DOCSLIB.ORG

Supporting Appendix

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supporting Appendix SUPPORTING APPENDIX TABLE OF CONTENTS Figure S1: Compartmentalized redox proteome under steady state conditions in P. tricornutum cells. Figure S2: Redox regulation of metabolic pathways. Figure S3: Evolutionary conservation of GOGAT reactive cysteines. Figure S4: Expression levels of P. tricornutum redox sensitive nitrogen metabolism genes in EST libraries. Figure S5: Redox regulation of primary nitrate assimilation in diatoms. Figure S6: Targeting the in vivo redox sensor roGFP to different subcellular compartments in P. tricornutum cells. Figure S7: Growth of P. tricornutum cultures under low nitrogen conditions. Figure S8: GSH depletion under nitrogen starvation and oxidative stress conditions. Figure S9: In vivo quantification of the oxidation state of redox sensitive cysteine in roGFP. Table S1: Diatom redox proteome under oxidative stress. A list of P. tricornutum redox-sensitive proteins which were identified in this study. Predicted protein localization, sensitive cysteine position and degree of oxidation under steady state and H2O2 treatment are included. When the identified peptide contains more than one cysteine, the cysteine position refers to the first cysteine. P-value ranges are marked by asterisks: *** P < 0.01, ** 0.01 < P < 0.05, * P < 0.1. Table S2: Biological function enriched in P. tricornutum redox-sensitive proteome. Significantly enriched terms (p<0.05) are included. Enrichment of Gene Ontology (GO) terms was analyzed using the Ontologizer software (http://compbio.charite.de/contao/index.php/ontologizer2.html). Table S3. List of abbreviations. Supplementary methods Figure S1: Compartmentalized redox proteome under steady state conditions in P. tricornutum cells. The thiol proteome distribution under steady state condition is presented based on prediction of their subcellular localization and their level of oxidation. Chl, chloroplast; Mit, mitochondria; Nuc, nucleus; SP, signal peptide; SA, signal anchor; NT, not targeted. TCA cycle Cofactors, Prosthetic Groups, Nucleosides and Nucleotide Calvin cycle and Nitrogen Compound Electron Carrier Biosynthesis Biosynthesis photorespiration Metabolism Amino Acids Biosynthesis Secondary Metabolite Biosynthesis Pentose Phosphate Aromatic Amines and Glycolysis Compound Polyamine Fatty Acid and Lipid Pathway Biosynthesis Biosynthesis Biosynthesis Figure S2: Redox regulation of metabolic pathways. Overview of P. tricornutum peroxide-sensitive proteins that are involved in metabolic network reactions. Redox proteomics data was mapped to metabolic-map diagrams using the DiatomCyc databases at http://www.diatomcyc.org/. Each node in the diagram represents a single metabolite and each line represents a single bioreaction. Reactions catalyzed by proteins that were found as redox-sensitive (ΔOX >10%) are marked in red. Figure S3: Evolutionary conservation of GOGAT reactive cysteines. Sequence comparison of GOGAT protein from 38 organism is shown. Highly conserved cysteines, Cys120 and Cys704, which were found as redox sensetive are highlithed. Multiple sequence alignment was done and visulized using MATLAB software. 