151
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DeLuca KF, Meppelink A, Broad AJ, Mick JE, Peersen OB, Pektas S, Lens SMA, DeLuca JG. Aurora A kinase phosphorylates Hec1 to regulate metaphase kinetochore-microtubule dynamics. J Cell Biol 2017; 217:163-177. [PMID: 29187526 PMCID: PMC5748988 DOI: 10.1083/jcb.201707160] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 10/23/2017] [Accepted: 10/30/2017] [Indexed: 01/04/2023] Open
Abstract
Precise regulation of kinetochore-microtubule attachments is essential for successful chromosome segregation. Central to this regulation is Aurora B kinase, which phosphorylates kinetochore substrates to promote microtubule turnover. A critical target of Aurora B is the N-terminal "tail" domain of Hec1, which is a component of the NDC80 complex, a force-transducing link between kinetochores and microtubules. Although Aurora B is regarded as the "master regulator" of kinetochore-microtubule attachment, other mitotic kinases likely contribute to Hec1 phosphorylation. In this study, we demonstrate that Aurora A kinase regulates kinetochore-microtubule dynamics of metaphase chromosomes, and we identify Hec1 S69, a previously uncharacterized phosphorylation target site in the Hec1 tail, as a critical Aurora A substrate for this regulation. Additionally, we demonstrate that Aurora A kinase associates with inner centromere protein (INCENP) during mitosis and that INCENP is competent to drive accumulation of the kinase to the centromere region of mitotic chromosomes. These findings reveal that both Aurora A and B contribute to kinetochore-microtubule attachment dynamics, and they uncover an unexpected role for Aurora A in late mitosis.
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Affiliation(s)
- Keith F DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO
| | - Amanda Meppelink
- Oncode Institute, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Amanda J Broad
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO
| | - Jeanne E Mick
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO
| | - Olve B Peersen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO
| | - Sibel Pektas
- Oncode Institute, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Susanne M A Lens
- Oncode Institute, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Jennifer G DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO
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152
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Toyoda Y, Cattin CJ, Stewart MP, Poser I, Theis M, Kurzchalia TV, Buchholz F, Hyman AA, Müller DJ. Genome-scale single-cell mechanical phenotyping reveals disease-related genes involved in mitotic rounding. Nat Commun 2017; 8:1266. [PMID: 29097687 PMCID: PMC5668354 DOI: 10.1038/s41467-017-01147-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/22/2017] [Indexed: 01/01/2023] Open
Abstract
To divide, most animal cells drastically change shape and round up against extracellular confinement. Mitotic cells facilitate this process by generating intracellular pressure, which the contractile actomyosin cortex directs into shape. Here, we introduce a genome-scale microcantilever- and RNAi-based approach to phenotype the contribution of > 1000 genes to the rounding of single mitotic cells against confinement. Our screen analyzes the rounding force, pressure and volume of mitotic cells and localizes selected proteins. We identify 49 genes relevant for mitotic rounding, a large portion of which have not previously been linked to mitosis or cell mechanics. Among these, depleting the endoplasmic reticulum-localized protein FAM134A impairs mitotic progression by affecting metaphase plate alignment and pressure generation by delocalizing cortical myosin II. Furthermore, silencing the DJ-1 gene uncovers a link between mitochondria-associated Parkinson's disease and mitotic pressure. We conclude that mechanical phenotyping is a powerful approach to study the mechanisms governing cell shape.
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Affiliation(s)
- Yusuke Toyoda
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.,Division of Cell Biology, Life Science Institute, Kurume University, Hyakunen-Kohen 1-1, Kurume, Fukuoka, 839-0864, Japan
| | - Cedric J Cattin
- Department of Biosystems Science and Engineering (D-BSSE), Eidgenössische Technische Hochschule (ETH) Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Martin P Stewart
- Department of Biosystems Science and Engineering (D-BSSE), Eidgenössische Technische Hochschule (ETH) Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.,Department of Chemical Engineering, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139-4307, USA.,The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139-4307, USA
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Mirko Theis
- UCC, Medical System biology, Medical Faculty Carl Gustav Carus, University of Technology Dresden, Am Tatzberg 47/49, 01307, Dresden, Germany
| | - Teymuras V Kurzchalia
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Frank Buchholz
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.,UCC, Medical System biology, Medical Faculty Carl Gustav Carus, University of Technology Dresden, Am Tatzberg 47/49, 01307, Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.
| | - Daniel J Müller
- Department of Biosystems Science and Engineering (D-BSSE), Eidgenössische Technische Hochschule (ETH) Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.
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153
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Ly T, Whigham A, Clarke R, Brenes-Murillo AJ, Estes B, Madhessian D, Lundberg E, Wadsworth P, Lamond AI. Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS. eLife 2017; 6:e27574. [PMID: 29052541 PMCID: PMC5650473 DOI: 10.7554/elife.27574] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 10/06/2017] [Indexed: 12/22/2022] Open
Abstract
The temporal regulation of protein abundance and post-translational modifications is a key feature of cell division. Recently, we analysed gene expression and protein abundance changes during interphase under minimally perturbed conditions (Ly et al., 2014, 2015). Here, we show that by using specific intracellular immunolabelling protocols, FACS separation of interphase and mitotic cells, including mitotic subphases, can be combined with proteomic analysis by mass spectrometry. Using this PRIMMUS (PRoteomic analysis of Intracellular iMMUnolabelled cell Subsets) approach, we now compare protein abundance and phosphorylation changes in interphase and mitotic fractions from asynchronously growing human cells. We identify a set of 115 phosphorylation sites increased during G2, termed 'early risers'. This set includes phosphorylation of S738 on TPX2, which we show is important for TPX2 function and mitotic progression. Further, we use PRIMMUS to provide the first a proteome-wide analysis of protein abundance remodeling between prophase, prometaphase and anaphase.
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Affiliation(s)
- Tony Ly
- Centre for Gene Regulation and Expression, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
- Wellcome Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
| | - Arlene Whigham
- CAST Flow Cytometry Facility, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Rosemary Clarke
- CAST Flow Cytometry Facility, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Alejandro J Brenes-Murillo
- Centre for Gene Regulation and Expression, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Brett Estes
- Department of BiologyUniversity of MassachusettsMassachusettsUnited States
- Program in Molecular and Cellular BiologyUniversity of MassachusettsMassachusettsUnited States
| | - Diana Madhessian
- Science for Life LaboratoryRoyal Institute of TechnologyStockholmSweden
| | - Emma Lundberg
- Science for Life LaboratoryRoyal Institute of TechnologyStockholmSweden
| | - Patricia Wadsworth
- Department of BiologyUniversity of MassachusettsMassachusettsUnited States
- Program in Molecular and Cellular BiologyUniversity of MassachusettsMassachusettsUnited States
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
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154
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Ali A, Veeranki SN, Chinchole A, Tyagi S. MLL/WDR5 Complex Regulates Kif2A Localization to Ensure Chromosome Congression and Proper Spindle Assembly during Mitosis. Dev Cell 2017. [PMID: 28633016 DOI: 10.1016/j.devcel.2017.05.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mixed-lineage leukemia (MLL), along with multisubunit (WDR5, RbBP5, ASH2L, and DPY30) complex catalyzes the trimethylation of H3K4, leading to gene activation. Here, we characterize a chromatin-independent role for MLL during mitosis. MLL and WDR5 localize to the mitotic spindle apparatus, and loss of function of MLL complex by RNAi results in defects in chromosome congression and compromised spindle formation. We report interaction of MLL complex with several kinesin and dynein motors. We further show that the MLL complex associates with Kif2A, a member of the Kinesin-13 family of microtubule depolymerase, and regulates the spindle localization of Kif2A during mitosis. We have identified a conserved WDR5 interaction (Win) motif, so far unique to the MLL family, in Kif2A. The Win motif of Kif2A engages in direct interactions with WDR5 for its spindle localization. Our findings highlight a non-canonical mitotic function of MLL complex, which may have a direct impact on chromosomal stability, frequently compromised in cancer.
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Affiliation(s)
- Aamir Ali
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, India; Graduate Studies, Manipal University, Manipal, India
| | - Sailaja Naga Veeranki
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, India
| | - Akash Chinchole
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, India; Graduate Studies, Manipal University, Manipal, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, India.
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155
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Rhodes J, Mazza D, Nasmyth K, Uphoff S. Scc2/Nipbl hops between chromosomal cohesin rings after loading. eLife 2017; 6:e30000. [PMID: 28914604 PMCID: PMC5621834 DOI: 10.7554/elife.30000] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/08/2017] [Indexed: 11/13/2022] Open
Abstract
The cohesin complex mediates DNA-DNA interactions both between (sister chromatid cohesion) and within chromosomes (DNA looping). It has been suggested that intra-chromosome loops are generated by extrusion of DNAs through the lumen of cohesin's ring. Scc2 (Nipbl) stimulates cohesin's ABC-like ATPase and is essential for loading cohesin onto chromosomes. However, it is possible that the stimulation of cohesin's ATPase by Scc2 also has a post-loading function, for example driving loop extrusion. Using fluorescence recovery after photobleaching (FRAP) and single-molecule tracking in human cells, we show that Scc2 binds dynamically to chromatin, principally through an association with cohesin. Scc2's movement within chromatin is consistent with a 'stop-and-go' or 'hopping' motion. We suggest that a low diffusion coefficient, a low stoichiometry relative to cohesin, and a high affinity for chromosomal cohesin enables Scc2 to move rapidly from one chromosomal cohesin complex to another, performing a function distinct from loading.
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Affiliation(s)
- James Rhodes
- Department of BiochemistryOxford UniversityOxfordUnited Kingdom
| | - Davide Mazza
- Istituto Scientifico Ospedale San RaffaeleCentro di Imaging SperimentaleMilanoItaly
- Fondazione CENEuropean Center for NanomedicineMilanoItaly
| | - Kim Nasmyth
- Department of BiochemistryOxford UniversityOxfordUnited Kingdom
| | - Stephan Uphoff
- Department of BiochemistryOxford UniversityOxfordUnited Kingdom
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156
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Üretmen Kagıalı ZC, Şentürk A, Özkan Küçük NE, Qureshi MH, Özlü N. Proteomics in Cell Division. Proteomics 2017; 17. [PMID: 28548456 DOI: 10.1002/pmic.201600100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/07/2017] [Indexed: 11/08/2022]
Abstract
Cell division requires a coordinated action of the cell cycle machinery, cytoskeletal elements, chromosomes, and membranes. Cell division studies have greatly benefitted from the mass spectrometry (MS)-based proteomic approaches for probing the biochemistry of highly dynamic complexes and their coordination with each other as a cell progresses into division. In this review, the authors first summarize a wide-range of proteomic studies that focus on the identification of sub-cellular components/protein complexes of the cell division machinery including kinetochores, mitotic spindle, midzone, and centrosomes. The authors also highlight MS-based large-scale analyses of the cellular components that are largely understudied during cell division such as the cell surface and lipids. Then, the authors focus on posttranslational modification analyses, especially phosphorylation and the resulting crosstalk with other modifications as a cell undergoes cell division. Combining proteomic approaches that probe the biochemistry of cell division components with functional genomic assays will lead to breakthroughs toward a systems-level understanding of cell division.
