Molecular Cloning of Cdna for Double-Strandedrna Adenosine

Total Page:16

File Type:pdf, Size:1020Kb

Molecular Cloning of Cdna for Double-Strandedrna Adenosine Proc. Natd. Acad. Sci. USA Vol. 91, pp. 11457-11461, November 1994 Biochemistry Molecular cloning of cDNA for double-stranded RNA adenosine deaminase, a candidate enzyme for nuclear RNA editing UNKYU KIM, YI WANG, TAMARA SANFORD, YONG ZENG, AND KAZUKO NISHIKURA* The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104 Communicated by David Botstein, August 1, 1994 ABSTRACT We have domed human cDNA e Ing dou- Determination of N-Terminal Sequence by Micosequenc- blesranded RNA deue (DRADA). DRADA IS ing. Approximately 100 pmol of purified bovine DRADA a ubtus uear me that conver multiple proteins (10) was fractionated by SDS/PAGE and transferred to inosin In doubeheIdcal RNA bsrat i t apparent onto a poly(vinylidine difluoride) membrane. The 93- and sequencespedfldty. The A-- Icove activity ofthe protein 88-kDa bands were cut out and sequenced by Edman degra- encoded by the coned cDNA was med by b t dation (11). In insect ees. Use ofthe domed DNA as a l r Reverse T s t om ee Chain Reaction (PCR). PlObe de lstate c ation sacros _ and Degenerate sets of oligonucleotides that represented the detected a s e trcri o 7 kb in RNA of ahuantnge codons for N-terminal peptide sequences were synthesized. anald. The deduced ay sr e of human DRADA For the 93-kDa protein, the sense primer was CGG;AAIC revealed a bipartite ner l an dgal, three res of CNGGNAAA/GGTNGA, and the antisense primer was a do t RNA b motf, and the presence of CGGGiATCCNGCT/CTCCTT/CTGGT/CTTNA, which sequences conserved In the ctlyic center ofother d correspond to amino acid residues PGKVE and AEQKL, includig a cytidine da isnvolved in the RNA editing of respectively. For the 88-kDa protein, the sense primer was B. These rucal pr ies are onsisetwith CiGAAIICAAA/GACNGGNTAC/TGTNGA, and the he enymic siture oDRADA, and strengthen the hypoth- antisense primer was CG(KIAICG/ATCG/ATCNGGG/ eds that DRADA carries out the RNA edit of tr pts T/AATG/ATCG/ATC, which correspond to residues KT- e ig gumte-gated ion annels in brain. GYVD and DDPIDD, respectively. Restriction sites (under- lined) for EcoRI for the sense primer and BamHI for the Double-stranded adenosine deaminase (DRADA) is an aden- antisense primer were included at the 5' end. In addition, osine deaminase specific for double-stranded RNA (dsRNA) internalprobes representing the residuesflankedby the sense (1, 2). DRADA deaminates multiple adenosines to inosines by and antisense primers were synthesized. The sequences of a hydrolytic deaminaton reaction (3). Although a relatively the internal probe were for the 93-kfla protein C/TTTG/ long double-helical RNA structure is required for efficient CAGC/CAGC/T/AGGCTCCTG and for the 88-kDa protein modification, the minimum length of the double-stranded CGGGATCCAT/CTGNCCA/GTTC/TTCT/GTT. The region for substrate recognition may be as short as 15 bp (4). first-strand cDNA synthesis was carried out (12) using total Theprecisebiologicalfunction(s) ofDRADA andthefullrange RNA prepared from the cultured bovine endothelial cell line, ofits substrate RNAs are currently not known (5). However, BFA-1C BPT (13). A portion of the PCR-amplified product several examples of in vivo interaction of the enzyme with was analyzed by Southern blot hybridization using the inter- cellular and viral gene transcripts