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Roy S, Adhikary H, D’Amours D. The SMC5/6 complex: folding chromosomes back into shape when genomes take a break. Nucleic Acids Res 2024; 52:2112-2129. [PMID: 38375830 PMCID: PMC10954462 DOI: 10.1093/nar/gkae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
High-level folding of chromatin is a key determinant of the shape and functional state of chromosomes. During cell division, structural maintenance of chromosome (SMC) complexes such as condensin and cohesin ensure large-scale folding of chromatin into visible chromosomes. In contrast, the SMC5/6 complex plays more local and context-specific roles in the structural organization of interphase chromosomes with important implications for health and disease. Recent advances in single-molecule biophysics and cryo-electron microscopy revealed key insights into the architecture of the SMC5/6 complex and how interactions connecting the complex to chromatin components give rise to its unique repertoire of interphase functions. In this review, we provide an integrative view of the features that differentiates the SMC5/6 complex from other SMC enzymes and how these enable dramatic reorganization of DNA folding in space during DNA repair reactions and other genome transactions. Finally, we explore the mechanistic basis for the dynamic targeting of the SMC5/6 complex to damaged chromatin and its crucial role in human health.
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Affiliation(s)
- Shamayita Roy
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Hemanta Adhikary
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Damien D’Amours
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
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2
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Kolbin D, Walker BL, Hult C, Stanton JD, Adalsteinsson D, Forest MG, Bloom K. Polymer Modeling Reveals Interplay between Physical Properties of Chromosomal DNA and the Size and Distribution of Condensin-Based Chromatin Loops. Genes (Basel) 2023; 14:2193. [PMID: 38137015 PMCID: PMC10742461 DOI: 10.3390/genes14122193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Transient DNA loops occur throughout the genome due to thermal fluctuations of DNA and the function of SMC complex proteins such as condensin and cohesin. Transient crosslinking within and between chromosomes and loop extrusion by SMCs have profound effects on high-order chromatin organization and exhibit specificity in cell type, cell cycle stage, and cellular environment. SMC complexes anchor one end to DNA with the other extending some distance and retracting to form a loop. How cells regulate loop sizes and how loops distribute along chromatin are emerging questions. To understand loop size regulation, we employed bead-spring polymer chain models of chromatin and the activity of an SMC complex on chromatin. Our study shows that (1) the stiffness of the chromatin polymer chain, (2) the tensile stiffness of chromatin crosslinking complexes such as condensin, and (3) the strength of the internal or external tethering of chromatin chains cooperatively dictate the loop size distribution and compaction volume of induced chromatin domains. When strong DNA tethers are invoked, loop size distributions are tuned by condensin stiffness. When DNA tethers are released, loop size distributions are tuned by chromatin stiffness. In this three-way interaction, the presence and strength of tethering unexpectedly dictates chromatin conformation within a topological domain.
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Affiliation(s)
- Daniel Kolbin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.K.); (J.D.S.)
| | - Benjamin L. Walker
- Department of Mathematics, University of California-Irvine, Irvine, CA 92697, USA;
| | - Caitlin Hult
- Department of Mathematics, Gettysburg College, Gettysburg, PA 17325, USA
| | - John Donoghue Stanton
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.K.); (J.D.S.)
| | - David Adalsteinsson
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.A.); (M.G.F.)
| | - M. Gregory Forest
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.A.); (M.G.F.)
- Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.K.); (J.D.S.)
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3
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Penzo A, Dubarry M, Brocas C, Zheng M, Mangione RM, Rougemaille M, Goncalves C, Lautier O, Libri D, Simon MN, Géli V, Dubrana K, Palancade B. A R-loop sensing pathway mediates the relocation of transcribed genes to nuclear pore complexes. Nat Commun 2023; 14:5606. [PMID: 37730746 PMCID: PMC10511428 DOI: 10.1038/s41467-023-41345-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023] Open
Abstract
Nuclear pore complexes (NPCs) have increasingly recognized interactions with the genome, as exemplified in yeast, where they bind transcribed or damaged chromatin. By combining genome-wide approaches with live imaging of model loci, we uncover a correlation between NPC association and the accumulation of R-loops, which are genotoxic structures formed through hybridization of nascent RNAs with their DNA templates. Manipulating hybrid formation demonstrates that R-loop accumulation per se, rather than transcription or R-loop-dependent damages, is the primary trigger for relocation to NPCs. Mechanistically, R-loop-dependent repositioning involves their recognition by the ssDNA-binding protein RPA, and SUMO-dependent interactions with NPC-associated factors. Preventing R-loop-dependent relocation leads to lethality in hybrid-accumulating conditions, while NPC tethering of a model hybrid-prone locus attenuates R-loop-dependent genetic instability. Remarkably, this relocation pathway involves molecular factors similar to those required for the association of stalled replication forks with NPCs, supporting the existence of convergent mechanisms for sensing transcriptional and genotoxic stresses.
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Affiliation(s)
- Arianna Penzo
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Marion Dubarry
- Marseille Cancer Research Center (CRCM), U1068, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR7258, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue, 13273, Marseille, France
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, F-69622, Villeurbanne, France
| | - Clémentine Brocas
- Université Paris Cité, Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Myriam Zheng
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Raphaël M Mangione
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Mathieu Rougemaille
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Coralie Goncalves
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Ophélie Lautier
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Domenico Libri
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Marie-Noëlle Simon
- Marseille Cancer Research Center (CRCM), U1068, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR7258, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue, 13273, Marseille, France
| | - Vincent Géli
- Marseille Cancer Research Center (CRCM), U1068, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR7258, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue, 13273, Marseille, France
| | - Karine Dubrana
- Université Paris Cité, Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Benoit Palancade
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France.
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4
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Soon HR, Gaunt JR, Bansal VA, Lenherr C, Sze SK, Ch’ng TH. Seizure enhances SUMOylation and zinc-finger transcriptional repression in neuronal nuclei. iScience 2023; 26:107707. [PMID: 37694138 PMCID: PMC10483055 DOI: 10.1016/j.isci.2023.107707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/29/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
A single episode of pilocarpine-induced status epilepticus can trigger the development of spontaneous recurrent seizures in a rodent model for epilepsy. The initial seizure-induced events in neuronal nuclei that lead to long-term changes in gene expression and cellular responses likely contribute toward epileptogenesis. Using a transgenic mouse model to specifically isolate excitatory neuronal nuclei, we profiled the seizure-induced nuclear proteome via tandem mass tag mass spectrometry and observed robust enrichment of nuclear proteins associated with the SUMOylation pathway. In parallel with nuclear proteome, we characterized nuclear gene expression by RNA sequencing which provided insights into seizure-driven transcriptional regulation and dynamics. Strikingly, we saw widespread downregulation of zinc-finger transcription factors, specifically proteins that harbor Krüppel-associated box (KRAB) domains. Our results provide a detailed snapshot of nuclear events induced by seizure activity and demonstrate a robust method for cell-type-specific nuclear profiling that can be applied to other cell types and models.
