DOCSLIB.ORG

Identification and Characterization of Zn (II)-Responsive Genes And

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Identification and Characterization of Zn (II)-Responsive Genes And MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of J. Allen Easton Candidate for the Degree: Doctor of Philosophy ______________________________________________ Director (Dr. Michael W. Crowder) ______________________________________________ Reader (Dr. John W. Hawes) ______________________________________________ Reader (Dr. Chris A. Makaroff) ______________________________________________ Reader (Dr. Gary A. Lorigan) ______________________________________________ Graduate School Representative (Dr. Gary Janssen) ABSTRACT IDENTIFICATION AND CHARACTERIZATION OF ZN(II)- RESPONSIVE GENES AND PROTEINS IN E. COLI By J. Allen Easton Transition metal ion homeostasis is absolutely crucial for the survival of all organisms. Zinc (Zn(II)) is perhaps one of the most important, yet least studied transition metals. Previous studies indicate that intracellular Zn(II) levels in E. coli are in the low millimolar range, yet there is less than one “free” Zn(II) ion per cell. All of the intracellular Zn(II) must then be bound and Zn(II) must be delivered from transporters and inserted into Zn(II)-metalloproteins. The cytoplasmic transport of transition metals, such as copper, iron, nickel, manganese, and arsenic, is accomplished by a group of proteins called metallochaperones. No such metallochaperone has been identified for Zn(II). In an effort to identify the Zn(II) metallochaperones in E. coli, proteomic and genomic studies were conducted. Proteomic studies were used to probe for the time-dependent response of E. coli to stress by Zn(II) excess. Genomic studies were used to probe for the transcriptional response of E. coli to stress by Zn(II) excess and deficiency. Several Zn(II)-metallochaperone candidates were identified, and these proteins were cloned, over-expressed, purified, and characterized. Trigger factor was found to be down-regulated at the proteomic level in response to excess Zn(II). Over-expression and characterization of trigger factor show that it tightly binds 0.5 Zn(II)/monomer; however, spectroscopic studies showed that Zn(II) binding is most likely adventitious. GatY/GatZ Zn(II)-responsive proteins that are part of the galactitol catabolic pathway. GatY was over-expressed and shown to bind 2 Zn(II) equivalents per enzyme. GatZ, reported to be necessary for GatY function, was tested for Zn(II)- binding and shown to not bind Zn(II). A transcript found to be highly up-regulated was ykgM. We cloned and over-expressed YkgM to elucidate why it is highly responsive to Zn(II). We determined that YkgM does not bind Zn(II), and may substitute for Zn(II)-containing ribosomal protein L31 in Zn(II)-limiting conditions. ZnuA was cloned, over-expressed, purified, and characterized. We found that ZnuA tightly binds 2 equivalents of Zn(II) per monomer. Our proteomic and genomic data suggest that there are no soluble, cytoplasmic Zn(II) metallochaperones in E. coli. Based on this conclusion, a novel model is hypothesized that explains Zn(II) transport in E. coli cytoplasm. Identification and Characterization of Zn(II)-responsive Genes and Proteins in E. coli A DISSERTATION Submitted to the Faculty of Miami University in partial Fulfillment of the requirements For the degree of Doctor of Philosophy Department of Chemistry and Biochemistry By J. Allen Easton Miami University Oxford, OH 2007 Dissertation Director: Dr. Michael W. Crowder TABLE OF CONTENTS Chapter 1: Introduction 1.1 The importance of Metal Ions 1 1.2 The importance of Zinc 3 1.3 Zinc homeostasis in eukaryotes 3 1.4 Zinc homeostasis in prokaryotes 6 1.5 Discovery of metallochaperones 9 1.6 Proteomic and genomic techniques 11 1.6.1 Proteomics 11 1.6.2 Genomics 18 1.7 Chapters of the dissertation 19 1.8 References 22 Chapter 2: Time-dependent