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Martinez D, Legrand A, Gronnier J, Decossas M, Gouguet P, Lambert O, Berbon M, Verron L, Grélard A, Germain V, Loquet A, Mongrand S, Habenstein B. Coiled-coil oligomerization controls localization of the plasma membrane REMORINs. J Struct Biol 2018; 206:12-19. [PMID: 29481850 DOI: 10.1016/j.jsb.2018.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 01/25/2018] [Accepted: 02/12/2018] [Indexed: 12/20/2022]
Abstract
REMORINs are nanodomain-organized proteins located in the plasma membrane and involved in cellular responses in plants. The dynamic assembly of the membrane nanodomains represents an essential tool of the versatile membrane barriers to control and modulate cellular functions. Nevertheless, the assembly mechanisms and protein organization strategies of nanodomains are poorly understood and many structural aspects are difficult to visualize. Using an ensemble of biophysical approaches, including solid-state nuclear magnetic resonance, cryo-electron microscopy and in vivo confocal imaging, we provide first insights on the role and the structural mechanisms of REMORIN trimerization. Our results suggest that the formation of REMORIN coiled-coil trimers is essential for membrane recruitment and promotes REMORIN assembly in vitro into long filaments by trimer-trimer interactions that might participate in nanoclustering into membrane domains in vivo.
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Affiliation(s)
- Denis Martinez
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Universite Bordeaux, Institut Polytechnique Bordeaux, All. Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Anthony Legrand
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Universite Bordeaux, Institut Polytechnique Bordeaux, All. Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Julien Gronnier
- Laboratoire de Biogènese Membranaire - UMR 5200 - CNRS, Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave d'Ornon Cédex, France
| | - Marion Decossas
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), CNRS, Universite Bordeaux, Institut Polytechnique Bordeaux, 14 All. Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Paul Gouguet
- Laboratoire de Biogènese Membranaire - UMR 5200 - CNRS, Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave d'Ornon Cédex, France
| | - Olivier Lambert
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), CNRS, Universite Bordeaux, Institut Polytechnique Bordeaux, 14 All. Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Mélanie Berbon
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Universite Bordeaux, Institut Polytechnique Bordeaux, All. Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Loris Verron
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Universite Bordeaux, Institut Polytechnique Bordeaux, All. Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Axelle Grélard
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Universite Bordeaux, Institut Polytechnique Bordeaux, All. Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Veronique Germain
- Laboratoire de Biogènese Membranaire - UMR 5200 - CNRS, Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave d'Ornon Cédex, France
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Universite Bordeaux, Institut Polytechnique Bordeaux, All. Geoffroy Saint-Hilaire, 33600 Pessac, France.
| | - Sébastien Mongrand
- Laboratoire de Biogènese Membranaire - UMR 5200 - CNRS, Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave d'Ornon Cédex, France.
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Universite Bordeaux, Institut Polytechnique Bordeaux, All. Geoffroy Saint-Hilaire, 33600 Pessac, France.
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102
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Won SJ, Cheung See Kit M, Martin BR. Protein depalmitoylases. Crit Rev Biochem Mol Biol 2018; 53:83-98. [PMID: 29239216 PMCID: PMC6009847 DOI: 10.1080/10409238.2017.1409191] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/21/2017] [Accepted: 11/21/2017] [Indexed: 12/13/2022]
Abstract
Protein depalmitoylation describes the removal of thioester-linked long chain fatty acids from cysteine residues in proteins. For many S-palmitoylated proteins, this process is promoted by acyl protein thioesterase enzymes, which catalyze thioester hydrolysis to solubilize and displace substrate proteins from membranes. The closely related enzymes acyl protein thioesterase 1 (APT1; LYPLA1) and acyl protein thioesterase 2 (APT2; LYPLA2) were initially identified from biochemical assays as G protein depalmitoylases, yet later were shown to accept a number of S-palmitoylated protein and phospholipid substrates. Leveraging the development of isoform-selective APT inhibitors, several studies report distinct roles for APT enzymes in growth factor and hormonal signaling. Recent crystal structures of APT1 and APT2 reveal convergent acyl binding channels, suggesting additional factors beyond acyl chain recognition mediate substrate selection. In addition to APT enzymes, the ABHD17 family of hydrolases contributes to the depalmitoylation of Ras-family GTPases and synaptic proteins. Overall, enzymatic depalmitoylation ensures efficient membrane targeting by balancing the palmitoylation cycle, and may play additional roles in signaling, growth, and cell organization. In this review, we provide a perspective on the biochemical, structural, and cellular analysis of protein depalmitoylases, and outline opportunities for future studies of systems-wide analysis of protein depalmitoylation.
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Affiliation(s)
- Sang Joon Won
- a Program in Chemical Biology , University of Michigan , Ann Arbor , MI , USA
| | | | - Brent R Martin
- a Program in Chemical Biology , University of Michigan , Ann Arbor , MI , USA
- b Department of Chemistry , University of Michigan , Ann Arbor , MI , USA
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103
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Sameni S, Malacrida L, Tan Z, Digman MA. Alteration in Fluidity of Cell Plasma Membrane in Huntington Disease Revealed by Spectral Phasor Analysis. Sci Rep 2018; 8:734. [PMID: 29335600 PMCID: PMC5768877 DOI: 10.1038/s41598-018-19160-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/22/2017] [Indexed: 12/18/2022] Open
Abstract
Huntington disease (HD) is a late-onset genetic neurodegenerative disorder caused by expansion of cytosine-adenine-guanine (CAG) trinucleotide in the exon 1 of the gene encoding the polyglutamine (polyQ). It has been shown that protein degradation and lipid metabolism is altered in HD. In many neurodegenerative disorders, impaired lipid homeostasis is one of the early events in the disease onset. Yet, little is known about how mutant huntingtin may affect phospholipids membrane fluidity. Here, we investigated how membrane fluidity in the living cells (differentiated PC12 and HEK293 cell lines) are affected using a hyperspectral imaging of widely used probes, LAURDAN. Using phasor approach, we characterized the fluorescence of LAURDAN that is sensitive to the polarity of the immediate environment. LAURDAN is affected by the physical order of phospholipids (lipid order) and reports the membrane fluidity. We also validated our results using a different fluorescent membrane probe, Nile Red (NR). The plasma membrane in the cells expressing expanded polyQ shows a shift toward increased membrane fluidity revealed by both LAURDAN and NR spectral phasors. This finding brings a new perspective in the understanding of the early stages of HD that can be used as a target for drug screening.
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Affiliation(s)
- Sara Sameni
- Laboratory for Fluorescence Dynamics, University of California Irvine, Irvine, CA, USA
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA
| | - Leonel Malacrida
- Laboratory for Fluorescence Dynamics, University of California Irvine, Irvine, CA, USA
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA
- Departamento de Fisiopatología, Hospital de Clinicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Zhiqun Tan
- Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, USA
| | - Michelle A Digman
- Laboratory for Fluorescence Dynamics, University of California Irvine, Irvine, CA, USA.
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA.
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104
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Suhaj A, Le Marois A, Williamson DJ, Suhling K, Lorenz CD, Owen DM. PRODAN differentially influences its local environment. Phys Chem Chem Phys 2018; 20:16060-16066. [DOI: 10.1039/c8cp00543e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
PRODAN influences its local environment at the nanoscale differently between ordered and disordered phases as shown by MD simulations.
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Affiliation(s)
- Adam Suhaj
- Department of Physics and Randall Division of Cell and Molecular Biophysics
- King's College London
- London
- UK
| | | | - David J. Williamson
- Randall Division of Cell and Molecular Biophysics
- King's College London
- London
- UK
| | | | | | - Dylan M. Owen
- Department of Physics and Randall Division of Cell and Molecular Biophysics
- King's College London
- London
- UK
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105
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Moore R, Pujol MG, Zhu Z, Smythe E. Interplay of Endocytosis and Growth Factor Receptor Signalling. ENDOCYTOSIS AND SIGNALING 2018; 57:181-202. [DOI: 10.1007/978-3-319-96704-2_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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106
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Thimiri Govinda Raj DB, Khan NA. Surface functionalization dependent subcellular localization of Superparamagnetic nanoparticle in plasma membrane and endosome. NANO CONVERGENCE 2018; 5:4. [PMID: 29492374 PMCID: PMC5813047 DOI: 10.1186/s40580-018-0136-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/31/2018] [Indexed: 05/22/2023]
Abstract
In this article, we elaborate the application of thermal decomposition based synthesis of Fe3O4 superparamagnetic nanoparticle (SPMNP) in subcellular fractionation context. Here, we performed surface functionalization of SPMNP with phospholipids and dimercaptosuccinic acid. Surprisingly, we observed surface functionalization dependent SPMNP localization in subcellular compartments such as plasma membrane, endosomes and lysosomes. By using SPMNP based subcellular localization with pulse-chase methodology, we could use SPMNP for high pure-high yield organelle (plasma membrane, endosomes and lysosome) fractionation. Further, SPMNP that are distinctly localized in subcellular compartments can be used as technology for subcellular fractionation that can complement existing tools for cell biology research. As a future perspective, isolated magnetic organelles can be extended to protein/protein complex purification for biochemical and structural biology studies.
