APPL1 Associates with Trka and GIPC1 and Is Required for Nerve Growth Factor-Mediated Signal Transduction
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Redefining the Specificity of Phosphoinositide-Binding by Human
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.20.163253; this version posted June 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Redefining the specificity of phosphoinositide-binding by human PH domain-containing proteins Nilmani Singh1†, Adriana Reyes-Ordoñez1†, Michael A. Compagnone1, Jesus F. Moreno Castillo1, Benjamin J. Leslie2, Taekjip Ha2,3,4,5, Jie Chen1* 1Department of Cell & Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801; 2Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205; 3Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218; 4Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205; 5Howard Hughes Medical Institute, Baltimore, MD 21205, USA †These authors contributed equally to this work. *Correspondence: [email protected]. bioRxiv preprint doi: https://doi.org/10.1101/2020.06.20.163253; this version posted June 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. ABSTRACT Pleckstrin homology (PH) domains are presumed to bind phosphoinositides (PIPs), but specific interaction with and regulation by PIPs for most PH domain-containing proteins are unclear. Here we employed a single-molecule pulldown assay to study interactions of lipid vesicles with full-length proteins in mammalian whole cell lysates. -
Supplementary Figures 1-14 and Supplementary References
SUPPORTING INFORMATION Spatial Cross-Talk Between Oxidative Stress and DNA Replication in Human Fibroblasts Marko Radulovic,1,2 Noor O Baqader,1 Kai Stoeber,3† and Jasminka Godovac-Zimmermann1* 1Division of Medicine, University College London, Center for Nephrology, Royal Free Campus, Rowland Hill Street, London, NW3 2PF, UK. 2Insitute of Oncology and Radiology, Pasterova 14, 11000 Belgrade, Serbia 3Research Department of Pathology and UCL Cancer Institute, Rockefeller Building, University College London, University Street, London WC1E 6JJ, UK †Present Address: Shionogi Europe, 33 Kingsway, Holborn, London WC2B 6UF, UK TABLE OF CONTENTS 1. Supplementary Figures 1-14 and Supplementary References. Figure S-1. Network and joint spatial razor plot for 18 enzymes of glycolysis and the pentose phosphate shunt. Figure S-2. Correlation of SILAC ratios between OXS and OAC for proteins assigned to the SAME class. Figure S-3. Overlap matrix (r = 1) for groups of CORUM complexes containing 19 proteins of the 49-set. Figure S-4. Joint spatial razor plots for the Nop56p complex and FIB-associated complex involved in ribosome biogenesis. Figure S-5. Analysis of the response of emerin nuclear envelope complexes to OXS and OAC. Figure S-6. Joint spatial razor plots for the CCT protein folding complex, ATP synthase and V-Type ATPase. Figure S-7. Joint spatial razor plots showing changes in subcellular abundance and compartmental distribution for proteins annotated by GO to nucleocytoplasmic transport (GO:0006913). Figure S-8. Joint spatial razor plots showing changes in subcellular abundance and compartmental distribution for proteins annotated to endocytosis (GO:0006897). Figure S-9. Joint spatial razor plots for 401-set proteins annotated by GO to small GTPase mediated signal transduction (GO:0007264) and/or GTPase activity (GO:0003924). -
Lowe Syndrome-Linked Endocytic Adaptors Direct Membrane Cycling
bioRxiv preprint doi: https://doi.org/10.1101/616664; this version posted April 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Lowe Syndrome-linked endocytic adaptors direct membrane 2 cycling kinetics with OCRL in Dictyostelium discoideum. 3 Running Title: F&H motifs and OCRL in Dictyostelium discoideum 4 Alexandre Luscher5+, Florian Fröhlich1,7+, Caroline Barisch5, Clare Littlewood 4, Joe Metcalfe4, 5 Florence Leuba5, Anita Palma6, Michelle Pirruccello1,2, Gianni Cesareni6, Massimiliano Stagi4, Tobias 6 C. Walther7, Thierry Soldati5*, Pietro De Camilli1,2,3*, Laura E. Swan1,2,4* 7 1. Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA 8 2. Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration, and 9 Repair, Yale University School of Medicine, New Haven, CT 06510, USA. 10 3. Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of 11 Medicine, New Haven, CT 06510, USA. 12 4. Department of Cellular and Molecular Physiology, University of Liverpool, Crown St, Liverpool, 13 L69 3BX, UK 14 5.Department of Biochemistry, Faculty of Science, University of Geneva, Science II, 30 quai Ernest- 15 Ansermet, 1211 Geneva-4, Switzerland 16 6.Department of Biology, University of Rome, Tor Vergata, Rome Italy 17 7. Department of Genetics and Complex Diseases, Harvard School of Public Health, Department of 18 Cell Biology, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA 02115, USA 19 + : contributed equally to this manuscript 20 *: Correspondence : [email protected]; [email protected]; [email protected] 21 Lead correspondence: [email protected] 22 1 bioRxiv preprint doi: https://doi.org/10.1101/616664; this version posted April 24, 2019. -
Table S1. Identified Proteins with Exclusive Expression in Cerebellum of Rats of Control, 10Mg F/L and 50Mg F/L Groups
Table S1. Identified proteins with exclusive expression in cerebellum of rats of control, 10mg F/L and 50mg F/L groups. Accession PLGS Protein Name Group IDa Score Q3TXS7 26S proteasome non-ATPase regulatory subunit 1 435 Control Q9CQX8 28S ribosomal protein S36_ mitochondrial 197 Control P52760 2-iminobutanoate/2-iminopropanoate deaminase 315 Control Q60597 2-oxoglutarate dehydrogenase_ mitochondrial 67 Control P24815 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 1 84 Control Q99L13 3-hydroxyisobutyrate dehydrogenase_ mitochondrial 114 Control P61922 4-aminobutyrate aminotransferase_ mitochondrial 470 Control P10852 4F2 cell-surface antigen heavy chain 220 Control Q8K010 5-oxoprolinase 197 Control P47955 60S acidic ribosomal protein P1 190 Control P70266 6-phosphofructo-2-kinase/fructose-2_6-bisphosphatase 1 113 Control Q8QZT1 Acetyl-CoA acetyltransferase_ mitochondrial 402 Control Q9R0Y5 Adenylate kinase isoenzyme 1 623 Control Q80TS3 Adhesion G protein-coupled receptor L3 59 Control B7ZCC9 Adhesion G-protein coupled receptor G4 139 Control Q6P5E6 ADP-ribosylation factor-binding protein GGA2 45 Control E9Q394 A-kinase anchor protein 13 60 Control Q80Y20 Alkylated DNA repair protein alkB homolog 8 111 Control P07758 Alpha-1-antitrypsin 1-1 78 Control P22599 Alpha-1-antitrypsin 1-2 78 Control Q00896 Alpha-1-antitrypsin 1-3 78 Control Q00897 Alpha-1-antitrypsin 1-4 78 Control P57780 Alpha-actinin-4 58 Control Q9QYC0 Alpha-adducin 270 Control Q9DB05 Alpha-soluble NSF attachment protein 156 Control Q6PAM1 Alpha-taxilin 161 -
Confirmation of Pathogenic Mechanisms by SARS-Cov-2–Host
Messina et al. Cell Death and Disease (2021) 12:788 https://doi.org/10.1038/s41419-021-03881-8 Cell Death & Disease ARTICLE Open Access Looking for pathways related to COVID-19: confirmation of pathogenic mechanisms by SARS-CoV-2–host interactome Francesco Messina 1, Emanuela Giombini1, Chiara Montaldo1, Ashish Arunkumar Sharma2, Antonio Zoccoli3, Rafick-Pierre Sekaly2, Franco Locatelli4, Alimuddin Zumla5, Markus Maeurer6,7, Maria R. Capobianchi1, Francesco Nicola Lauria1 and Giuseppe Ippolito 1 Abstract In the last months, many studies have clearly described several mechanisms of SARS-CoV-2 infection at cell and tissue level, but the mechanisms of interaction between host and SARS-CoV-2, determining the grade of COVID-19 severity, are still unknown. We provide a network analysis on protein–protein interactions (PPI) between viral and host proteins to better identify host biological responses, induced by both whole proteome of SARS-CoV-2 and specific viral proteins. A host-virus interactome was inferred, applying an explorative algorithm (Random Walk with Restart, RWR) triggered by 28 proteins of SARS-CoV-2. The analysis of PPI allowed to estimate the distribution of SARS-CoV-2 proteins in the host cell. Interactome built around one single viral protein allowed to define a different response, underlining as ORF8 and ORF3a modulated cardiovascular diseases and pro-inflammatory pathways, respectively. Finally, the network-based approach highlighted a possible direct action of ORF3a and NS7b to enhancing Bradykinin Storm. This network-based representation of SARS-CoV-2 infection could be a framework for pathogenic evaluation of specific 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; clinical outcomes. -
And Pancreatic Cancer: from the Role of Evs to the Interference with EV-Mediated Reciprocal Communication