20 nitrite reductase ornithine aminotransferase glutamate synthase 1 carbamoyl-phosphate synthase 16 serine hydroxymethyltransferase isocitrate nadp-dependent serine hydroxymethyltransferase glycine dehydrogenase 12 arginase glutamate synthase 8 Frequencies of ESTs of Frequencies 4 0 OS UA AA NS NR Figure S4: Expression levels of genes encoding redox-sensitive proteins participating in nitrogen metabolism in P. tricornutum EST libraries. Expression levels in five EST libraries derived from different nitrogen conditions is presented. Level of expression is presented as frequencies of ESTs in each library. UA, Urea Adapted, AA, Ammonium Adapted, NR, Nitrate Replete, OS, Original Standard, NS, Nitrate Starved. A B 50 50 N N 15 40 15 40 30 30 20 20 Atom % excess % Atom excess % Atom 10 10 0 0 0 20 40 60 80 100 120 140 0 20 40 60 80 100 120 140 Time (min) Time (min) Figure S5: Redox regulation of primary nitrate assimilation in diatoms. P. 15 tricornutum cells were supplied with N-nitrate under oxidative stress (150µM H2O2) 15 and control conditions (0µM H2O2) and the enrichment of N in glutamine labeled in amide and amino groups was detected using multiple reaction monitoring (MRM) applying the following parameters: 148.1>130.1 (A) and 148.1>131.1 (B). a Chl-roGFP H4 promoter OEE tp roGFP Mit-roGFP H4 promoter GSIII tp roGFP Nuc-roGFP H4 promoter H4 sp roGFP b BF roGFP Marker Overlay roGFP mitoTracker DAPI Chl Chlorophyll autoflorescence Mit Nuc 10µm Figure S6: Targeting the in vivo redox sensor roGFP to different subcellular compartments in P. tricornutum cells (a) Schematic representation of roGFP constructs. Histone H4 (H4) promoter was used for all constructs for constitutive expression of the roGFP protein. Mit-roGFP has mitochondrial transient peptide (GSIII), nuc-roGFP has a nuclear signal peptide (Histone H4), and chl-roGFP has chloroplastic transit peptide (OEE1). (b) Verification of roGFP subcellular localization. P. tricornutum cells expressing roGFP were viewed under a fluorescence microscope. Images of expression in the chloroplast, mitochondria and nucleus are shown. For each P. tricornutum strain images of bright field (BF), roGFP fluorescence (ex: 488nm, em: 525nm) and various sub-cellular markers are presented. Chlorophyll autofluorescence (ex: 500nm, em: > 650nm), mitoTracker stain (ex: 540nm, em: 630nm), and DAPI stain (ex: 350nm, em: 460nm) were used as markers for plastid, mitochondria, and nucleus localization, respectively. Scale bar: 10µm. Mit, mitochondria; Nuc, nucleus; Chl, chloroplast. 4 + N 3 - N ) 1 - 2 Cell·ml 6 10 ( Cell abandence Cell 1 0 0 10 20 30 40 50 60 70 Time (hr) Figure S7: Growth of P. tricornutum cultures under nitrogen-starved conditions. Cells from an exponential culture (~2•105 cells/ml) were washed with nitrogen-free ¯ media and resuspended in media containing 882µM NO3 (+Nitrate) or nitrogen-free media (-Nitrate). Subsequently, cell abundance was monitored over growth phase of 72hr. 1.2 1 0.8 ++ Nitrate Nitrate 0.6 -- Nitrate Nitrate GSH (AU) ++ Nitarte, Nitrate, H H22OO2 % of control% 0.4 -- Nitrate, Nitrate, H H2022O2 0.2 0 1 2 3 4 Day Figure S8: GSH depletion under nitrogen starvation and oxidative stress conditions. Cells were exposed to nitrogen replete or depleted media and GSH level were determined with or without addition of hydrogen peroxide (150µM, 2hr) by applying the specific GSH dye monochlorobimane. Fluorescence data was analyzed by flow cytometery and presented as percentage of monochlorobimane fluorescence of control (day 