1
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Scaramuzza S, Jones RM, Sadurni MM, Reynolds-Winczura A, Poovathumkadavil D, Farrell A, Natsume T, Rojas P, Cuesta CF, Kanemaki MT, Saponaro M, Gambus A. TRAIP resolves DNA replication-transcription conflicts during the S-phase of unperturbed cells. Nat Commun 2023; 14:5071. [PMID: 37604812 PMCID: PMC10442450 DOI: 10.1038/s41467-023-40695-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/08/2023] [Indexed: 08/23/2023] Open
Abstract
Cell division is the basis for the propagation of life and requires accurate duplication of all genetic information. DNA damage created during replication (replication stress) is a major cause of cancer, premature aging and a spectrum of other human disorders. Over the years, TRAIP E3 ubiquitin ligase has been shown to play a role in various cellular processes that govern genome integrity and faultless segregation. TRAIP is essential for cell viability, and mutations in TRAIP ubiquitin ligase activity lead to primordial dwarfism in patients. Here, we have determined the mechanism of inhibition of cell proliferation in TRAIP-depleted cells. We have taken advantage of the auxin induced degron system to rapidly degrade TRAIP within cells and to dissect the importance of various functions of TRAIP in different stages of the cell cycle. We conclude that upon rapid TRAIP degradation, specifically in S-phase, cells cease to proliferate, arrest in G2 stage of the cell cycle and undergo senescence. Our findings reveal that TRAIP works in S-phase to prevent DNA damage at transcription start sites, caused by replication-transcription conflicts.
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Affiliation(s)
- Shaun Scaramuzza
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
- Cancer Research UK - Manchester Institute, Manchester Cancer Research Centre, Manchester, UK
| | - Rebecca M Jones
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Martina Muste Sadurni
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Alicja Reynolds-Winczura
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Divyasree Poovathumkadavil
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Abigail Farrell
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Toyoaki Natsume
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Patricia Rojas
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Cyntia Fernandez Cuesta
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Marco Saponaro
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Agnieszka Gambus
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK.
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2
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Chung HJ, Lee JR, Kim TM, Kim S, Park K, Kim MJ, Jung E, Kim S, Lee EA, Ra JS, Hwang S, Lee JY, Schärer OD, Kim Y, Myung K, Kim H. ZNF212 promotes genomic integrity through direct interaction with TRAIP. Nucleic Acids Res 2023; 51:631-649. [PMID: 36594163 PMCID: PMC9881131 DOI: 10.1093/nar/gkac1226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 01/04/2023] Open
Abstract
TRAIP is a key factor involved in the DNA damage response (DDR), homologous recombination (HR) and DNA interstrand crosslink (ICL) repair. However, the exact functions of TRAIP in these processes in mammalian cells are not fully understood. Here we identify the zinc finger protein 212, ZNF212, as a novel binding partner for TRAIP and find that ZNF212 colocalizes with sites of DNA damage. The recruitment of TRAIP or ZNF212 to sites of DNA damage is mutually interdependent. We show that depletion of ZNF212 causes defects in the DDR and HR-mediated repair in a manner epistatic to TRAIP. In addition, an epistatic analysis of Zfp212, the mouse homolog of human ZNF212, in mouse embryonic stem cells (mESCs), shows that it appears to act upstream of both the Neil3 and Fanconi anemia (FA) pathways of ICLs repair. We find that human ZNF212 interacted directly with NEIL3 and promotes its recruitment to ICL lesions. Collectively, our findings identify ZNF212 as a new factor involved in the DDR, HR-mediated repair and ICL repair though direct interaction with TRAIP.
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Affiliation(s)
| | | | | | | | | | - Myung-Jin Kim
- Department of Biological Sciences, Research Institute of Women's Health and Digital Humanity Center, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Eunyoung Jung
- Department of Biological Sciences, Research Institute of Women's Health and Digital Humanity Center, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Subin Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Eun A Lee
- Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Sunyoung Hwang
- Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Orlando D Schärer
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea,Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Yonghwan Kim
- Correspondence may also be addressed to Yonghwan Kim. Tel: +82 2 710 9552;
| | - Kyungjae Myung
- Correspondence may also be addressed to Kyungjae Myung. Tel: +82 52 217 5323; Fax: +82 52 217 5519;
| | - Hongtae Kim
- To whom correspondence should be addressed. Tel: +82 52 217 5404; Fax: +82 52 217 5519;
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3
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Lo Furno E, Busseau I, Aze A, Lorenzi C, Saghira C, Danzi MC, Zuchner S, Maiorano D. Translesion DNA synthesis-driven mutagenesis in very early embryogenesis of fast cleaving embryos. Nucleic Acids Res 2021; 50:885-898. [PMID: 34939656 PMCID: PMC8789082 DOI: 10.1093/nar/gkab1223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/22/2021] [Accepted: 12/22/2021] [Indexed: 11/19/2022] Open
Abstract
In early embryogenesis of fast cleaving embryos, DNA synthesis is short and surveillance mechanisms preserving genome integrity are inefficient, implying the possible generation of mutations. We have analyzed mutagenesis in Xenopus laevis and Drosophila melanogaster early embryos. We report the occurrence of a high mutation rate in Xenopus and show that it is dependent upon the translesion DNA synthesis (TLS) master regulator Rad18. Unexpectedly, we observed a homology-directed repair contribution of Rad18 in reducing the mutation load. Genetic invalidation of TLS in the pre-blastoderm Drosophila embryo resulted in reduction of both the hatching rate and single-nucleotide variations on pericentromeric heterochromatin in adult flies. Altogether, these findings indicate that during very early Xenopus and Drosophila embryos TLS strongly contributes to the high mutation rate. This may constitute a previously unforeseen source of genetic diversity contributing to the polymorphisms of each individual with implications for genome evolution and species adaptation.
