Mechanism of Manganese Dysregulation of Dopamine Neuronal Activity
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Bioinformatic Analyses of Integral Membrane Transport Proteins Encoded Within the Genome of the Planctomycetes Species, Rhodopirellula Baltica
UC San Diego UC San Diego Previously Published Works Title Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica. Permalink https://escholarship.org/uc/item/0f85q1z7 Journal Biochimica et biophysica acta, 1838(1 Pt B) ISSN 0006-3002 Authors Paparoditis, Philipp Västermark, Ake Le, Andrew J et al. Publication Date 2014 DOI 10.1016/j.bbamem.2013.08.007 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Biochimica et Biophysica Acta 1838 (2014) 193–215 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbamem Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica Philipp Paparoditis a, Åke Västermark a,AndrewJ.Lea, John A. Fuerst b, Milton H. Saier Jr. a,⁎ a Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093–0116, USA b School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, 9072, Australia article info abstract Article history: Rhodopirellula baltica (R. baltica) is a Planctomycete, known to have intracellular membranes. Because of its un- Received 12 April 2013 usual cell structure and ecological significance, we have conducted comprehensive analyses of its transmembrane Received in revised form 8 August 2013 transport proteins. The complete proteome of R. baltica was screened against the Transporter Classification Data- Accepted 9 August 2013 base (TCDB) to identify recognizable integral membrane transport proteins. 342 proteins were identified with a Available online 19 August 2013 high degree of confidence, and these fell into several different classes. -
Slc1a3-2A-Creert2 Mice Reveal Unique Features of Bergmann Glia and Augment a Growing Collection of Cre Drivers and Effectors In
www.nature.com/scientificreports OPEN Slc1a3‑2A‑CreERT2 mice reveal unique features of Bergmann glia and augment a growing collection of Cre drivers and efectors in the 129S4 genetic background Lech Kaczmarczyk1,2, Nicole Reichenbach2, Nelli Blank2, Maria Jonson1, Lars Dittrich2, Gabor C. Petzold2,3 & Walker S. Jackson1,2* Genetic variation is a primary determinant of phenotypic diversity. In laboratory mice, genetic variation can be a serious experimental confounder, and thus minimized through inbreeding. However, generalizations of results obtained with inbred strains must be made with caution, especially when working with complex phenotypes and disease models. Here we compared behavioral characteristics of C57Bl/6—the strain most widely used in biomedical research—with those of 129S4. In contrast to 129S4, C57Bl/6 demonstrated high within‑strain and intra‑litter behavioral hyperactivity. Although high consistency would be advantageous, the majority of disease models and transgenic tools are in C57Bl/6. We recently established six Cre driver lines and two Cre efector lines in 129S4. To augment this collection, we genetically engineered a Cre line to study astrocytes in 129S4. It was validated with two Cre efector lines: calcium indicator gCaMP5g‑tdTomato and RiboTag—a tool widely used to study cell type‑specifc translatomes. These reporters are in diferent genomic loci, and in both the Cre was functional and astrocyte‑specifc. We found that calcium signals lasted longer and had a higher amplitude in cortical compared to hippocampal astrocytes, genes linked to a single neurodegenerative disease have highly divergent expression patterns, and that ribosome proteins are non‑uniformly expressed across brain regions and cell types. -
Cellular and Molecular Signatures in the Disease Tissue of Early
Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of -
Magnesium Is a Key Player in Neuronal Maturation and Neuropathology
