The T-Complex-Encoded Guanine Nucleotide Exchange Factor Fgd2 Reveals That Two Opposing Signaling Pathways Promote Transmission Ratio Distortion in the Mouse
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Structure and Function of the Fgd Family of Divergent FYVE Domain Proteins
Biochemistry and Cell Biology Structure and Function of the Fgd Family of Divergent FYVE Domain Proteins Journal: Biochemistry and Cell Biology Manuscript ID bcb-2018-0185.R1 Manuscript Type: Mini Review Date Submitted by the 03-Aug-2018 Author: Complete List of Authors: Eitzen, Gary; University of Alberta Faculty of Medicine and Dentistry Smithers, Cameron C.; University of Alberta, Biochemistry Murray, Allan; University of Alberta Faculty of Medicine and Dentistry Overduin, Michael; University of Alberta Faculty of Medicine and Dentistry Draft Fgd, Pleckstrin Homology domain, FYVE domain, Dbl Homology Domain, Keyword: Rho GEF Is the invited manuscript for consideration in a Special CSMB Special Issue Issue? : https://mc06.manuscriptcentral.com/bcb-pubs Page 1 of 37 Biochemistry and Cell Biology Title: Structure and Function of the Fgd Family of Divergent FYVE Domain Proteins Authors: Gary Eitzen1, Cameron C. Smithers2, Allan G Murray3 and Michael Overduin2* Draft 1Department of Cell Biology, 2Department of Biochemistry, 3Department of Medicine, University of Alberta, Edmonton, Alberta, Canada *Corresponding author. Michael Overduin Telephone: +1 780 492 3518 Fax: +1 780 492-0886 E-mail: [email protected] https://mc06.manuscriptcentral.com/bcb-pubs Biochemistry and Cell Biology Page 2 of 37 Abstract FYVE domains are highly conserved protein modules that typically bind phosphatidylinositol 3-phosphate (PI3P) on the surface of early endosomes. Along with pleckstrin homology (PH) and phox homology (PX) domains, FYVE domains are the principal readers of the phosphoinositide (PI) code that mediate specific recognition of eukaryotic organelles. Of all the human FYVE domain-containing proteins, those within the Faciogenital dysplasia (Fgd) subfamily are particularly divergent, and couple with GTPases to exert unique cellular functions. -
Regulation of Cdc42 and Its Effectors in Epithelial Morphogenesis Franck Pichaud1,2,*, Rhian F
© 2019. Published by The Company of Biologists Ltd | Journal of Cell Science (2019) 132, jcs217869. doi:10.1242/jcs.217869 REVIEW SUBJECT COLLECTION: ADHESION Regulation of Cdc42 and its effectors in epithelial morphogenesis Franck Pichaud1,2,*, Rhian F. Walther1 and Francisca Nunes de Almeida1 ABSTRACT An overview of Cdc42 Cdc42 – a member of the small Rho GTPase family – regulates cell Cdc42 was discovered in yeast and belongs to a large family of small – polarity across organisms from yeast to humans. It is an essential (20 30 kDa) GTP-binding proteins (Adams et al., 1990; Johnson regulator of polarized morphogenesis in epithelial cells, through and Pringle, 1990). It is part of the Ras-homologous Rho subfamily coordination of apical membrane morphogenesis, lumen formation and of GTPases, of which there are 20 members in humans, including junction maturation. In parallel, work in yeast and Caenorhabditis elegans the RhoA and Rac GTPases, (Hall, 2012). Rho, Rac and Cdc42 has provided important clues as to how this molecular switch can homologues are found in all eukaryotes, except for plants, which do generate and regulate polarity through localized activation or inhibition, not have a clear homologue for Cdc42. Together, the function of and cytoskeleton regulation. Recent studies have revealed how Rho GTPases influences most, if not all, cellular processes. important and complex these regulations can be during epithelial In the early 1990s, seminal work from Alan Hall and his morphogenesis. This complexity is mirrored by the fact that Cdc42 can collaborators identified Rho, Rac and Cdc42 as main regulators of exert its function through many effector proteins. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Molecular Mechanism of Membrane Targeting by the GRP1 PH Domain
