1
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Ólafsson G, Haase MAB, Boeke JD. Humanization reveals pervasive incompatibility of yeast and human kinetochore components. G3 (BETHESDA, MD.) 2023; 14:jkad260. [PMID: 37962556 PMCID: PMC10755175 DOI: 10.1093/g3journal/jkad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 06/29/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023]
Abstract
Kinetochores assemble on centromeres to drive chromosome segregation in eukaryotic cells. Humans and budding yeast share most of the structural subunits of the kinetochore, whereas protein sequences have diverged considerably. The conserved centromeric histone H3 variant, CenH3 (CENP-A in humans and Cse4 in budding yeast), marks the site for kinetochore assembly in most species. A previous effort to complement Cse4 in yeast with human CENP-A was unsuccessful; however, co-complementation with the human core nucleosome was not attempted. Previously, our lab successfully humanized the core nucleosome in yeast; however, this severely affected cellular growth. We hypothesized that yeast Cse4 is incompatible with humanized nucleosomes and that the kinetochore represented a limiting factor for efficient histone humanization. Thus, we argued that including the human CENP-A or a Cse4-CENP-A chimera might improve histone humanization and facilitate kinetochore function in humanized yeast. The opposite was true: CENP-A expression reduced histone humanization efficiency, was toxic to yeast, and disrupted cell cycle progression and kinetochore function in wild-type (WT) cells. Suppressors of CENP-A toxicity included gene deletions of subunits of 3 conserved chromatin remodeling complexes, highlighting their role in CenH3 chromatin positioning. Finally, we attempted to complement the subunits of the NDC80 kinetochore complex, individually and in combination, without success, in contrast to a previous study indicating complementation by the human NDC80/HEC1 gene. Our results suggest that limited protein sequence similarity between yeast and human components in this very complex structure leads to failure of complementation.
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Affiliation(s)
- Guðjón Ólafsson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Vilcek Institute of Graduate Biomedical Sciences, NYU School of Medicine, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 14 11201, USA
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2
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Cho C, Ganser C, Uchihashi T, Kato K, Song JJ. Structure of the human ATAD2 AAA+ histone chaperone reveals mechanism of regulation and inter-subunit communication. Commun Biol 2023; 6:993. [PMID: 37770645 PMCID: PMC10539301 DOI: 10.1038/s42003-023-05373-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
ATAD2 is a non-canonical ATP-dependent histone chaperone and a major cancer target. Despite widespread efforts to design drugs targeting the ATAD2 bromodomain, little is known about the overall structural organization and regulation of ATAD2. Here, we present the 3.1 Å cryo-EM structure of human ATAD2 in the ATP state, showing a shallow hexameric spiral that binds a peptide substrate at the central pore. The spiral conformation is locked by an N-terminal linker domain (LD) that wedges between the seam subunits, thus limiting ATP-dependent symmetry breaking of the AAA+ ring. In contrast, structures of the ATAD2-histone H3/H4 complex show the LD undocked from the seam, suggesting that H3/H4 binding unlocks the AAA+ spiral by allosterically releasing the LD. These findings, together with the discovery of an inter-subunit signaling mechanism, reveal a unique regulatory mechanism for ATAD2 and lay the foundation for developing new ATAD2 inhibitors.
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Affiliation(s)
- Carol Cho
- Department of Biological Sciences, KAIST Stem Cell Center, Basic Science 4.0 Institute, and KI for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea.
| | - Christian Ganser
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Takayuki Uchihashi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- Department of Physics and Institute for Glyco-core Research (iGCORE), Nagoya University, Chikusa-ku, Furo-cho, Nagoya, Aichi, 464-8602, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Ji-Joon Song
- Department of Biological Sciences, KAIST Stem Cell Center, Basic Science 4.0 Institute, and KI for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea.
