1
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Collombet S, Rall I, Dugast-Darzacq C, Heckert A, Halavatyi A, Le Saux A, Dailey G, Darzacq X, Heard E. RNA polymerase II depletion from the inactive X chromosome territory is not mediated by physical compartmentalization. Nat Struct Mol Biol 2023; 30:1216-1223. [PMID: 37291424 PMCID: PMC10442225 DOI: 10.1038/s41594-023-01008-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 04/28/2023] [Indexed: 06/10/2023]
Abstract
Subnuclear compartmentalization has been proposed to play an important role in gene regulation by segregating active and inactive parts of the genome in distinct physical and biochemical environments. During X chromosome inactivation (XCI), the noncoding Xist RNA coats the X chromosome, triggers gene silencing and forms a dense body of heterochromatin from which the transcription machinery appears to be excluded. Phase separation has been proposed to be involved in XCI, and might explain the exclusion of the transcription machinery by preventing its diffusion into the Xist-coated territory. Here, using quantitative fluorescence microscopy and single-particle tracking, we show that RNA polymerase II (RNAPII) freely accesses the Xist territory during the initiation of XCI. Instead, the apparent depletion of RNAPII is due to the loss of its chromatin stably bound fraction. These findings indicate that initial exclusion of RNAPII from the inactive X reflects the absence of actively transcribing RNAPII, rather than a consequence of putative physical compartmentalization of the inactive X heterochromatin domain.
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Affiliation(s)
| | - Isabell Rall
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Alec Heckert
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Agnes Le Saux
- Curie Institute, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, Paris, France
| | - Gina Dailey
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA.
| | - Edith Heard
- European Molecular Biology Laboratory, Heidelberg, Germany.
- Curie Institute, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, Paris, France.
- College de France, Paris, France.
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2
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Mocaer K, Mizzon G, Gunkel M, Halavatyi A, Steyer A, Oorschot V, Schorb M, Le Kieffre C, Yee DP, Chevalier F, Gallet B, Decelle J, Schwab Y, Ronchi P. Targeted volume correlative light and electron microscopy of an environmental marine microorganism. J Cell Sci 2023; 136:jcs261355. [PMID: 37455654 PMCID: PMC10445747 DOI: 10.1242/jcs.261355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Photosynthetic microalgae are responsible for an important fraction of CO2 fixation and O2 production on Earth. Three-dimensional (3D) ultrastructural characterization of these organisms in their natural environment can contribute to a deeper understanding of their cell biology. However, the low throughput of volume electron microscopy (vEM) methods along with the complexity and heterogeneity of environmental samples pose great technical challenges. In the present study, we used a workflow based on a specific electron microscopy sample preparation method compatible with both light and vEM imaging in order to target one cell among a complex natural community. This method revealed the 3D subcellular landscape of a photosynthetic dinoflagellate, which we identified as Ensiculifera tyrrhenica, with quantitative characterization of multiple organelles. We show that this cell contains a single convoluted chloroplast and show the arrangement of the flagellar apparatus with its associated photosensitive elements. Moreover, we observed partial chromatin unfolding, potentially associated with transcription activity in these organisms, in which chromosomes are permanently condensed. Together with providing insights in dinoflagellate biology, this proof-of-principle study illustrates an efficient tool for the targeted ultrastructural analysis of environmental microorganisms in heterogeneous mixes.