Supplemental Material can be found at: http://www.jlr.org/cgi/content/full/M800150-JLR200/DC1 Molecular mechanism of membrane targeting by the GRP1 PH domain † † † Ju He,* Rachel M. Haney, ,§ Mohsin Vora, Vladislav V. Verkhusha,** Robert V. Stahelin, ,§ and Tatiana G. Kutateladze1,* Department of Pharmacology,* University of Colorado Health Sciences Center, Aurora, CO; † Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, South Bend, IN; Department of Chemistry and Biochemistry and The Walther Center for Cancer Research,§ University of Notre Dame, South Bend, IN; and Department of Anatomy and Structural Biology,** Downloaded from Albert Einstein College of Medicine, Bronx, NY Abstract The general receptor for phosphoinositides iso- Supplementary key words general receptor for phosphoinositides iso- • • • form 1 (GRP1) is recruited to the plasma membrane in re- form 1 pleckstrin homology domain phosphoinositide phosphati- dylinositol 3,4,5-trisphosphate sponse to activation of phosphoinositide 3-kinases and www.jlr.org accumulation of phosphatidylinositol 3,4,5-trisphosphate ʼ [PtdIns(3,4,5)P3]. GRP1 s pleckstrin homology (PH) do- main recognizes PtdIns(3,4,5)P3 with high specificity and af- The signaling lipid phosphatidylinositol 3,4,5-trisphos- finity, however, the precise mechanism of its association phate [PtdIns(3,4,5)P3] is produced in plasma membranes at Albert Einstein College of Medicine Library on July 14, 2008 with membranes remains unclear. Here, we detail the mo- in response to stimulation of cell surface receptors by lecular basis of membrane anchoring by the GRP1 PH do- growth factors and hormones (1). Class I phosphoinositide main. Our data reveal a multivalent membrane docking (PI) 3-kinases phosphorylate the inositol headgroup of the involving PtdIns(3,4,5)P binding, regulated by pH and fa- 3 relatively abundant phosphatidylinositol 4,5-bisphosphate cilitated by electrostatic interactions with other anionic lip- [Ptdns(4,5)P2], transiently elevating the level of PtdIns ids. -
The PX Domain Protein Interaction Network in Yeast
The PX domain protein interaction network in yeast Zur Erlangung des akademischen Grades eines DOKTORS DER NATURWISSENSCHAFTEN (Dr. rer. nat.) der Fakultät für Chemie und Biowissenschaften der Universität Karlsruhe (TH) vorgelegte DISSERTATION von Dipl. Biol. Carolina S. Müller aus Buenos Aires Dekan: Prof. Dr. Manfred Kappes Referent: Dr. Nils Johnsson Korreferent: HD. Dr. Adam Bertl Tag der mündlichen Prüfung: 17.02.2005 I dedicate this work to my Parents and Alex TABLE OF CONTENTS Table of contents Introduction 1 Yeast as a model organism in proteome analysis 1 Protein-protein interactions 2 Protein Domains in Yeast 3 Classification of protein interaction domains 3 Phosphoinositides 5 Function 5 Structure 5 Biochemistry 6 Localization 7 Lipid Binding Domains 8 The PX domain 10 Function of PX domain containing proteins 10 PX domain structure and PI binding affinities 10 Yeast PX domain containing proteins 13 PX domain and protein-protein interactions 13 Lipid binding domains and protein-protein interactions 14 The PX-only proteins Grd19p and Ypt35p and their phenotypes 15 Aim of my PhD work 16 Project outline 16 Searching for interacting partners 16 Confirmation of obtained interactions via a 16 second independent method Mapping the interacting region 16 The Two-Hybrid System 17 Definition 17 Basic Principle of the classical Yeast-Two Hybrid System 17 Peptide Synthesis 18 SPOT synthesis technique 18 Analysis of protein- peptide contact sites based on SPOT synthesis 19 TABLE OF CONTENTS Experimental procedures 21 Yeast two-hybrid assay -