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Affiliation(s)
- Deepak B. Thimiri Govinda Raj
- Envirotransgene® Bio-solutions Global Chennai, Tamil Nadu, India
- Biotechnology Centre for Oslo, Centre for Molecular Medicine Norway (NCMM), Blindern, P.O. Box 1137, 0318 Oslo, Norway
| | - Niamat Ali Khan
- Laboratory of Lipid Metabolism and Cancer, O&N I, Herestraat 49, Box 902, 3000 Louvain, Belgium
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107
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Graessl M, Koch J, Calderon A, Kamps D, Banerjee S, Mazel T, Schulze N, Jungkurth JK, Patwardhan R, Solouk D, Hampe N, Hoffmann B, Dehmelt L, Nalbant P. An excitable Rho GTPase signaling network generates dynamic subcellular contraction patterns. J Cell Biol 2017; 216:4271-4285. [PMID: 29055010 PMCID: PMC5716289 DOI: 10.1083/jcb.201706052] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 08/25/2017] [Accepted: 09/08/2017] [Indexed: 12/22/2022] Open
Abstract
Rho GTPase-based signaling networks control cellular dynamics by coordinating protrusions and retractions in space and time. Here, we reveal a signaling network that generates pulses and propagating waves of cell contractions. These dynamic patterns emerge via self-organization from an activator-inhibitor network, in which the small GTPase Rho amplifies its activity by recruiting its activator, the guanine nucleotide exchange factor GEF-H1. Rho also inhibits itself by local recruitment of actomyosin and the associated RhoGAP Myo9b. This network structure enables spontaneous, self-limiting patterns of subcellular contractility that can explore mechanical cues in the extracellular environment. Indeed, actomyosin pulse frequency in cells is altered by matrix elasticity, showing that coupling of contractility pulses to environmental deformations modulates network dynamics. Thus, our study reveals a mechanism that integrates intracellular biochemical and extracellular mechanical signals into subcellular activity patterns to control cellular contractility dynamics.
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Affiliation(s)
- Melanie Graessl
- Department of Molecular Cell Biology, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Johannes Koch
- Department of Molecular Cell Biology, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Abram Calderon
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie, TU Dortmund University, Dortmund, Germany
| | - Dominic Kamps
- Department of Molecular Cell Biology, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie, TU Dortmund University, Dortmund, Germany
| | - Soumya Banerjee
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie, TU Dortmund University, Dortmund, Germany
| | - Tomáš Mazel
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie, TU Dortmund University, Dortmund, Germany
| | - Nina Schulze
- Department of Molecular Cell Biology, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Jana Kathrin Jungkurth
- Department of Molecular Cell Biology, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie, TU Dortmund University, Dortmund, Germany
| | - Rutuja Patwardhan
- Department of Molecular Cell Biology, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Djamschid Solouk
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie, TU Dortmund University, Dortmund, Germany
| | - Nico Hampe
- Institute of Complex Systems, Forschungszentrum Jülich, Jülich, Germany
| | - Bernd Hoffmann
- Institute of Complex Systems, Forschungszentrum Jülich, Jülich, Germany
| | - Leif Dehmelt
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie, TU Dortmund University, Dortmund, Germany
| | - Perihan Nalbant
- Department of Molecular Cell Biology, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
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108
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Damioli V, Salvadori A, Beretta GP, Ravelli C, Mitola S. Multi-physics interactions drive VEGFR2 relocation on endothelial cells. Sci Rep 2017; 7:16700. [PMID: 29196628 PMCID: PMC5711959 DOI: 10.1038/s41598-017-16786-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 11/04/2017] [Indexed: 12/31/2022] Open
Abstract
Vascular Endothelial Growth Factor Receptor-2 (VEGFR2) is a pro-angiogenic receptor, expressed on endothelial cells (ECs). Although biochemical pathways that follow the VEGFR2 activation are well established, knowledge about the dynamics of receptors on the plasma membrane remains limited. Ligand stimulation induces the polarization of ECs and the relocation of VEGFR2, either in cell protrusions or in the basal aspect in cells plated on ligand-enriched extracellular matrix (ECM). We develop a mathematical model in order to simulate the relocation of VEGFR2 on the cell membrane during the mechanical adhesion of cells onto a ligand-enriched substrate. Co-designing the in vitro experiments with the simulations allows identifying three phases of the receptor dynamics, which are controlled respectively by the high chemical reaction rate, by the mechanical deformation rate, and by the diffusion of free receptors on the membrane. The identification of the laws that regulate receptor polarization opens new perspectives toward developing innovative anti-angiogenic strategies through the modulation of EC activation.
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Affiliation(s)
- Valentina Damioli
- Università degli Studi di Brescia, DIMI Department of Mechanical and Industrial Engineering, Brescia, 25123, Italy
| | - Alberto Salvadori
- Università degli Studi di Brescia, DICATAM, Department of Civil, Environmental, Architectural Engineering and Mathematics, Brescia, 25123, Italy.,Laboratory for Preventive and Personalized Medicine (MPP Lab), Università degli Studi di Brescia, Brescia, 25123, Italy
| | - Gian Paolo Beretta
- Università degli Studi di Brescia, DIMI Department of Mechanical and Industrial Engineering, Brescia, 25123, Italy
| | - Cosetta Ravelli
- Università degli Studi di Brescia, DMMT, Department of Molecular and Translational Medicine, Brescia, 25123, Italy. .,Laboratory for Preventive and Personalized Medicine (MPP Lab), Università degli Studi di Brescia, Brescia, 25123, Italy.
| | - Stefania Mitola
- Università degli Studi di Brescia, DMMT, Department of Molecular and Translational Medicine, Brescia, 25123, Italy. .,Laboratory for Preventive and Personalized Medicine (MPP Lab), Università degli Studi di Brescia, Brescia, 25123, Italy.
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109
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A systematic exploration of the interactions between bacterial effector proteins and host cell membranes. Nat Commun 2017; 8:532. [PMID: 28912547 PMCID: PMC5599653 DOI: 10.1038/s41467-017-00700-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/20/2017] [Indexed: 01/08/2023] Open
Abstract
Membrane-bound organelles serve as platforms for the assembly of multi-protein complexes that function as hubs of signal transduction in eukaryotic cells. Microbial pathogens have evolved virulence factors that reprogram these host signaling responses, but the underlying molecular mechanisms are poorly understood. Here we test the ability of ~200 type III and type IV effector proteins from six Gram-negative bacterial species to interact with the eukaryotic plasma membrane and intracellular organelles. We show that over 30% of the effectors localize to yeast and mammalian cell membranes, including a subset of previously uncharacterized Legionella effectors that appear to be able to regulate yeast vacuolar fusion. A combined genetic, cellular, and biochemical approach supports that some of the tested bacterial effectors can bind to membrane phospholipids and may regulate membrane trafficking. Finally, we show that the type III effector IpgB1 from Shigella flexneri may bind to acidic phospholipids and regulate actin filament dynamics.Microbial pathogens secrete effector proteins into host cells to affect cellular functions. Here, the authors use a yeast-based screen to study around 200 effectors from six bacterial species, showing that over 30% of them interact with the eukaryotic plasma membrane or intracellular organelles.
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110
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Limitations of Qdot labelling compared to directly-conjugated probes for single particle tracking of B cell receptor mobility. Sci Rep 2017; 7:11379. [PMID: 28900238 PMCID: PMC5595841 DOI: 10.1038/s41598-017-11563-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/18/2017] [Indexed: 12/25/2022] Open
Abstract
Single-particle tracking (SPT) is a powerful method for exploring single-molecule dynamics in living cells with nanoscale spatiotemporal resolution. Photostability and bright fluorescence make quantum dots (Qdots) a popular choice for SPT. However, their large size could potentially alter the mobility of the molecule of interest. To test this, we labelled B cell receptors on the surface of B-lymphocytes with monovalent Fab fragments of antibodies that were either linked to Qdots via streptavidin or directly conjugated to the small organic fluorophore Cy3. Imaging of receptor mobility by total internal reflection fluorescence microscopy (TIRFM), followed by quantitative single-molecule diffusion and confinement analysis, definitively showed that Qdots sterically hinder lateral mobility regardless of the substrate to which the cells were adhered. Qdot labelling also drastically altered the frequency with which receptors transitioned between apparent slow- and fast-moving states and reduced the size of apparent confinement zones. Although we show that Qdot-labelled probes can detect large differences in receptor mobility, they fail to resolve subtle differences in lateral diffusion that are readily detectable using Cy3-labelled Fabs. Our findings highlight the utility and limitations of using Qdots for TIRFM and wide-field-based SPT, and have significant implications for interpreting SPT data.
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111
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Gronnier J, Crowet JM, Habenstein B, Nasir MN, Bayle V, Hosy E, Platre MP, Gouguet P, Raffaele S, Martinez D, Grelard A, Loquet A, Simon-Plas F, Gerbeau-Pissot P, Der C, Bayer EM, Jaillais Y, Deleu M, Germain V, Lins L, Mongrand S. Structural basis for plant plasma membrane protein dynamics and organization into functional nanodomains. eLife 2017; 6:e26404. [PMID: 28758890 PMCID: PMC5536944 DOI: 10.7554/elife.26404] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/13/2017] [Indexed: 12/31/2022] Open
Abstract
Plasma Membrane is the primary structure for adjusting to ever changing conditions. PM sub-compartmentalization in domains is thought to orchestrate signaling. Yet, mechanisms governing membrane organization are mostly uncharacterized. The plant-specific REMORINs are proteins regulating hormonal crosstalk and host invasion. REMs are the best-characterized nanodomain markers via an uncharacterized moiety called REMORIN C-terminal Anchor. By coupling biophysical methods, super-resolution microscopy and physiology, we decipher an original mechanism regulating the dynamic and organization of nanodomains. We showed that targeting of REMORIN is independent of the COP-II-dependent secretory pathway and mediated by PI4P and sterol. REM-CA is an unconventional lipid-binding motif that confers nanodomain organization. Analyses of REM-CA mutants by single particle tracking demonstrate that mobility and supramolecular organization are critical for immunity. This study provides a unique mechanistic insight into how the tight control of spatial segregation is critical in the definition of PM domain necessary to support biological function.
