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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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Xu MJ, Jordan PW. SMC5/6 Promotes Replication Fork Stability via Negative Regulation of the COP9 Signalosome. Int J Mol Sci 2024; 25:952. [PMID: 38256025 PMCID: PMC10815603 DOI: 10.3390/ijms25020952] [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: 12/04/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
It is widely accepted that DNA replication fork stalling is a common occurrence during cell proliferation, but there are robust mechanisms to alleviate this and ensure DNA replication is completed prior to chromosome segregation. The SMC5/6 complex has consistently been implicated in the maintenance of replication fork integrity. However, the essential role of the SMC5/6 complex during DNA replication in mammalian cells has not been elucidated. In this study, we investigate the molecular consequences of SMC5/6 loss at the replication fork in mouse embryonic stem cells (mESCs), employing the auxin-inducible degron (AID) system to deplete SMC5 acutely and reversibly in the defined cellular contexts of replication fork stall and restart. In SMC5-depleted cells, we identify a defect in the restart of stalled replication forks, underpinned by excess MRE11-mediated fork resection and a perturbed localization of fork protection factors to the stalled fork. Previously, we demonstrated a physical and functional interaction of SMC5/6 with the COP9 signalosome (CSN), a cullin deneddylase that enzymatically regulates cullin ring ligase (CRL) activity. Employing a combination of DNA fiber techniques, the AID system, small-molecule inhibition assays, and immunofluorescence microscopy analyses, we show that SMC5/6 promotes the localization of fork protection factors to stalled replication forks by negatively modulating the COP9 signalosome (CSN). We propose that the SMC5/6-mediated modulation of the CSN ensures that CRL activity and their roles in DNA replication fork stabilization are maintained to allow for efficient replication fork restart when a replication fork stall is alleviated.
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Affiliation(s)
- Michelle J. Xu
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Philip W. Jordan
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
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3
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Roy S, Zaker A, Mer A, D’Amours D. Large-scale phenogenomic analysis of human cancers uncovers frequent alterations affecting SMC5/6 complex components in breast cancer. NAR Cancer 2023; 5:zcad047. [PMID: 37705607 PMCID: PMC10495288 DOI: 10.1093/narcan/zcad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/09/2023] [Accepted: 08/22/2023] [Indexed: 09/15/2023] Open
Abstract
Cancer cells often experience large-scale alterations in genome architecture because of DNA damage and replication stress. Whether mutations in core regulators of chromosome structure can also lead to cancer-promoting loss in genome stability is not fully understood. To address this question, we conducted a systematic analysis of mutations affecting a global regulator of chromosome biology -the SMC5/6 complex- in cancer genomics cohorts. Analysis of 64 959 cancer samples spanning 144 tissue types and 199 different cancer genome studies revealed that the SMC5/6 complex is frequently altered in breast cancer patients. Patient-derived mutations targeting this complex associate with strong phenotypic outcomes such as loss of ploidy control and reduced overall survival. Remarkably, the phenotypic impact of several patient mutations can be observed in a heterozygous context, hence providing an explanation for a prominent role of SMC5/6 mutations in breast cancer pathogenesis. Overall, our findings suggest that genes encoding global effectors of chromosome architecture can act as key contributors to cancer development in humans.
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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
| | - Arvin Zaker
- Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Arvind Mer
- Department of Biochemistry, Microbiology & Immunology, 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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4
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González-Martín E, Jiménez J, Tallada VA. BiFCo: visualizing cohesin assembly/disassembly cycle in living cells. Life Sci Alliance 2023; 6:e202301945. [PMID: 37160310 PMCID: PMC10172768 DOI: 10.26508/lsa.202301945] [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: 01/24/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/11/2023] Open
Abstract
Cohesin is a highly conserved, ring-shaped protein complex found in all eukaryotes. It consists of at least two structural maintenance of chromosomes (SMC) proteins, SMC1 and SMC3 in humans (Psm1 and Psm3 in fission yeast), and the kleisin RAD21 (Rad21 in fission yeast). Mutations in its components or regulators can lead to genetic syndromes, known as cohesinopathies, and various types of cancer. Studies in several organisms have shown that only a small fraction of each subunit assembles into complexes, making it difficult to investigate dynamic chromatin loading and unloading using fluorescent fusions in vivo because of excess soluble components. In this study, we introduce bimolecular fluorescent cohesin (BiFCo), based on bimolecular fluorescent complementation in the fission yeast Schizosaccharomyces pombe BiFCo selectively excludes signals from individual proteins, enabling the monitoring of complex assembly and disassembly within a physiological context throughout the entire cell cycle in living cells. This versatile system can be expanded and adapted for various genetic backgrounds and other eukaryotic models, including human cells.
