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Odiba AS, Liao G, Ezechukwu CS, Zhang L, Hong Y, Fang W, Jin C, Gartner A, Wang B. Caenorhabditis elegans NSE3 homolog (MAGE-1) is involved in genome stability and acts in inter-sister recombination during meiosis. Genetics 2023; 225:iyad149. [PMID: 37579186 PMCID: PMC10691751 DOI: 10.1093/genetics/iyad149] [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: 05/26/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
Melanoma antigen (MAGE) genes encode for a family of proteins that share a common MAGE homology domain. These genes are conserved in eukaryotes and have been linked to a variety of cellular and developmental processes including ubiquitination and oncogenesis in cancer. Current knowledge on the MAGE family of proteins mainly comes from the analysis of yeast and human cell lines, and their functions have not been reported at an organismal level in animals. Caenorhabditis elegans only encodes 1 known MAGE gene member, mage-1 (NSE3 in yeast), forming part of the SMC-5/6 complex. Here, we characterize the role of mage-1/nse-3 in mitosis and meiosis in C. elegans. mage-1/nse-3 has a role in inter-sister recombination repair during meiotic recombination and for preserving chromosomal integrity upon treatment with a variety of DNA-damaging agents. MAGE-1 directly interacts with NSE-1 and NSE-4. In contrast to smc-5, smc-6, and nse-4 mutants which cause the loss of NSE-1 nuclear localization and strong cytoplasmic accumulation, mage-1/nse-3 mutants have a reduced level of NSE-1::GFP, remnant NSE-1::GFP being partially nuclear but largely cytoplasmic. Our data suggest that MAGE-1 is essential for NSE-1 stability and the proper functioning of the SMC-5/6 complex.
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Affiliation(s)
- Arome Solomon Odiba
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guiyan Liao
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Chiemekam Samuel Ezechukwu
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Lanlan Zhang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Ye Hong
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Wenxia Fang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Cheng Jin
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Anton Gartner
- IBS Center for Genomic Integrity, Department for Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea
| | - Bin Wang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
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2
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Lelkes E, Jemelková J, Holá M, Štefanovie B, Kolesár P, Vágnerová R, Dvořák Tomaštíková E, Pecinka A, Angelis KJ, Paleček JJ. Characterization of the conserved features of the NSE6 subunit of the Physcomitrium patens SMC5/6 complex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1084-1099. [PMID: 37191775 DOI: 10.1111/tpj.16282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/06/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023]
Abstract
Structural maintenance of chromosomes (SMC) complexes are molecular machines ensuring chromatin organization at higher levels. They play direct roles in cohesion, condensation, replication, transcription, and DNA repair. Their cores are composed of long-armed SMC, kleisin, and kleisin-associated subunits. Additional factors, like NSE6 within SMC5/6, bind to SMC core complexes and regulate their activities. In the human HsNSE6/SLF2, we recently identified a new CANIN domain. Here we tracked down its sequence homology to lower plants, selected the bryophyte Physcomitrium patens, and analyzed PpNSE6 protein-protein interactions to explore its conservation in detail. We identified a previously unrecognized core sequence motif conserved from yeasts to humans within the NSE6 CANIN domain. This motif mediates the interaction between NSE6 and its NSE5 partner in yeasts and plants. In addition, the CANIN domain and its preceding PpNSE6 sequences bind both PpSMC5 and PpSMC6 arms. Interestingly, we mapped the PpNSE6-binding site at the PpSMC5 arm right next to the PpNSE2-binding surface. The position of NSE6 at SMC arms suggests its role in the regulation of SMC5/6 dynamics. Consistent with the regulatory role of NSE6 subunits, Ppnse6 mutant lines were viable and sensitive to the DNA-damaging drug bleomycin and lost a large portion of rDNA copies. These moss mutants also exhibited reduced growth and developmental aberrations. Altogether, our data showed the conserved function of the NSE6 subunit and architecture of the SMC5/6 complex across species.
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Affiliation(s)
- Edit Lelkes
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Jitka Jemelková
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Marcela Holá
- Institute of Experimental Botany, Czech Academy of Sciences, Na Karlovce 1, 16000, Prague, Czech Republic
| | - Barbora Štefanovie
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Peter Kolesár
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Radka Vágnerová
- Institute of Experimental Botany, Czech Academy of Sciences, Na Karlovce 1, 16000, Prague, Czech Republic
| | - Eva Dvořák Tomaštíková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Karel J Angelis
- Institute of Experimental Botany, Czech Academy of Sciences, Na Karlovce 1, 16000, Prague, Czech Republic
| | - Jan J Paleček
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, 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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3
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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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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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Mahrik L, Stefanovie B, Maresova A, Princova J, Kolesar P, Lelkes E, Faux C, Helmlinger D, Prevorovsky M, Palecek JJ. The SAGA histone acetyltransferase module targets SMC5/6 to specific genes. Epigenetics Chromatin 2023; 16:6. [PMID: 36793083 PMCID: PMC9933293 DOI: 10.1186/s13072-023-00480-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Structural Maintenance of Chromosomes (SMC) complexes are molecular machines driving chromatin organization at higher levels. In eukaryotes, three SMC complexes (cohesin, condensin and SMC5/6) play key roles in cohesion, condensation, replication, transcription and DNA repair. Their physical binding to DNA requires accessible chromatin. RESULTS We performed a genetic screen in fission yeast to identify novel factors required for SMC5/6 binding to DNA. We identified 79 genes of which histone acetyltransferases (HATs) were the most represented. Genetic and phenotypic analyses suggested a particularly strong functional relationship between the SMC5/6 and SAGA complexes. Furthermore, several SMC5/6 subunits physically interacted with SAGA HAT module components Gcn5 and Ada2. As Gcn5-dependent acetylation facilitates the accessibility of chromatin to DNA-repair proteins, we first analysed the formation of DNA-damage-induced SMC5/6 foci in the Δgcn5 mutant. The SMC5/6 foci formed normally in Δgcn5, suggesting SAGA-independent SMC5/6 localization to DNA-damaged sites. Next, we used Nse4-FLAG chromatin-immunoprecipitation (ChIP-seq) analysis in unchallenged cells to assess SMC5/6 distribution. A significant portion of SMC5/6 accumulated within gene regions in wild-type cells, which was reduced in Δgcn5 and Δada2 mutants. The drop in SMC5/6 levels was also observed in gcn5-E191Q acetyltransferase-dead mutant. CONCLUSION Our data show genetic and physical interactions between SMC5/6 and SAGA complexes. The ChIP-seq analysis suggests that SAGA HAT module targets SMC5/6 to specific gene regions and facilitates their accessibility for SMC5/6 loading.
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Affiliation(s)
- L Mahrik
- 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
| | - B Stefanovie
- 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
| | - A Maresova
- Department of Cell Biology, Faculty of Science, Charles University, Vinicna 7, 12800, Prague, Czech Republic
| | - J Princova
- Department of Cell Biology, Faculty of Science, Charles University, Vinicna 7, 12800, Prague, Czech Republic
| | - P Kolesar
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, 61137, Brno, Czech Republic
| | - E Lelkes
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, 61137, Brno, Czech Republic
| | - C Faux
- Centre de Recherche en Biologie Cellulaire de Montpellier, University of Montpellier, CNRS, 1919 Route de Mende, 34293, Montpellier Cedex 05, France
| | - D Helmlinger
- Centre de Recherche en Biologie Cellulaire de Montpellier, University of Montpellier, CNRS, 1919 Route de Mende, 34293, Montpellier Cedex 05, France
| | - M Prevorovsky
- Department of Cell Biology, Faculty of Science, Charles University, Vinicna 7, 12800, Prague, Czech Republic.
| | - J 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.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
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6
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Ng WC, Kwek SS, Sun B, Yousefi M, Ong EZ, Tan HC, Puschnik AS, Chan KR, Ooi YS, Ooi EE. A fast-growing dengue virus mutant reveals a dual role of STING in response to infection. Open Biol 2022; 12:220227. [PMID: 36514984 PMCID: PMC9748785 DOI: 10.1098/rsob.220227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The four dengue viruses (DENVs) have evolved multiple mechanisms to ensure its survival. Among these mechanisms is the ability to regulate its replication rate, which may contribute to avoiding premature immune activation that limit infection dissemination: DENVs associated with dengue epidemics have shown slower replication rate than pre-epidemic strains. Correspondingly, wild-type DENVs replicate more slowly than their clinically attenuated derivatives. To understand how DENVs 'make haste slowly', we generated and screened for DENV2 mutants with accelerated replication that also induced high type-I interferon (IFN) expression in infected cells. We chanced upon a single NS2B-I114T amino acid substitution, in an otherwise highly conserved amino acid residue. Accelerated DENV2 replication damaged host DNA as mutant infection was dependent on host DNA damage repair factors, namely RAD21, EID3 and NEK5. DNA damage induced cGAS/STING signalling and activated early type-I IFN response that inhibited infection dissemination. Unexpectedly, STING activation also supported mutant DENV replication in infected cells through STING-induced autophagy. Our findings thus show that DENV NS2B has multi-faceted role in controlling DENV replication rate and immune evasion and suggest that the dual role of STING in supporting virus replication within infected cells but inhibiting infection dissemination could be particularly advantageous for live attenuated vaccine development.