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Affiliation(s)
| | - Aydanur Şentürk
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | | | - Mohammad Haroon Qureshi
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey.,Biomedical Sciences and Engineering, Koç University, Istanbul, Turkey
| | - Nurhan Özlü
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
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157
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Schmidt R, Fielmich LE, Grigoriev I, Katrukha EA, Akhmanova A, van den Heuvel S. Two populations of cytoplasmic dynein contribute to spindle positioning in C. elegans embryos. J Cell Biol 2017; 216:2777-2793. [PMID: 28739679 PMCID: PMC5584144 DOI: 10.1083/jcb.201607038] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 05/08/2017] [Accepted: 06/28/2017] [Indexed: 12/14/2022] Open
Abstract
The position of the mitotic spindle is tightly controlled in animal cells as it determines the plane and orientation of cell division. Contacts between cytoplasmic dynein and astral microtubules (MTs) at the cell cortex generate pulling forces that position the spindle. An evolutionarily conserved Gα-GPR-1/2Pins/LGN-LIN-5Mud/NuMA cortical complex interacts with dynein and is required for pulling force generation, but the dynamics of this process remain unclear. In this study, by fluorescently labeling endogenous proteins in Caenorhabditis elegans embryos, we show that dynein exists in two distinct cortical populations. One population directly depends on LIN-5, whereas the other is concentrated at MT plus ends and depends on end-binding (EB) proteins. Knockout mutants lacking all EBs are viable and fertile and display normal pulling forces and spindle positioning. However, EB protein-dependent dynein plus end tracking was found to contribute to force generation in embryos with a partially perturbed dynein function, indicating the existence of two mechanisms that together create a highly robust force-generating system.
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Affiliation(s)
- Ruben Schmidt
- Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, Netherlands
- Cell Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, Netherlands
| | - Lars-Eric Fielmich
- Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, Netherlands
| | - Ilya Grigoriev
- Cell Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, Netherlands
| | - Eugene A Katrukha
- Cell Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, Netherlands
| | - Anna Akhmanova
- Cell Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, Netherlands
| | - Sander van den Heuvel
- Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, Netherlands
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158
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di Pietro F, Valon L, Li Y, Goïame R, Genovesio A, Morin X. An RNAi Screen in a Novel Model of Oriented Divisions Identifies the Actin-Capping Protein Z β as an Essential Regulator of Spindle Orientation. Curr Biol 2017; 27:2452-2464.e8. [PMID: 28803871 DOI: 10.1016/j.cub.2017.06.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 05/06/2017] [Accepted: 06/20/2017] [Indexed: 10/19/2022]
Abstract
Oriented cell divisions are controlled by a conserved molecular cascade involving Gαi, LGN, and NuMA. We developed a new cellular model of oriented cell divisions combining micropatterning and localized recruitment of Gαi and performed an RNAi screen for regulators acting downstream of Gαi. Remarkably, this screen revealed a unique subset of dynein regulators as being essential for spindle orientation, shedding light on a core regulatory aspect of oriented divisions. We further analyze the involvement of one novel regulator, the actin-capping protein CAPZB. Mechanistically, we show that CAPZB controls spindle orientation independently of its classical role in the actin cytoskeleton by regulating the assembly, stability, and motor activity of the dynein/dynactin complex at the cell cortex, as well as the dynamics of mitotic microtubules. Finally, we show that CAPZB controls planar divisions in vivo in the developing neuroepithelium. This demonstrates the power of this in cellulo model of oriented cell divisions to uncover new genes required in spindle orientation in vertebrates.
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Affiliation(s)
- Florencia di Pietro
- Cell Division and Neurogenesis, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France; Sorbonne Universités, UPMC Université Paris 06, IFD, 4 Place Jussieu, 75252 Paris, France
| | - Léo Valon
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS, UPMC Université Paris 06, 75005 Paris, France
| | - Yingbo Li
- Cell Division and Neurogenesis, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France; Scientific Center for Computational Biology, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France
| | - Rosette Goïame
- Cell Division and Neurogenesis, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France
| | - Auguste Genovesio
- Scientific Center for Computational Biology, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France
| | - Xavier Morin
- Cell Division and Neurogenesis, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France.
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159
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Yalçın B, Zhao L, Stofanko M, O'Sullivan NC, Kang ZH, Roost A, Thomas MR, Zaessinger S, Blard O, Patto AL, Sohail A, Baena V, Terasaki M, O'Kane CJ. Modeling of axonal endoplasmic reticulum network by spastic paraplegia proteins. eLife 2017; 6. [PMID: 28742022 PMCID: PMC5576921 DOI: 10.7554/elife.23882] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 07/24/2017] [Indexed: 01/17/2023] Open
Abstract
Axons contain a smooth tubular endoplasmic reticulum (ER) network that is thought to be continuous with ER throughout the neuron; the mechanisms that form this axonal network are unknown. Mutations affecting reticulon or REEP proteins, with intramembrane hairpin domains that model ER membranes, cause an axon degenerative disease, hereditary spastic paraplegia (HSP). We show that Drosophila axons have a dynamic axonal ER network, which these proteins help to model. Loss of HSP hairpin proteins causes ER sheet expansion, partial loss of ER from distal motor axons, and occasional discontinuities in axonal ER. Ultrastructural analysis reveals an extensive ER network in axons, which shows larger and fewer tubules in larvae that lack reticulon and REEP proteins, consistent with loss of membrane curvature. Therefore HSP hairpin-containing proteins are required for shaping and continuity of axonal ER, thus suggesting roles for ER modeling in axon maintenance and function. DOI:http://dx.doi.org/10.7554/eLife.23882.001 The way we move – from simple motions like reaching out to grab something, to playing the piano or dancing – is coordinated in our brain. These processes involve many regions and steps, in which nerve cells transport signals along projections known as axons. Axons rely on sophisticated ‘engineering’ to work properly over long distances and are vulnerable to diseases that disrupt their engineering. For example, in genetic diseases called ‘hereditary spastic paraplegias’, damages to the ‘distal’ end of axons – the end furthest from the nerve cell body – cause paralysis of the lower body. Axons have several internal structures that make sure everything works properly. One of these structures is the endoplasmic reticulum, which is a network of tubular membranes that runs lengthwise along the axon. It is known that spastic paraplegias are sometimes caused by mutations affecting proteins that help to build and shape the endoplasmic reticulum, for example, the proteins of the reticulon and REEP families. However, until now it was not known how the ER forms its network in the axons and if this is influenced by these proteins. To see whether reticulons and REEPs affect the shape of the endoplasmic reticulum, Yalçιn et al. used healthy fruit fly larvae, and genetically modified ones that lacked the proteins. The results show that in healthy flies, the tubular network runs continuously along the axons. When either reticulon or REEP proteins were removed, the distal axons contained less endoplasmic reticulum. In mutant fly larvae that lacked both protein families, the endoplasmic reticulum was more interrupted and contained more gaps than in normal larvae. Using high-magnification electron microscopy confirmed these findings, and showed that the tubules of the endoplasmic reticulum in mutant axons were larger, but fewer. A next step will be to test whether these mutations also affect how the axons work and communicate over long distances. A better knowledge of the role of the endoplasmic reticulum in axons will help us to understand how damages to it could affect hereditary spastic paraplegias and other degenerative conditions. DOI:http://dx.doi.org/10.7554/eLife.23882.002
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Affiliation(s)
- Belgin Yalçın
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Lu Zhao
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Martin Stofanko
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Niamh C O'Sullivan
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Zi Han Kang
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Annika Roost
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Matthew R Thomas
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Sophie Zaessinger
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Olivier Blard
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Alex L Patto
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Anood Sohail
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Valentina Baena
- Department of Cell Biology, University of Connecticut Health Center, Farmington, United States
| | - Mark Terasaki
- Department of Cell Biology, University of Connecticut Health Center, Farmington, United States
| | - Cahir J O'Kane
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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160
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Korotkevich E, Niwayama R, Courtois A, Friese S, Berger N, Buchholz F, Hiiragi T. The Apical Domain Is Required and Sufficient for the First Lineage Segregation in the Mouse Embryo. Dev Cell 2017; 40:235-247.e7. [PMID: 28171747 PMCID: PMC5300053 DOI: 10.1016/j.devcel.2017.01.006] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 12/10/2016] [Accepted: 01/09/2017] [Indexed: 11/29/2022]
Abstract
Mammalian development begins with segregation of the extra-embryonic trophectoderm from the embryonic lineage in the blastocyst. While cell polarity and adhesion play key roles, the decisive cue driving this lineage segregation remains elusive. Here, to study symmetry breaking, we use a reduced system in which isolated blastomeres recapitulate the first lineage segregation. We find that in the 8-cell stage embryo, the apical domain recruits a spindle pole to ensure its differential distribution upon division. Daughter cells that inherit the apical domain adopt trophectoderm fate. However, the fate of apolar daughter cells depends on whether their position within the embryo facilitates apical domain formation by Cdh1-independent cell contact. Finally, we develop methods for transplanting apical domains and show that acquisition of this domain is not only required but also sufficient for the first lineage segregation. Thus, we provide mechanistic understanding that reconciles previous models for symmetry breaking in mouse development. A reduced system was established to study symmetry breaking in mouse development 8-cell stage blastomeres acquire the capacity to self-organize the apical domain The apical domain is required and sufficient for the first lineage segregation Contact asymmetry specifies cell fate, leading to self-organized embryo patterning
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Affiliation(s)
- Ekaterina Korotkevich
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Ritsuya Niwayama
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Aurélien Courtois
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Stefanie Friese
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Nicolas Berger
- Medical Systems Biology, UCC, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, 01062 Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, UCC, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, 01062 Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Takashi Hiiragi
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
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161
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Mierzwa BE, Chiaruttini N, Redondo-Morata L, von Filseck JM, König J, Larios J, Poser I, Müller-Reichert T, Scheuring S, Roux A, Gerlich DW. Dynamic subunit turnover in ESCRT-III assemblies is regulated by Vps4 to mediate membrane remodelling during cytokinesis. Nat Cell Biol 2017; 19:787-798. [PMID: 28604678 PMCID: PMC5493987 DOI: 10.1038/ncb3559] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 05/19/2017] [Indexed: 02/07/2023]
Abstract
The Endosomal Sorting Complex Required for Transport (ESCRT)-III mediates membrane fission in fundamental cellular processes, including cytokinesis. ESCRT-III is thought to form persistent filaments that over time increase their curvature to constrict membranes. Unexpectedly, we found that ESCRT-III at the midbody of human cells rapidly turns over subunits with cytoplasmic pools while gradually forming larger assemblies. ESCRT-III turnover depended on the ATPase VPS4, which accumulated at the midbody simultaneously with ESCRT-III subunits, and was required for assembly of functional ESCRT-III structures. In vitro, the Vps2/Vps24 subunits of ESCRT-III formed side-by-side filaments with Snf7 and inhibited further polymerization, but the growth inhibition was alleviated by the addition of Vps4 and ATP. High-speed atomic force microscopy further revealed highly dynamic arrays of growing and shrinking ESCRT-III spirals in presence of Vps4. Continuous ESCRT-III remodeling by subunit turnover might facilitate shape adaptions to variable membrane geometries, with broad implications for diverse cellular processes.