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Affiliation(s)
- Julien Gronnier
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de BordeauxBordeauxFrance
| | - Jean-Marc Crowet
- Laboratoire de Biophysique Moléculaire aux InterfacesGX ABT, Université de LiègeGemblouxBelgium
| | - Birgit Habenstein
- Institute of Chemistry and Biology of Membranes and Nanoobjects (UMR5248 CBMN), CNRS, Université de Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Mehmet Nail Nasir
- Laboratoire de Biophysique Moléculaire aux InterfacesGX ABT, Université de LiègeGemblouxBelgium
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des PlantesUniversité de Lyon, ENS de Lyon, Université Claude Bernard Lyon 1LyonFrance
| | - Eric Hosy
- Interdisciplinary Institute for Neuroscience, CNRS, University of BordeauxBordeauxFrance
| | - Matthieu Pierre Platre
- Laboratoire Reproduction et Développement des PlantesUniversité de Lyon, ENS de Lyon, Université Claude Bernard Lyon 1LyonFrance
| | - Paul Gouguet
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de BordeauxBordeauxFrance
| | | | - Denis Martinez
- Institute of Chemistry and Biology of Membranes and Nanoobjects (UMR5248 CBMN), CNRS, Université de Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Axelle Grelard
- Institute of Chemistry and Biology of Membranes and Nanoobjects (UMR5248 CBMN), CNRS, Université de Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Antoine Loquet
- Institute of Chemistry and Biology of Membranes and Nanoobjects (UMR5248 CBMN), CNRS, Université de Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Françoise Simon-Plas
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRSDijonFrance
| | - Patricia Gerbeau-Pissot
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRSDijonFrance
| | - Christophe Der
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRSDijonFrance
| | - Emmanuelle M Bayer
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de BordeauxBordeauxFrance
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des PlantesUniversité de Lyon, ENS de Lyon, Université Claude Bernard Lyon 1LyonFrance
| | - Magali Deleu
- Laboratoire de Biophysique Moléculaire aux InterfacesGX ABT, Université de LiègeGemblouxBelgium
| | - Véronique Germain
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de BordeauxBordeauxFrance
| | - Laurence Lins
- Laboratoire de Biophysique Moléculaire aux InterfacesGX ABT, Université de LiègeGemblouxBelgium
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de BordeauxBordeauxFrance
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112
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Spatial cycles mediated by UNC119 solubilisation maintain Src family kinases plasma membrane localisation. Nat Commun 2017; 8:114. [PMID: 28740133 PMCID: PMC5524651 DOI: 10.1038/s41467-017-00116-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 06/02/2017] [Indexed: 12/12/2022] Open
Abstract
The peripheral membrane proto-oncogene Src family protein tyrosine kinases relay growth factor signals to the cytoplasm of mammalian cells. We unravel the spatial cycles of solubilisation, trapping on perinuclear membrane compartments and vesicular transport that counter entropic equilibration to endomembranes for maintaining the enrichment and activity of Src family protein tyrosine kinases at the plasma membrane. The solubilising factor UNC119 sequesters myristoylated Src family protein tyrosine kinases from the cytoplasm, enhancing their diffusion to effectively release Src family protein tyrosine kinases on the recycling endosome by localised Arl2/3 activity. Src is then trapped on the recycling endosome via electrostatic interactions, whereas Fyn is quickly released to be kinetically trapped on the Golgi by palmitoyl acyl-transferase activity. Vesicular trafficking from these compartments restores enrichment of the Src family protein tyrosine kinases to the plasma membrane. Interference with these spatial cycles by UNC119 knockdown disrupts Src family protein tyrosine kinase localisation and signalling activity, indicating that UNC119 could be a drug target to affect oncogenic Src family protein tyrosine kinase signalling. The peripheral membrane proto-oncogene Src family protein tyrosine kinases (SFKs) transmit growth factor signals to the cytoplasm. Here the authors show that the solubilising factor UNC119 sequesters myristoylated SFKs to maintain its enrichment at the plasma membrane to enable signal transduction.
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113
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Basit H, Maher S, Forster RJ, Keyes TE. Electrochemically Triggered Release of Reagent to the Proximal Leaflet of a Microcavity Supported Lipid Bilayer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6691-6700. [PMID: 28614663 DOI: 10.1021/acs.langmuir.7b01069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
A novel and versatile approach to electrichemically triggering the release of a reagent, β-cyclodextrin (β-CD), selectively to the proximal leaflet of a supported lipid bilayer is described. Selective delivery is achieved by creating a spanning lipid bilayer across a microcavity array and exploiting the irreversible redox disassembly of the host-guest complex formed between thiolated ferrocene (Fc) and β-cyclodextrin (β-CD) in the presence of chloride. Self-assembled monolayers of the ferrocene-alkanethiols were formed regioselectively on the interior surface of highly ordered 2.8 μm cavities while the exterior top surface of the array was blocked with a monolayer of mercaptoethanol. The Fc monolayers were complexed with β-CD or β-CD-conjugated to streptavidin (β-CD-SA). Phospholipid bilayers were then assembled across the array via combined Langmuir-Blodgett/vesicle fusion leading to a spanning bilayer suspended across the aqueous filled microcavities. Upon application of a positive potential, ferrocene is oxidized to ferrocinium cation, disrupting the inclusion complex and leading to the release of the β-CD into the microcavity solution where it diffuses to the lower leaflet of the suspended bilayer. Disassembly of the supramolecular complex within the cavities and binding of the β-CD-SA to a biotinylated bilayer was followed by voltammetry and impedance spectroscopy where it caused a large increase in membrane resistance. For unmodified β-CD, the extraction of cholesterol from a cholesterol containing bilayer was evident in a decrease in the bilayer resistance. For the first time, this direct approach to targeted delivery of a reagent to the proximal layer of a lipid bilayer offers the potential to build models of bidirectional signaling (inside-out vs outside-in) in cell membrane model systems.
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Affiliation(s)
- H Basit
- School of Chemical Sciences, National Centre for Sensors Research, Dublin City University , Dublin 9, Ireland
| | - S Maher
- School of Chemical Sciences, National Centre for Sensors Research, Dublin City University , Dublin 9, Ireland
| | - R J Forster
- School of Chemical Sciences, National Centre for Sensors Research, Dublin City University , Dublin 9, Ireland
| | - T E Keyes
- School of Chemical Sciences, National Centre for Sensors Research, Dublin City University , Dublin 9, Ireland
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114
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Silberberg M, Grecco HE. pawFLIM: reducing bias and uncertainty to enable lower photon count in FLIM experiments. Methods Appl Fluoresc 2017. [DOI: 10.1088/2050-6120/aa72ab] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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115
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Goedhart J, van Unen J. Molecular perturbation strategies to examine spatiotemporal features of Rho GEF and Rho GTPase activity in living cells. Small GTPases 2017; 10:178-186. [PMID: 28521592 PMCID: PMC6548299 DOI: 10.1080/21541248.2017.1302551] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Much of our current knowledge of Rho GTPase networks and the regulation by Rho guanine exchange factors (Rho GEFs) and Rho GTPase activating proteins (Rho GAPs) is based on population-based techniques. Over the last decades, technologies that enable single cell analysis with high spatial and temporal resolution have revealed that Rho GTPase activity in cells is regulated on second timescales and at submicrometer length scales. Therefore, perturbation methods with matching spatial and temporal resolution are crucial to further our understanding of Rho GTPase signaling. Here, we give a brief overview of the components of Rho GTPase signaling networks and review a range of existing perturbation strategies that target a specific component of the Rho GTPase signaling module. The advantages and limitations of each perturbation method are discussed. Several recommendations are formulated to guide future studies aimed at addressing spatiotemporal aspects of Rho GEF and Rho GTPase signaling.
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Affiliation(s)
- Joachim Goedhart
- a Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam , Amsterdam , The Netherlands
| | - Jakobus van Unen
- a Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam , Amsterdam , The Netherlands
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116
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Membrane restructuring following in situ sialidase digestion of gangliosides: Complex model bilayers by synchrotron radiation reflectivity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:845-851. [DOI: 10.1016/j.bbamem.2017.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 12/30/2016] [Accepted: 01/08/2017] [Indexed: 12/13/2022]
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117
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Chen X, Venkatachalapathy M, Kamps D, Weigel S, Kumar R, Orlich M, Garrecht R, Hirtz M, Niemeyer CM, Wu YW, Dehmelt L. “Molecular Activity Painting”: Switch-like, Light-Controlled Perturbations inside Living Cells. Angew Chem Int Ed Engl 2017; 56:5916-5920. [DOI: 10.1002/anie.201611432] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/10/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Xi Chen
- Chemical Genomics Centre of the Max-Planck Society; Dortmund Germany
| | - Muthukumaran Venkatachalapathy
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
| | - Dominic Kamps
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
| | - Simone Weigel
- Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Ravi Kumar
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF); Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Michael Orlich
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
| | - Ruben Garrecht
- Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Michael Hirtz
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF); Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Yao-Wen Wu
- Chemical Genomics Centre of the Max-Planck Society; Dortmund Germany
| | - Leif Dehmelt
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
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118
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Chen X, Venkatachalapathy M, Kamps D, Weigel S, Kumar R, Orlich M, Garrecht R, Hirtz M, Niemeyer CM, Wu YW, Dehmelt L. “Molecular Activity Painting”: schaltbare, lichtgesteuerte Manipulation in lebenden Zellen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611432] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xi Chen
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
| | - Muthukumaran Venkatachalapathy
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
| | - Dominic Kamps
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
| | - Simone Weigel
- Institut für Biologische Grenzflächen; Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Ravi Kumar
- Institut für Nanotechnologie (INT) und Karlsruhe Nano Micro Facility (KNMF); Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Michael Orlich
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
| | - Ruben Garrecht
- Institut für Biologische Grenzflächen; Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Michael Hirtz
- Institut für Nanotechnologie (INT) und Karlsruhe Nano Micro Facility (KNMF); Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Christof M. Niemeyer
- Institut für Biologische Grenzflächen; Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Yao-Wen Wu
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
| | - Leif Dehmelt
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
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119
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Islam M, Mane S, Hyder E, Jones S, Ellis I. The motogenic effect of EGF and TGF-α on the migration of tumor cells from the oral region. TRANSLATIONAL RESEARCH IN ORAL ONCOLOGY 2017. [DOI: 10.1177/2057178x17698481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Mohammad Islam
- Unit of Cell and Molecular Biology, Dundee Dental School, University of Dundee, Dundee, Scotland, UK
| | - Shraddha Mane
- Unit of Cell and Molecular Biology, Dundee Dental School, University of Dundee, Dundee, Scotland, UK
| | - Erum Hyder
- Unit of Cell and Molecular Biology, Dundee Dental School, University of Dundee, Dundee, Scotland, UK
| | - Sarah Jones
- Unit of Cell and Molecular Biology, Dundee Dental School, University of Dundee, Dundee, Scotland, UK
| | - Ian Ellis
- Unit of Cell and Molecular Biology, Dundee Dental School, University of Dundee, Dundee, Scotland, UK
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120
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Koseska A, Bastiaens PI. Cell signaling as a cognitive process. EMBO J 2017; 36:568-582. [PMID: 28137748 PMCID: PMC5331751 DOI: 10.15252/embj.201695383] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/13/2016] [Accepted: 12/20/2016] [Indexed: 12/17/2022] Open
Abstract
Cellular identity as defined through morphology and function emerges from intracellular signaling networks that communicate between cells. Based on recursive interactions within and among these intracellular networks, dynamical solutions in terms of biochemical behavior are generated that can differ from those in isolated cells. In this way, cellular heterogeneity in tissues can be established, implying that cell identity is not intrinsically predetermined by the genetic code but is rather dynamically maintained in a cognitive manner. We address how to experimentally measure the flow of information in intracellular biochemical networks and demonstrate that even simple causality motifs can give rise to rich, context-dependent dynamic behavior. The concept how intercellular communication can result in novel dynamical solutions is applied to provide a contextual perspective on cell differentiation and tumorigenesis.
