51
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Verma P, Tandon R, Yadav G, Gaur V. Structural Aspects of DNA Repair and Recombination in Crop Improvement. Front Genet 2020; 11:574549. [PMID: 33024442 PMCID: PMC7516265 DOI: 10.3389/fgene.2020.574549] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
The adverse effects of global climate change combined with an exponentially increasing human population have put substantial constraints on agriculture, accelerating efforts towards ensuring food security for a sustainable future. Conventional plant breeding and modern technologies have led to the creation of plants with better traits and higher productivity. Most crop improvement approaches (conventional breeding, genome modification, and gene editing) primarily rely on DNA repair and recombination (DRR). Studying plant DRR can provide insights into designing new strategies or improvising the present techniques for crop improvement. Even though plants have evolved specialized DRR mechanisms compared to other eukaryotes, most of our insights about plant-DRRs remain rooted in studies conducted in animals. DRR mechanisms in plants include direct repair, nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), non-homologous end joining (NHEJ) and homologous recombination (HR). Although each DRR pathway acts on specific DNA damage, there is crosstalk between these. Considering the importance of DRR pathways as a tool in crop improvement, this review focuses on a general description of each DRR pathway, emphasizing on the structural aspects of key DRR proteins. The review highlights the gaps in our understanding and the importance of studying plant DRR in the context of crop improvement.
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Affiliation(s)
- Prabha Verma
- National Institute of Plant Genome Research, New Delhi, India
| | - Reetika Tandon
- National Institute of Plant Genome Research, New Delhi, India
| | - Gitanjali Yadav
- National Institute of Plant Genome Research, New Delhi, India
| | - Vineet Gaur
- National Institute of Plant Genome Research, New Delhi, India
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52
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Song J, Freeman AD, Knebel A, Gartner A, Lilley DM. Human ANKLE1 Is a Nuclease Specific for Branched DNA. J Mol Biol 2020; 432:5825-5834. [PMID: 32866453 PMCID: PMC7610144 DOI: 10.1016/j.jmb.2020.08.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 12/02/2022]
Abstract
All physical connections between sister chromatids must be broken before cells can divide, and eukaryotic cells have evolved multiple ways in which to process branchpoints connecting DNA molecules separated both spatially and temporally. A single DNA link between chromatids has the potential to disrupt cell cycle progression and genome integrity, so it is highly likely that cells require a nuclease that can process remaining unresolved and hemi-resolved DNA junctions and other branched species at the very late stages of mitosis. We argue that ANKLE1 probably serves this function in human cells (LEM-3 in Caenorhabditis elegans). LEM-3 has previously been shown to be located at the cell mid-body, and we show here that human ANKLE1 is a nuclease that cleaves a range of branched DNA species. It thus has the substrate selectivity consistent with an enzyme required to process a variety of unresolved and hemi-resolved branchpoints in DNA. Our results suggest that ANKLE1 acts as a catch-all enzyme of last resort that allows faithful chromosome segregation and cell division to occur.
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Affiliation(s)
- Junfang Song
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK
| | - Alasdair D.J. Freeman
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Axel Knebel
- MRC Protein Phosphorylation Unit, University of Dundee, Dundee DD1 5EH, UK
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - David M.J. Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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53
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Nguyen DD, Kim EY, Sang PB, Chai W. Roles of OB-Fold Proteins in Replication Stress. Front Cell Dev Biol 2020; 8:574466. [PMID: 33043007 PMCID: PMC7517361 DOI: 10.3389/fcell.2020.574466] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022] Open
Abstract
Accurate DNA replication is essential for maintaining genome stability. However, this stability becomes vulnerable when replication fork progression is stalled or slowed - a condition known as replication stress. Prolonged fork stalling can cause DNA damage, leading to genome instabilities. Thus, cells have developed several pathways and a complex set of proteins to overcome the challenge at stalled replication forks. Oligonucleotide/oligosaccharide binding (OB)-fold containing proteins are a group of proteins that play a crucial role in fork protection and fork restart. These proteins bind to single-stranded DNA with high affinity and prevent premature annealing and unwanted nuclease digestion. Among these OB-fold containing proteins, the best studied in eukaryotic cells are replication protein A (RPA) and breast cancer susceptibility protein 2 (BRCA2). Recently, another RPA-like protein complex CTC1-STN1-TEN1 (CST) complex has been found to counter replication perturbation. In this review, we discuss the latest findings on how these OB-fold containing proteins (RPA, BRCA2, CST) cooperate to safeguard DNA replication and maintain genome stability.
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Affiliation(s)
| | | | | | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, United States
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54
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CRL4Cdt2 ubiquitin ligase regulates Dna2 and Rad16 (XPF) nucleases by targeting Pxd1 for degradation. PLoS Genet 2020; 16:e1008933. [PMID: 32692737 PMCID: PMC7394458 DOI: 10.1371/journal.pgen.1008933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/31/2020] [Accepted: 06/15/2020] [Indexed: 01/19/2023] Open
Abstract
Structure-specific endonucleases (SSEs) play key roles in DNA replication, recombination, and repair. SSEs must be tightly regulated to ensure genome stability but their regulatory mechanisms remain incompletely understood. Here, we show that in the fission yeast Schizosaccharomyces pombe, the activities of two SSEs, Dna2 and Rad16 (ortholog of human XPF), are temporally controlled during the cell cycle by the CRL4Cdt2 ubiquitin ligase. CRL4Cdt2 targets Pxd1, an inhibitor of Dna2 and an activator of Rad16, for degradation in S phase. The ubiquitination and degradation of Pxd1 is dependent on CRL4Cdt2, PCNA, and a PCNA-binding degron motif on Pxd1. CRL4Cdt2-mediated Pxd1 degradation prevents Pxd1 from interfering with the normal S-phase functions of Dna2. Moreover, Pxd1 degradation leads to a reduction of Rad16 nuclease activity in S phase, and restrains Rad16-mediated single-strand annealing, a hazardous pathway of repairing double-strand breaks. These results demonstrate a new role of the CRL4Cdt2 ubiquitin ligase in genome stability maintenance and shed new light on how SSE activities are regulated during the cell cycle. Structure-specific endonucleases are enzymes that process DNA intermediates generated in DNA replication, recombination, and repair. Proper regulation of these enzymes is critical for maintaining genome stability. Dna2 and XPF are two such enzymes present across eukaryotes, from yeasts to humans. Here, we show that in the fission yeast Schizosaccharomyces pombe, the activities of Dna2 and Rad16 (the equivalent of human XPF) are temporally controlled during the cell cycle by the CRL4Cdt2 ubiquitin E3 ligase. In the S phase of the cell cycle, CRL4Cdt2 promotes the degradation of Pxd1, which is an inhibitor of Dna2 and an activator of Rad16. Through targeting Pxd1 for degradation, CRL4Cdt2 increases the activity of Dna2 in S phase and is important for the normal S-phase function of Dna2. Meanwhile, the degradation of Pxd1 reduces the activity of Rad16 in S phase, and curtails Rad16-dependent single-strand annealing, a mutagenic DNA repair pathway. Our findings uncover a new mechanism regulating two important endonucleases during the cell cycle, and reveal a new way of coordinating endonucleases to safeguard genome stability.
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55
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Kaushal S, Wollmuth CE, Das K, Hile SE, Regan SB, Barnes RP, Haouzi A, Lee SM, House NCM, Guyumdzhyan M, Eckert KA, Freudenreich CH. Sequence and Nuclease Requirements for Breakage and Healing of a Structure-Forming (AT)n Sequence within Fragile Site FRA16D. Cell Rep 2020; 27:1151-1164.e5. [PMID: 31018130 DOI: 10.1016/j.celrep.2019.03.103] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 02/07/2019] [Accepted: 03/27/2019] [Indexed: 01/20/2023] Open
Abstract
Common fragile sites (CFSs) are genomic regions that display gaps and breaks in human metaphase chromosomes under replication stress and are often deleted in cancer cells. We studied an ∼300-bp subregion (Flex1) of human CFS FRA16D in yeast and found that it recapitulates characteristics of CFS fragility in human cells. Flex1 fragility is dependent on the ability of a variable-length AT repeat to form a cruciform structure that stalls replication. Fragility at Flex1 is initiated by structure-specific endonuclease Mus81-Mms4 acting together with the Slx1-4/Rad1-10 complex, whereas Yen1 protects Flex1 against breakage. Sae2 is required for healing of Flex1 after breakage. Our study shows that breakage within a CFS can be initiated by nuclease cleavage at forks stalled at DNA structures. Furthermore, our results suggest that CFSs are not just prone to breakage but also are impaired in their ability to heal, and this deleterious combination accounts for their fragility.
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Affiliation(s)
- Simran Kaushal
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Charles E Wollmuth
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Kohal Das
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Suzanne E Hile
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Samantha B Regan
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Ryan P Barnes
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Alice Haouzi
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Soo Mi Lee
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Nealia C M House
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Michael Guyumdzhyan
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Kristin A Eckert
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA; Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA.
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56
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Niss K, Gomez-Casado C, Hjaltelin JX, Joeris T, Agace WW, Belling KG, Brunak S. Complete Topological Mapping of a Cellular Protein Interactome Reveals Bow-Tie Motifs as Ubiquitous Connectors of Protein Complexes. Cell Rep 2020; 31:107763. [PMID: 32553166 DOI: 10.1016/j.celrep.2020.107763] [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] [Received: 08/16/2019] [Revised: 02/03/2020] [Accepted: 05/21/2020] [Indexed: 11/18/2022] Open
Abstract
The network topology of a protein interactome is shaped by the function of each protein, making it a resource of functional knowledge in tissues and in single cells. Today, this resource is underused, as complete network topology characterization has proved difficult for large protein interactomes. We apply a matrix visualization and decoding approach to a physical protein interactome of a dendritic cell, thereby characterizing its topology with no prior assumptions of structure. We discover 294 proteins, each forming topological motifs called "bow-ties" that tie together the majority of observed protein complexes. The central proteins of these bow-ties have unique network properties, display multifunctional capabilities, are enriched for essential proteins, and are widely expressed in other cells and tissues. Collectively, the bow-tie motifs are a pervasive and previously unnoted topological trend in cellular interactomes. As such, these results provide fundamental knowledge on how intracellular protein connectivity is organized and operates.