Translational Response of E. coli to Excess Zn(II) 28 2.1 Summary 29 2.2 Introduction 30 2.3 Materials and methods 30 2.3.1 Growth medium and conditions 30 2.3.2 Acetone precipitation and sample cleanup for 2D gels 31 2.3.3 IEF and second dimension SDS-PAGE 31 2.3.4 Gel Imaging 31 2.3.5 In-gel trypsin digestion and MALDI-TOF analysis 31 2.3.6 Database analysis 32 2.4 Results and discussion 32 2.5 Acknowledgements 38 2.6 References 39 Chapter 3: Time-dependent response of Zn(II)-induced genes to TPEN 43 3.1 Summary 44 3.2 Introduction 45 ii 3.3 Materials and methods 46 3.3.1 Growth medium and conditions 46 3.3.2 RNA isolation and quality assessment 47 3.3.3 Real-time PCR primer design 47 3.3.4 Real-time PCR 47 3.3.5 Standard curves and data analysis 47 3.3.6 Iron/zinc rescue experiments 47 3.3.7 Total protein assay 49 3.3.8 Microarray sample preparation 49 3.3.9 Microarray data analysis 49 3.4 Results 50 3.4.1 TPEN stress 50 3.4.2 ZnSO4 stress 51 3.4.3 Total protein assay 51 3.4.4 Iron/zinc rescue experiments 52 3.4.5 cDNA microarrays 52 3.5 Discussion 59 3.6 Acknowledgements 60 3.7 References 61 Chapter 4: Non-specific Zn(II) binding to E. coli Trigger Factor 77 4.1 Summary 78 4.2 Introduction 79 4.3 Materials and methods 80 4.3.1 Cloning and over-expression of E. coli trigger factor 80 4.3.2 Metal analysis 81 4.3.3 Fluorescence spectra 81 4.3.4 Gel filtration chromatography 81 4.3.5 UV-Visible spectrum of Co(II)-substituted trigger factor 81 4.3.6 EPR spectroscopy of Co(II)-substituted trigger factor 82 4.3.7 NMR spectroscopy of Co(II)-substituted trigger factor 82 iii 4.3.8 Prolyl isomerase assay 82 4.3.9 Refolding of GAPDH 82 4.3.10 Refolding of tryptophanase 83 4.4. Results 83 4.5 Discussion 85 4.6 Acknowledgements 89 4.7 References 90 Chapter 5: Structure and metal binding properties of ZnuA, a periplasmic zinc transport protein from Escherichia coli 93 5.1 Summary 95 5.2 Introduction 96 5.3 Materials and methods 97 5.3.1 Cloning, expression, and purification of Eco-ZnuA 97 5.3.2 Eco-ZnuA Crystallization and structure determination 98 5.3.3 Model refinement 99 5.3.4 Sample preparation for spectroscopic studies 100 5.3.5 Circular dichroism (CD) spectroscopy 101 5.3.6 Spectroscopic analysis of Zn2+ binding to Eco-ZnuA 101 5.3.7 Spectroscopic studies of Co2+-substituted Eco-ZnuA 102 5.3.8 EXAFS studies of Zn2+-and Zn2+Co2+-substituted Eco-ZnuA 102 5.3.9 Fluorescence emission with ANS 103 5.4 Results 104 5.4.1 Overall structure of Eco-ZnuA 104 5.4.2 The primary metal-binding site 106 5.4.3 The second metal-binding site 110 5.4.4 Circular dichroism (CD spectroscopy 110 5.4.5 Zn2+ binding affinity of Eco-ZnuA 112 5.4.6 Spectroscopic studies of CoZnuA 115 5.4.7 EXAFS studies of Zn- and ZnCo-Substituted Eco-ZnuA 119 5.4.8 Metal specificity of ZnuA monitored by ANS fluorescence 120 iv 5.5 Discussion 123 5.5.1 Metal specificity 123 5.5.2 Metal stoichiometry 124 5.5.3 Mechanistic implications 124 5.6. Acknowledgements 126 5.7 References 127 5.8 Supplementary material 135 Chapter 6: Characterization of Zn(II)-responsive proteins in E. coli 143 6.1 Abstract 143 6.2 Introduction 144 6.2.1 GatY and GatZ 144 6.2.2 YkgM 145 6.3 Materials and methods 146 6.3.1 Cloning, over-expression, and purification of MBP-GatY and MBP-GatZ 146 6.3.2 Metal analyses 147 6.3.3 Aldolase assays 147 6.3.4 Cloning, over-expression, and purification of YkgM 147 6.3.5 Metal analyses 148 6.4 Results 148 6.4.1 GatY and GatZ 148 6.4.2 YkgM 149 6.5 Discussion 150 6.5.1 GatY/Z 150 6.5.2 YkgM 151 6.6 References 151 Chapter 7: Conclusion 159 7.1 Perspectives on metal ion homeostasis 159 7.2 Approaches taken 160 v 7.2.1 Proteomics 161 7.2.2 Genomics 162 7.2.3 Characterization 162 7.3 Future directions 164 7.3.1 Examination of ribosomal proteins 164 7.4 References 166 vi List of Tables: Table 2.1 Proteins with differential expression after Zn(II) stress for 30 minutes. 40 Table 2.2 Proteins with differential expression after Zn(II) stress for 4 hours. 