Structural Basis of Vps33a Recruitment to the Human HOPS Complex by Vps16
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A Yeast Phenomic Model for the Gene Interaction Network Modulating
Louie et al. Genome Medicine 2012, 4:103 http://genomemedicine.com/content/4/12/103 RESEARCH Open Access A yeast phenomic model for the gene interaction network modulating CFTR-ΔF508 protein biogenesis Raymond J Louie3†, Jingyu Guo1,2†, John W Rodgers1, Rick White4, Najaf A Shah1, Silvere Pagant3, Peter Kim3, Michael Livstone5, Kara Dolinski5, Brett A McKinney6, Jeong Hong2, Eric J Sorscher2, Jennifer Bryan4, Elizabeth A Miller3* and John L Hartman IV1,2* Abstract Background: The overall influence of gene interaction in human disease is unknown. In cystic fibrosis (CF) a single allele of the cystic fibrosis transmembrane conductance regulator (CFTR-ΔF508) accounts for most of the disease. In cell models, CFTR-ΔF508 exhibits defective protein biogenesis and degradation rather than proper trafficking to the plasma membrane where CFTR normally functions. Numerous genes function in the biogenesis of CFTR and influence the fate of CFTR-ΔF508. However it is not known whether genetic variation in such genes contributes to disease severity in patients. Nor is there an easy way to study how numerous gene interactions involving CFTR-ΔF would manifest phenotypically. Methods: To gain insight into the function and evolutionary conservation of a gene interaction network that regulates biogenesis of a misfolded ABC transporter, we employed yeast genetics to develop a ‘phenomic’ model, in which the CFTR-ΔF508-equivalent residue of a yeast homolog is mutated (Yor1-ΔF670), and where the genome is scanned quantitatively for interaction. We first confirmed that Yor1-ΔF undergoes protein misfolding and has reduced half-life, analogous to CFTR-ΔF. Gene interaction was then assessed quantitatively by growth curves for approximately 5,000 double mutants, based on alteration in the dose response to growth inhibition by oligomycin, a toxin extruded from the cell at the plasma membrane by Yor1. -
Vps8 Overexpression Inhibits HOPS- Dependent Trafficking Routes By
RESEARCH ADVANCE Vps8 overexpression inhibits HOPS- dependent trafficking routes by outcompeting Vps41/Lt Pe´ ter Lo˝ rincz1,2*, Lili Anna Kene´ z1, Sarolta To´ th1, Vikto´ ria Kiss3,A´ gnes Varga1, Tama´ s Csizmadia1, Zso´ fia Simon-Vecsei1, Ga´ bor Juha´ sz1,3* 1Department of Anatomy, Cell and Developmental Biology, Eo¨ tvo¨ s Lora´nd University, Budapest, Hungary; 2Premium Postdoctoral Research Program, Hungarian Academy of Sciences, Budapest, Hungary; 3Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary Abstract Two related multisubunit tethering complexes promote endolysosomal trafficking in all eukaryotes: Rab5-binding CORVET that was suggested to transform into Rab7-binding HOPS. We have previously identified miniCORVET, containing Drosophila Vps8 and three shared core proteins, which are required for endosome maturation upstream of HOPS in highly endocytic cells (Lo˝rincz et al., 2016a). Here, we show that Vps8 overexpression inhibits HOPS-dependent trafficking routes including late endosome maturation, autophagosome-lysosome fusion, crinophagy and lysosome-related organelle formation. Mechanistically, Vps8 overexpression abolishes the late endosomal localization of HOPS-specific Vps41/Lt and prevents HOPS assembly. Proper ratio of Vps8 to Vps41 is thus critical because Vps8 negatively regulates HOPS by outcompeting Vps41. Endosomal recruitment of miniCORVET- or HOPS-specific subunits requires proper complex assembly, and Vps8/miniCORVET is dispensable for autophagy, crinophagy and lysosomal biogenesis. These data together indicate the recruitment of these complexes to target membranes independent of each other in Drosophila, rather than their transformation during *For correspondence: vesicle maturation. [email protected] (PL); DOI: https://doi.org/10.7554/eLife.45631.001 [email protected] (GJ) Competing interests: The authors declare that no competing interests exist. -
New Approaches to Functional Process Discovery in HPV 16-Associated Cervical Cancer Cells by Gene Ontology
Cancer Research and Treatment 2003;35(4):304-313 New Approaches to Functional Process Discovery in HPV 16-Associated Cervical Cancer Cells by Gene Ontology Yong-Wan Kim, Ph.D.1, Min-Je Suh, M.S.1, Jin-Sik Bae, M.S.1, Su Mi Bae, M.S.1, Joo Hee Yoon, M.D.2, Soo Young Hur, M.D.2, Jae Hoon Kim, M.D.2, Duck Young Ro, M.D.2, Joon Mo Lee, M.D.2, Sung Eun Namkoong, M.D.2, Chong Kook Kim, Ph.D.3 and Woong Shick Ahn, M.D.2 1Catholic Research Institutes of Medical Science, 2Department of Obstetrics and Gynecology, College of Medicine, The Catholic University of Korea, Seoul; 3College of Pharmacy, Seoul National University, Seoul, Korea Purpose: This study utilized both mRNA differential significant genes of unknown function affected by the display and the Gene Ontology (GO) analysis to char- HPV-16-derived pathway. The GO analysis suggested that acterize the multiple interactions of a number of genes the cervical cancer cells underwent repression of the with gene expression profiles involved in the HPV-16- cancer-specific cell adhesive properties. Also, genes induced cervical carcinogenesis. belonging to DNA metabolism, such as DNA repair and Materials and Methods: mRNA differential displays, replication, were strongly down-regulated, whereas sig- with HPV-16 positive cervical cancer cell line (SiHa), and nificant increases were shown in the protein degradation normal human keratinocyte cell line (HaCaT) as a con- and synthesis. trol, were used. Each human gene has several biological Conclusion: The GO analysis can overcome the com- functions in the Gene Ontology; therefore, several func- plexity of the gene expression profile of the HPV-16- tions of each gene were chosen to establish a powerful associated pathway, identify several cancer-specific cel- cervical carcinogenesis pathway. -
The Mouse Organellar Biogenesis Mutant Buff Results from a Mutation in Vps33a, a Homologue of Yeast Vps33 and Drosophila Carnation
The mouse organellar biogenesis mutant buff results from a mutation in Vps33a, a homologue of yeast vps33 and Drosophila carnation Tamio Suzuki*†‡, Naoki Oiso*†, Rashi Gautam†§, Edward K. Novak§, Jean-Jacques Panthier¶, P. G. Suprabhaʈ, Thomas Vida**, Richard T. Swank§, and Richard A. Spritz*†† *Human Medical Genetics Program, University of Colorado Health Sciences Center, Denver, CO 80262; §Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263; ¶Institut National de la Recherche Agronomique, Ecole Nationale Ve´te´ rinaire d’Alfort, 94704 Maisons-Alfort Cedex, France; ʈCenter for Basic Neuroscience, University of Texas Southwestern, Dallas, TX 75390; and **Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, TX 77030 Communicated by Theodore T. Puck, Eleanor Roosevelt Institute for Cancer Research, Denver, CO, December 2, 2002 (received for review July 16, 2002) In the mouse, more than 16 loci are associated with mutant bf-mutant Vps33a does not. These results establish murine bf as phenotypes that include defective pigmentation, aberrant target- a murine homologue to the yeast vps33 mutant and suggest ing of lysosomal enzymes, prolonged bleeding, and immunodefi- VPS33A as a candidate gene for some cases of human HPS. ciency, the result of defective biogenesis of cytoplasmic organelles: melanosomes, lysosomes, and various storage granules. Many of Materials and Methods these mouse mutants are homologous to the human Hermansky– Mice and Backcross. Mice carrying the spontaneous mutation bf on Pudlak syndrome (HPS), Chediak–Higashi syndrome, and Griscelli the C57BL͞6J strain were obtained from The Jackson Labora- syndrome. We have mapped and positionally cloned one of these tory and were subsequently bred at Roswell Park Cancer Insti- mouse loci, buff (bf), which has a mutant phenotype similar to that tute. -
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. -
Mig-6 Controls EGFR Trafficking and Suppresses Gliomagenesis
Mig-6 controls EGFR trafficking and suppresses gliomagenesis Haoqiang Yinga,1, Hongwu Zhenga,1, Kenneth Scotta, Ruprecht Wiedemeyera, Haiyan Yana, Carol Lima, Joseph Huanga, Sabin Dhakala, Elena Ivanovab, Yonghong Xiaob,HaileiZhangb,JianHua, Jayne M. Stommela, Michelle A. Leea, An-Jou Chena, Ji-Hye Paika,OresteSegattoc, Cameron Brennand,e, Lisa A. Elferinkf,Y.AlanWanga,b, Lynda China,b,g, and Ronald A. DePinhoa,b,h,2 aDepartment of Medical Oncology, bBelfer Institute for Applied Cancer Science, Belfer Foundation Institute for Innovative Cancer Science, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115; cLaboratory of Immunology, Istituto Regina Elena, Rome 00158, Italy; dHuman Oncology and Pathogenesis Program and eDepartment of Neurosurgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10065; fDepartment of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555; gDepartment of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115; and hDepartment of Medicine and Genetics, Harvard Medical School, Boston, MA 02115 Edited* by Webster K. Cavenee, Ludwig Institute, University of California, La Jolla, CA, and approved March 8, 2010 (received for review December 23, 2009) Glioblastoma multiforme (GBM) is the most common and lethal structural aberrations that serve as a key pathological driving primary brain cancer that is driven by aberrant signaling of growth force for tumor progression and many of them remain to be factor receptors, particularly the epidermal growth factor receptor characterized (6, 7). GBM possesses a highly rearranged genome (EGFR). EGFR signaling is tightly regulated by receptor endocytosis and high-resolution genome analysis has uncovered myriad and lysosome-mediated degradation, although the molecular somatic alterations on the genomic and epigenetic levels (2, 3). -
Clathrin-Dependent Mechanisms Modulate the Subcellular Distribution of Class C Vps/HOPS Tether Subunits in Polarized and Nonpolarized Cells Stephanie A
Clathrin-dependent mechanisms modulate the subcellular distribution of class C Vps/HOPS tether subunits in polarized and nonpolarized cells Stephanie A. Zlatic, Emory University Karine Tornieri, Emory University Steven L'Hernault, Emory University Victor Faundez, Emory University Journal Title: Molecular Biology of the Cell Volume: Volume 22, Number 10 Publisher: American Society for Cell Biology | 2011-05-15, Pages 1699-1715 Type of Work: Article | Final Publisher PDF Publisher DOI: 10.1091/mbc.E10-10-0799 Permanent URL: http://pid.emory.edu/ark:/25593/f71wm Final published version: http://www.molbiolcell.org/content/22/10/1699 Copyright information: © 2011 Zlatic et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License This is an Open Access work distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License (http://creativecommons.org/licenses/by-nc-sa/3.0/). Accessed September 26, 2021 8:16 AM EDT M BoC | ARTICLE Clathrin-dependent mechanisms modulate the subcellular distribution of class C Vps/HOPS tether subunits in polarized and nonpolarized cells Stephanie A. Zlatica,b, Karine Tornierib, Steven W. L’Hernaulta,c,d, and Victor Faundeza,b,d aGraduate Program in Biochemistry, Cell, and Developmental Biology, bDepartment of Cell Biology, cBiology Department, and dCenter for Neurodegenerative Diseases, Emory University, Atlanta, GA 30322 ABSTRACT Coats define the composition of carriers budding from organelles. In addition, Monitoring Editor coats interact with membrane tethers required for vesicular fusion. -
UVRAG Is Required for Virus Entry Through Combinatorial Interaction with the Class C-Vps Complex and Snares