have been reported in recent nal probe. The 75-bp cDNA that hybridized to the internal years (5). Forinstance, DRADA seems responsible forgenesis probe was purified from the agarose gel, digested with EcoRI of defective measles virus with biased hypermutation, which and BamHI, and ligated with pBluescript KS+ plasmid. results in the lethal central nervous system disease measles Selected subclones, BUCi and BUC2, were sequenced to inclusion body encephalitis (6). Furthermore, the codingofthe confirm the identity. DRADA-treated mRNAs is expected to be s ficantly al- Screening of the Recombinant Library. A human natural tered, and therefore, the involvement ofDRADA in the RNA killer cell cDNA library was screened using BUC2 as a editing process has been suggested (5, 7, 8). Indeed, DRADA specific probe. The positive cDNA plasmid, HUC1, con- now seems to be responsible at least for the RNA editing of tained -4 kb ofinsert DNA, which hybridized to both BUCi glutamate-gated ion channel subunits (glutamate receptor, and BUC2 by Southern blot analysis. The insert of HUC1 GluR) in mammalian brains (9). was then used to rescreen the original cDNA library, from Toward our ultimate goal of better understanding the which additional overlapping cDNA clones, HUC2, HUC3, physiological functions of DRADA, we have isolated and and HUC4, were obtained. characterized cloned cDNA encoding human DRADA.J The Southern Blot Analyis. Southern blot hybridization was deduced primary structure ofDRADA revealed the presence carried out in buffer containing 2x SSC, lx Denhardt's of sequence motifs that underlie the functional and catalytic solution, 40% (vol/vol) formamide, 10% (wt/vol) dextran properties of this intriguing enzyme. sulfate, 1% SDS, denatured salmon sperm DNA (0.05 mg/ ml), and heat-denatured 32P-labeled probe (106 cpm/ml) at 3TC for 18 hr. The membrane was washed with 2x SSC/1% MATERIALS AND METHODS SDS at 370C for 30 mm. DRADA Assay. The DRADA enzymatic activity was as- of the Recom t Bacuviru DRADA Pro- sayed in vitro as described (10). The radioactivity of the tein. For afull-length construct, pVLDRADA140, Xba I-Kpn adenosine and inosine spots on TLC plates was quantified by a phosphor imaging system (Molecular Dynamics). Abbreviations: dsRNA, double-stranded RNA; DRADA, dsRNA adenosine deaminase; DRBM, dsRNA binding motif; GluR, gluta- mate receptor; RNP, ribonucleoprotein. The publication costs ofthis article were defrayed in part by page charge *To whom reprint requests should be addressed. payment. This article must therefore be hereby marked "advertisement" tThe sequence reported in this paper has been deposited in the in accordance with 18 U.S.C. §1734 solely to indicate this fact. GenBank data base (accession no. U10439). 11457 Downloaded by guest on September 27, 2021 11458 Biochemistry: Kim et al. Proc. Natl. Acad. Sci. USA 91 (1994) A B 1 MNPRQQYSL8 GYYYHPFQ ZHQLRYQQP GPG88P8SFL LKQII1LKGQ 51 LPK&PVIGKQ TPSLPPBLPG LRPRIPVLL& 8SYTRGRVDI RGVPRGVHA 101 SQGLQRGFQH PGPKGRSLPQ RGVDCL88HF QILSIYQDQZ QRILKILZZL kDa 151 CKQLAT!AED LBGKLGTYI ZINRVLYBLL TPPLWKIAVS 93 201 TOMQOiQSQOV VRPDQS8QGA PUSDPSLZPZ DRX8!TVBKD LZPIFIAV8A 88 251 QA&UIQBSGVV RPD8HSQO8P NSDPGLZPZD SNTSALZDP LBFLDNABIX 4,41-0=_ 83 301 NXICDYLFNV 8DSSALNLAK NIGLTKARDI XAVLIDIRQ Q RITP 351 PIWNLTDKR IURMQIKRMN 8VPZTAPA&X PITRA18CNIP? r-OwNkD r6 kD 0 401 NN TT?'NUKVZ GQIQPVIKLZ NMEARUPZPA RLKPPVNYNG PS8G 451 NGQWADDIP DDLN8IRAAP QIIRIIMIRIP