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SUMOylation- and GAR1-Dependent Regulation of Dyskerin Nuclear and Subnuclear Localization. Mol Cell Biol 2021; 41:MCB.00464-20. [PMID: 33526451 DOI: 10.1128/mcb.00464-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/20/2021] [Indexed: 12/29/2022] Open
Abstract
The nuclear and subnuclear compartmentalization of the telomerase-associated protein and H/ACA ribonucleoprotein component dyskerin is an important although incompletely understood aspect of H/ACA ribonucleoprotein function. Four SUMOylation sites were previously identified in the C-terminal nuclear/nucleolar localization signal (N/NoLS) of dyskerin. We found that a cytoplasmic localized C-terminal truncation variant of dyskerin lacking most of the C-terminal N/NoLS represents an under-SUMOylated variant of dyskerin compared to wild-type dyskerin. We demonstrate that mimicking constitutive SUMOylation of dyskerin using a SUMO3 fusion construct can drive nuclear accumulation of this variant and that the SUMO site K467 in this N/NoLS is particularly important for the subnuclear localization of dyskerin to the nucleolus in a mature H/ACA complex assembly- and SUMO-dependent manner. We also characterize a novel SUMO-interacting motif in the mature H/ACA complex component GAR1 that mediates the interaction between dyskerin and GAR1. Mislocalization of dyskerin, either in the cytoplasm or excluded from the nucleolus, disrupts dyskerin function and leads to reduced interaction of dyskerin with the telomerase RNA. These data indicate a role for dyskerin C-terminal N/NoLS SUMOylation in regulating the nuclear and subnuclear localization of dyskerin, which is essential for dyskerin function as both a telomerase-associated protein and as an H/ACA ribonucleoprotein.
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52
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The Sumo proteome of proliferating and neuronal-differentiating cells reveals Utf1 among key Sumo targets involved in neurogenesis. Cell Death Dis 2021; 12:305. [PMID: 33753728 PMCID: PMC7985304 DOI: 10.1038/s41419-021-03590-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 11/28/2022]
Abstract
Post-translational modification by covalent attachment of the Small ubiquitin-like modifier (Sumo) polypeptide regulates a multitude of processes in vertebrates. Despite demonstrated roles of Sumo in the development and function of the nervous system, the identification of key factors displaying a sumoylation-dependent activity during neurogenesis remains elusive. Through a SILAC (stable isotope labeling by/with amino acids in cell culture)-based proteomic approach, we have identified the Sumo proteome of the model cell line P19 under proliferation and neuronal differentiation conditions. More than 300 proteins were identified as putative Sumo targets differentially associated with one or the other condition. A group of proteins of interest were validated and investigated in functional studies. Among these, Utf1 was revealed as a new Sumo target. Gain-of-function experiments demonstrated marked differences between the effects on neurogenesis of overexpressing wild-type and sumoylation mutant versions of the selected proteins. While sumoylation of Prox1, Sall4a, Trim24, and Utf1 was associated with a positive effect on neurogenesis in P19 cells, sumoylation of Kctd15 was associated with a negative effect. Prox1, Sall4a, and Kctd15 were further analyzed in the vertebrate neural tube of living embryos, with similar results. Finally, a detailed analysis of Utf1 showed the sumoylation dependence of Utf1 function in controlling the expression of bivalent genes. Interestingly, this effect seems to rely on two mechanisms: sumoylation modulates binding of Utf1 to the chromatin and mediates recruitment of the messenger RNA-decapping enzyme Dcp1a through a conserved SIM (Sumo-interacting motif). Altogether, our results indicate that the combined sumoylation status of key proteins determines the proper progress of neurogenesis.
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53
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Roy D, Sadanandom A. SUMO mediated regulation of transcription factors as a mechanism for transducing environmental cues into cellular signaling in plants. Cell Mol Life Sci 2021; 78:2641-2664. [PMID: 33452901 PMCID: PMC8004507 DOI: 10.1007/s00018-020-03723-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/25/2020] [Accepted: 11/25/2020] [Indexed: 12/31/2022]
Abstract
Across all species, transcription factors (TFs) are the most frequent targets of SUMOylation. The effect of SUMO conjugation on the functions of transcription factors has been extensively studied in animal systems, with over 200 transcription factors being documented to be modulated by SUMOylation. This has resulted in the establishment of a number of paradigms that seek to explain the mechanisms by which SUMO regulates transcription factor functions. For instance, SUMO has been shown to modulate TF DNA binding activity; regulate both localization as well as the abundance of TFs and also influence the association of TFs with chromatin. With transcription factors being implicated as master regulators of the cellular signalling pathways that maintain phenotypic plasticity in all organisms, in this review, we will discuss how SUMO mediated regulation of transcription factor activity facilitates molecular pathways to mount an appropriate and coherent biological response to environmental cues.
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Affiliation(s)
- Dipan Roy
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Ari Sadanandom
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK.
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Collados Rodríguez M. The Fate of Speckled Protein 100 (Sp100) During Herpesviruses Infection. Front Cell Infect Microbiol 2021; 10:607526. [PMID: 33598438 PMCID: PMC7882683 DOI: 10.3389/fcimb.2020.607526] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/14/2020] [Indexed: 12/27/2022] Open
Abstract
The constitutive expression of Speckled-100 (Sp100) is known to restrict the replication of many clinically important DNA viruses. This pre-existing (intrinsic) immune defense to virus infection can be further upregulated upon interferon (IFN) stimulation as a component of the innate immune response. In humans, Sp100 is encoded by a single gene locus, which can produce alternatively spliced isoforms. The widely studied Sp100A, Sp100B, Sp100C and Sp100HMG have functions associated with the transcriptional regulation of viral and cellular chromatin, either directly through their characteristic DNA-binding domains, or indirectly through post-translational modification (PTM) and associated protein interaction networks. Sp100 isoforms are resident component proteins of promyelocytic leukemia-nuclear bodies (PML-NBs), dynamic nuclear sub-structures which regulate host immune defenses against many pathogens. In the case of human herpesviruses, multiple protein antagonists are expressed to relieve viral DNA genome transcriptional silencing imposed by PML-NB and Sp100-derived proteinaceous structures, thereby stimulating viral propagation, pathogenesis, and transmission to new hosts. This review details how different Sp100 isoforms are manipulated during herpesviruses HSV1, VZV, HCMV, EBV, and KSHV infection, identifying gaps in our current knowledge, and highlighting future areas of research.
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55
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Liang Z, Chan HYE, Lee MM, Chan MK. A SUMO1-Derived Peptide Targeting SUMO-Interacting Motif Inhibits α-Synuclein Aggregation. Cell Chem Biol 2021; 28:180-190.e6. [PMID: 33444530 DOI: 10.1016/j.chembiol.2020.12.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/06/2020] [Accepted: 12/17/2020] [Indexed: 11/17/2022]
Abstract
The accumulation of α-synuclein amyloid fibrils in the brain is linked to Parkinson's disease and other synucleinopathies. The intermediate species in the early aggregation phase of α-synuclein are involved in the emergence of amyloid toxicity and considered to be the most neurotoxic. The N-terminal region flanking the non-amyloid-β component domain of α-synuclein has been implicated in modulating its aggregation. Herein, we report the development of a SUMO1-derived peptide inhibitor (SUMO1(15-55)), which targets two SUMO-interacting motifs (SIMs) within this aggregation-regulating region and suppresses α-synuclein aggregation. Molecular modeling, site-directed mutagenesis, and binding studies are used to elucidate the mode of interaction, namely, via the binding of either of the two SIM sequences on α-synuclein to a putative hydrophobic binding groove on SUMO1(15-55). Subsequent studies show that SUMO1(15-55) also reduces α-synuclein-induced cytotoxicity in cell-based and Drosophila disease models.
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Affiliation(s)
- Zhaohui Liang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China; Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ho Yin Edwin Chan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China; Laboratory of Drosophila Research, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China; Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Marianne M Lee
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China; Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Michael K Chan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China; Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
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56
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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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57
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Haas J, Bloesel D, Bacher S, Kracht M, Schmitz ML. Chromatin Targeting of HIPK2 Leads to Acetylation-Dependent Chromatin Decondensation. Front Cell Dev Biol 2020; 8:852. [PMID: 32984337 PMCID: PMC7490299 DOI: 10.3389/fcell.2020.00852] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/10/2020] [Indexed: 11/13/2022] Open
Abstract
The protein kinase homeodomain-interacting protein kinase 2 (HIPK2) plays an important role in development and in the response to external cues. The kinase associates with an exceptionally large number of different transcription factors and chromatin regulatory proteins to direct distinct gene expression programs. In order to investigate the function of HIPK2 for chromatin compaction, HIPK2 was fused to the DNA-binding domains of Gal4 or LacI, thus allowing its specific targeting to binding sites for these transcription factors that were integrated in specific chromosome loci. Tethering of HIPK2 resulted in strong decompaction of euchromatic and heterochromatic areas. HIPK2-mediated heterochromatin decondensation started already 4 h after its chromatin association and required the functionality of its SUMO-interacting motif. This process was paralleled by disappearance of the repressive H3K27me3 chromatin mark, recruitment of the acetyltransferases CBP and p300 and increased histone acetylation at H3K18 and H4K5. HIPK2-mediated chromatin decompaction was strongly inhibited in the presence of a CBP/p300 inhibitor and completely blocked by the BET inhibitor JQ1, consistent with a causative role of acetylations for this process. Chromatin tethering of HIPK2 had only a minor effect on basal transcription, while it strongly boosted estrogen-triggered gene expression by acting as a transcriptional cofactor.
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Affiliation(s)
- Jana Haas
- Institute of Biochemistry, Justus-Liebig-University, Giessen, Germany.,Member of the German Center for Lung Research, Giessen, Germany
| | - Daniel Bloesel
- Institute of Biochemistry, Justus-Liebig-University, Giessen, Germany.,Member of the German Center for Lung Research, Giessen, Germany
| | - Susanne Bacher
- Institute of Biochemistry, Justus-Liebig-University, Giessen, Germany.,Member of the German Center for Lung Research, Giessen, Germany
| | - Michael Kracht
- Member of the German Center for Lung Research, Giessen, Germany.,Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University, Giessen, Germany
| | - M Lienhard Schmitz
- Institute of Biochemistry, Justus-Liebig-University, Giessen, Germany.,Member of the German Center for Lung Research, Giessen, Germany
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58
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Brüninghoff K, Aust A, Taupitz KF, Wulff S, Dörner W, Mootz HD. Identification of SUMO Binding Proteins Enriched after Covalent Photo-Cross-Linking. ACS Chem Biol 2020; 15:2406-2414. [PMID: 32786267 DOI: 10.1021/acschembio.0c00609] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Post-translational modification with the small ubiquitin-like modifier (SUMO) affects thousands of proteins in the human proteome and is implicated in numerous cellular processes. The main outcome of SUMO conjugation is a rewiring of protein-protein interactions through recognition of the modifier's surface by SUMO binding proteins. The SUMO-interacting motif (SIM) mediates binding to a groove on SUMO; however, the low affinity of this interaction and the poor conservation of SIM sequences complicates the isolation and identification of SIM proteins. To address these challenges, we have designed and biochemically characterized monomeric and multimeric SUMO-2 probes with a genetically encoded photo-cross-linker positioned next to the SIM binding groove. Following photoinduced covalent capture, even weak SUMO binders are not washed away during the enrichment procedure, and very stringent washing conditions can be applied to remove nonspecifically binding proteins. A total of 329 proteins were isolated from nuclear HeLa cell extracts and identified using mass spectrometry. We found the molecular design of our probes was corroborated by the presence of many established SUMO interacting proteins and the high percentage (>90%) of hits containing a potential SIM sequence, as predicted by bioinformatic analyses. Notably, 266 of the 329 proteins have not been previously reported as SUMO binders using traditional noncovalent enrichment procedures. We confirmed SUMO binding with purified proteins and mapped the position of the covalent cross-links for selected cases. We postulate a new SIM in MRE11, involved in DNA repair. The identified SUMO binding candidates will help to reveal the complex SUMO-mediated protein network.
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59
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Murphy P, Xu Y, Rouse SL, Jaffray EG, Plechanovová A, Matthews SJ, Carlos Penedo J, Hay RT. Functional 3D architecture in an intrinsically disordered E3 ligase domain facilitates ubiquitin transfer. Nat Commun 2020; 11:3807. [PMID: 32733036 PMCID: PMC7393505 DOI: 10.1038/s41467-020-17647-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 07/13/2020] [Indexed: 12/18/2022] Open
Abstract
The human genome contains an estimated 600 ubiquitin E3 ligases, many of which are single-subunit E3s (ssE3s) that can bind to both substrate and ubiquitin-loaded E2 (E2~Ub). Within ssE3s structural disorder tends to be located in substrate binding and domain linking regions. RNF4 is a ssE3 ligase with a C-terminal RING domain and disordered N-terminal region containing SUMO Interactions Motifs (SIMs) required to bind SUMO modified substrates. Here we show that, although the N-terminal region of RNF4 bears no secondary structure, it maintains a compact global architecture primed for SUMO interaction. Segregated charged regions within the RNF4 N-terminus promote compaction, juxtaposing RING domain and SIMs to facilitate substrate ubiquitination. Mutations that induce a more extended shape reduce ubiquitination activity. Our result offer insight into a key step in substrate ubiquitination by a member of the largest ubiquitin ligase subtype and reveal how a defined architecture within a disordered region contributes to E3 ligase function.
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Affiliation(s)
- Paul Murphy
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | - Yingqi Xu
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK
| | - Sarah L Rouse
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK
| | - Ellis G Jaffray
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | - Anna Plechanovová
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | - Steve J Matthews
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK
| | - J Carlos Penedo
- Centre of Biophotonics, School of Physics and Astronomy, University of St. Andrews, KY16 9SS, St. Andrews, UK
- Biomedical Sciences Research Complex, School of Biology, University of St. Andrews, KY16 9ST, St. Andrews, UK
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK.
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60
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Characterization of a C-Terminal SUMO-Interacting Motif Present in Select PIAS-Family Proteins. Structure 2020; 28:573-585.e5. [PMID: 32348746 DOI: 10.1016/j.str.2020.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/24/2020] [Accepted: 04/06/2020] [Indexed: 11/23/2022]
Abstract
The human PIAS proteins are small ubiquitin-like modifier (SUMO) E3 ligases that participate in important cellular functions. Several of these functions depend on a conserved SUMO-interacting motif (SIM) located in the central region of all PIAS proteins (SIM1). Recently, it was determined that Siz2, a yeast homolog of PIAS proteins, possesses a second SIM at its C terminus (SIM2). Sequence alignment indicates that a SIM2 is also present in PIAS1-3, but not PIAS4. Using biochemical and structural studies, we demonstrate PIAS-SIM2 binds to SUMO1, but that phosphorylation of the PIAS-SIM2 or acetylation of SUMO1 alter this interaction in a manner distinct from what is observed for the PIAS-SIM1. We also show that the PIAS-SIM2 plays a key role in formation of a UBC9-PIAS1-SUMO1 complex. These results provide insights into how post-translational modifications selectively regulate the specificity of multiple SIMs found in the PIAS proteins by exploiting the plasticity built into the SUMO-SIM binding interface.
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61
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Molecular mechanisms in SUMO conjugation. Biochem Soc Trans 2020; 48:123-135. [PMID: 31872228 DOI: 10.1042/bst20190357] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/28/2019] [Accepted: 12/04/2019] [Indexed: 01/25/2023]
Abstract
The small ubiquitin-like modifier (SUMO) is a post-translational modifier that can regulate the function of hundreds of proteins inside the cell. SUMO belongs to the ubiquitin-like family of proteins that can be attached to target proteins by a dedicated enzymatic cascade pathway formed by E1, E2 and E3 enzymes. SUMOylation is involved in many cellular pathways, having in most instances essential roles for their correct function. In this review, we want to highlight the latest research on the molecular mechanisms that lead to the formation of the isopeptidic bond between the lysine substrate and the C-terminus of SUMO. In particular, we will focus on the recent discoveries on the catalytic function of the SUMO E3 ligases revealed by structural and biochemical approaches. Also, we will discuss important questions regarding specificity in SUMO conjugation, which it still remains as a major issue due to the small number of SUMO E3 ligases discovered so far, in contrast with the large number of SUMO conjugated proteins in the cell.
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62
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Yau TY, Molina O, Courey AJ. SUMOylation in development and neurodegeneration. Development 2020; 147:147/6/dev175703. [PMID: 32188601 DOI: 10.1242/dev.175703] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In essentially all eukaryotes, proteins can be modified by the attachment of small ubiquitin-related modifier (SUMO) proteins to lysine side chains to produce branched proteins. This process of 'SUMOylation' plays essential roles in plant and animal development by altering protein function in spatially and temporally controlled ways. In this Primer, we explain the process of SUMOylation and summarize how SUMOylation regulates a number of signal transduction pathways. Next, we discuss multiple roles of SUMOylation in the epigenetic control of transcription. In addition, we evaluate the role of SUMOylation in the etiology of neurodegenerative disorders, focusing on Parkinson's disease and cerebral ischemia. Finally, we discuss the possibility that SUMOylation may stimulate survival and neurogenesis of neuronal stem cells.
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Affiliation(s)
- Tak-Yu Yau
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Oscar Molina
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Albert J Courey
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569, USA
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63
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Lindenmann U, Brand M, Gall F, Frasson D, Hunziker L, Kroslakova I, Sievers M, Riedl R. Discovery of a Class of Potent and Selective Non-competitive Sentrin-Specific Protease 1 Inhibitors. ChemMedChem 2020; 15:675-679. [PMID: 32083799 DOI: 10.1002/cmdc.202000067] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Indexed: 01/17/2023]
Abstract
Sentrin-specific proteases (SENPs) are responsible for the maturation of small ubiquitin-like modifiers (SUMOs) and the deconjugation of SUMOs from their substrate proteins. Studies on prostate cancer revealed an overexpression of SENP1, which promotes prostate cancer progression as well as metastasis. Therefore, SENP1 has been identified as a novel drug target against prostate cancer. Herein, we report the discovery and biological evaluation of potent and selective SENP1 inhibitors. A structure-activity relationship (SAR) of the newly identified pyridone scaffold revealed allosteric inhibitors with very attractive in vitro ADMET properties regarding plasma binding and plasma stability for this challenging target. This study also emphasizes the importance of biochemical mode of inhibition studies for de novo designed inhibitors.
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Affiliation(s)
- Urs Lindenmann
- Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
| | - Michael Brand
- Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
| | - Flavio Gall
- Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
| | - David Frasson
- Institute of Chemistry and Biotechnology, Center of Molecular Biology, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
| | - Lukas Hunziker
- Institute of Chemistry and Biotechnology, Center of Molecular Biology, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
| | - Ivana Kroslakova
- Institute of Chemistry and Biotechnology, Center of Molecular Biology, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
| | - Martin Sievers
- Institute of Chemistry and Biotechnology, Center of Molecular Biology, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
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64
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Guion LG, Sapp M. The Role of Promyelocytic Leukemia Nuclear Bodies During HPV Infection. Front Cell Infect Microbiol 2020; 10:35. [PMID: 32154186 PMCID: PMC7045071 DOI: 10.3389/fcimb.2020.00035] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/17/2020] [Indexed: 12/15/2022] Open
Abstract
Promyelocytic leukemia (PML) nuclear bodies (NBs) are highly dynamic subnuclear structures. Their name giving major component, PML protein, is essential for their formation. PML is present in many different isoforms due to differential splicing, which seem to contribute differently to PML NBs function. Sp100 and DAXX are also permanently residing in these structures. PML NBs disassemble in mitosis to form large cytoplasmic aggregates and reassemble after completion of cell division. Posttranslational modifications such as SUMOylation play important roles for protein association with PML NBs. In addition to the factors permanently associated with PML NBs, a large number of proteins may transiently reside in PML NBs dependent on cell stage, type, and condition. PML NBs have been indirectly implicated in a large number of cellular processes including apoptosis, transcriptional regulation, DNA repair and replication. They are considered hot spots for posttranslational modifications and may serve as readily accessible protein depots. However, a precise function has been difficult to assign. Many DNA viruses target PML NBs after entry often resulting in reorganization of these subnuclear structures. Antiviral activity has been assigned to PML NBs partially based on the observation that PML protein is an interferon stimulated gene. In contrast, human papillomavirus (HPV) infection requires the presence of PML protein suggesting that PML NBs may be essential to establish infection. This review will summarize and discuss recent advances in our understanding of the role of PML NBs and individual protein components in the establishment of HPV infection.
