1
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Banerjee A, Mathew S, Naqvi MM, Yilmaz SZ, Zacharopoulou M, Doruker P, Kumita JR, Yang SH, Gur M, Itzhaki LS, Gordon R, Bahar I. Influence of point mutations on PR65 conformational adaptability: Insights from molecular simulations and nanoaperture optical tweezers. SCIENCE ADVANCES 2024; 10:eadn2208. [PMID: 38820156 PMCID: PMC11141623 DOI: 10.1126/sciadv.adn2208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/29/2024] [Indexed: 06/02/2024]
Abstract
PR65 is the HEAT repeat scaffold subunit of the heterotrimeric protein phosphatase 2A (PP2A) and an archetypal tandem repeat protein. Its conformational mechanics plays a crucial role in PP2A function by opening/closing substrate binding/catalysis interface. Using in silico saturation mutagenesis, we identified PR65 "hinge" residues whose substitutions could alter its conformational adaptability and thereby PP2A function, and selected six mutations that were verified to be expressed and soluble. Molecular simulations and nanoaperture optical tweezers revealed consistent results on the specific effects of the mutations on the structure and dynamics of PR65. Two mutants observed in simulations to stabilize extended/open conformations exhibited higher corner frequencies and lower translational scattering in experiments, indicating a shift toward extended conformations, whereas another displayed the opposite features, confirmed by both simulations and experiments. The study highlights the power of single-molecule nanoaperture-based tweezers integrated with in silico approaches for exploring the effect of mutations on protein structure and dynamics.
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Affiliation(s)
- Anupam Banerjee
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Samuel Mathew
- Department of Electrical and Computer Engineering, University of Victoria, Victoria V8P 5C2, Canada
| | - Mohsin M. Naqvi
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Sema Z. Yilmaz
- Department of Mechanical Engineering, Istanbul Technical University, 34437 Istanbul, Turkey
| | - Maria Zacharopoulou
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Pemra Doruker
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Janet R. Kumita
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Shang-Hua Yang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Mert Gur
- Department of Mechanical Engineering, Istanbul Technical University, 34437 Istanbul, Turkey
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Laura S. Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Reuven Gordon
- Department of Electrical and Computer Engineering, University of Victoria, Victoria V8P 5C2, Canada
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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2
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Bastianello G, Porcella G, Beznoussenko GV, Kidiyoor G, Ascione F, Li Q, Cattaneo A, Matafora V, Disanza A, Quarto M, Mironov AA, Oldani A, Barozzi S, Bachi A, Costanzo V, Scita G, Foiani M. Cell stretching activates an ATM mechano-transduction pathway that remodels cytoskeleton and chromatin. Cell Rep 2023; 42:113555. [PMID: 38088930 DOI: 10.1016/j.celrep.2023.113555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/01/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023] Open
Abstract
Ataxia telangiectasia mutated (ATM) and ataxia telangiectasia and Rad3-related (ATR) DNA damage response (DDR) kinases contain elastic domains. ATM also responds to reactive oxygen species (ROS) and ATR to nuclear mechanical stress. Mre11 mediates ATM activation following DNA damage; ATM mutations cause ataxia telangiectasia (A-T). Here, using in vivo imaging, electron microscopy, proteomic, and mechano-biology approaches, we study how ATM responds to mechanical stress. We report that cytoskeleton and ROS, but not Mre11, mediate ATM activation following cell deformation. ATM deficiency causes hyper-stiffness, stress fiber accumulation, Yes-associated protein (YAP) nuclear enrichment, plasma and nuclear membrane alterations during interstitial migration, and H3 hyper-methylation. ATM locates to the actin cytoskeleton and, following cytoskeleton stress, promotes phosphorylation of key cytoskeleton and chromatin regulators. Our data contribute to explain some clinical features of patients with A-T and pinpoint the existence of an integrated mechano-response in which ATM and ATR have distinct roles unrelated to their canonical DDR functions.
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Affiliation(s)
- Giulia Bastianello
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy; Oncology and Haemato-Oncology Department, University of Milan, 20122 Milan, Italy.
| | | | | | - Gururaj Kidiyoor
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Flora Ascione
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Qingsen Li
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | | | | | - Andrea Disanza
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Micaela Quarto
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | | | - Amanda Oldani
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Sara Barozzi
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Angela Bachi
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Vincenzo Costanzo
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy; Oncology and Haemato-Oncology Department, University of Milan, 20122 Milan, Italy
| | - Giorgio Scita
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy; Oncology and Haemato-Oncology Department, University of Milan, 20122 Milan, Italy
| | - Marco Foiani
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy; Oncology and Haemato-Oncology Department, University of Milan, 20122 Milan, Italy.
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3
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Madan V, Albacete‐Albacete L, Jin L, Scaturro P, Watson JL, Muschalik N, Begum F, Boulanger J, Bauer K, Kiebler MA, Derivery E, Bullock SL. HEATR5B associates with dynein-dynactin and promotes motility of AP1-bound endosomal membranes. EMBO J 2023; 42:e114473. [PMID: 37872872 PMCID: PMC10690479 DOI: 10.15252/embj.2023114473] [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: 05/09/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/25/2023] Open
Abstract
The microtubule motor dynein mediates polarised trafficking of a wide variety of organelles, vesicles and macromolecules. These functions are dependent on the dynactin complex, which helps recruit cargoes to dynein's tail and activates motor movement. How the dynein-dynactin complex orchestrates trafficking of diverse cargoes is unclear. Here, we identify HEATR5B, an interactor of the adaptor protein-1 (AP1) clathrin adaptor complex, as a novel player in dynein-dynactin function. HEATR5B was recovered in a biochemical screen for proteins whose association with the dynein tail is augmented by dynactin. We show that HEATR5B binds directly to the dynein tail and dynactin and stimulates motility of AP1-associated endosomal membranes in human cells. We also demonstrate that the Drosophila HEATR5B homologue is an essential gene that selectively promotes dynein-based transport of AP1-bound membranes to the Golgi apparatus. As HEATR5B lacks the coiled-coil architecture typical of dynein adaptors, our data point to a non-canonical process orchestrating motor function on a specific cargo. We additionally show that HEATR5B promotes association of AP1 with endosomal membranes independently of dynein. Thus, HEATR5B co-ordinates multiple events in AP1-based trafficking.
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Affiliation(s)
- Vanesa Madan
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
- Present address:
AbcamCambridgeUK
| | - Lucas Albacete‐Albacete
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Li Jin
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | | | - Joseph L Watson
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Nadine Muschalik
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Farida Begum
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Jérôme Boulanger
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Karl Bauer
- Biomedical Center, Department for Cell Biology, Medical FacultyLudwig‐Maximilians‐University of MunichMunichGermany
| | - Michael A Kiebler
- Biomedical Center, Department for Cell Biology, Medical FacultyLudwig‐Maximilians‐University of MunichMunichGermany
| | - Emmanuel Derivery
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Simon L Bullock
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
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4
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Zhang H, Wu S, Itzhaki LS, Perrett S. Interaction between huntingtin exon 1 and HEAT repeat structure probed by chimeric model proteins. Protein Sci 2023; 32:e4810. [PMID: 37853955 PMCID: PMC10659953 DOI: 10.1002/pro.4810] [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: 06/29/2023] [Revised: 10/11/2023] [Accepted: 10/15/2023] [Indexed: 10/20/2023]
Abstract
Huntington disease (HD) is associated with aggregation of huntingtin (HTT) protein containing over 35 continuous Q residues within the N-terminal exon 1 encoded region. The C-terminal of the HTT protein consists mainly of HEAT repeat structure which serves as a scaffold for multiple cellular activities. Structural and biochemical analysis of the intact HTT protein has been hampered by its huge size (~300 kDa) and most in vitro studies to date have focused on the properties of the exon 1 region. To explore the interaction between HTT exon 1 and the HEAT repeat structure, we constructed chimeric proteins containing the N-terminal HTT exon 1 region and the HEAT repeat protein PR65/A. The results indicate that HTT exon 1 slightly destabilizes the downstream HEAT repeat structure and endows the HEAT repeat structure with more conformational flexibility. Wild-type and pathological lengths of polyQ did not show differences in the interaction between HTT exon 1 and the HEAT repeats. With the C-terminal fusion of PR65/A, HTT exon 1 containing pathological lengths of polyQ could still form amyloid fibrils, but the higher-order architecture of fibrils and kinetics of fibril formation were affected by the C-terminal fusion of HEAT repeats. This indicates that interaction between HTT exon 1 and HEAT repeat structure is compatible with both normal function of HTT protein and the pathogenesis of HD, and this study provides a potential model for further exploration.
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Affiliation(s)
- Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of the Chinese Academy of SciencesBeijingChina
- Institute of Basic Medical Sciences, Chinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
| | - Si Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of the Chinese Academy of SciencesBeijingChina
| | | | - Sarah Perrett
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of the Chinese Academy of SciencesBeijingChina
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5
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Zickler D, Kleckner N. Meiosis: Dances Between Homologs. Annu Rev Genet 2023; 57:1-63. [PMID: 37788458 DOI: 10.1146/annurev-genet-061323-044915] [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] [Indexed: 10/05/2023]
Abstract
The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding of the DNA events of recombination and of three processes that involve whole chromosomes: homolog pairing, crossover interference, and chiasma maturation. All of these processes are implemented by direct physical interaction of recombination complexes with underlying chromosome structures. Finally, we present convergent lines of evidence that the meiotic program may have evolved by coupling of this interaction to late-stage mitotic chromosome morphogenesis.
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Affiliation(s)
- Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA;
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6
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Bahar I, Banerjee A, Mathew S, Naqvi M, Yilmaz S, Zachoropoulou M, Doruker P, Kumita J, Yang SH, Gur M, Itzhaki L, Gordon R. Influence of Point Mutations on PR65 Conformational Adaptability: Insights from Nanoaperture Optical Tweezer Experiments and Molecular Simulations. RESEARCH SQUARE 2023:rs.3.rs-3599809. [PMID: 38014259 PMCID: PMC10680943 DOI: 10.21203/rs.3.rs-3599809/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
PR65 is the HEAT-repeat scaffold subunit of the heterotrimeric protein phosphatase 2A (PP2A) and an archetypal tandem-repeat protein, forming a spring-like architecture. PR65 conformational mechanics play a crucial role in PP2A function by opening/closing the substrate-binding/catalysis interface. Using in-silico saturation mutagenesis we identified "hinge" residues of PR65, whose substitutions are predicted to restrict its conformational adaptability and thereby disrupt PP2A function. Molecular simulations revealed that a subset of hinge mutations stabilized the extended/open conformation, whereas another had the opposite effect. By trapping in nanoaperture optical tweezer, we characterized PR65 motion and showed that the former mutants exhibited higher corner frequencies and lower translational scattering, indicating a shift towards extended conformations, whereas the latter showed the opposite behavior. Thus, experiments confirm the conformations predicted computationally. The study highlights the utility of nanoaperture-based tweezers for exploring structure and dynamics, and the power of integrating this single-molecule method with in silico approaches.