International Journal of Molecular Sciences Review Magnesium Is a Key Player in Neuronal Maturation and Neuropathology Ryu Yamanaka 1,2 , Yutaka Shindo 1 and Kotaro Oka 1,3,4,* 1 Center for Biosciences and Informatics, School of Fundamental Science and Technology Graduate School of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan 2 Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo-Onoda, Yamaguchi 756-0884, Japan 3 Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City 80708, Taiwan 4 Waseda Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku, Tokyo 162-8480, Japan * Correspondence: [email protected]; Tel.: +81-045-566-1789 Received: 16 June 2019; Accepted: 9 July 2019; Published: 12 July 2019 Abstract: Magnesium (Mg) is the second most abundant cation in mammalian cells, and it is essential for numerous cellular processes including enzymatic reactions, ion channel functions, metabolic cycles, cellular signaling, and DNA/RNA stabilities. Because of the versatile and universal nature of Mg2+, the homeostasis of intracellular Mg2+ is physiologically linked to growth, proliferation, differentiation, energy metabolism, and death of cells. On the cellular and tissue levels, maintaining Mg2+ within optimal levels according to the biological context, such as cell types, developmental stages, extracellular environments, and pathophysiological conditions, is crucial for development, normal functions, and diseases. Hence, Mg2+ is pathologically involved in cancers, diabetes, and neurodegenerative diseases, such as Parkinson’s disease, Alzheimer’s disease, and demyelination. In the research field regarding the roles and mechanisms of Mg2+ regulation, numerous controversies caused by its versatility and complexity still exist. -
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 -
Figure S1. HAEC ROS Production and ML090 NOX5-Inhibition
Figure S1. HAEC ROS production and ML090 NOX5-inhibition. (a) Extracellular H2O2 production in HAEC treated with ML090 at different concentrations and 24 h after being infected with GFP and NOX5-β adenoviruses (MOI 100). **p< 0.01, and ****p< 0.0001 vs control NOX5-β-infected cells (ML090, 0 nM). Results expressed as mean ± SEM. Fold increase vs GFP-infected cells with 0 nM of ML090. n= 6. (b) NOX5-β overexpression and DHE oxidation in HAEC. Representative images from three experiments are shown. Intracellular superoxide anion production of HAEC 24 h after infection with GFP and NOX5-β adenoviruses at different MOIs treated or not with ML090 (10 nM). MOI: Multiplicity of infection. Figure S2. Ontology analysis of HAEC infected with NOX5-β. Ontology analysis shows that the response to unfolded protein is the most relevant. Figure S3. UPR mRNA expression in heart of infarcted transgenic mice. n= 12-13. Results expressed as mean ± SEM. Table S1: Altered gene expression due to NOX5-β expression at 12 h (bold, highlighted in yellow). N12hvsG12h N18hvsG18h N24hvsG24h GeneName GeneDescription TranscriptID logFC p-value logFC p-value logFC p-value family with sequence similarity NM_052966 1.45 1.20E-17 2.44 3.27E-19 2.96 6.24E-21 FAM129A 129. member A DnaJ (Hsp40) homolog. NM_001130182 2.19 9.83E-20 2.94 2.90E-19 3.01 1.68E-19 DNAJA4 subfamily A. member 4 phorbol-12-myristate-13-acetate- NM_021127 0.93 1.84E-12 2.41 1.32E-17 2.69 1.43E-18 PMAIP1 induced protein 1 E2F7 E2F transcription factor 7 NM_203394 0.71 8.35E-11 2.20 2.21E-17 2.48 1.84E-18 DnaJ (Hsp40) homolog. -
How Do Bacterial Cells Ensure That Metalloproteins Get the Correct Metal?
REVIEWS How do bacterial cells ensure that metalloproteins get the correct metal? Kevin J. Waldron and Nigel J. Robinson Abstract | Protein metal-coordination sites are richly varied and exquisitely attuned to their inorganic partners, yet many metalloproteins still select the wrong metals when presented with mixtures of elements. Cells have evolved elaborate mechanisms to scavenge for sufficient metal atoms to meet their needs and to adjust their needs to match supply. Metal sensors, transporters and stores have often been discovered as metal-resistance determinants, but it is emerging that they perform a broader role in microbial physiology: they allow cells to overcome inadequate protein metal affinities to populate large numbers of metalloproteins with the right metals. It has been estimated that one-quarter to one-third of all Both monovalent (cuprous) copper, which is expected proteins require metals, although the exploitation of ele- to predominate in a reducing cytosol, and trivalent ments varies from cell to cell and has probably altered over (ferric) iron, which is expected to predominate in an the aeons to match geochemistry1–3 (BOX 1). The propor- oxidizing periplasm, are also highly competitive, as are tions have been inferred from the numbers of homologues several non-essential metals, such as cadmium, mercury of known metalloproteins, and other deduced metal- and silver6 (BOX 2). How can a cell simultaneously contain binding motifs, encoded within sequenced genomes. A some proteins that require copper or zinc and others that large experimental estimate was generated using native require uncompetitive metals, such as magnesium or polyacrylamide-gel electrophoresis of extracts from iron- manganese? In a most simplistic model in which pro- rich Ferroplasma acidiphilum followed by the detection of teins pick elements from a cytosol in which all divalent metal in protein spots using inductively coupled plasma metals are present and abundant, all proteins would bind mass spectrometry4. -
Critical Issues in the Study of Magnesium Transport Systems and Magnesium Deficiency Symptoms in Plants
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by UTokyo Repository Int. J. Mol. Sci. 2015, 16, 23076-23093; doi:10.3390/ijms160923076 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Review Critical Issues in the Study of Magnesium Transport Systems and Magnesium Deficiency Symptoms in Plants Natsuko I. Kobayashi and Keitaro Tanoi * Graduate School of Agricultural and Life Sciences, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +81-3-5841-8496; Fax: +81-3-5841-8193. Academic Editor: Hatem Rouached Received: 30 July 2015 / Accepted: 6 September 2015 / Published: 23 September 2015 Abstract: Magnesium (Mg) is the second most abundant cation in living cells. Over 300 enzymes are known to be Mg-dependent, and changes in the Mg concentration significantly affects the membrane potential. As Mg becomes deficient, starch accumulation and chlorosis, bridged by the generation of reactive oxygen species, are commonly found in Mg-deficient young mature leaves. These defects further cause the inhibition of photosynthesis and finally decrease the biomass. Recently, transcriptome analysis has indicated the transcriptinal downregulation of chlorophyll apparatus at the earlier stages of Mg deficiency, and also the potential involvement of complicated networks relating to hormonal signaling and circadian oscillation. However, the processes of the common symptoms as well as the networks between Mg deficiency and signaling are not yet fully understood. -
The Magnesium Transporter a Is Activated by Cardiolipin And
RESEARCH ARTICLE The magnesium transporter A is activated by cardiolipin and is highly sensitive to free magnesium in vitro Saranya Subramani1, Harmonie Perdreau-Dahl1,2, Jens Preben Morth1,2* 1Norwegian Centre of Molecular Medicine, Nordic EMBL Partnership University of Oslo, Oslo, Norway; 2Institute for Experimental Medical Research, Oslo University Hospital, Oslo, Norway Abstract The magnesium transporter A (MgtA) is a specialized P-type ATPase, believed to import Mg2+ into the cytoplasm. In Salmonella typhimurium and Escherichia coli, the virulence determining two-component system PhoQ/PhoP regulates the transcription of mgtA gene by sensing Mg2+ concentrations in the periplasm. However, the factors that affect MgtA function are not known. This study demonstrates, for the first time, that MgtA is highly dependent on anionic phospholipids and in particular, cardiolipin. Colocalization studies confirm that MgtA is found in the cardiolipin lipid domains in the membrane. The head group of cardiolipin plays major role in activation of MgtA suggesting that cardiolipin may act as a Mg2+ chaperone for MgtA. We further 2+ 2+ show that MgtA is highly sensitive to free Mg (Mg free) levels in the solution. MgtA is activated 2+ when the Mg free concentration is reduced below 10 mM and is strongly inhibited above 1 mM, 2+ indicating that Mg free acts as product inhibitor. Combined, our findings conclude that MgtA may act as a sensor as well as a transporter of Mg2+. DOI: 10.7554/eLife.11407.001 *For correspondence: j.p.morth@ ncmm.uio.no Introduction Competing interests: The Magnesium is the most abundant divalent cation in biological systems and is an essential require- 2+ authors declare that no ment for all living cells (Reinhart, 1988). -
General Aspects of Metal Ions As Signaling Agents in Health and Disease