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Affiliation(s)
- Kristoffer Niss
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Cristina Gomez-Casado
- Immunology Section, Lund University, BMC D14, 221-84 Lund, Sweden; Institute of Applied Molecular Medicine, Faculty of Medicine, San Pablo CEU University, 28925 Madrid, Spain
| | - Jessica X Hjaltelin
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Thorsten Joeris
- Immunology Section, Lund University, BMC D14, 221-84 Lund, Sweden
| | - William W Agace
- Immunology Section, Lund University, BMC D14, 221-84 Lund, Sweden; Mucosal Immunology Group, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Kirstine G Belling
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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57
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Saccharomyces cerevisiae Mus81-Mms4 prevents accelerated senescence in telomerase-deficient cells. PLoS Genet 2020; 16:e1008816. [PMID: 32469862 PMCID: PMC7286520 DOI: 10.1371/journal.pgen.1008816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 06/10/2020] [Accepted: 04/30/2020] [Indexed: 01/31/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) in human cells is a conserved process that is often activated in telomerase-deficient human cancers. This process exploits components of the recombination machinery to extend telomere ends, thus allowing for increased proliferative potential. Human MUS81 (Mus81 in Saccharomyces cerevisiae) is the catalytic subunit of structure-selective endonucleases involved in recombination and has been implicated in the ALT mechanism. However, it is unclear whether MUS81 activity at the telomere is specific to ALT cells or if it is required for more general aspects of telomere stability. In this study, we use S. cerevisiae to evaluate the contribution of the conserved Mus81-Mms4 endonuclease in telomerase-deficient yeast cells that maintain their telomeres by mechanisms akin to human ALT. Similar to human cells, we find that yeast Mus81 readily localizes to telomeres and its activity is important for viability after initial loss of telomerase. Interestingly, our analysis reveals that yeast Mus81 is not required for the survival of cells undergoing recombination-mediated telomere lengthening, i.e. for ALT itself. Rather we infer from genetic analysis that Mus81-Mms4 facilitates telomere replication during times of telomere instability. Furthermore, combining mus81 mutants with mutants of a yeast telomere replication factor, Rrm3, reveals that the two proteins function in parallel to promote normal growth during times of telomere stress. Combined with previous reports, our data can be interpreted in a consistent model in which both yeast and human MUS81-dependent nucleases participate in the recovery of stalled replication forks within telomeric DNA. Furthermore, this process becomes crucial under conditions of additional replication stress, such as telomere replication in telomerase-deficient cells. Cancer cell divisions require active chromosome lengthening through extension of their highly repetitive ends, called telomeres. This process is accomplished through two main mechanisms: the activity of an RNA-protein complex, telomerase, or through a telomerase-independent process termed alternative lengthening of telomeres (ALT). Human MUS81, the catalytic subunit of a set of structure-selective endonucleases, was found to be essential in human cells undergoing ALT and proposed to be directly involved in telomere lengthening. Using telomerase-deficient Saccharomyces cerevisiae cells as a model for ALT, we tested the hypothesis that Mus81-Mms4, the budding yeast homolog of human MUS81-dependent nucleases, is essential for telomere lengthening as proposed for human cells. Using genetic and molecular assays we confirm that Mus81-Mms4 is involved in telomere metabolism in yeast. However, to our surprise, we find that Mus81-Mms4 is not directly involved in recombination-based mechanisms of telomere lengthening. Rather it appears that Mus81-Mms4 is involved in resolving replication stress at telomeres, which is augmented in cells undergoing telomere instability. This model is consistent with observations in mammalian cells and suggest that cells undergoing telomere shortening experience replication stress at telomeres.
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58
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SLX4 interacts with RTEL1 to prevent transcription-mediated DNA replication perturbations. Nat Struct Mol Biol 2020; 27:438-449. [PMID: 32398829 DOI: 10.1038/s41594-020-0419-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 03/17/2020] [Indexed: 12/20/2022]
Abstract
The SLX4 tumor suppressor is a scaffold that plays a pivotal role in several aspects of genome protection, including homologous recombination, interstrand DNA crosslink repair and the maintenance of common fragile sites and telomeres. Here, we unravel an unexpected direct interaction between SLX4 and the DNA helicase RTEL1, which, until now, were viewed as having independent and antagonistic functions. We identify cancer and Hoyeraal-Hreidarsson syndrome-associated mutations in SLX4 and RTEL1, respectively, that abolish SLX4-RTEL1 complex formation. We show that both proteins are recruited to nascent DNA, tightly co-localize with active RNA pol II, and that SLX4, in complex with RTEL1, promotes FANCD2/RNA pol II co-localization. Importantly, disrupting the SLX4-RTEL1 interaction leads to DNA replication defects in unstressed cells, which are rescued by inhibiting transcription. Our data demonstrate that SLX4 and RTEL1 interact to prevent replication-transcription conflicts and provide evidence that this is independent of the nuclease scaffold function of SLX4.
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59
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Wang Y, Qian M, Qu Y, Yang N, Mu B, Liu K, Yang J, Zhou Y, Ni C, Zhong J, Guo X. Genome-Wide Screen of the Hippocampus in Aged Rats Identifies Mitochondria, Metabolism and Aging Processes Implicated in Sevoflurane Anesthesia. Front Aging Neurosci 2020; 12:122. [PMID: 32457595 PMCID: PMC7221025 DOI: 10.3389/fnagi.2020.00122] [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: 12/17/2019] [Accepted: 04/14/2020] [Indexed: 01/11/2023] Open
Abstract
Previous studies have shown multiple mechanisms and pathophysiological changes after anesthesia, and genome-wide studies have been implemented in the studies of brain aging and neurodegenerative diseases. However, the genome-wide gene expression patterns and modulation networks after general anesthesia remains to be elucidated. Therefore, whole transcriptome microarray analysis was used to explore the coding gene expression patterns in the hippocampus of aged rats after sevoflurane anesthesia. Six hundred and thirty one upregulated and 183 downregulated genes were screened out, then 44 enriched terms of biological process, 16 of molecular function and 18 of the cellular components were identified by Gene Ontology (GO) and KEGG analysis. Among them, oxidative stress, metabolism, aging, and neurodegeneration were the most enriched biological processes and changed functions. Thus, involved genes of these processes were selected for qPCR verification and a good consistency was confirmed. The potential signaling pathways were further constructed including mitochondrion and oxidative stress-related Hifs-Prkcd-Akt-Nfe2l2-Sod1 signaling, multiple metabolism signaling (Scd2, Scap-Hmgcs2, Aldh18a1-Glul and Igf1r), as well as aging and neurodegeneration related signaling (Spidr-Ercc4-Cdkn1a-Pmaip1 and Map1lc3b). These results provide potential therapeutic gene targets for brain function modulation and memory formation process after inhaled anesthesia in the elderly, which could be valuable for preventing postoperative brain disorders and diseases, such as perioperative neurocognitive disorders (PND), from the genetic level in the future.
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Affiliation(s)
- Yujie Wang
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Min Qian
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Yinyin Qu
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Ning Yang
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Bing Mu
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kaixi Liu
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Jing Yang
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Yang Zhou
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Cheng Ni
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Zhong
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiangyang Guo
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
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60
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Palmer N, Kaldis P. Less-well known functions of cyclin/CDK complexes. Semin Cell Dev Biol 2020; 107:54-62. [PMID: 32386818 DOI: 10.1016/j.semcdb.2020.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/31/2022]
Abstract
Cyclin-dependent kinases (CDKs) are activated by cyclins, which play important roles in dictating the actions of CDK/cyclin complexes. Cyclin binding influences the substrate specificity of these complexes in addition to their susceptibility to inhibition or degradation. CDK/cyclin complexes are best known to promote cell cycle progression in the mitotic cell cycle but are also crucial for important cellular processes not strictly associated with cellular division. This chapter primarily explores the understudied topic of CDK/cyclin complex functionality during the DNA damage response. We detail how CDK/cyclin complexes perform dual roles both as targets of DNA damage checkpoint signaling as well as effectors of DNA repair. Additionally, we discuss the potential CDK-independent roles of cyclins in these processes and the impact of such roles in human diseases such as cancer. Our goal is to place the spotlight on these important functions of cyclins either acting as independent entities or within CDK/cyclin complexes which have attracted less attention in the past. We consider that this will be important for a more complete understanding of the intricate functions of cell cycle proteins in the DNA damage response.
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Affiliation(s)
- Nathan Palmer
- Institute of Molecular and Cell Biology (IMCB), A⁎STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore; National University of Singapore (NUS), Department of Biochemistry, Singapore, 117597, Republic of Singapore
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), A⁎STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore; National University of Singapore (NUS), Department of Biochemistry, Singapore, 117597, Republic of Singapore; Department of Clinical Sciences, Lund University, Clinical Research Centre (CRC), Box 50332, SE-202 13, Malmö, Sweden.
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61
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Chromosome 16p13.3 Contiguous Gene Deletion Syndrome including the SLX4, DNASE1, TRAP1, and CREBBP Genes Presenting as a Relatively Mild Rubinstein-Taybi Syndrome Phenotype: A Case Report of a Saudi Boy. Case Rep Genet 2020; 2020:6143050. [PMID: 32181026 PMCID: PMC7064822 DOI: 10.1155/2020/6143050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 11/18/2022] Open
Abstract
The classic Rubinstein-Taybi syndrome Type 1 (RSTS1, OMIM 180849) is caused by heterozygous mutations or deletions of the CREBBP gene. Herein, we describe the case of a Saudi boy with chromosome 16p13.3 contiguous gene deletion syndrome (OMIM 610543) including the SLX4, DNASE1, TRAP1, and CREBBP genes, but presenting with a relatively mild RSTS1 syndrome phenotype. Compared with previously reported cases with severe phenotypes associated with 16p13.3 contiguous gene deletions, our patient had partial deletion of the CREBBP gene (with a preserved 5' region), which might explain his relatively mild phenotype.