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3
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Guruvaiah P, Chava S, Sun CW, Singh N, Penn CA, Gupta R. ATAD2 is a driver and a therapeutic target in ovarian cancer that functions by upregulating CENPE. Cell Death Dis 2023; 14:456. [PMID: 37479754 PMCID: PMC10362061 DOI: 10.1038/s41419-023-05993-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
Ovarian cancer is a complex disease associated with multiple genetic and epigenetic alterations. The emergence of treatment resistance in most patients causes ovarian cancer to become incurable, and novel therapies remain necessary. We identified epigenetic regulator ATPase family AAA domain-containing 2 (ATAD2) is overexpressed in ovarian cancer and is associated with increased incidences of metastasis and recurrence. Genetic knockdown of ATAD2 or its pharmacological inhibition via ATAD2 inhibitor BAY-850 suppressed ovarian cancer growth and metastasis in both in vitro and in vivo models. Transcriptome-wide mRNA expression profiling of ovarian cancer cells treated with BAY-850 revealed that ATAD2 inhibition predominantly alters the expression of centromere regulatory genes, particularly centromere protein E (CENPE). In ovarian cancer cells, changes in CENPE expression following ATAD2 inhibition resulted in cell-cycle arrest and apoptosis induction, which led to the suppression of ovarian cancer growth. Pharmacological CENPE inhibition phenotypically recapitulated the cellular changes induced by ATAD2 inhibition, and combined pharmacological inhibition of both ATAD2 and CENPE inhibited ovarian cancer cell growth more potently than inhibition of either alone. Thus, our study identified ATAD2 as regulators of ovarian cancer growth and metastasis that can be targeted either alone or in combination with CENPE inhibitors for effective ovarian cancer therapy.
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Affiliation(s)
- Praveen Guruvaiah
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Suresh Chava
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Chiao-Wang Sun
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Nirupama Singh
- Department of Pathology, Division of Laboratory Medicine, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Courtney A Penn
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Romi Gupta
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL, 35233, USA.
- O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, AL, 35233, USA.
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4
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Wang F, Feng X, He Q, Li H, Li H. The Saccharomyces cerevisiae Yta7 ATPase hexamer contains a unique bromodomain tier that functions in nucleosome disassembly. J Biol Chem 2023; 299:102852. [PMID: 36592926 PMCID: PMC9898759 DOI: 10.1016/j.jbc.2022.102852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 01/01/2023] Open
Abstract
The Saccharomyces cerevisiae Yta7 is a chromatin remodeler harboring a histone-interacting bromodomain (BRD) and two AAA+ modules. It is not well understood how Yta7 recognizes the histone H3 tail to promote nucleosome disassembly for DNA replication or RNA transcription. By cryo-EM analysis, here we show that Yta7 assembles a three-tiered hexamer with a top BRD tier, a middle AAA1 tier, and a bottom AAA2 tier. Unexpectedly, the Yta7 BRD stabilizes a four-stranded β-helix, termed BRD-interacting motif (BIM), of the largely disordered N-terminal region. The BIM motif is unique to the baker's yeast, and we show both BRD and BIM contribute to nucleosome recognition. We found that Yta7 binds both acetylated and nonacetylated H3 peptides but with a higher affinity for the unmodified peptide. This property is consistent with the absence of key residues of canonical BRDs involved in acetylated peptide recognition and the role of Yta7 in general nucleosome remodeling. Interestingly, the BRD tier exists in a spiral and a flat-ring form on top of the Yta7 AAA+ hexamer. The spiral is likely in a nucleosome-searching mode because the bottom BRD blocks the entry to the AAA+ chamber. The flat ring may be in a nucleosome disassembly state because the entry is unblocked and the H3 peptide has entered the AAA+ chamber and is stabilized by the AAA1 pore loops 1 and 2. Indeed, we show that the BRD tier is a flat ring when bound to the nucleosome. Overall, our study sheds light on the nucleosome disassembly by Yta7.
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Affiliation(s)
- Feng Wang
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Xiang Feng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Qing He
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Hua Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA.
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5
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A targetable MYBL2-ATAD2 axis governs cell proliferation in ovarian cancer. Cancer Gene Ther 2023; 30:192-208. [PMID: 36151333 DOI: 10.1038/s41417-022-00538-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/25/2022] [Accepted: 09/12/2022] [Indexed: 01/19/2023]
Abstract
The chromatin-modifying enzyme ATAD2 confers oncogenic competence and proliferative advantage in malignances. We previously identified ATAD2 as a marker and driver of cell proliferation in ovarian cancer (OC); however, the mechanisms whereby ATAD2 is regulated and involved in cell proliferation are still unclear. Here, we disclose that ATAD2 displays a classical G2/M gene signature, functioning to facilitate mitotic progression. ATAD2 ablation caused mitotic arrest and decreased the ability of OC cells to pass through nocodazole-arrested mitosis. ChIP-seq data analyses demonstrated that DREAM and MYBL2-MuvB (MMB), two switchable MuvB-based complexes, bind the CHR elements in the ATAD2 promoter, representing a typical feature and principle mechanism of the periodic regulation of G2/M genes. As a downstream target of MYBL2, ATAD2 deletion significantly impaired MYBL2-driven cell proliferation. Intriguingly, ATAD2 silencing also fed back to destabilize the MYBL2 protein. The significant coexpression of MYBL2 and ATAD2 at both the bulk tissue and single-cell levels highlights the existence of the MYBL2-ATAD2 signaling in OC patients. This signaling is activated during tumorigenesis and correlated with TP53 mutation, and its hyperactivation was found especially in high-grade serous and drug-resistant OCs. Disrupting this signaling by CRISPR/Cas9-mediated ATAD2 ablation inhibited the in vivo growth of OC in a subcutaneous tumor xenograft mouse model, while pharmacologically targeting this signaling with an ATAD2 inhibitor demonstrated high therapeutic efficacy in both drug-sensitive and drug-resistant OC cells. Collectively, we identified a novel MYBL2-ATAD2 proliferative signaling axis and highlighted its potential application in developing new therapeutic strategies, especially for high-grade serous and drug-resistant OCs.