1, nitrogen replete). Figure S9: In vivo quantification of the oxidation state of redox sensitive cysteine in roGFP. Exponential P. tricornutum cells were subjected to OxICAT labeling under steady state and oxidized conditions (150μM H2O2, 20 min). Mass spectra are shown for the peptide containing the Cys204 of roGFP which is responsible for the redox properties of the protein. Peptide mass signal with lower m/z value corresponds to the thiol reduced state, labeled with light 12C-ICAT reagent (blue) and higher m/z value corresponds to thiol oxidized state, which is labeled with heavy 13C-ICAT reagents (red). The difference in m/z between the ICAT labeled pairs is equal to 9.0 Da (difference in mass between light and heavy ICAT reagent) divided by the charge state of the peptide. As seen under steady state conditions, a majority of the protein is in its reduced state, while after H2O2 treatment most of the protein is in its oxidized state and the difference in degree of oxidation between these conditions is 41%. These results were comparable to the fluorescence measurement of the roGFP. Table S1 Protein Code Cystein FC intensity Protein annotation JGI code Peptide Name % oxidation rest % oxidation H2O2 deltaOxi p-value Localization NCBI position (H2O2 /rest) ROS metabolism and redox signalling alkyl hydroperoxide reductase thiol specific antioxidant mal allergen 217408144 12713 GCTLEAR 100 12.0 47.2 35.2 ** 6.64 SP peroxiredoxin 5, atypical 2-Cys peroxiredoxin 217405639 14898 VAIFGVPGAFTPGCSK 94 16.9 30.8 13.9 * 2.25 Chl thioredoxin h 217408133 56471 LAEENPDIEFVKVDVDEADDVAAHCGVR 69 35.3 45.5 10.2 ** 1.54 Cyt redoxin domain protein 217405724 22388 VVVFAIPGAFTPTCSSTHLPGYEAAYDK 98 17.8 29.9 12.1 ** 1.94 SP thioredoxin 219110721 8167 DELLDTIVGCVAK 170 22.0 37.9 15.9 ** 2.16 Chl peroxiredoxin q 217406452 21736 KPLVVYFYPADSTPGCTK 74 33.0 57.4 24.3 *** 2.77 Chl ascorbate peroxidase 219122837 47395 YGRVDASGPENCSAEGNLPDAEPGPDGK 158 12.5 34.6 22.0 * 3.77 Chl ascorbate peroxidase 219122837 47395 VDASGPENCSAEGNLPDAEPGPDGK 158 9.6 29.4 19.8 *** 3.91 Chl ascorbate peroxidase 219122832 54731 IDSNGPENCSK 125 12.3 23.0 10.7 * 2.10 Cyt dehydroascorbate reductase 219120379 36641 CSLESVLLR 167 20.5 38.5 18.1 * 2.48 Cyt cytochrome c peroxidase 219120259 13174 CPANGRLPDATQGAEHLR 127 16.6 27.3 10.7 ** 1.89 Cyt glutaredoxin 2 219123711 38124 DVLPTVYVYDHCPFCVR 73 46.2 69.5 23.3 2.64 SP Photosynthesis and Chlorophyll biosynthesis magnesium chelatase atpase subunit d 219112735 33017 DLKVAPSQMQYLCEEAIR 372 46.4 66.5 20.1 ** 2.31 Chl ferredoxin 219127706 49401 VKIPVNCQK 106 55.8 77.6 21.8 ** 2.73 Chl fucoxanthin Chlorophyll a c binding protein 219110471 54065 LAMLAAAGCMAQELANGK 186 3.2 13.4 10.2 ** 4.60 Chl pgr5-like protein 1a 217411614 42543 CYIDTGICK 192 49.8 60.4 10.6 * 1.53 Chl ferredoxin 219127706 49401 ACSTPLPTGK 126 20.9 43.9 22.9 * 2.84 Chl ferredoxin 118411008 SDCTISVHQEDELY 88 49.2 59.5 10.3
Load more

Recommended publications
  • (12) United States Patent (10) Patent No.: US 6,395,889 B1 Robison (45) Date of Patent: May 28, 2002