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Affiliation(s)
- Wy Ching Ng
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Swee Sen Kwek
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Bo Sun
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Meisam Yousefi
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Eugenia Z. Ong
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore,Viral Research and Experimental Medicine Center, SingHealth Duke-NUS Academic Medical Center, Singapore 169856, Singapore
| | - Hwee Cheng Tan
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | | | - Kuan Rong Chan
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Yaw Shin Ooi
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Eng Eong Ooi
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore,Viral Research and Experimental Medicine Center, SingHealth Duke-NUS Academic Medical Center, Singapore 169856, Singapore,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore,Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore
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7
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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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8
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Odiba AS, Ezechukwu CS, Liao G, Li S, Chen Z, Liu X, Fang W, Jin C, Wang B. Loss of NSE-4 Perturbs Genome Stability and DNA Repair in Caenorhabditis elegans. Int J Mol Sci 2022; 23:ijms23137202. [PMID: 35806213 PMCID: PMC9266361 DOI: 10.3390/ijms23137202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
The Structural Maintenance of Chromosomes (SMC) complex plays an important role in maintaining chromosome integrity, in which the SMC5/6 complex occupies a central position by facilitating mitotic and meiotic processes as well as DNA repair. NSE-4 Kleisin is critical for both the organization and function of the SMC5/6 complex, bridging NSE1 and NSE3 (MAGE related) with the head domains of the SMC5 and SMC6 proteins. Despite the conservation in protein sequence, no functional relevance of the NSE-4 homologous protein (NSE-4) in Caenorhabditis elegans has been reported. Here, we demonstrated the essential role of C. elegans NSE-4 in genome maintenance and DNA repair. Our results showed that NSE-4 is essential for the maintenance of chromosomal structure and repair of a range of chemically induced DNA damage. Furthermore, NSE-4 is involved in inter-sister repair during meiosis. NSE-4 localizes on the chromosome and is indispensable for the localization of NSE-1. Collectively, our data from this study provide further insight into the evolutionary conservation and diversification of NSE-4 function in the SMC-5/6 complex.
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Affiliation(s)
- Arome Solomon Odiba
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (A.S.O.); (C.S.E.); (S.L.); (W.F.); (C.J.)
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Department of Genetics and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria
| | - Chiemekam Samuel Ezechukwu
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (A.S.O.); (C.S.E.); (S.L.); (W.F.); (C.J.)
- Department of Zoology and Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria
| | - Guiyan Liao
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (A.S.O.); (C.S.E.); (S.L.); (W.F.); (C.J.)
- Correspondence: (G.L.); (B.W.)
| | - Siqiao Li
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (A.S.O.); (C.S.E.); (S.L.); (W.F.); (C.J.)
| | - Zhongliang Chen
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (Z.C.); (X.L.)
| | - Xihui Liu
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (Z.C.); (X.L.)
| | - Wenxia Fang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (A.S.O.); (C.S.E.); (S.L.); (W.F.); (C.J.)
| | - Cheng Jin
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (A.S.O.); (C.S.E.); (S.L.); (W.F.); (C.J.)
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Wang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (A.S.O.); (C.S.E.); (S.L.); (W.F.); (C.J.)
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (Z.C.); (X.L.)
- Correspondence: (G.L.); (B.W.)
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9
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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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10
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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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11
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Yoshikawa K. Necdin: A purposive integrator of molecular interaction networks for mammalian neuron vitality. Genes Cells 2021; 26:641-683. [PMID: 34338396 PMCID: PMC9290590 DOI: 10.1111/gtc.12884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/27/2021] [Accepted: 06/29/2021] [Indexed: 12/29/2022]
Abstract
Necdin was originally found in 1991 as a hypothetical protein encoded by a neural differentiation‐specific gene transcript in murine embryonal carcinoma cells. Virtually all postmitotic neurons and their precursor cells express the necdin gene (Ndn) during neuronal development. Necdin mRNA is expressed only from the paternal allele through genomic imprinting, a placental mammal‐specific epigenetic mechanism. Necdin and its homologous MAGE (melanoma antigen) family, which have evolved presumedly from a subcomplex component of the SMC5/6 complex, are expressed exclusively in placental mammals. Paternal Ndn‐mutated mice totally lack necdin expression and exhibit various types of neuronal abnormalities throughout the nervous system. Ndn‐null neurons are vulnerable to detrimental stresses such as DNA damage. Necdin also suppresses both proliferation and apoptosis of neural stem/progenitor cells. Functional analyses using Ndn‐manipulated cells reveal that necdin consistently exerts antimitotic, anti‐apoptotic and prosurvival effects. Necdin interacts directly with a number of regulatory proteins including E2F1, p53, neurotrophin receptors, Sirt1 and PGC‐1α, which serve as major hubs of protein–protein interaction networks for mitosis, apoptosis, differentiation, neuroprotection and energy homeostasis. This review focuses on necdin as a pleiotropic protein that integrates molecular interaction networks to promote neuronal vitality in modern placental mammals.
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12
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Parts L, Batté A, Lopes M, Yuen MW, Laver M, San Luis BJ, Yue JX, Pons C, Eray E, Aloy P, Liti G, van Leeuwen J. Natural variants suppress mutations in hundreds of essential genes. Mol Syst Biol 2021; 17:e10138. [PMID: 34042294 PMCID: PMC8156963 DOI: 10.15252/msb.202010138] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 01/04/2023] Open
Abstract
The consequence of a mutation can be influenced by the context in which it operates. For example, loss of gene function may be tolerated in one genetic background, and lethal in another. The extent to which mutant phenotypes are malleable, the architecture of modifiers and the identities of causal genes remain largely unknown. Here, we measure the fitness effects of ~ 1,100 temperature‐sensitive alleles of yeast essential genes in the context of variation from ten different natural genetic backgrounds and map the modifiers for 19 combinations. Altogether, fitness defects for 149 of the 580 tested genes (26%) could be suppressed by genetic variation in at least one yeast strain. Suppression was generally driven by gain‐of‐function of a single, strong modifier gene, and involved both genes encoding complex or pathway partners suppressing specific temperature‐sensitive alleles, as well as general modifiers altering the effect of many alleles. The emerging frequency of suppression and range of possible mechanisms suggest that a substantial fraction of monogenic diseases could be managed by modulating other gene products.
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Affiliation(s)
- Leopold Parts
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Department of Computer Science, University of Tartu, Tartu, Estonia
| | - Amandine Batté
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Maykel Lopes
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Michael W Yuen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Meredith Laver
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Bryan-Joseph San Luis
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Jia-Xing Yue
- University of Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Elise Eray
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Gianni Liti
- University of Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Jolanda van Leeuwen
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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13
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Jo A, Li S, Shin JW, Zhao X, Cho Y. Structure Basis for Shaping the Nse4 Protein by the Nse1 and Nse3 Dimer within the Smc5/6 Complex. J Mol Biol 2021; 433:166910. [PMID: 33676928 PMCID: PMC8173833 DOI: 10.1016/j.jmb.2021.166910] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/01/2021] [Accepted: 02/23/2021] [Indexed: 12/01/2022]
Abstract
The Smc5/6 complex facilitates chromosome replication and DNA break repair. Within this complex, a subcomplex composed of Nse1, Nse3 and Nse4 is thought to play multiple roles through DNA binding and regulating ATP-dependent activities of the complex. However, how the Nse1-Nse3-Nse4 subcomplex carries out these multiple functions remain unclear. To address this question, we determine the crystal structure of the Xenopus laevis Nse1-Nse3-Nse4 subcomplex at 1.7 Å resolution and examine how it interacts with DNA. Our structural analyses show that the Nse1-Nse3 dimer adopts a closed conformation and forms three interfaces with a segment of Nse4, forcing it into a Z-shaped conformation. The Nse1-Nse3-Nse4 structure provides an explanation for how the lung disease immunodeficiency and chromosome breakage syndrome-causing mutations could dislodge Nse4 from Nse1-Nse3. Our DNA binding and mutational analyses reveal that the N-terminal and the middle region of Nse4 contribute to DNA interaction and cell viability. Integrating our data with previous crosslink mass spectrometry data, we propose potential roles of the Nse1-Nse3-Nse4 complex in binding DNA within the Smc5/6 complex.
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Affiliation(s)
- Aera Jo
- Department of Life Science, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Shibai Li
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jin Woo Shin
- Department of Life Science, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yunje Cho
- Department of Life Science, Pohang University of Science and Technology, Pohang, Republic of Korea.