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Affiliation(s)
- Hui Rong Soon
- School of Biological Science, Nanyang Technological University, Singapore 636551, Singapore
| | - Jessica Ruth Gaunt
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Vibhavari Aysha Bansal
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Clara Lenherr
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
- Centre for Discovery Brain Science, The University of Edinburgh, Edinburgh, UK
| | - Siu Kwan Sze
- Faculty of Applied Health Sciences, Brock University, St. Catherines, ON, Canada
| | - Toh Hean Ch’ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
- School of Biological Science, Nanyang Technological University, Singapore 636551, Singapore
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5
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Salas-Lloret D, Jansen NS, Nagamalleswari E, van der Meulen C, Gracheva E, de Ru AH, Otte HAM, van Veelen PA, Pichler A, Goedhart J, Vertegaal AC, González-Prieto R. SUMO-activated target traps (SATTs) enable the identification of a comprehensive E3-specific SUMO proteome. SCIENCE ADVANCES 2023; 9:eadh2073. [PMID: 37531430 PMCID: PMC10396300 DOI: 10.1126/sciadv.adh2073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023]
Abstract
Ubiquitin and ubiquitin-like conjugation cascades consist of dedicated E1, E2, and E3 enzymes with E3s providing substrate specificity. Mass spectrometry-based approaches have enabled the identification of more than 6500 SUMO2/3 target proteins. The limited number of SUMO E3s provides the unique opportunity to systematically study E3 substrate wiring. We developed SUMO-activated target traps (SATTs) and systematically identified substrates for eight different SUMO E3s, PIAS1, PIAS2, PIAS3, PIAS4, NSMCE2, ZNF451, LAZSUL (ZNF451-3), and ZMIZ2. SATTs enabled us to identify 427 SUMO1 and 961 SUMO2/3 targets in an E3-specific manner. We found pronounced E3 substrate preference. Quantitative proteomics enabled us to measure substrate specificity of E3s, quantified using the SATT index. Furthermore, we developed the Polar SATTs web-based tool to browse the dataset in an interactive manner. Overall, we uncover E3-to-target wiring of 1388 SUMO substrates, highlighting unique and overlapping sets of substrates for eight different SUMO E3 ligases.
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Affiliation(s)
- Daniel Salas-Lloret
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Nicolette S. Jansen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Coen van der Meulen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Ekaterina Gracheva
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - H. Anne Marie Otte
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Andrea Pichler
- Max Plank Institute for Immunobiology and Epigenetics, Freiburg, Germany
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | | | | | - Román González-Prieto
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-CSIC-Universidad-Pablo de Olavide, Sevilla, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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6
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Peng XP, Zhao X. The multi-functional Smc5/6 complex in genome protection and disease. Nat Struct Mol Biol 2023; 30:724-734. [PMID: 37336994 PMCID: PMC10372777 DOI: 10.1038/s41594-023-01015-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/05/2023] [Indexed: 06/21/2023]
Abstract
Structural maintenance of chromosomes (SMC) complexes are ubiquitous genome regulators with a wide range of functions. Among the three types of SMC complexes in eukaryotes, cohesin and condensin fold the genome into different domains and structures, while Smc5/6 plays direct roles in promoting chromosomal replication and repair and in restraining pathogenic viral extra-chromosomal DNA. The importance of Smc5/6 for growth, genotoxin resistance and host defense across species is highlighted by its involvement in disease prevention in plants and animals. Accelerated progress in recent years, including structural and single-molecule studies, has begun to provide greater insights into the mechanisms underlying Smc5/6 functions. Here we integrate a broad range of recent studies on Smc5/6 to identify emerging features of this unique SMC complex and to explain its diverse cellular functions and roles in disease pathogenesis. We also highlight many key areas requiring further investigation for achieving coherent views of Smc5/6-driven mechanisms.
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Affiliation(s)
- Xiao P Peng
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Sloan Kettering Cancer Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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7
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Xun Q, Song Y, Mei M, Ding Y, Ding C. The SMC5/6 complex subunit MMS21 regulates stem cell proliferation in rice. PLANT CELL REPORTS 2023:10.1007/s00299-023-03030-9. [PMID: 37178216 DOI: 10.1007/s00299-023-03030-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023]
Abstract
KEY MESSAGE SMC5/6 complex subunit OsMMS21 is involved in cell cycle and hormone signaling and required for stem cell proliferation during shoot and root development in rice. The structural maintenance of chromosome (SMC)5/6 complex is required for nucleolar integrity and DNA metabolism. Moreover, METHYL METHANESULFONATE SENSITIVITY GENE 21 (MMS21), a SUMO E3 ligase that is part of the SMC5/6 complex, is essential for the root stem cell niche and cell cycle transition in Arabidopsis. However, its specific role in rice remains unclear. Here, OsSMC5 and OsSMC6 single heterozygous mutants were generated using CRISPR/Cas9 technology to elucidate the function of SMC5/6 subunits, including OsSMC5, OsSMC6, and OsMMS21, in cell proliferation in rice. ossmc5/ + and ossmc6/ + heterozygous single mutants did not yield homozygous mutants in their progeny, indicating that OsSMC5 and OsSMC6 both play necessary roles during embryo formation. Loss of OsMMS21 caused severe defects in both the shoot and roots in rice. Transcriptome analysis showed a significant decrease in the expression of genes involved in auxin signaling in the roots of osmms21 mutants. Moreover, the expression levels of the cycB2-1 and MCM genes, which are involved the cell cycle, were significantly lower in the shoots of the mutants, indicating that OsMMS21 was involved in both hormone signaling pathways and the cell cycle. Overall, these findings indicate that the SUMO E3 ligase OsMMS21 is required for both shoot and root stem cell niches, improving the understanding of the function of the SMC5/6 complex in rice.
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Affiliation(s)
- Qian Xun
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ye Song
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Min Mei
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanfeng Ding
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing, 210095, China
| | - Chengqiang Ding
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, China.
- Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing, 210095, China.
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Dvořák Tomaštíková E, Prochazkova K, Yang F, Jemelkova J, Finke A, Dorn A, Said M, Puchta H, Pecinka A. SMC5/6 complex-mediated SUMOylation stimulates DNA-protein cross-link repair in Arabidopsis. THE PLANT CELL 2023; 35:1532-1547. [PMID: 36705512 PMCID: PMC10118267 DOI: 10.1093/plcell/koad020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 11/23/2022] [Accepted: 01/23/2023] [Indexed: 05/10/2023]
Abstract
DNA-protein cross-links (DPCs) are highly toxic DNA lesions consisting of proteins covalently attached to chromosomal DNA. Unrepaired DPCs physically block DNA replication and transcription. Three DPC repair pathways have been identified in Arabidopsis (Arabidopsis thaliana) to date: the endonucleolytic cleavage of DNA by the structure-specific endonuclease MUS81; proteolytic degradation of the crosslinked protein by the metalloprotease WSS1A; and cleavage of the cross-link phosphodiester bonds by the tyrosyl phosphodiesterases TDP1 and TDP2. Here we describe the evolutionary conserved STRUCTURAL MAINTENANCE OF CHROMOSOMEs SMC5/6 complex as a crucial component involved in DPC repair. We identified multiple alleles of the SMC5/6 complex core subunit gene SMC6B via a forward-directed genetic screen designed to identify the factors involved in the repair of DPCs induced by the cytidine analog zebularine. We monitored plant growth and cell death in response to DPC-inducing chemicals, which revealed that the SMC5/6 complex is essential for the repair of several types of DPCs. Genetic interaction and sensitivity assays showed that the SMC5/6 complex works in parallel to the endonucleolytic and proteolytic pathways. The repair of zebularine-induced DPCs was associated with SMC5/6-dependent SUMOylation of the damage sites. Thus, we present the SMC5/6 complex as an important factor in plant DPC repair.