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62
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Robinson NJ, Morrison-Smith CD, Gooding AJ, Schiemann BJ, Jackson MW, Taylor DJ, Schiemann WP. SLX4IP and telomere dynamics dictate breast cancer metastasis and therapeutic responsiveness. Life Sci Alliance 2020; 3:3/4/e201900427. [PMID: 32071280 PMCID: PMC7032570 DOI: 10.26508/lsa.201900427] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 02/06/2023] Open
Abstract
An unbiased genetic screen established SLX4IP as an essential driver of telomere maintenance mechanism identity, metastatic progression, and therapeutic response of breast cancers. Metastasis is the leading cause of breast cancer-related death and poses a substantial clinical burden owing to a paucity of targeted treatment options. The clinical manifestations of metastasis occur years-to-decades after initial diagnosis and treatment because disseminated tumor cells readily evade detection and resist therapy, ultimately giving rise to recurrent disease. Using an unbiased genetic screen, we identified SLX4-interacting protein (SLX4IP) as a regulator of metastatic recurrence and established its relationship in governing telomere maintenance mechanisms (TMMs). Inactivation of SLX4IP suppressed alternative lengthening of telomeres (ALT), coinciding with activation of telomerase. Importantly, TMM selection dramatically influenced metastatic progression and survival of patients with genetically distinct breast cancer subtypes. Notably, pharmacologic and genetic modulation of TMMs elicited telomere-dependent cell death and prevented disease recurrence by disseminated tumor cells. This study illuminates SLX4IP as a potential predictive biomarker for breast cancer progression and metastatic relapse. SLX4IP expression correlates with TMM identity, which also carries prognostic value and informs treatment selection, thereby revealing new inroads into combating metastatic breast cancers.
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Affiliation(s)
- Nathaniel J Robinson
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | | | - Alex J Gooding
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Barbara J Schiemann
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Mark W Jackson
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - William P Schiemann
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
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63
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Chen X, Sun Y, Wang S, Ying K, Xiao L, Liu K, Zuo X, He J. Identification of a novel structure-specific endonuclease AziN that contributes to the repair of azinomycin B-mediated DNA interstrand crosslinks. Nucleic Acids Res 2020; 48:709-718. [PMID: 31713613 PMCID: PMC7145581 DOI: 10.1093/nar/gkz1067] [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: 06/27/2019] [Revised: 10/11/2019] [Accepted: 10/30/2019] [Indexed: 11/25/2022] Open
Abstract
DNA interstrand crosslinks (ICLs) induced by the highly genotoxic agent azinomycin B (AZB) can cause severe perturbation of DNA structure and even cell death. However, Streptomyces sahachiroi, the strain that produces AZB, seems almost impervious to this danger because of its diverse and distinctive self-protection machineries. Here, we report the identification of a novel endonuclease-like gene aziN that contributes to drug self-protection in S. sahachiroi. AziN expression conferred AZB resistance on native and heterologous host strains. The specific binding reaction between AziN and AZB was also verified in accordance with its homology to drug binding proteins, but no drug sequestering and deactivating effects could be detected. Intriguingly, due to the high affinity with the drug, AziN was discovered to exhibit specific recognition and binding capacity with AZB-mediated ICL structures, further inducing DNA strand breakage. Subsequent in vitro assays demonstrated the structure-specific endonuclease activity of AziN, which cuts both damaged strands at specific sites around AZB-ICLs. Unravelling the nuclease activity of AziN provides a good entrance point to illuminate the complex mechanisms of AZB-ICL repair.
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Affiliation(s)
- Xiaorong Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuedi Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shan Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kun Ying
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Le Xiao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Zuo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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64
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Zhang H, Chen Z, Ye Y, Ye Z, Cao D, Xiong Y, Srivastava M, Feng X, Tang M, Wang C, Tainer JA, Chen J. SLX4IP acts with SLX4 and XPF-ERCC1 to promote interstrand crosslink repair. Nucleic Acids Res 2019; 47:10181-10201. [PMID: 31495888 PMCID: PMC6821277 DOI: 10.1093/nar/gkz769] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 08/03/2019] [Accepted: 09/05/2019] [Indexed: 12/13/2022] Open
Abstract
Interstrand crosslinks (ICLs) are highly toxic DNA lesions that are repaired via a complex process requiring the coordination of several DNA repair pathways. Defects in ICL repair result in Fanconi anemia, which is characterized by bone marrow failure, developmental abnormalities, and a high incidence of malignancies. SLX4, also known as FANCP, acts as a scaffold protein and coordinates multiple endonucleases that unhook ICLs, resolve homologous recombination intermediates, and perhaps remove unhooked ICLs. In this study, we explored the role of SLX4IP, a constitutive factor in the SLX4 complex, in ICL repair. We found that SLX4IP is a novel regulatory factor; its depletion sensitized cells to treatment with ICL-inducing agents and led to accumulation of cells in the G2/M phase. We further discovered that SLX4IP binds to SLX4 and XPF-ERCC1 simultaneously and that disruption of one interaction also disrupts the other. The binding of SLX4IP to both SLX4 and XPF-ERCC1 not only is vital for maintaining the stability of SLX4IP protein, but also promotes the interaction between SLX4 and XPF-ERCC1, especially after DNA damage. Collectively, these results demonstrate a new regulatory role for SLX4IP in maintaining an efficient SLX4-XPF-ERCC1 complex in ICL repair.
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Affiliation(s)
- Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yin Ye
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zu Ye
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Dan Cao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yun Xiong
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mrinal Srivastava
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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65
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Lemmens B, Lindqvist A. DNA replication and mitotic entry: A brake model for cell cycle progression. J Cell Biol 2019; 218:3892-3902. [PMID: 31712253 PMCID: PMC6891093 DOI: 10.1083/jcb.201909032] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 12/22/2022] Open
Abstract
Lemmens and Lindqvist discuss how DNA replication and mitosis are coordinated and propose a cell cycle model controlled by brakes. The core function of the cell cycle is to duplicate the genome and divide the duplicated DNA into two daughter cells. These processes need to be carefully coordinated, as cell division before DNA replication is complete leads to genome instability and cell death. Recent observations show that DNA replication, far from being only a consequence of cell cycle progression, plays a key role in coordinating cell cycle activities. DNA replication, through checkpoint kinase signaling, restricts the activity of cyclin-dependent kinases (CDKs) that promote cell division. The S/G2 transition is therefore emerging as a crucial regulatory step to determine the timing of mitosis. Here we discuss recent observations that redefine the coupling between DNA replication and cell division and incorporate these insights into an updated cell cycle model for human cells. We propose a cell cycle model based on a single trigger and sequential releases of three molecular brakes that determine the kinetics of CDK activation.
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Affiliation(s)
- Bennie Lemmens
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet and Science for Life Laboratory, Stockholm, Sweden
| | - Arne Lindqvist
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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66
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Vpr and Its Cellular Interaction Partners: R We There Yet? Cells 2019; 8:cells8111310. [PMID: 31652959 PMCID: PMC6912716 DOI: 10.3390/cells8111310] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 12/17/2022] Open
Abstract
Vpr is a lentiviral accessory protein that is expressed late during the infection cycle and is packaged in significant quantities into virus particles through a specific interaction with the P6 domain of the viral Gag precursor. Characterization of the physiologically relevant function(s) of Vpr has been hampered by the fact that in many cell lines, deletion of Vpr does not significantly affect viral fitness. However, Vpr is critical for virus replication in primary macrophages and for viral pathogenesis in vivo. It is generally accepted that Vpr does not have a specific enzymatic activity but functions as a molecular adapter to modulate viral or cellular processes for the benefit of the virus. Indeed, many Vpr interacting factors have been described by now, and the goal of this review is to summarize our current knowledge of cellular proteins targeted by Vpr.
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67
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Differential mechanisms of tolerance to extreme environmental conditions in tardigrades. Sci Rep 2019; 9:14938. [PMID: 31624306 PMCID: PMC6797769 DOI: 10.1038/s41598-019-51471-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/29/2019] [Indexed: 01/17/2023] Open
Abstract
Tardigrades, also known as water bears, are small aquatic animals that inhabit marine, fresh water or limno-terrestrial environments. While all tardigrades require surrounding water to grow and reproduce, species living in limno-terrestrial environments (e.g. Ramazzottius varieornatus) are able to undergo almost complete dehydration by entering an arrested state known as anhydrobiosis, which allows them to tolerate ionic radiation, extreme temperatures and intense pressure. Previous studies based on comparison of the genomes of R. varieornatus and Hypsibius dujardini - a less tolerant tardigrade - have pointed to potential mechanisms that may partially contribute to their remarkable ability to resist extreme physical conditions. In this work, we have further annotated the genomes of both tardigrades using a guided approach in search for novel mechanisms underlying the extremotolerance of R. varieornatus. We have found specific amplifications of several genes, including MRE11 and XPC, and numerous missense variants exclusive of R. varieornatus in CHEK1, POLK, UNG and TERT, all of them involved in important pathways for DNA repair and telomere maintenance. Taken collectively, these results point to genomic features that may contribute to the enhanced ability to resist extreme environmental conditions shown by R. varieornatus.
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68
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Hoogenboom WS, Boonen RACM, Knipscheer P. The role of SLX4 and its associated nucleases in DNA interstrand crosslink repair. Nucleic Acids Res 2019; 47:2377-2388. [PMID: 30576517 PMCID: PMC6411836 DOI: 10.1093/nar/gky1276] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 12/11/2022] Open
Abstract
A key step in the Fanconi anemia pathway of DNA interstrand crosslink (ICL) repair is the ICL unhooking by dual endonucleolytic incisions. SLX4/FANCP is a large scaffold protein that plays a central role in ICL unhooking. It contains multiple domains that interact with many proteins including three different endonucleases and also acts in several other DNA repair pathways. While it is known that its interaction with the endonuclease XPF-ERCC1 is required for its function in ICL repair, which other domains act in this process is unclear. Here, we used Xenopus egg extracts to determine ICL repair specific features of SLX4. We show that the SLX4-interacting endonuclease SLX1 is not required for ICL repair and demonstrate that all essential SLX4 domains are located at the N-terminal half of the protein. The MLR domain is crucial for the recruitment of XPF-ERCC1 but also has an unanticipated function in recruiting SLX4 to the site of damage. Although we find the BTB is not essential for ICL repair in our system, dimerization of SLX4 could be important. Our data provide new insights into the mechanism by which SLX4 acts in ICL repair.
