DOCSLIB.ORG

Two Splice Variants of Human PEX19 Exhibit Distinct Functions in Peroxisomal Assembly

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Two Splice Variants of Human PEX19 Exhibit Distinct Functions in Peroxisomal Assembly Biochemical and Biophysical Research Communications 291, 1180–1186 (2002) doi:10.1006/bbrc.2002.6568, available online at http://www.idealibrary.com on Two Splice Variants of Human PEX19 Exhibit Distinct Functions in Peroxisomal Assembly Peter U. Mayerhofer, Tanja Kattenfeld, Adelbert A. Roscher, and Ania C. Muntau1 Dr. v. Hauner Children’s Hospital, Department of Clinical Chemistry and Biochemical Genetics, Ludwig-Maximilians-University Munich, Lindwurmstrasse 4, D-80337 Munich, Germany Received January 31, 2002 cific biological functions of the different predicted do- PEX19 has been shown to play a central role in the mains of the PEX19 protein. © 2002 Elsevier Science (USA) early steps of peroxisomal membrane synthesis. Com- Key Words: peroxisome biogenesis disorders; splice putational database analysis of the PEX19 sequence variants; farnesylation; peroxin; PEX; ABC half trans- revealed three different conserved domains: D1 (aa porter; peroxisomal membrane proteins. 1–87), D2 (aa 88–272), and D3 (aa 273–299). However, these domains have not yet been linked to specific biological functions. We elected to functionally char- The biogenesis of peroxisomes (reviewed by 1–3) is a acterize the proteins derived from two naturally oc- curring PEX19 splice variants: PEX19⌬E2 lacking the complex process including the biosynthesis of the per- N-terminal domain D1 and PEX19⌬E8 lacking the do- oxisomal membrane, the targeting and insertion of per- main D3. Both interact with peroxisomal ABC trans- oxisomal membrane proteins (PMPs) into this mem- porters (ALDP, ALDRP, PMP70) and with full-length brane, and the import of peroxisomal matrix enzymes PEX3 as shown by in vitro protein interaction studies. across the bilayer into the peroxisomal lumen. The PEX19⌬E8 also interacts with a PEX3 protein lack- proteins involved are termed “peroxins” and are en- ing the peroxisomal targeting region located at the coded by at least 23 different PEX genes. In most cases, N-terminus (⌬66aaPEX3), whereas PEX19⌬E2 does human PEX mutants display defects in the import of not. Functional complementation studies in PEX19- peroxisomal matrix proteins whereas the synthesis of deficient human fibroblasts revealed that transfection some peroxisomal membrane vesicles and the insertion of PEX19⌬E8-cDNA leads to restoration of both perox- of PMPs into these membrane remnants (“peroxisomal isomal membranes and of functional peroxisomes, ghosts”) remain unaffected. Only mutants in PEX3, whereas transfection of PEX19⌬E2-cDNA does not re- PEX16, and PEX19 appear to lack even such peroxiso- store peroxisomal biogenesis. Human PEX19 is partly mal ghosts (4–6), implicating a crucial role of these farnesylated in vitro and in vivo. The farnesylation proteins in the very early stage of peroxisomal mem- consensus motif CLIM is located in the PEX19 domain brane synthesis. D3. The finding that the protein derived from the Among these PEX19 is the only peroxin known to splice variant lacking D3 is able to interact with sev- own a C-terminal CAAX-box, thereby harboring the eral peroxisomal membrane proteins and to restore intrinsic property of being modified by posttransla- peroxisomal biogenesis challenges the previous as- tional farnesylation. In human, PEX19 is in part far- sumption that farnesylation of PEX19 is essential for nesylated in vivo and it has been suggested that far- its biological functionality. The data presented dem- nesylation is required for the peroxisomal localization onstrate a considerable functional diversity of the pro- of PEX19 (6). Whether farnesylation is essential for the teins encoded by two PEX19 splice variants and function of PEX19 in peroxisomal biogenesis (6) or has thereby provide first experimental evidence for spe- only an ancillary effect (7) remains unclear to date. PEX19 appears to be bimodally distributed between Abbreviations used: ABC, half transporter ATP binding cassette transporter; ALDP, adrenoleukodystrophy protein; ALDRP, adreno- the cytoplasm and the peroxisomes, with most of the leukodystrophy related protein; GFP, green fluorescent protein; protein in the cytoplasm (7). PEX19 protein has been GST, glutathione-S-transferase; PEX, peroxisomal assembly protein; shown to bind a wide variety of peroxisomal membrane PMP70, 70-kDa peroxisomal membrane protein; PMP(s), peroxiso- proteins including peroxins and peroxisomal ABC mal membrane protein(s). 