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6
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Tumor-Promoting ATAD2 and Its Preclinical Challenges. Biomolecules 2022; 12:biom12081040. [PMID: 36008934 PMCID: PMC9405547 DOI: 10.3390/biom12081040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023] Open
Abstract
ATAD2 has received extensive attention in recent years as one prospective oncogene with tumor-promoting features in many malignancies. ATAD2 is a highly conserved bromodomain family protein that exerts its biological functions by mainly AAA ATPase and bromodomain. ATAD2 acts as an epigenetic decoder and transcription factor or co-activator, which is engaged in cellular activities, such as transcriptional regulation, DNA replication, and protein modification. ATAD2 has been reported to be highly expressed in a variety of human malignancies, including gastrointestinal malignancies, reproductive malignancies, urological malignancies, lung cancer, and other types of malignancies. ATAD2 is involved in the activation of multiple oncogenic signaling pathways and is closely associated with tumorigenesis, progression, chemoresistance, and poor prognosis, but the oncogenic mechanisms vary in different cancer types. Moreover, the direct targeting of ATAD2’s bromodomain may be a very challenging task. In this review, we summarized the role of ATAD2 in various types of malignancies and pointed out the pharmacological direction.
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7
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Ekin U, Yuzugullu H, Ozen C, Korhan P, Bagirsakci E, Yilmaz F, Yuzugullu OG, Uzuner H, Alotaibi H, Kirmizibayrak PB, Atabey N, Karakülah G, Ozturk M. Evaluation of ATAD2 as a Potential Target in Hepatocellular Carcinoma. J Gastrointest Cancer 2021; 52:1356-1369. [PMID: 34738187 DOI: 10.1007/s12029-021-00732-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2021] [Indexed: 01/15/2023]
Abstract
PURPOSE Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide with lack of effective systemic chemotherapy. In this study, we aimed to evaluate the value of ATPase family AAA domain-containing protein 2 (ATAD2) as a biomarker and potential therapeutic target for HCC. METHODS The expression of ATAD2 was tested in different HCC patient cohorts by immunohistochemistry and comparative transcriptional analysis. The co-expression of ATAD2 and proliferation markers was compared during liver regeneration and malignancy with different bioinformatics tools. The cellular effects of ATAD2 inactivation in liver malignancy was tested on cell cycle, apoptosis, and colony formation ability as well as tumor formation using RNA interference. The genes affected by ATAD2 inactivation in three different HCC cell lines were identified by global gene expression profiling and bioinformatics tools. RESULTS ATAD2 overexpression is closely correlated with HCC tumor stage. There was gradual increase from dysplasia, well-differentiated and poorly-differentiated HCC, respectively. We also observed transient upregulation of ATAD2 expression during rat liver regeneration in parallel to changes in Ki-67 expression. ATAD2 knockdown resulted in apoptosis and decreased cell survival in vitro and decreased tumor formation in some HCC cell lines. However, three other HCC cell lines tested were not affected. Similarly, gene expression response to ATAD2 inactivation in different HCC cell lines was highly heterogeneous. CONCLUSIONS ATAD2 is a potential proliferation marker for liver regeneration and HCC. It may also serve as a therapeutic target despite heterogeneous response of malignant cells.