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Affiliation(s)
- Wouter S Hoogenboom
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rick A C M Boonen
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
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69
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Porebski B, Wild S, Kummer S, Scaglione S, Gaillard PHL, Gari K. WRNIP1 Protects Reversed DNA Replication Forks from SLX4-Dependent Nucleolytic Cleavage. iScience 2019; 21:31-41. [PMID: 31654852 PMCID: PMC6820244 DOI: 10.1016/j.isci.2019.10.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/15/2019] [Accepted: 10/02/2019] [Indexed: 11/30/2022] Open
Abstract
During DNA replication stress, stalled replication forks need to be stabilized to prevent fork collapse and genome instability. The AAA + ATPase WRNIP1 (Werner Helicase Interacting Protein 1) has been implicated in the protection of stalled replication forks from nucleolytic degradation, but the underlying molecular mechanism has remained unclear. Here we show that WRNIP1 exerts its protective function downstream of fork reversal. Unexpectedly though, WRNIP1 is not part of the well-studied BRCA2-dependent branch of fork protection but seems to protect the junction point of reversed replication forks from SLX4-mediated endonucleolytic degradation, possibly by directly binding to reversed replication forks. This function is specific to the shorter, less abundant, and less conserved variant of WRNIP1. Overall, our data suggest that in the absence of BRCA2 and WRNIP1 different DNA substrates are generated at reversed forks but that nascent strand degradation in both cases depends on the activity of exonucleases and structure-specific endonucleases. WRNIP1, as BRCA2, protects stalled replication forks downstream of fork reversal WRNIP1 and BRCA2 act in two different branches of the fork protection pathway WRNIP1 protects from SLX4-mediated nucleolytic cleavage, possibly by direct binding Fork protection function is specific to the shorter isoform of WRNIP1
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Affiliation(s)
- Bartlomiej Porebski
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland.
| | - Sebastian Wild
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Sandra Kummer
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Sarah Scaglione
- Centre de Recherche en Cancérologie de Marseille, CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Pierre-Henri L Gaillard
- Centre de Recherche en Cancérologie de Marseille, CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Kerstin Gari
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland.
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70
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Panier S, Maric M, Hewitt G, Mason-Osann E, Gali H, Dai A, Labadorf A, Guervilly JH, Ruis P, Segura-Bayona S, Belan O, Marzec P, Gaillard PHL, Flynn RL, Boulton SJ. SLX4IP Antagonizes Promiscuous BLM Activity during ALT Maintenance. Mol Cell 2019; 76:27-43.e11. [PMID: 31447390 PMCID: PMC6863466 DOI: 10.1016/j.molcel.2019.07.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 06/03/2019] [Accepted: 07/08/2019] [Indexed: 12/18/2022]
Abstract
Cancer cells acquire unlimited proliferative capacity by either re-expressing telomerase or inducing alternative lengthening of telomeres (ALT), which relies on telomere recombination. Here, we show that ALT recombination requires coordinate regulation of the SMX and BTR complexes to ensure the appropriate balance of resolution and dissolution activities at recombining telomeres. Critical to this control is SLX4IP, which accumulates at ALT telomeres and interacts with SLX4, XPF, and BLM. Loss of SLX4IP increases ALT-related phenotypes, which is incompatible with cell growth following concomitant loss of SLX4. Inactivation of BLM is sufficient to rescue telomere aggregation and the synthetic growth defect in this context, suggesting that SLX4IP favors SMX-dependent resolution by antagonizing promiscuous BLM activity during ALT recombination. Finally, we show that SLX4IP is inactivated in a subset of ALT-positive osteosarcomas. Collectively, our findings uncover an SLX4IP-dependent regulatory mechanism critical for telomere maintenance in ALT cancer cells.
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Affiliation(s)
| | - Marija Maric
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Graeme Hewitt
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Emily Mason-Osann
- Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Himabindu Gali
- Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Anqi Dai
- Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Adam Labadorf
- Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Jean-Hugues Guervilly
- Centre de Recherche en Cancérologie de Marseille, CRCM, CNRS, Aix Marseille Université, INSERM, Institut Paoli-Calmettes, 27 Boulevard Leï Roure, 13009 Marseille, France
| | - Philip Ruis
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Ondrej Belan
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Paulina Marzec
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Pierre-Henri L Gaillard
- Centre de Recherche en Cancérologie de Marseille, CRCM, CNRS, Aix Marseille Université, INSERM, Institut Paoli-Calmettes, 27 Boulevard Leï Roure, 13009 Marseille, France
| | - Rachel L Flynn
- Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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71
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Palma A, Pugliese GM, Murfuni I, Marabitti V, Malacaria E, Rinalducci S, Minoprio A, Sanchez M, Mazzei F, Zolla L, Franchitto A, Pichierri P. Phosphorylation by CK2 regulates MUS81/EME1 in mitosis and after replication stress. Nucleic Acids Res 2019; 46:5109-5124. [PMID: 29850896 PMCID: PMC6007509 DOI: 10.1093/nar/gky280] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 04/04/2018] [Indexed: 12/21/2022] Open
Abstract
The MUS81 complex is crucial for preserving genome stability through the resolution of branched DNA intermediates in mitosis. However, untimely activation of the MUS81 complex in S-phase is dangerous. Little is known about the regulation of the human MUS81 complex and how deregulated activation affects chromosome integrity. Here, we show that the CK2 kinase phosphorylates MUS81 at Serine 87 in late-G2/mitosis, and upon mild replication stress. Phosphorylated MUS81 interacts with SLX4, and this association promotes the function of the MUS81 complex. In line with a role in mitosis, phosphorylation at Serine 87 is suppressed in S-phase and is mainly detected in the MUS81 molecules associated with EME1. Loss of CK2-dependent MUS81 phosphorylation contributes modestly to chromosome integrity, however, expression of the phosphomimic form induces DSBs accumulation in S-phase, because of unscheduled targeting of HJ-like DNA intermediates, and generates a wide chromosome instability phenotype. Collectively, our findings describe a novel regulatory mechanism controlling the MUS81 complex function in human cells. Furthermore, they indicate that, genome stability depends mainly on the ability of cells to counteract targeting of branched intermediates by the MUS81/EME1 complex in S-phase, rather than on a correct MUS81 function in mitosis.
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Affiliation(s)
- Anita Palma
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Giusj Monia Pugliese
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Ivana Murfuni
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Veronica Marabitti
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Eva Malacaria
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Sara Rinalducci
- Proteomics, Metabolomics and Interactomics Lab, Department of Ecology and Biology, Università della Tuscia, Viale dell'Università snc, 01100 Viterbo, Italy
| | - Anna Minoprio
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Massimo Sanchez
- Core Facilities Center - Section of Cytometry, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Filomena Mazzei
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Lello Zolla
- Proteomics, Metabolomics and Interactomics Lab, Department of Ecology and Biology, Università della Tuscia, Viale dell'Università snc, 01100 Viterbo, Italy
| | - Annapaola Franchitto
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Pietro Pichierri
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
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72
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Hunter FW, Devaux JBL, Meng F, Hong CR, Khan A, Tsai P, Ketela TW, Sharma I, Kakadia PM, Marastoni S, Shalev Z, Hickey AJR, Print CG, Bohlander SK, Hart CP, Wouters BG, Wilson WR. Functional CRISPR and shRNA Screens Identify Involvement of Mitochondrial Electron Transport in the Activation of Evofosfamide. Mol Pharmacol 2019; 95:638-651. [PMID: 30979813 DOI: 10.1124/mol.118.115196] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 04/08/2019] [Indexed: 01/29/2023] Open
Abstract
Evofosfamide (TH-302) is a hypoxia-activated DNA-crosslinking prodrug currently in clinical development for cancer therapy. Oxygen-sensitive activation of evofosfamide depends on one-electron reduction, yet the reductases that catalyze this process in tumors are unknown. We used RNA sequencing, whole-genome CRISPR knockout, and reductase-focused short hairpin RNA screens to interrogate modifiers of evofosfamide activation in cancer cell lines. Involvement of mitochondrial electron transport in the activation of evofosfamide and the related nitroaromatic compounds EF5 and FSL-61 was investigated using 143B ρ 0 (ρ zero) cells devoid of mitochondrial DNA and biochemical assays in UT-SCC-74B cells. The potency of evofosfamide in 30 genetically diverse cancer cell lines correlated with the expression of genes involved in mitochondrial electron transfer. A whole-genome CRISPR screen in KBM-7 cells identified the DNA damage-response factors SLX4IP, C10orf90 (FATS), and SLFN11, in addition to the key regulator of mitochondrial function, YME1L1, and several complex I constituents as modifiers of evofosfamide sensitivity. A reductase-focused shRNA screen in UT-SCC-74B cells similarly identified mitochondrial respiratory chain factors. Surprisingly, 143B ρ 0 cells showed enhanced evofosfamide activation and sensitivity but had global transcriptional changes, including increased expression of nonmitochondrial flavoreductases. In UT-SCC-74B cells, evofosfamide oxidized cytochromes a, b, and c and inhibited respiration at complexes I, II, and IV without quenching reactive oxygen species production. Our results suggest that the mitochondrial electron transport chain contributes to evofosfamide activation and that predicting evofosfamide sensitivity in patients by measuring the expression of canonical bioreductive enzymes such as cytochrome P450 oxidoreductase is likely to be futile.