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Affiliation(s)
- Aneta Koseska
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Philippe Ih Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund, Dortmund, Germany
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121
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Park JH, Gurunathan S, Choi YJ, Han JW, Song H, Kim JH. Silver nanoparticles suppresses brain-derived neurotrophic factor-induced cell survival in the human neuroblastoma cell line SH-SY5Y. J IND ENG CHEM 2017. [DOI: 10.1016/j.jiec.2016.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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122
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APT2 Inhibition Restores Scribble Localization and S-Palmitoylation in Snail-Transformed Cells. Cell Chem Biol 2017; 24:87-97. [PMID: 28065656 DOI: 10.1016/j.chembiol.2016.12.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/28/2016] [Accepted: 12/13/2016] [Indexed: 11/23/2022]
Abstract
The multidomain scaffolding protein Scribble (Scrib) organizes key signaling complexes to specify basolateral cell polarity and suppress aberrant growth. In many human cancers, genetically normal Scrib mislocalizes from cell-cell junctions to the cytosol, correlating with enhanced growth signaling and malignancy. Here we confirm that expression of the epithelial-to-mesenchymal transcription factor (EMT-TF) Snail in benign epithelial cells leads to Scrib displacement from the plasma membrane, mimicking the mislocalization observed in aggressive cancers. Upon further examination, Snail promotes a transcriptional program that targets genes in the palmitoylation cycle, repressing many protein acyl transferases and elevating expression and activity of protein acyl thioesterase 2 (APT2). APT2 isoform-selective inhibition or knockdown rescued Scrib membrane localization and palmitoylation while attenuating MEK activation. Overall, inhibiting APT2 restores balance to the Scrib palmitoylation cycle, promoting membrane re-localization and growth attenuation. These findings emphasize the importance of S-palmitoylation as a post-translational gatekeeper of cell polarity-mediated tumor suppression.
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123
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Roob E, Trendel N, Rein Ten Wolde P, Mugler A. Cooperative Clustering Digitizes Biochemical Signaling and Enhances its Fidelity. Biophys J 2016; 110:1661-1669. [PMID: 27074690 DOI: 10.1016/j.bpj.2016.02.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/04/2016] [Accepted: 02/22/2016] [Indexed: 10/21/2022] Open
Abstract
Many membrane-bound molecules in cells form small clusters. It has been hypothesized that these clusters convert an analog extracellular signal into a digital intracellular signal and that this conversion increases signaling fidelity. However, the mechanism by which clusters digitize a signal and the subsequent effects on fidelity remain poorly understood. Here we demonstrate using a stochastic model of cooperative cluster formation that sufficient cooperation leads to digital signaling. We show that despite reducing the number of output states, which decreases fidelity, digitization also reduces noise in the system, which increases fidelity. The tradeoff between these effects leads to an optimal cluster size that agrees with experimental measurements.
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Affiliation(s)
- Edward Roob
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana
| | - Nicola Trendel
- Systems Biology Doctoral Training Centre, University of Oxford, Oxford, United Kingdom; FOM Institute AMOLF, Amsterdam, the Netherlands
| | | | - Andrew Mugler
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana; FOM Institute AMOLF, Amsterdam, the Netherlands.
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124
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Cocucci E, Kim JY, Bai Y, Pabla N. Role of Passive Diffusion, Transporters, and Membrane Trafficking-Mediated Processes in Cellular Drug Transport. Clin Pharmacol Ther 2016; 101:121-129. [PMID: 27804130 DOI: 10.1002/cpt.545] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 12/11/2022]
Abstract
Intracellular drug accumulation is thought to be dictated by two major processes, passive diffusion through the lipid membrane or membrane transporters. The relative role played by these distinct processes remains actively debated. Moreover, the role of membrane-trafficking in drug transport remains underappreciated and unexplored. Here we discuss the distinct processes involved in cellular drug distribution and propose that better experimental models are required to elucidate the differential contributions of various processes in intracellular drug accumulation.
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Affiliation(s)
- E Cocucci
- Division of Hematology, Department of Internal Medicine and Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, USA
| | - J Y Kim
- Division of Pharmaceutics, School of Pharmacy and Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, USA
| | - Y Bai
- Division of Pharmaceutics, School of Pharmacy and Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, USA
| | - N Pabla
- Division of Pharmaceutics, School of Pharmacy and Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, USA
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125
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Bernardino de la Serna J, Schütz GJ, Eggeling C, Cebecauer M. There Is No Simple Model of the Plasma Membrane Organization. Front Cell Dev Biol 2016; 4:106. [PMID: 27747212 PMCID: PMC5040727 DOI: 10.3389/fcell.2016.00106] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/14/2016] [Indexed: 12/29/2022] Open
Abstract
Ever since technologies enabled the characterization of eukaryotic plasma membranes, heterogeneities in the distributions of its constituents were observed. Over the years this led to the proposal of various models describing the plasma membrane organization such as lipid shells, picket-and-fences, lipid rafts, or protein islands, as addressed in numerous publications and reviews. Instead of emphasizing on one model we in this review give a brief overview over current models and highlight how current experimental work in one or the other way do not support the existence of a single overarching model. Instead, we highlight the vast variety of membrane properties and components, their influences and impacts. We believe that highlighting such controversial discoveries will stimulate unbiased research on plasma membrane organization and functionality, leading to a better understanding of this essential cellular structure.
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Affiliation(s)
- Jorge Bernardino de la Serna
- Science and Technology Facilities Council, Rutherford Appleton Laboratory, Central Laser Facility, Research Complex at Harwell Harwell, UK
| | - Gerhard J Schütz
- Institute of Applied Physics, Technische Universität Wien Wien, Austria
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford Headley Way, UK
| | - Marek Cebecauer
- Department of Biophysical Chemistry, J.Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences Prague, Czech Republic
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126
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Plasma Membrane Organization of Epidermal Growth Factor Receptor in Resting and Ligand-Bound States. Biophys J 2016; 109:1925-36. [PMID: 26536269 DOI: 10.1016/j.bpj.2015.09.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/24/2015] [Accepted: 09/08/2015] [Indexed: 12/21/2022] Open
Abstract
The spatial arrangement of the epidermal growth factor receptor (EGFR) on the cellular plasma membrane is one of the prime factors that control its downstream signaling pathways and related functions. However, the molecular organization, which spans the scale from nanometers to micrometer-size clusters, has not been resolved in detail, mainly due to a lack of techniques with the required spatiotemporal resolution. Therefore, we used imaging total internal reflection-fluorescence correlation spectroscopy to investigate EGFR dynamics on live CHO-K1 plasma membranes in resting and ligand-bound states. In combination with the fluorescence correlation spectroscopy diffusion law, this provides information on the subresolution organization of EGFR on cell membranes. We found that overall EGFR organization is sensitive to both cholesterol and the actin cytoskeleton. EGFR in the resting state is partly trapped in cholesterol-containing domains, whereas another fraction exhibits cholesterol independent trapping on the membrane. Disruption of the cytoskeleton leads to a broader range of EGFR diffusion coefficients and a reduction of hop diffusion. In the ligand-bound state we found a dose-dependent behavior. At 10 ng/mL EGF the EGFR is endocytosed and recycled to the membrane, whereas diffusion and organization do not change significantly. At 100 ng/mL EGF the EGFR forms clusters, which are subsequently internalized, whereas outside the clusters diffusivity increases and the organization of the receptor remains unchanged. After disruption of cholesterol-containing domains or actin cytoskeleton, EGF induces microscopic EGFR clusters on the membrane and endocytosis is inhibited.
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127
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Abstract
Lipid-modified GTPases in the Ras superfamily that mediate a variety of cell signaling processes were thought to be passively anchored to membranes. However, an increasing number of recent studies are finding that membrane binding of these proteins is hardly a passive process, and it involves the soluble catalytic domain as well as the lipid anchor. The catalytic domain adopts multiple orientations on the membrane surface due to internal fluctuations that are modulated by activation status and mutations. Distinct orientation preferences among small GTPases likely lead to differential signaling outcomes, as downstream effectors can sense different orientations. We review recent studies behind this important conclusion.