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Affiliation(s)
- Beata E Mierzwa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), AT-1030 Vienna, Austria
| | - Nicolas Chiaruttini
- Department of Biochemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | | | | | - Julia König
- Experimental Center, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Jorge Larios
- Department of Biochemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, D-01307 Dresden, Germany
| | - Thomas Müller-Reichert
- Experimental Center, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Simon Scheuring
- U1006 INSERM, Aix-Marseille Université, 13009 Marseille, France
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, CH-1211 Geneva, Switzerland.,Swiss National Centre for Competence in Research Programme Chemical Biology, CH-1211 Geneva, Switzerland
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), AT-1030 Vienna, Austria
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162
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Zhang K, Foster HE, Rondelet A, Lacey SE, Bahi-Buisson N, Bird AW, Carter AP. Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated. Cell 2017; 169:1303-1314.e18. [PMID: 28602352 PMCID: PMC5473941 DOI: 10.1016/j.cell.2017.05.025] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/17/2017] [Accepted: 05/12/2017] [Indexed: 12/17/2022]
Abstract
Cytoplasmic dynein-1 binds dynactin and cargo adaptor proteins to form a transport machine capable of long-distance processive movement along microtubules. However, it is unclear why dynein-1 moves poorly on its own or how it is activated by dynactin. Here, we present a cryoelectron microscopy structure of the complete 1.4-megadalton human dynein-1 complex in an inhibited state known as the phi-particle. We reveal the 3D structure of the cargo binding dynein tail and show how self-dimerization of the motor domains locks them in a conformation with low microtubule affinity. Disrupting motor dimerization with structure-based mutagenesis drives dynein-1 into an open form with higher affinity for both microtubules and dynactin. We find the open form is also inhibited for movement and that dynactin relieves this by reorienting the motor domains to interact correctly with microtubules. Our model explains how dynactin binding to the dynein-1 tail directly stimulates its motor activity.
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Affiliation(s)
- Kai Zhang
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Helen E Foster
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Arnaud Rondelet
- Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Samuel E Lacey
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Nadia Bahi-Buisson
- Department of Pediatric Neurology, Université Paris Descartes, Imaging Institute, INSERM U781, Paris, France
| | - Alexander W Bird
- Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
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163
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Botti V, McNicoll F, Steiner MC, Richter FM, Solovyeva A, Wegener M, Schwich OD, Poser I, Zarnack K, Wittig I, Neugebauer KM, Müller-McNicoll M. Cellular differentiation state modulates the mRNA export activity of SR proteins. J Cell Biol 2017; 216:1993-2009. [PMID: 28592444 PMCID: PMC5496613 DOI: 10.1083/jcb.201610051] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 03/22/2017] [Accepted: 04/24/2017] [Indexed: 01/22/2023] Open
Abstract
SR proteins connect nuclear pre-mRNA processing to mRNA export and translation. Botti et al. develop a quantitative nucleocytoplasmic shuttling assay and show that SR proteins are differentially modified and active in differentiated and pluripotent cells. SR proteins function in nuclear pre-mRNA processing, mRNA export, and translation. To investigate their cellular dynamics, we developed a quantitative assay, which detects differences in nucleocytoplasmic shuttling among seven canonical SR protein family members. As expected, SRSF2 and SRSF5 shuttle poorly in HeLa cells but surprisingly display considerable shuttling in pluripotent murine P19 cells. Combining individual-resolution cross-linking and immunoprecipitation (iCLIP) and mass spectrometry, we show that elevated arginine methylation of SRSF5 and lower phosphorylation levels of cobound SRSF2 enhance shuttling of SRSF5 in P19 cells by modulating protein–protein and protein–RNA interactions. Moreover, SRSF5 is bound to pluripotency-specific transcripts such as Lin28a and Pou5f1/Oct4 in the cytoplasm. SRSF5 depletion reduces and overexpression increases their cytoplasmic mRNA levels, suggesting that enhanced mRNA export by SRSF5 is required for the expression of pluripotency factors. Remarkably, neural differentiation of P19 cells leads to dramatically reduced SRSF5 shuttling. Our findings indicate that posttranslational modification of SR proteins underlies the regulation of their mRNA export activities and distinguishes pluripotent from differentiated cells.
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Affiliation(s)
- Valentina Botti
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - François McNicoll
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Michaela C Steiner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Florian M Richter
- Functional Proteomics Group, Institute for Biochemistry I, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anfisa Solovyeva
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marius Wegener
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Oliver D Schwich
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics Group, Institute for Biochemistry I, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Michaela Müller-McNicoll
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
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164
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Malinová A, Cvačková Z, Matějů D, Hořejší Z, Abéza C, Vandermoere F, Bertrand E, Staněk D, Verheggen C. Assembly of the U5 snRNP component PRPF8 is controlled by the HSP90/R2TP chaperones. J Cell Biol 2017; 216:1579-1596. [PMID: 28515276 PMCID: PMC5461031 DOI: 10.1083/jcb.201701165] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/22/2017] [Accepted: 04/04/2017] [Indexed: 12/23/2022] Open
Abstract
The pre-mRNA splicing factor PRPF8 is a crucial component of the U5 snRNP. Using quantitative proteomics, Malinová et al. show that assembly of the U5 snRNP is controlled by the HSP90/R2TP chaperones and that Retinitis pigmentosa–associated mutations in PRPF8 impair PRPF8 quality control and U5 snRNP chaperone-mediated assembly. Splicing is catalyzed by the spliceosome, a complex of five major small nuclear ribonucleoprotein particles (snRNPs). The pre-mRNA splicing factor PRPF8 is a crucial component of the U5 snRNP, and together with EFTUD2 and SNRNP200, it forms a central module of the spliceosome. Using quantitative proteomics, we identified assembly intermediates containing PRPF8, EFTUD2, and SNRNP200 in association with the HSP90/R2TP complex, its ZNHIT2 cofactor, and additional proteins. HSP90 and R2TP bind unassembled U5 proteins in the cytoplasm, stabilize them, and promote the formation of the U5 snRNP. We further found that PRPF8 mutants causing Retinitis pigmentosa assemble less efficiently with the U5 snRNP and bind more strongly to R2TP, with one mutant retained in the cytoplasm in an R2TP-dependent manner. We propose that the HSP90/R2TP chaperone system promotes the assembly of a key module of U5 snRNP while assuring the quality control of PRPF8. The proteomics data further reveal new interactions between R2TP and the tuberous sclerosis complex (TSC), pointing to a potential link between growth signals and the assembly of key cellular machines.
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Affiliation(s)
- Anna Malinová
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic.,Faculty of Science, Charles University in Prague, 128 00 Prague, Czech Republic
| | - Zuzana Cvačková
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Daniel Matějů
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Zuzana Hořejší
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Claire Abéza
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, University of Montpellier, 34293 Montpellier, France
| | - Franck Vandermoere
- Institut de Génomique Fonctionnelle, Centre National de la Recherche Scientifique, University of Montpellier, 34090 Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, University of Montpellier, 34293 Montpellier, France
| | - David Staněk
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Céline Verheggen
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, University of Montpellier, 34293 Montpellier, France
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165
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Cooper S, Bakal C. Accelerating Live Single-Cell Signalling Studies. Trends Biotechnol 2017; 35:422-433. [PMID: 28161141 DOI: 10.1016/j.tibtech.2017.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/24/2016] [Accepted: 01/06/2017] [Indexed: 12/21/2022]
Abstract
The dynamics of signalling networks that couple environmental conditions with cellular behaviour can now be characterised in exquisite detail using live single-cell imaging experiments. Recent improvements in our abilities to introduce fluorescent sensors into cells, coupled with advances in pipelines for quantifying and extracting single-cell data, mean that high-throughput systematic analyses of signalling dynamics are becoming possible. In this review, we consider current technologies that are driving progress in the scale and range of such studies. Moreover, we discuss novel approaches that are allowing us to explore how pathways respond to changes in inputs and even predict the fate of a cell based upon its signalling history and state.
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Affiliation(s)
- Sam Cooper
- The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK; Department of Computational Systems Medicine, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.
| | - Chris Bakal
- The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
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166
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Hanley ML, Yoo TY, Sonnett M, Needleman DJ, Mitchison TJ. Chromosomal passenger complex hydrodynamics suggests chaperoning of the inactive state by nucleoplasmin/nucleophosmin. Mol Biol Cell 2017; 28:1444-1456. [PMID: 28404751 PMCID: PMC5449145 DOI: 10.1091/mbc.e16-12-0860] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/27/2017] [Accepted: 04/04/2017] [Indexed: 01/30/2023] Open
Abstract
The chromosomal passenger complex (CPC) is a conserved, essential regulator of cell division. As such, significant anti-cancer drug development efforts have been focused on targeting it, most notably by inhibiting its AURKB kinase subunit. The CPC is activated by AURKB-catalyzed autophosphorylation on multiple subunits, but how this regulates CPC interactions with other mitotic proteins remains unclear. We investigated the hydrodynamic behavior of the CPC in Xenopus laevis egg cytosol using sucrose gradient sedimentation and in HeLa cells using fluorescence correlation spectroscopy. We found that autophosphorylation of the CPC decreases its sedimentation coefficient in egg cytosol and increases its diffusion coefficient in live cells, indicating a decrease in mass. Using immunoprecipitation coupled with mass spectrometry and immunoblots, we discovered that inactive, unphosphorylated CPC interacts with nucleophosmin/nucleoplasmin proteins, which are known to oligomerize into pentamers and decamers. Autophosphorylation of the CPC causes it to dissociate from nucleophosmin/nucleoplasmin. We propose that nucleophosmin/nucleoplasmin complexes serve as chaperones that negatively regulate the CPC and/or stabilize its inactive form, preventing CPC autophosphorylation and recruitment to chromatin and microtubules in mitosis.
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Affiliation(s)
- Mariah L Hanley
- Department of Systems Biology, Harvard Medical School, Boston, MA 02114-5701.,Department of Chemistry, Harvard University, Cambridge, MA 02138-2902
| | - Tae Yeon Yoo
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138-2902
| | - Matthew Sonnett
- Department of Systems Biology, Harvard Medical School, Boston, MA 02114-5701
| | - Daniel J Needleman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138-2902.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138-2902
| | - Timothy J Mitchison
- Department of Systems Biology, Harvard Medical School, Boston, MA 02114-5701
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167
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Mateju D, Franzmann TM, Patel A, Kopach A, Boczek EE, Maharana S, Lee HO, Carra S, Hyman AA, Alberti S. An aberrant phase transition of stress granules triggered by misfolded protein and prevented by chaperone function. EMBO J 2017; 36:1669-1687. [PMID: 28377462 PMCID: PMC5470046 DOI: 10.15252/embj.201695957] [Citation(s) in RCA: 321] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/13/2017] [Accepted: 03/07/2017] [Indexed: 12/11/2022] Open
Abstract
Stress granules (SG) are membrane‐less compartments involved in regulating mRNAs during stress. Aberrant forms of SGs have been implicated in age‐related diseases, such as amyotrophic lateral sclerosis (ALS), but the molecular events triggering their formation are still unknown. Here, we find that misfolded proteins, such as ALS‐linked variants of SOD1, specifically accumulate and aggregate within SGs in human cells. This decreases the dynamics of SGs, changes SG composition, and triggers an aberrant liquid‐to‐solid transition of in vitro reconstituted compartments. We show that chaperone recruitment prevents the formation of aberrant SGs and promotes SG disassembly when the stress subsides. Moreover, we identify a backup system for SG clearance, which involves transport of aberrant SGs to the aggresome and their degradation by autophagy. Thus, cells employ a system of SG quality control to prevent accumulation of misfolded proteins and maintain the dynamic state of SGs, which may have relevance for ALS and related diseases.
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Affiliation(s)
- Daniel Mateju
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Titus M Franzmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Avinash Patel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrii Kopach
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Edgar E Boczek
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Shovamayee Maharana
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Hyun O Lee
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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168
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Changing the field of carcinogenicity testing of human pharmaceuticals by emphasizing mode of action. CURRENT OPINION IN TOXICOLOGY 2017. [DOI: 10.1016/j.cotox.2017.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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169
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Ding X, Stewart M, Sharei A, Weaver JC, Langer RS, Jensen KF. High-throughput Nuclear Delivery and Rapid Expression of DNA via Mechanical and Electrical Cell-Membrane Disruption. Nat Biomed Eng 2017; 1. [PMID: 28932622 PMCID: PMC5602535 DOI: 10.1038/s41551-017-0039] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Nuclear transfection of DNA into mammalian cells is challenging yet critical for many biological and medical studies. Here, by combining cell squeezing and electric-field-driven transport in a device that integrates microfluidic channels with constrictions and microelectrodes, we demonstrate nuclear delivery of plasmid DNA within 1 hour after treatment, the most rapid DNA expression in a high-throughput setting (up to millions of cells per minute per device). Passing cells at high speed through microfluidic constrictions smaller than the cell diameter mechanically disrupts the cell membrane, allowing a subsequent electric field to further disrupt the nuclear envelope and drive DNA molecules into the cytoplasm and nucleus. By tracking the localization of the ESCRT-III (endosomal sorting complexes required for transport) protein CHMP4B, we show that the integrity of the nuclear envelope is recovered within 15 minutes of treatment. We also provide insight into subcellular delivery by comparing the performance of the disruption-and-field-enhanced method with those of conventional chemical, electroporation, and manual-injection systems.
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Affiliation(s)
- Xiaoyun Ding
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,The David Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Martin Stewart
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,The David Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Armon Sharei
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,The David Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - James C Weaver
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert S Langer
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,The David Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Klavs F Jensen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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170
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Akpınar M, Lesche M, Fanourgakis G, Fu J, Anasstasiadis K, Dahl A, Jessberger R. TDRD6 mediates early steps of spliceosome maturation in primary spermatocytes. PLoS Genet 2017; 13:e1006660. [PMID: 28263986 PMCID: PMC5358835 DOI: 10.1371/journal.pgen.1006660] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 03/20/2017] [Accepted: 02/26/2017] [Indexed: 12/24/2022] Open
Abstract
Tudor containing protein 6 (TDRD6) is a male germ line-specific protein essential for chromatoid body (ChB) structure, elongated spermatid development and male fertility. Here we show that in meiotic prophase I spermatocytes TDRD6 interacts with the key protein arginine methyl transferase PRMT5, which supports splicing. TDRD6 also associates with spliceosomal core protein SmB in the absence of RNA and in an arginine methylation dependent manner. In Tdrd6-/- diplotene spermatocytes PRMT5 association with SmB and arginine dimethylation of SmB are much reduced. TDRD6 deficiency impairs the assembly of spliceosomes, which feature 3.5-fold increased levels of U5 snRNPs. In the nucleus, these deficiencies in spliceosome maturation correlate with decreased numbers of SMN-positive bodies and Cajal bodies involved in nuclear snRNP maturation. Transcriptome analysis of TDRD6-deficient diplotene spermatocytes revealed high numbers of splicing defects such as aberrant usage of intron and exons as well as aberrant representation of splice junctions. Together, this study demonstrates a novel function of TDRD6 in spliceosome maturation and mRNA splicing in prophase I spermatocytes.
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Affiliation(s)
- Müge Akpınar
- Institute of Physiological Chemistry, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Mathias Lesche
- Deep Sequencing Group SFB 655, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Grigorios Fanourgakis
- Institute of Physiological Chemistry, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Jun Fu
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | | | - Andreas Dahl
- Deep Sequencing Group SFB 655, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Rolf Jessberger
- Institute of Physiological Chemistry, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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171
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Mishima M. Preparation of centralspindlin as an active heterotetramer of kinesin and GTPase activating protein subunits for in vitro structural and functional assays. Methods Cell Biol 2017; 137:371-385. [DOI: 10.1016/bs.mcb.2016.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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172
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Polak B, Risteski P, Lesjak S, Tolić IM. PRC1-labeled microtubule bundles and kinetochore pairs show one-to-one association in metaphase. EMBO Rep 2016; 18:217-230. [PMID: 28028032 PMCID: PMC5286359 DOI: 10.15252/embr.201642650] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 02/04/2023] Open
Abstract
In the mitotic spindle, kinetochore microtubules form k‐fibers, whereas overlap or interpolar microtubules form antiparallel arrays containing the cross‐linker protein regulator of cytokinesis 1 (PRC1). We have recently shown that an overlap bundle, termed bridging fiber, links outermost sister k‐fibers. However, the relationship between overlap bundles and k‐fibers throughout the spindle remained unknown. Here, we show that in a metaphase spindle more than 90% of overlap bundles act as a bridge between sister k‐fibers. We found that the number of PRC1‐GFP‐labeled bundles per spindle is nearly the same as the number of kinetochore pairs. Live‐cell imaging revealed that kinetochore movement in the equatorial plane of the spindle is highly correlated with the movement of the coupled PRC1‐GFP‐labeled fiber, whereas the correlation with other fibers decreases with increasing distance. Analysis of endogenous PRC1 localization confirmed the results obtained with PRC1‐GFP. PRC1 knockdown reduced the bridging fiber thickness and interkinetochore distance throughout the spindle, suggesting a function of PRC1 in bridging microtubule organization and force balance in the metaphase spindle.
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Affiliation(s)
- Bruno Polak
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Patrik Risteski
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sonja Lesjak
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Iva M Tolić
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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173
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Bradley M, Ramirez I, Cheung K, Gholkar AA, Torres JZ. Inducible LAP-tagged Stable Cell Lines for Investigating Protein Function, Spatiotemporal Localization and Protein Interaction Networks. J Vis Exp 2016. [PMID: 28060263 PMCID: PMC5226453 DOI: 10.3791/54870] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Multi-protein complexes, rather than single proteins acting in isolation, often govern molecular pathways regulating cellular homeostasis. Based on this principle, the purification of critical proteins required for the functioning of these pathways along with their native interacting partners has not only allowed the mapping of the protein constituents of these pathways, but has also provided a deeper understanding of how these proteins coordinate to regulate these pathways. Within this context, understanding a protein's spatiotemporal localization and its protein-protein interaction network can aid in defining its role within a pathway, as well as how its misregulation may lead to disease pathogenesis. To address this need, several approaches for protein purification such as tandem affinity purification (TAP) and localization and affinity purification (LAP) have been designed and used successfully. Nevertheless, in order to apply these approaches to pathway-scale proteomic analyses, these strategies must be supplemented with modern technological developments in cloning and mammalian stable cell line generation. Here, we describe a method for generating LAP-tagged human inducible stable cell lines for investigating protein subcellular localization and protein-protein interaction networks. This approach has been successfully applied to the dissection of multiple cellular pathways including cell division and is compatible with high-throughput proteomic analyses.
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Affiliation(s)
- Michelle Bradley
- Department of Chemistry and Biochemistry, University of California, Los Angeles
| | - Ivan Ramirez
- Department of Chemistry and Biochemistry, University of California, Los Angeles
| | - Keith Cheung
- Department of Chemistry and Biochemistry, University of California, Los Angeles
| | - Ankur A Gholkar
- Department of Chemistry and Biochemistry, University of California, Los Angeles
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry, University of California, Los Angeles; Molecular Biology Institute, University of California, Los Angeles; Jonsson Comprehensive Cancer Center, University of California, Los Angeles;
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174
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Kranjc T, Dempsey E, Cagney G, Nakamura N, Shields DC, Simpson JC. Functional characterisation of the YIPF protein family in mammalian cells. Histochem Cell Biol 2016; 147:439-451. [DOI: 10.1007/s00418-016-1527-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2016] [Indexed: 01/26/2023]
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175
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Lawrence KS, Tapley EC, Cruz VE, Li Q, Aung K, Hart KC, Schwartz TU, Starr DA, Engebrecht J. LINC complexes promote homologous recombination in part through inhibition of nonhomologous end joining. J Cell Biol 2016; 215:801-821. [PMID: 27956467 PMCID: PMC5166498 DOI: 10.1083/jcb.201604112] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/03/2016] [Accepted: 10/31/2016] [Indexed: 01/23/2023] Open
Abstract
The Caenorhabditis elegans SUN domain protein, UNC-84, functions in nuclear migration and anchorage in the soma. We discovered a novel role for UNC-84 in DNA damage repair and meiotic recombination. Loss of UNC-84 leads to defects in the loading and disassembly of the recombinase RAD-51. Similar to mutations in Fanconi anemia (FA) genes, unc-84 mutants and human cells depleted of Sun-1 are sensitive to DNA cross-linking agents, and sensitivity is rescued by the inactivation of nonhomologous end joining (NHEJ). UNC-84 also recruits FA nuclease FAN-1 to the nucleoplasm, suggesting that UNC-84 both alters the extent of repair by NHEJ and promotes the processing of cross-links by FAN-1. UNC-84 interacts with the KASH protein ZYG-12 for DNA damage repair. Furthermore, the microtubule network and interaction with the nucleoskeleton are important for repair, suggesting that a functional linker of nucleoskeleton and cytoskeleton (LINC) complex is required. We propose that LINC complexes serve a conserved role in DNA repair through both the inhibition of NHEJ and the promotion of homologous recombination at sites of chromosomal breaks.
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Affiliation(s)
- Katherine S Lawrence
- Department of Molecular and Cellular Biology; Biochemistry, Molecular Cellular, and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616
| | - Erin C Tapley
- Department of Molecular and Cellular Biology; Biochemistry, Molecular Cellular, and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616
| | - Victor E Cruz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Qianyan Li
- Department of Molecular and Cellular Biology; Biochemistry, Molecular Cellular, and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616
| | - Kayla Aung
- Department of Molecular and Cellular Biology; Biochemistry, Molecular Cellular, and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616
| | - Kevin C Hart
- Department of Molecular and Cellular Biology; Biochemistry, Molecular Cellular, and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Daniel A Starr
- Department of Molecular and Cellular Biology; Biochemistry, Molecular Cellular, and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616
| | - JoAnne Engebrecht
- Department of Molecular and Cellular Biology; Biochemistry, Molecular Cellular, and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616
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176
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Hiemstra S, Niemeijer M, Koedoot E, Wink S, Klip JE, Vlasveld M, de Zeeuw E, van Os B, White A, Water BVD. Comprehensive Landscape of Nrf2 and p53 Pathway Activation Dynamics by Oxidative Stress and DNA Damage. Chem Res Toxicol 2016; 30:923-933. [PMID: 27982581 DOI: 10.1021/acs.chemrestox.6b00322] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A quantitative dynamics pathway map of the Nrf2-mediated oxidative stress response and p53-related DNA damage response pathways as well as the cross-talk between these pathways has not systematically been defined. To allow the dynamic single cell evaluation of these pathways, we have used BAC-GFP recombineering to tag for each pathway's three key components: for the oxidative stress response, Keap1-GFP, Nrf2-GFP, and Srxn1-GFP; for the DNA damage response, 53bp1-GFP, p53-GFP, and p21-GFP. The dynamic activation of these individual components was assessed using quantitative high throughput confocal microscopy after treatment with a broad concentration range of diethyl maleate (DEM; to induce oxidative stress) and etoposide (to induce DNA damage). DEM caused a rapid activation of Nrf2, which returned to baseline levels at low concentrations but remained sustained at high concentrations. Srxn1-GFP induction and Keap1-GFP translocation to autophagosomes followed later, with upper boundaries reached at high concentrations, close to the onset of cell death. Etoposide caused rapid accumulation of 53bp1-GFP in DNA damage foci, which was later followed by the concentration dependent nuclear accumulation of p53-GFP and subsequent induction of p21-GFP. While etoposide caused activation of Srxn1-GFP, a modest activation of DNA damage reporters was observed for DEM at high concentrations. Interestingly, Nrf2 knockdown caused an inhibition of the DNA damage response at high concentrations of etoposide, while Keap1 knockdown caused an enhancement of the DNA damage response already at low concentrations of etoposide. Knockdown of p53 did not affect the oxidative stress response. Altogether, the current stress response landscapes provide insight in the time course responses of and cross-talk between oxidative stress and DNA-damage and defines the tipping points where cell injury may switch from adaptation to injury.
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Affiliation(s)
- Steven Hiemstra
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marije Niemeijer
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Esmee Koedoot
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Steven Wink
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Janna E Klip
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Matthijs Vlasveld
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Elisabeth de Zeeuw
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bram van Os
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | | | - Bob van de Water
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
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177
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Bendre S, Rondelet A, Hall C, Schmidt N, Lin YC, Brouhard GJ, Bird AW. GTSE1 tunes microtubule stability for chromosome alignment and segregation by inhibiting the microtubule depolymerase MCAK. J Cell Biol 2016; 215:631-647. [PMID: 27881713 PMCID: PMC5147003 DOI: 10.1083/jcb.201606081] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 10/04/2016] [Accepted: 10/21/2016] [Indexed: 12/21/2022] Open
Abstract
The microtubule depolymerase MCAK influences chromosomal instability (CIN), but what controls its activity remains unclear. Bendre et al. show that GTSE1, a protein found overexpressed in tumors, regulates microtubule stability and chromosome alignment during mitosis by inhibiting MCAK. High levels of GTSE1 are linked to chromosome missegregation and CIN. The dynamic regulation of microtubules (MTs) during mitosis is critical for accurate chromosome segregation and genome stability. Cancer cell lines with hyperstabilized kinetochore MTs have increased segregation errors and elevated chromosomal instability (CIN), but the genetic defects responsible remain largely unknown. The MT depolymerase MCAK (mitotic centromere-associated kinesin) can influence CIN through its impact on MT stability, but how its potent activity is controlled in cells remains unclear. In this study, we show that GTSE1, a protein found overexpressed in aneuploid cancer cell lines and tumors, regulates MT stability during mitosis by inhibiting MCAK MT depolymerase activity. Cells lacking GTSE1 have defects in chromosome alignment and spindle positioning as a result of MT instability caused by excess MCAK activity. Reducing GTSE1 levels in CIN cancer cell lines reduces chromosome missegregation defects, whereas artificially inducing GTSE1 levels in chromosomally stable cells elevates chromosome missegregation and CIN. Thus, GTSE1 inhibition of MCAK activity regulates the balance of MT stability that determines the fidelity of chromosome alignment, segregation, and chromosomal stability.
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Affiliation(s)
- Shweta Bendre
- Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Arnaud Rondelet
- Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Conrad Hall
- Department of Biology, McGill University, Montreal H3A 1B1, Quebec, Canada
| | - Nadine Schmidt
- Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Yu-Chih Lin
- Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Gary J Brouhard
- Department of Biology, McGill University, Montreal H3A 1B1, Quebec, Canada
| | - Alexander W Bird
- Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
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178
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Scharaw S, Iskar M, Ori A, Boncompain G, Laketa V, Poser I, Lundberg E, Perez F, Beck M, Bork P, Pepperkok R. The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR. J Cell Biol 2016; 215:543-558. [PMID: 27872256 PMCID: PMC5119934 DOI: 10.1083/jcb.201601090] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 09/07/2016] [Accepted: 10/17/2016] [Indexed: 12/24/2022] Open
Abstract
Maintenance of EGFR plasma membrane levels is critical for cell functioning. Scharaw et al. demonstrate that endosomal RNF11 is required for transcriptional up-regulation of COPII components, specifically facilitating EGFR transport in response to its lysosomal degradation after EGF stimulation. Stimulation of cells with epidermal growth factor (EGF) induces internalization and partial degradation of the EGF receptor (EGFR) by the endo-lysosomal pathway. For continuous cell functioning, EGFR plasma membrane levels are maintained by transporting newly synthesized EGFRs to the cell surface. The regulation of this process is largely unknown. In this study, we find that EGF stimulation specifically increases the transport efficiency of newly synthesized EGFRs from the endoplasmic reticulum to the plasma membrane. This coincides with an up-regulation of the inner coat protein complex II (COPII) components SEC23B, SEC24B, and SEC24D, which we show to be specifically required for EGFR transport. Up-regulation of these COPII components requires the transcriptional regulator RNF11, which localizes to early endosomes and appears additionally in the cell nucleus upon continuous EGF stimulation. Collectively, our work identifies a new regulatory mechanism that integrates the degradation and transport of EGFR in order to maintain its physiological levels at the plasma membrane.
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Affiliation(s)
- Sandra Scharaw
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Murat Iskar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Alessandro Ori
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Gaelle Boncompain
- Institut Curie, Paris Sciences et Lettres Research University, 75248 Paris, France.,Institut Curie, Centre National de la Recherche Scientifique UMR144, 75248 Paris, France
| | - Vibor Laketa
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Emma Lundberg
- Science for Life Laboratory, KTH Royal Institute of Technology, 17121 Solna, Sweden
| | - Franck Perez
- Institut Curie, Paris Sciences et Lettres Research University, 75248 Paris, France.,Institut Curie, Centre National de la Recherche Scientifique UMR144, 75248 Paris, France
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany.,Department of Bioinformatics, Biocenter, University of Wuerzburg, 97074 Wuerzburg, Germany
| | - Rainer Pepperkok
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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179
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Skogs M, Stadler C, Schutten R, Hjelmare M, Gnann C, Björk L, Poser I, Hyman A, Uhlén M, Lundberg E. Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins. J Proteome Res 2016; 16:147-155. [PMID: 27723985 DOI: 10.1021/acs.jproteome.6b00821] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Antibodies are indispensible research tools, yet the scientific community has not adopted standardized procedures to validate their specificity. Here we present a strategy to systematically validate antibodies for immunofluorescence (IF) applications using gene tagging. We have assessed the on- and off-target binding capabilities of 197 antibodies using 108 cell lines expressing EGFP-tagged target proteins at endogenous levels. Furthermore, we assessed batch-to-batch effects for 35 target proteins, showing that both the on- and off-target binding patterns vary significantly between antibody batches and that the proposed strategy serves as a reliable procedure for ensuring reproducibility upon production of new antibody batches. In summary, we present a systematic scheme for antibody validation in IF applications using endogenous expression of tagged proteins. This is an important step toward a reproducible approach for context- and application-specific antibody validation and improved reliability of antibody-based experiments and research data.
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Affiliation(s)
- Marie Skogs
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
| | - Charlotte Stadler
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
| | - Rutger Schutten
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
| | - Martin Hjelmare
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
| | - Christian Gnann
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
| | - Lars Björk
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
| | - Ina Poser
- Molecular Cell Biology and Genetics, Max Planck Institute , D- 01307 Dresden, Germany
| | - Anthony Hyman
- Molecular Cell Biology and Genetics, Max Planck Institute , D- 01307 Dresden, Germany
| | - Mathias Uhlén
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden
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180
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Pichon X, Bastide A, Safieddine A, Chouaib R, Samacoits A, Basyuk E, Peter M, Mueller F, Bertrand E. Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells. J Cell Biol 2016; 214:769-81. [PMID: 27597760 PMCID: PMC5021097 DOI: 10.1083/jcb.201605024] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 08/16/2016] [Indexed: 12/13/2022] Open
Abstract
Pichon et al. describe a method to visualize translation of single endogenous mRNPs in live cells and provide evidence for specialized translation factories, as well as measurements of translation elongation rate, ribosome loading, and movements of single polysomes. Translation is an essential step in gene expression. In this study, we used an improved SunTag system to label nascent proteins and image translation of single messenger ribonucleoproteins (mRNPs) in human cells. Using a dedicated reporter RNA, we observe that translation of single mRNPs stochastically turns on and off while they diffuse through the cytoplasm. We further measure a ribosome density of 1.3 per kilobase and an elongation rate of 13–18 amino acids per second. Tagging the endogenous POLR2A gene revealed similar elongation rates and ribosomal densities and that nearly all messenger RNAs (mRNAs) are engaged in translation. Remarkably, tagging of the heavy chain of dynein 1 (DYNC1H1) shows this mRNA accumulates in foci containing three to seven RNA molecules. These foci are translation sites and thus represent specialized translation factories. We also observe that DYNC1H1 polysomes are actively transported by motors, which may deliver the mature protein at appropriate cellular locations. The SunTag should be broadly applicable to study translational regulation in live single cells.
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Affiliation(s)
- Xavier Pichon
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Amandine Bastide
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Adham Safieddine
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Racha Chouaib
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Aubin Samacoits
- Unité Imagerie et Modélisation, Institut Pasteur, UMR3691, Centre National de la Recherche Scientifique, 75015 Paris, France
| | - Eugenia Basyuk
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Marion Peter
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Florian Mueller
- Unité Imagerie et Modélisation, Institut Pasteur, UMR3691, Centre National de la Recherche Scientifique, 75015 Paris, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
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181
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Tsanov N, Samacoits A, Chouaib R, Traboulsi AM, Gostan T, Weber C, Zimmer C, Zibara K, Walter T, Peter M, Bertrand E, Mueller F. smiFISH and FISH-quant - a flexible single RNA detection approach with super-resolution capability. Nucleic Acids Res 2016; 44:e165. [PMID: 27599845 PMCID: PMC5159540 DOI: 10.1093/nar/gkw784] [Citation(s) in RCA: 245] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/26/2016] [Indexed: 11/12/2022] Open
Abstract
Single molecule FISH (smFISH) allows studying transcription and RNA localization by imaging individual mRNAs in single cells. We present smiFISH (single molecule inexpensive FISH), an easy to use and flexible RNA visualization and quantification approach that uses unlabelled primary probes and a fluorescently labelled secondary detector oligonucleotide. The gene-specific probes are unlabelled and can therefore be synthesized at low cost, thus allowing to use more probes per mRNA resulting in a substantial increase in detection efficiency. smiFISH is also flexible since differently labelled secondary detector probes can be used with the same primary probes. We demonstrate that this flexibility allows multicolor labelling without the need to synthesize new probe sets. We further demonstrate that the use of a specific acrydite detector oligonucleotide allows smiFISH to be combined with expansion microscopy, enabling the resolution of transcripts in 3D below the diffraction limit on a standard microscope. Lastly, we provide improved, fully automated software tools from probe-design to quantitative analysis of smFISH images. In short, we provide a complete workflow to obtain automatically counts of individual RNA molecules in single cells.