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Affiliation(s)
- Emilio González-Martín
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Seville, Spain
| | - Juan Jiménez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Seville, Spain
| | - Víctor A Tallada
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Seville, Spain
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5
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Ibars E, Codina-Fabra J, Bellí G, Casas C, Tarrés M, Solé-Soler R, Lorite NP, Ximénez-Embún P, Muñoz J, Colomina N, Torres-Rosell J. Ubiquitin proteomics identifies RNA polymerase I as a target of the Smc5/6 complex. Cell Rep 2023; 42:112463. [PMID: 37141096 DOI: 10.1016/j.celrep.2023.112463] [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: 05/30/2022] [Revised: 12/29/2022] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Ubiquitination controls numerous cellular processes, and its deregulation is associated with many pathologies. The Nse1 subunit in the Smc5/6 complex contains a RING domain with ubiquitin E3 ligase activity and essential functions in genome integrity. However, Nse1-dependent ubiquitin targets remain elusive. Here, we use label-free quantitative proteomics to analyze the nuclear ubiquitinome of nse1-C274A RING mutant cells. Our results show that Nse1 impacts the ubiquitination of several proteins involved in ribosome biogenesis and metabolism that, importantly, extend beyond canonical functions of Smc5/6. In addition, our analysis suggests a connection between Nse1 and RNA polymerase I (RNA Pol I) ubiquitination. Specifically, Nse1 and the Smc5/6 complex promote ubiquitination of K408 and K410 in the clamp domain of Rpa190, a modification that induces its degradation in response to blocks in transcriptional elongation. We propose that this mechanism contributes to Smc5/6-dependent segregation of the rDNA array, the locus transcribed by RNA Pol I.
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Affiliation(s)
- Eva Ibars
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Joan Codina-Fabra
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Gemma Bellí
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Celia Casas
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Marc Tarrés
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Roger Solé-Soler
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Neus P Lorite
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Pilar Ximénez-Embún
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), Madrid, Spain; ProteoRed-ISCIII, Madrid, Spain
| | - Javier Muñoz
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), Madrid, Spain; ProteoRed-ISCIII, Madrid, Spain
| | - Neus Colomina
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Jordi Torres-Rosell
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain.
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6
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Grange LJ, Reynolds JJ, Ullah F, Isidor B, Shearer RF, Latypova X, Baxley RM, Oliver AW, Ganesh A, Cooke SL, Jhujh SS, McNee GS, Hollingworth R, Higgs MR, Natsume T, Khan T, Martos-Moreno GÁ, Chupp S, Mathew CG, Parry D, Simpson MA, Nahavandi N, Yüksel Z, Drasdo M, Kron A, Vogt P, Jonasson A, Seth SA, Gonzaga-Jauregui C, Brigatti KW, Stegmann APA, Kanemaki M, Josifova D, Uchiyama Y, Oh Y, Morimoto A, Osaka H, Ammous Z, Argente J, Matsumoto N, Stumpel CTRM, Taylor AMR, Jackson AP, Bielinsky AK, Mailand N, Le Caignec C, Davis EE, Stewart GS. Pathogenic variants in SLF2 and SMC5 cause segmented chromosomes and mosaic variegated hyperploidy. Nat Commun 2022; 13:6664. [PMID: 36333305 PMCID: PMC9636423 DOI: 10.1038/s41467-022-34349-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Embryonic development is dictated by tight regulation of DNA replication, cell division and differentiation. Mutations in DNA repair and replication genes disrupt this equilibrium, giving rise to neurodevelopmental disease characterized by microcephaly, short stature and chromosomal breakage. Here, we identify biallelic variants in two components of the RAD18-SLF1/2-SMC5/6 genome stability pathway, SLF2 and SMC5, in 11 patients with microcephaly, short stature, cardiac abnormalities and anemia. Patient-derived cells exhibit a unique chromosomal instability phenotype consisting of segmented and dicentric chromosomes with mosaic variegated hyperploidy. To signify the importance of these segmented chromosomes, we have named this disorder Atelís (meaning - incomplete) Syndrome. Analysis of Atelís Syndrome cells reveals elevated levels of replication stress, partly due to a reduced ability to replicate through G-quadruplex DNA structures, and also loss of sister chromatid cohesion. Together, these data strengthen the functional link between SLF2 and the SMC5/6 complex, highlighting a distinct role for this pathway in maintaining genome stability.