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14
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The Smc5/6 Core Complex Is a Structure-Specific DNA Binding and Compacting Machine. Mol Cell 2020; 80:1025-1038.e5. [PMID: 33301731 DOI: 10.1016/j.molcel.2020.11.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 10/13/2020] [Accepted: 11/04/2020] [Indexed: 01/09/2023]
Abstract
The structural organization of chromosomes is a crucial feature that defines the functional state of genes and genomes. The extent of structural changes experienced by genomes of eukaryotic cells can be dramatic and spans several orders of magnitude. At the core of these changes lies a unique group of ATPases-the SMC proteins-that act as major effectors of chromosome behavior in cells. The Smc5/6 proteins play essential roles in the maintenance of genome stability, yet their mode of action is not fully understood. Here we show that the human Smc5/6 complex recognizes unusual DNA configurations and uses the energy of ATP hydrolysis to promote their compaction. Structural analyses reveal subunit interfaces responsible for the functionality of the Smc5/6 complex and how mutations in these regions may lead to chromosome breakage syndromes in humans. Collectively, our results suggest that the Smc5/6 complex promotes genome stability as a DNA micro-compaction machine.
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15
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Vondrova L, Kolesar P, Adamus M, Nociar M, Oliver AW, Palecek JJ. A role of the Nse4 kleisin and Nse1/Nse3 KITE subunits in the ATPase cycle of SMC5/6. Sci Rep 2020; 10:9694. [PMID: 32546830 PMCID: PMC7297730 DOI: 10.1038/s41598-020-66647-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 05/20/2020] [Indexed: 12/03/2022] Open
Abstract
The SMC (Structural Maintenance of Chromosomes) complexes are composed of SMC dimers, kleisin and kleisin-interacting (HAWK or KITE) subunits. Mutual interactions of these subunits constitute the basal architecture of the SMC complexes. In addition, binding of ATP molecules to the SMC subunits and their hydrolysis drive dynamics of these complexes. Here, we developed new systems to follow the interactions between SMC5/6 subunits and the relative stability of the complex. First, we show that the N-terminal domain of the Nse4 kleisin molecule binds to the SMC6 neck and bridges it to the SMC5 head. Second, binding of the Nse1 and Nse3 KITE proteins to the Nse4 linker increased stability of the ATP-free SMC5/6 complex. In contrast, binding of ATP to SMC5/6 containing KITE subunits significantly decreased its stability. Elongation of the Nse4 linker partially suppressed instability of the ATP-bound complex, suggesting that the binding of the KITE proteins to the Nse4 linker constrains its limited size. Our data suggest that the KITE proteins may shape the Nse4 linker to fit the ATP-free complex optimally and to facilitate opening of the complex upon ATP binding. This mechanism suggests an important role of the KITE subunits in the dynamics of the SMC5/6 complexes.
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Affiliation(s)
- Lucie Vondrova
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Peter Kolesar
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Marek Adamus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Matej Nociar
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, United Kingdom
| | - Jan J Palecek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, 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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16
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Sanderson MR, Badior KE, Fahlman RP, Wevrick R. The necdin interactome: evaluating the effects of amino acid substitutions and cell stress using proximity-dependent biotinylation (BioID) and mass spectrometry. Hum Genet 2020; 139:1513-1529. [PMID: 32529326 DOI: 10.1007/s00439-020-02193-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023]
Abstract
Prader-Willi syndrome (PWS) is a neurodevelopmental disorder caused by the loss of function of a set of imprinted genes on chromosome 15q11-15q13. One of these genes, NDN, encodes necdin, a protein that is important for neuronal differentiation and survival. Loss of Ndn in mice causes defects in the formation and function of the nervous system. Necdin is a member of the melanoma-associated antigen gene (MAGE) protein family. The functions of MAGE proteins depend highly on their interactions with other proteins, and in particular MAGE proteins interact with E3 ubiquitin ligases and deubiquitinases to form MAGE-RING E3 ligase-deubiquitinase complexes. Here, we used proximity-dependent biotin identification (BioID) and mass spectrometry (MS) to determine the network of protein-protein interactions (interactome) of the necdin protein. This process yielded novel as well as known necdin-proximate proteins that cluster into a protein network. Next, we used BioID-MS to define the interactomes of necdin proteins carrying coding variants. Variant necdin proteins had interactomes that were distinct from wildtype necdin. BioID-MS is not only a useful tool to identify protein-protein interactions, but also to analyze the effects of variants of unknown significance on the interactomes of proteins involved in genetic disease.
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Affiliation(s)
| | - Katherine E Badior
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.,Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.,Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Rachel Wevrick
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada.
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17
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Adamus M, Lelkes E, Potesil D, Ganji SR, Kolesar P, Zabrady K, Zdrahal Z, Palecek JJ. Molecular Insights into the Architecture of the Human SMC5/6 Complex. J Mol Biol 2020; 432:3820-3837. [PMID: 32389690 DOI: 10.1016/j.jmb.2020.04.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 04/16/2020] [Accepted: 04/27/2020] [Indexed: 01/03/2023]
Abstract
A family of Structural Maintenance of Chromosome (SMC) complexes is essential for key cellular processes ensuring proper cohesion, condensation and replication. They share a common SMC-kleisin architecture allowing them to embrace DNA. In SMC5/6, the NSE1 and NSE3 KITE and NSE4 kleisin subunits form a stable subcomplex that binds DNA and regulates essential processes. In addition, NSE5 and NSE6 subunits associate with the core SMC5/6 complex and recruit it to DNA repair sites. The architecture of the SMC5/6 complex is crucial for its proper functioning, and mutations within the human SMC5/6 subunits result in severe syndromes. Therefore, we aimed to analyze interactions within the human SMC5/6 complex and determine its detailed architecture. Firstly, we analyzed different parts of SMC5/6 by crosslinking and MS/MS analysis. Our data suggested domain arrangements of hNSE1-hNSE3 and orientation of hNSE4 within the hNSE1-hNSE3-hNSE4 subcomplex. The crosslinking and electron microscopic analysis of the SMC5/6 core complex showed its rod-like architecture with juxtaposed hSMC5-hSMC6 arms. Additionally, we observed fully or partially opened hSMC5-hSMC6 shapes with the hNSE1-hNSE3-hNSE4 trimer localized in the SMC head domains. To complete mapping of the human SMC5/6 complex architecture, we analyzed positions of hNSE5-hNSE6 at the hSMC5-hSMC6 arms. We showed that hNSE6 binding to hNSE5 and the coiled-coil arm of hSMC6 is mediated by a conserved FAM178 domain, which we therefore renamed CANIN (Coiled-coil SMC6 And NSE5 INteracting) domain. Interestingly, hNSE6 bound both hSMC5 and hSMC6 arms, suggesting that hNSE6 may lock the arms and regulate the dynamics of the human SMC5/6 complex.
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Affiliation(s)
- M Adamus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic
| | - E Lelkes
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic
| | - D Potesil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - S R Ganji
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - P Kolesar
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic
| | - K Zabrady
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic
| | - Z Zdrahal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic
| | - J J Palecek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic.
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18
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Byska J, Jurcik A, Furmanova K, Kozlikova B, Palecek JJ. Visual Analysis of Protein-Protein Interaction Docking Models Using COZOID Tool. Methods Mol Biol 2020; 2074:81-94. [PMID: 31583632 DOI: 10.1007/978-1-4939-9873-9_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Networks of protein-protein interactions (PPI) constitute either stable or transient complexes in every cell. Most of the cellular complexes keep their function, and therefore stay similar, during evolution. The evolutionary constraints preserve most cellular functions via preservation of protein structures and interactions. The evolutionary conservation information is utilized in template-based approaches, like protein structure modeling or docking. Here we use the combination of the template-free docking method with conservation-based selection of the best docking model using our newly developed COZOID tool.We describe a step-by-step protocol for visual selection of docking models, based on their similarity to the original protein complex structure. Using the COZOID tool, we first analyze contact zones of the original complex structure and select contact amino acids for docking restraints. Then we model and dock the homologous proteins. Finally, we utilize different analytical modes of our COZOID tool to select the docking models most similar to the original complex structure.
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Affiliation(s)
- Jan Byska
- Department of Informatics, University of Bergen, Bergen, Norway
- Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Adam Jurcik
- Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | | | | | - Jan J Palecek
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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19
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Fu X, Luo L, Yi R, Ding B, Wang C, Zhang W, Wang X, Yang Y, Chen C, Fei X, Hu D, Xu R. Transcriptome profiling in Eid1-KO mice brain shows that Eid1 links cell proliferation in the brain. Gene 2019; 717:143998. [PMID: 31381951 DOI: 10.1016/j.gene.2019.143998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 07/19/2019] [Accepted: 07/22/2019] [Indexed: 01/01/2023]
Abstract
Eid1 is a member of the EID protein family, which regulates differentiation, transcription and acetyltransferase activity. Accumulating evidence suggests that Eid1 is relevant to neurological disorder, but the main function of Eid1 is still unclear, especially in the brain. To better understand this issue, we generated Eid1-knockout (Eid1-KO) mice and profiled its gene expression changes in the brain by RNA sequencing. This study identified 2531 genes differentially expressed in Eid1-KO mice compared with the wild-type, then qRT-PCR verification demonstrated that the transcriptomic data are reliable. By protein-protein interaction cluster analysis, 'regulation of cell proliferation' were unexpectedly discovered as important Eid1 functions. We then isolated neural progenitor cells (NPCs) and showed that the number of neurospheres and the proliferation rate of Eid1-KO NPCs were obviously lower than that in the control group, furthermore, CCK-8 and immunofluorescence assay clearly demonstrated that the Eid1-KO NPCs showed significantly less cell proliferation than the control group. To the best of our knowledge, this is the first comprehensive report of the Eid1-KO transcriptome of mice brain. Our analysis and experimental data provide a foundation for further studies on understanding function of Eid1 in the brain.