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Affiliation(s)
- Elena Lo Furno
- Genome Surveillance and Stability Laboratory, Institut de Génétique Humaine, Université de Montpellier, CNRS-UMR9002, 34000 Montpellier, France
| | - Isabelle Busseau
- Systemic Impact of Small Regulatory RNAs Laboratory, Institut de Génétique Humaine, Université de Montpellier, CNRS-UMR9002, 34000 Montpellier, France
| | - Antoine Aze
- Genome Surveillance and Stability Laboratory, Institut de Génétique Humaine, Université de Montpellier, CNRS-UMR9002, 34000 Montpellier, France
| | - Claudio Lorenzi
- Machine Learning and Gene Regulation Laboratory, Institut de Génétique Humaine, Université de Montpellier, CNRS-UMR9002, 34000 Montpellier, France
| | - Cima Saghira
- Department of Human Genetics, Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA
| | - Matt C Danzi
- Department of Human Genetics, Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA
| | - Stephan Zuchner
- Department of Human Genetics, Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA
| | - Domenico Maiorano
- Genome Surveillance and Stability Laboratory, Institut de Génétique Humaine, Université de Montpellier, CNRS-UMR9002, 34000 Montpellier, France
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4
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Bhat EA, Sajjad N, Rather IA, Sabir JSM, Hor YY. In vitro assembly complex formation of TRAIP CC and RAP 80 zinc finger motif revealed by our study. Saudi J Biol Sci 2021; 28:7511-7516. [PMID: 34867056 PMCID: PMC8626312 DOI: 10.1016/j.sjbs.2021.08.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 08/10/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
Background Tumor necrosis factor interacting protein (TRAIP/TRIP) is an important cell-signaling molecule that prevents the TNF-induced-nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation via direct interaction with TRAF 2 protein. TRAIP is a crucial downstream signaling molecule, implicated in several signaling pathways. Due to these multifunctional effects, TRAIP is more related to cellular mitosis, chromosome segregation, and DNA damage response. Tumor necrosis factor interacting protein is a downstream signaling molecule that contains a RING domain with E3 ubiquitin ligase activity at the N terminal side followed by coiled-coil and C terminal leucine zipper domain. Human TRAIP is constituted of 469 amino acids with 76% sequence similarity with the mouse TRAIP protein. Although, the main inhibitory function of TRAIP has been known for decades, however, in vitro interaction of TRAIPCC domain with RAP80 Zinc finger motif has not been reported yet. Besides, RAP80, the binding partner of TRAIPCC protein has been implicated in DNA damage response. Results Our in vitro study shows that the TRAIP CC (64-166) associates with the RAP80 zinc finger of corresponding amino acid 490-584. However, TRAIP CCLZ (66-260) and TRAIP RINGCC (1 = 157) failed to interact with the RAP80 zinc finger of corresponding amino acid 490-584. The current study reinforces TRAIP CC (64-166) and RAP80 zinc finger of corresponding amino acid 490-584 associates to form a complex. Moreover, SDS PAGE arbitrated the homogeneity of RAP80 Zinc finger and TRAIP CC of corresponding amino acid 490-584 and 64-166, respectively. Conclusion In vitro, a specific interaction was observed between the TRAIP CC (64-166) and the RAP80 zinc finger of the corresponding amino acid 490-584 and a specific binding area of the RAP80 zinc finger motif were investigated. The TRAIPCC region is required for the complex to bind to the RAP80-Zn finger motif. This strategy may be necessary for the RAP80 zinc finger activity to the TRAIP CC protein.