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Affiliation(s)
- Priyanka Prakash
- a Department of Integrative Biology and Pharmacology , University of Texas Health Science Center at Houston , Houston , TX , USA
| | - Alemayehu A Gorfe
- a Department of Integrative Biology and Pharmacology , University of Texas Health Science Center at Houston , Houston , TX , USA
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128
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Ryu YS, Wittenberg NJ, Suh JH, Lee SW, Sohn Y, Oh SH, Parikh AN, Lee SD. Continuity of Monolayer-Bilayer Junctions for Localization of Lipid Raft Microdomains in Model Membranes. Sci Rep 2016; 6:26823. [PMID: 27230411 PMCID: PMC4882513 DOI: 10.1038/srep26823] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/09/2016] [Indexed: 11/16/2022] Open
Abstract
We show that the selective localization of cholesterol-rich domains and associated ganglioside receptors prefer to occur in the monolayer across continuous monolayer-bilayer junctions (MBJs) in supported lipid membranes. For the MBJs, glass substrates were patterned with poly(dimethylsiloxane) (PDMS) oligomers by thermally-assisted contact printing, leaving behind 3 nm-thick PDMS patterns. The hydrophobicity of the transferred PDMS patterns was precisely tuned by the stamping temperature. Lipid monolayers were formed on the PDMS patterned surface while lipid bilayers were on the bare glass surface. Due to the continuity of the lipid membranes over the MBJs, essentially free diffusion of lipids was allowed between the monolayer on the PDMS surface and the upper leaflet of the bilayer on the glass substrate. The preferential localization of sphingomyelin, ganglioside GM1 and cholesterol in the monolayer region enabled to develop raft microdomains through coarsening of nanorafts. Our methodology provides a simple and effective scheme of non-disruptive manipulation of the chemical landscape associated with lipid phase separations, which leads to more sophisticated applications in biosensors and as cell culture substrates.
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Affiliation(s)
- Yong-Sang Ryu
- School of Electrical Engineering #032, Seoul National University, Kwanak P.O. Box 34, Seoul 151-600 Korea
| | - Nathan J. Wittenberg
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Jeng-Hun Suh
- School of Electrical Engineering #032, Seoul National University, Kwanak P.O. Box 34, Seoul 151-600 Korea
| | - Sang-Wook Lee
- School of Electrical Engineering #032, Seoul National University, Kwanak P.O. Box 34, Seoul 151-600 Korea
| | - Youngjoo Sohn
- Department of Anatomy, College of Korean Medicine, Institute of Oriental Medicine, Kyung Hee University, Seoul 130-701, Korea
| | - Sang-Hyun Oh
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Atul N. Parikh
- Departments of Biomedical Engineering and Chemical Engineering & Materials Science, University of California, Davis, California 95616, USA
| | - Sin-Doo Lee
- School of Electrical Engineering #032, Seoul National University, Kwanak P.O. Box 34, Seoul 151-600 Korea
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129
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Abstract
The growth and migration of neurons require continuous remodelling of the neuronal cytoskeleton, providing a versatile cellular framework for force generation and guided movement, in addition to structural support. Actin filaments and microtubules are central to the dynamic action of the cytoskeleton and rapid advances in imaging technologies are enabling ever more detailed visualisation of the dynamic intracellular networks that they form. However, these filaments do not act individually and an expanding body of evidence emphasises the importance of actin-microtubule crosstalk in orchestrating cytoskeletal dynamics. Here, we summarise our current understanding of the structure and dynamics of actin and microtubules in isolation, before reviewing both the mechanisms and the molecular players involved in mediating actin-microtubule crosstalk in neurons.
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Affiliation(s)
- Charlotte H Coles
- Laboratory for Axon Growth and Regeneration, German Center for Neurodegenerative Diseases (DZNE), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.
| | - Frank Bradke
- Laboratory for Axon Growth and Regeneration, German Center for Neurodegenerative Diseases (DZNE), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.
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130
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A phosphotyrosine switch regulates organic cation transporters. Nat Commun 2016; 7:10880. [PMID: 26979622 PMCID: PMC4799362 DOI: 10.1038/ncomms10880] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 01/28/2016] [Indexed: 12/21/2022] Open
Abstract
Membrane transporters are key determinants of therapeutic outcomes. They regulate systemic and cellular drug levels influencing efficacy as well as toxicities. Here we report a unique phosphorylation-dependent interaction between drug transporters and tyrosine kinase inhibitors (TKIs), which has uncovered widespread phosphotyrosine-mediated regulation of drug transporters. We initially found that organic cation transporters (OCTs), uptake carriers of metformin and oxaliplatin, were inhibited by several clinically used TKIs. Mechanistic studies showed that these TKIs inhibit the Src family kinase Yes1, which was found to be essential for OCT2 tyrosine phosphorylation and function. Yes1 inhibition in vivo diminished OCT2 activity, significantly mitigating oxaliplatin-induced acute sensory neuropathy. Along with OCT2, other SLC-family drug transporters are potentially part of an extensive 'transporter-phosphoproteome' with unique susceptibility to TKIs. On the basis of these findings we propose that TKIs, an important and rapidly expanding class of therapeutics, can functionally modulate pharmacologically important proteins by inhibiting protein kinases essential for their post-translational regulation.
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131
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Le Roux AL, Castro B, Garbacik ET, Garcia Parajo MF, Pons M. Single molecule fluorescence reveals dimerization of myristoylated Src N-terminal region on supported lipid bilayers. ChemistrySelect 2016. [DOI: 10.1002/slct.201600117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Anabel-Lise Le Roux
- Biomolecular NMR Laboratory; Organic Chemistry Department; University of Barcelona; Baldiri Reixac 10-12 08028 Barcelona Spain
- Institute for Research in Biomedicine (IRB-Barcelona); The Barcelona Institute of Science and Technology; Baldiri Reixac 10-12 08028 Barcelona Spain
| | - Bruno Castro
- ICFO- Institut de Ciencies Fotoniques; The Barcelona Institute of Science and Technology; 08860 Castelldefels (Barcelona) Spain
| | - Erik T. Garbacik
- ICFO- Institut de Ciencies Fotoniques; The Barcelona Institute of Science and Technology; 08860 Castelldefels (Barcelona) Spain
| | - Maria F. Garcia Parajo
- ICFO- Institut de Ciencies Fotoniques; The Barcelona Institute of Science and Technology; 08860 Castelldefels (Barcelona) Spain
- ICREA-Institució Catalana de Recerca i Estudis Avançats; 08010 Barcelona Spain
| | - Miquel Pons
- Biomolecular NMR Laboratory; Organic Chemistry Department; University of Barcelona; Baldiri Reixac 10-12 08028 Barcelona Spain
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132
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Villaseñor R, Kalaidzidis Y, Zerial M. Signal processing by the endosomal system. Curr Opin Cell Biol 2016; 39:53-60. [PMID: 26921695 DOI: 10.1016/j.ceb.2016.02.002] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/29/2016] [Accepted: 02/03/2016] [Indexed: 02/08/2023]
Abstract
Cells need to decode chemical or physical signals from their environment in order to make decisions on their fate. In the case of signalling receptors, ligand binding triggers a cascade of chemical reactions but also the internalization of the activated receptors in the endocytic pathway. Here, we highlight recent studies revealing a new role of the endosomal network in signal processing. The diversity of entry pathways and endosomal compartments is exploited to regulate the kinetics of receptor trafficking, and interactions with specific signalling adaptors and effectors. By governing the spatio-temporal distribution of signalling molecules, the endosomal system functions analogously to a digital-analogue computer that regulates the specificity and robustness of the signalling response.
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Affiliation(s)
- Roberto Villaseñor
- Roche Innovation Center Basel, Grenzacherstrasse, CH-4070 Basel, Switzerland.
| | - Yannis Kalaidzidis
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.
| | - Marino Zerial
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.