41 Table 3.1 Primers used for real-time PCR. 47 Table 3.2 Genes up-regulated by TPEN. 66 Table 3.3 Genes down-regulated by TPEN. 67 Table S1 Complete list of up-regulated genes in response to 30 min of TPEN stress. 68 Table S2 Down-regulated genes in response to 30 min of TPEN stress. 72 Table 5.1 Crystallographic Statistics. 132 Table 5.2 Thermodynamic parameters for apoZnuA and ZnZnuA folding. 133 Table 5.3 EXAFS curve fitting results for 1-ZnZnuA and CoZnZnuA 134 Table S1 Important interatomic distances and angles. 136 Table S2 Comparison of metal – ligand distances in various ZnZnuA structures. 137 vii List of Figures: Figure 1.1 A dose-response diagram for an essential element. 2 Figure 1.2 Zinc homeostasis in eukaryotes. 4 Figure 1.3 Zinc transport and homeostasis in prokaryotes. 8 Figure 1.4 Two-dimensional SDS-PAGE gel. 12 Figure 1.5 Spots of varying intensity. 13 Figure 1.6 Peptide mass spectrum from MALDI-TOF mass spectrometer. 15 Figure 1.7 MASCOT database search. 16 Figure 1.8 The database search results. 17 Figure 3.1 Time-dependent real-time PCR of Zur-regulated genes.
Load more

Recommended publications
  • Electronic Supplementary Material (ESI) for Analyst. This Journal Is © the Royal Society of Chemistry 2017
    Electronic Supplementary Material (ESI) for Analyst. This journal is © The Royal Society of Chemistry 2017 Supplemental Table 2. Proteins Increased in Either Blood or Horizon media Table 2A. Proteins Increased in Spores Produced on Horizon Soil Over Spores Produced on Blood Medium quasi.fdr Protein Protein Class/Name KEGG Pathway Names or Function (if ID Pathways found in KEGG) Amino Acid Metabolism bat00250, bat00280, Alanine, aspartate and glutamate metabolism, bat00410, Valine, leucine and isoleucine degradation, bat00640, beta-Alanine metabolism to acetyl CoA, 4.50E-07 BAS0310 4-aminobutyrate aminotransferase bat00650 Propanoate metabolism, Butanoate metabolism bat00270, bat00330, Cysteine and methionine metabolism, Arginine bat00410, and proline metabolism, beta-Alanine 3.84E-10 BAS5060 spermidine synthase bat00480 metabolism, Glutathione metabolism bat00270, bat00330, Cysteine and methionine metabolism, Arginine bat00410, and proline metabolism, beta-Alanine 2.30E-09 BAS5219 spermidine synthase bat00480 metabolism, Glutathione metabolism bat00250, Alanine, aspartate and glutamate metabolism, 6.94E-07 BAS0561 alanine dehydrogenase bat00430 Taurine and hypotaurine metabolism bat00250, Alanine, aspartate and glutamate metabolism, 5.23E-07 BAS4521 alanine dehydrogenase bat00430 Taurine and hypotaurine metabolism 0.005627 BAS5218 agmatinase, putative bat00330 Arginine and proline metabolism 2,3,4,5-tetrahydropyridine-2- carboxylate N-succinyltransferase, 1.40E-10 BAS3891 putative bat00300 Lysine biosynthesis bat00010, bat00020, Glycolysis
    [Show full text]
  • Bacterial-Type Plant Ferroxidases Tune Local Phosphate Sensing in Root Development
    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.19.436157; this version posted March 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Bacterial-type plant ferroxidases tune local phosphate sensing in root development Christin Naumann1, Marcus Heisters1,2, Wolfgang Brandt3, Philipp Janitza4, Carolin Alfs1, Nancy Tang1, Alicia Toto Nienguesso1,5, Joerg Ziegler1, Richard Imre6,7, Karl Mechtler6,7, Yasin Dagdas6, Wolfgang Hoehenwarter8, Gary Sawers9, Marcel Quint4, and Steffen Abel1,10,11 1Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany 2VEROVACCiNES GmbH, Halle (Saale), Germany 3Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany 4Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle- Wittenberg, Halle (Saale), Germany 5Department of Anatomy and Cell Biology, University Hospital Halle, Halle (Saale), Germany 6Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria 7Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria 9Institute of Biology/Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany 8Proteome Analytics, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany 10Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany 11Department of Plant Sciences, University of California, Davis, CA, USA 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.19.436157; this version posted March 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Fluctuating bioavailability of inorganic phosphate (Pi), often caused by complex Pi-metal interactions, guide root tip growth and root system architecture for maximizing the foraged soil volume.