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Affiliation(s)
- Karel Mocaer
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between the European Molecular Biology Laboratory and the Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Giulia Mizzon
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Department of Infectious Diseases, Molecular Virology, CIID, 69120 Heidelberg, Germany
- German Center for Infection Research, Heidelberg partner site, 69120 Heidelberg, Germany
| | - Manuel Gunkel
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Aliaksandr Halavatyi
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Anna Steyer
- EMBL Imaging Centre, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Viola Oorschot
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Martin Schorb
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Daniel P. Yee
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38054 Grenoble, France
| | - Fabien Chevalier
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38054 Grenoble, France
| | - Benoit Gallet
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France
| | - Johan Decelle
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38054 Grenoble, France
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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3
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Didaskalou S, Efstathiou C, Galtsidis S, Kesisova I, Halavatyi A, Elmali T, Tsolou A, Girod A, Koffa M. HURP localization in metaphase is the result of a multi-step process requiring its phosphorylation at Ser627 residue. Front Cell Dev Biol 2023; 11:981425. [PMID: 37484914 PMCID: PMC10361663 DOI: 10.3389/fcell.2023.981425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Faithful chromosome segregation during cell division requires accurate mitotic spindle formation. As mitosis occurs rapidly within the cell cycle, the proteins involved in mitotic spindle assembly undergo rapid changes, including their interactions with other proteins. The proper localization of the HURP protein on the kinetochore fibers, in close proximity to chromosomes, is crucial for ensuring accurate congression and segregation of chromosomes. In this study, we employ photoactivation and FRAP experiments to investigate the impact of alterations in microtubule flux and phosphorylation of HURP at the Ser627 residue on its dynamics. Furthermore, through immunoprecipitations assays, we demonstrate the interactions of HURP with various proteins, such as TPX2, Aurora A, Eg5, Dynein, Kif5B, and Importin β, in mammalian cells during mitosis. We also find that phosphorylation of HURP at Ser627 regulates its interaction with these partners during mitosis. Our findings suggest that HURP participates in at least two distinct complexes during metaphase to ensure its proper localization in close proximity to chromosomes, thereby promoting the bundling and stabilization of kinetochore fibers.
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Affiliation(s)
- Stylianos Didaskalou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Christos Efstathiou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
- Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sotirios Galtsidis
- Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ilοna Kesisova
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
- Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Aliaksandr Halavatyi
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tountzai Elmali
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Avgi Tsolou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Andreas Girod
- Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Maria Koffa
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
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4
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Jung J, Khan MM, Landry J, Halavatyi A, Machado P, Reiss M, Pepperkok R. Regulation of the COPII secretory machinery via focal adhesions and extracellular matrix signaling. J Cell Biol 2022; 221:213351. [PMID: 35829701 PMCID: PMC9284426 DOI: 10.1083/jcb.202110081] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 05/10/2022] [Accepted: 06/24/2022] [Indexed: 12/19/2022] Open
Abstract
Proteins that enter the secretory pathway are transported from their place of synthesis in the endoplasmic reticulum to the Golgi complex by COPII-coated carriers. The networks of proteins that regulate these components in response to extracellular cues have remained largely elusive. Using high-throughput microscopy, we comprehensively screened 378 cytoskeleton-associated and related proteins for their functional interaction with the coat protein complex II (COPII) components SEC23A and SEC23B. Among these, we identified a group of proteins associated with focal adhesions (FERMT2, MACF1, MAPK8IP2, NGEF, PIK3CA, and ROCK1) that led to the downregulation of SEC23A when depleted by siRNA. Changes in focal adhesions induced by plating cells on ECM also led to the downregulation of SEC23A and decreases in VSVG transport from ER to Golgi. Both the expression of SEC23A and the transport defect could be rescued by treatment with a focal adhesion kinase inhibitor. Altogether, our results identify a network of cytoskeleton-associated proteins connecting focal adhesions and ECM-related signaling with the gene expression of the COPII secretory machinery and trafficking.
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Affiliation(s)
- Juan Jung
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Muzamil Majid Khan
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Translational Lung Research Center Heidelberg, German Center for Lung Research, Heidelberg, Germany
| | - Jonathan Landry
- Core Facilities Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Aliaksandr Halavatyi
- Core Facilities Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Pedro Machado
- Core Facilities Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Miriam Reiss
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rainer Pepperkok
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Core Facilities Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Translational Lung Research Center Heidelberg, German Center for Lung Research, Heidelberg, Germany
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5
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Sánchez-Iranzo H, Halavatyi A, Diz-Muñoz A. Strength of interactions in the Notch gene regulatory network determines patterning and fate in the notochord. eLife 2022; 11:75429. [PMID: 35658971 PMCID: PMC9170247 DOI: 10.7554/elife.75429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Development of multicellular organisms requires the generation of gene expression patterns that determines cell fate and organ shape. Groups of genetic interactions known as Gene Regulatory Networks (GRNs) play a key role in the generation of such patterns. However, how the topology and parameters of GRNs determine patterning in vivo remains unclear due to the complexity of most experimental systems. To address this, we use the zebrafish notochord, an organ where coin-shaped precursor cells are initially arranged in a simple unidimensional geometry. These cells then differentiate into vacuolated and sheath cells. Using newly developed transgenic tools together with in vivo imaging, we identify jag1a and her6/her9 as the main components of a Notch GRN that generates a lateral inhibition pattern and determines cell fate. Making use of this experimental system and mathematical modeling we show that lateral inhibition patterning is promoted when ligand-receptor interactions are stronger within the same cell than in neighboring cells. Altogether, we establish the zebrafish notochord as an experimental system to study pattern generation, and identify and characterize how the properties of GRNs determine self-organization of gene patterning and cell fate.