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133
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Baumdick M, Brüggemann Y, Schmick M, Xouri G, Sabet O, Davis L, Chin JW, Bastiaens PIH. EGF-dependent re-routing of vesicular recycling switches spontaneous phosphorylation suppression to EGFR signaling. eLife 2015; 4. [PMID: 26609808 PMCID: PMC4716840 DOI: 10.7554/elife.12223] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 11/25/2015] [Indexed: 11/17/2022] Open
Abstract
Autocatalytic activation of epidermal growth factor receptor (EGFR) coupled to dephosphorylating activity of protein tyrosine phosphatases (PTPs) ensures robust yet diverse responses to extracellular stimuli. The inevitable tradeoff of this plasticity is spontaneous receptor activation and spurious signaling. We show that a ligand-mediated switch in EGFR trafficking enables suppression of spontaneous activation while maintaining EGFR’s capacity to transduce extracellular signals. Autocatalytic phosphorylation of tyrosine 845 on unliganded EGFR monomers is suppressed by vesicular recycling through perinuclear areas with high PTP1B activity. Ligand-binding results in phosphorylation of the c-Cbl docking tyrosine and ubiquitination of the receptor. This secondary signal relies on EGF-induced EGFR self-association and switches suppressive recycling to directional trafficking. The re-routing regulates EGFR signaling response by the transit-time to late endosomes where it is switched-off by high PTP1B activity. This ubiquitin-mediated switch in EGFR trafficking is a uniquely suited solution to suppress spontaneous activation while maintaining responsiveness to EGF. DOI:http://dx.doi.org/10.7554/eLife.12223.001 In living tissue, the ability of individual cells to grow is influenced by signal molecules in the environment around each cell. For example, after an injury, a molecule called epidermal growth factor can stimulate cells to grow to repair the wound. Epidermal growth factor binds to and activates a receptor protein called EGFR, which faces outwards from the cell surface. However, this signal needs to be switched off again afterwards to prevent the cells from growing too much. Epidermal growth factor activates EGFR by triggering a process called “autophosphorylation”, in which EGFR attaches molecules called phosphates to itself. To quench the signal, EGFRs that are bound to growth factors are removed from the cell surface and taken into the cell in small membrane bubbles called vesicles. Enzymes called phosphatases near the cell nucleus remove the phosphate groups and thereby switch the receptors off, before the receptors are ultimately destroyed. However, EGFR autophosphorylation can also happen spontaneously in the absence of growth factor, so it was not clear how the cell is able to distinguish between this spontaneous activation and a genuine signal. Baumdick, Brüggemann, Schmick, Xouri et al. used biochemical techniques to address this question. The experiments show that EGFRs that have become spontaneously active are also removed from the cell surface in vesicles. However, unlike the EGFRs that are bound to growth factors, the spontaneously active receptors are recycled back to the membrane. On the way, their activity is also switched off by encountering phosphatases so that they are not active when they reach the cell surface again. The experiments also show that EGFRs are targeted for destruction by the presence of a tag called ubiquitin, which is added to the receptor in response to the binding of growth factor. Therefore, Baumdick et al.’s findings show that epidermal growth factor controls a switch that alters the way active EGFRs are processed in cells. This system acts to suppress the spontaneous activation of EGFRs, whilst maintaining the ability of the cell to respond to epidermal growth factor. The next challenge is to understand how the location of the phosphatases inside the cell influences when and how the EGFRs respond to this external signal. DOI:http://dx.doi.org/10.7554/eLife.12223.002
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Affiliation(s)
- Martin Baumdick
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Yannick Brüggemann
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, Technical University of Dortmund, Dortmund, Germany
| | - Malte Schmick
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Georgia Xouri
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Ola Sabet
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Lloyd Davis
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Philippe I H Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, Technical University of Dortmund, Dortmund, Germany
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134
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Wehrens M, ten Wolde PR, Mugler A. Positive feedback can lead to dynamic nanometer-scale clustering on cell membranes. J Chem Phys 2015; 141:205102. [PMID: 25429963 DOI: 10.1063/1.4901888] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Clustering of molecules on biological membranes is a widely observed phenomenon. A key example is the clustering of the oncoprotein Ras, which is known to be important for signal transduction in mammalian cells. Yet, the mechanism by which Ras clusters form and are maintained remains unclear. Recently, it has been discovered that activated Ras promotes further Ras activation. Here we show using particle-based simulation that this positive feedback is sufficient to produce persistent clusters of active Ras molecules at the nanometer scale via a dynamic nucleation mechanism. Furthermore, we find that our cluster statistics are consistent with experimental observations of the Ras system. Interestingly, we show that our model does not support a Turing regime of macroscopic reaction-diffusion patterning, and therefore that the clustering we observe is a purely stochastic effect, arising from the coupling of positive feedback with the discrete nature of individual molecules. These results underscore the importance of stochastic and dynamic properties of reaction diffusion systems for biological behavior.
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Affiliation(s)
- Martijn Wehrens
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | | | - Andrew Mugler
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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135
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Phua SC, Lin YC, Inoue T. An intelligent nano-antenna: Primary cilium harnesses TRP channels to decode polymodal stimuli. Cell Calcium 2015; 58:415-22. [PMID: 25828566 PMCID: PMC4564334 DOI: 10.1016/j.ceca.2015.03.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 11/30/2022]
Abstract
The primary cilium is a solitary hair-like organelle on the cell surface that serves as an antenna sensing ever-changing environmental conditions. In this review, we will first recapitulate the molecular basis of the polymodal sensory function of the primary cilia, specifically focusing on transient receptor potential (TRP) channels that accumulate inside the organelle and conduct calcium ions (Ca(2+)). Each subfamily member, namely TRPP2 TRPP3, TRPC1 and TRPV4, is gated by multiple environmental factors, including chemical (receptor ligands, intracellular second messengers such as Ca(2+)), mechanical (fluid shear stress, hypo-osmotic swelling), or physical (temperature, voltage) stimuli. Both activity and heterodimer compositions of the TRP channels may be dynamically regulated for precise tuning to the varying dynamic ranges of the individual input stimuli. We will thus discuss the potential regulation of TRP channels by local second messengers. Despite its reported importance in embryonic patterning and tissue morphogenesis, the precise functional significance of the downstream Ca(2+) signals of the TRP channels remains unknown. We will close our review by featuring recent technological advances in visualizing and analyzing signal transduction inside the primary cilia, together with current perspectives illuminating the functional significance of intraciliary Ca(2+) signals.
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Affiliation(s)
- Siew Cheng Phua
- Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Institute for Basic Biomedical Sciences, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA.
| | - Yu-Chun Lin
- Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Institute for Basic Biomedical Sciences, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Takanari Inoue
- Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Institute for Basic Biomedical Sciences, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Precursory Research for Embryonic Science and Technology (PRESTO) Investigator, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
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136
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Veya L, Piguet J, Vogel H. Single Molecule Imaging Deciphers the Relation between Mobility and Signaling of a Prototypical G Protein-coupled Receptor in Living Cells. J Biol Chem 2015; 290:27723-35. [PMID: 26363070 DOI: 10.1074/jbc.m115.666677] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Indexed: 01/10/2023] Open
Abstract
Lateral diffusion enables efficient interactions between membrane proteins, leading to signal transmission across the plasma membrane. An open question is how the spatiotemporal distribution of cell surface receptors influences the transmembrane signaling network. Here we addressed this issue by studying the mobility of a prototypical G protein-coupled receptor, the neurokinin-1 receptor, during its different phases of cellular signaling. Attaching a single quantum dot to individual neurokinin-1 receptors enabled us to follow with high spatial and temporal resolution over long time regimes the fate of individual receptors at the plasma membrane. Single receptor trajectories revealed a very heterogeneous mobility distribution pattern with diffusion constants ranging from 0.0005 to 0.1 μm(2)/s comprising receptors freely diffusing and others confined in 100-600-nm-sized membrane domains as well as immobile receptors. A two-dimensional representation of mobility and confinement resolved two major, broadly distributed receptor populations, one showing high mobility and low lateral restriction and the other showing low mobility and high restriction. We found that about 40% of the receptors in the basal state are already confined in membrane domains and are associated with clathrin. After stimulation with an agonist, an additional 30% of receptors became further confined. Using inhibitors of clathrin-mediated endocytosis, we found that the fraction of confined receptors at the basal state depends on the quantity of membrane-associated clathrin and is correlated to a significant decrease of the canonical pathway activity of the receptors. This shows that the high plasticity of receptor mobility is of central importance for receptor homeostasis and fine regulation of receptor activity.
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Affiliation(s)
- Luc Veya
- From the Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Joachim Piguet
- From the Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Horst Vogel
- From the Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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137
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Lopez D. Molecular composition of functional microdomains in bacterial membranes. Chem Phys Lipids 2015; 192:3-11. [PMID: 26320704 DOI: 10.1016/j.chemphyslip.2015.08.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 08/10/2015] [Accepted: 08/24/2015] [Indexed: 12/14/2022]
Abstract
Membranes of eukaryotic cells organize a number of proteins related to signal transduction and membrane trafficking into microdomains, which are enriched in particular lipids, like cholesterol and sphingolipids and are commonly referred as to lipid rafts or membrane rafts. The existence of this type of signaling platforms was traditionally associated with eukaryotic membranes because prokaryotic cells were considered too simple organisms to require a sophisticated organization of their signaling networks. However, the research that have been performed during last years have shown that bacteria organize many signaling transduction processes in Functional Membrane Microdomains (FMMs), which are similar to the lipid rafts that are found in eukaryotic cells. The current knowledge of the existence of FMMs in bacteria is described in this review and the specific structural and biological properties of these membrane microdomains are introduced. The organization of FMMs in bacterial membranes reveals an unexpected level of sophistication in signaling transduction and membrane organization that is unprecedented in bacteria, suggesting that bacteria as more complex organisms than previously considered.
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Affiliation(s)
- Daniel Lopez
- Research Center for Infectious Diseases (ZINF), Institute for Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider Strasse (2), 97080 Würzburg, Germany; Spanish National Center for Biotechnology (CNB), Campus de Cantoblanco, Darwin 3, 28049 Madrid, Spain.
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138
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Ubiquitination switches EphA2 vesicular traffic from a continuous safeguard to a finite signalling mode. Nat Commun 2015; 6:8047. [PMID: 26292967 PMCID: PMC4560775 DOI: 10.1038/ncomms9047] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/11/2015] [Indexed: 01/15/2023] Open
Abstract
Autocatalytic phosphorylation of receptor tyrosine kinases (RTKs) enables diverse, context-dependent responses to extracellular signals but comes at the price of autonomous, ligand-independent activation. Using a conformational biosensor that reports on the kinase activity of the cell guidance ephrin receptor type-A (EphA2) in living cells, we observe that autonomous EphA2 activation is suppressed by vesicular recycling and dephosphorylation by protein tyrosine phosphatases 1B (PTP1B) near the pericentriolar recycling endosome. This spatial segregation of catalytically superior PTPs from RTKs at the plasma membrane is essential to preserve ligand responsiveness. Ligand-induced clustering, on the other hand, promotes phosphorylation of a c-Cbl docking site and ubiquitination of the receptor, thereby redirecting it to the late endosome/lysosome. We show that this switch from cyclic to unidirectional receptor trafficking converts a continuous suppressive safeguard mechanism into a transient ligand-responsive signalling mode.
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139
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Hara-Chikuma M, Satooka H, Watanabe S, Honda T, Miyachi Y, Watanabe T, Verkman AS. Aquaporin-3-mediated hydrogen peroxide transport is required for NF-κB signalling in keratinocytes and development of psoriasis. Nat Commun 2015; 6:7454. [PMID: 26100668 DOI: 10.1038/ncomms8454] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 05/10/2015] [Indexed: 12/23/2022] Open
Abstract
Aquaporin 3 (AQP3), a water/glycerol channel protein, has been found to transport hydrogen peroxide (H2O2). Here, we show that H2O2, imported via AQP3, is involved in nuclear factor-κB (NF-κB) signalling in keratinocytes and in the pathogenesis of psoriasis. IL-23-mediated induction of psoriasis is reduced in AQP3 knockout mice (AQP3(-/-)), and is accompanied by impaired NF-κB activation and intracellular H2O2 accumulation. In primary keratinocyte cultures, cellular import of H2O2 produced by membrane NADPH oxidase 2 (Nox2) in response to TNF-α is facilitated by AQP3 and required for NF-κB activation by regulation of protein phosphatase 2A. As AQP3 associates with Nox2, we propose that this interplay constitutes H2O2-mediated signalling in response to TNF-α stimulation. Collectively, these data indicate that AQP3-facilitated H2O2 transport is required for NF-κB activation in keratinocytes in the development of psoriasis.