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Affiliation(s)
- Lucile G Guion
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, Louisiana State University Health Sciences Center, Shreveport, LA, United States.,Feist Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, United States
| | - Martin Sapp
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, Louisiana State University Health Sciences Center, Shreveport, LA, United States.,Feist Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, United States
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PML nuclear body biogenesis and oligomerization-driven leukemogenesis. BLOOD SCIENCE 2020; 2:7-10. [PMID: 35399865 PMCID: PMC8975047 DOI: 10.1097/bs9.0000000000000034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 10/02/2019] [Indexed: 11/26/2022] Open
Abstract
PML nuclear bodies (NBs), which are increasingly recognized as the central hub of many cellular signaling events, are superassembled spherical complexes with diameters of 0.1–2 μm. Recent studies reveal that RING tetramerization and B1-box polymerization are key factors to the overall PML NBs assembly. The productive RBCC oligomerization allows subsequent PML biogenesis steps, including the PML auto-sumoylation and partners recruitment via SUMO–SIM interactions. In promyelocytic leukemia, the oncoprotein PML/RARα (P/R) inhibits PML NBs assembly and leads to a full-fledged leukemogenesis. In this review, we review the recent progress in PML and acute promyelocytic leukemia fields, highlighting the protein oligomerization as an important direction of future targeted therapy.
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Critical role of CRAG, a splicing variant of centaurin-γ3/AGAP3, in ELK1-dependent SRF activation at PML bodies. Sci Rep 2019; 9:20107. [PMID: 31882856 PMCID: PMC6934726 DOI: 10.1038/s41598-019-56559-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 12/10/2019] [Indexed: 11/08/2022] Open
Abstract
CRMP-5-associated GTPase (CRAG), a short splicing variant of centaurin-γ3/AGAP3, is predominantly expressed in the developing brain. We previously demonstrated that CRAG, but not centaurin-γ3, translocates to the nucleus and activates the serum response factor (SRF)-c-Fos pathway in cultured neuronal cells. However, the physiological relevance of CRAG in vivo is unknown. Here, we found that CRAG/centaurin-γ3-knockout mice showed intensively suppressed kainic acid-induced c-fos expression in the hippocampus. Analyses of molecular mechanisms underlying CRAG-mediated SRF activation revealed that CRAG has an essential role in GTPase activity, interacts with ELK1 (a co-activator of SRF), and activates SRF in an ELK1-dependent manner. Furthermore, CRAG and ELK1 interact with promyelocytic leukaemia bodies through SUMO-interacting motifs, which is required for SRF activation. These results suggest that CRAG plays a critical role in ELK1-dependent SRF-c-fos activation at promyelocytic leukaemia bodies in the developing brain.
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Wolmarans A, Kwantes A, LaPointe P. A novel method for site-specific chemical SUMOylation: SUMOylation of Hsp90 modulates co-chaperone binding in vitro. Biol Chem 2019; 400:487-500. [PMID: 30265648 DOI: 10.1515/hsz-2018-0251] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/14/2018] [Indexed: 12/27/2022]
Abstract
SUMO is covalently attached to lysine side chains in target proteins by the action of a cascade of E1, E2, and E3 ligases. Unlike ubiquitin, SUMO does not target proteins for degradation but rather plays a regulatory role in activating target proteins or directing them to multiprotein complexes. Isolating SUMOylated proteins from native sources is challenging because of the low stoichiometry of SUMOylation that occurs for any given target protein in cells. Here we report a novel strategy to couple SUMO to the site of a target lysine for the purpose of in vitro study. Introduction of a single cysteine after the C terminal diglycine motif and a cysteine in place of a target lysine in a substrate protein allows for efficient and specific crosslinking of SUMO using a homo-bifunctional maleimide crosslinker. We demonstrate that SUMO can be crosslinked in this manner to amino acid position 178 in the dimeric molecular chaperone, Hsp90. Chemically SUMOylated Hsp90 has very similar ATPase activity compared to unmodified Hsp90 but displays preferential co-chaperone binding in vivo. Our novel strategy can easily be applied to other SUMOylated or ubiquitinated target protein in vitro.
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Affiliation(s)
- Annemarie Wolmarans
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2H7, Alberta, Canada
| | - Allison Kwantes
- Department of Biology, The King's University, Edmonton T6B 2H3, Alberta, Canada
| | - Paul LaPointe
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2H7, Alberta, Canada
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68
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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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Abstract
The homologous recombination (HR) machinery plays multiple roles in genome maintenance. Best studied in the context of DNA double-stranded break (DSB) repair, recombination enzymes can cleave, pair, and unwind DNA molecules, and collaborate with regulatory proteins to execute multiple DNA processing steps before generating specific repair products. HR proteins also help to cope with problems arising from DNA replication, modulating impaired replication forks or filling DNA gaps. Given these important roles, it is not surprising that each HR step is subject to complex regulation to adjust repair efficiency and outcomes as well as to limit toxic intermediates. Recent studies have revealed intricate regulation of all steps of HR by the protein modifier SUMO, which has been increasingly recognized for its broad influence in nuclear functions. This review aims to connect established roles of SUMO with its newly identified effects on recombinational repair and stimulate further thought on many unanswered questions.
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Affiliation(s)
- Nalini Dhingra
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Xiaolan Zhao
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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70
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Kumar R, Sabapathy K. RNF4—A Paradigm for SUMOylation‐Mediated Ubiquitination. Proteomics 2019; 19:e1900185. [DOI: 10.1002/pmic.201900185] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/13/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Ramesh Kumar
- Cancer & Stem Cell Biology Program Duke–NUS Medical School 8 College Road Singapore 169857 Singapore
| | - Kanaga Sabapathy
- Cancer & Stem Cell Biology Program Duke–NUS Medical School 8 College Road Singapore 169857 Singapore
- Laboratory of Molecular Carcinogenesis Division of Cellular & Molecular Research Humphrey Oei Institute of Cancer Research National Cancer Centre Singapore 11 Hospital Drive Singapore 169610 Singapore
- Department of Biochemistry National University of Singapore 8 Medical Drive Singapore 117597 Singapore
- Institute of Molecular and Cellular Biology 61 Biopolis Drive Singapore 138673 Singapore
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71
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Identification of ARKL1 as a Negative Regulator of Epstein-Barr Virus Reactivation. J Virol 2019; 93:JVI.00989-19. [PMID: 31341047 DOI: 10.1128/jvi.00989-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 07/17/2019] [Indexed: 12/20/2022] Open
Abstract
Epstein-Barr virus (EBV) maintains a life-long infection due to the ability to alternate between latent and lytic modes of replication. Lytic reactivation starts with derepression of the Zp promoter controlling BZLF1 gene expression, which binds and is activated by the c-Jun transcriptional activator. Here, we identified the cellular Arkadia-like 1 (ARKL1) protein as a negative regulator of Zp and EBV reactivation. Silencing of ARKL1 in the context of EBV-positive gastric carcinoma (AGS) cells, nasopharyngeal carcinoma (NPC43) cells, and B (M81) cells led to increased lytic protein expression, whereas overexpression inhibited BZLF1 expression. Similar effects of ARKL1 modulation were seen on BZLF1 transcripts as well as on Zp activity in Zp reporter assays, showing that ARKL1 repressed Zp. Proteomic profiling of ARKL1-host interactions identified c-Jun as an ARKL1 interactor, and reporter assays for Jun transcriptional activity showed that ARKL1 inhibited Jun activity. The ARKL1-Jun interaction required ARKL1 sequences that we previously showed mediated binding to the CK2 kinase regulatory subunit CK2β, suggesting that CK2β might mediate the ARKL1-Jun interaction. This model was supported by the findings that silencing of CK2β, but not the CK2α catalytic subunit, abrogated the ARKL1-Jun interaction and phenocopied ARKL1 silencing in promoting EBV reactivation. Additionally, ARKL1 was associated with Zp in reporter assays and this was increased by additional CK2β. Together, the data indicate that ARKL1 is a negative regulator of Zp and EBV reactivation that acts by inhibiting Jun activity through a CK2β-mediated interaction.IMPORTANCE Epstein-Barr virus (EBV) maintains a life-long infection due to the ability to alternate between latent and lytic modes of replication and is associated with several types of cancer. We have identified a cellular protein (ARKL1) that acts to repress the reactivation of EBV from the latent to the lytic cycle. We show that ARKL1 acts to repress transcription of the EBV lytic switch protein by inhibiting the activity of the cellular transcription factor c-Jun. This not only provides a new mechanism of regulating EBV reactivation but also identifies a novel cellular function of ARKL1 as an inhibitor of Jun-mediated transcription.
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Kötter A, Mootz HD, Heuer A. Standard Binding Free Energy of a SIM–SUMO Complex. J Chem Theory Comput 2019; 15:6403-6410. [DOI: 10.1021/acs.jctc.9b00428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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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73
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The SUMO Pathway in Hematomalignancies and Their Response to Therapies. Int J Mol Sci 2019; 20:ijms20163895. [PMID: 31405039 PMCID: PMC6721055 DOI: 10.3390/ijms20163895] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/31/2019] [Accepted: 08/06/2019] [Indexed: 12/21/2022] Open
Abstract
SUMO (Small Ubiquitin-related MOdifier) is a post-translational modifier of the ubiquitin family controlling the function and fate of thousands of proteins. SUMOylation is deregulated in various hematological malignancies, where it participates in both tumorigenesis and cancer cell response to therapies. This is the case for Acute Promyelocytic Leukemias (APL) where SUMOylation, and subsequent destruction, of the PML-RARα fusion oncoprotein are triggered by arsenic trioxide, which is used as front-line therapy in combination with retinoic acid to cure APL patients. A similar arsenic-induced SUMO-dependent degradation was also documented for Tax, a human T-cell lymphotropic virus type I (HTLV1) viral protein implicated in Adult T-cell Leukemogenesis. SUMOylation also participates in Acute Myeloid Leukemia (AML) response to both chemo- and differentiation therapies, in particular through its ability to regulate gene expression. In Multiple Myeloma, many enzymes of the SUMO pathway are overexpressed and their high expression correlates with lower response to melphalan-based chemotherapies. B-cell lymphomas overexpressing the c-Myc oncogene also overexpress most components of the SUMO pathway and are highly sensitive to SUMOylation inhibition. Targeting the SUMO pathway with recently discovered pharmacological inhibitors, alone or in combination with current therapies, might therefore constitute a powerful strategy to improve the treatment of these cancers.