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Affiliation(s)
- Francis W Hunter
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - Jules B L Devaux
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - Fanying Meng
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - Cho Rong Hong
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - Aziza Khan
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - Peter Tsai
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - Troy W Ketela
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - Indumati Sharma
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - Purvi M Kakadia
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - Stefano Marastoni
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - Zvi Shalev
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - Anthony J R Hickey
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - Cristin G Print
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - Stefan K Bohlander
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - Charles P Hart
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - Bradly G Wouters
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
| | - William R Wilson
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences (F.W.H., C.R.H., A.K., I.S., W.R.W.), Maurice Wilkins Centre for Molecular Biodiscovery (F.W.H., A.J.R.H., C.G.P., W.R.W.), School of Biological Sciences, Faculty of Science (J.B.L.D., A.J.R.H.), and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences (P.T., P.M.K., C.G.P., S.K.B.), University of Auckland, Auckland, New Zealand; Threshold Pharmaceuticals, South San Francisco, California (F.M., C.P.H.); Princess Margaret Genomics Centre (T.W.K.) and Princess Margaret Cancer Centre (S.M., Z.S., B.G.W.), University Health Network, and Departments of Radiation Oncology (B.G.W.) and Medical Biophysics (B.G.W.), University of Toronto, Toronto, Ontario, Canada
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73
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Falquet B, Rass U. Structure-Specific Endonucleases and the Resolution of Chromosome Underreplication. Genes (Basel) 2019; 10:E232. [PMID: 30893921 PMCID: PMC6470701 DOI: 10.3390/genes10030232] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 12/11/2022] Open
Abstract
Complete genome duplication in every cell cycle is fundamental for genome stability and cell survival. However, chromosome replication is frequently challenged by obstacles that impede DNA replication fork (RF) progression, which subsequently causes replication stress (RS). Cells have evolved pathways of RF protection and restart that mitigate the consequences of RS and promote the completion of DNA synthesis prior to mitotic chromosome segregation. If there is entry into mitosis with underreplicated chromosomes, this results in sister-chromatid entanglements, chromosome breakage and rearrangements and aneuploidy in daughter cells. Here, we focus on the resolution of persistent replication intermediates by the structure-specific endonucleases (SSEs) MUS81, SLX1-SLX4 and GEN1. Their actions and a recently discovered pathway of mitotic DNA repair synthesis have emerged as important facilitators of replication completion and sister chromatid detachment in mitosis. As RS is induced by oncogene activation and is a common feature of cancer cells, any advances in our understanding of the molecular mechanisms related to chromosome underreplication have important biomedical implications.
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Affiliation(s)
- Benoît Falquet
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.
- Faculty of Natural Sciences, University of Basel, Petersplatz 10, CH-4003 Basel, Switzerland.
| | - Ulrich Rass
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
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74
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Savage SA, Walsh MF. Myelodysplastic Syndrome, Acute Myeloid Leukemia, and Cancer Surveillance in Fanconi Anemia. Hematol Oncol Clin North Am 2019; 32:657-668. [PMID: 30047418 DOI: 10.1016/j.hoc.2018.04.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Fanconi anemia (FA) is a DNA repair disorder associated with a high risk of cancer and bone marrow failure. Patients with FA may present with certain dysmorphic features, such as radial ray abnormalities, short stature, typical facies, bone marrow failure, or certain solid malignancies. Some patients may be recognized due to exquisite sensitivity after exposure to cancer therapy. FA is diagnosed by increased chromosomal breakage after exposure to clastogenic agents. It follows autosomal recessive and X-linked inheritance depending on the underlying genomic alterations. Recognizing patients with FA is important for therapeutic decisions, genetic counseling, and optimal clinical management.
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Affiliation(s)
- Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Room 6E456, MSC 9772, Bethesda, MD 20892-9772, USA
| | - Michael F Walsh
- Department of Medicine, Division of Solid Tumor, Memorial Sloan Kettering Cancer Center, 222 70th Street Room 412, New York, NY 10021, USA; Department of Medicine, Division of Clinical Cancer Genetics, Memorial Sloan Kettering Cancer Center, 222 70th Street Room 412, New York, NY 10021, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 222 70th Street Room 412, New York, NY 10021, USA.
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75
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Datta A, Brosh RM. Holding All the Cards-How Fanconi Anemia Proteins Deal with Replication Stress and Preserve Genomic Stability. Genes (Basel) 2019; 10:genes10020170. [PMID: 30813363 PMCID: PMC6409899 DOI: 10.3390/genes10020170] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/18/2022] Open
Abstract
Fanconi anemia (FA) is a hereditary chromosomal instability disorder often displaying congenital abnormalities and characterized by a predisposition to progressive bone marrow failure (BMF) and cancer. Over the last 25 years since the discovery of the first linkage of genetic mutations to FA, its molecular genetic landscape has expanded tremendously as it became apparent that FA is a disease characterized by a defect in a specific DNA repair pathway responsible for the correction of covalent cross-links between the two complementary strands of the DNA double helix. This pathway has become increasingly complex, with the discovery of now over 20 FA-linked genes implicated in interstrand cross-link (ICL) repair. Moreover, gene products known to be involved in double-strand break (DSB) repair, mismatch repair (MMR), and nucleotide excision repair (NER) play roles in the ICL response and repair of associated DNA damage. While ICL repair is predominantly coupled with DNA replication, it also can occur in non-replicating cells. DNA damage accumulation and hematopoietic stem cell failure are thought to contribute to the increased inflammation and oxidative stress prevalent in FA. Adding to its confounding nature, certain FA gene products are also engaged in the response to replication stress, caused endogenously or by agents other than ICL-inducing drugs. In this review, we discuss the mechanistic aspects of the FA pathway and the molecular defects leading to elevated replication stress believed to underlie the cellular phenotypes and clinical features of FA.
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Affiliation(s)
- Arindam Datta
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, MD 21224, USA.
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, MD 21224, USA.
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76
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M. AlDallal S. Quick glance at Fanconi anemia and BRCA2/FANCD1. AIMS MEDICAL SCIENCE 2019. [DOI: 10.3934/medsci.2019.4.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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77
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Kim SM, Forsburg SL. Regulation of Structure-Specific Endonucleases in Replication Stress. Genes (Basel) 2018; 9:genes9120634. [PMID: 30558228 PMCID: PMC6316474 DOI: 10.3390/genes9120634] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 12/16/2022] Open
Abstract
Replication stress results in various forms of aberrant replication intermediates that need to be resolved for faithful chromosome segregation. Structure-specific endonucleases (SSEs) recognize DNA secondary structures rather than primary sequences and play key roles during DNA repair and replication stress. Holliday junction resolvase MUS81 (methyl methane sulfonate (MMS), and UV-sensitive protein 81) and XPF (xeroderma pigmentosum group F-complementing protein) are a subset of SSEs that resolve aberrant replication structures. To ensure genome stability and prevent unnecessary DNA breakage, these SSEs are tightly regulated by the cell cycle and replication checkpoints. We discuss the regulatory network that control activities of MUS81 and XPF and briefly mention other SSEs involved in the resolution of replication intermediates.
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Affiliation(s)
- Seong Min Kim
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
| | - Susan L Forsburg
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
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78
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Faridounnia M, Folkers GE, Boelens R. Function and Interactions of ERCC1-XPF in DNA Damage Response. Molecules 2018; 23:E3205. [PMID: 30563071 PMCID: PMC6320978 DOI: 10.3390/molecules23123205] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/27/2018] [Accepted: 12/01/2018] [Indexed: 12/28/2022] Open
Abstract
Numerous proteins are involved in the multiple pathways of the DNA damage response network and play a key role to protect the genome from the wide variety of damages that can occur to DNA. An example of this is the structure-specific endonuclease ERCC1-XPF. This heterodimeric complex is in particular involved in nucleotide excision repair (NER), but also in double strand break repair and interstrand cross-link repair pathways. Here we review the function of ERCC1-XPF in various DNA repair pathways and discuss human disorders associated with ERCC1-XPF deficiency. We also overview our molecular and structural understanding of XPF-ERCC1.
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Affiliation(s)
- Maryam Faridounnia
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Gert E Folkers
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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79
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Viviescas MA, Cano MIN, Segatto M. Chaperones and Their Role in Telomerase Ribonucleoprotein Biogenesis and Telomere Maintenance. CURR PROTEOMICS 2018. [DOI: 10.2174/1570164615666180713103133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Telomere length maintenance is important for genome stability and cell division. In most
eukaryotes, telomeres are maintained by the telomerase ribonucleoprotein (RNP) complex, minimally
composed of the Telomerase Reverse Transcriptase (TERT) and the telomerase RNA (TER) components.
In addition to TERT and TER, other protein subunits are part of the complex and are involved in
telomerase regulation, assembly, disassembly, and degradation. Among them are some molecular
chaperones such as Hsp90 and its co-chaperone p23 which are found associated with the telomerase
RNP complex in humans, yeast and probably in protozoa. Hsp90 and p23 are necessary for the telomerase
RNP assembly and enzyme activity. In budding yeast, the Hsp90 homolog (Hsp82) is also responsible
for the association and dissociation of telomerase from the telomeric DNA by its direct interaction
with a telomere end-binding protein (Cdc13), responsible for regulating telomerase access to telomeres.
In addition, AAA+ ATPases, such as Pontin and Reptin, which are also considered chaperone-
like proteins, associate with the human telomerase complex by the direct interaction of Pontin with
TERT and dyskerin. They are probably responsible for telomerase RNP assembly since their depletion
impairs the accumulation of the complex. Moreover, various RNA chaperones, are also pivotal in the
assembly and migration of the mature telomerase complex and complex intermediates. In this review,
we will focus on the importance of molecular chaperones for telomerase RNP biogenesis and how they
impact telomere length maintenance and cellular homeostasis.
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Affiliation(s)
- Maria Alejandra Viviescas
- Genetics Department, Biosciences Institute, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | | | - Marcela Segatto
- Genetics Department, Biosciences Institute, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
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80
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Fan Y, Sanyal S, Bruzzone R. Breaking Bad: How Viruses Subvert the Cell Cycle. Front Cell Infect Microbiol 2018; 8:396. [PMID: 30510918 PMCID: PMC6252338 DOI: 10.3389/fcimb.2018.00396] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/22/2018] [Indexed: 01/10/2023] Open
Abstract
Interactions between the host and viruses during the course of their co-evolution have not only shaped cellular function and the immune system, but also the counter measures employed by viruses. Relatively small genomes and high replication rates allow viruses to accumulate mutations and continuously present the host with new challenges. It is therefore, no surprise that they either escape detection or modulate host physiology, often by redirecting normal cellular pathways to their own advantage. Viruses utilize a diverse array of strategies and molecular targets to subvert host cellular processes, while evading detection. These include cell-cycle regulation, major histocompatibility complex-restricted antigen presentation, intracellular protein transport, apoptosis, cytokine-mediated signaling, and humoral immune responses. Moreover, viruses routinely manipulate the host cell cycle to create a favorable environment for replication, largely by deregulating cell cycle checkpoints. This review focuses on our current understanding of the molecular aspects of cell cycle regulation that are often targeted by viruses. Further study of their interactions should provide fundamental insights into cell cycle regulation and improve our ability to exploit these viruses.
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Affiliation(s)
- Ying Fan
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong.,MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Sumana Sanyal
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong.,LKS Faculty of Medicine, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Roberto Bruzzone
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong.,Department of Cell Biology and Infection, Institut Pasteur, Paris, France
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81
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Liu Y, Freeman ADJ, Déclais AC, Lilley DMJ. A monovalent ion in the DNA binding interface of the eukaryotic junction-resolving enzyme GEN1. Nucleic Acids Res 2018; 46:11089-11098. [PMID: 30247722 PMCID: PMC6237754 DOI: 10.1093/nar/gky863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 01/07/2023] Open
Abstract
GEN1 is a member of the FEN/EXO family of structure-selective nucleases that cleave 1 nt 3' to a variety of branchpoints. For each, the H2TH motif binds a monovalent ion and plays an important role in binding one helical arm of the substrates. We investigate here the importance of this metal ion on substrate specificity and GEN1 structure. In the presence of K+ ions the substrate specificity is wider than in Na+, yet four-way junctions remain the preferred substrate. In a combination of K+ and Mg2+ second strand cleavage is accelerated 17-fold, ensuring bilateral cleavage of the junction. We have solved crystal structures of Chaetomium thermophilum GEN1 with Cs+, K+ and Na+ bound. With bound Cs+ the loop of the H2TH motif extends toward the active site so that D199 coordinates a Mg2+, buttressed by an interaction of the adjacent Y200. With the lighter ions bound the H2TH loop changes conformation and retracts away from the active site. We hypothesize this conformational change might play a role in second strand cleavage acceleration.
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Affiliation(s)
- Yijin Liu
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Alasdair DJ Freeman
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Anne-Cécile Déclais
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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82
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Abstract
The SLX4/FANCP tumor suppressor has emerged as a key player in the maintenance of genome stability, making pivotal contributions to the repair of interstrand cross-links, homologous recombination, and in response to replication stress genome-wide as well as at specific loci such as common fragile sites and telomeres. SLX4 does so in part by acting as a scaffold that controls and coordinates the XPF-ERCC1, MUS81-EME1, and SLX1 structure-specific endonucleases in different DNA repair and recombination mechanisms. It also interacts with other important DNA repair and cell cycle control factors including MSH2, PLK1, TRF2, and TOPBP1 as well as with ubiquitin and SUMO. This review aims at providing an up-to-date and comprehensive view on the key functions that SLX4 fulfills to maintain genome stability as well as to highlight and discuss areas of uncertainty and emerging concepts.
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Affiliation(s)
- Jean-Hugues Guervilly
- a CRCM, CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes , Marseille , France
| | - Pierre Henri Gaillard
- a CRCM, CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes , Marseille , France
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83
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Yates M, Maréchal A. Ubiquitylation at the Fork: Making and Breaking Chains to Complete DNA Replication. Int J Mol Sci 2018; 19:E2909. [PMID: 30257459 PMCID: PMC6213728 DOI: 10.3390/ijms19102909] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 12/11/2022] Open
Abstract
The complete and accurate replication of the genome is a crucial aspect of cell proliferation that is often perturbed during oncogenesis. Replication stress arising from a variety of obstacles to replication fork progression and processivity is an important contributor to genome destabilization. Accordingly, cells mount a complex response to this stress that allows the stabilization and restart of stalled replication forks and enables the full duplication of the genetic material. This response articulates itself on three important platforms, Replication Protein A/RPA-coated single-stranded DNA, the DNA polymerase processivity clamp PCNA and the FANCD2/I Fanconi Anemia complex. On these platforms, the recruitment, activation and release of a variety of genome maintenance factors is regulated by post-translational modifications including mono- and poly-ubiquitylation. Here, we review recent insights into the control of replication fork stability and restart by the ubiquitin system during replication stress with a particular focus on human cells. We highlight the roles of E3 ubiquitin ligases, ubiquitin readers and deubiquitylases that provide the required flexibility at stalled forks to select the optimal restart pathways and rescue genome stability during stressful conditions.
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Affiliation(s)
- Maïlyn Yates
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
| | - Alexandre Maréchal
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
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84
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Chan YW, West SC. A new class of ultrafine anaphase bridges generated by homologous recombination. Cell Cycle 2018; 17:2101-2109. [PMID: 30253678 PMCID: PMC6226235 DOI: 10.1080/15384101.2018.1515555] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/20/2018] [Indexed: 12/31/2022] Open
Abstract
Ultrafine anaphase bridges (UFBs) are a potential source of genome instability that is a hallmark of cancer. UFBs can arise from DNA catenanes at centromeres/rDNA loci, late replication intermediates induced by replication stress, and DNA linkages at telomeres. Recently, it was reported that DNA intertwinements generated by homologous recombination give rise to a new class of UFBs, which have been termed homologous recombination ultrafine bridges (HR-UFBs). HR-UFBs are decorated with PICH and BLM in anaphase, and are subsequently converted to RPA-coated, single-stranded DNA bridges. Breakage of these sister chromatid entanglements leads to DNA damage that can be repaired by non-homologous end joining in the next cell cycle, but the potential consequences include DNA rearrangements, chromosome translocations and fusions. Visualisation of these HR-UFBs, and knowledge of how they arise, provides a molecular basis to explain how upregulation of homologous recombination or failure to resolve recombination intermediates leads to the development of chromosomal instability observed in certain cancers.
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Affiliation(s)
- Ying Wai Chan
- Department of DNA Recombination and Repair, The Francis Crick Institute, London, UK
| | - Stephen C. West
- Department of DNA Recombination and Repair, The Francis Crick Institute, London, UK
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85
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Distinct roles of XPF-ERCC1 and Rad1-Rad10-Saw1 in replication-coupled and uncoupled inter-strand crosslink repair. Nat Commun 2018; 9:2025. [PMID: 29795289 PMCID: PMC5966407 DOI: 10.1038/s41467-018-04327-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 04/20/2018] [Indexed: 01/17/2023] Open
Abstract
Yeast Rad1-Rad10 (XPF-ERCC1 in mammals) incises UV, oxidation, and cross-linking agent-induced DNA lesions, and contributes to multiple DNA repair pathways. To determine how Rad1-Rad10 catalyzes inter-strand crosslink repair (ICLR), we examined sensitivity to ICLs from yeast deleted for SAW1 and SLX4, which encode proteins that interact physically with Rad1-Rad10 and bind stalled replication forks. Saw1, Slx1, and Slx4 are critical for replication-coupled ICLR in mus81 deficient cells. Two rad1 mutations that disrupt interactions between Rpa1 and Rad1-Rad10 selectively disable non-nucleotide excision repair (NER) function, but retain UV lesion repair. Mutations in the analogous region of XPF also compromised XPF interactions with Rpa1 and Slx4, and are proficient in NER but deficient in ICLR and direct repeat recombination. We propose that Rad1-Rad10 makes distinct contributions to ICLR depending on cell cycle phase: in G1, Rad1-Rad10 removes ICL via NER, whereas in S/G2, Rad1-Rad10 facilitates NER-independent replication-coupled ICLR.
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86
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Saugar I, Jiménez-Martín A, Tercero JA. Subnuclear Relocalization of Structure-Specific Endonucleases in Response to DNA Damage. Cell Rep 2018; 20:1553-1562. [PMID: 28813668 DOI: 10.1016/j.celrep.2017.07.059] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 05/09/2017] [Accepted: 07/20/2017] [Indexed: 12/25/2022] Open
Abstract
Structure-specific endonucleases contribute to the maintenance of genome integrity by cleaving DNA intermediates that need to be resolved for faithful DNA repair, replication, or recombination. Despite advances in the understanding of their function and regulation, it is less clear how these proteins respond to genotoxic stress. Here, we show that the structure-specific endonuclease Mus81-Mms4/EME1 relocalizes to subnuclear foci following DNA damage and colocalizes with the endonucleases Rad1-Rad10 (XPF-ERCC1) and Slx1-Slx4. Recruitment takes place into a class of stress foci defined by Cmr1/WDR76, a protein involved in preserving genome stability, and depends on the E2-ubiquitin-conjugating enzyme Rad6 and the E3-ubiquitin ligase Bre1. Foci dynamics show that, in the presence of DNA intermediates that need resolution by Mus81-Mms4, Mus81 foci persist until this endonuclease is activated by Mms4 phosphorylation. Our data suggest that subnuclear relocalization is relevant for the function of Mus81-Mms4 and, probably, of the endonucleases that colocalize with it.
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Affiliation(s)
- Irene Saugar
- Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Cantoblanco, 28049 Madrid, Spain
| | | | - José Antonio Tercero
- Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Cantoblanco, 28049 Madrid, Spain.
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87
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Che R, Zhang J, Nepal M, Han B, Fei P. Multifaceted Fanconi Anemia Signaling. Trends Genet 2018; 34:171-183. [PMID: 29254745 PMCID: PMC5858900 DOI: 10.1016/j.tig.2017.11.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/28/2017] [Indexed: 01/26/2023]
Abstract
In 1927 Guido Fanconi described a hereditary condition presenting panmyelopathy accompanied by short stature and hyperpigmentation, now better known as Fanconi anemia (FA). With this discovery the genetic and molecular basis underlying FA has emerged as a field of great interest. FA signaling is crucial in the DNA damage response (DDR) to mediate the repair of damaged DNA. This has attracted a diverse range of investigators, especially those interested in aging and cancer. However, recent evidence suggests FA signaling also regulates functions outside the DDR, with implications for many other frontiers of research. We discuss here the characteristics of FA functions and expand upon current perspectives regarding the genetics of FA, indicating that FA plays a role in a myriad of molecular and cellular processes.
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Affiliation(s)
- Raymond Che
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA; Graduate Program of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, USA
| | - Jun Zhang
- Department of Laboratory Medicine and Pathology, Mayo Clinic Foundation, USA
| | - Manoj Nepal
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA; Graduate Program of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, USA
| | - Bing Han
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA
| | - Peiwen Fei
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA; Graduate Program of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, USA.