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Affiliation(s)
- Xiaojun Fu
- Department of Neurosurgery, SanBo Brain Hospital, Capital Medical University, PR China
| | - Liang Luo
- Stem Cell Research Center, Seventh Medical Center of PLA General Hospital, Beijing, PR China; Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, PR China.
| | - Rui Yi
- Department of Health and Welfare, Seventh Medical Center, PLA General Hospital, PR China
| | - Boyun Ding
- Southern Medical University, Guangzhou, PR China
| | - Chongwu Wang
- Stem Cell Research Center, Seventh Medical Center of PLA General Hospital, Beijing, PR China
| | - Wei Zhang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, PR China
| | - Xujie Wang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, PR China
| | - Yunshu Yang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, PR China
| | - Chen Chen
- Stem Cell Research Center, Seventh Medical Center of PLA General Hospital, Beijing, PR China
| | - Xiaowei Fei
- Stem Cell Research Center, Seventh Medical Center of PLA General Hospital, Beijing, PR China
| | - Dahai Hu
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, PR China.
| | - Ruxiang Xu
- Stem Cell Research Center, Seventh Medical Center of PLA General Hospital, Beijing, PR China.
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20
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Abstract
Smc5 and Smc6, together with the kleisin Nse4, form the heart of the enigmatic and poorly understood Smc5/6 complex, which is frequently viewed as a cousin of cohesin and condensin with functions in DNA repair. As novel functions for cohesin and condensin complexes in the organization of long-range chromatin architecture have recently emerged, new unsuspected roles for Smc5/6 have also surfaced. Here, I aim to provide a comprehensive overview of our current knowledge of the Smc5/6 complex, including its long-established function in genome stability, its multiple roles in DNA repair, and its recently discovered connection to the transcription inhibition of hepatitis B virus genomes. In addition, I summarize new research that is beginning to tease out the molecular details of Smc5/6 structure and function, knowledge that will illuminate the nuclear activities of Smc5/6 in the stability and dynamics of eukaryotic genomes.
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Affiliation(s)
- Luis Aragón
- Cell Cycle Group, MRC London Institute of Medical Sciences, Hammersmith Hospital Campus, London W12 0NN, United Kingdom;
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21
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Díaz M, Pečinková P, Nowicka A, Baroux C, Sakamoto T, Gandha PY, Jeřábková H, Matsunaga S, Grossniklaus U, Pecinka A. The SMC5/6 Complex Subunit NSE4A Is Involved in DNA Damage Repair and Seed Development. THE PLANT CELL 2019; 31:1579-1597. [PMID: 31036599 PMCID: PMC6635853 DOI: 10.1105/tpc.18.00043] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/26/2019] [Accepted: 04/26/2019] [Indexed: 05/04/2023]
Abstract
The maintenance of genome integrity over cell divisions is critical for plant development and the correct transmission of genetic information to the progeny. A key factor involved in this process is the STRUCTURAL MAINTENANCE OF CHROMOSOME5 (SMC5) and SMC6 (SMC5/6) complex, related to the cohesin and condensin complexes that control sister chromatid alignment and chromosome condensation, respectively. Here, we characterize NON-SMC ELEMENT4 (NSE4) paralogs of the SMC5/6 complex in Arabidopsis (Arabidopsis thaliana). NSE4A is expressed in meristems and accumulates during DNA damage repair. Partial loss-of-function nse4a mutants are viable but hypersensitive to DNA damage induced by zebularine. In addition, nse4a mutants produce abnormal seeds, with noncellularized endosperm and embryos that maximally develop to the heart or torpedo stage. This phenotype resembles the defects in cohesin and condensin mutants and suggests a role for all three SMC complexes in differentiation during seed development. By contrast, NSE4B is expressed in only a few cell types, and loss-of-function mutants do not have any obvious abnormal phenotype. In summary, our study shows that the NSE4A subunit of the SMC5-SMC6 complex is essential for DNA damage repair in somatic tissues and plays a role in plant reproduction.
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Affiliation(s)
- Mariana Díaz
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), 50829 Cologne, Germany
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan
| | - Petra Pečinková
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), 50829 Cologne, Germany
| | - Anna Nowicka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), 50829 Cologne, Germany
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic
- Polish Academy of Sciences, Franciszek Gorski Institute of Plant Physiology, 30-239 Krakow, Poland
| | - Célia Baroux
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zürich, Switzerland
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan
| | - Priscilla Yuliani Gandha
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), 50829 Cologne, Germany
| | - Hana Jeřábková
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zürich, Switzerland
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), 50829 Cologne, Germany
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic
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22
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Zelkowski M, Zelkowska K, Conrad U, Hesse S, Lermontova I, Marzec M, Meister A, Houben A, Schubert V. Arabidopsis NSE4 Proteins Act in Somatic Nuclei and Meiosis to Ensure Plant Viability and Fertility. FRONTIERS IN PLANT SCIENCE 2019; 10:774. [PMID: 31281325 PMCID: PMC6596448 DOI: 10.3389/fpls.2019.00774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/28/2019] [Indexed: 05/02/2023]
Abstract
The SMC 5/6 complex together with cohesin and condensin is a member of the structural maintenance of chromosome (SMC) protein family. In non-plant organisms SMC5/6 is engaged in DNA repair, meiotic synapsis, genome organization and stability. In plants, the function of SMC5/6 is still enigmatic. Therefore, we analyzed the crucial δ-kleisin component NSE4 of the SMC5/6 complex in the model plant Arabidopsis thaliana. Two functional conserved Nse4 paralogs (Nse4A and Nse4B) are present in A. thaliana, which may have evolved via gene subfunctionalization. Due to its high expression level, Nse4A seems to be the more essential gene, whereas Nse4B appears to be involved mainly in seed development. The morphological characterization of A. thaliana T-DNA mutants suggests that the NSE4 proteins are essential for plant growth and fertility. Detailed investigations in wild-type and the mutants based on live cell imaging of transgenic GFP lines, fluorescence in situ hybridization (FISH), immunolabeling and super-resolution microscopy suggest that NSE4A acts in several processes during plant development, such as mitosis, meiosis and chromatin organization of differentiated nuclei, and that NSE4A operates in a cell cycle-dependent manner. Differential response of NSE4A and NSE4B mutants after induced DNA double strand breaks (DSBs) suggests their involvement in DNA repair processes.
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Affiliation(s)
- Mateusz Zelkowski
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Katarzyna Zelkowska
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Udo Conrad
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Susann Hesse
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Plant Cytogenomics Research Group, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Marek Marzec
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Armin Meister
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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23
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Fu X, Ding B, Wang C, Chen C, Wang J, Fei X, Xu R. EID1 plays a crucial role in proliferation of neural stem cell. Biochem Biophys Res Commun 2019; 512:763-769. [PMID: 30926163 DOI: 10.1016/j.bbrc.2019.03.138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 11/19/2022]
Abstract
EP300-interacting inhibitor of differentiation 1 (Eid1) regulates differentiation, transcription and acetyltransferase activity. But the main function of Eid1 in the brain is still unclear. To better understand this issue, we generated Eid1-knockout (Eid1-KO) mice. We found poorer learning and memory ability, and smaller volume of neonatal telencephalon in Eid1-KO group than wild-type (WT). Bioinformatics implied that Eid1 may directly regulate cell proliferation. We then isolated neural stem cells (NSCs) and discovered a slower proliferation rate in Eid1-KO NSCs. Moreover, based on bioinformatics results, we investigated the expression of phosphatidylinositol 3-kinase (PI3K)/AKT/GSK3β pathway by Western blotting assay, which showed attenuated in Eid1-KO group. Our data proved the first comprehensive report of Eid1 regulating NSCs proliferation via PI3K/AKT/GSK3β pathway, and provide a foundation for the role of EID1 in the brain.
