How Do Bacterial Cells Ensure That Metalloproteins Get the Correct Metal?
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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. -
Cobalt Publications Rejected As Not Acceptable for Plants and Invertebrates
Interim Final Eco-SSL Guidance: Cobalt Cobalt Publications Rejected as Not Acceptable for Plants and Invertebrates Published literature that reported soil toxicity to terrestrial invertebrates and plants was identified, retrieved and screened. Published literature was deemed Acceptable if it met all 11 study acceptance criteria (Fig. 3.3 in section 3 “DERIVATION OF PLANT AND SOIL INVERTEBRATE ECO-SSLs” and ATTACHMENT J in Standard Operating Procedure #1: Plant and Soil Invertebrate Literature Search and Acquisition ). Each study was further screened through nine specific study evaluation criteria (Table 3.2 Summary of Nine Study Evaluation Criteria for Plant and Soil Invertebrate Eco-SSLs, also in section 3 and ATTACHMENT A in Standard Operating Procedure #2: Plant and Soil Invertebrate Literature Evaluation and Data Extraction, Eco-SSL Derivation, Quality Assurance Review, and Technical Write-up.) Publications identified as Not Acceptable did not meet one or more of these criteria. All Not Acceptable publications have been assigned one or more keywords categorizing the reasons for rejection ( Table 1. Literature Rejection Categories in Standard Operating Procedure #4: Wildlife TRV Literature Review, Data Extraction and Coding). No Dose Abdel-Sabour, M. F., El Naggr, H. A., and Suliman, S. M. 1994. Use of Inorganic and Organic Compounds as Decontaminants for Cobalt T-60 and Cesium-134 by Clover Plant Grown on INSHAS Sandy Soil. Govt Reports Announcements & Index (GRA&I) 15, 17 p. No Control Adams, S. N. and Honeysett, J. L. 1964. Some Effects of Soil Waterlogging on the Cobalt and Copper Status of Pasture Plants Grown in Pots. Aust.J.Agric.Res. 15, 357-367 OM, pH Adams, S. -
Flavin-Containing Monooxygenases: Mutations, Disease and Drug Response Phillips, IR; Shephard, EA
Flavin-containing monooxygenases: mutations, disease and drug response Phillips, IR; Shephard, EA For additional information about this publication click this link. http://qmro.qmul.ac.uk/jspui/handle/123456789/1015 Information about this research object was correct at the time of download; we occasionally make corrections to records, please therefore check the published record when citing. For more information contact [email protected] Flavin-containing monooxygenases: mutations, disease and drug response Ian R. Phillips1 and Elizabeth A. Shephard2 1School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK 2Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK Corresponding author: Shephard, E.A. ([email protected]). and, thus, contribute to drug development. This review Flavin-containing monooxygenases (FMOs) metabolize considers the role of FMOs and their genetic variants in numerous foreign chemicals, including drugs, pesticides disease and drug response. and dietary components and, thus, mediate interactions between humans and their chemical environment. We Mechanism and structure describe the mechanism of action of FMOs and insights For catalysis FMOs require flavin adenine dinucleotide gained from the structure of yeast FMO. We then (FAD) as a prosthetic group, NADPH as a cofactor and concentrate on the three FMOs (FMOs 1, 2 and 3) that are molecular oxygen as a cosubstrate [5,6]. In contrast to most important for metabolism of foreign chemicals in CYPs FMOs accept reducing equivalents directly from humans, focusing on the role of the FMOs and their genetic NADPH and, thus, do not require accessory proteins. -
Undocumented Water Column Sink for Cadmium in Open Ocean Oxygen-Deficient Zones
Undocumented water column sink for cadmium in open ocean oxygen-deficient zones David J. Janssena, Tim M. Conwayb, Seth G. Johnb, James R. Christianc, Dennis I. Kramera, Tom F. Pedersena, and Jay T. Cullena,1 aSchool of Earth and Ocean Sciences, University of Victoria, Victoria, BC, Canada V8W 2Y2; bDepartment of Earth and Ocean Sciences, University of South Carolina, Columbia, SC 29208; and cFisheries and Oceans Canada, Victoria, BC, Canada V8W 3V6 Edited by Edward A. Boyle, Massachusetts Institute of Technology, Cambridge, MA, and approved April 4, 2014 (received for review February 6, 2014) 3− Cadmium (Cd) is a micronutrient and a tracer of biological this sink induces local changes in Cd:PO4 must be understood productivity and circulation in the ocean. The correlation between to correctly interpret paleoceanographic records. dissolved Cd and the major algal nutrients in seawater has led to the use of Cd preserved in microfossils to constrain past ocean nutrient Results and Discussion