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88
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Liu Y, Freeman A, Déclais AC, Gartner A, Lilley DMJ. Biochemical and Structural Properties of Fungal Holliday Junction-Resolving Enzymes. Methods Enzymol 2018; 600:543-568. [PMID: 29458774 DOI: 10.1016/bs.mie.2017.11.021] [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] [Indexed: 02/01/2023]
Abstract
Four-way Holliday junctions in DNA are the central intermediates of genetic recombination and must be processed into regular duplex species. One mechanism for achieving this is called resolution, brought about by structure-selective nucleases. GEN1 is an important junction-resolving enzyme in eukaryotic cells, a member of the FEN1/EXO1 superfamily of nucleases. While human GEN1 is difficult to work with because of aggregation, orthologs from thermophilic fungi have been identified using bioinformatics and have proved to have excellent properties. Here, the expression and purification of this enzyme from Chaetomium thermophilum is described, together with the means of investigating its biochemical properties. The enzyme is quite similar to junction-resolving enzymes from lower organisms, binding to junctions in dimeric form, introducing symmetrical bilateral cleavages, the second of which is accelerated to promote productive resolution. Crystallization of C. thermophilum GEN1 is described, and the structure of a DNA-product complex. Juxtaposition of complexes in the crystal lattice suggests how the structure of a dimeric enzyme with an intact junction is organized.
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Affiliation(s)
- Yijin Liu
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - Alasdair Freeman
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - Anne-Cécile Déclais
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - Anton Gartner
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom.
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89
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West SC, Chan YW. Genome Instability as a Consequence of Defects in the Resolution of Recombination Intermediates. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2018; 82:207-212. [PMID: 29348327 DOI: 10.1101/sqb.2017.82.034256] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The efficient processing of homologous recombination (HR) intermediates, which often contain four-way structures known as Holliday junctions (HJs), is required for proper chromosome segregation at mitosis. Eukaryotic cells possess three distinct pathways of resolution: (i) HJ dissolution mediated by BLM-topoisomerase IIIα-RMI1-RMI2 (BTR) complex, and HJ resolution catalyzed by either (ii) SLX1-SLX4-MUS81-EME1-XPF-ERCC1 (SMX complex) or (iii) GEN1. The BTR pathway acts at all times throughout the cell cycle, whereas the actions of SMX and GEN1 are restrained in S phase and become elevated late in the cell cycle to ensure the resolution of persistent recombination intermediates before mitotic division. By developing a "resolvase-deficient" model system in which the activities of MUS81 and GEN1 are compromised, we have explored the fate of unresolved recombination intermediates. We find that covalently linked sister chromatids promote the formation of a new class of ultrafine bridges at anaphase that we term HR-UFBs. These bridges are broken at cell division, leading to activation of the DNA damage checkpoint and repair by nonhomologous end joining (NHEJ) in the next cell cycle. As a consequence, high levels of gross chromosomal rearrangements and aberrations are observed, together with frequent cell death. These results show that the HJ resolvases provide essential functions for the resolution of recombination intermediates, even in cells that remain proficient for BTR-mediated HJ dissolution.
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Affiliation(s)
- Stephen C West
- The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Ying Wai Chan
- The Francis Crick Institute, London NW1 1AT, United Kingdom
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90
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Ranjha L, Howard SM, Cejka P. Main steps in DNA double-strand break repair: an introduction to homologous recombination and related processes. Chromosoma 2018; 127:187-214. [PMID: 29327130 DOI: 10.1007/s00412-017-0658-1] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 12/16/2022]
Abstract
DNA double-strand breaks arise accidentally upon exposure of DNA to radiation and chemicals or result from faulty DNA metabolic processes. DNA breaks can also be introduced in a programmed manner, such as during the maturation of the immune system, meiosis, or cancer chemo- or radiotherapy. Cells have developed a variety of repair pathways, which are fine-tuned to the specific needs of a cell. Accordingly, vegetative cells employ mechanisms that restore the integrity of broken DNA with the highest efficiency at the lowest cost of mutagenesis. In contrast, meiotic cells or developing lymphocytes exploit DNA breakage to generate diversity. Here, we review the main pathways of eukaryotic DNA double-strand break repair with the focus on homologous recombination and its various subpathways. We highlight the differences between homologous recombination and end-joining mechanisms including non-homologous end-joining and microhomology-mediated end-joining and offer insights into how these pathways are regulated. Finally, we introduce noncanonical functions of the recombination proteins, in particular during DNA replication stress.
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Affiliation(s)
- Lepakshi Ranjha
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Sean M Howard
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland. .,Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.
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91
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Chan YW, Fugger K, West SC. Unresolved recombination intermediates lead to ultra-fine anaphase bridges, chromosome breaks and aberrations. Nat Cell Biol 2018; 20:92-103. [PMID: 29255170 PMCID: PMC5742284 DOI: 10.1038/s41556-017-0011-1] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/16/2017] [Indexed: 01/21/2023]
Abstract
The resolution of joint molecules that link recombining sister chromatids is essential for chromosome segregation. Here, we determine the fate of unresolved recombination intermediates arising in cells lacking two nucleases required for resolution (GEN1 -/- knockout cells depleted of MUS81). We find that intermediates persist until mitosis and form a distinct class of anaphase bridges, which we term homologous recombination ultra-fine bridges (HR-UFBs). HR-UFBs are distinct from replication stress-associated UFBs, which arise at common fragile sites, and from centromeric UFBs. HR-UFBs are processed by BLM helicase to generate single-stranded RPA-coated bridges that are broken during mitosis. In the next cell cycle, DNA breaks activate the DNA damage checkpoint response, and chromosome fusions arise by non-homologous end joining. Consequently, the cells undergo cell cycle delay and massive cell death. These results lead us to present a model detailing how unresolved recombination intermediates can promote DNA damage and chromosomal instability.
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92
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Javadekar SM, Yadav R, Raghavan SC. DNA structural basis for fragility at peak III of BCL2 major breakpoint region associated with t(14;18) translocation. Biochim Biophys Acta Gen Subj 2017; 1862:649-659. [PMID: 29246583 DOI: 10.1016/j.bbagen.2017.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/23/2017] [Accepted: 12/07/2017] [Indexed: 12/23/2022]
Abstract
Maintaining genome integrity is crucial for normal cellular functions. DNA double-strand breaks (DSBs), when unrepaired, can potentiate chromosomal translocations. t(14;18) translocation involving BCL2 gene on chromosome 18 and IgH loci at chromosome 14, could lead to follicular lymphoma. Molecular basis for fragility of translocation breakpoint regions is an active area of investigation. Previously, formation of non-B DNA structures like G-quadruplex, triplex, B/A transition were investigated at peak I of BCL2 major breakpoint region (MBR); however, it is less understood at peak III. In vitro gel shift assays show faster mobility for MBR peak III sequences, unlike controls. CD studies of peak III sequences reveal a spectral pattern different from B-DNA. Although complementary C-rich stretches exhibit single-strandedness, corresponding guanine-rich sequences do not show DMS protection, ruling out G-quadruplex and triplex DNA. Extrachromosomal assay indicates that peak III halts transcription, unlike its mutated version. Taken together, multiple lines of evidence suggest formation of potential cruciform DNA structure at MBR peak III, which was also supported by in silico studies. Thus, our study reveals formation of non-B DNA structure which could be a basis for fragility at BCL2 breakpoint regions, eventually leading to chromosomal translocations.
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Affiliation(s)
- Saniya M Javadekar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Rakhee Yadav
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India.
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93
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Sobinoff AP, Pickett HA. Alternative Lengthening of Telomeres: DNA Repair Pathways Converge. Trends Genet 2017; 33:921-932. [DOI: 10.1016/j.tig.2017.09.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 08/30/2017] [Accepted: 09/08/2017] [Indexed: 02/08/2023]
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94
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Garcia-Exposito L, Bournique E, Bergoglio V, Bose A, Barroso-Gonzalez J, Zhang S, Roncaioli JL, Lee M, Wallace CT, Watkins SC, Opresko PL, Hoffmann JS, O'Sullivan RJ. Proteomic Profiling Reveals a Specific Role for Translesion DNA Polymerase η in the Alternative Lengthening of Telomeres. Cell Rep 2017; 17:1858-1871. [PMID: 27829156 PMCID: PMC5406014 DOI: 10.1016/j.celrep.2016.10.048] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 09/18/2016] [Accepted: 10/14/2016] [Indexed: 11/22/2022] Open
Abstract
Cancer cells rely on the activation of telomerase or the alternative lengthening of telomeres (ALT) pathways for telomere maintenance and survival. ALT involves homologous recombination (HR)-dependent exchange and/or HR-associated synthesis of telomeric DNA. Utilizing proximity-dependent biotinylation (BioID), we sought to determine the proteome of telomeres in cancer cells that employ these distinct telomere elongation mechanisms. Our analysis reveals that multiple DNA repair networks converge at ALT telomeres. These include the specialized translesion DNA synthesis (TLS) proteins FANCJ-RAD18-PCNA and, most notably, DNA polymerase eta (Polη). We observe that the depletion of Polη leads to increased ALT activity and late DNA polymerase δ (Polδ)-dependent synthesis of telomeric DNA in mitosis. We propose that Polη fulfills an important role in managing replicative stress at ALT telomeres, maintaining telomere recombination at tolerable levels and stimulating DNA synthesis by Polδ.
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Affiliation(s)
- Laura Garcia-Exposito
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Elodie Bournique
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France
| | - Valérie Bergoglio
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France
| | - Arindam Bose
- Department of Environmental and Occupational Health, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jonathan Barroso-Gonzalez
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Sufang Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Justin L Roncaioli
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Marietta Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Callen T Wallace
- Department of Cell Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jean-Sébastien Hoffmann
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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95
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Xu Y, Ning S, Wei Z, Xu R, Xu X, Xing M, Guo R, Xu D. 53BP1 and BRCA1 control pathway choice for stalled replication restart. eLife 2017; 6:30523. [PMID: 29106372 PMCID: PMC5683755 DOI: 10.7554/elife.30523] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/04/2017] [Indexed: 12/29/2022] Open
Abstract
The cellular pathways that restart stalled replication forks are essential for genome stability and tumor prevention. However, how many of these pathways exist in cells and how these pathways are selectively activated remain unclear. Here, we describe two major fork restart pathways, and demonstrate that their selection is governed by 53BP1 and BRCA1, which are known to control the pathway choice to repair double-strand DNA breaks (DSBs). Specifically, 53BP1 promotes a fork cleavage-free pathway, whereas BRCA1 facilitates a break-induced replication (BIR) pathway coupled with SLX-MUS complex-mediated fork cleavage. The defect in the first pathway, but not DSB repair, in a 53BP1 mutant is largely corrected by disrupting BRCA1, and vice versa. Moreover, PLK1 temporally regulates the switch of these two pathways through enhancing the assembly of the SLX-MUS complex. Our results reveal two distinct fork restart pathways, which are antagonistically controlled by 53BP1 and BRCA1 in a DSB repair-independent manner.