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Affiliation(s)
- Eijaz Ahmed Bhat
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PR China.,Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Nasreena Sajjad
- Department of Biochemistry, University of Kashmir, Hazratbal, Jammu and Kashmir, India
| | - Irfan A Rather
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jamal S M Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Yan-Yan Hor
- Department of Biotechnology, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea
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5
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Villa F, Fujisawa R, Ainsworth J, Nishimura K, Lie‐A‐Ling M, Lacaud G, Labib KPM. CUL2 LRR1 , TRAIP and p97 control CMG helicase disassembly in the mammalian cell cycle. EMBO Rep 2021; 22:e52164. [PMID: 33590678 PMCID: PMC7926238 DOI: 10.15252/embr.202052164] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/16/2020] [Accepted: 01/07/2021] [Indexed: 11/26/2022] Open
Abstract
The eukaryotic replisome is disassembled in each cell cycle, dependent upon ubiquitylation of the CMG helicase. Studies of Saccharomyces cerevisiae, Caenorhabditis elegans and Xenopus laevis have revealed surprising evolutionary diversity in the ubiquitin ligases that control CMG ubiquitylation, but regulated disassembly of the mammalian replisome has yet to be explored. Here, we describe a model system for studying the ubiquitylation and chromatin extraction of the mammalian CMG replisome, based on mouse embryonic stem cells. We show that the ubiquitin ligase CUL2LRR1 is required for ubiquitylation of the CMG-MCM7 subunit during S-phase, leading to disassembly by the p97 ATPase. Moreover, a second pathway of CMG disassembly is activated during mitosis, dependent upon the TRAIP ubiquitin ligase that is mutated in primordial dwarfism and mis-regulated in various cancers. These findings indicate that replisome disassembly in diverse metazoa is regulated by a conserved pair of ubiquitin ligases, distinct from those present in other eukaryotes.
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Affiliation(s)
- Fabrizio Villa
- The MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Ryo Fujisawa
- The MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Johanna Ainsworth
- The MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Kohei Nishimura
- The MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaJapan
| | - Michael Lie‐A‐Ling
- Cancer Research U.K. Manchester InstituteThe University of ManchesterAlderley ParkUK
| | - Georges Lacaud
- Cancer Research U.K. Manchester InstituteThe University of ManchesterAlderley ParkUK
| | - Karim PM Labib
- The MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
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6
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Mechanisms of eukaryotic replisome disassembly. Biochem Soc Trans 2021; 48:823-836. [PMID: 32490508 PMCID: PMC7329349 DOI: 10.1042/bst20190363] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/06/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
DNA replication is a complex process that needs to be executed accurately before cell division in order to maintain genome integrity. DNA replication is divided into three main stages: initiation, elongation and termination. One of the key events during initiation is the assembly of the replicative helicase at origins of replication, and this mechanism has been very well described over the last decades. In the last six years however, researchers have also focused on deciphering the molecular mechanisms underlying the disassembly of the replicative helicase during termination. Similar to replisome assembly, the mechanism of replisome disassembly is strictly regulated and well conserved throughout evolution, although its complexity increases in higher eukaryotes. While budding yeast rely on just one pathway for replisome disassembly in S phase, higher eukaryotes evolved an additional mitotic pathway over and above the default S phase specific pathway. Moreover, replisome disassembly has been recently found to be a key event prior to the repair of certain DNA lesions, such as under-replicated DNA in mitosis and inter-strand cross-links (ICLs) in S phase. Although replisome disassembly in human cells has not been characterised yet, they possess all of the factors involved in these pathways in model organisms, and de-regulation of many of them are known to contribute to tumorigenesis and other pathological conditions.
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7
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Bhat EA, Sajjad N, Sabir JSM, Kamli MR, Hakeem KR, Rather IA, Bahieldin A. Molecular cloning, expression, overproduction and characterization of human TRAIP Leucine zipper protein. Saudi J Biol Sci 2020; 27:1562-1565. [PMID: 32489294 PMCID: PMC7253899 DOI: 10.1016/j.sjbs.2020.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/01/2020] [Accepted: 03/05/2020] [Indexed: 11/26/2022] Open
Abstract
The TRAIP interacting protein is known as a negative regulator of TNF-induced-nuclear factor, kappa-light-chain-enhancer of activated B cell (NF-κB) by direct interaction with the adaptor protein TRAF2, which inhibits the function of TRAF2 via the RINGCC domain protein. The TRAIP protein is composed of 469 amino acids with an N-terminal RING motif that is followed by a coiled coil (CC) and leucine zipper domain. TRAIP proteins are critical in programmed cell death, cell proliferation and differentiation, and embryonic development. The critical functions of TRAIP together with the molecular inhibitory mechanism effect of TRAIP have been reported by two different studies and have opened up new research into the field of TRAF biology. In this study, we designed different constructs of the Leucine zipper domain to find the over –expressed construct for further studies. We successfully cloned the C-terminal TRAIP containing the leucine zipper domain. In addition, we have over-expressed and purified the TRAIP LZ for their biochemical characterization.
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Affiliation(s)
- Eijaz Ahmed Bhat
- Life Science Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Nasreena Sajjad
- Department of Biochemistry, University of Kashmir, Hazratbal, Jammu and Kashmir, India
| | - Jamal S M Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.,Centre of Excellence in Bionanoscience Research, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
| | - Majid Rasool Kamli
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.,Centre of Excellence in Bionanoscience Research, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
| | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
| | - Irfan A Rather
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.,Centre of Excellence in Bionanoscience Research, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
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8
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Marygold SJ, Attrill H, Speretta E, Warner K, Magrane M, Berloco M, Cotterill S, McVey M, Rong Y, Yamaguchi M. The DNA polymerases of Drosophila melanogaster. Fly (Austin) 2020; 14:49-61. [PMID: 31933406 PMCID: PMC7714529 DOI: 10.1080/19336934.2019.1710076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
DNA synthesis during replication or repair is a fundamental cellular process that is catalyzed by a set of evolutionary conserved polymerases. Despite a large body of research, the DNA polymerases of Drosophila melanogaster have not yet been systematically reviewed, leading to inconsistencies in their nomenclature, shortcomings in their functional (Gene Ontology, GO) annotations and an under-appreciation of the extent of their characterization. Here, we describe the complete set of DNA polymerases in D. melanogaster, applying nomenclature already in widespread use in other species, and improving their functional annotation. A total of 19 genes encode the proteins comprising three replicative polymerases (alpha-primase, delta, epsilon), five translesion/repair polymerases (zeta, eta, iota, Rev1, theta) and the mitochondrial polymerase (gamma). We also provide an overview of the biochemical and genetic characterization of these factors in D. melanogaster. This work, together with the incorporation of the improved nomenclature and GO annotation into key biological databases, including FlyBase and UniProtKB, will greatly facilitate access to information about these important proteins.