biomolecules Review General Aspects of Metal Ions as Signaling Agents in Health and Disease Karolina Krzywoszy ´nska 1,*, Danuta Witkowska 1,* , Jolanta Swi´ ˛atek-Kozłowska 1, Agnieszka Szebesczyk 1 and Henryk Kozłowski 1,2 1 Institute of Health Sciences, University of Opole, 68 Katowicka St., 45-060 Opole, Poland; [email protected] (J.S.-K.);´ [email protected] (A.S.); [email protected] (H.K.) 2 Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie St., 50-383 Wrocław, Poland * Correspondence: [email protected] (K.K.); [email protected] (D.W.); Tel.: +48-77-44-23-549 (K.K); +48-77-44-23-548 (D.W.) Received: 25 August 2020; Accepted: 2 October 2020; Published: 7 October 2020 Abstract: This review focuses on the current knowledge on the involvement of metal ions in signaling processes within the cell, in both physiological and pathological conditions. The first section is devoted to the recent discoveries on magnesium and calcium-dependent signal transduction—the most recognized signaling agents among metals. The following sections then describe signaling pathways where zinc, copper, and iron play a key role. There are many systems in which changes in intra- and extra-cellular zinc and copper concentrations have been linked to important downstream events, especially in nervous signal transduction. Iron signaling is mostly related with its homeostasis. However, it is also involved in a recently discovered type of programmed cell death, ferroptosis. The important differences in metal ion signaling, and its disease-leading alterations, are also discussed. -
Magnesium Deficiency Alters Expression of Genes Critical For
nutrients Article Magnesium Deficiency Alters Expression of Genes Critical for Muscle Magnesium Homeostasis and Physiology in Mice Dominique Bayle 1,Cécile Coudy-Gandilhon 1, Marine Gueugneau 1, Sara Castiglioni 2 , Monica Zocchi 2 , Magdalena Maj-Zurawska 3,4 , Adriana Palinska-Saadi 3,4, André Mazur 1, Daniel Béchet 1,* and Jeanette A. Maier 2,5 1 UNH, Unité de Nutrition Humaine, Université Clermont Auvergne, INRAE, F-63000 Clermont-Ferrand, France; [email protected] (D.B.); [email protected] (C.C.-G.); [email protected] (M.G.); [email protected] (A.M.) 2 Department of Biomedical and Clinical Sciences Luigi Sacco, Università di Milano, 20157 Milano, Italy; [email protected] (S.C.); [email protected] (M.Z.); [email protected] (J.A.M.) 3 Biological and Chemical Research Centre, University of Warsaw, PL-02-089 Warsaw, Poland; [email protected] (M.M.-Z.); [email protected] (A.P.-S.) 4 Faculty of Chemistry, University of Warsaw, PL-02-093 Warsaw, Poland 5 Interdisciplinary Centre for Nanostructured Materials and Interfaces (CIMaINa), Università di Milano, 20133 Milano, Italy * Correspondence: [email protected] Abstract: Chronic Mg2+ deficiency is the underlying cause of a broad range of health dysfunctions. Citation: Bayle, D.; As 25% of body Mg2+ is located in the skeletal muscle, Mg2+ transport and homeostasis systems Coudy-Gandilhon, C.; Gueugneau, (MgTHs) in the muscle are critical for whole-body Mg2+ homeostasis. In the present study, we as- M.; Castiglioni, S.; Zocchi, M.; sessed whether Mg2+ deficiency alters muscle fiber characteristics and major pathways regulating Maj-Zurawska, M.; Palinska-Saadi, muscle physiology. -
TRPM Channels in Human Diseases
cells Review TRPM Channels in Human Diseases 1,2, 1,2, 1,2 3 4,5 Ivanka Jimenez y, Yolanda Prado y, Felipe Marchant , Carolina Otero , Felipe Eltit , Claudio Cabello-Verrugio 1,6,7 , Oscar Cerda 2,8 and Felipe Simon 1,2,7,* 1 Faculty of Life Science, Universidad Andrés Bello, Santiago 8370186, Chile; [email protected] (I.J.); [email protected] (Y.P.); [email protected] (F.M.); [email protected] (C.C.-V.) 2 Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Universidad de Chile, Santiago 8380453, Chile; [email protected] 3 Faculty of Medicine, School of Chemistry and Pharmacy, Universidad Andrés Bello, Santiago 8370186, Chile; [email protected] 4 Vancouver Prostate Centre, Vancouver, BC V6Z 1Y6, Canada; [email protected] 5 Department of Urological Sciences, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada 6 Center for the Development of Nanoscience and Nanotechnology (CEDENNA), Universidad de Santiago de Chile, Santiago 7560484, Chile 7 Millennium Institute on Immunology and Immunotherapy, Santiago 8370146, Chile 8 Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile * Correspondence: [email protected] These authors contributed equally to this work. y Received: 4 November 2020; Accepted: 1 December 2020; Published: 4 December 2020 Abstract: The transient receptor potential melastatin (TRPM) subfamily belongs to the TRP cation channels family. Since the first cloning of TRPM1 in 1989, tremendous progress has been made in identifying novel members of the TRPM subfamily and their functions. The TRPM subfamily is composed of eight members consisting of four six-transmembrane domain subunits, resulting in homomeric or heteromeric channels.