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Affiliation(s)
- Mariko Hara-Chikuma
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroki Satooka
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Sachiko Watanabe
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Tetsuya Honda
- 1] Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan [2] Department of Dermatology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Yoshiki Miyachi
- Department of Dermatology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Takeshi Watanabe
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - A S Verkman
- Department of Medicine and Physiology, University of California, San Francisco, California 94143, USA
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140
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Vermaas JV, Baylon JL, Arcario MJ, Muller MP, Wu Z, Pogorelov TV, Tajkhorshid E. Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution. J Membr Biol 2015; 248:563-82. [PMID: 25998378 PMCID: PMC4490090 DOI: 10.1007/s00232-015-9806-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/30/2015] [Indexed: 12/24/2022]
Abstract
Biological membranes constitute a critical component in all living cells. In addition to providing a conducive environment to a wide range of cellular processes, including transport and signaling, mounting evidence has established active participation of specific lipids in modulating membrane protein function through various mechanisms. Understanding lipid-protein interactions underlying these mechanisms at a sufficiently high resolution has proven extremely challenging, partly due to the semi-fluid nature of the membrane. In order to address this challenge computationally, multiple methods have been developed, including an alternative membrane representation termed highly mobile membrane mimetic (HMMM) in which lateral lipid diffusion has been significantly enhanced without compromising atomic details. The model allows for efficient sampling of lipid-protein interactions at atomic resolution, thereby significantly enhancing the effectiveness of molecular dynamics simulations in capturing membrane-associated phenomena. In this review, after providing an overview of HMMM model development, we will describe briefly successful application of the model to study a variety of membrane processes, including lipid-dependent binding and insertion of peripheral proteins, the mechanism of phospholipid insertion into lipid bilayers, and characterization of optimal tilt angle of transmembrane helices. We conclude with practical recommendations for proper usage of the model in simulation studies of membrane processes.
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Affiliation(s)
- Josh V. Vermaas
- Beckman Institute, Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave. Urbana, IL 61801
| | - Javier L. Baylon
- Beckman Institute, Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave. Urbana, IL 61801
| | - Mark J. Arcario
- Beckman Institute, Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave. Urbana, IL 61801
| | - Melanie P. Muller
- Beckman Institute, Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave. Urbana, IL 61801
| | - Zhe Wu
- Beckman Institute, Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave. Urbana, IL 61801
| | - Taras V. Pogorelov
- Beckman Institute, Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave. Urbana, IL 61801
| | - Emad Tajkhorshid
- Beckman Institute, Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave. Urbana, IL 61801
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141
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Wedeking T, Löchte S, Richter CP, Bhagawati M, Piehler J, You C. Single Cell GFP-Trap Reveals Stoichiometry and Dynamics of Cytosolic Protein Complexes. NANO LETTERS 2015; 15:3610-3615. [PMID: 25901412 DOI: 10.1021/acs.nanolett.5b01153] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We developed in situ single cell pull-down (SiCPull) of GFP-tagged protein complexes based on micropatterned functionalized surface architectures. Cells cultured on these supports are lysed by mild detergents and protein complexes captured to the surface are probed in situ by total internal reflection fluorescence microscopy. Using SiCPull, we quantitatively mapped the lifetimes of various signal transducer and activator of transcription complexes by monitoring dissociation from the surface and defined their stoichiometry on the single molecule level.
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Affiliation(s)
- Tim Wedeking
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Sara Löchte
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | | | - Maniraj Bhagawati
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Changjiang You
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
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142
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Schmick M, Kraemer A, Bastiaens PIH. Ras moves to stay in place. Trends Cell Biol 2015; 25:190-7. [PMID: 25759176 DOI: 10.1016/j.tcb.2015.02.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 10/23/2022]
Abstract
Ras is a major intracellular signaling hub. This elevated position comes at a precarious cost: a single point mutation can cause aberrant signaling. The capacity of Ras for signaling is inextricably linked to its enrichment at the plasma membrane (PM). This PM localization is dynamically maintained by three essential elements: alteration of membrane affinities via lipidation and membrane-interaction motifs; trapping on specific membranes coupled with unidirectional vesicular transport to the PM; and regulation of diffusion via interaction with a solubilization factor. This system constitutes a cycle that primarily corrects for the entropic equilibration of Ras to all membranes that dilutes its signaling capacity. We illuminate how this reaction-diffusion system maintains an out-of-equilibrium localization of Ras GTPases and thereby confers signaling functionality to the PM.
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Affiliation(s)
- Malte Schmick
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Astrid Kraemer
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Philippe I H Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany.
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143
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Abstract
An interesting concept in the organization of cellular membranes is the proposed existence of lipid rafts. Membranes of eukaryotic cells organize signal transduction proteins into membrane rafts or lipid rafts that are enriched in particular lipids such as cholesterol and are important for the correct functionality of diverse cellular processes. The assembly of lipid rafts in eukaryotes has been considered a fundamental step during the evolution of cellular complexity, suggesting that bacteria and archaea were organisms too simple to require such a sophisticated organization of their cellular membranes. However, it was recently discovered that bacteria organize many signal transduction, protein secretion, and transport processes in functional membrane microdomains, which are equivalent to the lipid rafts of eukaryotic cells. This review contains the most significant advances during the last 4 years in understanding the structural and biological role of lipid rafts in bacteria. Furthermore, this review shows a detailed description of a number of molecular and genetic approaches related to the discovery of bacterial lipid rafts as well as an overview of the group of tentative lipid-protein and protein-protein interactions that give consistency to these sophisticated signaling platforms. Additional data suggesting that lipid rafts are widely distributed in bacteria are presented in this review. Therefore, we discuss the available techniques and optimized protocols for the purification and analysis of raft-associated proteins in various bacterial species to aid in the study of bacterial lipid rafts in other laboratories that could be interested in this topic. Overall, the discovery of lipid rafts in bacteria reveals a new level of sophistication in signal transduction and membrane organization that was unexpected for bacteria and shows that bacteria are more complex than previously appreciated.
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Affiliation(s)
- Marc Bramkamp
- Department of Biology I, University of Munich (LMU), Planegg/Martinsried, Germany
| | - Daniel Lopez
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
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144
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Banjade S, Rosen MK. Phase transitions of multivalent proteins can promote clustering of membrane receptors. eLife 2014; 3. [PMID: 25321392 PMCID: PMC4238058 DOI: 10.7554/elife.04123] [Citation(s) in RCA: 390] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/16/2014] [Indexed: 12/14/2022] Open
Abstract
Clustering of proteins into micrometer-sized structures at membranes is observed in many signaling pathways. Most models of clustering are specific to particular systems, and relationships between physical properties of the clusters and their molecular components are not well understood. We report biochemical reconstitution on supported lipid bilayers of protein clusters containing the adhesion receptor Nephrin and its cytoplasmic partners, Nck and N-WASP. With Nephrin attached to the bilayer, multivalent interactions enable these proteins to polymerize on the membrane surface and undergo two-dimensional phase separation, producing micrometer-sized clusters. Dynamics and thermodynamics of the clusters are modulated by the valencies and affinities of the interacting species. In the presence of the Arp2/3 complex, the clusters assemble actin filaments, suggesting that clustering of regulatory factors could promote local actin assembly at membranes. Interactions between multivalent proteins could be a general mechanism for cytoplasmic adaptor proteins to organize membrane receptors into micrometer-scale signaling zones. DOI:http://dx.doi.org/10.7554/eLife.04123.001 The membrane that surrounds a cell is made up of a mixture of lipid molecules and proteins. Membrane proteins perform a wide range of roles, including transmitting signals into, and out of, cells and helping neighboring cells to stick together. To perform these tasks, these proteins commonly need to bind to other molecules—collectively known as ligands—that are found either inside or outside the cell. Membrane proteins are able to move around within the membrane, and in many systems, ligand binding causes the membrane proteins to cluster together. Although this clustering has been seen in many different systems, no general principles that describe how clustering occurs had been found. Now, Banjade and Rosen have constructed an artificial cell membrane to investigate the clustering of a membrane protein called Nephrin, which is essential for kidneys to function correctly. When it is activated, Nephrin interacts with protein ligands called Nck and N-WASP that are found inside cells and helps filaments of a protein called actin to form. These filaments perform a number of roles including enabling cells to adhere to each other and to move. In Banjade and Rosen's artificial system, when a critical concentration of ligands was exceeded, clusters of Nephrin, Nck and N-WASP suddenly formed. This suggests that the clusters form through a physical process known as ‘phase separation’. Banjade and Rosen found that this critical concentration depends on how strongly the proteins interact and the number of sites they possess to bind each other. Within the clusters, the three proteins formed large polymer chains. The clusters were mobile and, over time, small clusters coalesced into larger clusters. Even though the clusters persisted for hours, individual proteins did not stay in a given cluster for long and instead continuously exchanged back-and-forth between the cluster and its surroundings. When actin and another protein complex that interacts with N-WASP were added to the artificial membrane system, actin filaments began to form at the protein clusters. Banjade and Rosen suggest that such clusters act as ‘signaling zones’ that coordinate the construction of the actin filaments. Regions that are also found in many other signaling proteins mediate the interactions between Nephrin, Nck and N-WASP. Banjade and Rosen therefore suggest that phase separation and protein polymer formation could explain how many different types of membrane proteins form clusters. DOI:http://dx.doi.org/10.7554/eLife.04123.002
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Affiliation(s)
- Sudeep Banjade
- Department of Biophysics, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Michael K Rosen
- Department of Biophysics, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
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145
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Emerging concepts in the regulation of the EGF receptor and other receptor tyrosine kinases. Trends Biochem Sci 2014; 39:437-46. [DOI: 10.1016/j.tibs.2014.08.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/04/2014] [Accepted: 08/07/2014] [Indexed: 11/21/2022]
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146
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Interactions of peripheral proteins with model membranes as viewed by molecular dynamics simulations. Biochem Soc Trans 2014; 42:1418-24. [DOI: 10.1042/bst20140144] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Many cellular signalling and related events are triggered by the association of peripheral proteins with anionic lipids in the cell membrane (e.g. phosphatidylinositol phosphates or PIPs). This association frequently occurs via lipid-binding modules, e.g. pleckstrin homology (PH), C2 and four-point-one, ezrin, radixin, moesin (FERM) domains, present in peripheral and cytosolic proteins. Multiscale simulation approaches that combine coarse-grained and atomistic MD simulations may now be applied with confidence to investigate the molecular mechanisms of the association of peripheral proteins with model bilayers. Comparisons with experimental data indicate that such simulations can predict specific peripheral protein–lipid interactions. We discuss the application of multiscale MD simulation and related approaches to investigate the association of peripheral proteins which contain PH, C2 or FERM-binding modules with lipid bilayers of differing phospholipid composition, including bilayers containing multiple PIP molecules.