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Affiliation(s)
- Steven J Marygold
- FlyBase, Department of Physiology, Development and Neuroscience, University of Cambridge , Cambridge, UK
| | - Helen Attrill
- FlyBase, Department of Physiology, Development and Neuroscience, University of Cambridge , Cambridge, UK
| | - Elena Speretta
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridgeshire, UK
| | - Kate Warner
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridgeshire, UK
| | - Michele Magrane
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridgeshire, UK
| | - Maria Berloco
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro" , Bari, Italy
| | - Sue Cotterill
- Department Basic Medical Sciences, St Georges University London , London, UK
| | - Mitch McVey
- Department of Biology, Tufts University , Medford, MA, USA
| | - Yikang Rong
- School of Life Sciences, Sun Yat-sen University , Guangzhou, China
| | - Masamitsu Yamaguchi
- Department of Applied Biology and Advanced Insect Research Promotion Center, Kyoto Institute of Technology , Kyoto, Japan
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9
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Chen Y, Li J, Cao F, Lam J, Cheng CC, Yu CH, Huen MS. Nucleolar residence of the seckel syndrome protein TRAIP is coupled to ribosomal DNA transcription. Nucleic Acids Res 2019; 46:10119-10131. [PMID: 30165463 PMCID: PMC6212796 DOI: 10.1093/nar/gky775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 08/16/2018] [Indexed: 12/30/2022] Open
Abstract
The RING finger protein TRAIP protects genome integrity and its mutation causes Seckel syndrome. TRAIP encodes a nucleolar protein that migrates to UV-induced DNA lesions via a direct interaction with the DNA replication clamp PCNA. Thus far, mechanistically how UV mobilizes TRAIP from the nucleoli remains unknown. We found that PCNA binding is dispensable for the nucleolus-nucleoplasm shuttling of TRAIP following cell exposure to UV irradiation, and that its redistribution did not rely on the master DNA damage kinases ATM and ATR. Interestingly, I-PpoI-induced ribosomal DNA damage led to TRAIP exclusion from the nucleoli, raising the possibility that active ribosomal DNA transcription may underlie TRAIP retention in the nuclear sub-compartments. Accordingly, chemical inhibition of RNA polymerase I activity led to TRAIP diffusion into the nucleoplasm, and was coupled with marked reduction of DNA/RNA hybrids in the nucleoli, suggesting that TRAIP may be sequestered via binding to nucleic acid structures in the nucleoli. Consistently, cell pre-treatment with DNase/RNase effectively released TRAIP from the nucleoli. Taken together, our study defines a bipartite mechanism that drives TRAIP trafficking in response to UV damage, and highlights the nucleolus as a stress sensor that contributes to orchestrating DNA damage responses.
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Affiliation(s)
- Yangzi Chen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Junshi Li
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Fakun Cao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Jason Lam
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Clooney Cy Cheng
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Cheng-Han Yu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Michael Sy Huen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R.,Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, PR China.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong S.A.R
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10
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Priego Moreno S, Jones RM, Poovathumkadavil D, Scaramuzza S, Gambus A. Mitotic replisome disassembly depends on TRAIP ubiquitin ligase activity. Life Sci Alliance 2019; 2:2/2/e201900390. [PMID: 30979826 PMCID: PMC6464043 DOI: 10.26508/lsa.201900390] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 01/08/2023] Open
Abstract
Analysis of the mitotic replisome disassembly pathway in X. laevis egg extract shows that any replisomes retained on chromatin past S-phase are unloaded through formation of K6- and K63-linked ubiquitin chains on Mcm7 by TRAIP ubiquitin ligase and p97/VCP activity. We have shown previously that the process of replication machinery (replisome) disassembly at the termination of DNA replication forks in the S-phase is driven through polyubiquitylation of one of the replicative helicase subunits (Mcm7) by Cul2LRR1 ubiquitin ligase. Interestingly, upon inhibition of this pathway in Caenorhabditis elegans embryos, the replisomes retained on chromatin were unloaded in the subsequent mitosis. Here, we show that this mitotic replisome disassembly pathway exists in Xenopus laevis egg extract and we determine the first elements of its regulation. The mitotic disassembly pathway depends on the formation of K6- and K63-linked ubiquitin chains on Mcm7 by TRAIP ubiquitin ligase and the activity of p97/VCP protein segregase. Unlike in lower eukaryotes, however, it does not require SUMO modifications. Importantly, we also show that this process can remove all replisomes from mitotic chromatin, including stalled ones, which indicates a wide application for this pathway over being just a “backup” for terminated replisomes. Finally, we characterise the composition of the replisome retained on chromatin until mitosis.