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Affiliation(s)
- Héctor Sánchez-Iranzo
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Aliaksandr Halavatyi
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alba Diz-Muñoz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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6
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Zimmerli CE, Allegretti M, Rantos V, Goetz SK, Obarska-Kosinska A, Zagoriy I, Halavatyi A, Hummer G, Mahamid J, Kosinski J, Beck M. Nuclear pores dilate and constrict in cellulo. Science 2021; 374:eabd9776. [PMID: 34762489 DOI: 10.1126/science.abd9776] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Christian E Zimmerli
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany.,Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Matteo Allegretti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Vasileios Rantos
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany.,EMBL Hamburg, 22607 Hamburg, Germany
| | - Sara K Goetz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Agnieszka Obarska-Kosinska
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,EMBL Hamburg, 22607 Hamburg, Germany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | | | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany.,EMBL Hamburg, 22607 Hamburg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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7
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Zimoń M, Huang Y, Trasta A, Halavatyi A, Liu JZ, Chen CY, Blattmann P, Klaus B, Whelan CD, Sexton D, John S, Huber W, Tsai EA, Pepperkok R, Runz H. Pairwise effects between lipid GWAS genes modulate lipid plasma levels and cellular uptake. Nat Commun 2021; 12:6411. [PMID: 34741066 PMCID: PMC8571362 DOI: 10.1038/s41467-021-26761-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 10/09/2021] [Indexed: 12/27/2022] Open
Abstract
Complex traits are characterized by multiple genes and variants acting simultaneously on a phenotype. However, studying the contribution of individual pairs of genes to complex traits has been challenging since human genetics necessitates very large population sizes, while findings from model systems do not always translate to humans. Here, we combine genetics with combinatorial RNAi (coRNAi) to systematically test for pairwise additive effects (AEs) and genetic interactions (GIs) between 30 lipid genome-wide association studies (GWAS) genes. Gene-based burden tests from 240,970 exomes show that in carriers with truncating mutations in both, APOB and either PCSK9 or LPL ("human double knock-outs") plasma lipid levels change additively. Genetics and coRNAi identify overlapping AEs for 12 additional gene pairs. Overlapping GIs are observed for TOMM40/APOE with SORT1 and NCAN. Our study identifies distinct gene pairs that modulate plasma and cellular lipid levels primarily via AEs and nominates putative drug target pairs for improved lipid-lowering combination therapies.