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Affiliation(s)
| | - Klara Prochazkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
| | - Fen Yang
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 77900 Olomouc, Czech Republic
| | - Jitka Jemelkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Functional Genomics and Proteomics, National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | | | - Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Mahmoud Said
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, 12619, Cairo, Egypt
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
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9
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Liang T, Li G, Lu Y, Hu M, Ma X. The Involvement of Ubiquitination and SUMOylation in Retroviruses Infection and Latency. Viruses 2023; 15:v15040985. [PMID: 37112965 PMCID: PMC10144533 DOI: 10.3390/v15040985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/15/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Retroviruses, especially the pathogenic human immunodeficiency virus type 1 (HIV-1), have severely threatened human health for decades. Retroviruses can form stable latent reservoirs via retroviral DNA integration into the host genome, and then be temporarily transcriptional silencing in infected cells, which makes retroviral infection incurable. Although many cellular restriction factors interfere with various steps of the life cycle of retroviruses and the formation of viral latency, viruses can utilize viral proteins or hijack cellular factors to evade intracellular immunity. Many post-translational modifications play key roles in the cross-talking between the cellular and viral proteins, which has greatly determined the fate of retroviral infection. Here, we reviewed recent advances in the regulation of ubiquitination and SUMOylation in the infection and latency of retroviruses, focusing on both host defense- and virus counterattack-related ubiquitination and SUMOylation system. We also summarized the development of ubiquitination- and SUMOylation-targeted anti-retroviral drugs and discussed their therapeutic potential. Manipulating ubiquitination or SUMOylation pathways by targeted drugs could be a promising strategy to achieve a "sterilizing cure" or "functional cure" of retroviral infection.
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Affiliation(s)
- Taizhen Liang
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China
| | - Guojie Li
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China
| | - Yunfei Lu
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China
| | - Meilin Hu
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China
| | - Xiancai Ma
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
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10
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Li W, Han Q, Zhu Y, Zhou Y, Zhang J, Wu W, Li Y, Liu L, Qiu Y, Hu K, Yin D. SUMOylation of RNF146 results in Axin degradation and activation of Wnt/β-catenin signaling to promote the progression of hepatocellular carcinoma. Oncogene 2023; 42:1728-1740. [PMID: 37029301 DOI: 10.1038/s41388-023-02689-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/09/2023]
Abstract
Aberrant SUMOylation contributes to the progression of hepatocellular carcinoma (HCC), yet the molecular mechanisms have not been well elucidated. RING-type E3 ubiquitin ligase RNF146 is a key regulator of the Wnt/β-catenin signaling pathway, which is frequently hyperactivated in HCC. Here, it is identified that RNF146 can be modified by SUMO3. By mutating all lysines in RNF146, we found that K19, K61, K174 and K175 are the major sites for SUMOylation. UBC9/PIAS3/MMS21 and SENP1/2/6 mediated the conjugation and deconjugation of SUMO3, respectively. Furthermore, SUMOylation of RNF146 promoted its nuclear localization, while deSUMOylation induced its cytoplasmic localization. Importantly, SUMOylation promotes the association of RNF146 with Axin to accelerate the ubiquitination and degradation of Axin. Intriguingly, only UBC9/PIAS3 and SENP1 can act at K19/K175 in RNF146 and affect its role in regulating the stability of Axin. In addition, inhibiting RNF146 SUMOylation suppressed the progression of HCC both in vitro and in vivo. And, patients with higher expression of RNF146 and UBC9 have the worst prognosis. Taken together, we conclude that RNF146 SUMOylation at K19/K175 promotes its association with Axin and accelerates Axin degradation, thereby enhancing β-catenin signaling and contributing to cancer progression. Our findings reveal that RNF146 SUMOylation is a potential therapeutic target in HCC.
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Affiliation(s)
- Wenjia Li
- Guangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, China
| | - Qingfang Han
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Research Centre for Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yuanxin Zhu
- Guangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Department of Orthopedics, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou, 510120, China
| | - Yingshi Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Department of Ultrasound Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Jingyuan Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Weijun Wu
- Department of Oncology Radiotherapy, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421000, China
| | - Yu Li
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Research Centre for Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yuntan Qiu
- Guangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.
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11
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Stabilization of DNA fork junctions by Smc5/6 complexes revealed by single-molecule imaging. Cell Rep 2022; 41:111778. [PMID: 36476856 PMCID: PMC9756111 DOI: 10.1016/j.celrep.2022.111778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 09/15/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
SMC complexes play key roles in genome maintenance, where they ensure efficient genome replication and segregation. The SMC complex Smc5/6 is a crucial player in DNA replication and repair, yet many molecular features that determine its roles are unclear. Here, we use single-molecule microscopy to investigate Smc5/6's interaction with DNA. We find that Smc5/6 forms oligomers that dynamically redistribute on dsDNA by 1D diffusion and statically bind to ssDNA. Using combined force manipulation and single-molecule microscopy, we generate ssDNA-dsDNA junctions that mimic structures present in DNA repair intermediates or replication forks. We show that Smc5/6 accumulates at these junction sites, stabilizes the fork, and promotes the retention of RPA. Our observations provide a model for the complex's enrichment at sites of replication stress and DNA lesions from where it coordinates the recruitment and activation of downstream repair proteins.
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12
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Hallett ST, Campbell Harry I, Schellenberger P, Zhou L, Cronin N, Baxter J, Etheridge T, Murray J, Oliver A. Cryo-EM structure of the Smc5/6 holo-complex. Nucleic Acids Res 2022; 50:9505-9520. [PMID: 35993814 PMCID: PMC9458440 DOI: 10.1093/nar/gkac692] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/14/2022] [Accepted: 07/30/2022] [Indexed: 01/06/2023] Open
Abstract
The Smc5/6 complex plays an essential role in the resolution of recombination intermediates formed during mitosis or meiosis, or as a result of the cellular response to replication stress. It also functions as a restriction factor preventing viral replication. Here, we report the cryogenic EM (cryo-EM) structure of the six-subunit budding yeast Smc5/6 holo-complex, reconstituted from recombinant proteins expressed in insect cells - providing both an architectural overview of the entire complex and an understanding of how the Nse1/3/4 subcomplex binds to the hetero-dimeric SMC protein core. In addition, we demonstrate that a region within the head domain of Smc5, equivalent to the 'W-loop' of Smc4 or 'F-loop' of Smc1, mediates an important interaction with Nse1. Notably, mutations that alter the surface-charge profile of the region of Nse1 which accepts the Smc5-loop, lead to a slow-growth phenotype and a global reduction in the chromatin-associated fraction of the Smc5/6 complex, as judged by single molecule localisation microscopy experiments in live yeast. Moreover, when taken together, our data indicates functional equivalence between the structurally unrelated KITE and HAWK accessory subunits associated with SMC complexes.
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Affiliation(s)
- Stephen T Hallett
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Isabella Campbell Harry
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Pascale Schellenberger
- Electron Microscopy Imaging Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Lihong Zhou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Nora B Cronin
- London Consortium for CryoEM (LonCEM) Facility, The Francis Crick Institute, London, UK
| | - Jonathan Baxter
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Thomas J Etheridge
- Correspondence may also be addressed to Thomas J. Etheridge. Tel: +44 1273 678123;
| | - Johanne M Murray
- Correspondence may also be addressed to Johanne M. Murray. Tel: +44 1273 877191;
| | - Antony W Oliver
- To whom correspondence should be addressed. Tel: +44 1273 678349;
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13
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Li S, Mutchler A, Zhu X, So S, Epps J, Guan D, Zhao X, Xue X. Multi-faceted regulation of the sumoylation of the Sgs1 DNA helicase. J Biol Chem 2022; 298:102092. [PMID: 35654140 PMCID: PMC9243176 DOI: 10.1016/j.jbc.2022.102092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/27/2022] Open
Abstract
Homologous recombination repairs DNA breaks and sequence gaps via the production of joint DNA intermediates such as Holliday junctions. Dissolving Holliday junctions into linear DNA repair products requires the activity of the Sgs1 helicase in yeast and of its homologs in other organisms. Recent studies suggest that the functions of these conserved helicases are regulated by sumoylation; however, the mechanisms that promote their sumoylation are not well understood. Here, we employed in vitro sumoylation systems and cellular assays to determine the roles of DNA and the scaffold protein Esc2 in Sgs1 sumoylation. We show that DNA binding enhances Sgs1 sumoylation in vitro. In addition, we demonstrate the Esc2’s midregion (MR) with DNA-binding activity is required for Sgs1 sumoylation. Unexpectedly, we found that the sumoylation-promoting effect of Esc2-MR is DNA independent, suggesting a second function for this domain. In agreement with our biochemical data, we found the Esc2-MR domain, like its SUMO E2-binding C-terminal domain characterized in previous studies, is required for proficient sumoylation of Sgs1 and its cofactors, Top3 and Rmi1, in cells. Taken together, these findings provide evidence that while DNA binding enhances Sgs1 sumoylation, Esc2-based stimulation of this modification is mediated by two distinct domains.