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7
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Pillai M, Lafortune P, Dabo A, Yu H, Park SS, Taluru H, Ahmed H, Bobrow D, Sattar Z, Jundi B, Reece J, Ortega RR, Soto B, Yewedalsew S, Foronjy R, Wyman A, Geraghty P, Ohlmeyer M. Small-Molecule Activation of Protein Phosphatase 2A Counters Bleomycin-Induced Fibrosis in Mice. ACS Pharmacol Transl Sci 2023; 6:1659-1672. [PMID: 37974628 PMCID: PMC10644462 DOI: 10.1021/acsptsci.3c00117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Indexed: 11/19/2023]
Abstract
The activity of protein phosphatase 2A (PP2A), a serine-threonine phosphatase, is reduced in the lung fibroblasts of idiopathic pulmonary fibrosis (IPF) patients. The objective of this study was to determine whether the reactivation of PP2A could reduce fibrosis and preserve the pulmonary function in a bleomycin (BLM) mouse model. Here, we present a new class of direct small-molecule PP2A activators, diarylmethyl-pyran-sulfonamide, exemplified by ATUX-1215. ATUX-1215 has improved metabolic stability and bioavailability compared to our previously described PP2A activators. Primary human lung fibroblasts were exposed to ATUX-1215 and an older generation PP2A activator in combination with TGFβ. ATUX-1215 treatment enhanced the PP2A activity, reduced the phosphorylation of ERK and JNK, and reduced the TGFβ-induced expression of ACTA2, FN1, COL1A1, and COL3A1. C57BL/6J mice were administered 5 mg/kg ATUX-1215 daily following intratracheal instillation of BLM. Three weeks later, forced oscillation and expiratory measurements were performed using the Scireq Flexivent System. ATUX-1215 prevented BLM-induced lung physiology changes, including the preservation of normal PV loop, compliance, tissue elastance, and forced vital capacity. PP2A activity was enhanced with ATUX-1215 and reduced collagen deposition within the lungs. ATUX-1215 also prevented the BLM induction of Acta2, Ccn2, and Fn1 gene expression. Treatment with ATUX-1215 reduced the phosphorylation of ERK, p38, JNK, and Akt and the secretion of IL-12p70, GM-CSF, and IL1α in BLM-treated animals. Delayed treatment with ATUX-1215 was also observed to slow the progression of lung fibrosis. In conclusion, our study indicates that the decrease in PP2A activity, which occurs in fibroblasts from the lungs of IPF subjects, could be restored with ATUX-1215 administration as an antifibrotic agent.
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Affiliation(s)
- Meshach Pillai
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Pascale Lafortune
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Abdoulaye Dabo
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Howard Yu
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Sangmi S. Park
- Department
of Cell Biology, The State University of
New York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Harsha Taluru
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Huma Ahmed
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Dylan Bobrow
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Zeeshan Sattar
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Bakr Jundi
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Joshua Reece
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Romy Rodriguez Ortega
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Brian Soto
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Selome Yewedalsew
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Robert Foronjy
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Anne Wyman
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
| | - Patrick Geraghty
- Department
of Medicine, The State University of New
York Downstate Health Sciences University, Brooklyn, New York 11203, United States
- Department
of Cell Biology, The State University of
New York Downstate Health Sciences University, Brooklyn, New York 11203, United States
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8
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Kovacs MT, Vallette M, Wiertsema P, Dingli F, Loew D, Nader GPDF, Piel M, Ceccaldi R. DNA damage induces nuclear envelope rupture through ATR-mediated phosphorylation of lamin A/C. Mol Cell 2023; 83:3659-3668.e10. [PMID: 37832547 PMCID: PMC10597398 DOI: 10.1016/j.molcel.2023.09.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 08/01/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
The integrity of the nuclear envelope (NE) is essential for maintaining the structural stability of the nucleus. Rupture of the NE has been frequently observed in cancer cells, especially in the context of mechanical challenges, such as physical confinement and migration. However, spontaneous NE rupture events, without any obvious physical challenges to the cell, have also been described. The molecular mechanism(s) of these spontaneous NE rupture events remain to be explored. Here, we show that DNA damage and subsequent ATR activation leads to NE rupture. Upon DNA damage, lamin A/C is phosphorylated in an ATR-dependent manner, leading to changes in lamina assembly and, ultimately, NE rupture. In addition, we show that cancer cells with intrinsic DNA repair defects undergo frequent events of DNA-damage-induced NE rupture, which renders them extremely sensitive to further NE perturbations. Exploiting this NE vulnerability could provide a new angle to complement traditional, DNA-damage-based chemotherapy.
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Affiliation(s)
| | - Marie Vallette
- Inserm U830, PSL Research University, Institut Curie, 75005 Paris, France
| | - Pauline Wiertsema
- Inserm U830, PSL Research University, Institut Curie, 75005 Paris, France
| | - Florent Dingli
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Spectrométrie de Masse Protéomique, 26 rue d'Ulm, Paris 75248 Cedex 05, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Spectrométrie de Masse Protéomique, 26 rue d'Ulm, Paris 75248 Cedex 05, France
| | | | - Matthieu Piel
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS, UMR 144, Paris, France
| | - Raphael Ceccaldi
- Inserm U830, PSL Research University, Institut Curie, 75005 Paris, France.
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9
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Negri ML, D'Annunzio S, Vitali G, Zippo A. May the force be with you: Nuclear condensates function beyond transcription control: Potential nongenetic functions of nuclear condensates in physiological and pathological conditions. Bioessays 2023; 45:e2300075. [PMID: 37530178 DOI: 10.1002/bies.202300075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 08/03/2023]
Abstract
Over the past decade, research has revealed biomolecular condensates' relevance in diverse cellular functions. Through a phase separation process, they concentrate macromolecules in subcompartments shaping the cellular organization and physiology. In the nucleus, biomolecular condensates assemble relevant biomolecules that orchestrate gene expression. We here hypothesize that chromatin condensates can also modulate the nongenetic functions of the genome, including the nuclear mechanical properties. The importance of chromatin condensates is supported by the genetic evidence indicating that mutations in their members are causative of a group of rare Mendelian diseases named chromatinopathies (CPs). Despite a broad spectrum of clinical features and the perturbations of the epigenetic machinery characterizing the CPs, recent findings highlighted negligible changes in gene expression. These data argue in favor of possible noncanonical functions of chromatin condensates in regulating the genome's spatial organization and, consequently, the nuclear mechanics. In this review, we discuss how condensates may impact nuclear mechanical properties, thus affecting the cellular response to mechanical cues and, eventually, cell fate and identity. Chromatin condensates organize macromolecules in the nucleus orchestrating the transcription regulation and mutations in their members are responsible for rare diseases named chromatinopathies. We argue that chromatin condensates, in concert with the nuclear lamina, may also govern the nuclear mechanical properties affecting the cellular response to external cues.
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Affiliation(s)
- Maria Luce Negri
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Sarah D'Annunzio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giulia Vitali
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessio Zippo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
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10
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Kleckner N. From phage genetics to chromosomes as mechanical objects. Nat Cell Biol 2023; 25:1075-1076. [PMID: 37474817 PMCID: PMC11007551 DOI: 10.1038/s41556-023-01200-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Nancy Kleckner is the Herchel Smith professor of molecular biology at Harvard University. She recalls the evolution of her research interests from pure genetics, through biochemistry and molecular biology of DNA, to the roles of mechanical forces for whole-chromosome spatial patterning and dynamics.
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Affiliation(s)
- Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
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11
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Avelar RA, Armstrong AJ, Carvette G, Gupta R, Puleo N, Colina JA, Joseph P, Sobeck AM, O'Connor CM, Raines B, Gandhi A, Dziubinski ML, Ma DS, Resnick K, Singh S, Zanotti K, Nagel C, Waggoner S, Thomas DG, Skala SL, Zhang J, Narla G, DiFeo A. Small-Molecule-Mediated Stabilization of PP2A Modulates the Homologous Recombination Pathway and Potentiates DNA Damage-Induced Cell Death. Mol Cancer Ther 2023; 22:599-615. [PMID: 36788429 PMCID: PMC10157366 DOI: 10.1158/1535-7163.mct-21-0880] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 05/17/2022] [Accepted: 02/09/2023] [Indexed: 02/16/2023]
Abstract
High-grade serous carcinoma (HGSC) is the most common and lethal ovarian cancer subtype. PARP inhibitors (PARPi) have become the mainstay of HGSC-targeted therapy, given that these tumors are driven by a high degree of genomic instability (GI) and homologous recombination (HR) defects. Nonetheless, approximately 30% of patients initially respond to treatment, ultimately relapsing with resistant disease. Thus, despite recent advances in drug development and an increased understanding of genetic alterations driving HGSC progression, mortality has not declined, highlighting the need for novel therapies. Using a small-molecule activator of protein phosphatase 2A (PP2A; SMAP-061), we investigated the mechanism by which PP2A stabilization induces apoptosis in patient-derived HGSC cells and xenograft (PDX) models alone or in combination with PARPi. We uncovered that PP2A genes essential for cellular transformation (B56α, B56γ, and PR72) and basal phosphatase activity (PP2A-A and -C) are heterozygously lost in the majority of HGSC. Moreover, loss of these PP2A genes correlates with worse overall patient survival. We show that SMAP-061-induced stabilization of PP2A inhibits the HR output by targeting RAD51, leading to chronic accumulation of DNA damage and ultimately apoptosis. Furthermore, combination of SMAP-061 and PARPi leads to enhanced apoptosis in both HR-proficient and HR-deficient HGSC cells and PDX models. Our studies identify PP2A as a novel regulator of HR and indicate PP2A modulators as a therapeutic therapy for HGSC. In summary, our findings further emphasize the potential of PP2A modulators to overcome PARPi insensitivity, given that targeting RAD51 presents benefits in overcoming PARPi resistance driven by BRCA1/2 mutation reversions.
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Affiliation(s)
- Rita A. Avelar
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
- The Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | | | - Gracie Carvette
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
- The Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Riya Gupta
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
- The Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Noah Puleo
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
- The Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Jose A. Colina
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
- The Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Peronne Joseph
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | - Alexander M. Sobeck
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
- The Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Caitlin M. O'Connor
- The Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
- Department of Internal Medicine, Genetic Medicine, University of Michigan, Ann Arbor, Michigan
| | - Brynne Raines
- The Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
- Department of Internal Medicine, Genetic Medicine, University of Michigan, Ann Arbor, Michigan
| | - Agharnan Gandhi
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
- The Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Michele L. Dziubinski
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
- The Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Daniel S. Ma
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | | | | | | | | | | | - Daffyd G. Thomas
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | | | - Junran Zhang
- Department of Radiation Oncology, Ohio State University, Columbus, Ohio
| | - Goutham Narla
- The Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
- Department of Internal Medicine, Genetic Medicine, University of Michigan, Ann Arbor, Michigan
| | - Analisa DiFeo
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
- The Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan
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12
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Kaynak BT, Dahmani ZL, Doruker P, Banerjee A, Yang SH, Gordon R, Itzhaki LS, Bahar I. Cooperative mechanics of PR65 scaffold underlies the allosteric regulation of the phosphatase PP2A. Structure 2023; 31:607-618.e3. [PMID: 36948205 PMCID: PMC10164121 DOI: 10.1016/j.str.2023.02.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/25/2023] [Accepted: 02/23/2023] [Indexed: 03/24/2023]
Abstract
PR65, a horseshoe-shaped scaffold composed of 15 HEAT (observed in Huntingtin, elongation factor 3, protein phosphatase 2A, and the yeast kinase TOR1) repeats, forms, together with catalytic and regulatory subunits, the heterotrimeric protein phosphatase PP2A. We examined the role of PR65 in enabling PP2A enzymatic activity with computations at various levels of complexity, including hybrid approaches that combine full-atomic and elastic network models. Our study points to the high flexibility of this scaffold allowing for end-to-end distance fluctuations of 40-50 Å between compact and extended conformations. Notably, the intrinsic dynamics of PR65 facilitates complexation with the catalytic subunit and is retained in the PP2A complex enabling PR65 to engage the two domains of the catalytic subunit and provide the mechanical framework for enzymatic activity, with support from the regulatory subunit. In particular, the intra-repeat coils at the C-terminal arm play an important role in allosterically mediating the collective dynamics of PP2A, pointing to target sites for modulating PR65 function.