distributions. However, linking Cd to marine biological processes Cadmium and other trace metals such as copper (Cu) and zinc requires constraints on marine sources and sinks of Cd. Here, we (Zn) are known to form solid sulfide precipitates in the ocean show a decoupling between Cd and major nutrients within oxygen- under conditions of anoxia where sulfide is present. For example, deficient zones (ODZs) in both the Northeast Pacific and North precipitation of Cd sulfide (CdS) (13) leading to dissolved Cd Atlantic Oceans, which we attribute to Cd sulfide (CdS) precipitation depletion is observed at oxic–anoxic interfaces in stratified basins in euxinic microenvironments around sinking biological particles. -
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 -
Citric Acid Cycle
CHEM464 / Medh, J.D. The Citric Acid Cycle Citric Acid Cycle: Central Role in Catabolism • Stage II of catabolism involves the conversion of carbohydrates, fats and aminoacids into acetylCoA • In aerobic organisms, citric acid cycle makes up the final stage of catabolism when acetyl CoA is completely oxidized to CO2. • Also called Krebs cycle or tricarboxylic acid (TCA) cycle. • It is a central integrative pathway that harvests chemical energy from biological fuel in the form of electrons in NADH and FADH2 (oxidation is loss of electrons). • NADH and FADH2 transfer electrons via the electron transport chain to final electron acceptor, O2, to form H2O. Entry of Pyruvate into the TCA cycle • Pyruvate is formed in the cytosol as a product of glycolysis • For entry into the TCA cycle, it has to be converted to Acetyl CoA. • Oxidation of pyruvate to acetyl CoA is catalyzed by the pyruvate dehydrogenase complex in the mitochondria • Mitochondria consist of inner and outer membranes and the matrix • Enzymes of the PDH complex and the TCA cycle (except succinate dehydrogenase) are in the matrix • Pyruvate translocase is an antiporter present in the inner mitochondrial membrane that allows entry of a molecule of pyruvate in exchange for a hydroxide ion. 1 CHEM464 / Medh, J.D. The Citric Acid Cycle The Pyruvate Dehydrogenase (PDH) complex • The PDH complex consists of 3 enzymes. They are: pyruvate dehydrogenase (E1), Dihydrolipoyl transacetylase (E2) and dihydrolipoyl dehydrogenase (E3). • It has 5 cofactors: CoASH, NAD+, lipoamide, TPP and FAD. CoASH and NAD+ participate stoichiometrically in the reaction, the other 3 cofactors have catalytic functions. -
Evaluation of the Trace Metal Supplements for a Synthetic Low Lactose Diet
Arch Dis Child: first published as 10.1136/adc.58.6.433 on 1 June 1983. Downloaded from Archives of Disease in Childhood, 1983, 58, 433-437 Evaluation of the trace metal supplements for a synthetic low lactose diet P J AGGETT, J MORE, J M THORN, H T DELVES, M CORNFIELD, AND B E CLAYTON Department of Chemical Pathology, Institute of Child Health, London SUMMARY A trace element supplement used with a synthetic low lactose milk (Galactomins 17 and 18) has been evaluated by means of metabolic balance studies in 4 infants with dissacharide intolerances. The supplement was considered satisfactory for iron and manganese but increases in its zinc and copper content are probably necessary to ensure adequate retentions ofthese metals. Diets used in the management of infants with synthetic low lactose milks (Galactomins 17 and 18, inborn errors of metabolism or dietary intolerances Cow and Gate Ltd) has been assessed. There may have an inadequate essential trace element are three similar Galactomin products which are content."-3 This deficiency may be quantitative in derived from demineralised casein and which are as much as these micronutrients are lost during prepared according to a formula elaborated in this manufacture of the diet, or it may be a qualitative department.5 They are used in the management of defect resulting from postulated interactions between dietary lactose intolerances (Galactomins 17, 18, and these elements and other inorganic and organic 19) and of inborn errors of galactose metabolism dietary constituents which reduce intestinal -
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. -
The Metallome As a Link Between the ``Omes'' in Autism Spectrum