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Affiliation(s)
- Shibai Li
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ashley Mutchler
- Materials Science, Engineering, and Commercialization Program, Texas State University, San Marcos, TX 78666, USA
| | - Xinji Zhu
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Stephen So
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - John Epps
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Danying Guan
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Xiaoyu Xue
- Materials Science, Engineering, and Commercialization Program, Texas State University, San Marcos, TX 78666, USA; Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA.
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14
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Smc5/6 Complex Promotes Rad3 ATR Checkpoint Signaling at the Perturbed Replication Fork through Sumoylation of the RecQ Helicase Rqh1. Mol Cell Biol 2022; 42:e0004522. [PMID: 35612306 DOI: 10.1128/mcb.00045-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Smc5/6, like cohesin and condensin, is a structural maintenance of chromosomes complex crucial for genome stability. Unlike cohesin and condensin, Smc5/6 carries an essential Nse2 subunit with SUMO E3 ligase activity. While screening for new DNA replication checkpoint mutants in fission yeast, we have identified two previously uncharacterized mutants in Smc5/6. Characterization of the mutants and a series of previously reported Smc5/6 mutants uncovered that sumoylation of the RecQ helicase Rqh1 by Nse2 facilitates the checkpoint signaling at the replication fork. We found that mutations that eliminate the sumoylation sites or the helicase activity of Rqh1 compromised the checkpoint signaling similar to a nse2 mutant lacking the ligase activity. Surprisingly, introducing a sumoylation site mutation to a helicase-inactive rqh1 mutant promoted cell survival under stress. These findings, together with other genetic data, support a mechanism that sumoylation of Rqh1 by Smc5/6-Nse2 recruits Rqh1 or modulates its helicase activity at the fork to facilitate the checkpoint signaling. Since the Smc5/6 complex, Rqh1, and the replication checkpoint are conserved in eukaryotes, a similar checkpoint mechanism may be operating in human cells.
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15
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The Role of SUMO E3 Ligases in Signaling Pathway of Cancer Cells. Int J Mol Sci 2022; 23:ijms23073639. [PMID: 35408996 PMCID: PMC8998487 DOI: 10.3390/ijms23073639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023] Open
Abstract
Small ubiquitin-like modifier (SUMO)ylation is a reversible post-translational modification that plays a crucial role in numerous aspects of cell physiology, including cell cycle regulation, DNA damage repair, and protein trafficking and turnover, which are of importance for cell homeostasis. Mechanistically, SUMOylation is a sequential multi-enzymatic process where SUMO E3 ligases recruit substrates and accelerate the transfer of SUMO onto targets, modulating their interactions, localization, activity, or stability. Accumulating evidence highlights the critical role of dysregulated SUMO E3 ligases in processes associated with the occurrence and development of cancers. In the present review, we summarize the SUMO E3 ligases, in particular, the novel ones recently identified, and discuss their regulatory roles in cancer pathogenesis.
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16
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Irwan ID, Bogerd HP, Cullen BR. Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency. Nat Microbiol 2022; 7:2101-2113. [PMID: 36376394 PMCID: PMC9712108 DOI: 10.1038/s41564-022-01264-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022]
Abstract
After viral entry and reverse transcription, HIV-1 proviruses that fail to integrate are epigenetically silenced, but the underlying mechanism has remained unclear. Using a genome-wide CRISPR/Cas9 knockout screen, we identified the host SMC5/6 complex as essential for this epigenetic silencing. We show that SMC5/6 binds to and then SUMOylates unintegrated chromatinized HIV-1 DNA. Inhibition of SUMOylation, either by point mutagenesis of the SMC5/6 component NSMCE2-a SUMO E3 ligase-or using the SUMOylation inhibitor TAK-981, prevents epigenetic silencing, enables transcription from unintegrated HIV-1 DNA and rescues the replication of integrase-deficient HIV-1. Finally, we show that blocking SMC5/6 complex expression, or inhibiting its SUMOylation activity, suppresses the establishment of latent HIV-1 infections in both CD4+ T cell lines and primary human T cells. Collectively, our data show that the SMC5/6 complex plays a direct role in mediating the establishment of HIV-1 latency by epigenetically silencing integration-competent HIV-1 proviruses before integration.
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Affiliation(s)
- Ishak D. Irwan
- grid.189509.c0000000100241216Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC USA
| | - Hal P. Bogerd
- grid.189509.c0000000100241216Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC USA
| | - Bryan R. Cullen
- grid.189509.c0000000100241216Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC USA
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17
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Varejão N, Lascorz J, Codina-Fabra J, Bellí G, Borràs-Gas H, Torres-Rosell J, Reverter D. Structural basis for the E3 ligase activity enhancement of yeast Nse2 by SUMO-interacting motifs. Nat Commun 2021; 12:7013. [PMID: 34853311 PMCID: PMC8636563 DOI: 10.1038/s41467-021-27301-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/09/2021] [Indexed: 01/02/2023] Open
Abstract
Post-translational modification of proteins by ubiquitin and ubiquitin-like modifiers, such as SUMO, are key events in protein homeostasis or DNA damage response. Smc5/6 is a nuclear multi-subunit complex that participates in the recombinational DNA repair processes and is required in the maintenance of chromosome integrity. Nse2 is a subunit of the Smc5/6 complex that possesses SUMO E3 ligase activity by the presence of a SP-RING domain that activates the E2~SUMO thioester for discharge on the substrate. Here we present the crystal structure of the SUMO E3 ligase Nse2 in complex with an E2-SUMO thioester mimetic. In addition to the interface between the SP-RING domain and the E2, the complex reveals how two SIM (SUMO-Interacting Motif) -like motifs in Nse2 are restructured upon binding the donor and E2-backside SUMO during the E3-dependent discharge reaction. Both SIM interfaces are essential in the activity of Nse2 and are required to cope with DNA damage. Nse2 is a SUMO E3 ligase component of the Smc5/6 multisubunit complex involved in the DNA repair and chromosome integrity. Here, the structure of the Nse2 in complex with an E2-SUMO thioester mimetic reveals the combined action of two SIM motifs during the E3- dependent conjugation reaction.
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Affiliation(s)
- Nathalia Varejão
- Institut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Jara Lascorz
- Institut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Joan Codina-Fabra
- IRBLLEIDA, Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Gemma Bellí
- IRBLLEIDA, Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Helena Borràs-Gas
- Institut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Jordi Torres-Rosell
- IRBLLEIDA, Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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18
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Cappadocia L, Kochańczyk T, Lima CD. DNA asymmetry promotes SUMO modification of the single-stranded DNA-binding protein RPA. EMBO J 2021; 40:e103787. [PMID: 34585421 PMCID: PMC8591536 DOI: 10.15252/embj.2019103787] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 11/23/2022] Open
Abstract
Repair of DNA double‐stranded breaks by homologous recombination (HR) is dependent on DNA end resection and on post‐translational modification of repair factors. In budding yeast, single‐stranded DNA is coated by replication protein A (RPA) following DNA end resection, and DNA–RPA complexes are then SUMO‐modified by the E3 ligase Siz2 to promote repair. Here, we show using enzymatic assays that DNA duplexes containing 3' single‐stranded DNA overhangs increase the rate of RPA SUMO modification by Siz2. The SAP domain of Siz2 binds DNA duplexes and makes a key contribution to this process as highlighted by models and a crystal structure of Siz2 and by assays performed using protein mutants. Enzymatic assays performed using DNA that can accommodate multiple RPA proteins suggest a model in which the SUMO‐RPA signal is amplified by successive rounds of Siz2‐dependent SUMO modification of RPA and dissociation of SUMO‐RPA at the junction between single‐ and double‐stranded DNA. Our results provide insights on how DNA architecture scaffolds a substrate and E3 ligase to promote SUMO modification in the context of DNA repair.