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Affiliation(s)
- Laura J Grange
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - John J Reynolds
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Farid Ullah
- Advanced Center for Genetic and Translational Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, Nantes Cedex 1, France
| | - Robert F Shearer
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Xenia Latypova
- Service de Génétique Médicale, CHU Nantes, Nantes Cedex 1, France
| | - Ryan M Baxley
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Antony W Oliver
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton, UK
| | - Anil Ganesh
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sophie L Cooke
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Satpal S Jhujh
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Gavin S McNee
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Robert Hollingworth
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Toyoaki Natsume
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka, Japan
| | - Tahir Khan
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
| | - Gabriel Á Martos-Moreno
- Hospital Infantil Universitario Niño Jesús, CIBER de fisiopatología de la obesidad y nutrición (CIBEROBN), Instituto de Salud Carlos III, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Christopher G Mathew
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - David Parry
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh, Scotland
| | - Michael A Simpson
- Department of Medical and Molecular Genetics, Faculty of Life Science and Medicine, Guy's Hospital, King's College London, London, UK
| | - Nahid Nahavandi
- Bioscientia Institute for Medical Diagnostics, Human Genetics, Ingelheim, Germany
| | - Zafer Yüksel
- Bioscientia Institute for Medical Diagnostics, Human Genetics, Ingelheim, Germany
| | - Mojgan Drasdo
- Bioscientia Institute for Medical Diagnostics, Human Genetics, Ingelheim, Germany
| | - Anja Kron
- Bioscientia Institute for Medical Diagnostics, Human Genetics, Ingelheim, Germany
| | - Petra Vogt
- Bioscientia Institute for Medical Diagnostics, Human Genetics, Ingelheim, Germany
| | - Annemarie Jonasson
- Bioscientia Institute for Medical Diagnostics, Human Genetics, Ingelheim, Germany
| | | | - Claudia Gonzaga-Jauregui
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, México
| | | | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Masato Kanemaki
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | | | - Yuri Uchiyama
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yukiko Oh
- Department of Paediatrics, Jichi Medical University School of Medicine, Tochigi, Japan
| | - Akira Morimoto
- Department of Paediatrics, Jichi Medical University School of Medicine, Tochigi, Japan
| | - Hitoshi Osaka
- Department of Paediatrics, Jichi Medical University School of Medicine, Tochigi, Japan
| | | | - Jesús Argente
- Hospital Infantil Universitario Niño Jesús, CIBER de fisiopatología de la obesidad y nutrición (CIBEROBN), Instituto de Salud Carlos III, Universidad Autónoma de Madrid, Madrid, Spain
- IMDEA Alimentación/IMDEA Food, Madrid, Spain
| | - Naomichi Matsumoto
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Constance T R M Stumpel
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Alexander M R Taylor
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Andrew P Jackson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh, Scotland
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Niels Mailand
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cedric Le Caignec
- Centre Hospitalier Universitaire Toulouse, Service de Génétique Médicale and ToNIC, Toulouse NeuroImaging Center, Inserm, UPS, Université de Toulouse, Toulouse, France.
| | - Erica E Davis
- Advanced Center for Genetic and Translational Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA.