SFY8HGL&P&&JYKILTZCQ FIG. 1. Cloning of cDNA en- 501 LINPIBOLL YAQFAQUC _ IZQBGPP PRFQVV INGEZPPPAN coding human DRADA. (A) The 551 AWQ8KVAKD AUNANTILL NIAKASX B8BHYS= K lC final purified fraction was ana- 601 TTP'P8AT8FF 8QBPVYLL HG RLLBKUGP ANZPKIQYCV lyzed by SDS/PAGE (7% gel) and 651 AVGAQTFP8V 8APSVQ MANZAKAL GAN8A DQPI 8 three protein bands were visual- 4W'1 701 BLDULiN VUKIQZLV RYLWEPVGG LLZYAPR.BF AABFUNDQB ized by silver staining. Lanes: 1 VLI 751 GPPNNPKIVY QAKVGGRNPP AVCABSKKQQKO DR and 2, molecular mass standards; 801 RlNfGPKVYPV TQABLRRTU LL8RBPZAQP KLPLTG8TF HDQE=IAiE 3, bovine DRADA. (B) The de- 851 CFIUL!81Q PsL8RKIL& AZImI8ZD UGVVVSLQG NUCVKGD8LB duced amino acid sequence of the I 901 IKGZITVIDCN ABIISRRGFI RPLYBL Y NSAEDBIF ZPAOGQ 136-kDa form of human DRADA 951 IXKTVSFNLY IZTAPCGDGA L1DKC8DRA KI8Y8OBYP VPUPIQQK is shown. The putative bipartite 1001 RUEVINOZOT IPVZ8BDIVP TDGIRLGZR LRTKSCBDKI LRUNVWLQG nuclear localization signal is 1051 ALLNIFLQPI YLKSVTLGYL FSQGHLTRAI CCRVTRDG8A FPDGLRRPFI boxed. The N-terminal sequences 1101 VIIHIPJKVQVS IYDKRQ8QK ?UT8VNWIL ADGYDLUILD TRNGVDGIPR of 93- and 88-kDa proteins are 1151 UKL8RVSIKN ILIZKKLC8 IPRYRRDTLLRL BGZAR DYNITARFIz indicated by arrows; three DRBM 1 2 3 1201 IGLIDUGYO WZSKPQINKN FYLCPV* repeats are indicated by lines. I (the 5'-end 3.7 kb of HUCI) and Kpn I-Xba I (the 3'-end 1 by PILEUP, BESTFIT, and GAP programs, and identification of kb of HUC2) fragments were ligated with pVL1393 (Invitro- various protein sequence motifs was by the MOTIFS program gen). For pVLDRADAA, a mutant lacking the C-terminal 346 (15). A homology search of the National Center for Biotech- amino acids, a new termination codon was created at residue nology Information peptide sequence database (Release 82.0) 880 by filling in the overhang ofXma III located downstream was performed by Internet electronic mail. ofthe dsRNA binding motifs (DRBMs). Infected Spodoptera frugiperdera (Sf9) cells were labeled with 50 pCi of [35S]me- RESULTS thionine (1 Ci = 37 GBq) for 1 hr (14), and the labeled protein was analyzed by SDS/PAGE and fluorography. Purification of DRADA Proteins and Isolation of DRADA Determination of the cDNA Sequence. DNA sequencing of cDNAs. By following the A I modification activity, we sets of nested deletion mutants of the cDNA clones was have purified (10) DRADA to homogeneity from bovine liver carried out with the model 373A DNA sequencing system nuclear extracts. The final fraction contained three DRADA (Applied Biosystems). polypeptides of93, 88, and 83 kDa (Fig. 1A). The N-terminal Sequence Analysis. The overlapping sequences were amino acid sequences of the 93-kDa and 88-kDa proteins aligned and combined by the FRAGMENT ASSEMBLY program were determined by microsequencing, and two short bovine (15). Alignments ofDRBM and deaminases were determined cDNA clones encoding the N termini were obtained. Using B - DRADA1 40 - DRADA A A Nuc DRBM pVLDRADA1 40 pVLDRADAA FIG. 2. Characterization of the recombinant DRADA pro- C teins. (A) Full-length DRADA140 and C-terminally truncated DRADAA constructs are shown. * - - pi (B) Forty-eight hours after infec- tion with recombinant or wild- type baculoviruses, SO9 cells were labeled with P5S]methionine and proteins were separated by SDS/ * * * * * -pA PAGE. (C) Crude extracts made after infection at various time Polyhedrin points were analyzed by a modi- fied-base assay using 20 ,g of extract as described (10).