UVRAG is required for virus entry through combinatorial interaction with the class C-Vps complex and SNAREs Sara Dolatshahi Pirooza, Shanshan Hea, Tian Zhanga, Xiaowei Zhanga, Zhen Zhaoa, Soohwan Oha, Douglas O’Connella, Payam Khalilzadeha, Samad Amini-Bavil-Olyaeea, Michael Farzanb, and Chengyu Lianga,1 aDepartment of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033; and bDepartment of Infectious Diseases, The Scripps Research Institute, Jupiter, FL 33458 Edited by Peter Palese, Icahn School of Medicine at Mount Sinai, New York, NY, and approved January 15, 2014 (received for review November 4, 2013) Enveloped viruses exploit the endomembrane system to enter host (R)-SNAREs embedded in the other (3). Specifically, syntaxin 7 cells. Through a cascade of membrane-trafficking events, virus-bearing (STX7; Qa), Vti1b (Qb), and STX8 (Qc) on the LE, when paired vesicles fuse with acidic endosomes and/or lysosomes mediated by with VAMP7 (R), mediate the LE fusion with the lysosome, but SNAREs triggering viral fusion. However, the molecular mechanisms when paired with VAMP8 (R), regulate homotypic fusion of the underlying this process remain elusive. Here, we found that UV- LEs (4). The upstream process regulating LE-associated SNARE radiation resistance-associated gene (UVRAG), an autophagic tumor pairing relies on the class C vacuolar protein sorting (Vps) complex suppressor, is required for the entry of the prototypic negative- (hereafter referred to as C-Vps), composed of Vps11, Vps16, strand RNA virus, including influenza A virus and vesicular stoma- Vps18, and Vps33 as core subunits (5, 6). A recent study indicated titis virus, by a mechanism independent of IFN and autophagy. -
Functions of Syntaxin 8 in Human Cytotoxic T Lymphocytes
Aus dem Bereich Biophysik Theoretische und Klinische Medizin der Medizinischen Fakultät der Universität des Saarlandes, Homburg/Saar Functions of Syntaxin 8 in human cytotoxic T lymphocytes Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften der Medizinischen Fakultät der UNIVERSITÄT DES SAARLANDES 2013 vorgelegt von: Shruthi. S. Bhat geb.am: 27.03.1985 in Manipal, India Tag des Promotionskolloquiums: __________________________________ Dekan: __________________________________ Vorsitzender: __________________________________ Berichterstatter: __________________________________ __________________________________ __________________________________ __________________________________ To my beloved parents and teachers Index INDEX I ABBREVIATIONS VI ZUSAMMENFASSUNG VII 1. INTRODUCTION 1 1.1. Immune system 1 1.2. Cell mediated and humoral immunity 2 1.3. Cytotoxic T Lymphocytes (CTLs) 4 1.3.1. T Cell Receptor complex 5 1.3.2. Immunological Synapse 6 1.3.3. Lytic granules, the secretory lysosomes in immune cells 7 1.3.3.1. Perforin 8 1.3.3.2. Granzymes, lytic granule serine proteases 9 1.3.4. Fas and Fas ligand pathway 11 1.4. Sorting, delivery and maturation of proteins and vesicles through endosomal pathway 12 1.5. SNARE proteins 15 1.6. SNARE and related proteins in immune cells 17 1.7. Syntaxin 8: the protein of interest 20 1.8. Aims of this study 21 2. MATERIALS AND METHODS 23 2.1. Antibodies and Reagents 23 2.2. Peripheral blood mononuclear cell (PBMC) isolation 23 2.3. Stimulation of PBLs with Staphylococcal enterotoxin A 24 2.4. Positive isolation of CD8+ T lymphocytes 25 2.5. Negative isolation of CD8+ T lymphocytes 26 2.6. siRNA transfection of CTLs 27 I Index 2.7. -
Diversification of CORVET Tethers Facilitates Transport Complexity in Tetrahymena Thermophila Daniela Sparvoli1,*, Martin Zoltner2,3, Chao-Yin Cheng1, Mark C