    USOO6395889B1 (12) United States Patent (10) Patent No.: US 6,395,889 B1 Robison (45) Date of Patent: May 28, 2002 (54) NUCLEIC ACID MOLECULES ENCODING WO WO-98/56804 A1 * 12/1998 ........... CO7H/21/02 HUMAN PROTEASE HOMOLOGS WO WO-99/0785.0 A1 * 2/1999 ... C12N/15/12 WO WO-99/37660 A1 * 7/1999 ........... CO7H/21/04 (75) Inventor: fish E. Robison, Wilmington, MA OTHER PUBLICATIONS Vazquez, F., et al., 1999, “METH-1, a human ortholog of (73) Assignee: Millennium Pharmaceuticals, Inc., ADAMTS-1, and METH-2 are members of a new family of Cambridge, MA (US) proteins with angio-inhibitory activity', The Journal of c: - 0 Biological Chemistry, vol. 274, No. 33, pp. 23349–23357.* (*) Notice: Subject to any disclaimer, the term of this Descriptors of Protease Classes in Prosite and Pfam Data patent is extended or adjusted under 35 bases. U.S.C. 154(b) by 0 days. * cited by examiner (21) Appl. No.: 09/392, 184 Primary Examiner Ponnathapu Achutamurthy (22) Filed: Sep. 9, 1999 ASSistant Examiner William W. Moore (51) Int. Cl." C12N 15/57; C12N 15/12; (74) Attorney, Agent, or Firm-Alston & Bird LLP C12N 9/64; C12N 15/79 (57) ABSTRACT (52) U.S. Cl. .................... 536/23.2; 536/23.5; 435/69.1; 435/252.3; 435/320.1 The invention relates to polynucleotides encoding newly (58) Field of Search ............................... 536,232,235. identified protease homologs. The invention also relates to 435/6, 226, 69.1, 252.3 the proteases. The invention further relates to methods using s s s/ - - -us the protease polypeptides and polynucleotides as a target for (56) References Cited diagnosis and treatment in protease-mediated disorders.
    [Show full text]
  • Itraq-Based Quantitative Proteomics Analysis Reveals the Mechanism Underlying the Weakening of Carbon Metabolism in Chlorotic Tea Leaves
    Article iTRAQ-Based Quantitative Proteomics Analysis Reveals the Mechanism Underlying the Weakening of Carbon Metabolism in Chlorotic Tea Leaves Fang Dong 1,2, Yuanzhi Shi 1,2, Meiya Liu 1,2, Kai Fan 1,2, Qunfeng Zhang 1,2,* and Jianyun Ruan 1,2 1 Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; [email protected] (F.D.); [email protected] (Y.S.); [email protected] (M.L.); [email protected] (K.F.); [email protected] (J.R.) 2 Key Laboratory for Plant Biology and Resource Application of Tea, the Ministry of Agriculture, Hangzhou 310008, China * Correspondence: [email protected]; Tel.: +86-571-8527-0665 Received: 7 November 2018; Accepted: 5 December 2018; Published: 7 December 2018 Abstract: To uncover mechanism of highly weakened carbon metabolism in chlorotic tea (Camellia sinensis) plants, iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic analyses were employed to study the differences in protein expression profiles in chlorophyll-deficient and normal green leaves in the tea plant cultivar “Huangjinya”. A total of 2110 proteins were identified in “Huangjinya”, and 173 proteins showed differential accumulations between the chlorotic and normal green leaves. Of these, 19 proteins were correlated with RNA expression levels, based on integrated analyses of the transcriptome and proteome. Moreover, the results of our analysis of differentially expressed proteins suggested that primary carbon metabolism (i.e., carbohydrate synthesis and transport) was inhibited in chlorotic tea leaves. The differentially expressed genes and proteins combined with photosynthetic phenotypic data indicated that 4-coumarate-CoA ligase (4CL) showed a major effect on repressing flavonoid metabolism, and abnormal developmental chloroplast inhibited the accumulation of chlorophyll and flavonoids because few carbon skeletons were provided as a result of a weakened primary carbon metabolism.