1 To whom correspondence and reprint requests should be ad- transporters (7–13). Among these, PEX19 has been dressed. Fax: ϩ49 89 5160 3343. E-mail: [email protected]. shown to interact with PEX3, another key component uni-muenchen.de. in early peroxisomal membrane synthesis, in yeast (8) 0006-291X/02 $35.00 1180 © 2002 Elsevier Science (USA) All rights reserved. Vol. 291, No. 5, 2002 BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS and human (4, 5, 14). In yeast, this particular protein- System (Promega) following standard protocols. For the genera- protein interplay appears to be a prerequisite for the tion of glutathione-S-transferase (GST) fusion proteins, different cDNAs of human PEX19-splice variants were subcloned into the generation of preperoxisomal structures that can ac- prokaryotic expression plasmid pGEX-3X (Pharmacia) as described quire and stabilize newly synthesized PMPs (15). elsewhere (16). Expression and affinity purification using gluta- PEX19 harbors distinct binding sites for PEX3 and thione-Sepharose 4B (Pharmacia) of the fusion proteins were per- PEX16 (13). However, these sites have not yet been formed as previously described (22). The various purified GST-fusion linked to a specific protein domain organization of proteins were bound to glutathione-Sepharose beads (Pharmacia) in PBSfor1hat4°C and washed three times in PBS. For the in vitro PEX19. interaction assay the GST-fusion proteins (0.5–1.5 ␮g protein bound We have previously cloned and characterized the to 1 ␮l bead suspension) were incubated with 5 ␮lofin vitro trans- human PEX19 gene, which is composed of eight exons lated, [35S]-labeled protein in 200 ␮l binding buffer (100 mM NaCl, 50 (16). On the transcriptional level, we identified differ- mM potassium phosphate pH 7.4, 1 mM MgCl2, 10% glycerol, 0.1% ent PEX19 splice variants (16). The unspliced variant Tween 20, 1.5% BSA) for2hat4°C. The beads were then pelleted and washed four times in 1 ml binding buffer not containing BSA. PEX19all encodes for the full-length PEX19 protein, Pellets were resuspended in SDS-sample buffer and boiled for 5 min whereas the variants PEX19⌬E2 and PEX19p⌬E8 are before being analyzed by SDS–PAGE according to standard proto- expected to lack N- or C-terminal parts of the protein. cols. To verify stability of the GST-fusion proteins and equal loading, Tissue- or cell-specific expression of splice variants gels were stained with Coomassie blue. The gels were dried and has been reported for many genes, e.g., for genes en- exposed to X-ray film for 24 h. coding cytokines or tyrosine kinases. Functional diver- Transfection, antibodies, and indirect immunofluorescence analy- sities of these variants, like distinct protein-protein sis. Plasmids were transfected into COS7 cells or into human PEX19-deficient fibroblasts using Lipofectamine (Life Technologies) interactions, are known (17–19). For PEX19, the splice following protocols provided by the manufacturer. To create stable variant PEX19all has been described to be the predom- transfectants, the fibroblasts were incubated with 500 ␮g/ml neomy- inant transcript in mRNA of several cells and tissues cin (SIGMA). For indirect immunofluorescence analysis, stable in human, although the variant PEX19⌬E2 has also transfectants were fixed with 3% formalin/PBS for 30 min and per- meabilized with 1% Triton X-100 for 5 min. Thereafter, cells were been reported to account for a significant level of total incubated for 1 h with a polyclonal rabbit antibody against catalase human PEX19 mRNA. Interestingly, the ratio between (Biodesign; 1:100 dilution) and/or a monoclonal mouse antibody PEX19all and PEX19⌬E2 expression was completely against ALDP (ALD-1D6, Euromedex; 1:100 dilution). The cells were reversed in uterine mRNA prepared from total human then washed 10 times with PBS and incubated for 1 h with secondary uterine tissue (16), but a possible biological impact of antibodies: Rhodamine (TRITC)-conjugated goat anti-mouse IgG and/or fluorescein (FITC)-conjugated goat anti-rabbit IgG (all Jack- these findings remained still unclear. Therefore, the son Immunoresearch Laboratory Inc.; 1:50 dilution). After 10 wash characterization of PEX19 splice variants as to their