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Affiliation(s)
- Xiaojun Fu
- Medical School of Chinese PLA & General Hospital of Chinese PLA, Beijing, PR China
| | - Boyun Ding
- Stem Cell Research Center, Neurosurgery Institute of PLA Army, Beijing, PR China
| | - Chongwu Wang
- Stem Cell Research Center, Neurosurgery Institute of PLA Army, Beijing, PR China
| | - Chen Chen
- Stem Cell Research Center, Neurosurgery Institute of PLA Army, Beijing, PR China
| | - Ji Wang
- Stem Cell Research Center, Neurosurgery Institute of PLA Army, Beijing, PR China
| | - Xiaowei Fei
- Stem Cell Research Center, Neurosurgery Institute of PLA Army, Beijing, PR China
| | - Ruxiang Xu
- Medical School of Chinese PLA & General Hospital of Chinese PLA, Beijing, PR China; Stem Cell Research Center, Neurosurgery Institute of PLA Army, Beijing, PR China.
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24
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Paleček JJ, Vondrová L, Zábrady K, Otočka J. Multicomponent Yeast Two-Hybrid System: Applications to Study Protein-Protein Interactions in SMC Complexes. Methods Mol Biol 2019; 2004:79-90. [PMID: 31147911 DOI: 10.1007/978-1-4939-9520-2_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Analysis of protein-protein interactions (PPI) is key for the understanding of most protein assemblies including structural maintenance of chromosomes (SMC) complexes. SMC complexes are composed of SMC proteins, kleisin, and kleisin-interacting subunits. These subunits interact in specific ways to constitute and regulate the closed structure of the complexes. Specifically, kleisin molecules bridge the SMC dimers and the kleisin-interacting subunits modulate stability of the bridge. Here we describe a multicomponent version of a yeast two-hybrid (Y2H) method and its application for analysis of the bridging role of the Nse4 kleisin in the SMC5/6 complex. Using this technique, we also show a stabilizing effect of KITE (kleisin-interacting tandem winged-helix element) proteins on SMC5/6.
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Affiliation(s)
- Jan Josef Paleček
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic. .,Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Lucie Vondrová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kateřina Zábrady
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Jakub Otočka
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
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25
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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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26
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Hwang G, Verver DE, Handel MA, Hamer G, Jordan PW. Depletion of SMC5/6 sensitizes male germ cells to DNA damage. Mol Biol Cell 2018; 29:3003-3016. [PMID: 30281394 PMCID: PMC6333175 DOI: 10.1091/mbc.e18-07-0459] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The structural maintenance of chromosomes complex SMC5/6 is thought to be essential for DNA repair and chromosome segregation during mitosis and meiosis. To determine the requirements of the SMC5/6 complex during mouse spermatogenesis we combined a conditional knockout allele for Smc5, with four germ cell–specific Cre-recombinase transgenes, Ddx4-Cre, Stra8-Cre, Spo11-Cre, and Hspa2-Cre, to mutate Smc5 in spermatogonia, in spermatocytes before meiotic entry, during early meiotic stages, and during midmeiotic stages, respectively. Conditional mutation of Smc5 resulted in destabilization of the SMC5/6 complex. Despite this, we observed only mild defects in spermatogenesis. Mutation of Smc5 mediated by Ddx4-Cre and Stra8-Cre resulted in partial loss of preleptotene spermatocytes; however, spermatogenesis progresses and mice are fertile. Mutation of Smc5 via Spo11-Cre or Hspa2-Cre did not result in detectable defects of spermatogenesis. Upon exposure to gamma irradiation or etoposide treatment, each conditional Smc5 mutant demonstrated an increase in the number of enlarged round spermatids with multiple acrosomes and supernumerary chromosome content. We propose that the SMC5/6 complex is not acutely required for premeiotic DNA replication and meiotic progression during mouse spermatogenesis; however, when germ cells are challenged by exogenous DNA damage, the SMC5/6 complex ensures genome integrity, and thus, fertility.
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Affiliation(s)
- G Hwang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
| | - D E Verver
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - M A Handel
- The Jackson Laboratory, Bar Harbor, ME 04609
| | - G Hamer
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - P W Jordan
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
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27
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Wang Y, Wang Y, Liu S, Liu Y, Xu H, Liang J, Zhu J, Zhang G, Su W, Dong W, Guo Q. Upregulation of EID3 sensitizes breast cancer cells to ionizing radiation-induced cellular senescence. Biomed Pharmacother 2018; 107:606-614. [PMID: 30114644 DOI: 10.1016/j.biopha.2018.08.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 07/23/2018] [Accepted: 08/06/2018] [Indexed: 10/28/2022] Open
Abstract
Previous studies have shown that BMS-345541 (BMS, a specific IκB kinase β inhibitor) sensitized various tumor cells including MCF-7 breast cancer cells to ionizing radiation (IR). However, the mechanisms of BMS action are unknown. Since the expression of E1A-like inhibitor of differentiation 3 (EID3) was highly upregulated in MCF-7 cells after BMS treatment, we investigated the role of EID3 in the response of MCF-7 cells to IR. We found that BMS induced EID3 expression in MCF-7 cells in a time- and dose-dependent manner. Knockdown of EID3 by specific shRNA attenuated BMS-induced radiosensitization in MCF-7 cells. In contrast, induction of EID3 expression in an inducible EID3 expressing MCF-7 cell line with doxycycline sensitized the cells to IR. EID3-mediated sensitization of MCF-7 cells to IR was not attributed to an increase in apoptosis. Instead, EID3-expressing MCF-7 cells exhibited significantly higher levels of senescence associated β-galactosidase (SA-β-gal) activity and higher levels of p21 and p57 than EID3-MCF-7 cells without induction of EID3 after exposure to IR. Similar findings were observed when EID3-expressing MCF-7 cells were treated with etoposide, a topoisomerase II inhibitor. Taken together, our findings reveal a novel function of EID3 and suggest that the induction of EID3 by BMS may be exploited as a new strategy to sensitize breast cancer cells to IR and chemotherapy by inducing cancer cell senescence.
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Affiliation(s)
- Yan Wang
- Department of Orthopedics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510182, PR China; Department of Pathophysiology, Guangzhou Medical University, Guangzhou, Guangdong 510182, PR China.
| | - Yuxuan Wang
- Department of Orthopedics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510182, PR China.
| | - Sihong Liu
- Department of Orthopedics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510182, PR China.
| | - Yamin Liu
- Department of Orthopedics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510182, PR China; Department of Pathophysiology, Guangzhou Medical University, Guangzhou, Guangdong 510182, PR China.
| | - Huihua Xu
- Department of Orthopedics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510182, PR China.
| | - Junbo Liang
- Department of Orthopedics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510182, PR China.
| | - Jianwei Zhu
- Department of Orthopedics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510182, PR China.
| | - Guiqiang Zhang
- Department of Orthopedics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510182, PR China.
| | - Wenzhou Su
- Department of Orthopedics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510182, PR China.
| | - Weihua Dong
- Department of Pathophysiology, Guangzhou Medical University, Guangzhou, Guangdong 510182, PR China.
| | - Qifeng Guo
- Department of Orthopedics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510182, PR China.
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28
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Furmanová K, Byška J, Gröller EM, Viola I, Paleček JJ, Kozlíková B. COZOID: contact zone identifier for visual analysis of protein-protein interactions. BMC Bioinformatics 2018; 19:125. [PMID: 29625561 PMCID: PMC5889581 DOI: 10.1186/s12859-018-2113-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/12/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Studying the patterns of protein-protein interactions (PPIs) is fundamental for understanding the structure and function of protein complexes. The exploration of the vast space of possible mutual configurations of interacting proteins and their contact zones is very time consuming and requires the proteomic expert knowledge. RESULTS In this paper, we propose a novel tool containing a set of visual abstraction techniques for the guided exploration of PPI configuration space. It helps proteomic experts to select the most relevant configurations and explore their contact zones at different levels of detail. The system integrates a set of methods that follow and support the workflow of proteomics experts. The first visual abstraction method, the Matrix view, is based on customized interactive heat maps and provides the users with an overview of all possible residue-residue contacts in all PPI configurations and their interactive filtering. In this step, the user can traverse all input PPI configurations and obtain an overview of their interacting amino acids. Then, the models containing a particular pair of interacting amino acids can be selectively picked and traversed. Detailed information on the individual amino acids in the contact zones and their properties is presented in the Contact-Zone list-view. The list-view provides a comparative tool to rank the best models based on the similarity of their contacts to the template-structure contacts. All these techniques are interactively linked with other proposed methods, the Exploded view and the Open-Book view, which represent individual configurations in three-dimensional space. These representations solve the high overlap problem associated with many configurations. Using these views, the structural alignment of the best models can also be visually confirmed. CONCLUSIONS We developed a system for the exploration of large sets of protein-protein complexes in a fast and intuitive way. The usefulness of our system has been tested and verified on several docking structures covering the three major types of PPIs, including coiled-coil, pocket-string, and surface-surface interactions. Our case studies prove that our tool helps to analyse and filter protein-protein complexes in a fraction of the time compared to using previously available techniques.