Recommended publications
  • 35 Disorders of Purine and Pyrimidine Metabolism
    35 Disorders of Purine and Pyrimidine Metabolism Georges van den Berghe, M.- Françoise Vincent, Sandrine Marie 35.1 Inborn Errors of Purine Metabolism – 435 35.1.1 Phosphoribosyl Pyrophosphate Synthetase Superactivity – 435 35.1.2 Adenylosuccinase Deficiency – 436 35.1.3 AICA-Ribosiduria – 437 35.1.4 Muscle AMP Deaminase Deficiency – 437 35.1.5 Adenosine Deaminase Deficiency – 438 35.1.6 Adenosine Deaminase Superactivity – 439 35.1.7 Purine Nucleoside Phosphorylase Deficiency – 440 35.1.8 Xanthine Oxidase Deficiency – 440 35.1.9 Hypoxanthine-Guanine Phosphoribosyltransferase Deficiency – 441 35.1.10 Adenine Phosphoribosyltransferase Deficiency – 442 35.1.11 Deoxyguanosine Kinase Deficiency – 442 35.2 Inborn Errors of Pyrimidine Metabolism – 445 35.2.1 UMP Synthase Deficiency (Hereditary Orotic Aciduria) – 445 35.2.2 Dihydropyrimidine Dehydrogenase Deficiency – 445 35.2.3 Dihydropyrimidinase Deficiency – 446 35.2.4 Ureidopropionase Deficiency – 446 35.2.5 Pyrimidine 5’-Nucleotidase Deficiency – 446 35.2.6 Cytosolic 5’-Nucleotidase Superactivity – 447 35.2.7 Thymidine Phosphorylase Deficiency – 447 35.2.8 Thymidine Kinase Deficiency – 447 References – 447 434 Chapter 35 · Disorders of Purine and Pyrimidine Metabolism Purine Metabolism Purine nucleotides are essential cellular constituents 4 The catabolic pathway starts from GMP, IMP and which intervene in energy transfer, metabolic regula- AMP, and produces uric acid, a poorly soluble tion, and synthesis of DNA and RNA. Purine metabo- compound, which tends to crystallize once its lism can be divided into three pathways: plasma concentration surpasses 6.5–7 mg/dl (0.38– 4 The biosynthetic pathway, often termed de novo, 0.47 mmol/l). starts with the formation of phosphoribosyl pyro- 4 The salvage pathway utilizes the purine bases, gua- phosphate (PRPP) and leads to the synthesis of nine, hypoxanthine and adenine, which are pro- inosine monophosphate (IMP).
    [Show full text]
  • Purine Metabolism in Cultured Endothelial Cells
    PURINE METABOLISM IN MAN-III Biochemical, Immunological, and Cancer Research Edited by Aurelio Rapado Fundacion Jimenez Diaz Madrid, Spain R.W.E. Watts M.R.C. Clinical Research Centre Harrow, England and Chris H.M.M. De Bruyn Department of Human Genetics University of Nijmegen Faculty of Medicine Nijmegen, The Netherlands PLENUM PRESS · NEW YORK AND LONDON Contents of Part Β I. PURINE METABOLISM PATHWAYS AND REGULATION A. De Novo Synthesis; Precursors and Regulation De Novo Purine Synthesis in Cultured Human Fibroblasts 1 R.B. Gordon, L. Thompson, L.A. Johnson, and B.T. Emmerson Comparative Metabolism of a New Antileishmanial Agent, Allopurinol Riboside, in the Parasite and the Host Cell 7 D. J. Nelson, S.W. LaFon, G.B. Elion, J.J. Marr, and R.L. Berens Purine Metabolism in Rat Skeletal Muscle 13 E. R. Tully and T.G. Sheehan Alterations in Purine Metabolism in Cultured Fibroblasts with HGPRT Deficiency and with PRPPP Synthetase Superactivity 19 E. