Mutation Leading to a Sulfatase Deficiency Is Associated
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The CLN5 Disease
Mia-Lisa Schmiedt Mia-Lisa Schmiedt Mia-Lisa Schmiedt The CLN5 disease − RESEARCH protein maturation, RESEARCH The CLN5 disease − protein maturation, trafficking and pathology trafficking and pathology The CLN5 disease −protein maturation, trafficking and pathology and trafficking maturation, The CLN5 disease −protein Neuronal ceroid lipofuscinoses (NCLs) are a group of hereditary neurode- generative disorders primarily affecting children. Characteristics for NCLs are accumulation of autofluorescent storage material, neuronal degenera- tion, motor disturbances, progressive loss of vision and premature death. One member of the NCL family is the CLN5 disease, a late infantile variant phenotype form, caused by mutations in the CLN5 gene. CLN5 encodes a lysosomal protein of unidentified function. This thesis work contributes to the basic understanding of the molecular and cell biological mechanisms underlying CLN5 disease. Real-time PCR studies indicated that Cln5 gene expression increases gradually in the mouse brain with age and its expres- sion is highest in microglia. This thesis project further presents that the CLN5 protein is cleaved in the ER, trimmed and finally traffics to lysosomes. CLN5 constructs carrying different disease causing mutations revealed that trafficking is disturbed with varying severity depending on the particular mutation. Also, this work provides novel aspects about the early events in the pathogenesis of CLN5 disease, late infantile variant, links Cln5 to lipid metabolism and strengthens the recently reported -
A New Michaelis Complex Leads to Efficient Transition State Charge Offset
Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset Charlotte M. Mitona,1, Stefanie Jonasa,2, Gerhard Fischera,3, Fernanda Duarteb,3,4, Mark F. Mohameda, Bert van Looa,5, Bálint Kintsesa,6, Shina C. L. Kamerlinb, Nobuhiko Tokurikia,c, Marko Hyvönena, and Florian Hollfeldera,7 aDepartment of Biochemistry, University of Cambridge, CB2 1GA Cambridge, United Kingdom; bDepartment of Chemistry, Biomedicinskt Centrum (BMC), Uppsala University, 751 23 Uppsala, Sweden; and cMichael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada Edited by Daniel Herschlag, Stanford University, Stanford, CA, and accepted by Editorial Board Member Michael A. Marletta May 31, 2018 (received for review January 31, 2018) The recruitment and evolutionary optimization of promiscuous catalytic residues but also occurs at the periphery of the catalytic enzymes is key to the rapid adaptation of organisms to changing machinery, even in positions as remote as the second and third environments. Our understanding of the precise mechanisms shells of the active site (23). In studies examining detailed evo- underlying enzyme repurposing is, however, limited: What are lutionary transitions, function-altering mutations led to the dis- the active-site features that enable the molecular recognition of placement of a catalytic metal ion or the repositioning of a multiple substrates with contrasting catalytic requirements? To nucleophile (24–26). In further cases, the position of the catalytic gain insights into the molecular determinants of adaptation in residues remained unaltered, but other structural features, for promiscuous enzymes, we performed the laboratory evolution of an arylsulfatase to improve its initially weak phenylphosphonate Significance hydrolase activity. -
An Interactive Web Application to Explore Regeneration-Associated Gene Expression and Chromatin Accessibility
Supplementary Materials Regeneration Rosetta: An interactive web application to explore regeneration-associated gene expression and chromatin accessibility Andrea Rau, Sumona P. Dhara, Ava J. Udvadia, Paul L. Auer 1. Table S1. List of cholesterol metabolic genes from MGI database 2. Table S2. List of differentially expressed transcripts during optic nerve regeneration in zebrafish using the MGI cholesterol metabolic gene queries in the Regeneration Rosetta app 3. Table S3. List of transcription factor encoding genes from brain cell bodies following spinal cord injury in lamprey over a course of 12 weeKs 4. Table S4. List of transcription factor encoding genes from spinal cell bodies following spinal cord injury in lamprey over a course of 12 weeks Ensembl ID MGI Gene ID Symbol Name ENSMUSG00000015243 MGI:99607 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1 