fnmol-14-695873 June 29, 2021 Time: 18:33 # 1 MINI REVIEW published: 05 July 2021 doi: 10.3389/fnmol.2021.695873 The Metallome as a Link Between the “Omes” in Autism Spectrum Disorders Janelle E. Stanton1,2, Sigita Malijauskaite2,3, Kieran McGourty2,3,4 and Andreas M. Grabrucker1,2,4* 1 Department of Biological Sciences, University of Limerick, Limerick, Ireland, 2 Bernal Institute, University of Limerick, Limerick, Ireland, 3 Department of Chemical Sciences, University of Limerick, Limerick, Ireland, 4 Health Research Institute, University of Limerick, Limerick, Ireland Metal dyshomeostasis plays a significant role in various neurological diseases such as Alzheimer’s disease, Parkinson’s disease, Autism Spectrum Disorders (ASD), and many more. Like studies investigating the proteome, transcriptome, epigenome, microbiome, etc., for years, metallomics studies have focused on data from their domain, i.e., trace metal composition, only. Still, few have considered the links between other “omes,” which may together result in an individual’s specific pathologies. In particular, ASD have been reported to have multitudes of possible causal effects. Metallomics Edited by: data focusing on metal deficiencies and dyshomeostasis can be linked to functions David Blum, INSERM U1172 Centre de Recherche of metalloenzymes, metal transporters, and transcription factors, thus affecting the Jean Pierre Aubert, France proteome and transcriptome. Furthermore, recent studies in ASD have emphasized Reviewed by: the gut-brain axis, with alterations in the microbiome being linked to changes in the Arnaud B. Nicot, metabolome and inflammatory processes. However, the microbiome and other “omes” INSERM U1064 Centre de Recherche en Transplantation et Immunologie, are heavily influenced by the metallome. -
Cofactor Strap Regulates Oxidative Phosphorylation and Mitochondrial P53 Activity Through ATP Synthase
Cell Death and Differentiation (2015) 22, 156–163 & 2015 Macmillan Publishers Limited All rights reserved 1350-9047/15 www.nature.com/cdd Cofactor Strap regulates oxidative phosphorylation and mitochondrial p53 activity through ATP synthase S Maniam1,4, AS Coutts1,4, MR Stratford2, J McGouran3, B Kessler3 and NB La Thangue*,1 Metabolic reprogramming is a hallmark of cancer cells. Strap (stress-responsive activator of p300) is a novel TPR motif OB-fold protein that contributes to p53 transcriptional activation. We show here that, in addition to its established transcriptional role, Strap is localised at mitochondria where one of its key interaction partners is ATP synthase. Significantly, the interaction between Strap and ATP synthase downregulates mitochondrial ATP production. Under glucose-limiting conditions, cancer cells are sensitised by mitochondrial Strap to apoptosis, which is rescued by supplementing cells with an extracellular source of ATP. Furthermore, Strap augments the apoptotic effects of mitochondrial p53. These findings define Strap as a dual regulator of cellular reprogramming: first as a nuclear transcription cofactor and second in the direct regulation of mitochondrial respiration. Cell Death and Differentiation (2015) 22, 156–163; doi:10.1038/cdd.2014.135; published online 29 August 2014 An established characteristic of tumour cells is their under- model whereby Strap unfolds to become more accessible lying metabolic changes.1 Early observations that during the DNA-damage response.12 tumour cells had persistently high -
Novel Derivatives of Nicotinamide Adenine Dinucleotide (NAD) and Their Biological Evaluation Against NAD- Consuming Enzymes
Novel derivatives of nicotinamide adenine dinucleotide (NAD) and their biological evaluation against NAD- Consuming Enzymes Giulia Pergolizzi University of East Anglia School of Pharmacy Thesis submitted for the degree of Doctor of Philosophy July, 2012 © This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that use of any information derived there from must be in accordance with current UK Copyright Law. In addition, any quotation or extract must include full attribution. ABSTRACT Nicotinamide adenine dinucleotide (β-NAD+) is a primary metabolite involved in fundamental biological processes. Its molecular structure with characteristic functional groups, such as the quaternary nitrogen of the nicotinamide ring, and the two high- energy pyrophosphate and nicotinamide N-glycosidic bonds, allows it to undergo different reactions depending on the reactive moiety. Well known as a redox substrate owing to the redox properties of the nicotinamide ring, β-NAD+ is also fundamental as a substrate of NAD+-consuming enzymes that cleave either high-energy bonds to catalyse their reactions. In this study, a panel of novel adenine-modified NAD+ derivatives was synthesized and biologically evaluated against different NAD+-consuming enzymes. The synthesis of NAD+ derivatives, modified in position 2, 6 or 8 of the adenine ring with aryl/heteroaryl groups, was accomplished by Suzuki-Miyaura cross-couplings. Their biological activity as inhibitors and/or non-natural substrates was assessed against a selected range of NAD+-consuming enzymes. The fluorescence of 8-aryl/heteroaryl NAD+ derivatives allowed their use as biochemical probes for the development of continuous biochemical assays to monitor NAD+-consuming enzyme activities.