biomedicines Review Extracellular Vesicles (EVs) and Pancreatic Cancer: From the Role of EVs to the Interference with EV-Mediated Reciprocal Communication 1, 1, 1 1 1 Sokviseth Moeng y, Seung Wan Son y, Jong Sun Lee , Han Yeoung Lee , Tae Hee Kim , Soo Young Choi 1, Hyo Jeong Kuh 2 and Jong Kook Park 1,* 1 Department of Biomedical Science and Research Institute for Bioscience & Biotechnology, Hallym University, Chunchon 24252, Korea; [email protected] (S.M.); [email protected] (S.W.S.); [email protected] (J.S.L.); [email protected] (H.Y.L.); [email protected] (T.H.K.); [email protected] (S.Y.C.) 2 Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; [email protected] * Correspondence: [email protected]; Tel.: +82-33-248-2114 These authors contributed equally. y Received: 29 June 2020; Accepted: 1 August 2020; Published: 3 August 2020 Abstract: Pancreatic cancer is malignant and the seventh leading cause of cancer-related deaths worldwide. However, chemotherapy and radiotherapy are—at most—moderately effective, indicating the need for new and different kinds of therapies to manage this disease. It has been proposed that the biologic properties of pancreatic cancer cells are finely tuned by the dynamic microenvironment, which includes extracellular matrix, cancer-associated cells, and diverse immune cells. Accumulating evidence has demonstrated that extracellular vesicles (EVs) play an essential role in communication between heterogeneous subpopulations of cells by transmitting multiplex biomolecules. EV-mediated cell–cell communication ultimately contributes to several aspects of pancreatic cancer, such as growth, angiogenesis, metastasis and therapeutic resistance. -
Integrin Traffic – the Update
ß 2015. Published by The Company of Biologists Ltd | Journal of Cell Science (2015) 128, 839–852 doi:10.1242/jcs.161653 COMMENTARY Integrin traffic – the update Nicola De Franceschi*, Hellyeh Hamidi*, Jonna Alanko*, Pranshu Sahgal and Johanna Ivaska` ABSTRACT thus integrin signalling, by tightly controlling specific integrin heterodimer availability at the cell surface. With increasing interest Integrins are a family of transmembrane cell surface molecules that on the biological relevance of integrin traffic, the number of constitute the principal adhesion receptors for the extracellular matrix adaptor and signalling proteins and cellular machineries identified (ECM) and are indispensable for the existence of multicellular as key regulators of this pathway is rapidly expanding and thus organisms. In vertebrates, 24 different integrin heterodimers exist reveals the complexity of integrin traffic regulation and the close with differing substrate specificity and tissue expression. Integrin– connection with the cytoskeletal and signalling apparatus of a cell. extracellular-ligand interaction provides a physical anchor for the cell Importantly, conceptual progress in the field has identified well- and triggers a vast array of intracellular signalling events that known cancer oncogenes and mutations as being crucial regulators determine cell fate. Dynamic remodelling of adhesions, through rapid of integrin traffic and, therefore, cell invasion and metastasis. endocytic and exocytic trafficking of integrin receptors, is an Mounting data highlights how integrin trafficking is deeply wired important mechanism employed by cells to regulate integrin–ECM into the cytoskeletal and signalling apparatus of a cell and how interactions, and thus cellular signalling, during processes such as integrin trafficking is tightly and spatially regulated in the cell. -
Structure of the APPL1 BAR-PH Domain and EMBO Characterization of Its Interaction with Rab5 Open
The EMBO Journal (2007) 26, 3484–3493 | & 2007 European Molecular Biology Organization | Some Rights Reserved 0261-4189/07 www.embojournal.org TTHEH E EEMBOMBO JJOURNALOURN AL Structure of the APPL1 BAR-PH domain and EMBO characterization of its interaction with Rab5 open This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits distribution, and reproductioninany medium, provided the original authorand source are credited. This license does not permit commercial exploitation or the creation of derivative works without specific permission. Guangyu Zhu1, Jia Chen2, Jay Liu3, Introduction Joseph S Brunzelle4, Bo Huang2, Endocytosis induced by ligandÀreceptor interaction has been Nancy Wakeham1, Simon Terzyan1, 2 2 3 directly linked to signal transduction mediated by Rab5 and Xuemei Li , Zihe Rao , Guangpu Li its effector APPL1 (Adaptor protein containing PH domain 1,2, and Xuejun C Zhang * PTB domain and Leucine zipper motif; Miaczynska et al, 1Crystallography Research Program, Oklahoma Medical Research 2004; Mao et al, 2006). The small GTPase Rab5 is a generally Foundation, Oklahoma City, OK, USA, 2National Laboratory of acknowledged prominent regulator of vesicle trafficking en- Biomacromolecules, Institute of Biophysics, Chinese Academy of route from the plasma membrane to early endosomes (Li, 3 Sciences, Beijing, China, Department of Biochemistry and Molecular 1996), whereas APPL1 (also called DIP13a) is identified with Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA and 4Department of Molecular Pharmacology and signaling pathways of adiponectin, insulin, EGF, follicle Biological Chemistry, Feinberg Medical School, Northwestern stimulating hormone receptor, neurotrophin receptor University, Chicago, IL, USA (TrkA), oxidative stress, and DCC-mediated apoptosis (Liu et al, 2002; Miaczynska et al, 2004; Lin et al, 2006; Mao et al, APPL1 is an effector of the small GTPase Rab5. -
Adaptor Protein APPL1 Couples Synaptic NMDA Receptor with Neuronal Prosurvival Phosphatidylinositol 3-Kinase/Akt Pathway
The Journal of Neuroscience, August 29, 2012 • 32(35):11919–11929 • 11919 Cellular/Molecular Adaptor Protein APPL1 Couples Synaptic NMDA Receptor with Neuronal Prosurvival Phosphatidylinositol 3-Kinase/Akt Pathway Yu-bin Wang, Jie-jie Wang, Shao-hua Wang, Shuang-Shuang Liu, Jing-yuan Cao, Xiao-ming Li, Shuang Qiu, and Jian-hong Luo Department of Neurobiology, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, Zhejiang Province Key Laboratory of Neurobiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China It is well known that NMDA receptors (NMDARs) can both induce neurotoxicity and promote neuronal survival under different circum- stances. Recent studies show that such paradoxical responses are related to the receptor location: the former to the extrasynaptic and the latter to the synaptic. The phosphoinositide 3-kinase (PI3K)/Akt kinase cascade is a key pathway responsible for the synaptic NMDAR- dependent neuroprotection. However, it is still unknown how synaptic NMDARs are coupled with the PI3K/Akt pathway. Here, we exploredtheroleofanadaptorprotein—adaptorproteincontainingpHdomain,PTBdomain,andleucinezippermotif(APPL1)—inthis signal coupling using rat cortical neurons. We found that APPL1 existed in postsynaptic densities and associated with the NMDAR complex through binding to PSD95 at its C-terminal PDZ-binding motif. NMDARs, APPL1, and the PI3K/Akt cascade formed a complex in rat cortical neurons. Synaptic NMDAR activity increased the association of this complex, induced activation of the PI3K/Akt pathway, and consequently protected neurons against starvation-induced apoptosis. Perturbing APPL1 interaction with PSD95 by a peptide comprising the APPL1 C-terminal PDZ-binding motif dissociated the PI3K/Akt pathway from NMDARs. -
Complex Rab4-Mediated Regulation of Endosomal Size and EGFR Activation
Published OnlineFirst February 4, 2020; DOI: 10.1158/1541-7786.MCR-19-0052 MOLECULAR CANCER RESEARCH | SIGNAL TRANSDUCTION AND FUNCTIONAL IMAGING Complex Rab4-Mediated Regulation of Endosomal Size and EGFR Activation Kate Tubbesing1, Jamie Ward1, Raymond Abini-Agbomson1, Aditi Malhotra1, Alena Rudkouskaya1, Janine Warren1, John Lamar1, Nina Martino1, Alejandro P. Adam1,2, and Margarida Barroso1 ABSTRACT ◥ Early sorting endosomes are responsible for the trafficking and exhibited prolonged and increased EGF-induced activation of function of transferrin receptor (TfR) and EGFR. These receptors EGFR upon phosphorylation at tyrosine-1068 (EGFR-p1068). play important roles in iron uptake and signaling and are critical for Rab4A overexpression in MCF10A cells produced EEA1-positive breast cancer development. However, the role of morphology, enlarged endosomes that displayed prolonged and amplified receptor composition, and signaling of early endosomes in breast EGF-induced EGFR-p1068 activation. Knockdown of Rab4A cancer remains poorly understood. A novel population of enlarged lead to increased endosomal size in MCF10A, but not in early endosomes was identified in breast cancer cells and tumor MDA-MB-231 cells. Nevertheless, Rab4A knockdown resulted xenografts but not in noncancerous MCF10A cells. Quantitative in enhanced EGF-induced activation of EGFR-p1068 in MDA- analysis of endosomal morphology, cargo sorting, EGFR activa- MB-231 as well as downstream signaling in MCF10A cells. tion, and Rab GTPase regulation was performed using super- Altogether, this extensive characterization of early endosomes resolution and confocal microscopy followed by 3D rendering. in breast cancer cells has identified a Rab4-modulated enlarged MDA-MB-231 breast cancer cells have fewer, but larger EEA1- early endosomal compartment as the site of prolonged and positive early endosomes compared with MCF10A cells. -