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Affiliation(s)
| | - Jan Byška
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Eduard M Gröller
- Institute of Visual Computing & Human-Centered Technology, TU Wien, Wien, Austria
| | - Ivan Viola
- Institute of Visual Computing & Human-Centered Technology, TU Wien, Wien, Austria
| | - Jan J Paleček
- National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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29
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Diaz M, Pecinka A. Scaffolding for Repair: Understanding Molecular Functions of the SMC5/6 Complex. Genes (Basel) 2018; 9:genes9010036. [PMID: 29329249 PMCID: PMC5793187 DOI: 10.3390/genes9010036] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/03/2018] [Accepted: 01/04/2018] [Indexed: 12/17/2022] Open
Abstract
Chromosome organization, dynamics and stability are required for successful passage through cellular generations and transmission of genetic information to offspring. The key components involved are Structural maintenance of chromosomes (SMC) complexes. Cohesin complex ensures proper chromatid alignment, condensin complex chromosome condensation and the SMC5/6 complex is specialized in the maintenance of genome stability. Here we summarize recent knowledge on the composition and molecular functions of SMC5/6 complex. SMC5/6 complex was originally identified based on the sensitivity of its mutants to genotoxic stress but there is increasing number of studies demonstrating its roles in the control of DNA replication, sister chromatid resolution and genomic location-dependent promotion or suppression of homologous recombination. Some of these functions appear to be due to a very dynamic interaction with cohesin or other repair complexes. Studies in Arabidopsis indicate that, besides its canonical function in repair of damaged DNA, the SMC5/6 complex plays important roles in regulating plant development, abiotic stress responses, suppression of autoimmune responses and sexual reproduction.
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Affiliation(s)
- Mariana Diaz
- Institute of Experimental Botany of the Czech Academy of Sciences (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900 Olomouc-Holice, Czech Republic.
- Max Planck Institute for Plant Breeding Research (MPIPZ), Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
| | - Ales Pecinka
- Institute of Experimental Botany of the Czech Academy of Sciences (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900 Olomouc-Holice, Czech Republic.
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30
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Lee AK, Potts PR. A Comprehensive Guide to the MAGE Family of Ubiquitin Ligases. J Mol Biol 2017; 429:1114-1142. [PMID: 28300603 DOI: 10.1016/j.jmb.2017.03.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/07/2017] [Accepted: 03/07/2017] [Indexed: 12/28/2022]
Abstract
Melanoma antigen (MAGE) genes are conserved in all eukaryotes and encode for proteins sharing a common MAGE homology domain. Although only a single MAGE gene exists in lower eukaryotes, the MAGE family rapidly expanded in eutherians and consists of more than 50 highly conserved genes in humans. A subset of MAGEs initially garnered interest as cancer biomarkers and immunotherapeutic targets due to their antigenic properties and unique expression pattern that is primary restricted to germ cells and aberrantly reactivated in various cancers. However, further investigation revealed that MAGEs not only drive tumorigenesis but also regulate pathways essential for diverse cellular and developmental processes. Therefore, MAGEs are implicated in a broad range of diseases including neurodevelopmental, renal, and lung disorders, and cancer. Recent biochemical and biophysical studies indicate that MAGEs assemble with E3 RING ubiquitin ligases to form MAGE-RING ligases (MRLs) and act as regulators of ubiquitination by modulating ligase activity, substrate specification, and subcellular localization. Here, we present a comprehensive guide to MAGEs highlighting the molecular mechanisms of MRLs and their physiological roles in germ cell and neural development, oncogenic functions in cancer, and potential as therapeutic targets in disease.
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Affiliation(s)
- Anna K Lee
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Patrick Ryan Potts
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA.
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31
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Li G, Zou W, Jian L, Qian J, Deng Y, Zhao J. Non-SMC elements 1 and 3 are required for early embryo and seedling development in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1039-1054. [PMID: 28207059 PMCID: PMC5441860 DOI: 10.1093/jxb/erx016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Early embryo development from the zygote is an essential stage in the formation of the seed, while seedling development is the beginning of the formation of an individual plant. AtNSE1 and AtNSE3 are subunits of the structural maintenance of chromosomes (SMC) 5/6 complex and have been identified as non-SMC elements, but their functions in Arabidopsis growth and development remain as yet unknown. In this study, we found that loss of function of AtNSE1 and AtNSE3 led to severe defects in early embryo development. Partially complemented mutants showed that the development of mutant seedlings was inhibited, that chromosome fragments occurred during anaphase, and that the cell cycle was delayed at G2/M, which led to the occurrence of endoreduplication. Further, a large number of DNA double-strand breaks (DSBs) occurred in the nse1 and nse3 mutants, and the expression of AtNSE1 and AtNSE3 was up-regulated following treatment of the plants with DSB inducer compounds, suggesting that AtNSE1 and AtNSE3 have a role in DNA damage repair. Therefore, we conclude that AtNSE1 and AtNSE3 facilitate DSB repair and contribute to maintaining genome stability and cell division in mitotic cells. Thus, we think that AtNSE1 and AtNSE3 may be crucial factors for maintaining proper early embryonic and post-embryonic development.
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Affiliation(s)
- Gang Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenxuan Zou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Liufang Jian
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Qian
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yingtian Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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32
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van der Crabben SN, Hennus MP, McGregor GA, Ritter DI, Nagamani SC, Wells OS, Harakalova M, Chinn IK, Alt A, Vondrova L, Hochstenbach R, van Montfrans JM, Terheggen-Lagro SW, van Lieshout S, van Roosmalen MJ, Renkens I, Duran K, Nijman IJ, Kloosterman WP, Hennekam E, Orange JS, van Hasselt PM, Wheeler DA, Palecek JJ, Lehmann AR, Oliver AW, Pearl LH, Plon SE, Murray JM, van Haaften G. Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease. J Clin Invest 2016; 126:2881-92. [PMID: 27427983 PMCID: PMC4966312 DOI: 10.1172/jci82890] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 05/12/2016] [Indexed: 11/27/2022] Open
Abstract
The structural maintenance of chromosomes (SMC) family of proteins supports mitotic proliferation, meiosis, and DNA repair to control genomic stability. Impairments in chromosome maintenance are linked to rare chromosome breakage disorders. Here, we have identified a chromosome breakage syndrome associated with severe lung disease in early childhood. Four children from two unrelated kindreds died of severe pulmonary disease during infancy following viral pneumonia with evidence of combined T and B cell immunodeficiency. Whole exome sequencing revealed biallelic missense mutations in the NSMCE3 (also known as NDNL2) gene, which encodes a subunit of the SMC5/6 complex that is essential for DNA damage response and chromosome segregation. The NSMCE3 mutations disrupted interactions within the SMC5/6 complex, leading to destabilization of the complex. Patient cells showed chromosome rearrangements, micronuclei, sensitivity to replication stress and DNA damage, and defective homologous recombination. This work associates missense mutations in NSMCE3 with an autosomal recessive chromosome breakage syndrome that leads to defective T and B cell function and acute respiratory distress syndrome in early childhood.
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Affiliation(s)
| | - Marije P. Hennus
- Department of Pediatric Intensive Care, Wilhelmina Children’s Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands
| | - Grant A. McGregor
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | | | | | - Owen S. Wells
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | | | - Ivan K. Chinn
- Texas Children’s Hospital, and
- Department of Pediatrics, Baylor College of Medicine, Houston Texas, USA
| | - Aaron Alt
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Lucie Vondrova
- Central European Institute of Technology and Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | | | | | | | | | - Ivo Renkens
- Department of Genetics (Center for Molecular Medicine) and
| | - Karen Duran
- Department of Genetics (Center for Molecular Medicine) and
| | | | | | - Eric Hennekam
- Department of Genetics (Center for Molecular Medicine) and
| | - Jordan S. Orange
- Texas Children’s Hospital, and
- Department of Pediatrics, Baylor College of Medicine, Houston Texas, USA
| | - Peter M. van Hasselt
- Department of Metabolic Diseases, Wilhelmina Children’s Hospital, UMCU, Utrecht, Netherlands
| | - David A. Wheeler
- Human Genome Sequencing Center
- Department of Molecular and Human Genetics
| | - Jan J. Palecek
- Central European Institute of Technology and Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Alan R. Lehmann
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Antony W. Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Laurence H. Pearl
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Sharon E. Plon
- Human Genome Sequencing Center
- Department of Molecular and Human Genetics
- Texas Children’s Hospital, and
- Department of Pediatrics, Baylor College of Medicine, Houston Texas, USA
| | - Johanne M. Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
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Zabrady K, Adamus M, Vondrova L, Liao C, Skoupilova H, Novakova M, Jurcisinova L, Alt A, Oliver AW, Lehmann AR, Palecek JJ. Chromatin association of the SMC5/6 complex is dependent on binding of its NSE3 subunit to DNA. Nucleic Acids Res 2016; 44:1064-79. [PMID: 26446992 PMCID: PMC4756808 DOI: 10.1093/nar/gkv1021] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 09/23/2015] [Accepted: 09/26/2015] [Indexed: 11/13/2022] Open
Abstract
SMC5/6 is a highly conserved protein complex related to cohesin and condensin, which are the key components of higher-order chromatin structures. The SMC5/6 complex is essential for proliferation in yeast and is involved in replication fork stability and processing. However, the precise mechanism of action of SMC5/6 is not known. Here we present evidence that the NSE1/NSE3/NSE4 sub-complex of SMC5/6 binds to double-stranded DNA without any preference for DNA-replication/recombination intermediates. Mutations of key basic residues within the NSE1/NSE3/NSE4 DNA-binding surface reduce binding to DNA in vitro. Their introduction into the Schizosaccharomyces pombe genome results in cell death or hypersensitivity to DNA damaging agents. Chromatin immunoprecipitation analysis of the hypomorphic nse3 DNA-binding mutant shows a reduced association of fission yeast SMC5/6 with chromatin. Based on our results, we propose a model for loading of the SMC5/6 complex onto the chromatin.