- Department of Pediatrics; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
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Smc5/6 silences episomal transcription by a three-step function. Nat Struct Mol Biol 2022; 29:922-931. [PMID: 36097294 DOI: 10.1038/s41594-022-00829-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 07/29/2022] [Indexed: 11/08/2022]
Abstract
In addition to its role in chromosome maintenance, the six-membered Smc5/6 complex functions as a restriction factor that binds to and transcriptionally silences viral and other episomal DNA. However, the underlying mechanism is unknown. Here, we show that transcriptional silencing by the human Smc5/6 complex is a three-step process. The first step is entrapment of the episomal DNA by a mechanism dependent on Smc5/6 ATPase activity and a function of its Nse4a subunit for which the Nse4b paralog cannot substitute. The second step results in Smc5/6 recruitment to promyelocytic leukemia nuclear bodies by SLF2 (the human ortholog of Nse6). The third step promotes silencing through a mechanism requiring Nse2 but not its SUMO ligase activity. By contrast, the related cohesin and condensin complexes fail to bind to or silence episomal DNA, indicating a property unique to Smc5/6.
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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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9
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KSHV RTA antagonizes SMC5/6 complex-induced viral chromatin compaction by hijacking the ubiquitin-proteasome system. PLoS Pathog 2022; 18:e1010744. [PMID: 35914008 PMCID: PMC9371351 DOI: 10.1371/journal.ppat.1010744] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 08/11/2022] [Accepted: 07/15/2022] [Indexed: 02/07/2023] Open
Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV) is a double-stranded DNA virus with the capacity to establish life-long latent infection. During latent infection, the viral genome persists as a circular episome that associates with cellular histones and exists as a nonintegrated minichromosome in the nucleus of infected cells. Chromatin structure and epigenetic programming are required for the proper control of viral gene expression and stable maintenance of viral DNA. However, there is still limited knowledge regarding how the host regulates the chromatin structure and maintenance of episomal DNA. Here, we found that the cellular protein structural maintenance of chromosome (SMC) complex SMC5/6 recognizes and associates with the KSHV genome to inhibit its replication. The SMC5/6 complex can bind to the KSHV genome and suppress KSHV gene transcription by condensing the viral chromatin and creating a repressive chromatin structure. Correspondingly, KSHV employs an antagonistic strategy by utilizing the viral protein RTA to degrade the SMC5/6 complex and antagonize the inhibitory effect of this complex on viral gene transcription. Interestingly, this antagonistic mechanism of RTA is evolutionarily conserved among γ-herpesviruses. Our work suggests that the SMC5/6 complex is a new host factor that restricts KSHV replication. KSHV can establish life-long latent infection. During latency, the viral genome is maintained as an extrachromosomal episome in the infected cells. We demonstrated that the host protein SMC5/6 complex associates with the KSHV genome and results in direct transcriptional inhibition by creating a transcriptionally repressive chromatin structure of the viral genome. RTA, the master switch protein of KSHV, can hijack the ubiquitin-proteasome system to degrade the SMC5/6 complex to antagonize its inhibitory effect on viral gene transcription. Interestingly, this function of RTA is evolutionarily conserved among γ-herpesviruses.