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Affiliation(s)
- Burak T Kaynak
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Zakaria L Dahmani
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Pemra Doruker
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anupam Banerjee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Shang-Hua Yang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Reuven Gordon
- Department of Electrical and Computer Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
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13
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Friedrich D, Marintchev A, Arthanari H. The metaphorical swiss army knife: The multitude and diverse roles of HEAT domains in eukaryotic translation initiation. Nucleic Acids Res 2022; 50:5424-5442. [PMID: 35552740 PMCID: PMC9177959 DOI: 10.1093/nar/gkac342] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/24/2022] Open
Abstract
Biomolecular associations forged by specific interaction among structural scaffolds are fundamental to the control and regulation of cell processes. One such structural architecture, characterized by HEAT repeats, is involved in a multitude of cellular processes, including intracellular transport, signaling, and protein synthesis. Here, we review the multitude and versatility of HEAT domains in the regulation of mRNA translation initiation. Structural and cellular biology approaches, as well as several biophysical studies, have revealed that a number of HEAT domain-mediated interactions with a host of protein factors and RNAs coordinate translation initiation. We describe the basic structural architecture of HEAT domains and briefly introduce examples of the cellular processes they dictate, including nuclear transport by importin and RNA degradation. We then focus on proteins in the translation initiation system featuring HEAT domains, specifically the HEAT domains of eIF4G, DAP5, eIF5, and eIF2Bϵ. Comparative analysis of their remarkably versatile interactions, including protein–protein and protein–RNA recognition, reveal the functional importance of flexible regions within these HEAT domains. Here we outline how HEAT domains orchestrate fundamental aspects of translation initiation and highlight open mechanistic questions in the area.
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Affiliation(s)
- Daniel Friedrich
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Assen Marintchev
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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14
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Synakewicz M, Eapen RS, Perez-Riba A, Rowling PJE, Bauer D, Weißl A, Fischer G, Hyvönen M, Rief M, Itzhaki LS, Stigler J. Unraveling the Mechanics of a Repeat-Protein Nanospring: From Folding of Individual Repeats to Fluctuations of the Superhelix. ACS NANO 2022. [PMID: 35258937 DOI: 10.1101/2021.03.27.437344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Tandem-repeat proteins comprise small secondary structure motifs that stack to form one-dimensional arrays with distinctive mechanical properties that are proposed to direct their cellular functions. Here, we use single-molecule optical tweezers to study the folding of consensus-designed tetratricopeptide repeats (CTPRs), superhelical arrays of short helix-turn-helix motifs. We find that CTPRs display a spring-like mechanical response in which individual repeats undergo rapid equilibrium fluctuations between partially folded and unfolded conformations. We rationalize the force response using Ising models and dissect the folding pathway of CTPRs under mechanical load, revealing how the repeat arrays form from the center toward both termini simultaneously. Most strikingly, we also directly observe the protein's superhelical tertiary structure in the force signal. Using protein engineering, crystallography, and single-molecule experiments, we show that the superhelical geometry can be altered by carefully placed amino acid substitutions, and we examine how these sequence changes affect intrinsic repeat stability and inter-repeat coupling. Our findings provide the means to dissect and modulate repeat-protein stability and dynamics, which will be essential for researchers to understand the function of natural repeat proteins and to exploit artificial repeats proteins in nanotechnology and biomedical applications.
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Affiliation(s)
- Marie Synakewicz
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom†
| | - Rohan S Eapen
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom†
| | - Albert Perez-Riba
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom†
| | - Pamela J E Rowling
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom†
| | - Daniela Bauer
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Andreas Weißl
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Gerhard Fischer
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Matthias Rief
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom†
| | - Johannes Stigler
- Gene Center Munich, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 München, Germany
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15
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Synakewicz M, Eapen RS, Perez-Riba A, Rowling PJE, Bauer D, Weißl A, Fischer G, Hyvönen M, Rief M, Itzhaki LS, Stigler J. Unraveling the Mechanics of a Repeat-Protein Nanospring: From Folding of Individual Repeats to Fluctuations of the Superhelix. ACS NANO 2022; 16:3895-3905. [PMID: 35258937 PMCID: PMC8944806 DOI: 10.1021/acsnano.1c09162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Tandem-repeat proteins comprise small secondary structure motifs that stack to form one-dimensional arrays with distinctive mechanical properties that are proposed to direct their cellular functions. Here, we use single-molecule optical tweezers to study the folding of consensus-designed tetratricopeptide repeats (CTPRs), superhelical arrays of short helix-turn-helix motifs. We find that CTPRs display a spring-like mechanical response in which individual repeats undergo rapid equilibrium fluctuations between partially folded and unfolded conformations. We rationalize the force response using Ising models and dissect the folding pathway of CTPRs under mechanical load, revealing how the repeat arrays form from the center toward both termini simultaneously. Most strikingly, we also directly observe the protein's superhelical tertiary structure in the force signal. Using protein engineering, crystallography, and single-molecule experiments, we show that the superhelical geometry can be altered by carefully placed amino acid substitutions, and we examine how these sequence changes affect intrinsic repeat stability and inter-repeat coupling. Our findings provide the means to dissect and modulate repeat-protein stability and dynamics, which will be essential for researchers to understand the function of natural repeat proteins and to exploit artificial repeats proteins in nanotechnology and biomedical applications.
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Affiliation(s)
- Marie Synakewicz
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Rohan S. Eapen
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Albert Perez-Riba
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Pamela J. E. Rowling
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Daniela Bauer
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Andreas Weißl
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Gerhard Fischer
- Department
of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Marko Hyvönen
- Department
of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Matthias Rief
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Laura S. Itzhaki
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Johannes Stigler
- Gene
Center Munich, Ludwig-Maximilians-Universität
München, Feodor-Lynen-Straße 25, 81377 München, Germany
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16
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Sule A, Golding SE, Ahmad SF, Watson J, Ahmed MH, Kellogg GE, Bernas T, Koebley S, Reed JC, Povirk LF, Valerie K. ATM phosphorylates PP2A subunit A resulting in nuclear export and spatiotemporal regulation of the DNA damage response. Cell Mol Life Sci 2022; 79:603. [PMID: 36434396 PMCID: PMC9700600 DOI: 10.1007/s00018-022-04550-5] [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: 04/24/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/26/2022]
Abstract
Ataxia telangiectasia mutated (ATM) is a serine-threonine protein kinase and important regulator of the DNA damage response (DDR). One critical ATM target is the structural subunit A (PR65-S401) of protein phosphatase 2A (PP2A), known to regulate diverse cellular processes such as mitosis and cell growth as well as dephosphorylating many proteins during the recovery from the DDR. We generated mouse embryonic fibroblasts expressing PR65-WT, -S401A (cannot be phosphorylated), and -S401D (phospho-mimetic) transgenes. Significantly, S401 mutants exhibited extensive chromosomal aberrations, impaired DNA double-strand break (DSB) repair and underwent increased mitotic catastrophe after radiation. Both S401A and the S401D cells showed impaired DSB repair (nonhomologous end joining and homologous recombination repair) and exhibited delayed DNA damage recovery, which was reflected in reduced radiation survival. Furthermore, S401D cells displayed increased ERK and AKT signaling resulting in enhanced growth rate further underscoring the multiple roles ATM-PP2A signaling plays in regulating prosurvival responses. Time-lapse video and cellular localization experiments showed that PR65 was exported to the cytoplasm after radiation by CRM1, a nuclear export protein, in line with the very rapid pleiotropic effects observed. A putative nuclear export sequence (NES) close to S401 was identified and when mutated resulted in aberrant PR65 shuttling. Our study demonstrates that the phosphorylation of a single, critical PR65 amino acid (S401) by ATM fundamentally controls the DDR, and balances DSB repair quality, cell survival and growth by spatiotemporal PR65 nuclear-cytoplasmic shuttling mediated by the nuclear export receptor CRM1.
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Affiliation(s)
- Amrita Sule
- Department of Radiation Oncology, Virginia Commonwealth University, Richmond, VA, 23298-0058, USA
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Sarah E Golding
- Department of Radiation Oncology, Virginia Commonwealth University, Richmond, VA, 23298-0058, USA
| | - Syed F Ahmad
- Department of Radiation Oncology, Virginia Commonwealth University, Richmond, VA, 23298-0058, USA
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - James Watson
- Department of Radiation Oncology, Virginia Commonwealth University, Richmond, VA, 23298-0058, USA
| | - Mostafa H Ahmed
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Glen E Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, 23298, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Tytus Bernas
- Department of Anatomy, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Sean Koebley
- Department of Physics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Jason C Reed
- Department of Physics, Virginia Commonwealth University, Richmond, VA, 23298, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Lawrence F Povirk
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, 23298, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Kristoffer Valerie
- Department of Radiation Oncology, Virginia Commonwealth University, Richmond, VA, 23298-0058, USA.
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, 23298, USA.
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA.
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17
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Sergienko NM, Donner DG, Delbridge LMD, McMullen JR, Weeks KL. Protein phosphatase 2A in the healthy and failing heart: New insights and therapeutic opportunities. Cell Signal 2021; 91:110213. [PMID: 34902541 DOI: 10.1016/j.cellsig.2021.110213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023]
Abstract
Protein phosphatases have emerged as critical regulators of phosphoprotein homeostasis in settings of health and disease. Protein phosphatase 2A (PP2A) encompasses a large subfamily of enzymes that remove phosphate groups from serine/threonine residues within phosphoproteins. The heterogeneity in PP2A structure, which arises from the grouping of different catalytic, scaffolding and regulatory subunit isoforms, creates distinct populations of catalytically active enzymes (i.e. holoenzymes) that localise to different parts of the cell. This structural complexity, combined with other regulatory mechanisms, such as interaction of PP2A heterotrimers with accessory proteins and post-translational modification of the catalytic and/or regulatory subunits, enables PP2A holoenzymes to target phosphoprotein substrates in a highly specific manner. In this review, we summarise the roles of PP2A in cardiac physiology and disease. PP2A modulates numerous processes that are vital for heart function including calcium handling, contractility, β-adrenergic signalling, metabolism and transcription. Dysregulation of PP2A has been observed in human cardiac disease settings, including heart failure and atrial fibrillation. Efforts are underway, particularly in the cancer field, to develop therapeutics targeting PP2A activity. The development of small molecule activators of PP2A (SMAPs) and other compounds that selectively target specific PP2A holoenzymes (e.g. PP2A/B56α and PP2A/B56ε) will improve understanding of the function of different PP2A species in the heart, and may lead to the development of therapeutics for normalising aberrant protein phosphorylation in settings of cardiac remodelling and dysfunction.
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Affiliation(s)
- Nicola M Sergienko
- Baker Heart and Diabetes Institute, Melbourne VIC 3004, Australia; Central Clinical School, Monash University, Clayton VIC 3800, Australia
| | - Daniel G Donner
- Baker Heart and Diabetes Institute, Melbourne VIC 3004, Australia; Baker Department of Cardiometabolic Health, The University of Melbourne, Parkville VIC 3010, Australia
| | - Lea M D Delbridge
- Department of Anatomy and Physiology, The University of Melbourne, Parkville VIC 3010, Australia
| | - Julie R McMullen
- Baker Heart and Diabetes Institute, Melbourne VIC 3004, Australia; Baker Department of Cardiometabolic Health, The University of Melbourne, Parkville VIC 3010, Australia; Department of Physiology and Department of Medicine Alfred Hospital, Monash University, Clayton VIC 3800, Australia; Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora VIC 3086, Australia; Department of Diabetes, Central Clinical School, Monash University, Clayton VIC 3800, Australia.
| | - Kate L Weeks
- Baker Heart and Diabetes Institute, Melbourne VIC 3004, Australia; Department of Anatomy and Physiology, The University of Melbourne, Parkville VIC 3010, Australia; Baker Department of Cardiometabolic Health, The University of Melbourne, Parkville VIC 3010, Australia; Department of Diabetes, Central Clinical School, Monash University, Clayton VIC 3800, Australia.