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Affiliation(s)
- Sara Priego Moreno
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Rebecca M Jones
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Divyasree Poovathumkadavil
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Shaun Scaramuzza
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Agnieszka Gambus
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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11
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Regulation of Mammalian DNA Replication via the Ubiquitin-Proteasome System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1042:421-454. [PMID: 29357069 DOI: 10.1007/978-981-10-6955-0_19] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Proper regulation of DNA replication ensures the faithful transmission of genetic material essential for optimal cellular and organismal physiology. Central to this regulation is the activity of a set of enzymes that induce or reverse posttranslational modifications of various proteins critical for the initiation, progression, and termination of DNA replication. This is particularly important when DNA replication proceeds in cancer cells with elevated rates of genomic instability and increased proliferative capacities. Here, we describe how DNA replication in mammalian cells is regulated via the activity of the ubiquitin-proteasome system as well as the consequence of derailed ubiquitylation signaling involved in this important cellular activity.
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Lee KA, Cho KC, Kim B, Jang IH, Nam K, Kwon YE, Kim M, Hyeon DY, Hwang D, Seol JH, Lee WJ. Inflammation-Modulated Metabolic Reprogramming Is Required for DUOX-Dependent Gut Immunity in Drosophila. Cell Host Microbe 2018; 23:338-352.e5. [DOI: 10.1016/j.chom.2018.01.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/07/2017] [Accepted: 01/23/2018] [Indexed: 12/22/2022]
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Lee NS, Kim S, Jung YW, Kim H. Eukaryotic DNA damage responses: Homologous recombination factors and ubiquitin modification. Mutat Res 2017; 809:88-98. [PMID: 28552167 DOI: 10.1016/j.mrfmmm.2017.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/17/2017] [Accepted: 04/30/2017] [Indexed: 12/20/2022]
Abstract
To prevent genomic instability disorders, cells have developed a DNA damage response. The response involves various proteins that sense damaged DNA, transduce damage signals, and effect DNA repair. In addition, ubiquitin modifications modulate the signaling pathway depending on cellular context. Among various types of DNA damage, double-stranded breaks are highly toxic to genomic integrity. Homologous recombination (HR) repair is an essential mechanism that fixes DNA damage because of its high level of accuracy. Although factors in the repair pathway are well established, pinpointing the exact mechanisms of repair and devising therapeutic applications requires more studies. Moreover, essential functions of ubiquitin modification in the DNA damage signaling pathway have emerged. In this review, to explore the eukaryotic DNA damage response, we will mention the functions of main factors in the HR repair pathway and ubiquitin modification.
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Affiliation(s)
- Nam Soo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Soomi Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Yong Woo Jung
- Department of Pharmacy, Korea University, Sejong 30019, South Korea.
| | - Hongtae Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea; Center for Neuroscience Imaging Research, Institute for Basic Science, Sungkyunkwan University, Suwon 16419, South Korea.
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Zhao L, Washington MT. Translesion Synthesis: Insights into the Selection and Switching of DNA Polymerases. Genes (Basel) 2017; 8:genes8010024. [PMID: 28075396 PMCID: PMC5295019 DOI: 10.3390/genes8010024] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/04/2017] [Accepted: 01/04/2017] [Indexed: 01/05/2023] Open
Abstract
DNA replication is constantly challenged by DNA lesions, noncanonical DNA structures and difficult-to-replicate DNA sequences. Two major strategies to rescue a stalled replication fork and to ensure continuous DNA synthesis are: (1) template switching and recombination-dependent DNA synthesis; and (2) translesion synthesis (TLS) using specialized DNA polymerases to perform nucleotide incorporation opposite DNA lesions. The former pathway is mainly error-free, and the latter is error-prone and a major source of mutagenesis. An accepted model of translesion synthesis involves DNA polymerase switching steps between a replicative DNA polymerase and one or more TLS DNA polymerases. The mechanisms that govern the selection and exchange of specialized DNA polymerases for a given DNA lesion are not well understood. In this review, recent studies concerning the mechanisms of selection and switching of DNA polymerases in eukaryotic systems are summarized.
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Affiliation(s)
- Linlin Zhao
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI 48859, USA.