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Affiliation(s)
- Katerina Zabrady
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Marek Adamus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Lucie Vondrova
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Chunyan Liao
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Hana Skoupilova
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Marketa Novakova
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Lenka Jurcisinova
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Aaron Alt
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Antony W Oliver
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Alan R Lehmann
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Jan J Palecek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
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Kozakova L, Vondrova L, Stejskal K, Charalabous P, Kolesar P, Lehmann AR, Uldrijan S, Sanderson CM, Zdrahal Z, Palecek JJ. The melanoma-associated antigen 1 (MAGEA1) protein stimulates the E3 ubiquitin-ligase activity of TRIM31 within a TRIM31-MAGEA1-NSE4 complex. Cell Cycle 2015; 14:920-30. [PMID: 25590999 PMCID: PMC4614679 DOI: 10.1080/15384101.2014.1000112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The MAGE (Melanoma-associated antigen) protein family members are structurally related to each other by a MAGE-homology domain comprised of 2 winged helix motifs WH/A and WH/B. This family specifically evolved in placental mammals although single homologs designated NSE3 (non-SMC element) exist in most eukaryotes. NSE3, together with its partner proteins NSE1 and NSE4 form a tight subcomplex of the structural maintenance of chromosomes SMC5–6 complex. Previously, we showed that interactions of the WH/B motif of the MAGE proteins with their NSE4/EID partners are evolutionarily conserved (including the MAGEA1-NSE4 interaction). In contrast, the interaction of the WH/A motif of NSE3 with NSE1 diverged in the MAGE paralogs. We hypothesized that the MAGE paralogs acquired new RING-finger-containing partners through their evolution and form MAGE complexes reminiscent of NSE1-NSE3-NSE4 trimers. In this work, we employed the yeast 2-hybrid system to screen a human RING-finger protein library against several MAGE baits. We identified a number of potential MAGE-RING interactions and confirmed several of them (MDM4, PCGF6, RNF166, TRAF6, TRIM8, TRIM31, TRIM41) in co-immunoprecipitation experiments. Among these MAGE-RING pairs, we chose to examine MAGEA1-TRIM31 in detail and showed that both WH/A and WH/B motifs of MAGEA1 bind to the coiled-coil domain of TRIM31 and that MAGEA1 interaction stimulates TRIM31 ubiquitin-ligase activity. In addition, TRIM31 directly binds to NSE4, suggesting the existence of a TRIM31-MAGEA1-NSE4 complex reminiscent of the NSE1-NSE3-NSE4 trimer. These results suggest that MAGEA1 functions as a co-factor of TRIM31 ubiquitin-ligase and that the TRIM31-MAGEA1-NSE4 complex may have evolved from an ancestral NSE1-NSE3-NSE4 complex.
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Affiliation(s)
- Lucie Kozakova
- a From the Mendel Center for Plant Genomics and Proteomics; Central European Institute of Technology; Masaryk University ; Brno , Czech Republic
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Peptidic degron in EID1 is recognized by an SCF E3 ligase complex containing the orphan F-box protein FBXO21. Proc Natl Acad Sci U S A 2015; 112:15372-7. [PMID: 26631746 DOI: 10.1073/pnas.1522006112] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
EP300-interacting inhibitor of differentiation 1 (EID1) belongs to a protein family implicated in the control of transcription, differentiation, DNA repair, and chromosomal maintenance. EID1 has a very short half-life, especially in G0 cells. We discovered that EID1 contains a peptidic, modular degron that is necessary and sufficient for its polyubiquitylation and proteasomal degradation. We found that this degron is recognized by an Skp1, Cullin, and F-box (SCF)-containing ubiquitin ligase complex that uses the F-box Only Protein 21 (FBXO21) as its substrate recognition subunit. SCF(FBXO21) polyubiquitylates EID1 both in vitro and in vivo and is required for the efficient degradation of EID1 in both cycling and quiescent cells. The EID1 degron partially overlaps with its retinoblastoma tumor suppressor protein-binding domain and is congruent with a previously defined melanoma-associated antigen-binding motif shared by EID family members, suggesting that binding to retinoblastoma tumor suppressor and melanoma-associated antigen family proteins could affect the polyubiquitylation and turnover of EID family members in cells.
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Palecek JJ, Gruber S. Kite Proteins: a Superfamily of SMC/Kleisin Partners Conserved Across Bacteria, Archaea, and Eukaryotes. Structure 2015; 23:2183-2190. [DOI: 10.1016/j.str.2015.10.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/23/2015] [Accepted: 10/01/2015] [Indexed: 10/22/2022]
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Taniura H, Tanabe N, Bando Y, Arai N. Nse1 and Nse4, subunits of the Smc5-Smc6 complex, are involved in Dictyostelium development upon starvation. Dev Growth Differ 2015; 57:430-443. [PMID: 26036668 DOI: 10.1111/dgd.12223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 04/06/2015] [Accepted: 04/22/2015] [Indexed: 11/29/2022]
Abstract
The Smc5-Smc6 complex contains a heterodimeric core of two SMC proteins and non-Smc elements (Nse1-6), and plays an important role in DNA repair. We investigated the functional roles of Nse4 and Nse1 in Dictyostelium discoideum. Nse4 and Nse3 expressed as Flag-tagged fusion proteins were highly enriched in nuclei, while Nse1 was localized in whole cells. Using yeast two-hybrid assays, only the interaction between Nse3 and Nse1 was detected among the combinations. However, all of the interactions among these three proteins were recognized by co-immunoprecipitation assay using cell lysates prepared from the cells expressing green fluorescent protein (GFP)- or Flag-tagged fusion proteins. GFP-tagged Nse1, which localized in whole cells, was translocated to nuclei when co-expressed with Flag-tagged Nse3 or Nse4. RNAi-mediated Nse1 and Nse4 knockdown cells (Nse1 KD and Nse4 KD cells) were generated and found to be more sensitive to UV-induced cell death than control cells. Upon starvation, Nse1 and Nse4 KD cells had increases in the number of smaller fruiting bodies that formed on non-nutrient agar plates or aggregates that formed under submerged culture. We found a reduction in the mRNA level of pdsA, in vegetative and 8 h-starved Nse4 KD cells, and pdsA knockdown cells displayed effects similar to Nse4 KD cells. Our results suggest that Nse4 and Nse1 are involved in not only the cellular DNA damage response but also cellular development in D. discoideum.
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Affiliation(s)
- Hideo Taniura
- Laboratory of Neurochemistry, College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Naoya Tanabe
- Laboratory of Neurochemistry, College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Yumi Bando
- Laboratory of Neurochemistry, College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Natsumi Arai
- Laboratory of Neurochemistry, College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
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38
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Affiliation(s)
- Melania E Zanchetta
- Cluster in Biomedicine; Trieste, Italy
- Dipartimento di Scienze della Vita; Università degli Studi di Trieste; Trieste, Italy
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Gur I, Fujiwara K, Hasegawa K, Yoshikawa K. Necdin promotes ubiquitin-dependent degradation of PIAS1 SUMO E3 ligase. PLoS One 2014; 9:e99503. [PMID: 24911587 PMCID: PMC4049815 DOI: 10.1371/journal.pone.0099503] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/15/2014] [Indexed: 01/09/2023] Open
Abstract
Necdin, a pleiotropic protein that promotes differentiation and survival of mammalian neurons, is a member of MAGE (melanoma antigen) family proteins that share a highly conserved MAGE homology domain. Several MAGE proteins interact with ubiquitin E3 ligases and modulate their activities. However, it remains unknown whether MAGE family proteins interact with SUMO (small ubiquitin-like modifier) E3 ligases such as PIAS (protein inhibitor of activated STAT) family, Nsmce2/Mms21 and Cbx4/Pc2. In the present study, we examined whether necdin interacts with these SUMO E3 ligases. Co-immunoprecipitation analysis revealed that necdin, MAGED1, MAGEF1 and MAGEL2 bound to PIAS1 but not to Nsmce2 or Cbx4. These SUMO E3 ligases bound to MAGEA1 but failed to interact with necdin-like 2/MAGEG1. Necdin bound to PIAS1 central domains that are highly conserved among PIAS family proteins and suppressed PIAS1-dependent sumoylation of the substrates STAT1 and PML (promyelocytic leukemia protein). Remarkably, necdin promoted degradation of PIAS1 via the ubiquitin-proteasome pathway. In transfected HEK293A cells, amino- and carboxyl-terminally truncated mutants of PIAS1 bound to necdin but failed to undergo necdin-dependent ubiquitination. Both PIAS1 and necdin were associated with the nuclear matrix, where the PIAS1 terminal deletion mutants failed to localize, implying that the nuclear matrix is indispensable for necdin-dependent ubiquitination of PIAS1. Our data suggest that necdin suppresses PIAS1 both by inhibiting SUMO E3 ligase activity and by promoting ubiquitin-dependent degradation.