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10
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Gong X, Tian X, Xie H, Li Z. The structural maintenance of chromosomes 5 is a possible biomarker for individualized treatment of colorectal cancer. Cancer Med 2022; 12:3276-3287. [PMID: 35894836 PMCID: PMC9939147 DOI: 10.1002/cam4.5074] [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: 02/18/2022] [Revised: 06/16/2022] [Accepted: 07/03/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Although the understanding of resistance to oxaliplatin (OXA) chemotherapy in colorectal cancer (CRC) has been sought for many years, drug tolerance remains a major challenge for cancer therapy. Revealing the molecular mechanism of OXA resistance could help to explain the poor prognosis of patients. METHODS Gene expression omnibus (GEO) database was searched, GSE83129, which contains RNA profiling in metastatic CRC patients treated first-line with OXA, was chosen for the following analysis. Differential expressed genes (DEGs) between the adenocarcinoma and adjacent_normal team, respectively, in the OXA responders and no-responders were analyzed. The Gene Ontology (GO) and hub genes in the protein-protein interaction (PPI) network were used for the molecular mechanism of OXA resistance. Tumor-related databases were used for the clinical relevance of the structural maintenance of chromosomes 5 (SMC5) in CRC. The in vitro assays were used to detect the molecular function of SMC5 in CRC cells. Quantitative real-time PCR (qRT-PCR) and western blot were used to detect the expression of the structural maintenance of chromosomes 5/6 (SMC5/6) complex components upon OXA and raltitrexed (RTX) treatment. CCK-8 was used to detect the cell viability of cells with different treatment. RESULTS SMC5 was downregulated in CRC tissues of OXA no-response patients. Lower expression of SMC5 was correlated with a poor prognosis in CRC patients, improved this gene expression, inhibited the CRC cell growth and invasion in vitro. Furthermore, SMC5 was downregulated upon OXA treatment in CRC cells, while RTX would reverse its expression, and the combination of these two drugs restored the SMC5 level to the normal situation. Finally, RTX treatment enhanced the OXA cytotoxicity. CONCLUSION SMC5 is a tumor suppressor, that low expression of this gene is benefit for the development of CRC. Combination treatment with RTX and OXA may be more suitable for those OXA no-responders with lower SMC5.
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Affiliation(s)
- Xiaoxia Gong
- School of Life Science and Technology, MOE Key Laboratory of Developmental Genes and Human DiseasesSoutheast UniversityNanjingChina
| | - Xiaowei Tian
- General Surgery DepartmentQingdao Municipal Hospital affiliated to Qingdao UniversityQingdaoChina
| | - Hao Xie
- School of Life Science and Technology, MOE Key Laboratory of Developmental Genes and Human DiseasesSoutheast UniversityNanjingChina
| | - Zhaoshui Li
- Qingdao Medical CollegeQingdao UniversityQingdaoChina
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11
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Post-Translational Modifications of PCNA: Guiding for the Best DNA Damage Tolerance Choice. J Fungi (Basel) 2022; 8:jof8060621. [PMID: 35736104 PMCID: PMC9225081 DOI: 10.3390/jof8060621] [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: 04/29/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 02/01/2023] Open
Abstract
The sliding clamp PCNA is a multifunctional homotrimer mainly linked to DNA replication. During this process, cells must ensure an accurate and complete genome replication when constantly challenged by the presence of DNA lesions. Post-translational modifications of PCNA play a crucial role in channeling DNA damage tolerance (DDT) and repair mechanisms to bypass unrepaired lesions and promote optimal fork replication restart. PCNA ubiquitination processes trigger the following two main DDT sub-pathways: Rad6/Rad18-dependent PCNA monoubiquitination and Ubc13-Mms2/Rad5-mediated PCNA polyubiquitination, promoting error-prone translation synthesis (TLS) or error-free template switch (TS) pathways, respectively. However, the fork protection mechanism leading to TS during fork reversal is still poorly understood. In contrast, PCNA sumoylation impedes the homologous recombination (HR)-mediated salvage recombination (SR) repair pathway. Focusing on Saccharomyces cerevisiae budding yeast, we summarized PCNA related-DDT and repair mechanisms that coordinately sustain genome stability and cell survival. In addition, we compared PCNA sequences from various fungal pathogens, considering recent advances in structural features. Importantly, the identification of PCNA epitopes may lead to potential fungal targets for antifungal drug development.