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Affiliation(s)
- Magdalena Zimoń
- grid.4709.a0000 0004 0495 846XMolecular Medicine Partnership Unit (MMPU), University of Heidelberg/EMBL, Heidelberg, Germany ,Cell Biology and Biophysics Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Yunfeng Huang
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - Anthi Trasta
- grid.4709.a0000 0004 0495 846XMolecular Medicine Partnership Unit (MMPU), University of Heidelberg/EMBL, Heidelberg, Germany ,Cell Biology and Biophysics Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Aliaksandr Halavatyi
- Advanced Light Microscopy Facility (ALMF), European Molecular Biological Laboratory, Heidelberg, Germany
| | - Jimmy Z. Liu
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - Chia-Yen Chen
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Psychiatric and Neurodevelopmental Genetics Unit, Mass General Hospital, Boston, MA USA
| | - Peter Blattmann
- grid.4709.a0000 0004 0495 846XMolecular Medicine Partnership Unit (MMPU), University of Heidelberg/EMBL, Heidelberg, Germany ,Cell Biology and Biophysics Unit, European Molecular Biological Laboratory, Heidelberg, Germany ,grid.508389.f0000 0004 6414 2411Idorsia Pharmaceuticals Ltd, Basel, Switzerland
| | - Bernd Klaus
- Genome Biology Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Christopher D. Whelan
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - David Sexton
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - Sally John
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Ellen A. Tsai
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - Rainer Pepperkok
- grid.4709.a0000 0004 0495 846XMolecular Medicine Partnership Unit (MMPU), University of Heidelberg/EMBL, Heidelberg, Germany ,Cell Biology and Biophysics Unit, European Molecular Biological Laboratory, Heidelberg, Germany ,Advanced Light Microscopy Facility (ALMF), European Molecular Biological Laboratory, Heidelberg, Germany
| | - Heiko Runz
- grid.4709.a0000 0004 0495 846XMolecular Medicine Partnership Unit (MMPU), University of Heidelberg/EMBL, Heidelberg, Germany ,grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
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8
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Khan MM, Poeckel D, Halavatyi A, Zukowska-Kasprzyk J, Stein F, Vappiani J, Sevin DC, Tischer C, Zinn N, Eley JD, Gudmann NS, Muley T, Winter H, Fisher AJ, Nanthakumar CB, Bergamini G, Pepperkok R. An integrated multiomic and quantitative label-free microscopy-based approach to study pro-fibrotic signalling in ex vivo human precision-cut lung slices. Eur Respir J 2021; 58:13993003.00221-2020. [PMID: 33361096 PMCID: PMC8318569 DOI: 10.1183/13993003.00221-2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 12/09/2020] [Indexed: 12/17/2022]
Abstract
Fibrosis can affect any organ, resulting in the loss of tissue architecture and function with often life-threatening consequences. Pathologically, fibrosis is characterised by the expansion of connective tissue due to excessive deposition of extracellular matrix (ECM) proteins, including the fibrillar forms of collagen. A significant limitation for discovering cures for fibrosis is the availability of suitable human models and techniques to quantify mature fibrillar collagen deposition as close as possible to human physiological conditions. Here we have extensively characterised an ex vivo cultured human lung tissue-derived, precision-cut lung slices (hPCLS) model using label-free second harmonic generation (SHG) light microscopy to quantify fibrillar collagen deposition and mass spectrometry-based techniques to obtain a proteomic and metabolomic fingerprint of hPCLS in ex vivo culture. We demonstrate that hPCLS are viable and metabolically active, with mesenchymal, epithelial, endothelial and immune cell types surviving for at least 2 weeks in ex vivo culture. Analysis of hPCLS-conditioned supernatants showed a strong induction of pulmonary fibrosis-related ECM proteins upon transforming growth factor-β1 (TGF-β1) stimulation. This upregulation of ECM proteins was not translated into an increased deposition of fibrillar collagen. In support of this observation, we revealed the presence of a pro-ECM degradation activity in our ex vivo cultures of hPCLS, inhibition of which by a metalloproteinase inhibitor resulted in increased collagen deposition in response to TGF-β1 stimulation. Together the data show that an integrated approach of measuring soluble pro-fibrotic markers alongside quantitative SHG-based analysis of fibrillar collagen is a valuable tool for studying pro-fibrotic signalling and testing anti-fibrotic agents. Multiomic and label-free imaging-based characterisation of ex vivo cultured human precision-cut lung slices (hPCLS) reveals that MMP signalling is a rate-limiting factor necessary for deposition of fibrillar collagen in ECM of hPCLShttps://bit.ly/3rcUa0e
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Affiliation(s)
- Muzamil Majid Khan
