A Unique PDZ Domain and Arrestin-Like Fold Interaction Reveals
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Sorting Nexins in Protein Homeostasis Sara E. Hanley1,And Katrina F
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 6 November 2020 doi:10.20944/preprints202011.0241.v1 Sorting nexins in protein homeostasis Sara E. Hanley1,and Katrina F. Cooper2* 1Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, 08084, USA 1 [email protected] 2 [email protected] * [email protected] Tel: +1 (856)-566-2887 1Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, 08084, USA Abstract: Sorting nexins (SNXs) are a highly conserved membrane-associated protein family that plays a role in regulating protein homeostasis. This family of proteins is unified by their characteristic phox (PX) phosphoinositides binding domain. Along with binding to membranes, this family of SNXs also comprises a diverse array of protein-protein interaction motifs that are required for cellular sorting and protein trafficking. SNXs play a role in maintaining the integrity of the proteome which is essential for regulating multiple fundamental processes such as cell cycle progression, transcription, metabolism, and stress response. To tightly regulate these processes proteins must be expressed and degraded in the correct location and at the correct time. The cell employs several proteolysis mechanisms to ensure that proteins are selectively degraded at the appropriate spatiotemporal conditions. SNXs play a role in ubiquitin-mediated protein homeostasis at multiple levels including cargo localization, recycling, degradation, and function. In this review, we will discuss the role of SNXs in three different protein homeostasis systems: endocytosis lysosomal, the ubiquitin-proteasomal, and the autophagy-lysosomal system. The highly conserved nature of this protein family by beginning with the early research on SNXs and protein trafficking in yeast and lead into their important roles in mammalian systems. -
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. -
Sorting Nexin 27 Regulates the Lysosomal Degradation of Aquaporin-2 Protein in the Kidney Collecting Duct
cells Article Sorting Nexin 27 Regulates the Lysosomal Degradation of Aquaporin-2 Protein in the Kidney Collecting Duct Hyo-Jung Choi 1,2, Hyo-Ju Jang 1,3, Euijung Park 1,3, Stine Julie Tingskov 4, Rikke Nørregaard 4, Hyun Jun Jung 5 and Tae-Hwan Kwon 1,3,* 1 Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Taegu 41944, Korea; [email protected] (H.-J.C.); [email protected] (H.-J.J.); [email protected] (E.P.) 2 New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Taegu 41061, Korea 3 BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, School of Medicine, Kyungpook National University, Taegu 41944, Korea 4 Department of Clinical Medicine, Aarhus University, Aarhus 8200, Denmark; [email protected] (S.J.T.); [email protected] (R.N.) 5 Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; [email protected] * Correspondence: [email protected]; Tel.: +82-53-420-4825; Fax: +82-53-422-1466 Received: 30 March 2020; Accepted: 11 May 2020; Published: 13 May 2020 Abstract: Sorting nexin 27 (SNX27), a PDZ (Postsynaptic density-95/Discs large/Zonula occludens 1) domain-containing protein, cooperates with a retromer complex, which regulates intracellular trafficking and the abundance of membrane proteins. Since the carboxyl terminus of aquaporin-2 (AQP2c) has a class I PDZ-interacting motif (X-T/S-X-F), the role of SNX27 in the regulation of AQP2 was studied. Co-immunoprecipitation assay of the rat kidney demonstrated an interaction of SNX27 with AQP2. -
Atypical Parkinsonism–Associated Retromer Mutant Alters Endosomal Sorting of Specific Cargo Proteins