- Science of Advanced Materials Program, Central Michigan University, Mount Pleasant, MI 48859, USA.
| | - M Todd Washington
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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Barnes R, Eckert K. Maintenance of Genome Integrity: How Mammalian Cells Orchestrate Genome Duplication by Coordinating Replicative and Specialized DNA Polymerases. Genes (Basel) 2017; 8:genes8010019. [PMID: 28067843 PMCID: PMC5295014 DOI: 10.3390/genes8010019] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/19/2016] [Accepted: 12/27/2016] [Indexed: 12/30/2022] Open
Abstract
Precise duplication of the human genome is challenging due to both its size and sequence complexity. DNA polymerase errors made during replication, repair or recombination are central to creating mutations that drive cancer and aging. Here, we address the regulation of human DNA polymerases, specifically how human cells orchestrate DNA polymerases in the face of stress to complete replication and maintain genome stability. DNA polymerases of the B-family are uniquely adept at accurate genome replication, but there are numerous situations in which one or more additional DNA polymerases are required to complete genome replication. Polymerases of the Y-family have been extensively studied in the bypass of DNA lesions; however, recent research has revealed that these polymerases play important roles in normal human physiology. Replication stress is widely cited as contributing to genome instability, and is caused by conditions leading to slowed or stalled DNA replication. Common Fragile Sites epitomize “difficult to replicate” genome regions that are particularly vulnerable to replication stress, and are associated with DNA breakage and structural variation. In this review, we summarize the roles of both the replicative and Y-family polymerases in human cells, and focus on how these activities are regulated during normal and perturbed genome replication.
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Affiliation(s)
- Ryan Barnes
- Biomedical Sciences Graduate Program, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| | - Kristin Eckert
- Departments of Pathology and Biochemistry & Molecular Biology, The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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Feng W, Guo Y, Huang J, Deng Y, Zang J, Huen MSY. TRAIP regulates replication fork recovery and progression via PCNA. Cell Discov 2016; 2:16016. [PMID: 27462463 PMCID: PMC4923944 DOI: 10.1038/celldisc.2016.16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 03/23/2016] [Indexed: 12/24/2022] Open
Abstract
PCNA is a central scaffold that coordinately assembles replication and repair machineries at DNA replication forks for faithful genome duplication. Here, we describe TRAIP (RNF206) as a novel PCNA-interacting factor that has important roles during mammalian replicative stress responses. We show that TRAIP encodes a nucleolar protein that migrates to stalled replication forks, and that this is accomplished by its targeting of PCNA via an evolutionarily conserved PIP box on its C terminus. Accordingly, inactivation of TRAIP or its interaction with the PCNA clamp compromised replication fork recovery and progression, and leads to chromosome instability. Together, our findings establish TRAIP as a component of the mammalian replicative stress response network, and implicate the TRAIP-PCNA axis in recovery of stalled replication forks.
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Affiliation(s)
- Wanjuan Feng
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R., China; Centre for Cancer Research, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R., China
| | - Yingying Guo
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R., China
| | - Jun Huang
- Life Sciences Institute, Zhejiang University, Zhejiang, China
| | - Yiqun Deng
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Jianye Zang
- School of Life Sciences, University of Science of Technology of China , Hefei, China
| | - Michael Shing-Yan Huen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R., China; Centre for Cancer Research, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R., China; State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong S.A.R., China
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17
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The TRAF-interacting protein (TRAIP) is a novel E2F target with peak expression in mitosis. Oncotarget 2016; 6:20933-45. [PMID: 26369285 PMCID: PMC4673240 DOI: 10.18632/oncotarget.3055] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 11/08/2014] [Indexed: 12/17/2022] Open
Abstract
The TRAF-interacting protein (TRAIP) is an E3 ubiquitin ligase required for cell proliferation. TRAIP mRNA is downregulated in human keratinocytes after inhibition of the PI3K/AKT/mTOR signaling. Since E2F transcription factors are downstream of PI3K/AKT/mTOR we investigated whether they regulate TRAIP expression. E2F1 expression significantly increased the TRAIP mRNA level in HeLa cells. Reporter assays with the 1400bp 5′-upstream promoter in HeLa cells and human keratinocytes showed that E2F1-, E2F2- and E2F4-induced upregulation of TRAIP expression is mediated by 168bp upstream of the translation start site. Mutating the E2F binding site within this fragment reduced the E2F1- and E2F2-dependent promoter activities and protein-DNA complex formation in gel shift assays. Abundance of TRAIP mRNA and protein was regulated by the cell cycle with a peak in G2/M. Expression of GFP and TRAIP-GFP demonstrated that TRAIP-GFP protein has a lower steady-state concentration than GFP despite similar mRNA levels. Cycloheximide inhibition experiments indicated that the TRAIP protein has a half-life of around four hours. Therefore, the combination of cell cycle-dependent transcription of the TRAIP gene by E2F and rapid protein degradation leads to cell cycle-dependent expression with a maximum in G2/M. These findings suggest that TRAIP has important functions in mitosis and tumorigenesis.