- European Molecular Biology Laboratory, Heidelberg, Germany.,Discovery Biology, Cellzome GmbH, GSK, Heidelberg, Germany.,Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Daniel Poeckel
- Discovery Biology, Cellzome GmbH, GSK, Heidelberg, Germany
| | - Aliaksandr Halavatyi
- European Molecular Biology Laboratory, Heidelberg, Germany.,Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | | | - Frank Stein
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Daniel C Sevin
- Discovery Biology, Cellzome GmbH, GSK, Heidelberg, Germany
| | | | - Nico Zinn
- Discovery Biology, Cellzome GmbH, GSK, Heidelberg, Germany
| | | | | | - Thomas Muley
- Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Biobank Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | - Hauke Winter
- Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Biobank Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | - Andrew J Fisher
- Newcastle University Translational and Clinical Research Institute and Institute of Transplantation, Newcastle upon Tyne Hospitals, Newcastle upon Tyne, UK
| | | | - Giovanna Bergamini
- Discovery Biology, Cellzome GmbH, GSK, Heidelberg, Germany.,G. Bergamini and R. Pepperkok contributed equally to this article as lead authors and supervised the work
| | - Rainer Pepperkok
- European Molecular Biology Laboratory, Heidelberg, Germany .,Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,G. Bergamini and R. Pepperkok contributed equally to this article as lead authors and supervised the work
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9
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Fuqua T, Jordan J, Halavatyi A, Tischer C, Richter K, Crocker J. An open-source semi-automated robotics pipeline for embryo immunohistochemistry. Sci Rep 2021; 11:10314. [PMID: 33986394 PMCID: PMC8119710 DOI: 10.1038/s41598-021-89676-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/19/2021] [Indexed: 11/09/2022] Open
Abstract
A significant challenge for developmental systems biology is balancing throughput with controlled conditions that minimize experimental artifacts. Large-scale developmental screens such as unbiased mutagenesis surveys have been limited in their applicability to embryonic systems, as the technologies for quantifying precise expression patterns in whole animals has not kept pace with other sequencing-based technologies. Here, we outline an open-source semi-automated pipeline to chemically fixate, stain, and 3D-image Drosophila embryos. Central to this pipeline is a liquid handling robot, Flyspresso, which automates the steps of classical embryo fixation and staining. We provide the schematics and an overview of the technology for an engineer or someone equivalently trained to reproduce and further improve upon Flyspresso, and highlight the Drosophila embryo fixation and colorimetric or antibody staining protocols. Additionally, we provide a detailed overview and stepwise protocol for our adaptive-feedback pipeline for automated embryo imaging on confocal microscopes. We demonstrate the efficiency of this pipeline compared to classical techniques, and how it can be repurposed or scaled to other protocols and biological systems. We hope our pipeline will serve as a platform for future research, allowing a broader community of users to build, execute, and share similar experiments.
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Affiliation(s)
- Timothy Fuqua
- European Molecular Biology Laboratory, Heidelberg, Germany.,Collaboration for Joint PhD Degree Between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Jeff Jordan
- Janelia Research Campus, 19700 Helix Dr, Ashburn, VA, 20147, USA
| | | | | | | | - Justin Crocker
- European Molecular Biology Laboratory, Heidelberg, Germany.
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10
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Fuqua T, Jordan J, van Breugel ME, Halavatyi A, Tischer C, Polidoro P, Abe N, Tsai A, Mann RS, Stern DL, Crocker J. Dense and pleiotropic regulatory information in a developmental enhancer. Nature 2020; 587:235-239. [PMID: 33057197 DOI: 10.1038/s41586-020-2816-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/22/2020] [Indexed: 01/08/2023]
Abstract
Changes in gene regulation underlie much of phenotypic evolution1. However, our understanding of the potential for regulatory evolution is biased, because most evidence comes from either natural variation or limited experimental perturbations2. Using an automated robotics pipeline, we surveyed an unbiased mutation library for a developmental enhancer in Drosophila melanogaster. We found that almost all mutations altered gene expression and that parameters of gene expression-levels, location, and state-were convolved. The widespread pleiotropic effects of most mutations may constrain the evolvability of developmental enhancers. Consistent with these observations, comparisons of diverse Drosophila larvae revealed apparent biases in the phenotypes influenced by the enhancer. Developmental enhancers may encode a higher density of regulatory information than has been appreciated previously, imposing constraints on regulatory evolution.
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Affiliation(s)
- Timothy Fuqua
- European Molecular Biology Laboratory, Heidelberg, Germany.,Joint PhD Collaboration, EMBL and Faculty of Biosciences Heidelberg University, Heidelberg, Germany
| | | | | | | | | | | | - Namiko Abe
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Albert Tsai
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Richard S Mann
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | | | - Justin Crocker
- European Molecular Biology Laboratory, Heidelberg, Germany.
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11
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Serçin Ö, Reither S, Roidos P, Ballin N, Palikyras S, Baginska A, Rein K, Llamazares M, Halavatyi A, Winter H, Muley T, Jurkowska RZ, Abdollahi A, Zenke FT, Neumann B, Mardin BR. A solid-phase transfection platform for arrayed CRISPR screens. Mol Syst Biol 2020; 16:e9611. [PMID: 33438803 PMCID: PMC7273733 DOI: 10.15252/msb.209611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024] Open
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12
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Serçin Ö, Reither S, Roidos P, Ballin N, Palikyras S, Baginska A, Rein K, Llamazares M, Halavatyi A, Winter H, Muley T, Jurkowska RZ, Abdollahi A, Zenke FT, Neumann B, Mardin BR. A solid-phase transfection platform for arrayed CRISPR screens. Mol Syst Biol 2019; 15:e8983. [PMID: 31885201 PMCID: PMC6926425 DOI: 10.15252/msb.20198983] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 11/24/2019] [Accepted: 11/27/2019] [Indexed: 12/24/2022] Open
Abstract
Arrayed CRISPR-based screens emerge as a powerful alternative to pooled screens making it possible to investigate a wide range of cellular phenotypes that are typically not amenable to pooled screens. Here, we describe a solid-phase transfection platform that enables CRISPR-based genetic screens in arrayed format with flexible readouts. We demonstrate efficient gene knockout upon delivery of guide RNAs and Cas9/guide RNA ribonucleoprotein complexes into untransformed and cancer cell lines. In addition, we provide evidence that our platform can be easily adapted to high-throughput screens and we use this approach to study oncogene addiction in tumor cells. Finally demonstrating that the human primary cells can also be edited using this method, we pave the way for rapid testing of potential targeted therapies.
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Affiliation(s)
| | - Sabine Reither
- Advanced Light Microscopy FacilityEuropean Molecular Biology LaboratoryHeidelbergGermany
| | | | | | | | | | | | | | - Aliaksandr Halavatyi
- Advanced Light Microscopy FacilityEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Hauke Winter
- Department of SurgeryThoraxklinik at University Hospital HeidelbergHeidelbergGermany
- Translational Lung Research Center (TLRC) HeidelbergMember of the German Center for Lung Research (DZL)HeidelbergGermany
| | - Thomas Muley
- Translational Lung Research Center (TLRC) HeidelbergMember of the German Center for Lung Research (DZL)HeidelbergGermany
- Thoraxklinik at University Hospital HeidelbergHeidelbergGermany
| | | | - Amir Abdollahi
- Division of Molecular and Translational Radiation OncologyNational Center for Tumor Diseases (NCT)and German Cancer Research Center (DKFZ), Heidelberg University HospitalHeidelbergGermany
- Clinical Cooperation Unit Translational Radiation OncologyGerman Cancer Consortium (DKTK) Core Center HeidelbergHeidelbergGermany
| | - Frank T Zenke
- Translational Innovation Platform OncologyMerck KGaADarmstadtGermany
| | - Beate Neumann
- Advanced Light Microscopy FacilityEuropean Molecular Biology LaboratoryHeidelbergGermany
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13
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Frey D, Dittrich A, Kühbandner I, Halavatyi A, Hagner M, Guerra M, Wege S, Halls V, Herth F, Schultz C, Mall M. P219 Small-molecule FRET flow cytometry: a novel technique to monitor surface-associated protease activity in cystic fibrosis. J Cyst Fibros 2019. [DOI: 10.1016/s1569-1993(19)30512-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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Hadzic E, Catillon M, Halavatyi A, Medves S, Van Troys M, Moes M, Baird MA, Davidson MW, Schaffner-Reckinger E, Ampe C, Friederich E. Delineating the Tes Interaction Site in Zyxin and Studying Cellular Effects of Its Disruption. PLoS One 2015; 10:e0140511. [PMID: 26509500 PMCID: PMC4624954 DOI: 10.1371/journal.pone.0140511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/25/2015] [Indexed: 01/21/2023] Open
Abstract
Focal adhesions are integrin-based structures that link the actin cytoskeleton and the extracellular matrix. They play an important role in various cellular functions such as cell signaling, cell motility and cell shape. To ensure and fine tune these different cellular functions, adhesions are regulated by a large number of proteins. The LIM domain protein zyxin localizes to focal adhesions where it participates in the regulation of the actin cytoskeleton. Because of its interactions with a variety of binding partners, zyxin has been proposed to act as a molecular scaffold. Here, we studied the interaction of zyxin with such a partner: Tes. Similar to zyxin, Tes harbors three highly conserved LIM domains of which the LIM1 domain directly interacts with zyxin. Using different zyxin variants in pull-down assays and ectopic recruitment experiments, we identified the Tes binding site in zyxin and showed that four highly conserved amino acids are crucial for its interaction with Tes. Based upon these findings, we used a zyxin mutant defective in Tes-binding to assess the functional consequences of abrogating the zyxin-Tes interaction in focal adhesions. Performing fluorescence recovery after photobleaching, we showed that zyxin recruits Tes to focal adhesions and modulates its turnover in these structures. However, we also provide evidence for zyxin-independent localization of Tes to focal adhesions. Zyxin increases focal adhesion numbers and reduces focal adhesion lifetimes, but does so independent of Tes. Quantitative analysis showed that the loss of interaction between zyxin and Tes affects the process of cell spreading. We conclude that zyxin influences focal adhesion dynamics, that it recruits Tes and that this interaction is functional in regulating cell spreading.
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Affiliation(s)
- Ermin Hadzic
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxemburg, Luxembourg
| | - Marie Catillon
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxemburg, Luxembourg
| | - Aliaksandr Halavatyi
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxemburg, Luxembourg
| | - Sandrine Medves
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxemburg, Luxembourg
| | | | - Michèle Moes
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxemburg, Luxembourg
| | - Michelle A. Baird
- National High Magnetic Field Laboratory and Department of Biological Science, The Florida State University, Tallahassee, Florida, United States of America
| | - Michael W. Davidson
- National High Magnetic Field Laboratory and Department of Biological Science, The Florida State University, Tallahassee, Florida, United States of America
| | - Elisabeth Schaffner-Reckinger
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxemburg, Luxembourg
| | - Christophe Ampe
- Department of Biochemistry, Ghent University, Ghent, Belgium
- * E-mail:
| | - Evelyne Friederich
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxemburg, Luxembourg
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15
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Verissimo F, Halavatyi A, Pepperkok R, Weiss M. A microtubule-independent role of p150glued in secretory cargo concentration at endoplasmic reticulum exit sites. J Cell Sci 2015; 128:4160-70. [PMID: 26459637 DOI: 10.1242/jcs.172395] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 10/05/2015] [Indexed: 01/08/2023] Open
Abstract
Newly synthesized proteins are sorted into COPII-coated transport carriers at the endoplasmic reticulum (ER). Assembly of the COPII coat complex, which occurs at ER exit sites (ERES), is initiated by membrane association and GTP loading of SAR1, followed by the recruitment of the SEC23-SEC24 and SEC13-SEC31 subcomplexes. Both of these two subcomplexes stimulate GTP hydrolysis and coat disassembly. This inherent disassembly capacity of COPII complexes needs to be regulated to allow sufficient time for cargo sorting and transport carrier formation. By performing fluorescence recovery after photobleaching (FRAP) and mathematical modeling, we show that p150(glued) (also known as DCTN1), a component of the dynactin complex, stabilizes the COPII pre-budding complex on ER membranes in a microtubule-independent manner. Concentration of the secretory marker ts-O45-G at ERES is reduced in the presence of a C-terminal p150(glued) fragment that prevents binding of endogenous p150(glued) to SEC23. A similar cargo reduction is observed upon p150(glued) knockdown. Taken together, our data suggest that cargo concentration at ERES is regulated by p150(glued) to coordinate protein sorting and transport carrier formation with the subsequent long-range transport towards the Golgi complex along microtubules.
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Affiliation(s)
- Fatima Verissimo
- Cell Biology and Biophysics Unit, EMBL, Meyerhofstraße 1, Heidelberg D-69117, Germany
| | - Aliaksandr Halavatyi
- Cell Biology and Biophysics Unit, EMBL, Meyerhofstraße 1, Heidelberg D-69117, Germany
| | - Rainer Pepperkok
- Cell Biology and Biophysics Unit, EMBL, Meyerhofstraße 1, Heidelberg D-69117, Germany
| | - Matthias Weiss
- Experimental Physics I, Universitaetsstr. 30, University of Bayreuth, Bayreuth D-95440, Germany
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16
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Al Tanoury Z, Schaffner-Reckinger E, Halavatyi A, Hoffmann C, Moes M, Hadzic E, Catillon M, Yatskou M, Friederich E. Quantitative kinetic study of the actin-bundling protein L-plastin and of its impact on actin turn-over. PLoS One 2010; 5:e9210. [PMID: 20169155 PMCID: PMC2821400 DOI: 10.1371/journal.pone.0009210] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 01/26/2010] [Indexed: 12/05/2022] Open
Abstract
Background Initially detected in leukocytes and cancer cells derived from solid tissues, L-plastin/fimbrin belongs to a large family of actin crosslinkers and is considered as a marker for many cancers. Phosphorylation of L-plastin on residue Ser5 increases its F-actin binding activity and is required for L-plastin-mediated cell invasion. Methodology/Principal Findings To study the kinetics of L-plastin and the impact of L-plastin Ser5 phosphorylation on L-plastin dynamics and actin turn-over in live cells, simian Vero cells were transfected with GFP-coupled WT-L-plastin, Ser5 substitution variants (S5/A, S5/E) or actin and analyzed by fluorescence recovery after photobleaching (FRAP). FRAP data were explored by mathematical modeling to estimate steady-state reaction parameters. We demonstrate that in Vero cell focal adhesions L-plastin undergoes rapid cycles of association/dissociation following a two-binding-state model. Phosphorylation of L-plastin increased its association rates by two-fold, whereas dissociation rates were unaffected. Importantly, L-plastin affected actin turn-over by decreasing the actin dissociation rate by four-fold, increasing thereby the amount of F-actin in the focal adhesions, all these effects being promoted by Ser5 phosphorylation. In MCF-7 breast carcinoma cells, phorbol 12-myristate 13-acetate (PMA) treatment induced L-plastin translocation to de novo actin polymerization sites in ruffling membranes and spike-like structures and highly increased its Ser5 phosphorylation. Both inhibition studies and siRNA knock-down of PKC isozymes pointed to the involvement of the novel PKC-δ isozyme in the PMA-elicited signaling pathway leading to L-plastin Ser5 phosphorylation. Furthermore, the L-plastin contribution to actin dynamics regulation was substantiated by its association with a protein complex comprising cortactin, which is known to be involved in this process. Conclusions/Significance Altogether these findings quantitatively demonstrate for the first time that L-plastin contributes to the fine-tuning of actin turn-over, an activity which is regulated by Ser5 phosphorylation promoting its high affinity binding to the cytoskeleton. In carcinoma cells, PKC-δ signaling pathways appear to link L-plastin phosphorylation to actin polymerization and invasion.
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Affiliation(s)
- Ziad Al Tanoury
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg
| | - Elisabeth Schaffner-Reckinger
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg
| | - Aliaksandr Halavatyi
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg
| | - Céline Hoffmann
- Laboratory of Plant Molecular Biology, Public Research Center for Health (CRP-Santé), Strassen, Luxembourg
| | - Michèle Moes
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg
| | - Ermin Hadzic
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg
| | - Marie Catillon
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg
| | - Mikalai Yatskou
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg
| | - Evelyne Friederich
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg
- * E-mail:
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