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74
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Abrieu A, Liakopoulos D. How Does SUMO Participate in Spindle Organization? Cells 2019; 8:E801. [PMID: 31370271 PMCID: PMC6721559 DOI: 10.3390/cells8080801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin-like protein SUMO is a regulator involved in most cellular mechanisms. Recent studies have discovered new modes of function for this protein. Of particular interest is the ability of SUMO to organize proteins in larger assemblies, as well as the role of SUMO-dependent ubiquitylation in their disassembly. These mechanisms have been largely described in the context of DNA repair, transcriptional regulation, or signaling, while much less is known on how SUMO facilitates organization of microtubule-dependent processes during mitosis. Remarkably however, SUMO has been known for a long time to modify kinetochore proteins, while more recently, extensive proteomic screens have identified a large number of microtubule- and spindle-associated proteins that are SUMOylated. The aim of this review is to focus on the possible role of SUMOylation in organization of the spindle and kinetochore complexes. We summarize mitotic and microtubule/spindle-associated proteins that have been identified as SUMO conjugates and present examples regarding their regulation by SUMO. Moreover, we discuss the possible contribution of SUMOylation in organization of larger protein assemblies on the spindle, as well as the role of SUMO-targeted ubiquitylation in control of kinetochore assembly and function. Finally, we propose future directions regarding the study of SUMOylation in regulation of spindle organization and examine the potential of SUMO and SUMO-mediated degradation as target for antimitotic-based therapies.
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Affiliation(s)
- Ariane Abrieu
- CRBM, CNRS UMR5237, Université de Montpellier, 1919 route de Mende, 34090 Montpellier, France.
| | - Dimitris Liakopoulos
- CRBM, CNRS UMR5237, Université de Montpellier, 1919 route de Mende, 34090 Montpellier, France.
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75
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Welch MA, Forster LA, Atlas SI, Baro DJ. SUMOylating Two Distinct Sites on the A-type Potassium Channel, Kv4.2, Increases Surface Expression and Decreases Current Amplitude. Front Mol Neurosci 2019; 12:144. [PMID: 31213982 PMCID: PMC6554448 DOI: 10.3389/fnmol.2019.00144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/17/2019] [Indexed: 12/15/2022] Open
Abstract
Post-translational conjugation of Small Ubiquitin-like Modifier (SUMO) peptides to lysine (K) residues on target proteins alters their interactions. SUMOylation of a target protein can either promote its interaction with other proteins that possess SUMO binding domains, or it can prevent target protein interactions that normally occur in the absence of SUMOylation. One subclass of voltage-gated potassium channels that mediates an A-type current, IA, exists as a ternary complex comprising Kv4 pore-forming subunits, Kv channel interacting proteins (KChIP) and transmembrane dipeptidyl peptidase like proteins (DPPL). SUMOylation could potentially regulate intra- and/or intermolecular interactions within the complex. This study began to test this hypothesis and showed that Kv4.2 channels were SUMOylated in the rat brain and in human embryonic kidney (HEK) cells expressing a GFP-tagged mouse Kv4.2 channel (Kv4.2g). Prediction software identified two putative SUMOylation sites in the Kv4.2 C-terminus at K437 and K579. These sites were conserved across mouse, rat, and human Kv4.2 channels and across mouse Kv4 isoforms. Increasing Kv4.2g SUMOylation at each site by ~30% produced a significant ~22%–50% decrease in IA Gmax, and a ~70%–95% increase in channel surface expression. Site-directed mutagenesis of Kv4.2g showed that K437 SUMOylation regulated channel surface expression, while K579 SUMOylation controlled IA Gmax. The K579R mutation mimicked and occluded the SUMOylation-mediated decrease in IA Gmax, suggesting that SUMOylation at K579 blocked an intra- or inter-protein interaction involving K579. The K437R mutation did not obviously alter channel surface expression or biophysical properties, but it did block the SUMOylation-mediated increase in channel surface expression. Interestingly, enhancing K437 SUMOylation in the K579R mutant roughly doubled channel surface expression, but produced no change in IA Gmax, suggesting that the newly inserted channels were electrically silent. This is the first report that Kv4.2 channels are SUMOylated and that SUMOylation can independently regulate Kv4.2 surface expression and IA Gmax in opposing directions. The next step will be to determine if/how SUMOylation affects Kv4 interactions within the ternary complex.
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Affiliation(s)
- Meghyn A Welch
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Lori A Forster
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
| | - Selin I Atlas
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Deborah J Baro
- Department of Biology, Georgia State University, Atlanta, GA, United States.,Neuroscience Institute, Georgia State University, Atlanta, GA, United States
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76
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SUMO1 Modification Facilitates Avibirnavirus Replication by Stabilizing Polymerase VP1. J Virol 2019; 93:JVI.02227-18. [PMID: 30842328 DOI: 10.1128/jvi.02227-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/23/2019] [Indexed: 02/06/2023] Open
Abstract
SUMOylation is a posttranslational modification that has crucial roles in diverse cellular biological pathways and in various viral life cycles. In this study, we found that the VP1 protein, the RNA-dependent RNA polymerase of avibirnavirus infectious bursal disease virus (IBDV), regulates virus replication by SUMOylation during infection. Our data demonstrated that the polymerase VP1 is efficiently modified by small ubiquitin-like modifier 1 (SUMO1) in avibirnavirus-infected cell lines. Mutation analysis showed that residues 404I and 406I within SUMO interaction motif 3 of VP1 constitute the critical site for SUMO1 modification. Protein stability assays showed that SUMO1 modification enhanced significantly the stability of polymerase VP1 by inhibiting K48-linked ubiquitination. A reverse genetic approach showed that only IBDV with I404C/T and I406C/F mutations of VP1 could be rescued successfully with decreased replication ability. Our data demonstrated that SUMO1 modification is essential to sustain the stability of polymerase VP1 during IBDV replication and provides a potential target for designing antiviral drugs targeting IBDV.IMPORTANCE SUMOylation is an extensively discussed posttranslational modification in diverse cellular biological pathways. However, there is limited understanding about SUMOylation of viral proteins of IBDV during infection. In the present study, we revealed a SUMO1 modification of VP1 protein, the RNA-dependent RNA polymerase of avibirnavirus infectious bursal disease virus (IBDV). The required site of VP1 SUMOylation comprised residues 404I and 406I of SUMO interaction motif 3, which was essential for maintaining its stability by inhibiting K48-linked ubiquitination. We also showed that IBDV with SUMOylation-deficient VP1 had decreased replication ability. These data demonstrated that the SUMOylation of IBDV VP1 played an important role in maintaining IBDV replication.
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Kaur A, Gourav, Kumar S, Jaiswal N, Vashisht A, Kumar D, Gahlay GK, Mithu VS. NMR characterization of conformational fluctuations and noncovalent interactions of SUMO protein from Drosophila melanogaster (dSmt3). Proteins 2019; 87:658-667. [PMID: 30958586 DOI: 10.1002/prot.25690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 03/15/2019] [Accepted: 04/04/2019] [Indexed: 11/09/2022]
Abstract
Structural heterogeneity in the native-state ensemble of dSmt3, the only small ubiquitin-like modifier (SUMO) in Drosophila melanogaster, was investigated and compared with its human homologue SUMO1. Temperature dependence of amide proton's chemical shift was studied to identify amino acids possessing alternative structural conformations in the native state. Effect of small concentration of denaturant (1M urea) on this population was also monitored to assess the ruggedness of near-native energy landscape. Owing to presence of many such amino acids, especially in the β2 -loop-α region, the native state of dSmt3 seems more flexible in comparison to SUMO1. Information about backbone dynamics in ns-ps timescale was quantified from the measurement of 15 N-relaxation experiments. Furthermore, the noncovalent interaction of dSmt3 and SUMO1 with Daxx12 (Daxx729 DPEEIIVLSDSD740 ), a [V/I]-X-[V/I]-[V/I]-based SUMO interaction motif, was characterized using Bio-layer Interferometery and NMR spectroscopy. Daxx12 fits itself in the groove formed by β2 -loop-α structural region in both dSmt3 and SUMO1, but the binding is stronger with the former. Flexibility of β2 -loop-α region in dSmt3 is suspected to assist its interaction with Daxx12. Our results highlight the role of native-state flexibility in assisting noncovalent interactions of SUMO proteins especially in organisms where a single SUMO isoform has to tackle multiple substrates single handedly.
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Affiliation(s)
- Anupreet Kaur
- Department of Chemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Gourav
- Department of Chemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Sandeep Kumar
- Department of Chemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Nancy Jaiswal
- Centre of Biomedical Research, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Lucknow, Uttar Pradesh, India
| | - Ashutosh Vashisht
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Dinesh Kumar
- Centre of Biomedical Research, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Lucknow, Uttar Pradesh, India
| | - Gagandeep K Gahlay
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Venus S Mithu
- Department of Chemistry, Guru Nanak Dev University, Amritsar, Punjab, India
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78
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Wei SC, Tsai CH, Hsu WT, Chao YC. Baculovirus IE2 Interacts with Viral DNA through Daxx To Generate an Organized Nuclear Body Structure for Gene Activation in Vero Cells. J Virol 2019; 93:e00149-19. [PMID: 30728268 PMCID: PMC6450129 DOI: 10.1128/jvi.00149-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/14/2022] Open
Abstract
Upon virus infection of a cell, the uncoated DNA is usually blocked by the host intrinsic immune system inside the nucleus. Although it is crucial for the virus to counteract the host intrinsic immune system and access its genome, little is known about how viruses can knock down host restriction and identify their blocked genomes for later viral gene activation and replication. We found that upon baculovirus transduction into Vero E6 cells, the invading viral DNA is trapped by the cellular death domain-associated protein (Daxx) and histone H3.3 in the nucleus, resulting in gene inactivation. IE2, a baculovirus transactivator, targets host Daxx through IE2 SUMO-interacting motifs (SIMs) to indirectly access viral DNA and forms unique nuclear body structures, which we term clathrate cage-like apparatus (CCLAs), at the early transduction stage. At the later transduction stage, CCLAs gradually enlarge, and IE2 continues to closely interact with viral DNA but no longer associates with Daxx. The association with Daxx is essential for IE2 CCLA formation, and the enlarged CCLAs are capable of transactivating viral but not chromosomal DNA of Vero E6 cells. Our study reveals that baculovirus IE2 counteracts the cellular intrinsic immune system by specifically targeting Daxx and H3.3 to associate with viral DNA indirectly and efficiently. IE2 then utilizes this association with viral DNA to establish a unique CCLA cellular nanomachinery, which is visible under light microscopy as an enclosed environment for proper viral gene expression.IMPORTANCE The major breakthrough of this work is that viral protein IE2 localizes and transactivates its own viral DNA through a most unlikely route, i.e., host proteins Daxx and H3.3, which are designed to efficiently restrict viral DNA from expression. By interacting with these host intrinsic immune factors, IE2 can thus target the viral DNA and then form a unique spherical nuclear body, which we name the CCLA, to enclose the viral DNA and necessary factors to assist in high-level transactivation. Our study represents one of the most complete investigations of nuclear body formation. In addition, so far only RNA or protein molecules have been reported as potential nucleators for initiating nuclear body formation; our study may represent the first example showing that DNA can be a nucleator for a new class of nuclear body formation.
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Affiliation(s)
- Sung-Chan Wei
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Chih-Hsuan Tsai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
- Molecular and Cell Biology, Taiwan International Graduate Program, National Defense Medical Center and Academia Sinica, Taipei, Taiwan, Republic of China
| | - Wei-Ting Hsu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Yu-Chan Chao
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
- Molecular and Cell Biology, Taiwan International Graduate Program, National Defense Medical Center and Academia Sinica, Taipei, Taiwan, Republic of China
- Department of Plant Pathology and Microbiology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan, Republic of China
- Department of Life Sciences, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China
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79
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Noncovalent SUMO-interaction motifs in HIV integrase play important roles in SUMOylation, cofactor binding, and virus replication. Virol J 2019; 16:42. [PMID: 30940169 PMCID: PMC6446281 DOI: 10.1186/s12985-019-1134-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/21/2019] [Indexed: 12/12/2022] Open
Abstract
Background HIV integrase (IN) and its cellular cofactors, including lens-epithelium-derived growth factor (LEDGF/p75), Ku70, p300, and Rad52, are subject to small ubiquitin-like modifier (SUMO) modification. In addition to covalent SUMOylation, SUMO paralogs can also noncovalently bind proteins through SUMO-interacting motifs (SIMs). However, little is known about whether HIV IN contains SIMs and the roles of these motifs. Results We searched for the amino acid sequence of HIV IN and investigated three putative SIMs of IN: SIM1 72VILV75, SIM2 200IVDI203 and SIM3 257IKVV260. Our mutational analysis showed that 200IVDI203 and 257IKVV260 are two bona fide SIMs that mediate IN-SUMO noncovalent interactions. Additionally, a cell-based SUMOylation assay revealed that IN SIMs negatively regulate the SUMOylation of IN, as well as the interaction between IN and SUMO E2 conjugation enzyme Ubc9. Conversely, IN SIMs are required for its interactions with LEDGF/p75 but not with Ku70. Furthermore, our study reveals that SIM2 and SIM3 are required for the nuclear localization of IN. Finally, we investigated the impact of IN SIM2 and SIM3 on HIV single cycle replication in CD4+ C8166 T cells, and the results showed that viruses carrying IN SIM mutants are replication defective at the steps of the early viral life cycle, including reverse transcription, nuclear import and integration. Conclusion Our data suggested that the INSIM-SUMO interaction constitutes a new regulatory mechanism of IN functions and might be important for HIV-1 replication.
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80
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Identification of two independent SUMO-interacting motifs in Fas-associated factor 1 (FAF1): Implications for mineralocorticoid receptor (MR)-mediated transcriptional regulation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:1282-1297. [PMID: 30935967 DOI: 10.1016/j.bbamcr.2019.03.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/19/2019] [Accepted: 03/26/2019] [Indexed: 01/23/2023]
Abstract
Fas-associated factor 1 (FAF1) was originally isolated as a Fas-associated factor and was subsequently found to interact with numerous other proteins that are involved in various cellular events including Fas-mediated apoptosis, nuclear factor (NF)-κB, Wnt/β-catenin, and transforming growth factor (TGF)-β signaling pathways, mineralocorticoid receptor (MR)-mediated transactivation, and ubiquitin-dependent processes. Herein, we defined two small ubiquitin-like modifier (SUMO)-interacting motifs (SIMs) within FAF1 and demonstrated to be crucial for transcriptional modulation of the MR. Our study demonstrated that the SIMs of FAF1 do not play a significant role in regulating its subcellular localization, Fas-mediated apoptosis, or NF-κB or Wnt/β-catenin pathways. Remarkably, FAF1 interacts with the sumoylated MR and represses aldosterone-activated MR transactivation in a SIM-dependent manner. Moreover, silencing of endogenous FAF1 in cells resulted in an increase in the induction of MR target genes by aldosterone, indicating that FAF1 functions as an MR co-repressor. We further provide evidence to suggest that the mechanisms of FAF1/SIM-mediated MR transrepression involve inhibition of MR N/C interactions and promotion of MR polyubiquitination and degradation. Sumoylation has been linked to impacting of repressive properties on several transcription factors and cofactors. Our findings therefore provide mechanistic insights underlying SUMO-dependent transcriptional repression of the MR.
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81
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Shastrula PK, Sierra I, Deng Z, Keeney F, Hayden JE, Lieberman PM, Janicki SM. PML is recruited to heterochromatin during S phase and represses DAXX-mediated histone H3.3 chromatin assembly. J Cell Sci 2019; 132:jcs.220970. [PMID: 30796101 DOI: 10.1242/jcs.220970] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 02/09/2019] [Indexed: 12/18/2022] Open
Abstract
The incorporation of the histone H3 variant, H3.3, into chromatin by the H3.3-specific chaperone DAXX and the ATP-dependent chromatin remodeling factor ATRX is a critical mechanism for silencing repetitive DNA. DAXX and ATRX are also components of promyelocytic nuclear bodies (PML-NBs), which have been identified as sites of H3.3 chromatin assembly. Here, we use a transgene array that can be visualized in single living cells to investigate the mechanisms that recruit PML-NB proteins (i.e. PML, DAXX, ATRX, and SUMO-1, SUMO-2 and SUMO-3) to heterochromatin and their functions in H3.3 chromatin assembly. We show that DAXX and PML are recruited to the array through distinct SUMOylation-dependent mechanisms. Additionally, PML is recruited during S phase and its depletion increases H3.3 deposition. Since this effect is abrogated when PML and DAXX are co-depleted, it is likely that PML represses DAXX-mediated H3.3 chromatin assembly. Taken together, these results suggest that, at heterochromatin, PML-NBs coordinate H3.3 chromatin assembly with DNA replication, which has important implications for understanding how transcriptional silencing is established and maintained.
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Affiliation(s)
- Prashanth Krishna Shastrula
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA.,University of the Sciences in Philadelphia, Department of Biological Sciences, 600 South 43rd Street, Philadelphia, PA 19104, USA
| | - Isabel Sierra
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Zhong Deng
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Frederick Keeney
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - James E Hayden
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Paul M Lieberman
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Susan M Janicki
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
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82
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Zhao X. SUMO-Mediated Regulation of Nuclear Functions and Signaling Processes. Mol Cell 2019; 71:409-418. [PMID: 30075142 DOI: 10.1016/j.molcel.2018.07.027] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/06/2018] [Accepted: 07/23/2018] [Indexed: 12/23/2022]
Abstract
Since the discovery of SUMO twenty years ago, SUMO conjugation has become a widely recognized post-translational modification that targets a myriad of proteins in many processes. Great progress has been made in understanding the SUMO pathway enzymes, substrate sumoylation, and the interplay between sumoylation and other regulatory mechanisms in a variety of contexts. As these research directions continue to generate insights into SUMO-based regulation, several mechanisms by which sumoylation and desumoylation can orchestrate large biological effects are emerging. These include the ability to target multiple proteins within the same cellular structure or process, respond dynamically to external and internal stimuli, and modulate signaling pathways involving other post-translational modifications. Focusing on nuclear function and intracellular signaling, this review highlights a broad spectrum of historical data and recent advances with the aim of providing an overview of mechanisms underlying SUMO-mediated global effects to stimulate further inquiry into intriguing roles of SUMO.
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Affiliation(s)
- Xiaolan Zhao
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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83
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Srinivasan S, Shankar SR, Wang Y, Taneja R. SUMOylation of G9a regulates its function as an activator of myoblast proliferation. Cell Death Dis 2019; 10:250. [PMID: 30867409 PMCID: PMC6416281 DOI: 10.1038/s41419-019-1465-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/13/2019] [Accepted: 02/20/2019] [Indexed: 02/03/2023]
Abstract
The lysine methyltransferase G9a plays a role in many cellular processes. It is a potent repressor of gene expression, a function attributed to its ability to methylate histone and non-histone proteins. Paradoxically, in some instances, G9a can activate gene expression. However, regulators of G9a expression and activity are poorly understood. In this study, we report that endogenous G9a is SUMOylated in proliferating skeletal myoblasts. There are four potential SUMOylation consensus motifs in G9a. Mutation of all four acceptor lysine residues [K79, K152, K256, and K799] inhibits SUMOylation. Interestingly, SUMOylation does not impact G9a-mediated repression of MyoD transcriptional activity or myogenic differentiation. In contrast, SUMO-defective G9a is unable to enhance proliferation of myoblasts. Using complementation experiments, we show that the proliferation defect of primary myoblasts from conditional G9a-deficient mice is rescued by re-expression of wild-type, but not SUMOylation-defective, G9a. Mechanistically, SUMOylation acts as signal for PCAF (P300/CBP-associated factor) recruitment at E2F1-target genes. This results in increased histone H3 lysine 9 acetylation marks at E2F1-target gene promoters that are required for S-phase progression. Our studies provide evidence by which SUMO modification of G9a influences the chromatin environment to impact cell cycle progression.
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Affiliation(s)
- Shruti Srinivasan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117593, Singapore, Singapore
| | - Shilpa Rani Shankar
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117593, Singapore, Singapore
| | - Yaju Wang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117593, Singapore, Singapore
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117593, Singapore, Singapore.