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Affiliation(s)
- Laurent Cappadocia
- Structural Biology Program, Sloan Kettering Institute, New York, NY, USA.,Department of Chemistry, Université du Québec à Montréal, Montréal, QC, Canada
| | - Tomasz Kochańczyk
- Structural Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, New York, NY, USA.,Howard Hughes Medical Institute, Sloan Kettering Institute, New York, NY, USA
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19
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The SUMO ligase MMS21 profoundly influences maize development through its impact on genome activity and stability. PLoS Genet 2021; 17:e1009830. [PMID: 34695110 PMCID: PMC8568144 DOI: 10.1371/journal.pgen.1009830] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/04/2021] [Accepted: 09/20/2021] [Indexed: 12/04/2022] Open
Abstract
The post-translational addition of SUMO plays essential roles in numerous eukaryotic processes including cell division, transcription, chromatin organization, DNA repair, and stress defense through its selective conjugation to numerous targets. One prominent plant SUMO ligase is METHYL METHANESULFONATE-SENSITIVE (MMS)-21/HIGH-PLOIDY (HPY)-2/NON-SMC-ELEMENT (NSE)-2, which has been connected genetically to development and endoreduplication. Here, we describe the potential functions of MMS21 through a collection of UniformMu and CRISPR/Cas9 mutants in maize (Zea mays) that display either seed lethality or substantially compromised pollen germination and seed/vegetative development. RNA-seq analyses of leaves, embryos, and endosperm from mms21 plants revealed a substantial dysregulation of the maize transcriptome, including the ectopic expression of seed storage protein mRNAs in leaves and altered accumulation of mRNAs associated with DNA repair and chromatin dynamics. Interaction studies demonstrated that MMS21 associates in the nucleus with the NSE4 and STRUCTURAL MAINTENANCE OF CHROMOSOMES (SMC)-5 components of the chromatin organizer SMC5/6 complex, with in vitro assays confirming that MMS21 will SUMOylate SMC5. Comet assays measuring genome integrity, sensitivity to DNA-damaging agents, and protein versus mRNA abundance comparisons implicated MMS21 in chromatin stability and transcriptional controls on proteome balance. Taken together, we propose that MMS21-directed SUMOylation of the SMC5/6 complex and other targets enables proper gene expression by influencing chromatin structure. The post-translational addition of SUMO to other proteins by the MMS21 SUMO ligase has been implicated in a plethora of biological processes in plants but the identit(ies) of its targets and the biological consequences of their modification remain poorly resolved. Here, we address this issue by characterizing a collection of maize mms21 mutants using genetic, biochemical, transcriptomic and proteomic approaches. Our results revealed that mms21 mutations substantially compromise pollen germination and seed/vegetative development, dysregulate the maize transcriptome, including the ectopic expression of seed storage protein mRNAs in leaves, increase DNA damage, and alter the proteome/transcriptome balance. Interaction studies showed that MMS21 associates in the nucleus with the NON-SMC-ELEMENT (NSE)-4 and STRUCTURAL MAINTENANCE OF CHROMOSOMES (SMC)-5 components of the chromatin organizer SMC5/6 complex responsible for DNA-damage repair and chromatin accessibility. Our data demonstrate that MMS21 is crucial for plant development likely through its maintenance of DNA repair, balanced transcription, and genome stability.
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20
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Dodat F, Mader S, Lévesque D. Minireview: What is Known about SUMOylation Among NR4A Family Members? J Mol Biol 2021; 433:167212. [PMID: 34437889 DOI: 10.1016/j.jmb.2021.167212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/16/2021] [Accepted: 08/16/2021] [Indexed: 02/06/2023]
Abstract
NR4A receptors, including NUR77 (NR4A1), NURR1 (NR4A2) and NOR-1 (NR4A3), form a family of nuclear receptors that act as transcription factors to regulate many physiological and pathological processes such as cell cycle and apoptosis, lipid metabolism, inflammation, carcinogenesis, vascular and neuronal functions. In the absence of known endogenous ligand modulating their physiological functions, the NR4A family remains a class of orphan receptors. However, several post-translational modifications (PTMs), including SUMOylation, have been shown to regulate the expression and/or activity of these receptors. Addition of Small Ubiquitin-like MOdifier (SUMO) proteins is a dynamic and reversible enzymatic process that regulates multiple essential functions of proteins, including nuclear receptors. This review aims at summarizing what is known about the impact of SUMOylation on NR4A family member transcriptional activities and physiological functions.
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MESH Headings
- Animals
- Apoptosis/genetics
- Carcinogenesis/genetics
- Carcinogenesis/metabolism
- Carcinogenesis/pathology
- Cell Cycle/genetics
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Eukaryotic Cells/cytology
- Eukaryotic Cells/metabolism
- Humans
- Inflammation
- Lipid Metabolism/genetics
- Multigene Family
- Nuclear Receptor Subfamily 4, Group A, Member 1/genetics
- Nuclear Receptor Subfamily 4, Group A, Member 1/metabolism
- Nuclear Receptor Subfamily 4, Group A, Member 2/genetics
- Nuclear Receptor Subfamily 4, Group A, Member 2/metabolism
- Protein Processing, Post-Translational
- Receptors, Steroid/genetics
- Receptors, Steroid/metabolism
- Receptors, Thyroid Hormone/genetics
- Receptors, Thyroid Hormone/metabolism
- Small Ubiquitin-Related Modifier Proteins/genetics
- Small Ubiquitin-Related Modifier Proteins/metabolism
- Sumoylation
- Transcription, Genetic
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Affiliation(s)
- Fatéma Dodat
- Faculté de Pharmacie, Université de Montréal, Montréal, QC, Canada; Institut de Recherche en Immunologie et Cancérologie (IRIC) and Département de biochimie et de médecine moléculaire, Faculté de médecine, Université de Montréal, Montréal, QC, Canada.
| | - Sylvie Mader
- Institut de Recherche en Immunologie et Cancérologie (IRIC) and Département de biochimie et de médecine moléculaire, Faculté de médecine, Université de Montréal, Montréal, QC, Canada
| | - Daniel Lévesque
- Faculté de Pharmacie, Université de Montréal, Montréal, QC, Canada
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21
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Smc5/6, an atypical SMC complex with two RING-type subunits. Biochem Soc Trans 2021; 48:2159-2171. [PMID: 32964921 DOI: 10.1042/bst20200389] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 01/06/2023]
Abstract
The Smc5/6 complex plays essential roles in chromosome segregation and repair, by promoting disjunction of sister chromatids. The core of the complex is constituted by an heterodimer of Structural Maintenance of Chromosomes (SMC) proteins that use ATP hydrolysis to dynamically associate with and organize chromosomes. In addition, the Smc5/6 complex contains six non-SMC subunits. Remarkably, and differently to other SMC complexes, the Nse1 and Nse2 subunits contain RING-type domains typically found in E3 ligases, pointing to the capacity to regulate other proteins and complexes through ubiquitin-like modifiers. Nse2 codes for a C-terminal SP-RING domain with SUMO ligase activity, assisting Smc5/6 functions in chromosome segregation through sumoylation of several chromosome-associated proteins. Nse1 codes for a C-terminal NH-RING domain and, although it has been proposed to have ubiquitin ligase activity, no Smc5/6-dependent ubiquitylation target has been described to date. Here, we review the function of the two RING domains of the Smc5/6 complex in the broader context of SMC complexes as global chromosome organizers of the genome.