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García-Rodríguez N, Wong RP, Ulrich HD. Functions of Ubiquitin and SUMO in DNA Replication and Replication Stress. Front Genet 2016; 7:87. [PMID: 27242895 PMCID: PMC4865505 DOI: 10.3389/fgene.2016.00087] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 04/27/2016] [Indexed: 12/14/2022] Open
Abstract
Complete and faithful duplication of its entire genetic material is one of the essential prerequisites for a proliferating cell to maintain genome stability. Yet, during replication DNA is particularly vulnerable to insults. On the one hand, lesions in replicating DNA frequently cause a stalling of the replication machinery, as most DNA polymerases cannot cope with defective templates. This situation is aggravated by the fact that strand separation in preparation for DNA synthesis prevents common repair mechanisms relying on strand complementarity, such as base and nucleotide excision repair, from working properly. On the other hand, the replication process itself subjects the DNA to a series of hazardous transformations, ranging from the exposure of single-stranded DNA to topological contortions and the generation of nicks and fragments, which all bear the risk of inducing genomic instability. Dealing with these problems requires rapid and flexible responses, for which posttranslational protein modifications that act independently of protein synthesis are particularly well suited. Hence, it is not surprising that members of the ubiquitin family, particularly ubiquitin itself and SUMO, feature prominently in controlling many of the defensive and restorative measures involved in the protection of DNA during replication. In this review we will discuss the contributions of ubiquitin and SUMO to genome maintenance specifically as they relate to DNA replication. We will consider cases where the modifiers act during regular, i.e., unperturbed stages of replication, such as initiation, fork progression, and termination, but also give an account of their functions in dealing with lesions, replication stalling and fork collapse.
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19
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Harley ME, Murina O, Leitch A, Higgs MR, Bicknell LS, Yigit G, Blackford AN, Zlatanou A, Mackenzie KJ, Reddy K, Halachev M, McGlasson S, Reijns MAM, Fluteau A, Martin CA, Sabbioneda S, Elcioglu NH, Altmüller J, Thiele H, Greenhalgh L, Chessa L, Maghnie M, Salim M, Bober MB, Nürnberg P, Jackson SP, Hurles ME, Wollnik B, Stewart GS, Jackson AP. TRAIP promotes DNA damage response during genome replication and is mutated in primordial dwarfism. Nat Genet 2016; 48:36-43. [PMID: 26595769 PMCID: PMC4697364 DOI: 10.1038/ng.3451] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/26/2015] [Indexed: 12/11/2022]
Abstract
DNA lesions encountered by replicative polymerases threaten genome stability and cell cycle progression. Here we report the identification of mutations in TRAIP, encoding an E3 RING ubiquitin ligase, in patients with microcephalic primordial dwarfism. We establish that TRAIP relocalizes to sites of DNA damage, where it is required for optimal phosphorylation of H2AX and RPA2 during S-phase in response to ultraviolet (UV) irradiation, as well as fork progression through UV-induced DNA lesions. TRAIP is necessary for efficient cell cycle progression and mutations in TRAIP therefore limit cellular proliferation, providing a potential mechanism for microcephaly and dwarfism phenotypes. Human genetics thus identifies TRAIP as a component of the DNA damage response to replication-blocking DNA lesions.
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Affiliation(s)
- Margaret E Harley
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Olga Murina
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrea Leitch
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Louise S Bicknell
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Gökhan Yigit
- Institute of Human Genetics, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | | | - Anastasia Zlatanou
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Karen J Mackenzie
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Kaalak Reddy
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Mihail Halachev
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Sarah McGlasson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Martin A M Reijns
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Adeline Fluteau
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Carol-Anne Martin
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | | | - Nursel H Elcioglu
- Department of Pediatric Genetics, Marmara University Pendik Hospital, Istanbul, Turkey
| | - Janine Altmüller
- Institute of Human Genetics, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Lynn Greenhalgh
- Cheshire and Merseyside Clinical Genetics Service, Liverpool Women's Hospital, Liverpool, L12 2AP, UK
| | - Luciana Chessa
- Department of Clinical and Molecular Medicine, University Sapienza, A.O.S. Andrea, I-00189 Roma, Italy
| | - Mohamad Maghnie
- Department of Pediatrics, IRCCS, Giannina Gaslini, University of Genova, 16147 Genova, Italy
| | - Mahmoud Salim
- Department of Pediatric Genetics, Marmara University Pendik Hospital, Istanbul, Turkey
| | - Michael B Bober
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware 19803, USA
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Stephen P Jackson
- The Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | | | - Bernd Wollnik
- Institute of Human Genetics, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
- Institute of Human Genetics, University Medical Centre Göttingen, 37073 Göttingen, Germany
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Andrew P Jackson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
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Hoffmann S, Smedegaard S, Nakamura K, Mortuza GB, Räschle M, Ibañez de Opakua A, Oka Y, Feng Y, Blanco FJ, Mann M, Montoya G, Groth A, Bekker-Jensen S, Mailand N. TRAIP is a PCNA-binding ubiquitin ligase that protects genome stability after replication stress. J Cell Biol 2015; 212:63-75. [PMID: 26711499 PMCID: PMC4700480 DOI: 10.1083/jcb.201506071] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/02/2015] [Indexed: 12/02/2022] Open
Abstract
The E3 ubiquitin ligase TRAIP associates with replication forks through direct interaction with PCNA, promoting checkpoint signaling and genome stability after replication stress. Cellular genomes are highly vulnerable to perturbations to chromosomal DNA replication. Proliferating cell nuclear antigen (PCNA), the processivity factor for DNA replication, plays a central role as a platform for recruitment of genome surveillance and DNA repair factors to replication forks, allowing cells to mitigate the threats to genome stability posed by replication stress. We identify the E3 ubiquitin ligase TRAIP as a new factor at active and stressed replication forks that directly interacts with PCNA via a conserved PCNA-interacting peptide (PIP) box motif. We show that TRAIP promotes ATR-dependent checkpoint signaling in human cells by facilitating the generation of RPA-bound single-stranded DNA regions upon replication stress in a manner that critically requires its E3 ligase activity and is potentiated by the PIP box. Consequently, loss of TRAIP function leads to enhanced chromosomal instability and decreased cell survival after replication stress. These findings establish TRAIP as a PCNA-binding ubiquitin ligase with an important role in protecting genome integrity after obstacles to DNA replication.