JCB: Report Atypical parkinsonism–associated retromer mutant alters endosomal sorting of specific cargo proteins Kirsty J. McMillan,1 Matthew Gallon,1* Adam P. Jellett,1* Thomas Clairfeuille,3 Frances C. Tilley,1 Ian McGough,1 Chris M. Danson,1 Kate J. Heesom,2 Kevin A. Wilkinson,1 Brett M. Collins,3 and Peter J. Cullen1 1School of Biochemistry and 2Proteomics Facility, School of Biochemistry, University of Bristol, Bristol BS8 1TD, England, UK 3Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia The retromer complex acts as a scaffold for endosomal protein complexes that sort integral membrane proteins to vari- ous cellular destinations. The retromer complex is a heterotrimer of VPS29, VPS35, and VPS26. Two of these paral- ogues, VPS26A and VPS26B, are expressed in humans. Retromer dysfunction is associated with neurodegenerative disease, and recently, three VPS26A mutations (p.K93E, p.M112V, and p.K297X) were discovered to be associated with atypical parkinsonism. Here, we apply quantitative proteomics to provide a detailed description of the retromer interac- tome. By establishing a comparative proteomic methodology, we identify how this interactome is perturbed in atypical parkinsonism-associated VPS26A mutants. In particular, we describe a selective defect in the association of VPS26A (p.K297X) with the SNX27 cargo adaptor. By showing how a retromer mutant leads to altered endosomal sorting of specific PDZ ligand–containing cargo proteins, we reveal a new mechanism for perturbed endosomal cargo sorting in atypical parkinsonism. Introduction Retromer is a highly conserved heterotrimer of VPS29, homologue (WASH) complex (McGough et al., 2014a; Za- VPS35, and VPS26. -
VPS26A Rabbit Pab
Leader in Biomolecular Solutions for Life Science VPS26A Rabbit pAb Catalog No.: A14265 Basic Information Background Catalog No. This gene belongs to a group of vacuolar protein sorting (VPS) genes. The encoded A14265 protein is a component of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. Observed MW The close structural similarity between the yeast and human proteins that make up this 38kDa complex suggests a similarity in function. Expression studies in yeast and mammalian cells indicate that this protein interacts directly with VPS35, which serves as the core of Calculated MW the retromer complex. Alternative splicing results in multiple transcript variants 28kDa/38kDa encoding different isoforms. Category Primary antibody Applications WB, IF Cross-Reactivity Human, Mouse, Rat Recommended Dilutions Immunogen Information WB 1:500 - 1:2000 Gene ID Swiss Prot 9559 O75436 IF 1:50 - 1:200 Immunogen Recombinant fusion protein containing a sequence corresponding to amino acids 208-327 of human VPS26A (NP_004887.2). Synonyms VPS26A;HB58;Hbeta58;PEP8A;VPS26 Contact Product Information www.abclonal.com Source Isotype Purification Rabbit IgG Affinity purification Storage Store at -20℃. Avoid freeze / thaw cycles. Buffer: PBS with 0.02% sodium azide,50% glycerol,pH7.3. Validation Data Western blot analysis of extracts of various cell lines, using VPS26A antibody (A14265) at 1:1000 dilution. Secondary antibody: HRP Goat Anti-Rabbit IgG (H+L) (AS014) at 1:10000 dilution. Lysates/proteins: 25ug per lane. Blocking buffer: 3% nonfat dry milk in TBST. Detection: ECL Basic Kit (RM00020). Exposure time: 5s. -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Molecular Mechanism for the Subversion of the Retromer Coat By
Molecular mechanism for the subversion of the PNAS PLUS retromer coat by the Legionella effector RidL Miguel Romano-Morenoa, Adriana L. Rojasa, Chad D. Williamsonb, David C. Gershlickb, María Lucasa, Michail N. Isupovc, Juan S. Bonifacinob, Matthias P. Machnerd,1, and Aitor Hierroa,e,1 aStructural Biology Unit, Centro de Investigación Cooperativa en Biociencias, 48160 Derio, Spain; bCell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892; cThe Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter EX4 4SB, United Kingdom; dDivision of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892; and eIKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain Edited by Ralph R. Isberg, Howard Hughes Medical Institute and Tufts University School of Medicine, Boston, MA, and approved November 13, 2017 (received for review August 30, 2017) Microbial pathogens employ sophisticated virulence strategies to VAMP7 together with several Rab GTPases that function along cause infections in humans. The intracellular pathogen Legionella distinct trafficking pathways (18), and the Tre-2/Bub2/Cdc16 pneumophila encodes RidL to hijack the host scaffold protein domain family member 5 (TBC1D5), a GTPase-activating pro- VPS29, a component of retromer and retriever complexes critical for tein (GAP) that causes Rab7 inactivation and redistribution to endosomal cargo recycling. Here, we determined the crystal structure the cytosol (14). of L. pneumophila RidL in complex with the human VPS29–VPS35 Recent biochemical and structural characterization of single retromer subcomplex. A hairpin loop protruding from RidL inserts subunits and subcomplexes from retromer have provided insights into a conserved pocket on VPS29 that is also used by cellular ligands, into its modular architecture and mechanisms of action. -