    [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]
  • Serine Proteases with Altered Sensitivity to Activity-Modulating
    (19) & (11) EP 2 045 321 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 08.04.2009 Bulletin 2009/15 C12N 9/00 (2006.01) C12N 15/00 (2006.01) C12Q 1/37 (2006.01) (21) Application number: 09150549.5 (22) Date of filing: 26.05.2006 (84) Designated Contracting States: • Haupts, Ulrich AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 51519 Odenthal (DE) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • Coco, Wayne SK TR 50737 Köln (DE) •Tebbe, Jan (30) Priority: 27.05.2005 EP 05104543 50733 Köln (DE) • Votsmeier, Christian (62) Document number(s) of the earlier application(s) in 50259 Pulheim (DE) accordance with Art. 76 EPC: • Scheidig, Andreas 06763303.2 / 1 883 696 50823 Köln (DE) (71) Applicant: Direvo Biotech AG (74) Representative: von Kreisler Selting Werner 50829 Köln (DE) Patentanwälte P.O. Box 10 22 41 (72) Inventors: 50462 Köln (DE) • Koltermann, André 82057 Icking (DE) Remarks: • Kettling, Ulrich This application was filed on 14-01-2009 as a 81477 München (DE) divisional application to the application mentioned under INID code 62. (54) Serine proteases with altered sensitivity to activity-modulating substances (57) The present invention provides variants of ser- screening of the library in the presence of one or several ine proteases of the S1 class with altered sensitivity to activity-modulating substances, selection of variants with one or more activity-modulating substances. A method altered sensitivity to one or several activity-modulating for the generation of such proteases is disclosed, com- substances and isolation of those polynucleotide se- prising the provision of a protease library encoding poly- quences that encode for the selected variants.
    [Show full text]
  • Anti-Inflammatory Role of Curcumin in LPS Treated A549 Cells at Global Proteome Level and on Mycobacterial Infection
    Anti-inflammatory Role of Curcumin in LPS Treated A549 cells at Global Proteome level and on Mycobacterial infection. Suchita Singh1,+, Rakesh Arya2,3,+, Rhishikesh R Bargaje1, Mrinal Kumar Das2,4, Subia Akram2, Hossain Md. Faruquee2,5, Rajendra Kumar Behera3, Ranjan Kumar Nanda2,*, Anurag Agrawal1 1Center of Excellence for Translational Research in Asthma and Lung Disease, CSIR- Institute of Genomics and Integrative Biology, New Delhi, 110025, India. 2Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India. 3School of Life Sciences, Sambalpur University, Jyoti Vihar, Sambalpur, Orissa, 768019, India. 4Department of Respiratory Sciences, #211, Maurice Shock Building, University of Leicester, LE1 9HN 5Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia- 7003, Bangladesh. +Contributed equally for this work. S-1 70 G1 S 60 G2/M 50 40 30 % of cells 20 10 0 CURI LPSI LPSCUR Figure S1: Effect of curcumin and/or LPS treatment on A549 cell viability A549 cells were treated with curcumin (10 µM) and/or LPS or 1 µg/ml for the indicated times and after fixation were stained with propidium iodide and Annexin V-FITC. The DNA contents were determined by flow cytometry to calculate percentage of cells present in each phase of the cell cycle (G1, S and G2/M) using Flowing analysis software. S-2 Figure S2: Total proteins identified in all the three experiments and their distribution betwee curcumin and/or LPS treated conditions. The proteins showing differential expressions (log2 fold change≥2) in these experiments were presented in the venn diagram and certain number of proteins are common in all three experiments.
    [Show full text]
  • Assembly of an Active Enzyme by the Linkage of Two Protein Modules
    Proc. Natl. Acad. Sci. USA Vol. 94, pp. 1069–1073, February 1997 Biochemistry Assembly of an active enzyme by the linkage of two protein modules A. E. NIXON,M.S.WARREN, AND S. J. BENKOVIC* 152 Davey Laboratory, Department of Chemistry, Pennsylvania State University, University Park, PA 16802-6300 Contributed by S. J. Benkovic, December 9, 1996 ABSTRACT The feasibility of creating new enzyme activ- design enzymes with novel properties. Previous approaches to ities from enzymes of known function has precedence in view the design of proteins with novel activities have included of protein evolution based on the concepts of molecular catalytic antibodies (8, 9); introduction of metal ion binding recruitment and exon shuffling. The enzymes encoded by the sites, such as the one engineered into trypsin to allow either Escherichia coli genes purU and purN, N10-formyltetrahydro- control of the proteolytic activity (10) or to regulate specificity folate hydrolase and glycinamide ribonucleotide (GAR) trans- (11); creation of hybrid enzymes through exchange of subunits formylase, respectively, catalyze similiar yet distinct reactions. to create hybrid oligomers (12); replacement of structural N10-formyltetrahydrofolate hydrolase uses water to cleave elements such as the DNA binding domain of GCN4 with that N10-formyltetrahydrofolate into tetrahydrofolate and for- of CyEBP (13); mutation of multiple individual residues to mate, whereas GAR transformylase catalyses the transfer of change the cofactor specificity of glutathione reductase from formyl from N10-formyltetrahydrofolate to GAR to yield NADPH to NADH (14), modulation of the substrate speci- formyl-GAR and tetrahydrofolate. The two enzymes show ficity of aspartate aminotransferase (15); and changing the significant homology ('60%) in the carboxyl-terminal region specificity of subtilisin (16) and a-lytic protease (17) through which, from the GAR transformylase crystal structure and mutation of single functional groups.
    [Show full text]
  • Resolution of Carbon Metabolism and Sulfur-Oxidation Pathways of Metallosphaera Cuprina Ar-4 Via Comparative Proteomics
    JOURNAL OF PROTEOMICS 109 (2014) 276– 289 Available online at www.sciencedirect.com ScienceDirect www.elsevier.com/locate/jprot Resolution of carbon metabolism and sulfur-oxidation pathways of Metallosphaera cuprina Ar-4 via comparative proteomics Cheng-Ying Jianga, Li-Jun Liua, Xu Guoa, Xiao-Yan Youa, Shuang-Jiang Liua,c,⁎, Ansgar Poetschb,⁎⁎ aState Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China bPlant Biochemistry, Ruhr University Bochum, Bochum, Germany cEnvrionmental Microbiology and Biotechnology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China ARTICLE INFO ABSTRACT Article history: Metallosphaera cuprina is able to grow either heterotrophically on organics or autotrophically Received 16 March 2014 on CO2 with reduced sulfur compounds as electron donor. These traits endowed the species Accepted 6 July 2014 desirable for application in biomining. In order to obtain a global overview of physiological Available online 14 July 2014 adaptations on the proteome level, proteomes of cytoplasmic and membrane fractions from cells grown autotrophically on CO2 plus sulfur or heterotrophically on yeast extract Keywords: were compared. 169 proteins were found to change their abundance depending on growth Quantitative proteomics condition. The proteins with increased abundance under autotrophic growth displayed Bioleaching candidate enzymes/proteins of M. cuprina for fixing CO2 through the previously identified Autotrophy 3-hydroxypropionate/4-hydroxybutyrate cycle and for oxidizing elemental sulfur as energy Heterotrophy source. The main enzymes/proteins involved in semi- and non-phosphorylating Entner– Industrial microbiology Doudoroff (ED) pathway and TCA cycle were less abundant under autotrophic growth. Also Extremophile some transporter proteins and proteins of amino acid metabolism changed their abundances, suggesting pivotal roles for growth under the respective conditions.