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84
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Garvin AJ, Walker AK, Densham RM, Chauhan AS, Stone HR, Mackay HL, Jamshad M, Starowicz K, Daza-Martin M, Ronson GE, Lanz AJ, Beesley JF, Morris JR. The deSUMOylase SENP2 coordinates homologous recombination and nonhomologous end joining by independent mechanisms. Genes Dev 2019; 33:333-347. [PMID: 30796017 PMCID: PMC6411010 DOI: 10.1101/gad.321125.118] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/21/2018] [Indexed: 12/18/2022]
Abstract
SUMOylation (small ubiquitin-like modifier) in the DNA double-strand break (DSB) response regulates recruitment, activity, and clearance of repair factors. However, our understanding of a role for deSUMOylation in this process is limited. Here we identify different mechanistic roles for deSUMOylation in homologous recombination (HR) and nonhomologous end joining (NHEJ) through the investigation of the deSUMOylase SENP2. We found that regulated deSUMOylation of MDC1 prevents excessive SUMOylation and its RNF4-VCP mediated clearance from DSBs, thereby promoting NHEJ. In contrast, we show that HR is differentially sensitive to SUMO availability and SENP2 activity is needed to provide SUMO. SENP2 is amplified as part of the chromosome 3q amplification in many cancers. Increased SENP2 expression prolongs MDC1 focus retention and increases NHEJ and radioresistance. Collectively, our data reveal that deSUMOylation differentially primes cells for responding to DSBs and demonstrates the ability of SENP2 to tune DSB repair responses.
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Affiliation(s)
- Alexander J Garvin
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Alexandra K Walker
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Ruth M Densham
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Anoop Singh Chauhan
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Helen R Stone
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Hannah L Mackay
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Mohammed Jamshad
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Katarzyna Starowicz
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Manuel Daza-Martin
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - George E Ronson
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Alexander J Lanz
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - James F Beesley
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Joanna R Morris
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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85
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Abstract
Posttranslational modification with small ubiquitin-like modifier (SUMO) plays an important role in many biological processes. SUMO-targeted ubiquitin E3 ligases (STUbLs) are part of the really interesting new gene (RING)-type family of ubiquitin E3 ligases. STUbLs recognize their SUMO-modified substrates via SUMO-interaction motifs and ubiquitinate them via the RING domain. As a result, they form a link between the ubiquitin and SUMO signaling pathways. STUbL activity is required for the maintenance of genome stability, the repair of damaged DNA and to target SUMO-modified proteins for degradation by the proteasome. In vitro assays for STUbL activity have been developed and used to identify their cognate ubiquitin-conjugating enzymes (E2s), to determine their substrate requirements, and to characterize the types of ubiquitin chains linked to substrates. While we have focused on the STUbL RING finger protein 4 (RNF4) the methods we describe can be extended to other STUbLs. We also describe an assay for RNF4 ubiquitination activity based on fluorescence polarization, suitable for high-throughput compound screening in drug discovery.
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86
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SUMOylation of PCNA by PIAS1 and PIAS4 promotes template switch in the chicken and human B cell lines. Proc Natl Acad Sci U S A 2018; 115:12793-12798. [PMID: 30487218 DOI: 10.1073/pnas.1716349115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA damage tolerance (DDT) releases replication blockage caused by damaged nucleotides on template strands employing two alternative pathways, error-prone translesion DNA synthesis (TLS) and error-free template switch (TS). Lys164 of proliferating cell nuclear antigen (PCNA) is SUMOylated during the physiological cell cycle. To explore the role for SUMOylation of PCNA in DDT, we characterized chicken DT40 and human TK6 B cells deficient in the PIAS1 and PIAS4 small ubiquitin-like modifier (SUMO) E3 ligases. DT40 cells have a unique advantage in the phenotypic analysis of DDT as they continuously diversify their immunoglobulin (Ig) variable genes by TLS and TS [Ig gene conversion (GC)], both relieving replication blocks at abasic sites without accompanying by DNA breakage. Remarkably, PIAS1 -/- /PIAS4 -/- cells displayed a multifold decrease in SUMOylation of PCNA at Lys164 and over a 90% decrease in the rate of TS. Likewise, PIAS1 -/- /PIAS4 -/- TK6 cells showed a shift of DDT from TS to TLS at a chemosynthetic UV lesion inserted into the genomic DNA. The PCNA K164R/K164R mutation caused a ∼90% decrease in the rate of Ig GC and no additional impact on PIAS1 -/- /PIAS4 -/- cells. This epistatic relationship between the PCNA K164R/K164R and the PIAS1 -/- /PIAS4 -/- mutations suggests that PIAS1 and PIAS4 promote TS mainly through SUMOylation of PCNA at Lys164. This idea is further supported by the data that overexpression of a PCNA-SUMO1 chimeric protein restores defects in TS in PIAS1 -/- /PIAS4 -/- cells. In conclusion, SUMOylation of PCNA at Lys164 promoted by PIAS1 and PIAS4 ensures the error-free release of replication blockage during physiological DNA replication in metazoan cells.
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87
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Molecular interaction between human SUMO-I and histone like DNA binding protein of Helicobacter pylori (Hup) investigated by NMR and other biophysical tools. Int J Biol Macromol 2018; 123:446-456. [PMID: 30439429 DOI: 10.1016/j.ijbiomac.2018.11.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/29/2018] [Accepted: 11/11/2018] [Indexed: 02/07/2023]
Abstract
The proteins secreted by bacteria contribute to immune mediated gastric inflammation and epithelial damage; thus aid bacterial invasion in host tissue, and may also interact with host proteins, conspirating a mechanism against host-immune system. The Histone-like DNA binding protein is one of the most abundant nucleoid-associated proteins in Helicobacter pylori (H. pylori). The protein -referred here as Hup- is also secreted in vitro by H. pylori, thus it may have its role in disease pathogenesis. This is possible only if Hup interact with some human proteins including Small-Ubiquitin-like-Modifier (SUMO) proteins. Studies have established that SUMO-proteins participate in various innate-immune pathways and thus promote an efficient immune response to combat pathogenic infections. Sequence analysis revealed the presence of two SUMO interacting motifs (SIMs) and several positively charged lysine residues on the protein surface of Hup. Additionally, SUMO-proteins epitomize negatively charged surface which confers them the ability to bind to DNA/RNA binding proteins. Based on the presence of SIMs as well as charge complementarity between the proteins, it is legitimate to consider that Hup protein would bind to SUMO-proteins. The present study has been undertaken to establish this interaction for the first time using NMR in combination with ITC and other biophysical techniques.
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88
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Augustine RC, Vierstra RD. SUMOylation: re-wiring the plant nucleus during stress and development. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:143-154. [PMID: 30014889 DOI: 10.1016/j.pbi.2018.06.006] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 06/11/2018] [Accepted: 06/25/2018] [Indexed: 05/08/2023]
Abstract
Conjugation of small ubiquitin-related modifier (SUMO) to intracellular proteins provides a dynamic regulatory mechanism that enables plants to rapidly defend against environmental challenges. SUMOylation of mostly nuclear proteins is among the fastest stress responses observed but precisely how this post-translational modification provides stress resilience remains unclear. Here, we describe the plant SUMO system and its expanding target catalog, which implicates this modification in DNA repair, chromatin modification/remodeling, transcriptional activation/repression, epigenetics, and RNA metabolism, with a likely outcome being extensive nuclear re-wiring to withstand stress. In parallel, studies have linked SUMO to developmental programs such as gametogenesis and gene silencing. The accumulating data support the notion that SUMOylation substantially influences the transcriptional and epigenetic landscapes to promote stress tolerance and developmental progression.
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Affiliation(s)
- Robert C Augustine
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
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89
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Benlloch R, Lois LM. Sumoylation in plants: mechanistic insights and its role in drought stress. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4539-4554. [PMID: 29931319 DOI: 10.1093/jxb/ery233] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/11/2018] [Indexed: 05/20/2023]
Abstract
Post-translational modification by SUMO is an essential process that has a major role in the regulation of plant development and stress responses. Such diverse biological functions are accompanied by functional diversification among the SUMO conjugation machinery components and regulatory mechanisms that has just started to be identified in plants. In this review, we focus on the current knowledge of the SUMO conjugation system in plants in terms of components, substrate specificity, cognate interactions, enzyme activity, and subcellular localization. In addition, we analyze existing data on the role of SUMOylation in plant drought tolerance in model plants and crop species, paying attention to the genetic approaches used to stimulate or inhibit endogenous SUMO conjugation. The role in drought tolerance of potential SUMO targets identified in proteomic analyses is also discussed. Overall, the complexity of SUMOylation and the multiple genetic and environmental factors that are integrated to confer drought tolerance highlight the need for significant efforts to understand the interplay between SUMO and drought.
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Affiliation(s)
- Reyes Benlloch
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - L Maria Lois
- Center for Research in Agricultural Genomics-CRAG, Edifici CRAG-Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
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90
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SUMOs Mediate the Nuclear Transfer of p38 and p-p38 during Helicobacter Pylori Infection. Int J Mol Sci 2018; 19:ijms19092482. [PMID: 30135361 PMCID: PMC6163533 DOI: 10.3390/ijms19092482] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 08/13/2018] [Accepted: 08/17/2018] [Indexed: 12/23/2022] Open
Abstract
The p38 mitogen activated protein kinase (MAPK) signaling pathway has been suggested to play a significant role in the gastric mucosal inflammatory response to chronic Helicobacter pylori (H. pylori) infection. Nuclear translocation is thought to be important for p38 function, but no nuclear translocation signals have been found in the protein and no nuclear carrier proteins have been identified for p38. We have investigated the role of small ubiquitin-related modifier (SUMO) in the nuclear transfer of p38 in response to H. pylori infection. Exposure of human AGS cells to H. pylori induced the activation of p38 and the expression of SUMOs, especially SUMO-2. SUMO knockdown counteracted the effect of H. pylori infection by decreasing the resulting p38 mediated cellular apoptosis through a reduction in the nuclear fraction of phosphorylated p38. We identified a non-covalent interaction between SUMOs and p38 via SUMO interaction motifs (SIMs), and showed that SUMO-dependent nuclear transfer of p38 was decreased upon mutation of its SIMs. This study has identified a new pathway of p38 nuclear translocation, in response to H. pylori infection. We conclude that in the presence of H. pylori SUMO-2 has a major role in regulating nuclear levels of p38, through non-covalent SUMO-p38 interactions, independent of the p38 phosphorylation state.
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91
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Chanda A, Sarkar A, Bonni S. The SUMO System and TGFβ Signaling Interplay in Regulation of Epithelial-Mesenchymal Transition: Implications for Cancer Progression. Cancers (Basel) 2018; 10:cancers10080264. [PMID: 30096838 PMCID: PMC6115711 DOI: 10.3390/cancers10080264] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/06/2018] [Accepted: 08/06/2018] [Indexed: 02/07/2023] Open
Abstract
Protein post-translational modification by the small ubiquitin-like modifier (SUMO), or SUMOylation, can regulate the stability, subcellular localization or interactome of a protein substrate with key consequences for cellular processes including the Epithelial-Mesenchymal Transition (EMT). The secreted protein Transforming Growth Factor beta (TGFβ) is a potent inducer of EMT in development and homeostasis. Importantly, the ability of TGFβ to induce EMT has been implicated in promoting cancer invasion and metastasis, resistance to chemo/radio therapy, and maintenance of cancer stem cells. Interestingly, TGFβ-induced EMT and the SUMO system intersect with important implications for cancer formation and progression, and novel therapeutics identification.