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Affiliation(s)
- Saskia Hoffmann
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Stine Smedegaard
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kyosuke Nakamura
- Biotech Research and Innovation Center, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Gulnahar B Mortuza
- Macromolecular Crystallography Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Markus Räschle
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Alain Ibañez de Opakua
- Structural Biology Unit, Center for Cooperative Research in Biosciences, 48160 Derio, Bizkaia, Spain
| | - Yasuyoshi Oka
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Yunpeng Feng
- Biotech Research and Innovation Center, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Francisco J Blanco
- Structural Biology Unit, Center for Cooperative Research in Biosciences, 48160 Derio, Bizkaia, Spain IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Guillermo Montoya
- Macromolecular Crystallography Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anja Groth
- Biotech Research and Innovation Center, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Simon Bekker-Jensen
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Niels Mailand
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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McIntyre J, Woodgate R. Regulation of translesion DNA synthesis: Posttranslational modification of lysine residues in key proteins. DNA Repair (Amst) 2015; 29:166-79. [PMID: 25743599 PMCID: PMC4426011 DOI: 10.1016/j.dnarep.2015.02.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 01/30/2023]
Abstract
Posttranslational modification of proteins often controls various aspects of their cellular function. Indeed, over the past decade or so, it has been discovered that posttranslational modification of lysine residues plays a major role in regulating translesion DNA synthesis (TLS) and perhaps the most appreciated lysine modification is that of ubiquitination. Much of the recent interest in ubiquitination stems from the fact that proliferating cell nuclear antigen (PCNA) was previously shown to be specifically ubiquitinated at K164 and that such ubiquitination plays a key role in regulating TLS. In addition, TLS polymerases themselves are now known to be ubiquitinated. In the case of human polymerase η, ubiquitination at four lysine residues in its C-terminus appears to regulate its ability to interact with PCNA and modulate TLS. Within the past few years, advances in global proteomic research have revealed that many proteins involved in TLS are, in fact, subject to a previously underappreciated number of lysine modifications. In this review, we will summarize the known lysine modifications of several key proteins involved in TLS; PCNA and Y-family polymerases η, ι, κ and Rev1 and we will discuss the potential regulatory effects of such modification in controlling TLS in vivo.
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Affiliation(s)
- Justyna McIntyre
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
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22
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Chapard C, Meraldi P, Gleich T, Bachmann D, Hohl D, Huber M. TRAIP is a regulator of the spindle assembly checkpoint. J Cell Sci 2014; 127:5149-56. [PMID: 25335891 DOI: 10.1242/jcs.152579] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Accurate chromosome segregation during mitosis is temporally and spatially coordinated by fidelity-monitoring checkpoint systems. Deficiencies in these checkpoint systems can lead to chromosome segregation errors and aneuploidy, and promote tumorigenesis. Here, we report that the TRAF-interacting protein (TRAIP), a ubiquitously expressed nucleolar E3 ubiquitin ligase important for cellular proliferation, is localized close to mitotic chromosomes. Its knockdown in HeLa cells by RNA interference (RNAi) decreased the time of early mitosis progression from nuclear envelope breakdown (NEB) to anaphase onset and increased the percentages of chromosome alignment defects in metaphase and lagging chromosomes in anaphase compared with those of control cells. The decrease in progression time was corrected by the expression of wild-type but not a ubiquitin-ligase-deficient form of TRAIP. TRAIP-depleted cells bypassed taxol-induced mitotic arrest and displayed significantly reduced kinetochore levels of MAD2 (also known as MAD2L1) but not of other spindle checkpoint proteins in the presence of nocodazole. These results imply that TRAIP regulates the spindle assembly checkpoint, MAD2 abundance at kinetochores and the accurate cellular distribution of chromosomes. The TRAIP ubiquitin ligase activity is functionally required for the spindle assembly checkpoint control.
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Affiliation(s)
- Christophe Chapard
- Service of Dermatology, Lausanne University Hospital, CHUV, 1011 Lausanne, Switzerland
| | - Patrick Meraldi
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva, Switzerland
| | - Tobias Gleich
- Service of Dermatology, Lausanne University Hospital, CHUV, 1011 Lausanne, Switzerland
| | - Daniel Bachmann
- Service of Dermatology, Lausanne University Hospital, CHUV, 1011 Lausanne, Switzerland
| | - Daniel Hohl
- Service of Dermatology, Lausanne University Hospital, CHUV, 1011 Lausanne, Switzerland
| | - Marcel Huber
- Service of Dermatology, Lausanne University Hospital, CHUV, 1011 Lausanne, Switzerland
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