SNX17 Recruits USP9X to Antagonize MIB1-Mediated Ubiquitination and Degradation of PCM1 During Serum-Starvation-Induced Ciliogenesis
cells Article SNX17 Recruits USP9X to Antagonize MIB1-Mediated Ubiquitination and Degradation of PCM1 during Serum-Starvation-Induced Ciliogenesis Pengtao Wang 1,2,3,4, Jianhong Xia 2,3, Leilei Zhang 2,3, Shaoyang Zhao 2,3, Shengbiao Li 2,3, Haiyun Wang 2,3, Shan Cheng 4, Heying Li 2,3, Wenguang Yin 2,3, Duanqing Pei 2,3,5,* and Xiaodong Shu 2,3,4,5,6,* 1 School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; [email protected] 2 CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; [email protected] (J.X.); [email protected] (L.Z.); [email protected] (S.Z.); [email protected] (S.L.); [email protected] (H.W.); [email protected] (H.L.); [email protected] (W.Y.) 3 Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China 4 Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; [email protected] 5 Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China 6 Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 511436, China * Correspondence: [email protected] (D.P.); [email protected] (X.S.); Tel.: +86-20-3201-5310 (X.S.) Academic Editor: Tomer Avidor-Reiss Received: 13 September 2019; Accepted: 27 October 2019; Published: 29 October 2019 Abstract: Centriolar satellites are non-membrane cytoplasmic granules that deliver proteins to centrosome during centrosome biogenesis and ciliogenesis. -
Structural Basis of Mammalian Mucin Processing by the Human Gut O
ARTICLE https://doi.org/10.1038/s41467-020-18696-y OPEN Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila ✉ ✉ Beatriz Trastoy 1,4, Andreas Naegeli2,4, Itxaso Anso 1,4, Jonathan Sjögren 2 & Marcelo E. Guerin 1,3 Akkermansia muciniphila is a mucin-degrading bacterium commonly found in the human gut that promotes a beneficial effect on health, likely based on the regulation of mucus thickness 1234567890():,; and gut barrier integrity, but also on the modulation of the immune system. In this work, we focus in OgpA from A. muciniphila,anO-glycopeptidase that exclusively hydrolyzes the peptide bond N-terminal to serine or threonine residues substituted with an O-glycan. We determine the high-resolution X-ray crystal structures of the unliganded form of OgpA, the complex with the glycodrosocin O-glycopeptide substrate and its product, providing a comprehensive set of snapshots of the enzyme along the catalytic cycle. In combination with O-glycopeptide chemistry, enzyme kinetics, and computational methods we unveil the molecular mechanism of O-glycan recognition and specificity for OgpA. The data also con- tribute to understanding how A. muciniphila processes mucins in the gut, as well as analysis of post-translational O-glycosylation events in proteins. 1 Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain. 2 Genovis AB, Box 790, 22007 Lund, Sweden. 3 IKERBASQUE, Basque Foundation for Science, 48013 ✉ Bilbao, Spain. 4These authors contributed equally: Beatriz Trastoy, Andreas Naegeli, Itxaso Anso. -
Atypical Parkinsonism–Associated Retromer Mutant Alters Endosomal Sorting of Specific Cargo Proteins
Published August 15, 2016 JCB: Report Atypical parkinsonism–associated retromer mutant alters endosomal sorting of specific cargo proteins Kirsty J. McMillan,1 Matthew Gallon,1* Adam P. Jellett,1* Thomas Clairfeuille,3 Frances C. Tilley,1 Ian McGough,1 Chris M. Danson,1 Kate J. Heesom,2 Kevin A. Wilkinson,1 Brett M. Collins,3 and Peter J. Cullen1 1School of Biochemistry and 2Proteomics Facility, School of Biochemistry, University of Bristol, Bristol BS8 1TD, England, UK 3Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia The retromer complex acts as a scaffold for endosomal protein complexes that sort integral membrane proteins to vari- ous cellular destinations. The retromer complex is a heterotrimer of VPS29, VPS35, and VPS26. Two of these paral- ogues, VPS26A and VPS26B, are expressed in humans. Retromer dysfunction is associated with neurodegenerative disease, and recently, three VPS26A mutations (p.K93E, p.M112V, and p.K297X) were discovered to be associated with atypical