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Affiliation(s)
- Nikolay Tsanov
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Aubin Samacoits
- Unité Imagerie et Modélisation, Institut Pasteur and CNRS UMR 3691, 28 rue du Docteur Roux, 75015 Paris, France.,C3BI, USR 3756 IP CNRS - Paris, France
| | - Racha Chouaib
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France.,ER045, Laboratory of Stem Cells, DSST, PRASE, Lebanese University, Beirut, Lebanon
| | - Abdel-Meneem Traboulsi
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Thierry Gostan
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Christian Weber
- Unité Imagerie et Modélisation, Institut Pasteur and CNRS UMR 3691, 28 rue du Docteur Roux, 75015 Paris, France.,C3BI, USR 3756 IP CNRS - Paris, France
| | - Christophe Zimmer
- Unité Imagerie et Modélisation, Institut Pasteur and CNRS UMR 3691, 28 rue du Docteur Roux, 75015 Paris, France.,C3BI, USR 3756 IP CNRS - Paris, France
| | - Kazem Zibara
- ER045, Laboratory of Stem Cells, DSST, PRASE, Lebanese University, Beirut, Lebanon.,Biology Department, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Thomas Walter
- MINES ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, 77300 Fontainebleau, France.,Institut Curie, 75248 Paris Cedex, France.,INSERM, U900, 75248 Paris Cedex, France
| | - Marion Peter
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France .,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France .,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Florian Mueller
- Unité Imagerie et Modélisation, Institut Pasteur and CNRS UMR 3691, 28 rue du Docteur Roux, 75015 Paris, France .,C3BI, USR 3756 IP CNRS - Paris, France
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182
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Saha S, Weber CA, Nousch M, Adame-Arana O, Hoege C, Hein MY, Osborne-Nishimura E, Mahamid J, Jahnel M, Jawerth L, Pozniakovski A, Eckmann CR, Jülicher F, Hyman AA. Polar Positioning of Phase-Separated Liquid Compartments in Cells Regulated by an mRNA Competition Mechanism. Cell 2016; 166:1572-1584.e16. [PMID: 27594427 DOI: 10.1016/j.cell.2016.08.006] [Citation(s) in RCA: 222] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/21/2016] [Accepted: 08/01/2016] [Indexed: 12/21/2022]
Abstract
P granules are non-membrane-bound RNA-protein compartments that are involved in germline development in C. elegans. They are liquids that condense at one end of the embryo by localized phase separation, driven by gradients of polarity proteins such as the mRNA-binding protein MEX-5. To probe how polarity proteins regulate phase separation, we combined biochemistry and theoretical modeling. We reconstitute P granule-like droplets in vitro using a single protein PGL-3. By combining in vitro reconstitution with measurements of intracellular concentrations, we show that competition between PGL-3 and MEX-5 for mRNA can regulate the formation of PGL-3 droplets. Using theory, we show that, in a MEX-5 gradient, this mRNA competition mechanism can drive a gradient of P granule assembly with similar spatial and temporal characteristics to P granule assembly in vivo. We conclude that gradients of polarity proteins can position RNP granules during development by using RNA competition to regulate local phase separation.
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Affiliation(s)
- Shambaditya Saha
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Christoph A Weber
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | - Marco Nousch
- Martin Luther University, 06120 Halle (Saale), Germany
| | - Omar Adame-Arana
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | - Carsten Hoege
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Marco Y Hein
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | - Julia Mahamid
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Marcus Jahnel
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Louise Jawerth
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | - Andrej Pozniakovski
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | | | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
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183
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A Surveillance Function of the HSPB8-BAG3-HSP70 Chaperone Complex Ensures Stress Granule Integrity and Dynamism. Mol Cell 2016; 63:796-810. [PMID: 27570075 DOI: 10.1016/j.molcel.2016.07.021] [Citation(s) in RCA: 222] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/28/2016] [Accepted: 07/20/2016] [Indexed: 12/29/2022]
Abstract
Stress granules (SGs) are ribonucleoprotein complexes induced by stress. They sequester mRNAs and disassemble when the stress subsides, allowing translation restoration. In amyotrophic lateral sclerosis (ALS), aberrant SGs cannot disassemble and therefore accumulate and are degraded by autophagy. However, the molecular events causing aberrant SG formation and the molecular players regulating this transition are largely unknown. We report that defective ribosomal products (DRiPs) accumulate in SGs and promote a transition into an aberrant state that renders SGs resistant to RNase. We show that only a minor fraction of aberrant SGs is targeted by autophagy, whereas the majority disassembles in a process that requires assistance by the HSPB8-BAG3-HSP70 chaperone complex. We further demonstrate that HSPB8-BAG3-HSP70 ensures the functionality of SGs and restores proteostasis by targeting DRiPs for degradation. We propose a system of chaperone-mediated SG surveillance, or granulostasis, which regulates SG composition and dynamics and thus may play an important role in ALS.
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184
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An endosomal tether undergoes an entropic collapse to bring vesicles together. Nature 2016; 537:107-111. [PMID: 27556945 PMCID: PMC5142606 DOI: 10.1038/nature19326] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 07/19/2016] [Indexed: 12/16/2022]
Abstract
An early step in intracellular transport is the selective recognition of
a vesicle by its appropriate target membrane, a process regulated by Rab GTPases
via the recruitment of tethering effectors1–4. Membrane tethering
confers higher selectivity and efficiency to membrane fusion than the pairing of
SNAREs alone5,6,7. Here, we
addressed the mechanism whereby a tethered vesicle comes closer towards its
target membrane for fusion by reconstituting an endosomal asymmetric tethering
machinery consisting of the dimeric coiled-coil protein EEA16,7
recruited to phosphatidylinositol 3-phosphate membranes and binding vesicles
harboring Rab5. Surprisingly, structural analysis revealed that Rab5:GTP induces
an allosteric conformational change in EEA1, from extended to flexible and
collapsed. Through dynamic analysis by optical tweezers we confirmed that EEA1
captures a vesicle at a distance corresponding to its extended conformation, and
directly measured its flexibility and the forces induced during the tethering
reaction. Expression of engineered EEA1 variants defective in the conformational
change induced prominent clusters of tethered vesicles in vivo.
Our results suggest a new mechanism in which Rab5 induces a change in
flexibility of EEA1, generating an entropic collapse force that
pulls the captured vesicle toward the target membrane to initiate docking and
fusion.
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185
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Unsal E, Degirmenci B, Harmanda B, Erman B, Ozlu N. A small molecule identified through an in silico screen inhibits Aurora B-INCENP interaction. Chem Biol Drug Des 2016; 88:783-794. [PMID: 27390292 DOI: 10.1111/cbdd.12816] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 07/07/2016] [Accepted: 06/18/2016] [Indexed: 12/23/2022]
Abstract
Aurora B is a serine/threonine kinase that has a central role in the regulation of mitosis. The observation of Aurora B overexpression in cancer makes it a promising target to develop antitumoral inhibitors. We describe a new potential inhibitor that exclusively targets the interaction site of Aurora B and its activator INCENP. We performed a structure-based virtual screening and determined five potential candidates of 200 000 compounds, which selectively bind to the Aurora B::INCENP interaction site, but not to the ATP-binding site (kinase pocket) of Aurora B or other related kinases. Further characterization in vivo validated the inhibitory role of one of these five compounds in Aurora B::INCENP complex formation and exhibited hallmarks of Aurora inhibition such as chromosome congression and segregation defects that interfere with the progression into cytokinesis and result in multinuclear cells. Our results provide an alternative approach on the way of exploring specific kinase inhibitors.
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Affiliation(s)
- Esra Unsal
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Bahar Degirmenci
- Department of Chemical and Biological Engineering, Koç University, Istanbul, Turkey
| | - Büşra Harmanda
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Burak Erman
- Department of Chemical and Biological Engineering, Koç University, Istanbul, Turkey
| | - Nurhan Ozlu
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey.
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186
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Weigt D, Hopf C, Médard G. Studying epigenetic complexes and their inhibitors with the proteomics toolbox. Clin Epigenetics 2016; 8:76. [PMID: 27437033 PMCID: PMC4950666 DOI: 10.1186/s13148-016-0244-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/05/2016] [Indexed: 12/27/2022] Open
Abstract
Some epigenetic modifier proteins have become validated clinical targets. With a few small molecule inhibitors already approved by national health administrations and many more in the pharmaceutical industry pipelines, there is a need for technologies that can promote full comprehension of the molecular action of these drugs. Proteomics, with its relatively unbiased nature, can contribute to a thorough understanding of the complexity of the megadalton complexes, which write, read and erase the histone code, and it can help study the on-target and off-target effect of the drugs designed to modulate their action. This review on the one hand gathers the published affinity probes able to decipher small molecule targets and off-targets in a close-to-native environment. These are small molecule analogues of epigenetic drugs conceived as protein target enrichment tools after they have engaged them in cells or lysates. Such probes, which have been designed for deacetylases, bromodomains, demethylases, and methyltransferases not only enrich their direct protein targets but also their stable interactors, which can be identified by mass spectrometry. Hence, they constitute a tool to study the epigenetic complexes together with other techniques also reviewed here: immunoaffinity purification with antibodies against native protein complex constituents or epitope tags, affinity matrices designed to bind recombinantly tagged protein, and enrichment of the complexes using histone tail peptides as baits. We expect that this toolbox will be adopted by more and more researchers willing to harness the spectacular advances in mass spectrometry to the epigenetic field.
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Affiliation(s)
- David Weigt
- />Center for Applied Research in Biomedical Mass Spectrometry (ABIMAS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- />HBIGS International Graduate School of Molecular and Cellular Biology, Heidelberg University, Im Neuenheimer Feld 501, 69120 Heidelberg, Germany
| | - Carsten Hopf
- />Center for Applied Research in Biomedical Mass Spectrometry (ABIMAS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- />HBIGS International Graduate School of Molecular and Cellular Biology, Heidelberg University, Im Neuenheimer Feld 501, 69120 Heidelberg, Germany
| | - Guillaume Médard
- />Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
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187
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Liu H, Liang C, Kollipara RK, Matsui M, Ke X, Jeong BC, Wang Z, Yoo KS, Yadav GP, Kinch LN, Grishin NV, Nam Y, Corey DR, Kittler R, Liu Q. HP1BP3, a Chromatin Retention Factor for Co-transcriptional MicroRNA Processing. Mol Cell 2016; 63:420-32. [PMID: 27425409 DOI: 10.1016/j.molcel.2016.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/26/2016] [Accepted: 06/09/2016] [Indexed: 02/08/2023]
Abstract
Recent studies suggest that the microprocessor (Drosha-DGCR8) complex can be recruited to chromatin to catalyze co-transcriptional processing of primary microRNAs (pri-miRNAs) in mammalian cells. However, the molecular mechanism of co-transcriptional miRNA processing is poorly understood. Here we find that HP1BP3, a histone H1-like chromatin protein, specifically associates with the microprocessor and promotes global miRNA biogenesis in human cells. Chromatin immunoprecipitation (ChIP) studies reveal genome-wide co-localization of HP1BP3 and Drosha and HP1BP3-dependent Drosha binding to actively transcribed miRNA loci. Moreover, HP1BP3 specifically binds endogenous pri-miRNAs and facilitates the Drosha/pri-miRNA association in vivo. Knockdown of HP1BP3 compromises pri-miRNA processing by causing premature release of pri-miRNAs from the chromatin. Taken together, these studies suggest that HP1BP3 promotes co-transcriptional miRNA processing via chromatin retention of nascent pri-miRNA transcripts. This work significantly expands the functional repertoire of the H1 family of proteins and suggests the existence of chromatin retention factors for widespread co-transcriptional miRNA processing.