steps in PBS, the cells were embedded in an antifading reagent ability to interact with other peroxisomal proteins and (Vectashield, Vector Laboratories Inc.). Fluorescence microscopy was to initiate early peroxisomal membrane synthesis performed using an Axiovert 135 inverted fluorescence microscope could provide insights into the potential biological rel- (Zeiss). evance of these PEX19 splice variants. Furthermore, the definition of functional regions of PEX19 by the RESULTS characterization of truncated PEX19 splice variants Domain Structure of the Human PEX19 Protein could contribute to the knowledge on specific protein in Relation to PEX19 Splice Variants domains within PEX19. Computational database analysis of the full-length PEX19 protein sequence using the NCBI-BLASTP pro- MATERIALS AND METHODS gram and the ProDom database revealed three differ- Computational analysis. Database searches for the prediction of ent conserved domains in
Load more

Recommended publications
  • Peroxisome: the New Player in Ferroptosis
    Signal Transduction and Targeted Therapy www.nature.com/sigtrans RESEARCH HIGHLIGHT OPEN Peroxisome: the new player in ferroptosis Daolin Tang1,2 and Guido Kroemer 3,4,5 Signal Transduction and Targeted Therapy (2020) 5:273; https://doi.org/10.1038/s41392-020-00404-3 A recent paper published in Nature by Zou et al. reported that peroxisomes was positively correlated with susceptibility to peroxisomes, membrane-bound oxidative organelles, contribute ferroptosis. Therefore, peroxisomes may be added to the list of to ferroptosis through the biosynthesis of plasmalogens for lipid organelles that can initiate the ferroptotic cell death.5 peroxidation (Fig. 1).1 These observations provide new insights Subsequently, the author explored how peroxisomes affect the into the lipid metabolic basis of ferroptotic cell death. sensitivity of cells to ferroptosis. Peroxisomal enzymes involved in Cell death, which is essential for organismal homeostasis, the synthesis of plasmalogens, such as alkylglycerone phosphate exhibits multiple subroutines with different molecular mechan- synthase (AGPS), fatty acyl-CoA reductase 1 (FAR1), and glycer- isms and signaling cascades.2 Within the expanding typology of onephosphate O-acyltransferase (GNPAT), were significantly regulated cell death pathways, ferroptosis is an iron-dependent enriched among the CRISPR targets that confer cytoprotection. non-apoptotic cell death caused by unrestrained lipid peroxida- Lipidomic analysis revealed that the production of plasmalogens tion culminating in irreversible plasma membrane
    [Show full text]
  • PEX2 Is the E3 Ubiquitin Ligase Required for Pexophagy During Starvation
    JCB: Article PEX2 is the E3 ubiquitin ligase required for pexophagy during starvation Graeme Sargent,1,6 Tim van Zutphen,7 Tatiana Shatseva,6 Ling Zhang,3 Valeria Di Giovanni,3 Robert Bandsma,2,3,4,5 and Peter Kijun Kim1,6 1Cell Biology Department, 2Department of Paediatric Laboratory Medicine, 3Physiology and Experimental Medicine Program, Research Institute, 4Division of Gastroenterology, Hepatology and Nutrition, and 5Centre for Global Child Health, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada 6Biochemistry Department, University of Toronto, Toronto, ON M5S 1A8, Canada 7Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, 9700 AD Groningen, Netherlands Peroxisomes are metabolic organelles necessary for anabolic and catabolic lipid reactions whose numbers are highly dynamic based on the metabolic need of the cells. One mechanism to regulate peroxisome numbers is through an auto- phagic process called pexophagy. In mammalian cells, ubiquitination of peroxisomal membrane proteins signals pexo- phagy; however, the E3 ligase responsible for mediating ubiquitination is not known. Here, we report that the peroxisomal E3 ubiquitin ligase peroxin 2 (PEX2) is the causative agent for mammalian pexophagy. Expression of PEX2 leads to Downloaded from gross ubiquitination of peroxisomes and degradation of peroxisomes in an NBR1-dependent autophagic process. We identify PEX5 and PMP70 as substrates of PEX2 that are ubiquitinated during amino acid starvation. We also find that PEX2 expression is up-regulated during both amino acid starvation and rapamycin treatment, suggesting that the mTORC1 pathway regulates pexophagy by regulating PEX2 expression levels. Finally, we validate our findings in vivo using an animal model.
    [Show full text]
  • Combinatorial Genomic Data Refute the Human Chromosome 2 Evolutionary Fusion and Build a Model of Functional Design for Interstitial Telomeric Repeats
    The Proceedings of the International Conference on Creationism Volume 8 Print Reference: Pages 222-228 Article 32 2018 Combinatorial Genomic Data Refute the Human Chromosome 2 Evolutionary Fusion and Build a Model of Functional Design for Interstitial Telomeric Repeats Jeffrey P. Tomkins Institute for Creation Research Follow this and additional works at: https://digitalcommons.cedarville.edu/icc_proceedings Part of the Biology Commons, and the Genomics Commons DigitalCommons@Cedarville provides a publication platform for fully open access journals, which means that all articles are available on the Internet to all users immediately upon publication. However, the opinions and sentiments expressed by the authors of articles published in our journals do not necessarily indicate the endorsement or reflect the views of DigitalCommons@Cedarville, the Centennial Library, or Cedarville University and its employees. The authors are solely responsible for the content of their work. Please address questions to [email protected]. Browse the contents of this volume of The Proceedings of the International Conference on Creationism. Recommended Citation Tomkins, J.P. 2018. Combinatorial genomic data refute the human chromosome 2 evolutionary fusion and build a model of functional design for interstitial telomeric repeats. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. Whitmore, pp. 222–228. Pittsburgh, Pennsylvania: Creation Science Fellowship. Tomkins, J.P. 2018. Combinatorial genomic data refute the human chromosome 2 evolutionary fusion and build a model of functional design for interstitial telomeric repeats. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. Whitmore, pp. 222–228. Pittsburgh, Pennsylvania: Creation Science Fellowship. COMBINATORIAL GENOMIC DATA REFUTE THE HUMAN CHROMOSOME 2 EVOLUTIONARY FUSION AND BUILD A MODEL OF FUNCTIONAL DESIGN FOR INTERSTITIAL TELOMERIC REPEATS Jeffrey P.
    [Show full text]
  • Autophagy -   Autophagy
    EMBO Molecular Medicine cross-journal focus Autophagy - Autophagy EDITORS Andrea Leibfried Editor [email protected] | T + Andrea worked with Jan Lohmann on stem cell maintenance in the plant Arabidopsis before moving to the eld of trafcking. In she obtained her PhD from the Université Pierre et Marie Curie in Paris, for which she studied DE-Cadherin trafcking in Drosophila with Yohanns Bellaiche at the Curie Institute. She then went to Anne Ephrussi’s lab at the EMBL in Heidelberg to work on oocyte polarity and mRNA trafcking in Drosophila. Andrea joined The EMBO Journal in . Nonia Pariente Senior Editor [email protected] | T + Nonia joined EMBO Reports in August . She studied biochemistry and molecular biology in Madrid’s Autónoma University, where she also gained her PhD on the generation of new antiviral strategies against RNA viruses. She did a four-year post-doc at UCLA focusing on the development of new strategies for gene therapy. Céline Carret Editor [email protected] | T + Céline Carret completed her PhD at the University of Montpellier, France, characterising host immunodominant antigens to ght babesiosis, a parasitic disease caused by a unicellular EMBO Apicomplexan parasite closely related to the malaria agent Plasmodium. She further developed Molecular her post-doctoral career on malaria working at the Wellcome Trust Sanger Institute in Cambridge, Medicine UK and Instituto de Medicina Molecular in Lisbon, Portugal. Céline joined EMBO Molecular Medicine as a Scientic Editor in March . Maria Polychronidou Editor [email protected] | T + Maria received her PhD from the University of Heidelberg, where she studied the role of nuclear membrane proteins in development and aging.
    [Show full text]
  • Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Nutrition Publications and Other Works Nutrition 12-19-2010 Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P. Stewart Marshall University Hyoung Y. Kim University of Tennessee - Knoxville, [email protected] Arnold M. Saxton University of Tennessee - Knoxville, [email protected] Jung H. Kim Marshall University Follow this and additional works at: https://trace.tennessee.edu/utk_nutrpubs Part of the Animal Sciences Commons, and the Nutrition Commons Recommended Citation BMC Genomics 2010, 11:713 doi:10.1186/1471-2164-11-713 This Article is brought to you for free and open access by the Nutrition at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Nutrition Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Stewart et al. BMC Genomics 2010, 11:713 http://www.biomedcentral.com/1471-2164/11/713 RESEARCH ARTICLE Open Access Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P Stewart1, Hyoung Yon Kim2, Arnold M Saxton3, Jung Han Kim1* Abstract Background: Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/ JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia.
    [Show full text]
  • Research Article Label-Free Proteomics of the Fetal Pancreas Identifies Deficits in the Peroxisome in Rats with Intrauterine Growth Restriction
    Hindawi Oxidative Medicine and Cellular Longevity Volume 2019, Article ID 1520753, 15 pages https://doi.org/10.1155/2019/1520753 Research Article Label-Free Proteomics of the Fetal Pancreas Identifies Deficits in the Peroxisome in Rats with Intrauterine Growth Restriction Xiaomei Liu ,1 Yanyan Guo ,1 Jun Wang ,1,2 Linlin Gao ,3 and Caixia Liu 1 1Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China 2Department of Obstetrics and Gynecology, Benxi Central Hospital of China Medical University, Benxi 117022, China 3Medical Research Center, Shengjing Hospital, China Medical University, Shenyang 110004, China Correspondence should be addressed to Xiaomei Liu; [email protected] Received 14 May 2019; Revised 31 August 2019; Accepted 9 September 2019; Published 3 November 2019 Guest Editor: Roberta Cascella Copyright © 2019 Xiaomei Liu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Aim. The objective of the present study was to identify differentially expressed proteins (DEPs) in the pancreas of a fetus with intrauterine growth restriction (IUGR) and to investigate the molecular mechanisms leading to adulthood diabetes in IUGR. Methods. The IUGR rat model was induced by maternal protein malnutrition. The fetal pancreas was collected at embryonic day 20 (E20). Protein was extracted, pooled, and subjected to label-free quantitative proteomic analysis. Bioinformatics analysis (GO and IPA) was performed to define the pathways and networks associated with DEPs. LC-MS results were confirmed by western blotting and/or quantitative PCR (q-PCR).
    [Show full text]
  • Common Variants in SOX-2 and Congenital Cataract Genes Contribute to Age-Related Nuclear Cataract
    ARTICLE https://doi.org/10.1038/s42003-020-01421-2 OPEN Common variants in SOX-2 and congenital cataract genes contribute to age-related nuclear cataract Ekaterina Yonova-Doing et al.# 1234567890():,; Nuclear cataract is the most common type of age-related cataract and a leading cause of blindness worldwide. Age-related nuclear cataract is heritable (h2 = 0.48), but little is known about specific genetic factors underlying this condition. Here we report findings from the largest to date multi-ethnic meta-analysis of genome-wide association studies (discovery cohort N = 14,151 and replication N = 5299) of the International Cataract Genetics Consortium. We confirmed the known genetic association of CRYAA (rs7278468, P = 2.8 × 10−16) with nuclear cataract and identified five new loci associated with this dis- ease: SOX2-OT (rs9842371, P = 1.7 × 10−19), TMPRSS5 (rs4936279, P = 2.5 × 10−10), LINC01412 (rs16823886, P = 1.3 × 10−9), GLTSCR1 (rs1005911, P = 9.8 × 10−9), and COMMD1 (rs62149908, P = 1.2 × 10−8). The results suggest a strong link of age-related nuclear cat- aract with congenital cataract and eye development genes, and the importance of common genetic variants in maintaining crystalline lens integrity in the aging eye. #A list of authors and their affiliations appears at the end of the paper. COMMUNICATIONS BIOLOGY | (2020) 3:755 | https://doi.org/10.1038/s42003-020-01421-2 | www.nature.com/commsbio 1 ARTICLE COMMUNICATIONS BIOLOGY | https://doi.org/10.1038/s42003-020-01421-2 ge-related cataract is the leading cause of blindness, structure (meta-analysis genomic inflation factor λ = 1.009, accounting for more than one-third of blindness Supplementary Table 4 and Supplementary Fig.
    [Show full text]
  • Peroxisomal Disorders and Their Mouse Models Point to Essential Roles of Peroxisomes for Retinal Integrity
    International Journal of Molecular Sciences Review Peroxisomal Disorders and Their Mouse Models Point to Essential Roles of Peroxisomes for Retinal Integrity Yannick Das, Daniëlle Swinkels and Myriam Baes * Lab of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; [email protected] (Y.D.); [email protected] (D.S.) * Correspondence: [email protected] Abstract: Peroxisomes are multifunctional organelles, well known for their role in cellular lipid homeostasis. Their importance is highlighted by the life-threatening diseases caused by peroxisomal dysfunction. Importantly, most patients suffering from peroxisomal biogenesis disorders, even those with a milder disease course, present with a number of ocular symptoms, including retinopathy. Patients with a selective defect in either peroxisomal α- or β-oxidation or ether lipid synthesis also suffer from vision problems. In this review, we thoroughly discuss the ophthalmological pathology in peroxisomal disorder patients and, where possible, the corresponding animal models, with a special emphasis on the retina. In addition, we attempt to link the observed retinal phenotype to the underlying biochemical alterations. It appears that the retinal pathology is highly variable and the lack of histopathological descriptions in patients hampers the translation of the findings in the mouse models. Furthermore, it becomes clear that there are still large gaps in the current knowledge on the contribution of the different metabolic disturbances to the retinopathy, but branched chain fatty acid accumulation and impaired retinal PUFA homeostasis are likely important factors. Citation: Das, Y.; Swinkels, D.; Baes, Keywords: peroxisome; Zellweger; metabolism; fatty acid; retina M. Peroxisomal Disorders and Their Mouse Models Point to Essential Roles of Peroxisomes for Retinal Integrity.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • 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.
    [Show full text]
  • Supplementary Material
    BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Neurol Neurosurg Psychiatry Page 1 / 45 SUPPLEMENTARY MATERIAL Appendix A1: Neuropsychological protocol. Appendix A2: Description of the four cases at the transitional stage. Table A1: Clinical status and center proportion in each batch. Table A2: Complete output from EdgeR. Table A3: List of the putative target genes. Table A4: Complete output from DIANA-miRPath v.3. Table A5: Comparison of studies investigating miRNAs from brain samples. Figure A1: Stratified nested cross-validation. Figure A2: Expression heatmap of miRNA signature. Figure A3: Bootstrapped ROC AUC scores. Figure A4: ROC AUC scores with 100 different fold splits. Figure A5: Presymptomatic subjects probability scores. Figure A6: Heatmap of the level of enrichment in KEGG pathways. Kmetzsch V, et al. J Neurol Neurosurg Psychiatry 2021; 92:485–493. doi: 10.1136/jnnp-2020-324647 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Neurol Neurosurg Psychiatry Appendix A1. Neuropsychological protocol The PREV-DEMALS cognitive evaluation included standardized neuropsychological tests to investigate all cognitive domains, and in particular frontal lobe functions. The scores were provided previously (Bertrand et al., 2018). Briefly, global cognitive efficiency was evaluated by means of Mini-Mental State Examination (MMSE) and Mattis Dementia Rating Scale (MDRS). Frontal executive functions were assessed with Frontal Assessment Battery (FAB), forward and backward digit spans, Trail Making Test part A and B (TMT-A and TMT-B), Wisconsin Card Sorting Test (WCST), and Symbol-Digit Modalities test.
    [Show full text]
  • Multiple Pathways for Protein Transport to Peroxisomes
    Review Multiple Pathways for Protein Transport to Peroxisomes P.K. Kim 1,2 and E.H. Hettema 3 1 - Program in Cell Biology, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8 2 - Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8 3 - Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire S10 2TN, United Kingdom Correspondence to E.H. Hettema: [email protected] http://dx.doi.org/10.1016/j.jmb.2015.02.005 Edited by S. High Abstract Peroxisomes are unique among the organelles of the endomembrane system. Unlike other organelles that derive most if not all of their proteins from the ER (endoplasmic reticulum), peroxisomes contain dedicated machineries for import of matrix proteins and insertion of membrane proteins. However, peroxisomes are also able to import a subset of their membrane proteins from the ER. One aspect of peroxisome biology that has remained ill defined is the role the various import pathways play in peroxisome maintenance. In this review, we discuss the available data on matrix and membrane protein import into peroxisomes. © 2015 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Introduction dependent on consumption of energy in the form of ATP. Several aspects of peroxisomal protein transport Peroxisomes are organelles found in almost all distinguish it from other translocation systems. For eukaryotic cells. They are bounded by a single example, peroxisomal proteins can fold, acquire membrane and are usually spherical.
    [Show full text]