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147
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Srivastava A, Voth GA. Solvent-Free, Highly Coarse-Grained Models for Charged Lipid Systems. J Chem Theory Comput 2014; 10:4730-4744. [PMID: 25328498 PMCID: PMC4196741 DOI: 10.1021/ct500474a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Indexed: 12/13/2022]
Abstract
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We
present a methodology to develop coarse-grained lipid models
such that electrostatic interactions between the coarse-grained sites
can be derived accurately from an all-atom molecular dynamics trajectory
and expressed as an effective pairwise electrostatic potential with
appropriate screening functions. The reference nonbonded forces from
the all-atom trajectory are decomposed into separate electrostatic
and van der Waals (vdW) forces, based on the multiscale coarse-graining
method. The coarse-grained electrostatic potential is assumed to be
a general function of unknown variables and the final site–site
interactions are obtained variationally, where the residual of the
electrostatic forces from the assumed field is minimized. The resulting
electrostatic interactions are fitted to screened electrostatics functions,
with a special treatment for distance-dependent dielectrics and screened
dipole–dipole interactions. The vdW interactions are derived
separately. The resulting charged hybrid coarse-graining method is
applied to various solvent-free three-site models of anionic lipid
systems.
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Affiliation(s)
- Anand Srivastava
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, The University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, The University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
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148
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Bernardo-Faura M, Massen S, Falk CS, Brady NR, Eils R. Data-derived modeling characterizes plasticity of MAPK signaling in melanoma. PLoS Comput Biol 2014; 10:e1003795. [PMID: 25188314 PMCID: PMC4154640 DOI: 10.1371/journal.pcbi.1003795] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 06/24/2014] [Indexed: 01/05/2023] Open
Abstract
The majority of melanomas have been shown to harbor somatic mutations in the RAS-RAF-MEK-MAPK and PI3K-AKT pathways, which play a major role in regulation of proliferation and survival. The prevalence of these mutations makes these kinase signal transduction pathways an attractive target for cancer therapy. However, tumors have generally shown adaptive resistance to treatment. This adaptation is achieved in melanoma through its ability to undergo neovascularization, migration and rearrangement of signaling pathways. To understand the dynamic, nonlinear behavior of signaling pathways in cancer, several computational modeling approaches have been suggested. Most of those models require that the pathway topology remains constant over the entire observation period. However, changes in topology might underlie adaptive behavior to drug treatment. To study signaling rearrangements, here we present a new approach based on Fuzzy Logic (FL) that predicts changes in network architecture over time. This adaptive modeling approach was used to investigate pathway dynamics in a newly acquired experimental dataset describing total and phosphorylated protein signaling over four days in A375 melanoma cell line exposed to different kinase inhibitors. First, a generalized strategy was established to implement a parameter-reduced FL model encoding non-linear activity of a signaling network in response to perturbation. Next, a literature-based topology was generated and parameters of the FL model were derived from the full experimental dataset. Subsequently, the temporal evolution of model performance was evaluated by leaving time-defined data points out of training. Emerging discrepancies between model predictions and experimental data at specific time points allowed the characterization of potential network rearrangement. We demonstrate that this adaptive FL modeling approach helps to enhance our mechanistic understanding of the molecular plasticity of melanoma. Signal transduction pathways can be described as static routes, transmitting extrinsic signals to the nucleus to induce a transcriptional response. In contrast to this reductionist view, the emerging paradigm is that signaling networks undergo dynamic crosstalk, both in disease and physiological conditions. To understand complex pathway behavior, it is necessary to develop methods to identify pathway interactions that are active as a consequence of stimuli and, importantly, to describe their evolution in time. To that end, we developed a method relying on prior knowledge networks in order to predict signaling crosstalk evolution, in response to perturbation and over time. The challenge we addressed was to establish a method dependent on information related to the topology of reported interactions, and not their mechanistic characteristics, and at the same time complex enough to reproduce the behavior of the signaling intermediates. The work presented here demonstrates that such an approach can be used to predict mechanisms that melanoma uses to rearrange its signaling and maintain its abnormal proliferation upon treatment.
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Affiliation(s)
- Marti Bernardo-Faura
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Bioquant, Heidelberg University, Heidelberg, Germany
| | - Stefan Massen
- Lysosomal Systems Biology, German Cancer Research Center (DKFZ), Bioquant, Heidelberg, Germany
- Institute of Transplant Immunology, IFB-Tx, Hannover Medical School, Hannover, Germany
| | - Christine S. Falk
- Institute of Transplant Immunology, IFB-Tx, Hannover Medical School, Hannover, Germany
- German Center for Infectious Diseases (DZIF) TTU-IICH, Hannover, Germany
| | - Nathan R. Brady
- Systems Biology of Cell Death Mechanisms, German Cancer Research Center (DKFZ), Bioquant, Heidelberg, Germany
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Bioquant, Heidelberg University, Heidelberg, Germany
- * E-mail:
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149
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Iversen L, Tu HL, Lin WC, Christensen SM, Abel SM, Iwig J, Wu HJ, Gureasko J, Rhodes C, Petit RS, Hansen SD, Thill P, Yu CH, Stamou D, Chakraborty AK, Kuriyan J, Groves JT. Molecular kinetics. Ras activation by SOS: allosteric regulation by altered fluctuation dynamics. Science 2014; 345:50-4. [PMID: 24994643 DOI: 10.1126/science.1250373] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation, through protein and membrane interactions, govern activity of SOS. We characterized the specific activity of individual SOS molecules catalyzing nucleotide exchange in H-Ras. Single-molecule kinetic traces revealed that SOS samples a broad distribution of turnover rates through stochastic fluctuations between distinct, long-lived (more than 100 seconds), functional states. The expected allosteric activation of SOS by Ras-guanosine triphosphate (GTP) was conspicuously absent in the mean rate. However, fluctuations into highly active states were modulated by Ras-GTP. This reveals a mechanism in which functional output may be determined by the dynamical spectrum of rates sampled by a small number of enzymes, rather than the ensemble average.
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Affiliation(s)
- Lars Iversen
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hsiung-Lin Tu
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Wan-Chen Lin
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sune M Christensen
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Steven M Abel
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Jeff Iwig
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hung-Jen Wu
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jodi Gureasko
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher Rhodes
- Department of Mechanical Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rebecca S Petit
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Scott D Hansen
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Peter Thill
- Department of Chemistry, MIT, Cambridge, MA 02139, USA
| | - Cheng-Han Yu
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Dimitrios Stamou
- Department of Chemistry and Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Department of Chemistry, MIT, Cambridge, MA 02139, USA. Department of Biological Engineering, MIT, Cambridge, MA 02139, USA. Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA. Department of Physics, MIT, Cambridge, MA 02139, USA. Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
| | - John Kuriyan
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. Physical Biosciences and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jay T Groves
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. Mechanobiology Institute, National University of Singapore, Singapore. Physical Biosciences and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Berkeley Education Alliance for Research in Singapore, 1 Create Way, CREATE tower level 11, University Town, Singapore 138602.
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150
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Nastou KC, Tsaousis GN, Kremizas KE, Litou ZI, Hamodrakas SJ. The human plasma membrane peripherome: visualization and analysis of interactions. BIOMED RESEARCH INTERNATIONAL 2014; 2014:397145. [PMID: 25057483 PMCID: PMC4095733 DOI: 10.1155/2014/397145] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/04/2014] [Indexed: 12/11/2022]
Abstract
A major part of membrane function is conducted by proteins, both integral and peripheral. Peripheral membrane proteins temporarily adhere to biological membranes, either to the lipid bilayer or to integral membrane proteins with noncovalent interactions. The aim of this study was to construct and analyze the interactions of the human plasma membrane peripheral proteins (peripherome hereinafter). For this purpose, we collected a dataset of peripheral proteins of the human plasma membrane. We also collected a dataset of experimentally verified interactions for these proteins. The interaction network created from this dataset has been visualized using Cytoscape. We grouped the proteins based on their subcellular location and clustered them using the MCL algorithm in order to detect functional modules. Moreover, functional and graph theory based analyses have been performed to assess biological features of the network. Interaction data with drug molecules show that ~10% of peripheral membrane proteins are targets for approved drugs, suggesting their potential implications in disease. In conclusion, we reveal novel features and properties regarding the protein-protein interaction network created by peripheral proteins of the human plasma membrane.
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Affiliation(s)
- Katerina C. Nastou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 15701 Athens, Greece
| | - Georgios N. Tsaousis
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 15701 Athens, Greece
| | - Kimon E. Kremizas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 15701 Athens, Greece
| | - Zoi I. Litou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 15701 Athens, Greece
| | - Stavros J. Hamodrakas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 15701 Athens, Greece
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