ENSMUSG00000026944 MGI:99606 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2 ENSMUSG00000024030 MGI:107704 Abcg1 ATP binding cassette subfamily G member 1 ENSMUSG00000026003 MGI:87866 Acadl acyl-Coenzyme A dehydrogenase, long-chain ENSMUSG00000018574 MGI:895149 Acadvl acyl-Coenzyme A dehydrogenase, very long chain ENSMUSG00000038641 MGI:2384785 Akr1d1 aldo-keto reductase family 1, member D1 ENSMUSG00000028553 MGI:1353627 Angptl3 angiopoietin-like 3 ENSMUSG00000031996 MGI:88047 Aplp2 amyloid beta (A4) precursor-like protein 2 ENSMUSG00000032083 MGI:88049 Apoa1 apolipoprotein A-I ENSMUSG00000005681 MGI:88050 Apoa2 apolipoprotein A-II ENSMUSG00000032080 MGI:88051 Apoa4 -
Genotyping of Breech Flystrike Resource – Update
Project No: ON-00515 Contract No: PO4500010753 AWI Project Manager: Bridget Peachey Contractor Name: CSIRO Agriculture and Food Prepared by: Dr Sonja Dominik Publication Date: July 2019 Genotyping of breech flystrike resource – update Published by Australian Wool Innovation Limited, Level 6, 68 Harrington Street, THE ROCKS, NSW, 2000 This publication should only be used as a general aid and is not a substitute for specific advice. To the extent permitted by law, we exclude all liability for loss or damage arising from the use of the information in this publication. AWI invests in research, development, innovation and marketing activities along the global supply chain for Australian wool. AWI is grateful for its funding, which is primarily provided by Australian woolgrowers through a wool levy and by the Australian Government which provides a matching contribution for eligible R&D activities © 2019 Australian Wool Innovation Ltd. All rights reserved. Contents Executive Summary .................................................................................................................... 3 1 Introduction/Hypothesis .................................................................................................... 5 2 Literature Review ............................................................................................................... 6 3 Project Objectives .............................................................................................................. 8 4 Success in Achieving Objectives ........................................................................................ -
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. -
1 Metabolic Dysfunction Is Restricted to the Sciatic Nerve in Experimental
Page 1 of 255 Diabetes Metabolic dysfunction is restricted to the sciatic nerve in experimental diabetic neuropathy Oliver J. Freeman1,2, Richard D. Unwin2,3, Andrew W. Dowsey2,3, Paul Begley2,3, Sumia Ali1, Katherine A. Hollywood2,3, Nitin Rustogi2,3, Rasmus S. Petersen1, Warwick B. Dunn2,3†, Garth J.S. Cooper2,3,4,5* & Natalie J. Gardiner1* 1 Faculty of Life Sciences, University of Manchester, UK 2 Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK 3 Centre for Endocrinology and Diabetes, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, UK 4 School of Biological Sciences, University of Auckland, New Zealand 5 Department of Pharmacology, Medical Sciences Division, University of Oxford, UK † Present address: School of Biosciences, University of Birmingham, UK *Joint corresponding authors: Natalie J. Gardiner and Garth J.S. Cooper Email: [email protected]; [email protected] Address: University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, United Kingdom Telephone: +44 161 275 5768; +44 161 701 0240 Word count: 4,490 Number of tables: 1, Number of figures: 6 Running title: Metabolic dysfunction in diabetic neuropathy 1 Diabetes Publish Ahead of Print, published online October 15, 2015 Diabetes Page 2 of 255 Abstract High glucose levels in the peripheral nervous system (PNS) have been implicated in the pathogenesis of diabetic neuropathy (DN). However our understanding of the molecular mechanisms which cause the marked distal pathology is incomplete. Here we performed a comprehensive, system-wide analysis of the PNS of a rodent model of DN. -
Palmitoyl-Protein Thioesterase 1 Deficiency in Drosophila Melanogaster Causes Accumulation