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Affiliation(s)
- Umut Ekin
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Haluk Yuzugullu
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.,Institut Albert Bonniot, Grenoble, France
| | - Cigdem Ozen
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.,Present Address: Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Bioinformatics group, Dresden, Germany
| | - Peyda Korhan
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Ezgi Bagirsakci
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Funda Yilmaz
- Department of Pathology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Ozge Gursoy Yuzugullu
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.,Institut Albert Bonniot, Grenoble, France
| | - Hamdiye Uzuner
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Hani Alotaibi
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | | | - Nese Atabey
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Faculty of Medicine, Izmir Tinaztepe University, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Mehmet Ozturk
- Izmir Biomedicine and Genome Center, Izmir, Turkey. .,Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey. .,Institut Albert Bonniot, Grenoble, France. .,Faculty of Medicine, Izmir Tinaztepe University, Izmir, Turkey.
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8
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Wang T, Perazza D, Boussouar F, Cattaneo M, Bougdour A, Chuffart F, Barral S, Vargas A, Liakopoulou A, Puthier D, Bargier L, Morozumi Y, Jamshidikia M, Garcia-Saez I, Petosa C, Rousseaux S, Verdel A, Khochbin S. ATAD2 controls chromatin-bound HIRA turnover. Life Sci Alliance 2021; 4:4/12/e202101151. [PMID: 34580178 PMCID: PMC8500222 DOI: 10.26508/lsa.202101151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/18/2022] Open
Abstract
Taking advantage of the evolutionary conserved nature of ATAD2, we report here a series of parallel functional studies in human, mouse, and Schizosaccharomyces pombe to investigate ATAD2's conserved functions. In S. pombe, the deletion of ATAD2 ortholog, abo1, leads to a dramatic decrease in cell growth, with the appearance of suppressor clones recovering normal growth. The identification of the corresponding suppressor mutations revealed a strong genetic interaction between Abo1 and the histone chaperone HIRA. In human cancer cell lines and in mouse embryonic stem cells, we observed that the KO of ATAD2 leads to an accumulation of HIRA. A ChIP-seq mapping of nucleosome-bound HIRA and FACT in Atad2 KO mouse ES cells demonstrated that both chaperones are trapped on nucleosomes at the transcription start sites of active genes, resulting in the abnormal presence of a chaperone-bound nucleosome on the TSS-associated nucleosome-free regions. Overall, these data highlight an important layer of regulation of chromatin dynamics ensuring the turnover of histone-bound chaperones.
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Affiliation(s)
- Tao Wang
- Centre National de la Recherche Scientifique (CNRS), Unite Mixte de Recherche (UMR) 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France
| | - Daniel Perazza
- Centre National de la Recherche Scientifique (CNRS), Unite Mixte de Recherche (UMR) 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France
| | - Fayçal Boussouar
- Centre National de la Recherche Scientifique (CNRS), Unite Mixte de Recherche (UMR) 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France
| | - Matteo Cattaneo
- Centre National de la Recherche Scientifique (CNRS), Unite Mixte de Recherche (UMR) 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France
| | - Alexandre Bougdour
- Centre National de la Recherche Scientifique (CNRS), Unite Mixte de Recherche (UMR) 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France
| | - Florent Chuffart
- Centre National de la Recherche Scientifique (CNRS), Unite Mixte de Recherche (UMR) 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France
| | - Sophie Barral
- Centre National de la Recherche Scientifique (CNRS), Unite Mixte de Recherche (UMR) 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France
| | - Alexandra Vargas
- Centre National de la Recherche Scientifique (CNRS), Unite Mixte de Recherche (UMR) 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France
| | - Ariadni Liakopoulou
- Centre National de la Recherche Scientifique (CNRS), Unite Mixte de Recherche (UMR) 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France
| | - Denis Puthier
- Aix Marseille Université, INSERM, Theories and Approaches of Genomic Complexity (TAGC), Transcriptomique et Genomique Marseille-Luminy (TGML), Marseille, France
| | - Lisa Bargier
- Aix Marseille Université, INSERM, Theories and Approaches of Genomic Complexity (TAGC), Transcriptomique et Genomique Marseille-Luminy (TGML), Marseille, France
| | - Yuichi Morozumi
- Centre National de la Recherche Scientifique (CNRS), Unite Mixte de Recherche (UMR) 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France.,Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Mahya Jamshidikia
- Centre National de la Recherche Scientifique (CNRS), Unite Mixte de Recherche (UMR) 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France
| | - Isabel Garcia-Saez
- Université Grenoble Alpes/CNRS/CEA, Institut de Biologie Structurale, Grenoble, France
| | - Carlo Petosa
- Université Grenoble Alpes/CNRS/CEA, Institut de Biologie Structurale, Grenoble, France
| | - Sophie Rousseaux
- Centre National de la Recherche Scientifique (CNRS), Unite Mixte de Recherche (UMR) 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France
| | - André Verdel
- Centre National de la Recherche Scientifique (CNRS), Unite Mixte de Recherche (UMR) 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France
| | - Saadi Khochbin
- Centre National de la Recherche Scientifique (CNRS), Unite Mixte de Recherche (UMR) 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France
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9
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VE-822, a novel DNA Holliday junction stabilizer, inhibits homologous recombination repair and triggers DNA damage response in osteogenic sarcomas. Biochem Pharmacol 2021; 193:114767. [PMID: 34537248 DOI: 10.1016/j.bcp.2021.114767] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/20/2022]
Abstract
Homologous recombination repair (HRR) is crucial for genomic stability of cancer cells and is an attractive target in cancer therapy. Holliday junction (HJ) is a four-way DNA intermediate that performs an essential role in homology-directed repair. However, few studies about regulatory mechanisms of HJs have been reported. In this study, to better understand the biological effects of HJs, VE-822 was identified as an effective DNA HJ stabilizer to promote the assembly of HJs both in vitro and in cells. This compound could inhibit the HRR level, activate DNA-PKCS to trigger DNA damage response (DDR) and induce telomeric DNA damage via stabilizing DNA HJs. Furthermore, VE-822 was demonstrated to sensitize the osteosarcoma cells to doxorubicin (Dox) by enhancing DNA damage and cellular apoptosis. This work thus reports one novel HJ stabilizer, and provide a potential anticancer strategy through the modulation of DNA HJs.
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10
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Chacin E, Bansal P, Reusswig KU, Diaz-Santin LM, Ortega P, Vizjak P, Gómez-González B, Müller-Planitz F, Aguilera A, Pfander B, Cheung ACM, Kurat CF. A CDK-regulated chromatin segregase promoting chromosome replication. Nat Commun 2021; 12:5224. [PMID: 34471130 PMCID: PMC8410769 DOI: 10.1038/s41467-021-25424-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 08/05/2021] [Indexed: 11/09/2022] Open
Abstract
The replication of chromosomes during S phase is critical for cellular and organismal function. Replicative stress can result in genome instability, which is a major driver of cancer. Yet how chromatin is made accessible during eukaryotic DNA synthesis is poorly understood. Here, we report the characterization of a chromatin remodeling enzyme-Yta7-entirely distinct from classical SNF2-ATPase family remodelers. Yta7 is a AAA+ -ATPase that assembles into ~1 MDa hexameric complexes capable of segregating histones from DNA. The Yta7 chromatin segregase promotes chromosome replication both in vivo and in vitro. Biochemical reconstitution experiments using purified proteins revealed that the enzymatic activity of Yta7 is regulated by S phase-forms of Cyclin-Dependent Kinase (S-CDK). S-CDK phosphorylation stimulates ATP hydrolysis by Yta7, promoting nucleosome disassembly and chromatin replication. Our results present a mechanism for how cells orchestrate chromatin dynamics in co-ordination with the cell cycle machinery to promote genome duplication during S phase.
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Affiliation(s)
- Erika Chacin
- Molecular Biology Division, Biomedical Center Munich, Ludwig-Maximilians-Universität, Munich, Planegg-Martinsried, Germany
| | - Priyanka Bansal
- Molecular Biology Division, Biomedical Center Munich, Ludwig-Maximilians-Universität, Munich, Planegg-Martinsried, Germany
| | - Karl-Uwe Reusswig
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Planegg-Martinsried, Germany
| | - Luis M Diaz-Santin
- Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology, University College London, London, UK.,Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck College, London, UK
| | - Pedro Ortega
- Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER, University of Seville-CSIC, Seville, Spain
| | - Petra Vizjak
- Molecular Biology Division, Biomedical Center Munich, Ludwig-Maximilians-Universität, Munich, Planegg-Martinsried, Germany
| | - Belen Gómez-González
- Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER, University of Seville-CSIC, Seville, Spain
| | - Felix Müller-Planitz
- Molecular Biology Division, Biomedical Center Munich, Ludwig-Maximilians-Universität, Munich, Planegg-Martinsried, Germany.,Institute of Physiological Chemistry, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Andrés Aguilera
- Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER, University of Seville-CSIC, Seville, Spain
| | - Boris Pfander
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Planegg-Martinsried, Germany
| | - Alan C M Cheung
- Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology, University College London, London, UK.,Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck College, London, UK.,School of Biochemistry, University of Bristol, Bristol, UK
| | - Christoph F Kurat
- Molecular Biology Division, Biomedical Center Munich, Ludwig-Maximilians-Universität, Munich, Planegg-Martinsried, Germany.