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Affiliation(s)
- Haoming Liu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chunyang Liang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rahul K Kollipara
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Masayuki Matsui
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiong Ke
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Byung-Cheon Jeong
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhiqiang Wang
- International Institute for Integrated Sleep Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Kyoung Shin Yoo
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gaya P Yadav
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lisa N Kinch
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nicholas V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yunsun Nam
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David R Corey
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ralf Kittler
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qinghua Liu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; International Institute for Integrated Sleep Medicine, University of Tsukuba, Tsukuba 305-8575, Japan; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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188
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Christ L, Wenzel EM, Liestøl K, Raiborg C, Campsteijn C, Stenmark H. ALIX and ESCRT-I/II function as parallel ESCRT-III recruiters in cytokinetic abscission. J Cell Biol 2016; 212:499-513. [PMID: 26929449 PMCID: PMC4772496 DOI: 10.1083/jcb.201507009] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Cytokinetic abscission, the final stage of cell division, is mediated by the ESCRT machinery. Here, Christ et al. dissect the regulation of ESCRT-III recruitment and abscission timing and identify an intersection with abscission checkpoint signaling in cells with chromatin bridges. Cytokinetic abscission, the final stage of cell division where the two daughter cells are separated, is mediated by the endosomal sorting complex required for transport (ESCRT) machinery. The ESCRT-III subunit CHMP4B is a key effector in abscission, whereas its paralogue, CHMP4C, is a component in the abscission checkpoint that delays abscission until chromatin is cleared from the intercellular bridge. How recruitment of these components is mediated during cytokinesis remains poorly understood, although the ESCRT-binding protein ALIX has been implicated. Here, we show that ESCRT-II and the ESCRT-II–binding ESCRT-III subunit CHMP6 cooperate with ESCRT-I to recruit CHMP4B, with ALIX providing a parallel recruitment arm. In contrast to CHMP4B, we find that recruitment of CHMP4C relies predominantly on ALIX. Accordingly, ALIX depletion leads to furrow regression in cells with chromosome bridges, a phenotype associated with abscission checkpoint signaling failure. Collectively, our work reveals a two-pronged recruitment of ESCRT-III to the cytokinetic bridge and implicates ALIX in abscission checkpoint signaling.
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Affiliation(s)
- Liliane Christ
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, N-0379 Oslo, Norway Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, N-0379 Oslo, Norway
| | - Eva M Wenzel
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, N-0379 Oslo, Norway Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, N-0379 Oslo, Norway
| | - Knut Liestøl
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, N-0379 Oslo, Norway Department of Informatics, University of Oslo, N-0373 Oslo, Norway
| | - Camilla Raiborg
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, N-0379 Oslo, Norway Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, N-0379 Oslo, Norway
| | - Coen Campsteijn
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, N-0379 Oslo, Norway Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, N-0379 Oslo, Norway
| | - Harald Stenmark
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, N-0379 Oslo, Norway Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, N-0379 Oslo, Norway
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189
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Wink S, Hiemstra S, Herpers B, van de Water B. High-content imaging-based BAC-GFP toxicity pathway reporters to assess chemical adversity liabilities. Arch Toxicol 2016; 91:1367-1383. [PMID: 27358234 PMCID: PMC5316409 DOI: 10.1007/s00204-016-1781-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 06/21/2016] [Indexed: 11/04/2022]
Abstract
Adaptive cellular stress responses are paramount in the healthy control of cell and tissue homeostasis and generally activated during toxicity in a chemical-specific manner. Here, we established a platform containing a panel of distinct adaptive stress response reporter cell lines based on BAC-transgenomics GFP tagging in HepG2 cells. Our current panel of eleven BAC-GFP HepG2 reporters together contains (1) upstream sensors, (2) downstream transcription factors and (3) their respective target genes, representing the oxidative stress response pathway (Keap1/Nrf2/Srxn1), the unfolded protein response in the endoplasmic reticulum (Xbp1/Atf4/BiP/Chop) and the DNA damage response (53bp1/p53/p21). Using automated confocal imaging and quantitative single-cell image analysis, we established that all reporters allowed the time-resolved, sensitive and mode-of-action-specific activation of the individual BAC-GFP reporter cell lines as defined by a panel of pathway-specific training compounds. Implementing the temporal pathway activity information increased the discrimination of training compounds. For a set of >30 hepatotoxicants, the induction of Srxn1, BiP, Chop and p21 BAC-GFP reporters correlated strongly with the transcriptional responses observed in cryopreserved primary human hepatocytes. Together, our data indicate that a phenotypic adaptive stress response profiling platform will allow a high throughput and time-resolved classification of chemical-induced stress responses, thus assisting in the future mechanism-based safety assessment of chemicals.
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Affiliation(s)
- Steven Wink
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Steven Hiemstra
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Bram Herpers
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Bob van de Water
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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190
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The infectious BAC genomic DNA expression library: a high capacity vector system for functional genomics. Sci Rep 2016; 6:28644. [PMID: 27353647 PMCID: PMC4926088 DOI: 10.1038/srep28644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/13/2016] [Indexed: 01/24/2023] Open
Abstract
Gene dosage plays a critical role in a range of cellular phenotypes, yet most cellular expression systems use heterologous cDNA-based vectors which express proteins well above physiological levels. In contrast, genomic DNA expression vectors generate physiologically-relevant levels of gene expression by carrying the whole genomic DNA locus of a gene including its regulatory elements. Here we describe the first genomic DNA expression library generated using the high-capacity herpes simplex virus-1 amplicon technology to deliver bacterial artificial chromosomes (BACs) into cells by viral transduction. The infectious BAC (iBAC) library contains 184,320 clones with an average insert size of 134.5 kb. We show in a Chinese hamster ovary (CHO) disease model cell line and mouse embryonic stem (ES) cells that this library can be used for genetic rescue studies in a range of contexts including the physiological restoration of Ldlr deficiency, and viral receptor expression. The iBAC library represents an important new genetic analysis tool openly available to the research community.
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191
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Ettinger A, Kosodo Y, Huttner WB. Specific membrane dynamics during neural stem cell division. Methods Cell Biol 2016; 137:143-172. [PMID: 28065302 DOI: 10.1016/bs.mcb.2016.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Neural stem and progenitor cells in the developing cerebral cortex, but also when grown in culture, display a range of distinct phenomena during cytokinesis. Cleavage furrow ingression in neural progenitor cells can bisect their basal processes and, later on, result in midbody formation at the apical surface. After abscission, these midbodies are released as membrane-bound particles into the extracellular space, in contrast to uptake and degradation of postabscission midbodies in other cell types. Whether these cellular dynamics are unique to neural stem cells, or more ubiquitously found, and what biological significance these processes have for cell differentiation or cell-cell communication, are open questions that require a combination of approaches. Here, we discuss techniques to study the specific membrane dynamics underlying the basal process splitting and postabscission midbody release in neural stem cells. We provide some basic concepts and protocols to isolate, enrich and stain released midbodies, and follow midbody dynamics over time. Moreover, we discuss techniques to prepare cortical sections for high-voltage electron microscopy to visualize the fine basal processes of progenitor cells.
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Affiliation(s)
- A Ettinger
- Institute of Epigenetics and Stem Cells, Munich, Germany
| | - Y Kosodo
- Korea Brain Research Institute, Daegu, Korea
| | - W B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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192
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Partridge EC, Watkins TA, Mendenhall EM. Every transcription factor deserves its map: Scaling up epitope tagging of proteins to bypass antibody problems. Bioessays 2016; 38:801-11. [PMID: 27311628 DOI: 10.1002/bies.201600028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Genome-wide identification of transcription factor binding sites with the ChIP-seq method is an extremely important scientific endeavor - one that should ideally be performed for every transcription factor in as many cell types as possible. A major hurdle on the way to this goal is the necessity for a specific, ChIP-grade antibody for each transcription factor of interest, which is often not available. Here, we describe CETCh-seq, a recently published method utilizing genome engineering with the CRISPR/Cas9 system to circumvent the need for a specific antibody. Using the CETCh-seq method, targeted genomic editing results in an epitope-tagged transcription factor, which is recognized by a well-characterized, standard antibody, efficacious for ChIP-seq. We have used CETCh-seq in human cancer cell lines as well as mouse embryonic stem cells. We find that roughly 60% of transcription factors tagged using CETCh-seq produce a high quality ChIP-seq map, a significant improvement over traditional antibody-based methods.
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Affiliation(s)
| | | | - Eric M Mendenhall
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,University of Alabama in Huntsville, AL, USA
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193
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Zheng X, Ramani A, Soni K, Gottardo M, Zheng S, Ming Gooi L, Li W, Feng S, Mariappan A, Wason A, Widlund P, Pozniakovsky A, Poser I, Deng H, Ou G, Riparbelli M, Giuliano C, Hyman AA, Sattler M, Gopalakrishnan J, Li H. Molecular basis for CPAP-tubulin interaction in controlling centriolar and ciliary length. Nat Commun 2016; 7:11874. [PMID: 27306797 PMCID: PMC4912634 DOI: 10.1038/ncomms11874] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 05/09/2016] [Indexed: 02/05/2023] Open
Abstract
Centrioles and cilia are microtubule-based structures, whose precise formation requires controlled cytoplasmic tubulin incorporation. How cytoplasmic tubulin is recognized for centriolar/ciliary-microtubule construction remains poorly understood. Centrosomal-P4.1-associated-protein (CPAP) binds tubulin via its PN2-3 domain. Here, we show that a C-terminal loop-helix in PN2-3 targets β-tubulin at the microtubule outer surface, while an N-terminal helical motif caps microtubule's α-β surface of β-tubulin. Through this, PN2-3 forms a high-affinity complex with GTP-tubulin, crucial for defining numbers and lengths of centriolar/ciliary-microtubules. Surprisingly, two distinct mutations in PN2-3 exhibit opposite effects on centriolar/ciliary-microtubule lengths. CPAP(F375A), with strongly reduced tubulin interaction, causes shorter centrioles and cilia exhibiting doublet- instead of triplet-microtubules. CPAP(EE343RR) that unmasks the β-tubulin polymerization surface displays slightly reduced tubulin-binding affinity inducing over-elongation of newly forming centriolar/ciliary-microtubules by enhanced dynamic release of its bound tubulin. Thus CPAP regulates delivery of its bound-tubulin to define the size of microtubule-based cellular structures using a 'clutch-like' mechanism.
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Affiliation(s)
- Xiangdong Zheng
- Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.,MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anand Ramani
- Institute for Biochemistry I and Center for Molecular Medicine of the University of Cologne, Robert-Koch-Str. 21, Cologne 50931, Germany
| | - Komal Soni
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany.,Biomolecular NMR at Center for Integrated Protein Science Munich and Department Chemie, Technische Universität München, Lichtenbergstr. 4, Garching 85747, Germany
| | - Marco Gottardo
- Department of Life Sciences, University of Siena, Siena 53100, Italy
| | - Shuangping Zheng
- Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.,MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Li Ming Gooi
- Institute for Biochemistry I and Center for Molecular Medicine of the University of Cologne, Robert-Koch-Str. 21, Cologne 50931, Germany
| | - Wenjing Li
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shan Feng
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Aruljothi Mariappan
- Institute for Biochemistry I and Center for Molecular Medicine of the University of Cologne, Robert-Koch-Str. 21, Cologne 50931, Germany
| | - Arpit Wason
- Institute for Biochemistry I and Center for Molecular Medicine of the University of Cologne, Robert-Koch-Str. 21, Cologne 50931, Germany
| | - Per Widlund
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauer Str. 108, Dresden 01307, Germany
| | - Andrei Pozniakovsky
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauer Str. 108, Dresden 01307, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauer Str. 108, Dresden 01307, Germany
| | - Haiteng Deng
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guangshuo Ou
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Maria Riparbelli
- Department of Life Sciences, University of Siena, Siena 53100, Italy
| | - Callaini Giuliano
- Department of Life Sciences, University of Siena, Siena 53100, Italy
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauer Str. 108, Dresden 01307, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany.,Biomolecular NMR at Center for Integrated Protein Science Munich and Department Chemie, Technische Universität München, Lichtenbergstr. 4, Garching 85747, Germany
| | - Jay Gopalakrishnan
- Institute for Biochemistry I and Center for Molecular Medicine of the University of Cologne, Robert-Koch-Str. 21, Cologne 50931, Germany
| | - Haitao Li
- Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.,MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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194
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Kloet SL, Makowski MM, Baymaz HI, van Voorthuijsen L, Karemaker ID, Santanach A, Jansen PWTC, Di Croce L, Vermeulen M. The dynamic interactome and genomic targets of Polycomb complexes during stem-cell differentiation. Nat Struct Mol Biol 2016; 23:682-690. [PMID: 27294783 PMCID: PMC4939079 DOI: 10.1038/nsmb.3248] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 05/17/2016] [Indexed: 12/16/2022]
Abstract
Although the core subunits of Polycomb group (PcG) complexes are well characterized, little is known about the dynamics of these protein complexes during cellular differentiation. We used quantitative interaction proteomics and genome-wide profiling to study PcG proteins in mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs). We found that the stoichiometry and genome-wide binding of PRC1 and PRC2 were highly dynamic during neural differentiation. Intriguingly, we observed a downregulation and loss of PRC2 from chromatin marked with trimethylated histone H3 K27 (H3K27me3) during differentiation, whereas PRC1 was retained at these sites. Additionally, we found PRC1 at enhancer and promoter regions independently of PRC2 binding and H3K27me3. Finally, overexpression of NPC-specific PRC1 interactors in ESCs led to increased Ring1b binding to, and decreased expression of, NPC-enriched Ring1b-target genes. In summary, our integrative analyses uncovered dynamic PcG subcomplexes and their widespread colocalization with active chromatin marks during differentiation.