    [Show full text]
  • Dioxygen Activation in Soluble Methane Monooxygenase
    Dioxygen Activation in Soluble Methane Monooxygenase The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Tinberg, Christine E., and Stephen J. Lippard. “Dioxygen Activation in Soluble Methane Monooxygenase.” Accounts of Chemical Research 44.4 (2011): 280–288. As Published http://dx.doi.org/10.1021/ar1001473 Publisher American Chemical Society Version Author's final manuscript Citable link http://hdl.handle.net/1721.1/69856 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. Dioxygen Activation in Soluble Methane Monooxygenase† Christine E. Tinberg and Stephen J. Lippard* Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 RECEIVED DATE (to be automatically inserted after your manuscript is accepted if required according to the journal that you are submitting your paper to) * To whom correspondence should be addressed. E-mail: [email protected]. Telephone: (617) 253-1892. Fax: (617) 258-8150. †Work from our laboratory discussed in this Account was funded by grant GM032134 from the National Institute of General Medical Sciences. 1 CONSPECTUS The controlled oxidation of methane to methanol is a chemical transformation of great industrial importance that is underutilized because of inefficient and costly synthetic procedures. Methane monooxygenase enzymes (MMOs) from methanotrophic bacteria achieve this chemistry efficiently under ambient conditions. In this Account we discuss the first step in the oxidation of methane at the carboxylate-bridged diiron active site of the soluble MMO (sMMO), namely, the reductive activation of atmospheric O2.
    [Show full text]
  • Geometric and Electronic Structure Differences Between the Type 3 Copper Sites of the Multicopper Oxidases and Hemocyanin/Tyrosinase
    Geometric and electronic structure differences between the type 3 copper sites of the multicopper oxidases and hemocyanin/tyrosinase Jungjoo Yoon, Satoshi Fujii1, and Edward I. Solomon2 Department of Chemistry, Stanford University, Stanford, CA 94305-5080 Contributed by Edward I. Solomon, February 25, 2009 (sent for review January 31, 2009) The coupled binuclear ‘‘type 3’’ Cu sites are found in hemocyanin (Hc), tyrosinase (Tyr), and the multicopper oxidases (MCOs), such as laccase (Lc), and play vital roles in O2 respiration. Although all type 3 Cu sites share the same ground state features, those of Hc/Tyr have very different ligand-binding properties relative to those of the MCOs. In particular, the type 3 Cu site in the MCOs (LcT3)isa part of the trinuclear Cu cluster, and if the third (i.e., type 2) Cu is T3 removed, the Lc site does not react with O2. Density functional ؊1 theory calculations indicate that O2 binding in Hc is Ϸ9 kcal mol more favorable than for LcT3. The difference is mostly found in the Ϸ ؊1 total energy difference of the deoxy states ( 7 kcal mol ), where Fig. 1. O2 binding in the type 3 Cu sites of Hc/Tyr and MCOs. the stabilization of deoxy LcT3 derives from its long equilibrium Cu–Cu distance of Ϸ5.5–6.5 Å, relative to Ϸ4.2 Å in deoxy Hc/Tyr. The O2 binding in Hc is driven by the electrostatic destabilization Cu–Cu distance of Ϸ3.6 Å (Fig. 1A) (7, 8, 10). The side-on 2Ϫ ␲ of the deoxy Hc site, in which the two Cu(I) centers are kept close geometry promotes a large overlap between the O2 * and the together by the protein for facile 2-electron reduction of O2.