© 2020. Published by The Company of Biologists Ltd | Journal of Cell Science (2020) 133, jcs238659. doi:10.1242/jcs.238659 RESEARCH ARTICLE Diversification of CORVET tethers facilitates transport complexity in Tetrahymena thermophila Daniela Sparvoli1,*, Martin Zoltner2,3, Chao-Yin Cheng1, Mark C. Field2 and Aaron P. Turkewitz1,‡ ABSTRACT Key determinants for ensuring productive membrane interactions In endolysosomal networks, two hetero-hexameric tethers called are SNARE proteins, with distinct paralogs present at each HOPS and CORVET are found widely throughout eukaryotes. The compartment (Gerst, 1999). SNARE complex assembly drives unicellular ciliate Tetrahymena thermophila possesses elaborate formation of a fusion pore, together with complexes called tethers endolysosomal structures, but curiously both it and related protozoa that act upstream of SNAREs (Baker and Hughson, 2016). The lack the HOPS tether and several other trafficking proteins, while homotypic-fusion-and-protein-sorting (HOPS) and class-C-core- retaining the related CORVET complex. Here, we show that vacuole/endosome-tethering (CORVET) complexes are cytoplasmic Tetrahymena encodes multiple paralogs of most CORVET hetero-hexamers that bridge compartments by binding Rab GTPases at subunits, which assemble into six distinct complexes. Each two membranes, and subsequently chaperoning SNARE assembly complex has a unique subunit composition and, significantly, shows (Baker and Hughson, 2016; Horazdovsky et al., 1996; Nickerson unique localization, indicating participation -
Analysis of Mir-34A-5P Over-Expression by Qrt-PCR
Supplementary material files Supplementary Figure 1: Analysis of miR-34a-5p over-expression by qRT-PCR. Primary CD4+ T cells were transfected either with allstars negative control (ANC) or miR-34a-5p mimic. 48 h post transfection the total RNA was isolated and analyzed by qRT-PCR using a specific hsa-miR-34a-5p primer. Supplementary Figure 2: FACS Controls CD4+ T cells were stained for CD4 and co-stained for CD11A or the respective isotype controls for 30 min at 4°C. Cells were analyzed by flow cytometry. Gated CD4+ T cells (A) were analyzed for CD11A expression (B, dark grey) in comparison to isotype controls (light grey). CD8+ T cells were stained for CD8 and co-stained for CD11A or the respective isotype controls for 30 min at 4°C. Cells were analyzed by flow cytometry. Gated CD8+ T cells (C) were analyzed for CD11A expression (D, dark grey) in comparison to isotype controls (light grey). Supplementary Table 1 target cloning sequence ID gene primers (restriction sites are underlined) 5'-VAMP2-SpeI ggactagtccatcatcctcatcatcatc VAMP2 NM_014232.2 3'-VAMP2-NaeI gccggccctcaatcagttcacccaatgag 5'-IKBKE-SpeI ggactagtcacatgaggcatcctgaag IKBKE NM_014002.3 3'-IKBKE-SacI cgagctcgcatagaaagaacaggaggctc 5'-MYH9-SpeI ggactagtcgaagaggtagatggcaaagc MYH9 NM_002473.5 3'-MYH9-SacI cgagctccctttgtgacagcaactggg 5'-MARCH8-SpeI ggactagtgtgtgcgggttgtcattttc MARCH8 NM_001282866.1 3'-MARCH8-SacI cgagctccagaatgcactgagagtggg 5'-KLRK1-SpeI ggactagtgagactgtgcactctatgcctc KLRK1 NM_007360.3 3'-KLRK1-SacI cgagctcccttcttaactgtgaacctgtg 5'-CD11A-SpeI ggactagtgagaaggactctgagagtgg -
Variation in Protein Coding Genes Identifies Information
bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 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. Animal complexity and information flow 1 1 2 3 4 5 Variation in protein coding genes identifies information flow as a contributor to 6 animal complexity 7 8 Jack Dean, Daniela Lopes Cardoso and Colin Sharpe* 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Institute of Biological and Biomedical Sciences 25 School of Biological Science 26 University of Portsmouth, 27 Portsmouth, UK 28 PO16 7YH 29 30 * Author for correspondence 31 [email protected] 32 33 Orcid numbers: 34 DLC: 0000-0003-2683-1745 35 CS: 0000-0002-5022-0840 36 37 38 39 40 41 42 43 44 45 46 47 48 49 Abstract bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 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. Animal complexity and information flow 2 1 Across the metazoans there is a trend towards greater organismal complexity. How 2 complexity is generated, however, is uncertain. Since C.elegans and humans have 3 approximately the same number of genes, the explanation will depend on how genes are 4 used, rather than their absolute number.