The Endosomal Protein Appl1 Mediates Akt Substrate Specificity and Cell Survival in Vertebrate Development
The Endosomal Protein Appl1 Mediates Akt Substrate Specificity and Cell Survival in Vertebrate Development Annette Schenck,1,4 Livia Goto-Silva,1 Claudio Collinet,1 Muriel Rhinn,2,5 Angelika Giner,1 Bianca Habermann,1,3 Michael Brand,2 and Marino Zerial1,* 1Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany 2Biotechnology Center and Center for Regenerative Therapies, University of Technology Dresden, Tatzberg 47-51, 01307 Dresden, Germany 3Scionics Computer Innovation GmbH, Tatzberg 47, 01307 Dresden, Germany 4Present address: Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands. 5Present address: Institut de Ge´ ne´ tique et de Biologie Mole´ culaire et Cellulaire, CNRS/INSERM/ULP, Boite Postal 10142, 67404 Illkirch Cedex, France. *Correspondence: [email protected] DOI 10.1016/j.cell.2008.02.044 SUMMARY grown in the past decade, uncovering central signaling hubs such protein kinase B (Akt) and mitogen-activated protein During development of multicellular organisms, cells kinases (MAPK) (Dhillon et al., 2007; Manning and Cantley, respond to extracellular cues through nonlinear sig- 2007). However, our understanding of the mechanisms underly- nal transduction cascades whose principal compo- ing the specificity of signal transmission and processing requires nents have been identified. Nevertheless, the molec- new conceptual advances. Signaling components such as ular mechanisms underlying specificity of cellular kinases often possess various potential substrates, leading to responses remain poorly understood. Spatial distri- highly branched signaling networks rather than linear cascades. This poses the problem of how a physiological response can be bution of signaling proteins may contribute to signal- elicited with high specificity, with information flowing through ing specificity. -
Mutations and Protein Interaction Landscape Reveal Key Cellular Events Perturbed in Upper Motor Neurons with HSP and PLS
brain sciences Article Mutations and Protein Interaction Landscape Reveal Key Cellular Events Perturbed in Upper Motor Neurons with HSP and PLS Oge Gozutok 1, Benjamin Ryan Helmold 1 and P. Hande Ozdinler 1,2,3,4,* 1 Department of Neurology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave, Chicago, IL 60611, USA; [email protected] (O.G.); [email protected] (B.R.H.) 2 Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60611, USA 3 Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA 4 Feinberg School of Medicine, Les Turner ALS Center at Northwestern University, Chicago, IL 60611, USA * Correspondence: [email protected]; Tel.: +1-(312)-503-2774 Abstract: Hereditary spastic paraplegia (HSP) and primary lateral sclerosis (PLS) are rare motor neuron diseases, which affect mostly the upper motor neurons (UMNs) in patients. The UMNs display early vulnerability and progressive degeneration, while other cortical neurons mostly remain functional. Identification of numerous mutations either directly linked or associated with HSP and PLS begins to reveal the genetic component of UMN diseases. Since each of these mutations are identified on genes that code for a protein, and because cellular functions mostly depend on protein- protein interactions, we hypothesized that the mutations detected in patients and the alterations in Citation: Gozutok, O.; Helmold, B.R.; protein interaction domains would hold the key to unravel the underlying causes of their vulnerability. Ozdinler, P.H. Mutations and Protein In an effort to bring a mechanistic insight, we utilized computational analyses to identify interaction Interaction Landscape Reveal Key Cellular Events Perturbed in Upper partners of proteins and developed the protein-protein interaction landscape with respect to HSP Motor Neurons with HSP and PLS.