    [Show full text]
  • Supplementary Table S1. Table 1. List of Bacterial Strains Used in This Study Suppl
    Supplementary Material Supplementary Tables: Supplementary Table S1. Table 1. List of bacterial strains used in this study Supplementary Table S2. List of plasmids used in this study Supplementary Table 3. List of primers used for mutagenesis of P. intermedia Supplementary Table 4. List of primers used for qRT-PCR analysis in P. intermedia Supplementary Table 5. List of the most highly upregulated genes in P. intermedia OxyR mutant Supplementary Table 6. List of the most highly downregulated genes in P. intermedia OxyR mutant Supplementary Table 7. List of the most highly upregulated genes in P. intermedia grown in iron-deplete conditions Supplementary Table 8. List of the most highly downregulated genes in P. intermedia grown in iron-deplete conditions Supplementary Figures: Supplementary Figure 1. Comparison of the genomic loci encoding OxyR in Prevotella species. Supplementary Figure 2. Distribution of SOD and glutathione peroxidase genes within the genus Prevotella. Supplementary Table S1. Bacterial strains Strain Description Source or reference P. intermedia V3147 Wild type OMA14 isolated from the (1) periodontal pocket of a Japanese patient with periodontitis V3203 OMA14 PIOMA14_I_0073(oxyR)::ermF This study E. coli XL-1 Blue Host strain for cloning Stratagene S17-1 RP-4-2-Tc::Mu aph::Tn7 recA, Smr (2) 1 Supplementary Table S2. Plasmids Plasmid Relevant property Source or reference pUC118 Takara pBSSK pNDR-Dual Clonetech pTCB Apr Tcr, E. coli-Bacteroides shuttle vector (3) plasmid pKD954 Contains the Porpyromonas gulae catalase (4)
    [Show full text]
  • 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
    [Show full text]
  • Supporting Information
    Supporting Information Lee et al. 10.1073/pnas.0903619106 SI Materials and Methods The tobramycin sensitivities for strains expressing the rmtD Plasmids. Plasmid p(amgRSϩ) was constructed by inserting a 2.4 ribosomal methylase gene were determined by a 2-fold broth kb PCR fragment carrying the region from 206 bp upstream of dilution test. Inocula were prepared by growing cells at 37 °C for the amgR start codon to 60 bp downstream of the amgS 16 h in LB lacking NaCl. Cells were diluted to approximately ϫ 6 termination codon into a derivative of pUCP19 (1). Plasmid 3.3 10 cells/ml based on OD600. After a 90 min incubation at 37 °C, 10 ␮l aliquots were distributed to wells (in 96-well format) pRmtD was constructed by inserting the 2.3 kb HindIII-XbaI ␮ fragment carrying rmtD from pPA95B1 (2) into a derivative of containing 125 l LB buffered with 0.1 M MOPS at pH 7.6 pUCP19 (1). Plasmids used for complementation studies (Table containing different concentrations of tobramycin. MICs were 1) were constructed in pUCP19 derivatives by inserting PCR determined after incubation for 24 h at 37 °C. fragments corresponding to the genes tested. Plasmid pIbsC was Transcriptional Profiling. MPAO1 and ⌬amgRS transcriptomes constructed by inserting a 1.8 kb PCR fragment carrying the were compared under tobramycin-treated and -untreated con- arabinose-inducible ibsC construct (P -ibsC) from pAZ3-ibsC bad ditions. Samples were prepared in duplicate from independent (3) into a derivative of pUCP19 (4), resulting in pIbsC. The cultures grown in 15 ml LB lacking NaCl.