High Throughput Strategies Aimed at Closing the GAP in Our Knowledge of Rho Gtpase Signaling
cells Review High Throughput strategies Aimed at Closing the GAP in Our Knowledge of Rho GTPase Signaling Manel Dahmene 1, Laura Quirion 2 and Mélanie Laurin 1,3,* 1 Oncology Division, CHU de Québec–Université Laval Research Center, Québec, QC G1V 4G2, Canada; [email protected] 2 Montréal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada; [email protected] 3 Université Laval Cancer Research Center, Québec, QC G1R 3S3, Canada * Correspondence: [email protected] Received: 21 May 2020; Accepted: 7 June 2020; Published: 9 June 2020 Abstract: Since their discovery, Rho GTPases have emerged as key regulators of cytoskeletal dynamics. In humans, there are 20 Rho GTPases and more than 150 regulators that belong to the RhoGEF, RhoGAP, and RhoGDI families. Throughout development, Rho GTPases choregraph a plethora of cellular processes essential for cellular migration, cell–cell junctions, and cell polarity assembly. Rho GTPases are also significant mediators of cancer cell invasion. Nevertheless, to date only a few molecules from these intricate signaling networks have been studied in depth, which has prevented appreciation for the full scope of Rho GTPases’ biological functions. Given the large complexity involved, system level studies are required to fully grasp the extent of their biological roles and regulation. Recently, several groups have tackled this challenge by using proteomic approaches to map the full repertoire of Rho GTPases and Rho regulators protein interactions. These studies have provided in-depth understanding of Rho regulators specificity and have contributed to expand Rho GTPases’ effector portfolio. Additionally, new roles for understudied family members were unraveled using high throughput screening strategies using cell culture models and mouse embryos. -
Membrane Insertion of the FYVE Domain Is Modulated by Ph Ju He,1 Mohsin Vora,2 Rachel M
proteins STRUCTURE O FUNCTION O BIOINFORMATICS Membrane insertion of the FYVE domain is modulated by pH Ju He,1 Mohsin Vora,2 Rachel M. Haney,2,3 Grigory S. Filonov,4 Catherine A. Musselman,1 Christopher G. Burd,5 Andrei G. Kutateladze,6 Vladislav V. Verkhusha,4 Robert V. Stahelin,2,3,7* and Tatiana G. Kutateladze1* 1 Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, Colorado 80045 2 Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, South Bend, Indiana 46617 3 Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 4 Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461 5 Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104 6 Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80210 7 The Walther Center for Cancer Research, University of Notre Dame, Notre Dame, Indiana 46556 INTRODUCTION ABSTRACT Phosphoinositide (PI) 3-kinases regulate membrane trafficking, pro- The FYVE domain associates with phosphati- tein sorting and signaling by generating phosphatidylinositol (PtdIns) dylinositol 3-phosphate [PtdIns(3)P] in mem- derivatives phosphorylated at the third position of the inositol ring.1,2 branes of early endosomes and penetrates bilayers. Here, we detail principles of mem- Of the four known products of PI 3-kinases, PtdIns 3-phosphate brane anchoring and show that the FYVE do- [PtdIns(3)P] is the most abundant and is constitutively produced in the main insertion into PtdIns(3)P-enriched cytosolic leaflet of membranes of early endosomes. -