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18
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Sarkar R, Petrushenko ZM, Dawson DS, Rybenkov VV. Ycs4 Subunit of Saccharomyces cerevisiae Condensin Binds DNA and Modulates the Enzyme Turnover. Biochemistry 2021; 60:3385-3397. [PMID: 34723504 DOI: 10.1021/acs.biochem.1c00473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Condensins play a key role in higher order chromosome organization. In budding yeast Saccharomyces cerevisiae, a condensin complex consists of five subunits: two conserved structural maintenance of chromosome subunits, Smc2 and Smc4, a kleisin Brn1, and two HEAT repeat subunits, Ycg1, which possesses a DNA binding activity, and Ycs4, which can transiently associate with Smc4 and thereby disrupt its association with the Smc2 head. We characterized here DNA binding activity of the non-SMC subunits using an agnostic, model-independent approach. To this end, we mapped the DNA interface of the complex using sulfo-NHS biotin labeling. Besides the known site on Ycg1, we found a patch of lysines at the C-terminal domain of Ycs4 that were protected from biotinylation in the presence of DNA. Point mutations at the predicted protein-DNA interface reduced both Ycs4 binding to DNA and the DNA stimulated ATPase activity of the reconstituted condensin, whereas overproduction of the mutant Ycs4 was detrimental for yeast viability. Notably, the DNA binding site on Ycs4 partially overlapped with its interface with SMC4, revealing an intricate interplay between DNA binding, engagement of the Smc2-Smc4 heads, and ATP hydrolysis and suggesting a mechanism for ATP-modulated loading and translocation of condensins on DNA.
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Affiliation(s)
- Rupa Sarkar
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Zoya M Petrushenko
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Dean S Dawson
- Oklahoma Medical Research Foundation, 825 N.E. 13th Street, Oklahoma City, Oklahoma 73104, United States
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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19
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Barvitenko N, Aslam M, Lawen A, Saldanha C, Skverchinskaya E, Uras G, Manca A, Pantaleo A. Two Motors and One Spring: Hypothetic Roles of Non-Muscle Myosin II and Submembrane Actin-Based Cytoskeleton in Cell Volume Sensing. Int J Mol Sci 2021; 22:7967. [PMID: 34360739 PMCID: PMC8347689 DOI: 10.3390/ijms22157967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/16/2021] [Accepted: 07/23/2021] [Indexed: 12/12/2022] Open
Abstract
Changes in plasma membrane curvature and intracellular ionic strength are two key features of cell volume perturbations. In this hypothesis we present a model of the responsible molecular apparatus which is assembled of two molecular motors [non-muscle myosin II (NMMII) and protrusive actin polymerization], a spring [a complex between the plasma membrane (PM) and the submembrane actin-based cytoskeleton (smACSK) which behaves like a viscoelastic solid] and the associated signaling proteins. We hypothesize that this apparatus senses changes in both the plasma membrane curvature and the ionic strength and in turn activates signaling pathways responsible for regulatory volume increase (RVI) and regulatory volume decrease (RVD). During cell volume changes hydrostatic pressure (HP) changes drive alterations in the cell membrane curvature. HP difference has opposite directions in swelling versus shrinkage, thus allowing distinction between them. By analogy with actomyosin contractility that appears to sense stiffness of the extracellular matrix we propose that NMMII and actin polymerization can actively probe the transmembrane gradient in HP. Furthermore, NMMII and protein-protein interactions in the actin cortex are sensitive to ionic strength. Emerging data on direct binding to and regulating activities of transmembrane mechanosensors by NMMII and actin cortex provide routes for signal transduction from transmembrane mechanosensors to cell volume regulatory mechanisms.
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Affiliation(s)
| | - Muhammad Aslam
- Department of Internal Medicine I, Experimental Cardiology, Justus Liebig University, 35392 Giessen, Germany;
| | - Alfons Lawen
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia;
| | - Carlota Saldanha
- Institute of Biochemistry, Institute of Molecular Medicine, Faculty of Medicine University of Lisbon, 1649-028 Lisboa, Portugal;
| | | | - Giuseppe Uras
- Department of Clinical and Movement Neurosciences, Institute of Neurology, University College London, London NW3 2PF, UK;
| | - Alessia Manca
- Department of Biomedical Science, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy;
| | - Antonella Pantaleo
- Department of Biomedical Science, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy;
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20
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Biallelic hypomorphic mutations in HEATR5B, encoding HEAT repeat-containing protein 5B, in a neurological syndrome with pontocerebellar hypoplasia. Eur J Hum Genet 2021; 29:957-964. [PMID: 33824466 DOI: 10.1038/s41431-021-00832-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/12/2021] [Accepted: 02/09/2021] [Indexed: 11/09/2022] Open
Abstract
HEAT repeats are 37-47 amino acid flexible tandem repeat structural motifs occurring in a wide variety of eukaryotic proteins with diverse functions. Due to their ability to undergo elastic conformational changes, they often serve as scaffolds at sites of protein interactions. Here, we describe four affected children from two families presenting with pontocerebellar hypoplasia manifest clinically with neonatal seizures, severe intellectual disability, and motor delay. Whole exome sequencing identified biallelic variants at predicted splice sites in intron 31 of HEATR5B, encoding the HEAT repeat-containing protein 5B segregating in a recessive fashion. Aberrant splicing was found in patient fibroblasts, which correlated with reduced levels of HEATR5B protein. HEATR5B is expressed during brain development in human, and we failed to recover live-born homozygous Heatr5b knockout mice. Taken together, our results implicate loss of HEATR5B in pontocerebellar hypoplasia.
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21
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Chu L, Liang Z, Mukhina MV, Fisher JK, Hutchinson JW, Kleckner NE. One-dimensional spatial patterning along mitotic chromosomes: A mechanical basis for macroscopic morphogenesis. Proc Natl Acad Sci U S A 2020; 117:26749-26755. [PMID: 33051295 PMCID: PMC7604413 DOI: 10.1073/pnas.2013709117] [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] [Indexed: 01/22/2023] Open
Abstract
Spatial patterns are ubiquitous in both physical and biological systems. We have recently discovered that mitotic chromosomes sequentially acquire two interesting morphological patterns along their structural axes [L. Chu et al., Mol. Cell, 10.1016/j.molcel.2020.07.002 (2020)]. First, axes of closely conjoined sister chromosomes acquire regular undulations comprising nearly planar arrays of sequential half-helices of similar size and alternating handedness, accompanied by periodic kinks. This pattern, which persists through all later stages, provides a case of the geometric form known as a "perversion." Next, as sister chromosomes become distinct parallel units, their individual axes become linked by bridges, which are themselves miniature axes. These bridges are dramatically evenly spaced. Together, these effects comprise a unique instance of spatial patterning in a subcellular biological system. We present evidence that axis undulations and bridge arrays arise by a single continuous mechanically promoted progression, driven by stress within the chromosome axes. We further suggest that, after sister individualization, this same stress also promotes chromosome compaction by rendering the axes susceptible to the requisite molecular remodeling. Thus, by this scenario, the continuous presence of mechanical stress within the chromosome axes could potentially underlie the entire morphogenetic chromosomal program. Direct analogies with meiotic chromosomes suggest that the same effects could underlie interactions between homologous chromosomes as required for gametogenesis. Possible mechanical bases for generation of axis stress and resultant deformations are discussed. Together, these findings provide a perspective on the macroscopic changes of organized chromosomes.
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Affiliation(s)
- Lingluo Chu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Zhangyi Liang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Maria V Mukhina
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | | | - John W Hutchinson
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
| | - Nancy E Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138;
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22
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Kidiyoor GR, Li Q, Bastianello G, Bruhn C, Giovannetti I, Mohamood A, Beznoussenko GV, Mironov A, Raab M, Piel M, Restuccia U, Matafora V, Bachi A, Barozzi S, Parazzoli D, Frittoli E, Palamidessi A, Panciera T, Piccolo S, Scita G, Maiuri P, Havas KM, Zhou ZW, Kumar A, Bartek J, Wang ZQ, Foiani M. ATR is essential for preservation of cell mechanics and nuclear integrity during interstitial migration. Nat Commun 2020; 11:4828. [PMID: 32973141 PMCID: PMC7518249 DOI: 10.1038/s41467-020-18580-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/25/2020] [Indexed: 12/17/2022] Open
Abstract
ATR responds to mechanical stress at the nuclear envelope and mediates envelope-associated repair of aberrant topological DNA states. By combining microscopy, electron microscopic analysis, biophysical and in vivo models, we report that ATR-defective cells exhibit altered nuclear plasticity and YAP delocalization. When subjected to mechanical stress or undergoing interstitial migration, ATR-defective nuclei collapse accumulating nuclear envelope ruptures and perinuclear cGAS, which indicate loss of nuclear envelope integrity, and aberrant perinuclear chromatin status. ATR-defective cells also are defective in neuronal migration during development and in metastatic dissemination from circulating tumor cells. Our findings indicate that ATR ensures mechanical coupling of the cytoskeleton to the nuclear envelope and accompanying regulation of envelope-chromosome association. Thus the repertoire of ATR-regulated biological processes extends well beyond its canonical role in triggering biochemical implementation of the DNA damage response. The nucleus is a mechanically stiff organelle of the cell and the DNA damage response protein ATR can localize to the nuclear envelope upon mechanical stress. Here, the authors show that ATR may contribute to the integrity of the nuclear envelope and may play a role in cell migration.
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Affiliation(s)
| | - Qingsen Li
- IFOM- FIRC Institute of Molecular Oncology, Milan, Italy
| | | | | | | | - Adhil Mohamood
- IFOM- FIRC Institute of Molecular Oncology, Milan, Italy
| | | | | | | | | | | | | | - Angela Bachi
- IFOM- FIRC Institute of Molecular Oncology, Milan, Italy
| | - Sara Barozzi
- IFOM- FIRC Institute of Molecular Oncology, Milan, Italy
| | | | | | | | | | - Stefano Piccolo
- IFOM- FIRC Institute of Molecular Oncology, Milan, Italy.,University of Padova, Padova, Italy
| | - Giorgio Scita
- IFOM- FIRC Institute of Molecular Oncology, Milan, Italy.,University of Milan, Milan, Italy
| | - Paolo Maiuri
- IFOM- FIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Zhong-Wei Zhou
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany.,School of Medicine, Sun Yat-Sen University, Shenzhen, China
| | - Amit Kumar
- Genome and Cell Integrity Lab, CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Jiri Bartek
- Danish Cancer Society Research Center, Copenhagen, Denmark.,Karolinska Institute, Stockholm, Sweden
| | - Zhao-Qi Wang
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany.,Friedrich-Schiller University, Jena, Germany
| | - Marco Foiani
- IFOM- FIRC Institute of Molecular Oncology, Milan, Italy. .,University of Milan, Milan, Italy.
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23
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Jung T, Shin B, Tamo G, Kim H, Vijayvargia R, Leitner A, Marcaida MJ, Astorga-Wells J, Jung R, Aebersold R, Peraro MD, Hebert H, Seong IS, Song JJ. The Polyglutamine Expansion at the N-Terminal of Huntingtin Protein Modulates the Dynamic Configuration and Phosphorylation of the C-Terminal HEAT Domain. Structure 2020; 28:1035-1050.e8. [PMID: 32668197 PMCID: PMC11059206 DOI: 10.1016/j.str.2020.06.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 04/01/2020] [Accepted: 06/23/2020] [Indexed: 11/15/2022]
Abstract
The polyQ expansion in huntingtin protein (HTT) is the prime cause of Huntington's disease (HD). The recent cryoelectron microscopy (cryo-EM) structure of HTT-HAP40 complex provided the structural information on its HEAT-repeat domains. Here, we present analyses of the impact of polyQ length on the structure and function of HTT via an integrative structural and biochemical approach. The cryo-EM analysis of normal (Q23) and disease (Q78) type HTTs shows that the structures of apo HTTs significantly differ from the structure of HTT in a HAP40 complex and that the polyQ expansion induces global structural changes in the relative movements among the HTT domains. In addition, we show that the polyQ expansion alters the phosphorylation pattern across HTT and that Ser2116 phosphorylation in turn affects the global structure and function of HTT. These results provide a molecular basis for the effect of the polyQ segment on HTT structure and activity, which may be important for HTT pathology.