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Affiliation(s)
- Yixi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Shaokai Ning
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Zheng Wei
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Ran Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Xinlin Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Mengtan Xing
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Rong Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
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96
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Bhattacharjee S, Nandi S. DNA damage response and cancer therapeutics through the lens of the Fanconi Anemia DNA repair pathway. Cell Commun Signal 2017; 15:41. [PMID: 29017571 PMCID: PMC5635482 DOI: 10.1186/s12964-017-0195-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/03/2017] [Indexed: 01/01/2023] Open
Abstract
Fanconi Anemia (FA) is a rare, inherited genomic instability disorder, caused by mutations in genes involved in the repair of interstrand DNA crosslinks (ICLs). The FA signaling network contains a unique nuclear protein complex that mediates the monoubiquitylation of the FANCD2 and FANCI heterodimer, and coordinates activities of the downstream DNA repair pathway including nucleotide excision repair, translesion synthesis, and homologous recombination. FA proteins act at different steps of ICL repair in sensing, recognition and processing of DNA lesions. The multi-protein network is tightly regulated by complex mechanisms, such as ubiquitination, phosphorylation, and degradation signals that are critical for the maintenance of genome integrity and suppressing tumorigenesis. Here, we discuss recent advances in our understanding of how the FA proteins participate in ICL repair and regulation of the FA signaling network that assures the safeguard of the genome. We further discuss the potential application of designing small molecule inhibitors that inhibit the FA pathway and are synthetic lethal with DNA repair enzymes that can be used for cancer therapeutics.
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97
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Mazumdar J, Chowdhury P, Bhattacharya T, Mondal BC, Ghosh U. Patients with Congenital Limb Anomaly Show Short Telomere, Shutdown of Telomerase and Deregulated Expression of Various Telomere-Associated Proteins in Peripheral Blood Mononuclear Cells-A Case Series. J Clin Diagn Res 2017; 11:GR01-GR06. [PMID: 28969156 DOI: 10.7860/jcdr/2017/26960.10516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/24/2017] [Indexed: 11/24/2022]
Abstract
Congenital limb anomalies are outcome of improper bone formation during embryonic development when cells divide, differentiate with high rate. So, telomerase activity is essential to maintain telomere length for such highly dividing cells. Here, we report four cases of congenital limb anomalies with detailed structures of limbs along with other clinical manifestations of age less than two years. We compared telomere length, expression of telomerase and telomere-associated genes of Peripheral Blood Mononuclear Cells (PBMC) in patient and four age-matched normal individual. Patient-1 was diagnosed with congenital limb hypogenesis ectrodactyly sequence, an autosomal dominant disorder, showing absence of digits and fibula in upper and lower limb respectively. Both mother and grandmother of Patient-1 showed similar hypogenesis of limbs. Patient-2 showed bilateral clenched hand with arthrogryposis, microcephaly and holoprosencephaly. Both Patient-3 and Patient-4 has no radius in upper limb. Additionally, Paient-3 showed right sided orbital Space Occupying Lesion (SOL) and Paranasal Sinuses (PNS) whereas Patient-4 showed fused kidney with fanconi anaemia. Furthermore, all the patients showed shorter telomere length, inactive telomerase and de-regulated expression of telomere-associated proteins in PBMC compared with age-matched control group. So, we can conclude that congenital limb anomalies may be linked with telomeropathy and a study with large number of samples is required to firmly establish such association.
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Affiliation(s)
- Jayitri Mazumdar
- Senior Resident, Department of Paediatrics, Calcutta National Medical College and Hospital, Kolkata, West Bengal, India
| | - Priyanka Chowdhury
- Resaerch Scholar, Department of Biochemistry and Biophysics, University of Kalyani, West Bengal, India
| | - Tunisha Bhattacharya
- RMO Cum Clinical Tutor, Department of Paediatrics, Calcutta National Medical College and Hospital, Kolkata, West Bengal, India
| | - Badal Chandra Mondal
- Professor, Department of Paediatrics, Murshidabad Medical College, Berhampore, West Bengal, India
| | - Utpal Ghosh
- Assistant Professor, Department of Biochemistry and Biophysics, University of Kalyani, West Bengal, India
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98
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Reyes ED, Kulej K, Pancholi NJ, Akhtar LN, Avgousti DC, Kim ET, Bricker DK, Spruce LA, Koniski SA, Seeholzer SH, Isaacs SN, Garcia BA, Weitzman MD. Identifying Host Factors Associated with DNA Replicated During Virus Infection. Mol Cell Proteomics 2017; 16:2079-2097. [PMID: 28972080 DOI: 10.1074/mcp.m117.067116] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 07/14/2017] [Indexed: 01/22/2023] Open
Abstract
Viral DNA genomes replicating in cells encounter a myriad of host factors that facilitate or hinder viral replication. Viral proteins expressed early during infection modulate host factors interacting with viral genomes, recruiting proteins to promote viral replication, and limiting access to antiviral repressors. Although some host factors manipulated by viruses have been identified, we have limited knowledge of pathways exploited during infection and how these differ between viruses. To identify cellular processes manipulated during viral replication, we defined proteomes associated with viral genomes during infection with adenovirus, herpes simplex virus and vaccinia virus. We compared enrichment of host factors between virus proteomes and confirmed association with viral genomes and replication compartments. Using adenovirus as an illustrative example, we uncovered host factors deactivated by early viral proteins, and identified a subgroup of nucleolar proteins that aid virus replication. Our data sets provide valuable resources of virus-host interactions that affect proteins on viral genomes.
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Affiliation(s)
- Emigdio D Reyes
- From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,§Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Katarzyna Kulej
- From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,§Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Neha J Pancholi
- §Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,¶Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Lisa N Akhtar
- ‖Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Daphne C Avgousti
- From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,§Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Eui Tae Kim
- §Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Daniel K Bricker
- From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,§Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Lynn A Spruce
- **Protein and Proteomics Core, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sarah A Koniski
- §Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Steven H Seeholzer
- **Protein and Proteomics Core, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Stuart N Isaacs
- ‡‡Division of Infectious Diseases, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Benjamin A Garcia
- §§Epigenetics Program, Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Matthew D Weitzman
- From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; .,§Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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99
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Di Marco S, Hasanova Z, Kanagaraj R, Chappidi N, Altmannova V, Menon S, Sedlackova H, Langhoff J, Surendranath K, Hühn D, Bhowmick R, Marini V, Ferrari S, Hickson ID, Krejci L, Janscak P. RECQ5 Helicase Cooperates with MUS81 Endonuclease in Processing Stalled Replication Forks at Common Fragile Sites during Mitosis. Mol Cell 2017; 66:658-671.e8. [PMID: 28575661 DOI: 10.1016/j.molcel.2017.05.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 02/14/2017] [Accepted: 05/04/2017] [Indexed: 11/18/2022]
Abstract
The MUS81-EME1 endonuclease cleaves late replication intermediates at common fragile sites (CFSs) during early mitosis to trigger DNA-repair synthesis that ensures faithful chromosome segregation. Here, we show that these DNA transactions are promoted by RECQ5 DNA helicase in a manner dependent on its Ser727 phosphorylation by CDK1. Upon replication stress, RECQ5 associates with CFSs in early mitosis through its physical interaction with MUS81 and promotes MUS81-dependent mitotic DNA synthesis. RECQ5 depletion or mutational inactivation of its ATP-binding site, RAD51-interacting domain, or phosphorylation site causes excessive binding of RAD51 to CFS loci and impairs CFS expression. This leads to defective chromosome segregation and accumulation of CFS-associated DNA damage in G1 cells. Biochemically, RECQ5 alleviates the inhibitory effect of RAD51 on 3'-flap DNA cleavage by MUS81-EME1 through its RAD51 filament disruption activity. These data suggest that RECQ5 removes RAD51 filaments stabilizing stalled replication forks at CFSs and hence facilitates CFS cleavage by MUS81-EME1.
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Affiliation(s)
- Stefano Di Marco
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Zdenka Hasanova
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5/A7, Brno 62500, Czech Republic
| | - Radhakrishnan Kanagaraj
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Nagaraja Chappidi
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Veronika Altmannova
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5/A7, Brno 62500, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, Brno 656 91, Czech Republic
| | - Shruti Menon
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Hana Sedlackova
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5/A7, Brno 62500, Czech Republic
| | - Jana Langhoff
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kalpana Surendranath
- Department of Biomedical Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK
| | - Daniela Hühn
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Rahul Bhowmick
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Insitute Building 18.1, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Victoria Marini
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5/A7, Brno 62500, Czech Republic
| | - Stefano Ferrari
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Insitute Building 18.1, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Lumir Krejci
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5/A7, Brno 62500, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, Brno 656 91, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic.
| | - Pavel Janscak
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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100
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Sobinoff AP, Allen JA, Neumann AA, Yang SF, Walsh ME, Henson JD, Reddel RR, Pickett HA. BLM and SLX4 play opposing roles in recombination-dependent replication at human telomeres. EMBO J 2017; 36:2907-2919. [PMID: 28877996 DOI: 10.15252/embj.201796889] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 08/03/2017] [Accepted: 08/09/2017] [Indexed: 11/09/2022] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomere lengthening pathway that predominates in aggressive tumors of mesenchymal origin; however, the underlying mechanism of telomere synthesis is not fully understood. Here, we show that the BLM-TOP3A-RMI (BTR) dissolvase complex is required for ALT-mediated telomere synthesis. We propose that recombination intermediates formed during strand invasion are processed by the BTR complex, initiating rapid and extensive POLD3-dependent telomere synthesis followed by dissolution, with no overall exchange of telomeric DNA. This process is counteracted by the SLX4-SLX1-ERCC4 complex, which promotes resolution of the recombination intermediate, resulting in telomere exchange in the absence of telomere extension. Our data are consistent with ALT being a conservative DNA replication process, analogous to break-induced replication, which is dependent on BTR and counteracted by SLX4 complex-mediated resolution events.
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Affiliation(s)
- Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Joshua Am Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Axel A Neumann
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Sile F Yang
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Monica E Walsh
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Jeremy D Henson
- Cancer Cell Immortality Group, Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
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