    [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]
  • Microbial Production of Methyl Anthranilate, a Grape Flavor Compound
    Microbial production of methyl anthranilate, a grape flavor compound Zi Wei Luoa,b,1, Jae Sung Choa,b,1, and Sang Yup Leea,b,c,d,2 aMetabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology, 34141 Daejeon, Republic of Korea; bSystems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Korea Advanced Institute of Science and Technology, 34141 Daejeon, Republic of Korea; cBioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology, 34141 Daejeon, Republic of Korea; and dBioInformatics Research Center, Korea Advanced Institute of Science and Technology, 34141 Daejeon, Republic of Korea Contributed by Sang Yup Lee, April 5, 2019 (sent for review March 6, 2019; reviewed by Jay D. Keasling and Blaine A. Pfeifer) Methyl anthranilate (MANT) is a widely used compound to give While these biotransformation procedures are considered more grape scent and flavor, but is currently produced by petroleum-based natural and ecofriendly compared with chemical synthesis, their processes. Here, we report the direct fermentative production of actual use is limited due to low yields, long reaction times, and MANT from glucose by metabolically engineered Escherichia coli and formation of byproducts (5). In addition, the chemical and bio- Corynebacterium glutamicum strains harboring a synthetic plant- transformation processes mentioned
    [Show full text]
  • Davidge JBC Supplementary.Pdf
    promoting access to White Rose research papers Universities of Leeds, Sheffield and York http://eprints.whiterose.ac.uk/ White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/7923/ (includes links to Main Article, Supplementary Material and Figures) Published paper Davidge, K.S., Sanguinetti, G., Yee, C.H., Cox, A.G., McLeod, C.W., Monk, C.E., Mann, B.E., Motterlini, R. and Poole, R.K. (2009) Carbon monoxide-releasing antibacterial molecules target respiration and global transcriptional regulators. Journal of Biological Chemistry, 284 (7). pp. 4516-4524. http://dx.doi.org/10.1074/jbc.M808210200 Supplementary Material White Rose Research Online [email protected] Supplementary Material Carbon monoxide-releasing antibacterial molecules target respiration and global transcriptional regulators Kelly S Davidge, Guido Sanguinetti, Chu Hoi Yee, Alan G Cox, Cameron W McLeod, Claire E Monk, Brian E Mann, Roberto Motterlini and Robert K Poole Contents Page Number Supplementary Figure S1 3 Inhibition by CORM-3 of E. coli cultures grown in defined medium anaerobically and aerobically Supplementary Figure S2 4 Viability assays showing survival of anaerobically and aerobically E. coli in defined growth medium Supplementary Figure S3 5 Reaction of terminal oxidases in vivo on addition of RuCl2(DMSO)4 to intact cells in a dual-wavelength spectrophotometer Supplementary Figure S4 6 CORM-3 generates carbonmonoxycytochrome bd in vivo and depresses synthesis of cytochrome bo' Supplementary Figure S5 7 Expression of spy-lacZ activity
    [Show full text]
  • Insensitive 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthaset LISA M
    JOURNAL OF BACTERIOLOGY, Nov. 1990, p. 6581-6584 Vol. 172, No. 11 0021-9193/90/116581-04$02.00/0 Copyright X 1990, American Society for Microbiology Cloning of an aroF Allele Encoding a Tyrosine- Insensitive 3-Deoxy-D-arabino-Heptulosonate 7-Phosphate Synthaset LISA M. WEAVER AND KLAUS M. HERRMANN* Department ofBiochemistry, Purdue University, West Lafayette, Indiana 47907 Received 9 May 1990/Accepted 10 August 1990 In Escherichia coli, genes aroF+, aroG+, and aroH+ encode isoenzymes of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthases that are feedback inhibited by tyrosine, phenylalanine, and tryptophan, respectively. A single base pair change in aroF causes a Pro-148-to-Leu-148 substitution and results in a tyrosine-insensitive enzyme. In bacteria and plants, the aromatic amino acids phenyl- plasmid, designated pLW22, contained an 8-kb insert that alanine, tyrosine, and tryptophan are synthesized via the hybridized to the 714-bp DdeI (Fig. 1) aroF probe (6, 11). shikimate pathway (7, 13). The first enzyme of this pathway Digestion of pLW22 with HindIII-BglII gave a 950-bp frag- is 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) ment that hybridized to the probe. This result was unex- synthase (EC 4.1.2.15). In Escherichia coli, the three un- pected, since the corresponding wild-type fragment is 1.8 kb linked genes aroF+, aroG+, and aroH+ (1) encode three in size. Subsequent detailed restriction analysis and hybrid- isoenzymes of DAHP synthase that are sensitive to tyrosine, ization of pLW22 with the 796-bp DdeI (Fig. 1) aroF probe phenylalanine, and tryptophan, respectively (2).
    [Show full text]
  • Letters to Nature
    letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997).
    [Show full text]