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Affiliation(s)
- Taeyang Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), KI for the BioCentury, Daejeon 34141, Korea; School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, 141 52 Huddinge, Sweden; Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Baehyun Shin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Giorgio Tamo
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Hyeongju Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), KI for the BioCentury, Daejeon 34141, Korea
| | - Ravi Vijayvargia
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Maria J Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Juan Astorga-Wells
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, 171 65 Solna, Sweden; HDxperts AB, 183 48 Täby, Sweden
| | - Roy Jung
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland; Faculty of Science, University of Zürich, Zürich, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Hans Hebert
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, 141 52 Huddinge, Sweden; Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden.
| | - Ihn Sik Seong
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Harvard Medical School, Boston, MA 02114, USA.
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), KI for the BioCentury, Daejeon 34141, Korea.
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24
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Wei H, Zhang HL, Wang XC, Xie JZ, An DD, Wan L, Wang JZ, Zeng Y, Shu XJ, Westermarck J, Lu YM, Ohlmeyer M, Liu R. Direct Activation of Protein Phosphatase 2A (PP2A) by Tricyclic Sulfonamides Ameliorates Alzheimer's Disease Pathogenesis in Cell and Animal Models. Neurotherapeutics 2020; 17:1087-1103. [PMID: 32096091 PMCID: PMC7609734 DOI: 10.1007/s13311-020-00841-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is a multifactorial neurodegenerative disease for which there are limited therapeutic strategies. Protein phosphatase 2A (PP2A) activity is decreased in AD brains, which promotes the hyperphosphorylation of Tau and APP, thus participate in the formation of neurofibrillary tangles (NFTs) and β-amyloid (Aβ) overproduction. In this study, the effect of synthetic tricyclic sulfonamide PP2A activators (aka SMAPs) on reducing AD-like pathogenesis was evaluated in AD cell models and AD-like hyperhomocysteinemia (HHcy) rat models. SMAPs effectively increased PP2A activity, and decreased tau phosphorylation and Aβ40/42 levels in AD cell models. In HHcy-AD rat models, cognitive impairments induced by HHcy were rescued by SMAP administration. HHcy-induced tau hyperphosphorylation and Aβ overproduction were ameliorated through increasing PP2A activity on compound treatment. Importantly, SMAP therapy also prevented neuronal cell spine loss and neuronal synapse impairment in the hippocampus of HHcy-AD rats. In summary, our data reveal that pharmacological PP2A reactivation may be a novel therapeutic strategy for AD treatment, and that the tricyclic sulfonamides constitute a novel candidate class of AD therapeutic.
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Affiliation(s)
- Hui Wei
- Department of Pathophysiology, Key Laboratory of Ministry of Education for Neurological Disorders, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui-Liang Zhang
- Department of Pathophysiology, Key Laboratory of Ministry of Education for Neurological Disorders, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-Chuan Wang
- Department of Pathophysiology, Key Laboratory of Ministry of Education for Neurological Disorders, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia-Zhao Xie
- Department of Pathophysiology, Key Laboratory of Ministry of Education for Neurological Disorders, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dan-Dan An
- Department of Pathophysiology, Key Laboratory of Ministry of Education for Neurological Disorders, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lu Wan
- Department of Pathophysiology, Key Laboratory of Ministry of Education for Neurological Disorders, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jian-Zhi Wang
- Department of Pathophysiology, Key Laboratory of Ministry of Education for Neurological Disorders, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Zeng
- Clinical Laboratory, The Central Hospital of Wuhan, Wuhan, China
| | - Xi-Ji Shu
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, China
| | - Jukka Westermarck
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - You-Ming Lu
- The Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, China
| | - Michael Ohlmeyer
- Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Atux Iskay LLC, Plainsboro, NJ, USA.
| | - Rong Liu
- Department of Pathophysiology, Key Laboratory of Ministry of Education for Neurological Disorders, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- The Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, China.
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25
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Jong CJ, Merrill RA, Wilkerson EM, Herring LE, Graves LM, Strack S. Reduction of protein phosphatase 2A (PP2A) complexity reveals cellular functions and dephosphorylation motifs of the PP2A/B'δ holoenzyme. J Biol Chem 2020; 295:5654-5668. [PMID: 32156701 PMCID: PMC7186168 DOI: 10.1074/jbc.ra119.011270] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/21/2020] [Indexed: 12/17/2022] Open
Abstract
Protein phosphatase 2A (PP2A) is a large enzyme family responsible for most cellular Ser/Thr dephosphorylation events. PP2A substrate specificity, localization, and regulation by second messengers rely on more than a dozen regulatory subunits (including B/R2, B'/R5, and B″/R3), which form the PP2A heterotrimeric holoenzyme by associating with a dimer comprising scaffolding (A) and catalytic (C) subunits. Because of partial redundancy and high endogenous expression of PP2A holoenzymes, traditional approaches of overexpressing, knocking down, or knocking out PP2A regulatory subunits have yielded only limited insights into their biological roles and substrates. To this end, here we sought to reduce the complexity of cellular PP2A holoenzymes. We used tetracycline-inducible expression of pairs of scaffolding and regulatory subunits with complementary charge-reversal substitutions in their interaction interfaces. For each of the three regulatory subunit families, we engineered A/B charge-swap variants that could bind to one another, but not to endogenous A and B subunits. Because endogenous Aα was targeted by a co-induced shRNA, endogenous B subunits were rapidly degraded, resulting in expression of predominantly a single PP2A heterotrimer composed of the A/B charge-swap pair and the endogenous catalytic subunit. Using B'δ/PPP2R5D, we show that PP2A complexity reduction, but not PP2A overexpression, reveals a role of this holoenzyme in suppression of extracellular signal-regulated kinase signaling and protein kinase A substrate dephosphorylation. When combined with global phosphoproteomics, the PP2A/B'δ reduction approach identified consensus dephosphorylation motifs in its substrates and suggested that residues surrounding the phosphorylation site play roles in PP2A substrate specificity.
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Affiliation(s)
- Chian Ju Jong
- Department of Neuroscience and Pharmacology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242
| | - Ronald A Merrill
- Department of Neuroscience and Pharmacology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242
| | - Emily M Wilkerson
- Michael Hooker Proteomics Facility, University of North Carolina, Chapel Hill, North Carolina 27516
| | - Laura E Herring
- Michael Hooker Proteomics Facility, University of North Carolina, Chapel Hill, North Carolina 27516
| | - Lee M Graves
- Michael Hooker Proteomics Facility, University of North Carolina, Chapel Hill, North Carolina 27516
| | - Stefan Strack
- Department of Neuroscience and Pharmacology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242.
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26
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Zhang Y, Zhao C, Cao B, Ye J, Huang H, Hu L, Tian W, He X. Structural insights into the intramolecular interactions of centromere protein CENP-I. J Mol Recognit 2020; 33:e2837. [PMID: 32017295 DOI: 10.1002/jmr.2837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/05/2020] [Accepted: 01/14/2020] [Indexed: 01/04/2023]
Abstract
In mitosis, the accurate segregation of sister chromosomes relies on kinetochore, a multiple subunits complex assembled on centromere of each sister chromosome. As a core component of inner kinetochore, CENP-I plays important functions to mediate kinetochore assembly and supports the faithful chromosome segregation. The structures of the N-terminus and C-terminus of CENP-I homologs in complex with CENP-H/K have been reported, respectively. Unfortunately, the intramolecular interactions of CENP-I are poorly understood, and how CENP-I interacts with CENP-M remains unknown. Here, we verified a unique helix α11, which forms the intramolecular interactions with N-terminal HEAT repeats in fungal CENP-I. Deletion of the helix α11 exposed the hydrophobic surface and resulted in the in vitro protein aggregation of N-terminal HEAT repeats of fungal CENP-I. The corresponding helix and its intramolecular interaction are highly conserved in human CENP-I. Deletion of the corresponding helix in human CENP-I dramatically reduced the functional activity to interact with CENP-H and CENP-M. Mutations of the conserved residues on the helix in human CENP-I significantly weakened the binding to CENP-M, but not CENP-H, in HeLa cells. Therefore, our findings for the first time unveiled a conserved helix of CENP-I, which is important for the intramolecular interaction and function, and would be helpful for understanding the structure basis of how CENP-I mediates the kinetochore assembly during cell cycle and mitosis.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Congcong Zhao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Beibei Cao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jingjing Ye
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Huang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Liqiao Hu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Tian
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaojing He
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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27
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O'Connor CM, Leonard D, Wiredja D, Avelar RA, Wang Z, Schlatzer D, Bryson B, Tokala E, Taylor SE, Upadhyay A, Sangodkar J, Gingras AC, Westermarck J, Xu W, DiFeo A, Brautigan DL, Haider S, Jackson M, Narla G. Inactivation of PP2A by a recurrent mutation drives resistance to MEK inhibitors. Oncogene 2020; 39:703-717. [PMID: 31541192 PMCID: PMC6980487 DOI: 10.1038/s41388-019-1012-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/26/2019] [Accepted: 08/09/2019] [Indexed: 12/27/2022]
Abstract
The serine/threonine Protein Phosphatase 2A (PP2A) functions as a tumor suppressor by negatively regulating multiple oncogenic signaling pathways. The canonical PP2A holoenzyme comprises a scaffolding subunit (PP2A Aα/β), which serves as the platform for binding of both the catalytic C subunit and one regulatory B subunit. Somatic heterozygous missense mutations in PPP2R1A, the gene encoding the PP2A Aα scaffolding subunit, have been identified across multiple cancer types, but the effects of the most commonly mutated residue, Arg-183, on PP2A function have yet to be fully elucidated. In this study, we used a series of cellular and in vivo models and discovered that the most frequent Aα R183W mutation formed alternative holoenzymes by binding of different PP2A regulatory subunits compared with wild-type Aα, suggesting a rededication of PP2A functions. Unlike wild-type Aα, which suppressed tumorigenesis, the R183W mutant failed to suppress tumor growth in vivo through activation of the MAPK pathway in RAS-mutant transformed cells. Furthermore, cells expressing R183W were less sensitive to MEK inhibitors. Taken together, our results demonstrate that the R183W mutation in PP2A Aα scaffold abrogates the tumor suppressive actions of PP2A, thereby potentiating oncogenic signaling and reducing drug sensitivity of RAS-mutant cells.
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Affiliation(s)
- Caitlin M O'Connor
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Daniel Leonard
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Danica Wiredja
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA
| | - Rita A Avelar
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Zhizhi Wang
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Daniela Schlatzer
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA
| | - Benjamin Bryson
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Eesha Tokala
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah E Taylor
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Aditya Upadhyay
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Jaya Sangodkar
- Department of Internal Medicine: Genetic Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jukka Westermarck
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Wenqing Xu
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Analisa DiFeo
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
| | - David L Brautigan
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, University College London, London, UK
| | - Mark Jackson
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Goutham Narla
- Department of Internal Medicine: Genetic Medicine, University of Michigan, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
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28
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Chauhan N, Wagh V, Joshi P, Jariyal H. ATM and ATR checkpoint kinase pathways: A concise review. ADVANCES IN HUMAN BIOLOGY 2020. [DOI: 10.4103/aihb.aihb_78_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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29
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Kleinberger T. Biology of the adenovirus E4orf4 protein: from virus infection to cancer cell death. FEBS Lett 2019; 594:1891-1917. [DOI: 10.1002/1873-3468.13704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/24/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Tamar Kleinberger
- Department of Molecular Microbiology the Rappaport Faculty of Medicine Technion –Israel Institute of Technology Haifa Israel
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30
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Manalastas-Cantos K, Kschonsak M, Haering CH, Svergun DI. Solution structure and flexibility of the condensin HEAT-repeat subunit Ycg1. J Biol Chem 2019; 294:13822-13829. [PMID: 31350339 DOI: 10.1074/jbc.ra119.008661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/24/2019] [Indexed: 02/03/2023] Open
Abstract
High-resolution structural analysis of flexible proteins is frequently challenging and requires the synergistic application of different experimental techniques. For these proteins, small-angle X-ray scattering (SAXS) allows for a quantitative assessment and modeling of potentially flexible and heterogeneous structural states. Here, we report SAXS characterization of the condensin HEAT-repeat subunit Ycg1Cnd3 in solution, complementing currently available high-resolution crystallographic models. We show that the free Ycg1 subunit is flexible in solution but becomes considerably more rigid when bound to its kleisin-binding partner protein Brn1Cnd2 The analysis of SAXS and dynamic and static multiangle light scattering data furthermore reveals that Ycg1 tends to oligomerize with increasing concentrations in the absence of Brn1. Based on these data, we present a model of the free Ycg1 protein constructed by normal mode analysis, as well as tentative models of Ycg1 dimers and tetramers. These models enable visualization of the conformational transitions that Ycg1 has to undergo to adopt a closed rigid shape and thereby create a DNA-binding surface in the condensin complex.
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Affiliation(s)
| | - Marc Kschonsak
- European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | | | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22607, Germany
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31
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O'Connor CM, Hoffa MT, Taylor SE, Avelar RA, Narla G. Protein phosphatase 2A Aα regulates Aβ protein expression and stability. J Biol Chem 2019; 294:5923-5934. [PMID: 30796164 PMCID: PMC6463732 DOI: 10.1074/jbc.ra119.007593] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/14/2019] [Indexed: 11/06/2022] Open
Abstract
Protein phosphatase 2A (PP2A) represses many oncogenic signaling pathways and is an important tumor suppressor. PP2A comprises three distinct subunits and forms through a highly regulated biogenesis process, with the scaffolding A subunit existing as two highly related isoforms, Aα and Aβ. PP2A's tumor-suppressive functions have been intensely studied, and PP2A inactivation has been shown to be a prerequisite for tumor formation. Interestingly, although partial loss of the Aα isoform is growth promoting, complete Aα loss has no transformative properties. Additionally, in cancer patients, Aα is found to be inactivated in a haploinsufficient manner. Using both cellular and in vivo systems, colorectal and endometrial cancer cell lines, and biochemical and cellular assays, here we examined why the complete loss of Aα does not promote tumorigenesis. CRISPR/Cas9-mediated homozygous Aα deletion resulted in decreased colony formation and tumor growth across multiple cell lines. Protein expression analysis of PP2A family members revealed that the Aα deletion markedly up-regulates Aβ protein expression by increasing Aβ protein stability. Aβ knockdown in control and Aα knockout cell lines indicated that Aβ is necessary for cell survival in the Aα knockout cells. In the setting of Aα deficiency, co-immunoprecipitation analysis revealed increased binding of specific PP2A regulatory subunits to Aβ, and knockdown of these regulatory subunits restored colony-forming ability. Taken together, our results uncover a mechanism by which PP2A Aα regulates Aβ protein stability and activity and suggests why homozygous loss of Aα is rarely seen in cancer patients.
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Affiliation(s)
- Caitlin M O'Connor
- From the Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Matthew T Hoffa
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan, Ann Arbor, Michigan 48109
| | - Sarah E Taylor
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Rita A Avelar
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109
| | - Goutham Narla
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan, Ann Arbor, Michigan 48109.
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32
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Perez-Riba A, Synakewicz M, Itzhaki LS. Folding cooperativity and allosteric function in the tandem-repeat protein class. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0188. [PMID: 29735741 DOI: 10.1098/rstb.2017.0188] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2018] [Indexed: 01/08/2023] Open
Abstract
The term allostery was originally developed to describe structural changes in one binding site induced by the interaction of a partner molecule with a distant binding site, and it has been studied in depth in the field of enzymology. Here, we discuss the concept of action at a distance in relation to the folding and function of the solenoid class of tandem-repeat proteins such as tetratricopeptide repeats (TPRs) and ankyrin repeats. Distantly located repeats fold cooperatively, even though only nearest-neighbour interactions exist in these proteins. A number of repeat-protein scaffolds have been reported to display allosteric effects, transferred through the repeat array, that enable them to direct the activity of the multi-subunit enzymes within which they reside. We also highlight a recently identified group of tandem-repeat proteins, the RRPNN subclass of TPRs, recent crystal structures of which indicate that they function as allosteric switches to modulate multiple bacterial quorum-sensing mechanisms. We believe that the folding cooperativity of tandem-repeat proteins and the biophysical mechanisms that transform them into allosteric switches are intimately intertwined. This opinion piece aims to combine our understanding of the two areas and develop ideas on their common underlying principles.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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Affiliation(s)
- Albert Perez-Riba
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Marie Synakewicz
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
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Major P, Embley TM, Williams TA. Phylogenetic Diversity of NTT Nucleotide Transport Proteins in Free-Living and Parasitic Bacteria and Eukaryotes. Genome Biol Evol 2018; 9:480-487. [PMID: 28164241 PMCID: PMC5381601 DOI: 10.1093/gbe/evx015] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2017] [Indexed: 01/24/2023] Open
Abstract
Plasma membrane-located nucleotide transport proteins (NTTs) underpin the lifestyle of important obligate intracellular bacterial and eukaryotic pathogens by importing energy and nucleotides from infected host cells that the pathogens can no longer make for themselves. As such their presence is often seen as a hallmark of an intracellular lifestyle associated with reductive genome evolution and loss of primary biosynthetic pathways. Here, we investigate the phylogenetic distribution of NTT sequences across the domains of cellular life. Our analysis reveals an unexpectedly broad distribution of NTT genes in both host-associated and free-living prokaryotes and eukaryotes. We also identify cases of within-bacteria and bacteria-to-eukaryote horizontal NTT transfer, including into the base of the oomycetes, a major clade of parasitic eukaryotes. In addition to identifying sequences that retain the canonical NTT structure, we detected NTT gene fusions with HEAT-repeat and cyclic nucleotide binding domains in Cyanobacteria, pathogenic Chlamydiae and Oomycetes. Our results suggest that NTTs are versatile functional modules with a much wider distribution and a broader range of potential roles than has previously been appreciated.
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Affiliation(s)
- Peter Major
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - T Martin Embley
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Tom A Williams
- School of Earth Sciences, University of Bristol, United Kingdom
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Caterino M, Squillaro T, Montesarchio D, Giordano A, Giancola C, Melone MAB. Huntingtin protein: A new option for fixing the Huntington's disease countdown clock. Neuropharmacology 2018. [PMID: 29526547 DOI: 10.1016/j.neuropharm.2018.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Huntington's disease is a dreadful, incurable disorder. It springs from the autosomal dominant mutation in the first exon of the HTT gene, which encodes for the huntingtin protein (HTT) and results in progressive neurodegeneration. Thus far, all the attempted approaches to tackle the mutant HTT-induced toxicity causing this disease have failed. The mutant protein comes with the aberrantly expanded poly-glutamine tract. It is primarily to blame for the build-up of β-amyloid-like HTT aggregates, deleterious once broadened beyond the critical ∼35-37 repeats threshold. Recent experimental findings have provided valuable information on the molecular basis underlying this HTT-driven neurodegeneration. These findings indicate that the poly-glutamine siding regions and many post-translation modifications either abet or counter the poly-glutamine tract. This review provides an overall, up-to-date insight into HTT biophysics and structural biology, particularly discussing novel pharmacological options to specifically target the mutated protein and thus inhibit its functions and toxicity.
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Affiliation(s)
- Marco Caterino
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Tiziana Squillaro
- Department of Medical, Surgical, Neurological, Metabolic Sciences, and Aging, 2nd Division of Neurology, Center for Rare Diseases, University of Campania "Luigi Vanvitelli", Napoli, Italy; InterUniversity Center for Research in Neurosciences, University of Campania "Luigi Vanvitelli", Napoli, Italy
| | - Daniela Montesarchio
- InterUniversity Center for Research in Neurosciences, University of Campania "Luigi Vanvitelli", Napoli, Italy; Department of Chemical Sciences, University of Napoli Federico II, Via Cintia 21, 80126, Napoli, Italy
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA; Department of Medicine, Surgery and Neuroscience University of Siena, Siena, Italy
| | - Concetta Giancola
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy; InterUniversity Center for Research in Neurosciences, University of Campania "Luigi Vanvitelli", Napoli, Italy.
| | - Mariarosa A B Melone
- Department of Medical, Surgical, Neurological, Metabolic Sciences, and Aging, 2nd Division of Neurology, Center for Rare Diseases, University of Campania "Luigi Vanvitelli", Napoli, Italy; InterUniversity Center for Research in Neurosciences, University of Campania "Luigi Vanvitelli", Napoli, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA.
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35
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Therapeutic targeting of PP2A. Int J Biochem Cell Biol 2017; 96:182-193. [PMID: 29107183 DOI: 10.1016/j.biocel.2017.10.008] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/13/2017] [Accepted: 10/16/2017] [Indexed: 12/19/2022]
Abstract
Protein phosphatase 2A (PP2A) is a major serine/threonine phosphatase that regulates many cellular processes. Given the central role of PP2A in regulating diverse biological functions and its dysregulation in many diseases, including cancer, PP2A directed therapeutics have become of great interest. The main approaches leveraged thus far can be categorized as follows: 1) inhibiting endogenous inhibitors of PP2A, 2) targeted disruption of post translational modifications on PP2A subunits, or 3) direct targeting of PP2A. Additional insight into the structural, molecular, and biological framework driving the efficacy of these therapeutic strategies will provide a foundation for the refinement and development of novel and clinically tractable PP2A targeted therapies.
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Abstract
Huntingtin (HTT) is an essential protein during early embryogenesis and the development of the central nervous system (CNS). Conditional knock-out of mouse Huntingtin (Htt) expression in the CNS beginning during neural development, as well as reducing Htt expression only during embryonic and early postnatal stages, results in neurodegeneration in the adult brain. These findings suggest that HTT is important for the development and/or maintenance of the CNS, but they do not address the question of whether HTT is required specifically in the adult CNS for its normal functions and/or homeostasis. Recently, it was reported that although removing Htt expression in young adult mice causes lethality due to acute pancreatitis, loss of Htt expression in the adult brain is well tolerated and does not result in either motor deficits or neurodegeneration for up to 7 months after Htt inactivation. However, recent studies have also demonstrated that HTT participates in several cellular functions that are important for neuronal homeostasis and survival including sensing reactive oxygen species (ROS), DNA damage repair, and stress responses, in addition to its role in selective macroautophagy. In this review, HTT's functions in development and in the adult CNS will be discussed in the context of these recent discoveries, together with a discussion of their potential impact on the design of therapeutic strategies for Huntington's disease (HD) aimed at lowering total HTT expression.
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Affiliation(s)
| | - Scott O. Zeitlin
- Correspondence to: Scott O. Zeitlin, Ph.D., Department of Neuroscience, University of Virginia School of Medicine, 409 Lane Rd., Box 801392, MR4-5022, Charlottesville, VA 22908, USA. Tel.: +1 434 924 5011; Fax: +1 434 982 4380; E-mail:
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Maiuri T, Mocle AJ, Hung CL, Xia J, van Roon-Mom WMC, Truant R. Huntingtin is a scaffolding protein in the ATM oxidative DNA damage response complex. Hum Mol Genet 2017; 26:395-406. [PMID: 28017939 DOI: 10.1093/hmg/ddw395] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/11/2016] [Indexed: 11/15/2022] Open
Abstract
Huntington's disease (HD) is an age-dependent neurodegenerative disease. DNA repair pathways have recently been implicated as the most predominant modifiers of age of onset in HD patients. We report that endogenous huntingtin protein directly participates in oxidative DNA damage repair. Using novel chromobodies to detect endogenous human huntingtin in live cells, we show that localization of huntingtin to DNA damage sites is dependent on the kinase activity of ataxia telangiectasia mutated (ATM) protein. Super-resolution microscopy and biochemical assays revealed that huntingtin co-localizes with and scaffolds proteins of the DNA damage response pathway in response to oxidative stress. In HD patient fibroblasts bearing typical clinical HD allele lengths, we demonstrate that there is deficient oxidative DNA damage repair. We propose that DNA damage in HD is caused by dysfunction of the mutant huntingtin protein in DNA repair, and accumulation of DNA oxidative lesions due to elevated reactive oxygen species may contribute to the onset of HD.
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Affiliation(s)
- Tamara Maiuri
- Department of Biochemistry and Biomedical Research, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Canada L8N3Z5
| | - Andrew J Mocle
- Department of Biochemistry and Biomedical Research, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Canada L8N3Z5
| | - Claudia L Hung
- Department of Biochemistry and Biomedical Research, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Canada L8N3Z5
| | - Jianrun Xia
- Department of Biochemistry and Biomedical Research, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Canada L8N3Z5
| | - Willeke M C van Roon-Mom
- Center for Human and Clinical Genetics, Leiden University Medical Center, Postzone S4-0P, P.O. Box 9600 2300RC Leiden, The Netherlands
| | - Ray Truant
- Department of Biochemistry and Biomedical Research, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Canada L8N3Z5
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Ratovitski T, O’Meally RN, Jiang M, Chaerkady R, Chighladze E, Stewart JC, Wang X, Arbez N, Roby E, Alexandris A, Duan W, Vijayvargia R, Seong IS, Lavery DJ, Cole RN, Ross CA. Post-Translational Modifications (PTMs), Identified on Endogenous Huntingtin, Cluster within Proteolytic Domains between HEAT Repeats. J Proteome Res 2017; 16:2692-2708. [PMID: 28653853 PMCID: PMC5560079 DOI: 10.1021/acs.jproteome.6b00991] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Post-translational modifications (PTMs) of proteins regulate various cellular processes. PTMs of polyglutamine-expanded huntingtin (Htt) protein, which causes Huntington's disease (HD), are likely modulators of HD pathogenesis. Previous studies have identified and characterized several PTMs on exogenously expressed Htt fragments, but none of them were designed to systematically characterize PTMs on the endogenous full-length Htt protein. We found that full-length endogenous Htt, which was immunoprecipitated from HD knock-in mouse and human post-mortem brain, is suitable for detection of PTMs by mass spectrometry. Using label-free and mass tag labeling-based approaches, we identified near 40 PTMs, of which half are novel (data are available via ProteomeXchange with identifier PXD005753). Most PTMs were located in clusters within predicted unstructured domains rather than within the predicted α-helical structured HEAT repeats. Using quantitative mass spectrometry, we detected significant differences in the stoichiometry of several PTMs between HD and WT mouse brain. The mass-spectrometry identification and quantitation were verified using phospho-specific antibodies for selected PTMs. To further validate our findings, we introduced individual PTM alterations within full-length Htt and identified several PTMs that can modulate its subcellular localization in striatal cells. These findings will be instrumental in further assembling the Htt PTM framework and highlight several PTMs as potential therapeutic targets for HD.
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Affiliation(s)
- Tamara Ratovitski
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 600 North Wolfe Street, CMSC 8-121, Baltimore, Maryland 21287, United States
| | - Robert N. O’Meally
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, 733 North Broadway Street, Suite 371 BRB, Baltimore, Maryland 21287, United States
| | - Mali Jiang
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 600 North Wolfe Street, CMSC 8-121, Baltimore, Maryland 21287, United States
| | - Raghothama Chaerkady
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, 733 North Broadway Street, Suite 371 BRB, Baltimore, Maryland 21287, United States
| | - Ekaterine Chighladze
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 600 North Wolfe Street, CMSC 8-121, Baltimore, Maryland 21287, United States
| | - Jacqueline C. Stewart
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 600 North Wolfe Street, CMSC 8-121, Baltimore, Maryland 21287, United States
| | - Xiaofang Wang
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 600 North Wolfe Street, CMSC 8-121, Baltimore, Maryland 21287, United States
| | - Nicolas Arbez
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 600 North Wolfe Street, CMSC 8-121, Baltimore, Maryland 21287, United States
| | - Elaine Roby
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 600 North Wolfe Street, CMSC 8-121, Baltimore, Maryland 21287, United States
| | - Athanasios Alexandris
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 600 North Wolfe Street, CMSC 8-121, Baltimore, Maryland 21287, United States
| | - Wenzhen Duan
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 600 North Wolfe Street, CMSC 8-121, Baltimore, Maryland 21287, United States
- Department of Neurology and Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
- Departments of Pharmacology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
| | - Ravi Vijayvargia
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ihn Sik Seong
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Daniel J. Lavery
- CHDI Foundation/CHDI Management, Inc., Princeton, New Jersey 08540, United States
| | - Robert N. Cole
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, 733 North Broadway Street, Suite 371 BRB, Baltimore, Maryland 21287, United States
| | - Christopher A. Ross
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 600 North Wolfe Street, CMSC 8-121, Baltimore, Maryland 21287, United States
- Department of Neurology and Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
- Departments of Pharmacology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
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Blackford AN, Jackson SP. ATM, ATR, and DNA-PK: The Trinity at the Heart of the DNA Damage Response. Mol Cell 2017; 66:801-817. [PMID: 28622525 DOI: 10.1016/j.molcel.2017.05.015] [Citation(s) in RCA: 1151] [Impact Index Per Article: 164.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/28/2017] [Accepted: 05/16/2017] [Indexed: 01/09/2023]
Abstract
In vertebrate cells, the DNA damage response is controlled by three related kinases: ATM, ATR, and DNA-PK. It has been 20 years since the cloning of ATR, the last of the three to be identified. During this time, our understanding of how these kinases regulate DNA repair and associated events has grown profoundly, although major questions remain unanswered. Here, we provide a historical perspective of their discovery and discuss their established functions in sensing and responding to genotoxic stress. We also highlight what is known regarding their structural similarities and common mechanisms of regulation, as well as emerging non-canonical roles and how our knowledge of ATM, ATR, and DNA-PK is being translated to benefit human health.
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Affiliation(s)
- Andrew N Blackford
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
| | - Stephen P Jackson
- Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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40
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Abstract
The Thomas Hunt Morgan Medal is awarded to an individual Genetics Society of America member for lifetime achievement in the field of genetics. It recognizes the full body of work of an exceptional geneticist. The 2016 recipient is Nancy Kleckner, who has made many significant contributions to our understanding of chromosomes and the mechanisms of inheritance. Kleckner has made seminal achievements in several different research areas, including bacterial transposition, chromosome organization, and meiosis. She has repeatedly combined traditional genetic approaches with molecular biology, microscopy, physics, and modeling-unprecedented applications of these methods at the time, but which have now become commonplace. Indeed, she is widely recognized as one of the leaders in bringing meiosis research into the modern era. Notably, her laboratory played a key role in elucidating the mechanism that initiates meiotic recombination, has helped to decipher the "strand gymnastics" of recombination, and is beginning to provide insight into the enigmatic phenomenon of crossover interference.
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41
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Golloshi R, Sanders JT, McCord RP. Genome organization during the cell cycle: unity in division. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 9. [PMID: 28510289 DOI: 10.1002/wsbm.1389] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/12/2017] [Accepted: 03/14/2017] [Indexed: 12/11/2022]
Abstract
During the cell cycle, the genome must undergo dramatic changes in structure, from a decondensed, yet highly organized interphase structure to a condensed, generic mitotic chromosome and then back again. For faithful cell division, the genome must be replicated and chromosomes and sister chromatids physically segregated from one another. Throughout these processes, there is feedback and tension between the information-storing role and the physical properties of chromosomes. With a combination of recent techniques in fluorescence microscopy, chromosome conformation capture (Hi-C), biophysical experiments, and computational modeling, we can now attribute mechanisms to many long-observed features of chromosome structure changes during cell division. Apparent conflicts that arise when integrating the concepts from these different proposed mechanisms emphasize that orchestrating chromosome organization during cell division requires a complex system of factors rather than a simple pathway. Cell division is both essential for and threatening to proper genome organization. As interphase three-dimensional (3D) genome structure is quite static at a global level, cell division provides an important window of opportunity to make substantial changes in 3D genome organization in daughter cells, allowing for proper differentiation and development. Mistakes in the process of chromosome condensation or rebuilding the structure after mitosis can lead to diseases such as cancer, premature aging, and neurodegeneration. WIREs Syst Biol Med 2017, 9:e1389. doi: 10.1002/wsbm.1389 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Rosela Golloshi
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
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42
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Thomason PA, King JS, Insall RH. Mroh1, a lysosomal regulator localized by WASH-generated actin. J Cell Sci 2017; 130:1785-1795. [PMID: 28424231 PMCID: PMC5450189 DOI: 10.1242/jcs.197210] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/29/2017] [Indexed: 02/06/2023] Open
Abstract
The steps leading to constitutive exocytosis are poorly understood. In Dictyostelium WASH complex mutants, exocytosis is blocked, so cells that take up fluorescent dextran from the medium retain it and remain fluorescent. Here, we establish a FACS-based method to select cells that retain fluorescent dextran, allowing identification of mutants with disrupted exocytosis. Screening a pool of random mutants identified members of the WASH complex, as expected, and multiple mutants in the conserved HEAT-repeat-containing protein Mroh1. In mroh1 mutants, endosomes develop normally until the stage where lysosomes neutralize to postlysosomes, but thereafter the WASH complex is recycled inefficiently, and subsequent exocytosis is substantially delayed. Mroh1 protein localizes to lysosomes in mammalian and Dictyostelium cells. In Dictyostelium, it accumulates on lysosomes as they mature and is removed, together with the WASH complex, shortly before the postlysosomes are exocytosed. WASH-generated F-actin is required for correct subcellular localization; in WASH complex mutants, and immediately after latrunculin treatment, Mroh1 relocalizes from the cytoplasm to small vesicles. Thus, Mroh1 is involved in a late and hitherto undefined actin-dependent step in exocytosis.
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Affiliation(s)
- Peter A Thomason
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Jason S King
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Robert H Insall
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
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43
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Kinoshita K, Hirano T. Dynamic organization of mitotic chromosomes. Curr Opin Cell Biol 2017; 46:46-53. [PMID: 28214612 DOI: 10.1016/j.ceb.2017.01.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/30/2017] [Indexed: 12/19/2022]
Abstract
The assembly of rod-shaped chromosomes during mitosis is an essential prerequisite for faithful segregation of genetic information into daughter cells. Despite the long history of chromosome research, it is only recently that we have acquired powerful approaches and crucial tools that help to unlock the secret of this seemingly complex process. In particular, in vitro assays, mammalian genetics, Hi-C analyses and computer simulations have provided valuable information during the past two years. These studies are now beginning to elucidate how the core components of mitotic chromosomes, namely, histones, topoisomerase IIα and condensins, cooperate with each other to convert very long stretches of DNA into rod-shaped chromosomes.
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Affiliation(s)
- Kazuhisa Kinoshita
- Chromosome Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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44
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Cretu C, Schmitzová J, Ponce-Salvatierra A, Dybkov O, De Laurentiis EI, Sharma K, Will CL, Urlaub H, Lührmann R, Pena V. Molecular Architecture of SF3b and Structural Consequences of Its Cancer-Related Mutations. Mol Cell 2016; 64:307-319. [PMID: 27720643 DOI: 10.1016/j.molcel.2016.08.036] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/25/2016] [Accepted: 08/30/2016] [Indexed: 11/17/2022]
Abstract
SF3b is a heptameric protein complex of the U2 small nuclear ribonucleoprotein (snRNP) that is essential for pre-mRNA splicing. Mutations in the largest SF3b subunit, SF3B1/SF3b155, are linked to cancer and lead to alternative branch site (BS) selection. Here we report the crystal structure of a human SF3b core complex, revealing how the distinctive conformation of SF3b155's HEAT domain is maintained by multiple contacts with SF3b130, SF3b10, and SF3b14b. Protein-protein crosslinking enabled the localization of the BS-binding proteins p14 and U2AF65 within SF3b155's HEAT-repeat superhelix, which together with SF3b14b forms a composite RNA-binding platform. SF3b155 residues, the mutation of which leads to cancer, contribute to the tertiary structure of the HEAT superhelix and its surface properties in the proximity of p14 and U2AF65. The molecular architecture of SF3b reveals the spatial organization of cancer-related SF3b155 mutations and advances our understanding of their effects on SF3b structure and function.