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22
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Taschner M, Basquin J, Steigenberger B, Schäfer IB, Soh YM, Basquin C, Lorentzen E, Räschle M, Scheltema RA, Gruber S. Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding. EMBO J 2021; 40:e107807. [PMID: 34191293 PMCID: PMC8327961 DOI: 10.15252/embj.2021107807] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic cells employ three SMC (structural maintenance of chromosomes) complexes to control DNA folding and topology. The Smc5/6 complex plays roles in DNA repair and in preventing the accumulation of deleterious DNA junctions. To elucidate how specific features of Smc5/6 govern these functions, we reconstituted the yeast holo‐complex. We found that the Nse5/6 sub‐complex strongly inhibited the Smc5/6 ATPase by preventing productive ATP binding. This inhibition was relieved by plasmid DNA binding but not by short linear DNA, while opposing effects were observed without Nse5/6. We uncovered two binding sites for Nse5/6 on Smc5/6, based on an Nse5/6 crystal structure and cross‐linking mass spectrometry data. One binding site is located at the Smc5/6 arms and one at the heads, the latter likely exerting inhibitory effects on ATP hydrolysis. Cysteine cross‐linking demonstrated that the interaction with Nse5/6 anchored the ATPase domains in a non‐productive state, which was destabilized by ATP and DNA. Under similar conditions, the Nse4/3/1 module detached from the ATPase. Altogether, we show how DNA substrate selection is modulated by direct inhibition of the Smc5/6 ATPase by Nse5/6.
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Affiliation(s)
- Michael Taschner
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Jérôme Basquin
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Barbara Steigenberger
- Max Planck Institute of Biochemistry, Martinsried, Germany.,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Utrecht, The Netherlands
| | | | - Young-Min Soh
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Claire Basquin
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
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Etheridge TJ, Villahermosa D, Campillo-Funollet E, Herbert AD, Irmisch A, Watson AT, Dang HQ, Osborne MA, Oliver AW, Carr AM, Murray JM. Live-cell single-molecule tracking highlights requirements for stable Smc5/6 chromatin association in vivo. eLife 2021; 10:e68579. [PMID: 33860765 PMCID: PMC8075580 DOI: 10.7554/elife.68579] [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: 03/19/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022] Open
Abstract
The essential Smc5/6 complex is required in response to replication stress and is best known for ensuring the fidelity of homologous recombination. Using single-molecule tracking in live fission yeast to investigate Smc5/6 chromatin association, we show that Smc5/6 is chromatin associated in unchallenged cells and this depends on the non-SMC protein Nse6. We define a minimum of two Nse6-dependent sub-pathways, one of which requires the BRCT-domain protein Brc1. Using defined mutants in genes encoding the core Smc5/6 complex subunits, we show that the Nse3 double-stranded DNA binding activity and the arginine fingers of the two Smc5/6 ATPase binding sites are critical for chromatin association. Interestingly, disrupting the single-stranded DNA (ssDNA) binding activity at the hinge region does not prevent chromatin association but leads to elevated levels of gross chromosomal rearrangements during replication restart. This is consistent with a downstream function for ssDNA binding in regulating homologous recombination.
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Affiliation(s)
- Thomas J Etheridge
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Desiree Villahermosa
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Eduard Campillo-Funollet
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Alex David Herbert
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Anja Irmisch
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Adam T Watson
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Hung Q Dang
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Mark A Osborne
- Chemistry Department, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Antony M Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Johanne M Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
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24
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Functions of nuclear receptors SUMOylation. Clin Chim Acta 2021; 516:27-33. [PMID: 33476589 DOI: 10.1016/j.cca.2021.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/18/2022]
Abstract
The nuclear receptor superfamily is a family of ligand-activated transcription factors that play a key role in cell metabolism and human diseases. They can be modified after translation, such as acetylation, ubiquitination, phosphorylation and SUMOylation. Crosstalk between SUMO and ubiquitin, phosphorylation and acetylation regulates a variety of metabolic and physiological activities. Nuclear receptors play an important role in lipid metabolism, inflammation, bile acid homeostasis and autophagy. SUMOylation nuclear receptors can regulate their function and affect cell metabolism. It also provides a potential therapeutic target for atherosclerosis, tumor and other metabolic and inflammation-related diseases. This review focuses on the function of SUMOylation nuclear receptors.
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25
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Matityahu A, Onn I. Hit the brakes - a new perspective on the loop extrusion mechanism of cohesin and other SMC complexes. J Cell Sci 2021; 134:jcs247577. [PMID: 33419949 DOI: 10.1242/jcs.247577] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The three-dimensional structure of chromatin is determined by the action of protein complexes of the structural maintenance of chromosome (SMC) family. Eukaryotic cells contain three SMC complexes, cohesin, condensin, and a complex of Smc5 and Smc6. Initially, cohesin was linked to sister chromatid cohesion, the process that ensures the fidelity of chromosome segregation in mitosis. In recent years, a second function in the organization of interphase chromatin into topologically associated domains has been determined, and loop extrusion has emerged as the leading mechanism of this process. Interestingly, fundamental mechanistic differences exist between mitotic tethering and loop extrusion. As distinct molecular switches that aim to suppress loop extrusion in different biological contexts have been identified, we hypothesize here that loop extrusion is the default biochemical activity of cohesin and that its suppression shifts cohesin into a tethering mode. With this model, we aim to provide an explanation for how loop extrusion and tethering can coexist in a single cohesin complex and also apply it to the other eukaryotic SMC complexes, describing both similarities and differences between them. Finally, we present model-derived molecular predictions that can be tested experimentally, thus offering a new perspective on the mechanisms by which SMC complexes shape the higher-order structure of chromatin.
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Affiliation(s)
- Avi Matityahu
- 8 Henrietta Szold St., The Azrieli Faculty of Medicine, Bar-Ilan University, P.O. Box 1589 Safed, Israel
| | - Itay Onn
- 8 Henrietta Szold St., The Azrieli Faculty of Medicine, Bar-Ilan University, P.O. Box 1589 Safed, Israel
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26
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Jmii S, Cappadocia L. Plant SUMO E3 Ligases: Function, Structural Organization, and Connection With DNA. FRONTIERS IN PLANT SCIENCE 2021; 12:652170. [PMID: 33897743 PMCID: PMC8064691 DOI: 10.3389/fpls.2021.652170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/22/2021] [Indexed: 05/04/2023]
Abstract
Protein modification by the small ubiquitin-like modifier (SUMO) plays an important role in multiple plant processes, including growth, development, and the response to abiotic stresses. Mechanistically, SUMOylation is a sequential multi-enzymatic process where SUMO E3 ligases accelerate SUMO conjugation while also influencing target identity and interactions. This review explores the biological functions of plant SUMO E3 ligases [SAP AND MIZ1 DOMAIN-CONTAINING LIGASE (SIZs), METHYL METHANESULFONATE-SENSITIVITY PROTEIN 21 (MMS21s), and PROTEIN INHIBITOR OF ACTIVATED STAT-LIKE (PIALs)] in relation to their molecular activities and domains. We also explore the sub-cellular localization of SUMO E3 ligases and review evidence suggesting a connection between certain SUMO E3 ligases and DNA that contributes to gene expression regulation.