parkinsonism. Here, we apply quantitative proteomics to provide a detailed description of the retromer interac- tome. By establishing a comparative proteomic methodology, we identify how this interactome is perturbed in atypical parkinsonism-associated VPS26A mutants. In particular, we describe a selective defect in the association of VPS26A (p.K297X) with the SNX27 cargo adaptor. By showing how a retromer mutant leads to altered endosomal sorting of Downloaded from specific PDZ ligand–containing cargo proteins, we reveal a new mechanism for perturbed endosomal cargo sorting in atypical parkinsonism. Introduction on October 26, 2016 Retromer is a highly conserved heterotrimer of VPS29, homologue (WASH) complex (McGough et al., 2014a; Za- VPS35, and VPS26. -
Novel Crosstalk Between Vps26a and Nox4 Signaling During Neurogenesis
Cell Death & Differentiation (2019) 26:1582–1599 https://doi.org/10.1038/s41418-018-0226-0 ARTICLE Novel crosstalk between Vps26a and Nox4 signaling during neurogenesis 1,2,3 2,4 1,2,4 1,2 1,2 1,2 Seon-A Choi ● Young-Hyun Kim ● Young-Ho Park ● Hae-Jun Yang ● Pil-Soo Jeong ● Jae-Jin Cha ● 1,2 1,2,4 1,2,4 1,2 1,2 1,2,4 Seung-Bin Yoon ● Ji-Su Kim ● Bong-Seok Song ● Jong-Hee Lee ● Bo-Woong Sim ● Jae-Won Huh ● 5 1,2,4 3 6 7 8,9 In-Sung Song ● Sang-Rae Lee ● Min-Kyu Kim ● Jin-Man Kim ● Yun Soo Bae ● Kazuhiko Imakawa ● 1,2,4 2,4 Sun-Uk Kim ● Kyu-Tae Chang Received: 20 March 2018 / Revised: 21 September 2018 / Accepted: 28 September 2018 / Published online: 21 November 2018 © The Author(s) 2018. This article is published with open access Abstract Despite numerous studies on the molecular switches governing the conversion of stemness to differentiation in embryonic stem cells (ESCs), little is known about the involvement of the retromer complex. Under neural differentiation conditions, Vps26a deficiency (Vps26a-/-) or knockdown suppressed the loss of stemness and subsequent neurogenesis from ESCs or embryonic carcinoma cells, respectively, as evidenced by the long-lasting expression of stemness markers and the slow 1234567890();,: 1234567890();,: appearance of neuronal differentiation markers. Interestingly, relatively low reactive oxygen species (ROS) levels were generated during differentiation of Vps26a-/- ESCs, and treatment with an antioxidant or inhibitor of NADPH oxidase (Nox), a family of ROS-generating enzymes, led to restoration of stemness in wild-type cells to the level of Vps26a-/- cells during neurogenesis. -
Sorting Nexin-27 Regulates AMPA Receptor Trafficking Through The
RESEARCH ARTICLE Sorting nexin-27 regulates AMPA receptor trafficking through the synaptic adhesion protein LRFN2 Kirsty J McMillan1†*, Paul J Banks2†, Francesca LN Hellel1, Ruth E Carmichael1, Thomas Clairfeuille3, Ashley J Evans1, Kate J Heesom4, Philip Lewis4, Brett M Collins3, Zafar I Bashir2, Jeremy M Henley1, Kevin A Wilkinson1*, Peter J Cullen1* 1School of Biochemistry, University of Bristol, Bristol, United Kingdom; 2School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom; 3Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia; 4Proteomics facility, School of Biochemistry, University of Bristol, Bristol, United Kingdom Abstract The endosome-associated cargo adaptor sorting nexin-27 (SNX27) is linked to various neuropathologies through sorting of integral proteins to the synaptic surface, most notably AMPA receptors. To provide a broader view of SNX27-associated pathologies, we performed proteomics in rat primary neurons to identify SNX27-dependent cargoes, and identified proteins linked to excitotoxicity, epilepsy, intellectual disabilities, and working memory deficits. Focusing on the *For correspondence: synaptic adhesion molecule LRFN2, we established that SNX27 binds to LRFN2 and regulates its [email protected] endosomal sorting. Furthermore, LRFN2 associates with AMPA receptors and knockdown of (KJMM); LRFN2 results in decreased surface AMPA receptor expression, reduced synaptic activity, and [email protected] attenuated hippocampal long-term potentiation. Overall, our study provides an additional (KAW); mechanism by which SNX27 can control AMPA receptor-mediated synaptic transmission and [email protected] (PJC) plasticity indirectly through the sorting of LRFN2 and offers molecular insight into the perturbed †These authors contributed function of SNX27 and LRFN2 in a range of neurological conditions.