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12
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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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13
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Kolesar P, Stejskal K, Potesil D, Murray JM, Palecek JJ. Role of Nse1 Subunit of SMC5/6 Complex as a Ubiquitin Ligase. Cells 2022; 11:165. [PMID: 35011726 PMCID: PMC8750328 DOI: 10.3390/cells11010165] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/15/2021] [Accepted: 01/01/2022] [Indexed: 11/16/2022] Open
Abstract
Structural Maintenance of Chromosomes (SMC) complexes are important for many aspects of the chromosomal organization. Unlike cohesin and condensin, the SMC5/6 complex contains a variant RING domain carried by its Nse1 subunit. RING domains are characteristic for ubiquitin ligases, and human NSE1 has been shown to possess ubiquitin-ligase activity in vitro. However, other studies were unable to show such activity. Here, we confirm Nse1 ubiquitin-ligase activity using purified Schizosaccharomyces pombe proteins. We demonstrate that the Nse1 ligase activity is stimulated by Nse3 and Nse4. We show that Nse1 specifically utilizes Ubc13/Mms2 E2 enzyme and interacts directly with ubiquitin. We identify the Nse1 mutation (R188E) that specifically disrupts its E3 activity and demonstrate that the Nse1-dependent ubiquitination is particularly important under replication stress. Moreover, we determine Nse4 (lysine K181) as the first known SMC5/6-associated Nse1 substrate. Interestingly, abolition of Nse4 modification at K181 leads to suppression of DNA-damage sensitivity of other SMC5/6 mutants. Altogether, this study brings new evidence for Nse1 ubiquitin ligase activity, significantly advancing our understanding of this enigmatic SMC5/6 function.
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Affiliation(s)
- Peter Kolesar
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Karel Stejskal
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (K.S.); (D.P.)
| | - David Potesil
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (K.S.); (D.P.)
| | - Johanne M. Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RH, UK;
| | - Jan J. Palecek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (K.S.); (D.P.)
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14
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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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15
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Hallett ST, Schellenberger P, Zhou L, Beuron F, Morris E, Murray JM, Oliver AW. Nse5/6 is a negative regulator of the ATPase activity of the Smc5/6 complex. Nucleic Acids Res 2021; 49:4534-4549. [PMID: 33849072 PMCID: PMC8096239 DOI: 10.1093/nar/gkab234] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
The multi-component Smc5/6 complex plays a critical role in the resolution of recombination intermediates formed during mitosis and meiosis, and in the cellular response to replication stress. Using recombinant proteins, we have reconstituted a series of defined Saccharomyces cerevisiae Smc5/6 complexes, visualised them by negative stain electron microscopy, and tested their ability to function as an ATPase. We find that only the six protein ‘holo-complex’ is capable of turning over ATP and that its activity is significantly increased by the addition of double-stranded DNA to reaction mixes. Furthermore, stimulation is wholly dependent on functional ATP-binding pockets in both Smc5 and Smc6. Importantly, we demonstrate that budding yeast Nse5/6 acts as a negative regulator of Smc5/6 ATPase activity, binding to the head-end of the complex to suppress turnover, irrespective of the DNA-bound status of the complex.
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Affiliation(s)
- Stephen T Hallett
- 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
| | | | - Ed Morris
- The Institute of Cancer Research, London, UK
| | - Johanne M Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
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16
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Integrative analysis reveals unique structural and functional features of the Smc5/6 complex. Proc Natl Acad Sci U S A 2021; 118:2026844118. [PMID: 33941673 DOI: 10.1073/pnas.2026844118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Structural maintenance of chromosomes (SMC) complexes are critical chromatin modulators. In eukaryotes, the cohesin and condensin SMC complexes organize chromatin, while the Smc5/6 complex directly regulates DNA replication and repair. The molecular basis for the distinct functions of Smc5/6 is poorly understood. Here, we report an integrative structural study of the budding yeast Smc5/6 holo-complex using electron microscopy, cross-linking mass spectrometry, and computational modeling. We show that the Smc5/6 complex possesses several unique features, while sharing some architectural characteristics with other SMC complexes. In contrast to arm-folded structures of cohesin and condensin, Smc5 and Smc6 arm regions do not fold back on themselves. Instead, these long filamentous regions interact with subunits uniquely acquired by the Smc5/6 complex, namely the Nse2 SUMO ligase and the Nse5/Nse6 subcomplex, with the latter also serving as a linchpin connecting distal parts of the complex. Our 3.0-Å resolution cryoelectron microscopy structure of the Nse5/Nse6 core further reveals a clasped-hand topology and a dimeric interface important for cell growth. Finally, we provide evidence that Nse5/Nse6 uses its SUMO-binding motifs to contribute to Nse2-mediated sumoylation. Collectively, our integrative study identifies distinct structural features of the Smc5/6 complex and functional cooperation among its coevolved unique subunits.
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