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Affiliation(s)
- Ibrahim Gur
- Laboratory of Regulation of Neuronal Development, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Kazushiro Fujiwara
- Laboratory of Regulation of Neuronal Development, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Koichi Hasegawa
- Laboratory of Regulation of Neuronal Development, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Kazuaki Yoshikawa
- Laboratory of Regulation of Neuronal Development, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
- * E-mail:
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The Smc5/Smc6/MAGE complex confers resistance to caffeine and genotoxic stress in Drosophila melanogaster. PLoS One 2013; 8:e59866. [PMID: 23555814 PMCID: PMC3610895 DOI: 10.1371/journal.pone.0059866] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 02/19/2013] [Indexed: 12/20/2022] Open
Abstract
The SMC5/6 protein complex consists of the Smc5, Smc6 and Non-Smc-Element (Nse) proteins and is important for genome stability in many species. To identify novel components in the DNA repair pathway, we carried out a genetic screen to identify mutations that confer reduced resistance to the genotoxic effects of caffeine, which inhibits the ATM and ATR DNA damage response proteins. This approach identified inactivating mutations in CG5524 and MAGE, homologs of genes encoding Smc6 and Nse3 in yeasts. The fact that Smc5 mutants are also caffeine-sensitive and that Mage physically interacts with Drosophila homologs of Nse proteins suggests that the structure of the Smc5/6 complex is conserved in Drosophila. Although Smc5/6 proteins are required for viability in S. cerevisiae, they are not essential under normal circumstances in Drosophila. However, flies carrying mutations in Smc5, Smc6 and MAGE are hypersensitive to genotoxic agents such as ionizing radiation, camptothecin, hydroxyurea and MMS, consistent with the Smc5/6 complex serving a conserved role in genome stability. We also show that mutant flies are not compromised for pre-mitotic cell cycle checkpoint responses. Rather, caffeine-induced apoptosis in these mutants is exacerbated by inhibition of ATM or ATR checkpoint kinases but suppressed by Rad51 depletion, suggesting a functional interaction involving homologous DNA repair pathways that deserves further scrutiny. Our insights into the SMC5/6 complex provide new challenges for understanding the role of this enigmatic chromatin factor in multi-cellular organisms.
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Meek DW, Marcar L. MAGE-A antigens as targets in tumour therapy. Cancer Lett 2012; 324:126-32. [PMID: 22634429 DOI: 10.1016/j.canlet.2012.05.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 05/10/2012] [Accepted: 05/13/2012] [Indexed: 10/28/2022]
Abstract
MAGE-A proteins constitute a sub-family of Cancer-Testis Antigens which are expressed mainly, but not exclusively, in germ cells. They are also expressed in various human cancers where they are associated with, and may drive, malignancy. MAGE-A proteins are highly immunogenic and are considered as potential targets for cancer vaccines and/or immuno-therapy. Moreover, recent advances in our understanding of their molecular pathology have revealed interactions that offer potential as therapeutic targets. Here we review recent progress in this area and consider how these interactions might be exploited, especially for the treatment of malignant cancers for which available treatments are inadequate.
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Affiliation(s)
- David W Meek
- Division of Cancer Research, Medical Research Institute, College of Medicine, Dentistry and Nursing, University of Dundee, Ninewells Hospital, Dundee DD1 9SY, United Kingdom.
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Guerineau M, Kriz Z, Kozakova L, Bednarova K, Janos P, Palecek J. Analysis of the Nse3/MAGE-binding domain of the Nse4/EID family proteins. PLoS One 2012; 7:e35813. [PMID: 22536443 PMCID: PMC3335016 DOI: 10.1371/journal.pone.0035813] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 03/22/2012] [Indexed: 11/21/2022] Open
Abstract
Background The Nse1, Nse3 and Nse4 proteins form a tight sub-complex of the large SMC5-6 protein complex. hNSE3/MAGEG1, the mammalian ortholog of Nse3, is the founding member of the MAGE (melanoma-associated antigen) protein family and the Nse4 kleisin subunit is related to the EID (E1A-like inhibitor of differentiation) family of proteins. We have recently shown that human MAGE proteins can interact with NSE4/EID proteins through their characteristic conserved hydrophobic pocket. Methodology/Principal Findings Using mutagenesis and protein-protein interaction analyses, we have identified a new Nse3/MAGE-binding domain (NMBD) of the Nse4/EID proteins. This short domain is located next to the Nse4 N-terminal kleisin motif and is conserved in all NSE4/EID proteins. The central amino acid residues of the human NSE4b/EID3 domain were essential for its binding to hNSE3/MAGEG1 in yeast two-hybrid assays suggesting they form the core of the binding domain. PEPSCAN ELISA measurements of the MAGEC2 binding affinity to EID2 mutant peptides showed that similar core residues contribute to the EID2-MAGEC2 interaction. In addition, the N-terminal extension of the EID2 binding domain took part in the EID2-MAGEC2 interaction. Finally, docking and molecular dynamic simulations enabled us to generate a structure model for EID2-MAGEC2. Combination of our experimental data and the structure modeling showed how the core helical region of the NSE4/EID domain binds into the conserved pocket characteristic of the MAGE protein family. Conclusions/Significance We have identified a new Nse4/EID conserved domain and characterized its binding to Nse3/MAGE proteins. The conservation and binding of the interacting surfaces suggest tight co-evolution of both Nse4/EID and Nse3/MAGE protein families.
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Affiliation(s)
- Marc Guerineau
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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The mouse Mageb18 gene encodes a ubiquitously expressed type I MAGE protein and regulates cell proliferation and apoptosis in melanoma B16-F0 cells. Biochem J 2012; 443:779-88. [DOI: 10.1042/bj20112054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Although many cancer vaccines have been developed against type I MAGE (melanoma antigen) genes owing to their shared tumour-specific expression properties, studies about their expression and functions are relatively limited. In the present study, we first identify a non-testis-specific type I MAGE gene, Mageb18 (melanoma antigen family B 18). Mouse Mageb18 is also expressed in digestion- and immune-related tissues as well as testis, and its expression in testis is age-dependent. Mageb18 is expressed in many mouse-derived cell lines, and DNA demethylation and histone acetylation mediate the reactivation of Mageb18 in Mageb18-negtive H22 and C6 cells. We also show that mouse Mageb18 encodes a 46 kDa protein which is predominantly localized in the cytoplasm. In testis, the endogenous MAGEB18 protein is mainly expressed in proliferative spermatogonia and primary and secondary spermatocytes, but less so in spermatids. Finally, we demonstrate that knockdown of MAGEB18 inhibits the growth of B16-F0 cells and induces apoptosis, which correlates with increased levels of TP53 (tumour protein 53), p21, Bax and caspase 3. The results of the present study thus uncover an important phenomenon that the expression of certain type I MAGE genes, at least for Mageb18, is non-testis-specific. Although they can regulate various malignant phenotypes of cancer cells, it is necessary to study further their expression pattern in normal tissues before using them to develop more effective and safer cancer vaccines.
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The Nse2/Mms21 SUMO ligase of the Smc5/6 complex in the maintenance of genome stability. FEBS Lett 2011; 585:2907-13. [PMID: 21550342 DOI: 10.1016/j.febslet.2011.04.067] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 04/22/2011] [Accepted: 04/27/2011] [Indexed: 01/21/2023]
Abstract
There exist three highly-conserved structural maintenance of chromosomes (Smc) complexes that ensure genome stability during eukaryotic cell division. There are the well-characterized cohesin and condensin complexes and the third Smc complex, Smc5/6. Nse2/Mms21, a SUMO ligase, is a component of the Smc5/6 complex and recent data have indicated that Nse1 may function as a ubiquitin ligase. Smc5/6 regulates sister chromatid cohesion, homologous recombination and chromatin structure and conformation. This review examines the functions of Smc5/6 in DNA repair and the maintenance of genomic integrity and explores the roles of the associated SUMO and ubiquitin ligases. Recent findings have indicated that Smc5/6 may play a topological role in chromosome dynamics, which may help understand the complexity of its activities.
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