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27
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Gutierrez-Escribano P, Hormeño S, Madariaga-Marcos J, Solé-Soler R, O'Reilly FJ, Morris K, Aicart-Ramos C, Aramayo R, Montoya A, Kramer H, Rappsilber J, Torres-Rosell J, Moreno-Herrero F, Aragon L. Purified Smc5/6 Complex Exhibits DNA Substrate Recognition and Compaction. Mol Cell 2020; 80:1039-1054.e6. [PMID: 33301732 PMCID: PMC7758880 DOI: 10.1016/j.molcel.2020.11.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 10/12/2020] [Accepted: 11/04/2020] [Indexed: 02/03/2023]
Abstract
Eukaryotic SMC complexes, cohesin, condensin, and Smc5/6, use ATP hydrolysis to power a plethora of functions requiring organization and restructuring of eukaryotic chromosomes in interphase and during mitosis. The Smc5/6 mechanism of action and its activity on DNA are largely unknown. Here we purified the budding yeast Smc5/6 holocomplex and characterized its core biochemical and biophysical activities. Purified Smc5/6 exhibits DNA-dependent ATP hydrolysis and SUMO E3 ligase activity. We show that Smc5/6 binds DNA topologically with affinity for supercoiled and catenated DNA templates. Employing single-molecule assays to analyze the functional and dynamic characteristics of Smc5/6 bound to DNA, we show that Smc5/6 locks DNA plectonemes and can compact DNA in an ATP-dependent manner. These results demonstrate that the Smc5/6 complex recognizes DNA tertiary structures involving juxtaposed helices and might modulate DNA topology by plectoneme stabilization and local compaction.
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Affiliation(s)
| | - Silvia Hormeño
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Julene Madariaga-Marcos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Roger Solé-Soler
- Institut de Recerca Biomèdica de Lleida (IRBLLEIDA), Department of Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Francis J O'Reilly
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Kyle Morris
- Microscopy Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ricardo Aramayo
- Microscopy Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Alex Montoya
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jordi Torres-Rosell
- Institut de Recerca Biomèdica de Lleida (IRBLLEIDA), Department of Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Luis Aragon
- Cell Cycle Group, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK.
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28
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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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29
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Keiten-Schmitz J, Schunck K, Müller S. SUMO Chains Rule on Chromatin Occupancy. Front Cell Dev Biol 2020; 7:343. [PMID: 31998715 PMCID: PMC6965010 DOI: 10.3389/fcell.2019.00343] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 12/03/2019] [Indexed: 12/22/2022] Open
Abstract
The dynamic and reversible post-translational modification of proteins and protein complexes with the ubiquitin-related SUMO modifier regulates a wide variety of nuclear functions, such as transcription, replication and DNA repair. SUMO can be attached as a monomer to its targets, but can also form polymeric SUMO chains. While monoSUMOylation is generally involved in the assembly of protein complexes, multi- or polySUMOylation may have very different consequences. The evolutionary conserved paradigmatic signaling process initiated by multi- or polySUMOylation is the SUMO-targeted Ubiquitin ligase (StUbL) pathway, where the presence of multiple SUMO moieties primes ubiquitylation by the mammalian E3 ubiquitin ligases RNF4 or RNF111, or the yeast Slx5/8 heterodimer. The mammalian SUMO chain-specific isopeptidases SENP6 or SENP7, or yeast Ulp2, counterbalance chain formation thereby limiting StUbL activity. Many facets of SUMO chain signaling are still incompletely understood, mainly because only a limited number of polySUMOylated substrates have been identified. Here we summarize recent work that revealed a highly interconnected network of candidate polySUMO modified proteins functioning in DNA damage response and chromatin organization. Based on these datasets and published work on distinct polySUMO-regulated processes we discuss overarching concepts in SUMO chain function. We propose an evolutionary conserved role of polySUMOylation in orchestrating chromatin dynamics and genome stability networks by balancing chromatin-residency of protein complexes. This concept will be exemplified in processes, such as centromere/kinetochore organization, sister chromatid cohesion, DNA repair and replication.
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Affiliation(s)
- Jan Keiten-Schmitz
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
| | - Kathrin Schunck
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
| | - Stefan Müller
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
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30
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Zapatka M, Pociño-Merino I, Heluani-Gahete H, Bermúdez-López M, Tarrés M, Ibars E, Solé-Soler R, Gutiérrez-Escribano P, Apostolova S, Casas C, Aragon L, Wellinger R, Colomina N, Torres-Rosell J. Sumoylation of Smc5 Promotes Error-free Bypass at Damaged Replication Forks. Cell Rep 2019; 29:3160-3172.e4. [DOI: 10.1016/j.celrep.2019.10.123] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 12/15/2022] Open
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31
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Winczura A, Appanah R, Tatham MH, Hay RT, De Piccoli G. The S phase checkpoint promotes the Smc5/6 complex dependent SUMOylation of Pol2, the catalytic subunit of DNA polymerase ε. PLoS Genet 2019; 15:e1008427. [PMID: 31765407 PMCID: PMC6876773 DOI: 10.1371/journal.pgen.1008427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/16/2019] [Indexed: 12/31/2022] Open
Abstract
Replication fork stalling and accumulation of single-stranded DNA trigger the S phase checkpoint, a signalling cascade that, in budding yeast, leads to the activation of the Rad53 kinase. Rad53 is essential in maintaining cell viability, but its targets of regulation are still partially unknown. Here we show that Rad53 drives the hyper-SUMOylation of Pol2, the catalytic subunit of DNA polymerase ε, principally following replication forks stalling induced by nucleotide depletion. Pol2 is the main target of SUMOylation within the replisome and its modification requires the SUMO-ligase Mms21, a subunit of the Smc5/6 complex. Moreover, the Smc5/6 complex co-purifies with Pol ε, independently of other replisome components. Finally, we map Pol2 SUMOylation to a single site within the N-terminal catalytic domain and identify a SUMO-interacting motif at the C-terminus of Pol2. These data suggest that the S phase checkpoint regulate Pol ε during replication stress through Pol2 SUMOylation and SUMO-binding ability.
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Affiliation(s)
- Alicja Winczura
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Rowin Appanah
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Michael H. Tatham
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, United Kingdom
| | - Ronald T. Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, United Kingdom
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32
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Using Cell Cycle-Restricted Alleles to Study the Chromatin Dynamics and Functions of the Structural Maintenance of Chromosomes (SMC) Complexes In Vivo. Methods Mol Biol 2019. [PMID: 31147905 DOI: 10.1007/978-1-4939-9520-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
SMC complexes play fundamental functions in chromosome architecture and organization as well as in DNA replication and repair throughout the cell cycle. The essential nature of the SMC components makes the study of their specific functions challenging. In this chapter, we describe the application of cell cycle tags to S. cerevisiae SMC genes. The cell cycle tags regulate both gene expression and protein degradation, allowing for restriction of the gene of interest to either the S or the G2/M phase. In case of SMC genes, the tags lead to valuable mutants that can bring insights into cell cycle specific essential functions, chromatin binding pattern and functional interactions. Here, we describe the generation of the cell cycle-restricted mutants in diploid and haploid cells and the validation of their functionality with several approaches.
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33
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Brc1 Promotes the Focal Accumulation and SUMO Ligase Activity of Smc5-Smc6 during Replication Stress. Mol Cell Biol 2019; 39:MCB.00271-18. [PMID: 30348841 DOI: 10.1128/mcb.00271-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/12/2018] [Indexed: 11/20/2022] Open
Abstract
As genetic instability drives disease or loss of cell fitness, cellular safeguards have evolved to protect the genome, especially during sensitive cell cycle phases, such as DNA replication. Fission yeast Brc1 has emerged as a key factor in promoting cell survival when replication forks are stalled or collapsed. Brc1 is a multi-BRCT protein that is structurally related to the budding yeast Rtt107 and human PTIP DNA damage response factors, but functional similarities appear limited. Brc1 is a dosage suppressor of a mutation in the essential Smc5-Smc6 genome stability complex and is thought to act in a bypass pathway. In this study, we reveal an unexpectedly intimate connection between Brc1 and Smc5-Smc6 function. Brc1 is required for the accumulation of the Smc5-Smc6 genome stability complex in foci during replication stress and for activation of the intrinsic SUMO ligase activity of the complex by collapsed replication forks. Moreover, we show that the chromatin association and SUMO ligase activity of Smc5-Smc6 require the Nse5-Nse6 heterodimer, explaining how this nonessential cofactor critically supports the DNA repair roles of Smc5-Smc6. We also found that Brc1 interacts with Nse5-Nse6, as well as gamma-H2A, so it can tether Smc5-Smc6 at replicative DNA lesions to promote survival.