Genetics: Published Articles Ahead of Print, published on February 1, 2006 as 10.1534/genetics.105.053306 Palmitoyl-protein thioesterase 1 deficiency in Drosophila melanogaster causes accumulation of abnormal storage material and reduced lifespan Anthony J. Hickey*,†,1, Heather L. Chotkowski*, Navjot Singh*, Jeffrey G. Ault*, Christopher A. Korey‡,2, Marcy E. MacDonald‡, and Robert L. Glaser*,†,3 * Wadsworth Center, New York State Department of Health, Albany, NY 12201-2002 † Department of Biomedical Sciences, State University of New York, Albany, NY 12201-0509 ‡ Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114 1 current address: Albany Medical College, Albany, NY 12208 2 current address: Department of Biology, College of Charleston, Charleston, SC 294243 3 corresponding author: Wadsworth Center, NYS Dept. Health, P. O. Box 22002, Albany, NY 12201-2002 E-mail: [email protected] 1 running title: Phenotypes of Ppt1-deficient Drosophila key words: Batten disease infantile neuronal ceroid lipofuscinosis palmitoyl-protein thioesterase CLN1 Drosophila corresponding author: Robert L. Glaser Wadsworth Center, NYS Dept. Health P. O. Box 22002 Albany, NY 12201-2002 E-mail: [email protected] phone: 518-473-4201 fax: 518-474-3181 2 ABSTRACT Human neuronal ceroid lipofuscinoses (NCLs) are a group of genetic neurodegenerative diseases characterized by progressive death of neurons in the central nervous system (CNS) and accumulation of abnormal lysosomal storage material. Infantile NCL (INCL), the most severe form of NCL, is caused by mutations in the Ppt1 gene, which encodes the lysosomal enzyme palmitoyl-protein thioesterase 1 (Ppt1). We generated mutations in the Ppt1 ortholog of Drosophila melanogaster in order to characterize phenotypes caused by Ppt1-deficiency in flies. -
Genome-Wide Analysis of ATP-Binding
Tian et al. BMC Genomics (2017) 18:330 DOI 10.1186/s12864-017-3706-6 RESEARCH ARTICLE Open Access Genome-wide analysis of ATP-binding cassette (ABC) transporters in the sweetpotato whitefly, Bemisia tabaci Lixia Tian1, Tianxue Song2, Rongjun He1, Yang Zeng1, Wen Xie1, Qingjun Wu1, Shaoli Wang1, Xuguo Zhou3* and Youjun Zhang1* Abstract Background: ABC transporter superfamily is one of the largest and ubiquitous groups of proteins. Because of their role in detoxification, insect ABC transporters have gained more attention in recent years. In this study, we annotated ABC transporters from a newly sequenced sweetpotato whitefly genome. Bemisia tabaci Q biotype is an emerging global invasive species that has caused extensive damages to field crops as well as ornamental plants. Results: A total of 55 ABC transporters containing all eight described subfamilies (A to H) were identified in the B. tabaci Q genome, including 8 ABCAs, 3 ABCBs, 6 ABCCs, 2 ABCDs, 1 ABCE, 3 ABCFs, 23 ABCGs and 9 ABCHs. In comparison to other species, subfamilies G and H in both phloem- and blood-sucking arthropods are expanded. The temporal expression profiles of these 55 ABC transporters throughout B. tabaci developmental stages and their responses to imidacloprid, a neonicotinoid insecticide, were investigated using RNA-seq analysis. Furthermore, the mRNA expression of 24 ABC transporters (44% of the total) representing all eight subfamilies was confirmed by the quantitative real-time PCR (RT-qPCR). Furthermore, mRNA expression levels estimated by RT-qPCR and RNA-seq analyses were significantly correlated (r =0.684,p <0.01). Conclusions: It is the first genome-wide analysis of the entire repertoire of ABC transporters in B. -
Yeast Genome Gazetteer P35-65
gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal -
5' Untranslated Region Elements Show High Abundance and Great
International Journal of Molecular Sciences Article 0 5 Untranslated Region Elements Show High Abundance and Great Variability in Homologous ABCA Subfamily Genes Pavel Dvorak 1,2,* , Viktor Hlavac 2,3 and Pavel Soucek 2,3 1 Department of Biology, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic 2 Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; [email protected] (V.H.); [email protected] (P.S.) 3 Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic * Correspondence: [email protected]; Tel.: +420-377593263 Received: 7 October 2020; Accepted: 20 November 2020; Published: 23 November 2020 Abstract: The 12 members of the ABCA subfamily in humans are known for their ability to transport cholesterol and its derivatives, vitamins, and xenobiotics across biomembranes. Several ABCA genes are causatively linked to inborn diseases, and the role in cancer progression and metastasis is studied intensively. The regulation of translation initiation is implicated as the major mechanism in the processes of post-transcriptional modifications determining final protein levels. In the current bioinformatics study, we mapped the features of the 50 untranslated regions (50UTR) known to have the potential to regulate translation, such as the length of 50UTRs, upstream ATG codons, upstream open-reading frames, introns, RNA G-quadruplex-forming sequences, stem loops, and Kozak consensus motifs, in the DNA sequences of all members of the subfamily. Subsequently, the conservation of the features, correlations among them, ribosome profiling data as well as protein levels in normal human tissues were examined. The 50UTRs of ABCA genes contain above-average numbers of upstream ATGs, open-reading frames and introns, as well as conserved ones, and these elements probably play important biological roles in this subfamily, unlike RG4s. -