Supp Table 6.Pdf
Supplementary Table 6. Processes associated to the 2037 SCL candidate target genes ID Symbol Entrez Gene Name Process NM_178114 AMIGO2 adhesion molecule with Ig-like domain 2 adhesion NM_033474 ARVCF armadillo repeat gene deletes in velocardiofacial syndrome adhesion NM_027060 BTBD9 BTB (POZ) domain containing 9 adhesion NM_001039149 CD226 CD226 molecule adhesion NM_010581 CD47 CD47 molecule adhesion NM_023370 CDH23 cadherin-like 23 adhesion NM_207298 CERCAM cerebral endothelial cell adhesion molecule adhesion NM_021719 CLDN15 claudin 15 adhesion NM_009902 CLDN3 claudin 3 adhesion NM_008779 CNTN3 contactin 3 (plasmacytoma associated) adhesion NM_015734 COL5A1 collagen, type V, alpha 1 adhesion NM_007803 CTTN cortactin adhesion NM_009142 CX3CL1 chemokine (C-X3-C motif) ligand 1 adhesion NM_031174 DSCAM Down syndrome cell adhesion molecule adhesion NM_145158 EMILIN2 elastin microfibril interfacer 2 adhesion NM_001081286 FAT1 FAT tumor suppressor homolog 1 (Drosophila) adhesion NM_001080814 FAT3 FAT tumor suppressor homolog 3 (Drosophila) adhesion NM_153795 FERMT3 fermitin family homolog 3 (Drosophila) adhesion NM_010494 ICAM2 intercellular adhesion molecule 2 adhesion NM_023892 ICAM4 (includes EG:3386) intercellular adhesion molecule 4 (Landsteiner-Wiener blood group)adhesion NM_001001979 MEGF10 multiple EGF-like-domains 10 adhesion NM_172522 MEGF11 multiple EGF-like-domains 11 adhesion NM_010739 MUC13 mucin 13, cell surface associated adhesion NM_013610 NINJ1 ninjurin 1 adhesion NM_016718 NINJ2 ninjurin 2 adhesion NM_172932 NLGN3 neuroligin -
Supplementary Table 1
Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7 -
1 Fibrillar Αβ Triggers Microglial Proteome Alterations and Dysfunction in Alzheimer Mouse 1 Models 2 3 4 Laura Sebastian
bioRxiv preprint doi: https://doi.org/10.1101/861146; this version posted December 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Fibrillar triggers microglial proteome alterations and dysfunction in Alzheimer mouse 2 models 3 4 5 Laura Sebastian Monasor1,10*, Stephan A. Müller1*, Alessio Colombo1, Jasmin König1,2, Stefan 6 Roth3, Arthur Liesz3,4, Anna Berghofer5, Takashi Saito6,7, Takaomi C. Saido6, Jochen Herms1,4,8, 7 Michael Willem9, Christian Haass1,4,9, Stefan F. Lichtenthaler 1,4,5# & Sabina Tahirovic1# 8 9 1 German Center for Neurodegenerative Diseases (DZNE) Munich, 81377 Munich, Germany 10 2 Faculty of Chemistry, Technical University of Munich, Garching, Germany 11 3 Institute for Stroke and Dementia Research (ISD), Ludwig-Maximilians Universität München, 12 81377 Munich, Germany 13 4 Munich Cluster for Systems Neurology (SyNergy), Munich, Germany 14 5 Neuroproteomics, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, 15 Munich, Germany 16 6 Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science Institute, Wako, 17 Saitama 351-0198, Japan 18 7 Department of Neurocognitive Science, Nagoya City University Graduate School of Medical 19 Science, Nagoya, Aichi 467-8601, Japan 20 8 Center for Neuropathology and Prion Research, Ludwig-Maximilians-Universität München, 81377 21 Munich, Germany 22 9 Biomedical Center (BMC), Ludwig-Maximilians Universität München, 81377 Munich, Germany 23 10 Graduate School of Systemic Neuroscience, Ludwig-Maximilians-University Munich, Munich, 24 Germany. 25 *Contributed equally 26 #Correspondence: [email protected] and [email protected] 27 28 Running title: 29 Microglial proteomic signatures of AD 30 Keywords: Alzheimer’s disease / microglia / proteomic signatures / neuroinflammation / 31 phagocytosis 32 1 bioRxiv preprint doi: https://doi.org/10.1101/861146; this version posted December 2, 2019. -