    [Show full text]
  • Downloaded Using the Database on Presence of This Metal for 24 H
    fmicb-11-01834 August 10, 2020 Time: 12:25 # 1 ORIGINAL RESEARCH published: 10 August 2020 doi: 10.3389/fmicb.2020.01834 Metabolic Adaptation of Paracoccidioides brasiliensis in Response to in vitro Copper Deprivation Guilherme Petito1,2†, Juliana Santana de Curcio1†, Maristela Pereira1, Alexandre Melo Bailão1, Juliano Domiraci Paccez1, Gabriel Brum Tristão1, Camila Oliveira Barbosa de Morais1, Marcelo Valle de Souza3, Agenor de Castro Moreira Santos Junior3, Wagner Fontes3, Carlos André Ornelas Ricart3 and Célia Maria de Almeida Soares1* Edited by: 1 Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil, Carlos Pelleschi Taborda, 2 Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Federal de Goiás, Goiânia, Brazil, University of São Paulo, Brazil 3 Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, Brazil Reviewed by: Rosana Puccia, Federal University of São Paulo, Brazil Copper is an essential micronutrient for the performance of important biochemical Sandro Rogerio Almeida, processes such as respiration detoxification, and uptake of metals like iron. Studies University of São Paulo, Brazil Elizabeth R. Ballou, have shown that copper deprivation is a strategy used by the host against pathogenic University of Birmingham, fungi such as Cryptoccocus neoformans and Candida albicans during growth and United Kingdom development of infections in the lungs and kidneys. Although there are some *Correspondence: studies, little is known about the impact of copper deprivation in members of the Célia Maria de Almeida Soares [email protected] Paracoccidioides genus. Therefore, using isobaric tag labeling (iTRAQ)-Based proteomic †These authors have contributed approach and LC-MS/MS, we analyzed the impact of in vitro copper deprivation in equally to this work the metabolism of Paracoccidioides brasiliensis.
    [Show full text]
  • Generate Metabolic Map Poster
    Authors: Pallavi Subhraveti Anamika Kothari Quang Ong Ron Caspi An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Peter D Karp Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Csac1394711Cyc: Candidatus Saccharibacteria bacterium RAAC3_TM7_1 Cellular Overview Connections between pathways are omitted for legibility. Tim Holland TM7C00001G0420 TM7C00001G0109 TM7C00001G0953 TM7C00001G0666 TM7C00001G0203 TM7C00001G0886 TM7C00001G0113 TM7C00001G0247 TM7C00001G0735 TM7C00001G0001 TM7C00001G0509 TM7C00001G0264 TM7C00001G0176 TM7C00001G0342 TM7C00001G0055 TM7C00001G0120 TM7C00001G0642 TM7C00001G0837 TM7C00001G0101 TM7C00001G0559 TM7C00001G0810 TM7C00001G0656 TM7C00001G0180 TM7C00001G0742 TM7C00001G0128 TM7C00001G0831 TM7C00001G0517 TM7C00001G0238 TM7C00001G0079 TM7C00001G0111 TM7C00001G0961 TM7C00001G0743 TM7C00001G0893 TM7C00001G0630 TM7C00001G0360 TM7C00001G0616 TM7C00001G0162 TM7C00001G0006 TM7C00001G0365 TM7C00001G0596 TM7C00001G0141 TM7C00001G0689 TM7C00001G0273 TM7C00001G0126 TM7C00001G0717 TM7C00001G0110 TM7C00001G0278 TM7C00001G0734 TM7C00001G0444 TM7C00001G0019 TM7C00001G0381 TM7C00001G0874 TM7C00001G0318 TM7C00001G0451 TM7C00001G0306 TM7C00001G0928 TM7C00001G0622 TM7C00001G0150 TM7C00001G0439 TM7C00001G0233 TM7C00001G0462 TM7C00001G0421 TM7C00001G0220 TM7C00001G0276 TM7C00001G0054 TM7C00001G0419 TM7C00001G0252 TM7C00001G0592 TM7C00001G0628 TM7C00001G0200 TM7C00001G0709 TM7C00001G0025 TM7C00001G0846 TM7C00001G0163 TM7C00001G0142 TM7C00001G0895 TM7C00001G0930 Detoxification Carbohydrate Biosynthesis DNA combined with a 2'- di-trans,octa-cis a 2'- Amino Acid Degradation an L-methionyl- TM7C00001G0190 superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E.