Thioesterase Superfamily Member 1 Undergoes Stimulus-Coupled Conformational Reorganization to Regulate Metabolism in Mice
ARTICLE https://doi.org/10.1038/s41467-021-23595-x OPEN Thioesterase superfamily member 1 undergoes stimulus-coupled conformational reorganization to regulate metabolism in mice Yue Li 1,2, Norihiro Imai3, Hayley T. Nicholls 3, Blaine R. Roberts 4, Samaksh Goyal 1,2, Tibor I. Krisko 3, Lay-Hong Ang 1,2, Matthew C. Tillman4, Anne M. Roberts4, Mahnoor Baqai 1,2, Eric A. Ortlund 4, ✉ ✉ David E. Cohen 3 & Susan J. Hagen 1,2 1234567890():,; In brown adipose tissue, thermogenesis is suppressed by thioesterase superfamily member 1 (Them1), a long chain fatty acyl-CoA thioesterase. Them1 is highly upregulated by cold ambient temperature, where it reduces fatty acid availability and limits thermogenesis. Here, we show that Them1 regulates metabolism by undergoing conformational changes in response to β-adrenergic stimulation that alter Them1 intracellular distribution. Them1 forms metabolically active puncta near lipid droplets and mitochondria. Upon stimulation, Them1 is phosphorylated at the N-terminus, inhibiting puncta formation and activity and resulting in a diffuse intracellular localization. We show by correlative light and electron microscopy that Them1 puncta are biomolecular condensates that are inhibited by phosphorylation. Thus, Them1 forms intracellular biomolecular condensates that limit fatty acid oxidation and sup- press thermogenesis. During a period of energy demand, the condensates are disrupted by phosphorylation to allow for maximal thermogenesis. The stimulus-coupled reorganization of Them1 provides fine-tuning of thermogenesis and energy expenditure. 1 Division of General Surgery, Department of Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA. 2 Department of Surgery, Harvard Medical School, Boston, MA, USA. 3 Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA. -
CLN8 Mutations Presenting with a Phenotypic Continuum of Neuronal Ceroid Lipofuscinosis—Literature Review and Case Report
G C A T T A C G G C A T genes Article CLN8 Mutations Presenting with a Phenotypic Continuum of Neuronal Ceroid Lipofuscinosis—Literature Review and Case Report Magdalena Badura-Stronka 1,*,†, Anna Winczewska-Wiktor 2,†, Anna Pietrzak 3,†, Adam Sebastian Hirschfeld 1, Tomasz Zemojtel 4, Katarzyna Woły ´nska 1, Katarzyna Bednarek-Rajewska 5, Monika Seget-Dubaniewicz 5, Agnieszka Matheisel 6, Anna Latos-Bielenska 1 and Barbara Steinborn 2 1 Chair and Department of Medical Genetics, Poznan University of Medical Sciences, 60-352 Poznan, Poland; [email protected] (A.S.H.); [email protected] (K.W.); [email protected] (A.L.-B.) 2 Chair and Department of Developmental Neurology, Poznan University of Medical Sciences, 60-355 Poznan, Poland; [email protected] (A.W.-W.); [email protected] (B.S.) 3 Department of Neurology, 10th Military Research Hospital and Polyclinic, 85-681 Bydgoszcz, Poland; [email protected] 4 BIH Genomics Core Unit, Campus Mitte, Charite University Medicine, 13353 Berlin, Germany; [email protected] 5 Department of Clinical Pathology, Poznan University of Medical Sciences, 60-355 Poznan, Poland; [email protected] (K.B.-R.); [email protected] (M.S.-D.) 6 Citation: Badura-Stronka, M.; Department of Developmental Neurology, Gdansk Medical University, 80-307 Gdansk, Poland; Winczewska-Wiktor, A.; Pietrzak, A.; [email protected] * Correspondence: [email protected] Hirschfeld, A.S.; Zemojtel, T.; † These authors contributed equally to this work. Woły´nska,K.; Bednarek-Rajewska, K.; Seget-Dubaniewicz, M.; Matheisel, A.; Latos-Bielenska, A.; Steinborn, B. Abstract: CLN8 is a ubiquitously expressed membrane-spanning protein that localizes primarily CLN8 Mutations Presenting with a in the ER, with partial localization in the ER-Golgi intermediate compartment.