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34
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Oravcová M, Boddy MN. Recruitment, loading, and activation of the Smc5-Smc6 SUMO ligase. Curr Genet 2019; 65:669-676. [PMID: 30600397 DOI: 10.1007/s00294-018-0922-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/14/2018] [Accepted: 12/15/2018] [Indexed: 12/21/2022]
Abstract
Duplication of the genome poses one of the most significant threats to genetic integrity, cellular fitness, and organismal health. Therefore, numerous mechanisms have evolved that maintain replication fork stability in the face of DNA damage and allow faithful genome duplication. The fission yeast BRCT-domain-containing protein Brc1, and its budding yeast orthologue Rtt107, has emerged as a "hub" factor that integrates multiple replication fork protection mechanisms. Notably, the cofactors and pathways through which Brc1, Rtt107, and their human orthologue (PTIP) act have appeared largely distinct. This either represents true evolutionary functional divergence, or perhaps an incomplete genetic and biochemical analysis of each protein. In this regard, we recently showed that like Rtt107, Brc1 supports key functions of the Smc5-Smc6 complex, including its recruitment into DNA repair foci, chromatin association, and SUMO ligase activity. Furthermore, fission yeast cells lacking the Nse5-Nse6 genome stability factor were found to exhibit defects in Smc5-Smc6 function, similar to but more severe than those in cells lacking Brc1. Here, we place these findings in context with the known functions of Brc1, Rtt107, and Smc5-Smc6, present data suggesting a role for acetylation in Smc5-Smc6 chromatin loading, and discuss wider implications for genome stability.
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Affiliation(s)
- Martina Oravcová
- Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Michael N Boddy
- Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA.
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35
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Palecek JJ. SMC5/6: Multifunctional Player in Replication. Genes (Basel) 2018; 10:genes10010007. [PMID: 30583551 PMCID: PMC6356406 DOI: 10.3390/genes10010007] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 12/13/2022] Open
Abstract
The genome replication process is challenged at many levels. Replication must proceed through different problematic sites and obstacles, some of which can pause or even reverse the replication fork (RF). In addition, replication of DNA within chromosomes must deal with their topological constraints and spatial organization. One of the most important factors organizing DNA into higher-order structures are Structural Maintenance of Chromosome (SMC) complexes. In prokaryotes, SMC complexes ensure proper chromosomal partitioning during replication. In eukaryotes, cohesin and SMC5/6 complexes assist in replication. Interestingly, the SMC5/6 complexes seem to be involved in replication in many ways. They stabilize stalled RFs, restrain RF regression, participate in the restart of collapsed RFs, and buffer topological constraints during RF progression. In this (mini) review, I present an overview of these replication-related functions of SMC5/6.
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Affiliation(s)
- Jan J Palecek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
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36
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Rosa MTG, Almeida DM, Pires IS, da Rosa Farias D, Martins AG, da Maia LC, de Oliveira AC, Saibo NJM, Oliveira MM, Abreu IA. Insights into the transcriptional and post-transcriptional regulation of the rice SUMOylation machinery and into the role of two rice SUMO proteases. BMC PLANT BIOLOGY 2018; 18:349. [PMID: 30541427 PMCID: PMC6291987 DOI: 10.1186/s12870-018-1547-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 11/20/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND SUMOylation is an essential eukaryotic post-translation modification that, in plants, regulates numerous cellular processes, ranging from seed development to stress response. Using rice as a model crop plant, we searched for potential regulatory points that may influence the activity of the rice SUMOylation machinery genes. RESULTS We analyzed the presence of putative cis-acting regulatory elements (CREs) within the promoter regions of the rice SUMOylation machinery genes and found CREs related to different cellular processes, including hormone signaling. We confirmed that the transcript levels of genes involved in target-SUMOylation, containing ABA- and GA-related CREs, are responsive to treatments with these hormones. Transcriptional analysis in Nipponbare (spp. japonica) and LC-93-4 (spp. indica), showed that the transcript levels of all studied genes are maintained in the two subspecies, under normal growth. OsSUMO3 is an exceptional case since it is expressed at low levels or is not detectable at all in LC-93-4 roots and shoots, respectively. We revealed post-transcriptional regulation by alternative splicing (AS) for all genes studied, except for SUMO coding genes, OsSIZ2, OsOTS3, and OsELS2. Some AS forms have the potential to alter protein domains and catalytic centers. We also performed the molecular and phenotypic characterization of T-DNA insertion lines of some of the genes under study. Knockouts of OsFUG1 and OsELS1 showed increased SUMOylation levels and non-overlapping phenotypes. The fug1 line showed a dwarf phenotype, and significant defects in fertility, seed weight, and panicle architecture, while the els1 line showed early flowering and decreased plant height. We suggest that OsELS1 is an ortholog of AtEsd4, which was also supported by our phylogenetic analysis. CONCLUSIONS Overall, we provide a comprehensive analysis of the rice SUMOylation machinery and discuss possible effects of the regulation of these genes at the transcriptional and post-transcriptional level. We also contribute to the characterization of two rice SUMO proteases, OsELS1 and OsFUG1.
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Affiliation(s)
- Margarida T. G. Rosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República, 2780-157 Oeiras, Portugal
| | - Diego M. Almeida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República, 2780-157 Oeiras, Portugal
- IBET, Av. da República, 2780-157 Oeiras, Portugal
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes (BPMP), Institut National de la Recherche Agronomique (INRA), Université de Montpellier (UM), Montpellier, France
| | - Inês S. Pires
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República, 2780-157 Oeiras, Portugal
- Frontiers Media SA, Avenue du Tribunal-Fédéral 34, CH-1015 Lausanne, Switzerland
| | - Daniel da Rosa Farias
- Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS Brazil
| | - Alice G. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República, 2780-157 Oeiras, Portugal
| | - Luciano Carlos da Maia
- Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS Brazil
| | - António Costa de Oliveira
- Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS Brazil
| | - Nelson J. M. Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República, 2780-157 Oeiras, Portugal
| | - M. Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República, 2780-157 Oeiras, Portugal
| | - Isabel A. Abreu
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República, 2780-157 Oeiras, Portugal
- IBET, Av. da República, 2780-157 Oeiras, Portugal
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37
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Gil-Garcia M, Bañó-Polo M, Varejão N, Jamroz M, Kuriata A, Díaz-Caballero M, Lascorz J, Morel B, Navarro S, Reverter D, Kmiecik S, Ventura S. Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein Solubility. Mol Pharm 2018; 15:3846-3859. [DOI: 10.1021/acs.molpharmaceut.8b00341] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Marcos Gil-Garcia
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - Manuel Bañó-Polo
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - Nathalia Varejão
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - Michal Jamroz
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, 00-927 Warsaw, Poland
| | - Aleksander Kuriata
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, 00-927 Warsaw, Poland
| | - Marta Díaz-Caballero
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - Jara Lascorz
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - Bertrand Morel
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - Sebastian Kmiecik
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, 00-927 Warsaw, Poland
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
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38
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Affiliation(s)
- Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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