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Affiliation(s)
- Constantin Cretu
- Research Group Macromolecular Crystallography, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jana Schmitzová
- Research Group Macromolecular Crystallography, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Almudena Ponce-Salvatierra
- Research Group Macromolecular Crystallography, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Max Planck Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Olexandr Dybkov
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Evelina I De Laurentiis
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kundan Sharma
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Vladimir Pena
- Research Group Macromolecular Crystallography, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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45
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Yoshimura SH, Hirano T. HEAT repeats - versatile arrays of amphiphilic helices working in crowded environments? J Cell Sci 2016; 129:3963-3970. [PMID: 27802131 DOI: 10.1242/jcs.185710] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cellular proteins do not work in isolation. Instead, they often function as part of large macromolecular complexes, which are transported and concentrated into specific cellular compartments and function in a highly crowded environment. A central theme of modern cell biology is to understand how such macromolecular complexes are assembled efficiently and find their destinations faithfully. In this Opinion article, we will focus on HEAT repeats, flexible arrays of amphiphilic helices found in many eukaryotic proteins, such as karyopherins and condensins, and discuss how these uniquely designed helical repeats might underlie dynamic protein-protein interactions and support cellular functions in crowded environments. We will make bold speculations on functional similarities between the action of HEAT repeats and intrinsically disordered regions (IDRs) in macromolecular phase separation. Potential contributions of HEAT-HEAT interactions, as well as cooperation between HEATs and IDRs, to mesoscale organelle assembly will be discussed.
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Affiliation(s)
- Shige H Yoshimura
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN, Saitama 351-0198, Japan
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Abstract
Studying protein folding and protein design in globular proteins presents significant challenges because of the two related features, topological complexity and co-operativity. In contrast, tandem-repeat proteins have regular and modular structures composed of linearly arrayed motifs. This means that the biophysics of even giant repeat proteins is highly amenable to dissection and to rational design. Here we discuss what has been learnt about the folding mechanisms of tandem-repeat proteins. The defining features that have emerged are: (i) accessibility of multiple distinct routes between denatured and native states, both at equilibrium and under kinetic conditions; (ii) different routes are favoured for folding compared with unfolding; (iii) unfolding energy barriers are broad, reflecting stepwise unravelling of an array repeat by repeat; (iv) highly co-operative unfolding at equilibrium and the potential for exceptionally high thermodynamic stabilities by introducing consensus residues; (v) under force, helical-repeat structures are very weak with non-co-operative unfolding leading to elasticity and buffering effects. This level of understanding should enable us to create repeat proteins with made-to-measure folding mechanisms, in which one can dial into the sequence the order of repeat folding, number of pathways taken, step size (co-operativity) and fine-structure of the kinetic energy barriers.
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Rakesh R, Joseph AP, Bhaskara RM, Srinivasan N. Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps. RNA Biol 2016; 13:1025-1040. [PMID: 27618338 DOI: 10.1080/15476286.2016.1218590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Pre-mRNA splicing in eukaryotes is performed by the spliceosome, a highly complex macromolecular machine. SF3b is a multi-protein complex which recognizes the branch point adenosine of pre-mRNA as part of a larger U2 snRNP or U11/U12 di-snRNP in the dynamic spliceosome machinery. Although a cryo-EM map is available for human SF3b complex, the structure and relative spatial arrangement of all components in the complex are not yet known. We have recognized folds of domains in various proteins in the assembly and generated comparative models. Using an integrative approach involving structural and other experimental data, guided by the available cryo-EM density map, we deciphered a pseudo-atomic model of the closed form of SF3b which is found to be a "fuzzy complex" with highly flexible components and multiplicity of folds. Further, the model provides structural information for 5 proteins (SF3b10, SF3b155, SF3b145, SF3b130 and SF3b14b) and localization information for 4 proteins (SF3b10, SF3b145, SF3b130 and SF3b14b) in the assembly for the first time. Integration of this model with the available U11/U12 di-snRNP cryo-EM map enabled elucidation of an open form. This now provides new insights on the mechanistic features involved in the transition between closed and open forms pivoted by a hinge region in the SF3b155 protein that also harbors cancer causing mutations. Moreover, the open form guided model of the 5' end of U12 snRNA, which includes the branch point duplex, shows that the architecture of SF3b acts as a scaffold for U12 snRNA: pre-mRNA branch point duplex formation with potential implications for branch point adenosine recognition fidelity.
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Affiliation(s)
- Ramachandran Rakesh
- a Molecular Biophysics Unit, Indian Institute of Science , Bangalore , India
| | - Agnel Praveen Joseph
- b National Center for Biological Sciences, TIFR, GKVK Campus , Bangalore , India
| | - Ramachandra M Bhaskara
- a Molecular Biophysics Unit, Indian Institute of Science , Bangalore , India.,b National Center for Biological Sciences, TIFR, GKVK Campus , Bangalore , India
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Abstract
ATR (Ataxia Telangiectasia and Rad3-related) is a member of the Phosphatidylinositol 3-kinase-related kinases (PIKKs) family, amongst six other vertebrate proteins known so far. ATR is indispensable for cell survival and its essential role is in sensing DNA damage and initiating appropriate repair responses. In this review we highlight emerging and recent observations connecting ATR to alternative roles in controlling the nuclear envelope, nucleolus, centrosome and other organelles in response to both internal and external stress conditions. We propose that ATR functions control cell plasticity by sensing structural deformations of different cellular components, including DNA and initiating appropriate repair responses, most of which are yet to be understood completely.
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Affiliation(s)
- Gururaj Rao Kidiyoor
- Istituto FIRC di Oncologia Molecolare, Milan, Italy; University of Milan, Milan, Italy
| | - Amit Kumar
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, M.G. Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), India
| | - Marco Foiani
- Istituto FIRC di Oncologia Molecolare, Milan, Italy; University of Milan, Milan, Italy.
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Vijayvargia R, Epand R, Leitner A, Jung TY, Shin B, Jung R, Lloret A, Singh Atwal R, Lee H, Lee JM, Aebersold R, Hebert H, Song JJ, Seong IS. Huntingtin's spherical solenoid structure enables polyglutamine tract-dependent modulation of its structure and function. eLife 2016; 5:e11184. [PMID: 27003594 PMCID: PMC4846397 DOI: 10.7554/elife.11184] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 03/13/2016] [Indexed: 11/14/2022] Open
Abstract
The polyglutamine expansion in huntingtin protein causes Huntington’s disease. Here, we investigated structural and biochemical properties of huntingtin and the effect of the polyglutamine expansion using various biophysical experiments including circular dichroism, single-particle electron microscopy and cross-linking mass spectrometry. Huntingtin is likely composed of five distinct domains and adopts a spherical α-helical solenoid where the amino-terminal and carboxyl-terminal regions fold to contain a circumscribed central cavity. Interestingly, we showed that the polyglutamine expansion increases α-helical properties of huntingtin and affects the intramolecular interactions among the domains. Our work delineates the structural characteristics of full-length huntingtin, which are affected by the polyglutamine expansion, and provides an elegant solution to the apparent conundrum of how the extreme amino-terminal polyglutamine tract confers a novel property on huntingtin, causing the disease. DOI:http://dx.doi.org/10.7554/eLife.11184.001 Huntington’s disease is an inherited disorder that occurs in adulthood and sometimes in children. It causes progressive damage to the brain and people with the condition develop memory loss, movement difficulties, confusion, and other symptoms of mental decline. Eventually, the disease leads to death. Mutations in the gene that encodes a protein called huntingtin cause Huntington’s disease. Individuals who inherit just one copy of the mutated gene develop the condition. No treatments currently exist that can slow or stop disease progression. Genetic and molecular studies are beginning to shed light on how mutations in the gene encoding huntingtin cause the disease. Normally, the protein has a section near its tail end made up of the amino acid glutamine repeated around 23 times. Mutations that increase the number of glutamines to more than 38 cause Huntington’s disease. The more extra glutamines there are in this region of the protein, the earlier in life the disease symptoms begin. But it was not clear how these extra glutamines near the tail of huntingtin affect the structure and behavior of a protein that is more than 3,000 amino acids long. Now, Vijayvargia et al. have revealed why the tail end of huntingtin is so important. Several biophysical methods were used to determine the three-dimensional structure of the huntingtin protein. These methods revealed that the protein folds up into a hollow sphere and that its tail end is able to interact with the entire length of the protein and physically touches its opposite end. To see this in more detail, Vijayvargia et al. used another experimental technique called crosslinking mass spectrometry to confirm which parts of the huntingtin protein are in close contact with each other. Together with the structural data, these experiments suggest that the stretch of glutamines is in the position to bring about subtle, but widespread, changes throughout the huntingtin protein. That is to say, that having more glutamines slightly changes the curve of the sphere and alters the way different parts of the protein interact. Together the new findings explain why mutations that alter the tail of huntingtin affect the rest of the protein. Further work will now aim to provide a more-detailed structure of the huntingtin protein and to investigate what other roles of huntingtin are affected by the increased number of glutamines in the protein’s tail. These insights may help scientists understand how the mutated protein causes brain decline. DOI:http://dx.doi.org/10.7554/eLife.11184.002
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Affiliation(s)
- Ravi Vijayvargia
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, United States.,Department of Neurology, Harvard Medical School, Boston, United States
| | - Raquel Epand
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Tae-Yang Jung
- Department of Biological Sciences, Cancer Metastasis Control Center, KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.,Department of Biosciences and Nutrition, Karolinska Institute, Solna, Sweden.,School of Technology and Health, KTH Royal Institute of Technology, Novum, Sweden
| | - Baehyun Shin
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, United States.,Department of Neurology, Harvard Medical School, Boston, United States
| | - Roy Jung
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, United States.,Department of Neurology, Harvard Medical School, Boston, United States
| | - Alejandro Lloret
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, United States.,Department of Neurology, Harvard Medical School, Boston, United States
| | - Randy Singh Atwal
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, United States.,Department of Neurology, Harvard Medical School, Boston, United States
| | - Hyeongseok Lee
- Department of Biological Sciences, Cancer Metastasis Control Center, KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jong-Min Lee
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, United States.,Department of Neurology, Harvard Medical School, Boston, United States
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Hans Hebert
- Department of Biosciences and Nutrition, Karolinska Institute, Solna, Sweden.,School of Technology and Health, KTH Royal Institute of Technology, Novum, Sweden
| | - Ji-Joon Song
- Department of Biological Sciences, Cancer Metastasis Control Center, KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Ihn Sik Seong
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, United States.,Department of Neurology, Harvard Medical School, Boston, United States
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50
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Abstract
Condensins are large protein complexes that play a central role in chromosome organization and segregation in the three domains of life. They display highly characteristic, rod-shaped structures with SMC (structural maintenance of chromosomes) ATPases as their core subunits and organize large-scale chromosome structure through active mechanisms. Most eukaryotic species have two distinct condensin complexes whose balanced usage is adapted flexibly to different organisms and cell types. Studies of bacterial condensins provide deep insights into the fundamental mechanisms of chromosome segregation. This Review surveys both conserved features and rich variations of condensin-based chromosome organization and discusses their evolutionary implications.
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Affiliation(s)
- Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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