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11
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Kang Y, Cho C, Lee KS, Song JJ, Lee JY. Single-Molecule Imaging Reveals the Mechanism Underlying Histone Loading of Schizosaccharomyces pombe AAA+ ATPase Abo1. Mol Cells 2021; 44:79-87. [PMID: 33658433 PMCID: PMC7941004 DOI: 10.14348/molcells.2021.2242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/26/2021] [Accepted: 02/09/2021] [Indexed: 11/27/2022] Open
Abstract
Chromatin dynamics is essential for maintaining genomic integrity and regulating gene expression. Conserved bromodomain-containing AAA+ ATPases play important roles in nucleosome organization as histone chaperones. Recently, the high-resolution cryo-electron microscopy structures of Schizosaccharomyces pombe Abo1 revealed that it forms a hexameric ring and undergoes a conformational change upon ATP hydrolysis. In addition, single-molecule imaging demonstrated that Abo1 loads H3-H4 histones onto DNA in an ATP hydrolysis-dependent manner. However, the molecular mechanism by which Abo1 loads histones remains unknown. Here, we investigated the details concerning Abo1-mediated histone loading onto DNA and the Abo1- DNA interaction using single-molecule imaging techniques and biochemical assays. We show that Abo1 does not load H2A-H2B histones. Interestingly, Abo1 deposits multiple copies of H3-H4 histones as the DNA length increases and requires at least 80 bp DNA. Unexpectedly, Abo1 weakly binds DNA regardless of ATP, and neither histone nor DNA stimulates the ATP hydrolysis activity of Abo1. Based on our results, we propose an allosteric communication model in which the ATP hydrolysis of Abo1 changes the configuration of histones to facilitate their deposition onto DNA.
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Affiliation(s)
- Yujin Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- These authors contributed equally to this work
| | - Carol Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- These authors contributed equally to this work
| | - Kyung Suk Lee
- Department of Physics Education, Kongju National University, Gongju 32588, Korea
| | - Ji-Joon Song
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
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12
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Sridhar S, Hori T, Nakagawa R, Fukagawa T, Sanyal K. Bridgin connects the outer kinetochore to centromeric chromatin. Nat Commun 2021; 12:146. [PMID: 33420015 PMCID: PMC7794384 DOI: 10.1038/s41467-020-20161-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/10/2020] [Indexed: 11/29/2022] Open
Abstract
The microtubule-binding outer kinetochore is coupled to centromeric chromatin through CENP-CMif2, CENP-TCnn1, and CENP-UAme1 linker pathways originating from the constitutive centromere associated network (CCAN) of the inner kinetochore. Here, we demonstrate the recurrent loss of most CCAN components, including certain kinetochore linkers during the evolution of the fungal phylum of Basidiomycota. By kinetochore interactome analyses in a model basidiomycete and human pathogen Cryptococcus neoformans, a forkhead-associated domain containing protein “bridgin” was identified as a kinetochore component along with other predicted kinetochore proteins. In vivo and in vitro functional analyses of bridgin reveal its ability to connect the outer kinetochore with centromeric chromatin to ensure accurate chromosome segregation. Unlike established CCAN-based linkers, bridgin is recruited at the outer kinetochore establishing its role as a distinct family of kinetochore proteins. Presence of bridgin homologs in non-fungal lineages suggests an ancient divergent strategy exists to bridge the outer kinetochore with centromeric chromatin. The kinetochore is a multi-complex structure that helps attach chromosomes to spindle microtubules, ensuring accurate chromosome segregation during cell division. Kinetochores are thought to be evolutionarily conserved, but which components are conserved is unclear. Here, the authors report that some members of the fungal phylum of Basidomycota lack many conventional kinetochore linker proteins. Instead, they possess a human Ki67-like protein that bridges the outer part of the kinetochore to centromere DNA, which may compensate for the loss of a conventional linker.
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Affiliation(s)
- Shreyas Sridhar
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research (JNCASR), Bangalore, India, 560064.,Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tetsuya Hori
- Laboratory of Chromosome Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Reiko Nakagawa
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Tatsuo Fukagawa
- Laboratory of Chromosome Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research (JNCASR), Bangalore, India, 560064. .,Laboratory of Chromosome Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
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