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Affiliation(s)
- Ayan Chanda
- Department of Biochemistry and Molecular Biology, The Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.
| | - Anusi Sarkar
- Department of Biochemistry and Molecular Biology, The Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.
| | - Shirin Bonni
- Department of Biochemistry and Molecular Biology, The Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.
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92
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Greenlee M, Alonso A, Rahman M, Meednu N, Davis K, Tabb V, Cook R, Miller RK. The TOG protein Stu2/XMAP215 interacts covalently and noncovalently with SUMO. Cytoskeleton (Hoboken) 2018; 75:290-306. [PMID: 29729126 PMCID: PMC6712953 DOI: 10.1002/cm.21449] [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: 02/07/2018] [Revised: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 01/21/2023]
Abstract
Stu2p is the yeast member of the XMAP215/Dis1/ch‐TOG family of microtubule‐associated proteins that promote microtubule polymerization. However, the factors that regulate its activity are not clearly understood. Here we report that Stu2p in the budding yeast Saccharomyces cerevisiae interacts with SUMO by covalent and noncovalent mechanisms. Stu2p interacted by two‐hybrid analysis with the yeast SUMO Smt3p, its E2 Ubc9p, and the E3 Nfi1p. A region of Stu2p containing the dimerization domain was both necessary and sufficient for interaction with SUMO and Ubc9p. Stu2p was found to be sumoylated both in vitro and in vivo. Stu2p copurified with SUMO in a pull‐down assay and vice versa. Stu2p also bound to a nonconjugatable form of SUMO, suggesting that Stu2p can interact noncovalently with SUMO. In addition, Stu2p interacted with the STUbL enzyme Ris1p. Stu2p also copurified with ubiquitin in a pull‐down assay, suggesting that it can be modified by both SUMO and ubiquitin. Tubulin, a major binding partner of Stu2p, also interacted noncovalently with SUMO. By two‐hybrid analysis, the beta‐tubulin Tub2p interacted with SUMO independently of the microtubule stressor, benomyl. Together, these findings raise the possibility that the microtubule polymerization activities mediated by Stu2p are regulated through sumoylation pathways.
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Affiliation(s)
- Matt Greenlee
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, 74078
| | - Annabel Alonso
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, 74078
| | - Maliha Rahman
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, 74078
| | - Nida Meednu
- Department of Biology, University of Rochester, Rochester, New York, 14627
| | - Kayla Davis
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, 74078
| | - Victoria Tabb
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, 74078
| | - River Cook
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, 74078
| | - Rita K Miller
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, 74078
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93
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Lazar NH, Nevonen KA, O'Connell B, McCann C, O'Neill RJ, Green RE, Meyer TJ, Okhovat M, Carbone L. Epigenetic maintenance of topological domains in the highly rearranged gibbon genome. Genome Res 2018; 28:983-997. [PMID: 29914971 PMCID: PMC6028127 DOI: 10.1101/gr.233874.117] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 06/01/2018] [Indexed: 12/27/2022]
Abstract
The relationship between evolutionary genome remodeling and the three-dimensional structure of the genome remain largely unexplored. Here, we use the heavily rearranged gibbon genome to examine how evolutionary chromosomal rearrangements impact genome-wide chromatin interactions, topologically associating domains (TADs), and their epigenetic landscape. We use high-resolution maps of gibbon–human breaks of synteny (BOS), apply Hi-C in gibbon, measure an array of epigenetic features, and perform cross-species comparisons. We find that gibbon rearrangements occur at TAD boundaries, independent of the parameters used to identify TADs. This overlap is supported by a remarkable genetic and epigenetic similarity between BOS and TAD boundaries, namely presence of CpG islands and SINE elements, and enrichment in CTCF and H3K4me3 binding. Cross-species comparisons reveal that regions orthologous to BOS also correspond with boundaries of large (400–600 kb) TADs in human and other mammalian species. The colocalization of rearrangement breakpoints and TAD boundaries may be due to higher chromatin fragility at these locations and/or increased selective pressure against rearrangements that disrupt TAD integrity. We also examine the small portion of BOS that did not overlap with TAD boundaries and gave rise to novel TADs in the gibbon genome. We postulate that these new TADs generally lack deleterious consequences. Last, we show that limited epigenetic homogenization occurs across breakpoints, irrespective of their time of occurrence in the gibbon lineage. Overall, our findings demonstrate remarkable conservation of chromatin interactions and epigenetic landscape in gibbons, in spite of extensive genomic shuffling.
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Affiliation(s)
- Nathan H Lazar
- Bioinformatics and Computational Biology Division, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Kimberly A Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Brendan O'Connell
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Christine McCann
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, USA.,Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, USA.,Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Thomas J Meyer
- Bioinformatics and Computational Biology Division, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Lucia Carbone
- Bioinformatics and Computational Biology Division, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA.,Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA.,Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA.,Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
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94
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Yang Y, Xia Z, Wang X, Zhao X, Sheng Z, Ye Y, He G, Zhou L, Zhu H, Xu N, Liang S. Small-Molecule Inhibitors Targeting Protein SUMOylation as Novel Anticancer Compounds. Mol Pharmacol 2018; 94:885-894. [PMID: 29784649 DOI: 10.1124/mol.118.112300] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/16/2018] [Indexed: 02/05/2023] Open
Abstract
SUMOylation, one of post-translational modifications, is covalently modified on lysine residues of a target protein through an enzymatic cascade reaction similar to protein ubiquitination. Along with identification of many SUMOylated proteins, protein SUMOylation has been proven to regulate multiple biologic activities including transcription, cell cycle, DNA repair, and innate immunity. The dysregulation of protein SUMOylation and deSUMOylation modification is linked with carcinogenesis and tumor progression. The SUMOylation-associated enzymes are usually elevated in various cancers, which function as cancer biomarkers to relate to poor outcomes for patients. Considering the significance of protein SUMOylation in regulating diverse biologic functions in cancer progression, numerous small-molecule inhibitors targeting protein SUMOylation pathway are developed as potentially clinical anticancer therapeutics. Here, we systematically summarize the latest progresses of associations of small ubiquitin-like modifier (SUMO) enzymes with cancers and small-molecular inhibitors against human cancers by targeting SUMOylation enzymes. We also compared the pros and cons of several special anticancer inhibitors targeting SUMO pathway. As more efforts are invested in this field, small-molecule inhibitors targeting the SUMOylation modification pathway are promising for development into novel anticancer drugs.
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Affiliation(s)
- Yanfang Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu (Y.Ya., Z.X., X.W., X.Z., Z.S., Y.Ye., G.H., L.Z., N.X., S.L.); Departments of Nephrology (Z.X.) and Neurosurgery (L.Z.), West China Hospital, Sichuan University, Chengdu; and Laboratory of Cell and Molecular Biology, and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences, Beijing (H.Z., N.X.), People's Republic of China
| | - Zijing Xia
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu (Y.Ya., Z.X., X.W., X.Z., Z.S., Y.Ye., G.H., L.Z., N.X., S.L.); Departments of Nephrology (Z.X.) and Neurosurgery (L.Z.), West China Hospital, Sichuan University, Chengdu; and Laboratory of Cell and Molecular Biology, and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences, Beijing (H.Z., N.X.), People's Republic of China
| | - Xixi Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu (Y.Ya., Z.X., X.W., X.Z., Z.S., Y.Ye., G.H., L.Z., N.X., S.L.); Departments of Nephrology (Z.X.) and Neurosurgery (L.Z.), West China Hospital, Sichuan University, Chengdu; and Laboratory of Cell and Molecular Biology, and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences, Beijing (H.Z., N.X.), People's Republic of China
| | - Xinyu Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu (Y.Ya., Z.X., X.W., X.Z., Z.S., Y.Ye., G.H., L.Z., N.X., S.L.); Departments of Nephrology (Z.X.) and Neurosurgery (L.Z.), West China Hospital, Sichuan University, Chengdu; and Laboratory of Cell and Molecular Biology, and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences, Beijing (H.Z., N.X.), People's Republic of China
| | - Zenghua Sheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu (Y.Ya., Z.X., X.W., X.Z., Z.S., Y.Ye., G.H., L.Z., N.X., S.L.); Departments of Nephrology (Z.X.) and Neurosurgery (L.Z.), West China Hospital, Sichuan University, Chengdu; and Laboratory of Cell and Molecular Biology, and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences, Beijing (H.Z., N.X.), People's Republic of China
| | - Yang Ye
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu (Y.Ya., Z.X., X.W., X.Z., Z.S., Y.Ye., G.H., L.Z., N.X., S.L.); Departments of Nephrology (Z.X.) and Neurosurgery (L.Z.), West China Hospital, Sichuan University, Chengdu; and Laboratory of Cell and Molecular Biology, and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences, Beijing (H.Z., N.X.), People's Republic of China
| | - Gu He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu (Y.Ya., Z.X., X.W., X.Z., Z.S., Y.Ye., G.H., L.Z., N.X., S.L.); Departments of Nephrology (Z.X.) and Neurosurgery (L.Z.), West China Hospital, Sichuan University, Chengdu; and Laboratory of Cell and Molecular Biology, and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences, Beijing (H.Z., N.X.), People's Republic of China
| | - Liangxue Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu (Y.Ya., Z.X., X.W., X.Z., Z.S., Y.Ye., G.H., L.Z., N.X., S.L.); Departments of Nephrology (Z.X.) and Neurosurgery (L.Z.), West China Hospital, Sichuan University, Chengdu; and Laboratory of Cell and Molecular Biology, and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences, Beijing (H.Z., N.X.), People's Republic of China
| | - Hongxia Zhu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu (Y.Ya., Z.X., X.W., X.Z., Z.S., Y.Ye., G.H., L.Z., N.X., S.L.); Departments of Nephrology (Z.X.) and Neurosurgery (L.Z.), West China Hospital, Sichuan University, Chengdu; and Laboratory of Cell and Molecular Biology, and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences, Beijing (H.Z., N.X.), People's Republic of China
| | - Ningzhi Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu (Y.Ya., Z.X., X.W., X.Z., Z.S., Y.Ye., G.H., L.Z., N.X., S.L.); Departments of Nephrology (Z.X.) and Neurosurgery (L.Z.), West China Hospital, Sichuan University, Chengdu; and Laboratory of Cell and Molecular Biology, and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences, Beijing (H.Z., N.X.), People's Republic of China
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu (Y.Ya., Z.X., X.W., X.Z., Z.S., Y.Ye., G.H., L.Z., N.X., S.L.); Departments of Nephrology (Z.X.) and Neurosurgery (L.Z.), West China Hospital, Sichuan University, Chengdu; and Laboratory of Cell and Molecular Biology, and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences, Beijing (H.Z., N.X.), People's Republic of China
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95
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McManus FP, Bourdeau V, Acevedo M, Lopes-Paciencia S, Mignacca L, Lamoliatte F, Rojas Pino JW, Ferbeyre G, Thibault P. Quantitative SUMO proteomics reveals the modulation of several PML nuclear body associated proteins and an anti-senescence function of UBC9. Sci Rep 2018; 8:7754. [PMID: 29773808 PMCID: PMC5958138 DOI: 10.1038/s41598-018-25150-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 03/28/2018] [Indexed: 12/13/2022] Open
Abstract
Several regulators of SUMOylation have been previously linked to senescence but most targets of this modification in senescent cells remain unidentified. Using a two-step purification of a modified SUMO3, we profiled the SUMO proteome of senescent cells in a site-specific manner. We identified 25 SUMO sites on 23 proteins that were significantly regulated during senescence. Of note, most of these proteins were PML nuclear body (PML-NB) associated, which correlates with the increased number and size of PML-NBs observed in senescent cells. Interestingly, the sole SUMO E2 enzyme, UBC9, was more SUMOylated during senescence on its Lys-49. Functional studies of a UBC9 mutant at Lys-49 showed a decreased association to PML-NBs and the loss of UBC9’s ability to delay senescence. We thus propose both pro- and anti-senescence functions of protein SUMOylation.