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Affiliation(s)
- Susan L Kloet
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands
| | - Matthew M Makowski
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands
| | - H Irem Baymaz
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands
| | - Lisa van Voorthuijsen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands
| | - Ino D Karemaker
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands
| | - Alexandra Santanach
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Biomedical Genetics, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Biomedical Genetics, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands.,Cancer GenomiCs.nl (CGC.nl) Consortium, Center for Molecular Medicine, UMC Utrecht, The Netherlands
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195
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Baker O, Gupta A, Obst M, Zhang Y, Anastassiadis K, Fu J, Stewart AF. RAC-tagging: Recombineering And Cas9-assisted targeting for protein tagging and conditional analyses. Sci Rep 2016; 6:25529. [PMID: 27216209 PMCID: PMC4877586 DOI: 10.1038/srep25529] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/13/2016] [Indexed: 11/30/2022] Open
Abstract
A fluent method for gene targeting to establish protein tagged and ligand inducible conditional loss-of-function alleles is described. We couple new recombineering applications for one-step cloning of gRNA oligonucleotides and rapid generation of short-arm (~1 kb) targeting constructs with the power of Cas9-assisted targeting to establish protein tagged alleles in embryonic stem cells at high efficiency. RAC (Recombineering And Cas9)-tagging with Venus, BirM, APEX2 and the auxin degron is facilitated by a recombineering-ready plasmid series that permits the reuse of gene-specific reagents to insert different tags. Here we focus on protein tagging with the auxin degron because it is a ligand-regulated loss-of-function strategy that is rapid and reversible. Furthermore it includes the additional challenge of biallelic targeting. Despite high frequencies of monoallelic RAC-targeting, we found that simultaneous biallelic targeting benefits from long-arm (>4 kb) targeting constructs. Consequently an updated recombineering pipeline for fluent generation of long arm targeting constructs is also presented.
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Affiliation(s)
- Oliver Baker
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Ashish Gupta
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Mandy Obst
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Youming Zhang
- Shandong University–Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Shanda Nanlu 27, 250100 Jinan, People’s Republic of China
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Jun Fu
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
- Shandong University–Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Shanda Nanlu 27, 250100 Jinan, People’s Republic of China
| | - A. Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
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196
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Abstract
Protein-protein interactions (PPIs) underlie most, if not all, cellular functions. The comprehensive mapping of these complex networks of stable and transient associations thus remains a key goal, both for systems biology-based initiatives (where it can be combined with other 'omics' data to gain a better understanding of functional pathways and networks) and for focused biological studies. Despite the significant challenges of such an undertaking, major strides have been made over the past few years. They include improvements in the computation prediction of PPIs and the literature curation of low-throughput studies of specific protein complexes, but also an increase in the deposition of high-quality data from non-biased high-throughput experimental PPI mapping strategies into publicly available databases.
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Affiliation(s)
- Virja Mehta
- Department of Cellular and Molecular Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
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197
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Guerrera D, Shah J, Vasileva E, Sluysmans S, Méan I, Jond L, Poser I, Mann M, Hyman AA, Citi S. PLEKHA7 Recruits PDZD11 to Adherens Junctions to Stabilize Nectins. J Biol Chem 2016; 291:11016-29. [PMID: 27044745 DOI: 10.1074/jbc.m115.712935] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Indexed: 01/07/2023] Open
Abstract
PLEKHA7 is a junctional protein implicated in stabilization of the cadherin protein complex, hypertension, cardiac contractility, glaucoma, microRNA processing, and susceptibility to bacterial toxins. To gain insight into the molecular basis for the functions of PLEKHA7, we looked for new PLEKHA7 interactors. Here, we report the identification of PDZ domain-containing protein 11 (PDZD11) as a new interactor of PLEKHA7 by yeast two-hybrid screening and by mass spectrometry analysis of PLEKHA7 immunoprecipitates. We show that PDZD11 (17 kDa) is expressed in epithelial and endothelial cells, where it forms a complex with PLEKHA7, as determined by co-immunoprecipitation analysis. The N-terminal Trp-Trp (WW) domain of PLEKHA7 interacts directly with the N-terminal 44 amino acids of PDZD11, as shown by GST-pulldown assays. Immunofluorescence analysis shows that PDZD11 is localized at adherens junctions in a PLEKHA7-dependent manner, because its junctional localization is abolished by knock-out of PLEKHA7, and is rescued by re-expression of exogenous PLEKHA7. The junctional recruitment of nectin-1 and nectin-3 and their protein levels are decreased via proteasome-mediated degradation in epithelial cells where either PDZD11 or PLEKHA7 have been knocked-out. PDZD11 forms a complex with nectin-1 and nectin-3, and its PDZ domain interacts directly with the PDZ-binding motif of nectin-1. PDZD11 is required for the efficient assembly of apical junctions of epithelial cells at early time points in the calcium-switch model. These results show that the PLEKHA7-PDZD11 complex stabilizes nectins to promote efficient early junction assembly and uncover a new molecular mechanism through which PLEKHA7 recruits PDZ-binding membrane proteins to epithelial adherens junctions.
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Affiliation(s)
- Diego Guerrera
- From the Department of Cell Biology and Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211-4 Geneva, Switzerland
| | - Jimit Shah
- From the Department of Cell Biology and Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211-4 Geneva, Switzerland
| | - Ekaterina Vasileva
- From the Department of Cell Biology and Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211-4 Geneva, Switzerland
| | - Sophie Sluysmans
- From the Department of Cell Biology and Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211-4 Geneva, Switzerland
| | - Isabelle Méan
- From the Department of Cell Biology and Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211-4 Geneva, Switzerland
| | - Lionel Jond
- From the Department of Cell Biology and Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211-4 Geneva, Switzerland
| | - Ina Poser
- the Max Planck Institute for Cell Biology and Genetics, 01307 Dresden, Germany, and
| | - Matthias Mann
- the Max Planck Institute for Biochemistry, 82152 Martinsried, Germany
| | - Anthony A Hyman
- the Max Planck Institute for Cell Biology and Genetics, 01307 Dresden, Germany, and
| | - Sandra Citi
- From the Department of Cell Biology and Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211-4 Geneva, Switzerland,
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198
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FBXW7 and USP7 regulate CCDC6 turnover during the cell cycle and affect cancer drugs susceptibility in NSCLC. Oncotarget 2016; 6:12697-709. [PMID: 25885523 PMCID: PMC4494967 DOI: 10.18632/oncotarget.3708] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/03/2015] [Indexed: 11/25/2022] Open
Abstract
CCDC6 gene product is a pro-apoptotic protein substrate of ATM, whose loss or inactivation enhances tumour progression. In primary tumours, the impaired function of CCDC6 protein has been ascribed to CCDC6 rearrangements and to somatic mutations in several neoplasia. Recently, low levels of CCDC6 protein, in NSCLC, have been correlated with tumor prognosis. However, the mechanisms responsible for the variable levels of CCDC6 in primary tumors have not been described yet. We show that CCDC6 turnover is regulated in a cell cycle dependent manner. CCDC6 undergoes a cyclic variation in the phosphorylated status and in protein levels that peak at G2 and decrease in mitosis. The reduced stability of CCDC6 in the M phase is dependent on mitotic kinases and on degron motifs that are present in CCDC6 and direct the recruitment of CCDC6 to the FBXW7 E3 Ubl. The de-ubiquitinase enzyme USP7 appears responsible of the fine tuning of the CCDC6 stability, affecting cells behaviour and drug response. Thus, we propose that the amount of CCDC6 protein in primary tumors, as reported in lung, may depend on the impairment of the CCDC6 turnover due to altered protein-protein interaction and post-translational modifications and may be critical in optimizing personalized therapy.
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199
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Raab M, Gentili M, de Belly H, Thiam HR, Vargas P, Jimenez AJ, Lautenschlaeger F, Voituriez R, Lennon-Duménil AM, Manel N, Piel M. ESCRT III repairs nuclear envelope ruptures during cell migration to limit DNA damage and cell death. Science 2016; 352:359-62. [PMID: 27013426 DOI: 10.1126/science.aad7611] [Citation(s) in RCA: 624] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/25/2016] [Indexed: 12/18/2022]
Abstract
In eukaryotic cells, the nuclear envelope separates the genomic DNA from the cytoplasmic space and regulates protein trafficking between the two compartments. This barrier is only transiently dissolved during mitosis. Here, we found that it also opened at high frequency in migrating mammalian cells during interphase, which allowed nuclear proteins to leak out and cytoplasmic proteins to leak in. This transient opening was caused by nuclear deformation and was rapidly repaired in an ESCRT (endosomal sorting complexes required for transport)-dependent manner. DNA double-strand breaks coincided with nuclear envelope opening events. As a consequence, survival of cells migrating through confining environments depended on efficient nuclear envelope and DNA repair machineries. Nuclear envelope opening in migrating leukocytes could have potentially important consequences for normal and pathological immune responses.
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Affiliation(s)
- M Raab
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France. Institut Pierre-Gilles de Gennes, PSL Research University, F-75005 Paris, France
| | - M Gentili
- Institut Curie, PSL Research University, INSERM, U 932, F-75005 Paris, France
| | - H de Belly
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - H R Thiam
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - P Vargas
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France. Institut Pierre-Gilles de Gennes, PSL Research University, F-75005 Paris, France
| | - A J Jimenez
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - F Lautenschlaeger
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - Raphaël Voituriez
- Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Paris, France. Laboratoire Jean Perrin, CNRS UMR 8237, Université Pierre et Marie Curie, Paris, France
| | - A M Lennon-Duménil
- Institut Curie, PSL Research University, INSERM, U 932, F-75005 Paris, France
| | - N Manel
- Institut Curie, PSL Research University, INSERM, U 932, F-75005 Paris, France
| | - M Piel
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France. Institut Pierre-Gilles de Gennes, PSL Research University, F-75005 Paris, France.
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200
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Sudhir PR, Chen CH. Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology. Int J Mol Sci 2016; 17:432. [PMID: 27011181 PMCID: PMC4813282 DOI: 10.3390/ijms17030432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 03/08/2016] [Accepted: 03/16/2016] [Indexed: 12/24/2022] Open
Abstract
A protein complex consists of two or more proteins that are linked together through protein-protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples.
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Affiliation(s)
| | - Chung-Hsuan Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
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