    [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]
  • Metligdb: a Web-Based Database for the Identification of Chemical Groups
    computer programs Journal of Applied MetLigDB: a web-based database for the Crystallography identification of chemical groups to design ISSN 0021-8898 metalloprotein inhibitors Received 12 April 2011 Accepted 10 June 2011 Hwanho Choi,‡ Hongsuk Kang‡ and Hwangseo Park* Department of Bioscience and Biotechnology, Sejong University, 98 Kunja-dong, Kwangjin-ku, Seoul 143-747, Korea. Correspondence e-mail: [email protected] MetLigDB (http://silver.sejong.ac.kr/MetLigDB) is a publicly accessible web- based database through which the interactions between a variety of chelating groups and various central metal ions in the active site of metalloproteins can be explored in detail. Additional information can also be retrieved, including protein and inhibitor names, the amino acid residues coordinated to the central metal ion, and the binding affinity of the inhibitor for the target metalloprotein. Although many metalloproteins have been considered promising targets for drug discovery, it is difficult to discover new inhibitors because of the difficulty in designing a suitable chelating moiety to impair the catalytic activity of the central metal ion. Because both common and specific chelating groups can be identified for varying metal ions and the associated coordination environments, # 2011 International Union of Crystallography MetLigDB is expected to give users insight into designing new inhibitors of Printed in Singapore – all rights reserved metalloproteins for drug discovery. 1. Introduction 2008), the coordination geometry around the metal ion (Castagnetto The importance of metal ions in biological systems is increasingly et al., 2002; Andreini, Bertini, Cavallaro, Holliday & Thornton, 2009), drawing attention, as indicated by the recent emergence of terms such catalytic mechanisms (Andreini, Bertini, Cavallaro, Najmanovich & as metallome and metallomics (Shi & Chance, 2008).
    [Show full text]
  • The Life of a Professor Email Print
    Log In ACS ACS Publications C&EN CAS About Subscribe Advertise Contact Join ACS Serving The Chemical, Life Sciences & Laboratory Worlds Search Adv anced Search Home Magazine News Departments Collections Blogs Multimedia Jobs Home > Volume 92 Issue 11 > The Lif e Of A Prof essor Volume 92 Issue 11 | pp. 14-18 Issue Date: March 17, 2014 0 0 MOST POPULAR COVER STORIES: TRAILBLAZER AND MENTOR Viewed Commented Shared The Life Of A Professor Email Print Spider Silk Poised For Commercial Department: Science & Technology, ACS News | Collection: Life Sciences Entry News Channels: JACS In C&EN Keywords: Priestley Medal, Stephen Lippard Controversy Clouds E-Cigarettes Reports Make Progress In Transforming C–H Bonds Into Druglike Motifs I am honored to receive the 2014 Priestley Medal. The award is a tribute to the talented Cover Stories students, both graduate and undergraduate, as well as postdoctoral associates who Global Top 50 have trained with me over nearly 50 years. I am proud of these individuals, for their Trailblazer And Mentor Milk Proteins Protect Fabrics From courage in agreeing to venture onto new snowfields to place the first footprints, for their The Life Of A Professor Fire relentless pursuit of the truth, and for their creative ideas and clever experiments that *Most Viewed in the last 7 days brought insight where previously there was often confusion. Of equal importance are the many collaborators who have greatly facilitated our ability to Advertisement make progress in areas beyond our knowledge base. If “professor” stands for “professional student,” these individuals have been my teachers. I thank them, the ACS Board of Directors who award this medal, and those who entered and supported my nomination.
    [Show full text]