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Affiliation(s)
- Francis P McManus
- Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Véronique Bourdeau
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Mariana Acevedo
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Stéphane Lopes-Paciencia
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Lian Mignacca
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Frédéric Lamoliatte
- Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3C 3J7, Canada.,Department of Chemistry, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - John W Rojas Pino
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Gerardo Ferbeyre
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada.
| | - Pierre Thibault
- Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3C 3J7, Canada. .,Department of Chemistry, Université de Montréal, Montréal, QC H3C 3J7, Canada.
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96
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Matmati S, Vaurs M, Escandell JM, Maestroni L, Nakamura TM, Ferreira MG, Géli V, Coulon S. The fission yeast Stn1-Ten1 complex limits telomerase activity via its SUMO-interacting motif and promotes telomeres replication. SCIENCE ADVANCES 2018; 4:eaar2740. [PMID: 29774234 PMCID: PMC5955624 DOI: 10.1126/sciadv.aar2740] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/29/2018] [Indexed: 06/01/2023]
Abstract
Mammalian CST (CTC1-STN1-TEN1) complex fulfills numerous functions including rescue of the stalled replication forks and termination of telomerase action. In fission yeast lacking the CTC1 ortholog, the Stn1-Ten1 complex restricts telomerase action via its sumoylation-mediated interaction with Tpz1TPP1. We identify a small ubiquitin-like modifier (SUMO)-interacting motif (SIM) in the carboxyl-terminal part of Stn1 and show that this domain is crucial for SUMO and Tpz1-SUMO interactions. Point mutations in the SIM (Stn1-226) lead to telomere elongation, impair Stn1-Ten1 recruitment to telomeres, and enhance telomerase binding, revealing that Stn1 SIM domain contributes to the inhibition of telomerase activity at chromosome ends. Our results suggest that Stn1-Ten1 promotes DNA synthesis at telomeres to limit single-strand DNA accumulation. We further demonstrate that Stn1 functions in the replication of telomeric and subtelomeric regions in a Taz1-independent manner. Genetic analysis reveals that misregulation of origin firing and/or telomerase inhibition circumvents the replication defects of the stn1-226 mutant. Together, our results show that the Stn1-Ten1 complex has a dual function at telomeres by limiting telomerase action and promoting chromosome end replication.
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Affiliation(s)
- Samah Matmati
- CRCM, CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Equipe Labellisée Ligue, 27 Boulevard Lei Roure, Marseille, France
| | - Mélina Vaurs
- CRCM, CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Equipe Labellisée Ligue, 27 Boulevard Lei Roure, Marseille, France
| | - José M. Escandell
- Telomere and Genome Stability Laboratory, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Laetitia Maestroni
- CRCM, CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Equipe Labellisée Ligue, 27 Boulevard Lei Roure, Marseille, France
| | - Toru M. Nakamura
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Miguel G. Ferreira
- Telomere and Genome Stability Laboratory, Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Institute for Research on Cancer and Aging, Nice, Faculty of Medicine, CNRS UMR7284, INSERM U1081, University of Nice Sophia Antipolis, Nice, France
| | - Vincent Géli
- CRCM, CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Equipe Labellisée Ligue, 27 Boulevard Lei Roure, Marseille, France
| | - Stéphane Coulon
- CRCM, CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Equipe Labellisée Ligue, 27 Boulevard Lei Roure, Marseille, France
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97
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Probing ubiquitin and SUMO conjugation and deconjugation. Biochem Soc Trans 2018; 46:423-436. [PMID: 29588386 DOI: 10.1042/bst20170086] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 02/25/2018] [Accepted: 02/28/2018] [Indexed: 12/24/2022]
Abstract
Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins including small Ubl modifier (SUMO) are small proteins which are covalently linked to target proteins to regulate their functions. In this review, we discuss the current state of the art and point out what we feel this field urgently needs in order to delineate the wiring of the system. We discuss what is needed to unravel the connections between different components of the conjugation machineries for ubiquitylation and SUMOylation, and to unravel the connections between the conjugation machineries and their substrates. Chemical probes are key tools to probe signal transduction by these small proteins that may help understand their action. This rapidly moving field has resulted in various small molecules that will help us to further understand Ub and SUMO function and that may lead to the development of new drugs.
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98
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Abstract
The Anaphase Promoting Complex/Cyclosome (APC/C) is a ubiquitin E3 ligase that functions as the gatekeeper to mitotic exit. APC/C activity is controlled by an interplay of multiple pathways during mitosis, including the spindle assembly checkpoint (SAC), that are not yet fully understood. Here, we show that sumoylation of the APC4 subunit of the APC/C peaks during mitosis and is critical for timely APC/C activation and anaphase onset. We have also identified a functionally important SUMO interacting motif in the cullin-homology domain of APC2 located near the APC4 sumoylation sites and APC/C catalytic core. Our findings provide evidence of an important regulatory role for SUMO modification and binding in affecting APC/C activation and mitotic exit.
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Affiliation(s)
- Christine C Lee
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Baltimore, United States
| | - Bing Li
- Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Hongtao Yu
- Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Michael J Matunis
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Baltimore, United States
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99
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Leonen CJA, Upadhyay E, Chatterjee C. Studies of biochemical crosstalk in chromatin with semisynthetic histones. Curr Opin Chem Biol 2018; 45:27-34. [PMID: 29494828 DOI: 10.1016/j.cbpa.2018.02.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/08/2018] [Accepted: 02/11/2018] [Indexed: 01/26/2023]
Abstract
Reversible post-translational modifications of histone proteins in eukaryotic chromatin are closely tied to gene function and cellular development. Specific combinations of histone modifications, or marks, are implicated in distinct DNA-templated processes mediated by a range of chromatin-associated enzymes that install, erase and interpret the histone code. Mechanistic studies of the precise biochemical relationship between sets of marks and their effects on chromatin function are significantly complicated by the dynamic nature and heterogeneity of marks in cellular chromatin. Protein semisynthesis is a chemical technique that enables the piecewise assembly of uniformly and site-specifically modified histones in quantities sufficient for biophysical and biochemical analyses. Recent pioneering efforts in semisynthesis have yielded access to histones site-specifically modified by entire proteins, such as ubiquitin (Ub) and the small ubiquitin-like modifier (SUMO). Herein, we highlight key studies of biochemical crosstalk involving Ub and SUMO in chromatin that were enabled by histone semisynthesis.
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Affiliation(s)
| | - Esha Upadhyay
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States.
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100
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Iribarren PA, Di Marzio LA, Berazategui MA, De Gaudenzi JG, Alvarez VE. SUMO polymeric chains are involved in nuclear foci formation and chromatin organization in Trypanosoma brucei procyclic forms. PLoS One 2018; 13:e0193528. [PMID: 29474435 PMCID: PMC5825156 DOI: 10.1371/journal.pone.0193528] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/13/2018] [Indexed: 01/10/2023] Open
Abstract
SUMOylation is a post-translational modification conserved in eukaryotic organisms that involves the covalent attachment of the small ubiquitin-like protein SUMO to internal lysine residues in target proteins. This tag usually alters the interaction surface of the modified protein and can be translated into changes in its biological activity, stability or subcellular localization, among other possible outputs. SUMO can be attached as a single moiety or as SUMO polymers in case there are internal acceptor sites in SUMO itself. These chains have been shown to be important for proteasomal degradation as well as for the formation of subnuclear structures such as the synaptonemal complex in Saccharomyces cerevisiae or promyelocytic leukemia nuclear bodies in mammals. In this work, we have examined SUMO chain formation in the protozoan parasite Trypanosoma brucei. Using a recently developed bacterial strain engineered to produce SUMOylated proteins we confirmed the ability of TbSUMO to form polymers and determined the type of linkage using site-directed mutational analysis. By generating transgenic procyclic parasites unable to form chains we demonstrated that although not essential for normal growth, SUMO polymerization determines the localization of the modified proteins in the nucleus. In addition, FISH analysis of telomeres showed a differential positioning depending on the polySUMOylation abilities of the cells. Thus, our observations suggest that TbSUMO chains might play a role in establishing interaction platforms contributing to chromatin organization.
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Affiliation(s)
- Paula Ana Iribarren
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
| | - Lucía Ayelén Di Marzio
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
| | - María Agustina Berazategui
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
| | - Javier Gerardo De Gaudenzi
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
- * E-mail: (VEA); (JGDG)
| | - Vanina Eder Alvarez
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
- * E-mail: (VEA); (JGDG)
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