1 Novel Expression Signatures Identified by Transcriptional Analysis
ARD Online First, published on October 7, 2009 as 10.1136/ard.2009.108043 Ann Rheum Dis: first published as 10.1136/ard.2009.108043 on 7 October 2009. Downloaded from Novel expression signatures identified by transcriptional analysis of separated leukocyte subsets in SLE and vasculitis 1Paul A Lyons, 1Eoin F McKinney, 1Tim F Rayner, 1Alexander Hatton, 1Hayley B Woffendin, 1Maria Koukoulaki, 2Thomas C Freeman, 1David RW Jayne, 1Afzal N Chaudhry, and 1Kenneth GC Smith. 1Cambridge Institute for Medical Research and Department of Medicine, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0XY, UK 2Roslin Institute, University of Edinburgh, Roslin, Midlothian, EH25 9PS, UK Correspondence should be addressed to Dr Paul Lyons or Prof Kenneth Smith, Department of Medicine, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0XY, UK. Telephone: +44 1223 762642, Fax: +44 1223 762640, E-mail: [email protected] or [email protected] Key words: Gene expression, autoimmune disease, SLE, vasculitis Word count: 2,906 The Corresponding Author has the right to grant on behalf of all authors and does grant on behalf of all authors, an exclusive licence (or non-exclusive for government employees) on a worldwide basis to the BMJ Publishing Group Ltd and its Licensees to permit this article (if accepted) to be published in Annals of the Rheumatic Diseases and any other BMJPGL products to exploit all subsidiary rights, as set out in their licence (http://ard.bmj.com/ifora/licence.pdf). http://ard.bmj.com/ on September 29, 2021 by guest. Protected copyright. 1 Copyright Article author (or their employer) 2009. -
FGD2 (V-15): Sc-11114
SAN TA C RUZ BI OTEC HNOL OG Y, INC . FGD2 (V-15): sc-11114 BACKGROUND APPLICATIONS Fgd1 gene mutations result in faciogenital dysplasia (FGDY, Aarskog syn - FGD2 (V-15) is recommended for detection of FGD2 of mouse, rat and human drome),an X-linked developmental disorder that adversely affects the forma tion origin by Western Blotting (starting dilution 1:200, dilution range 1:100- of multiple skeletal structures. FGD1 maps to human chromosome Xp11.21 1:1000), immunoprecipitation [1-2 µg per 100-500 µg of total protein (1 ml and shares a high degree of sequence identity with the FGD2 (6p21.2) and of cell lysate)], immunofluorescence (starting dilution 1:50, dilution range the FGD3 (9q22) proteins. FGD1 encodes a guanine nucleotide exchange fac - 1:50-1:500) and solid phase ELISA (starting dilution 1:30, dilution range tor that specifically activates the Rho GTPase Cdc42. FGD2 is present in sev - 1:30- 1:3000). eral diverse tissues during embryogenesis, suggesting a role in embryonic Suitable for use as control antibody for FGD2 siRNA (h): sc-41713, FGD2 development. FGD3 stimulates fibroblasts to form filopodia, which are actin siRNA (m): sc-41714, FGD2 shRNA Plasmid (h): sc-41713-SH, FGD2 shRNA microspikes formed upon the stimulation of Cdc42. All FGD family members Plasmid (m): sc-41714-SH, FGD2 shRNA (h) Lentiviral Particles: sc-41713-V contain equivalent signaling domains and a conserved structural organiza tion, and FGD2 shRNA (m) Lentiviral Particles: sc-41714-V. which strongly suggests that these signaling domains form a canonical core structure for members of the FGD family of RhoGEF proteins.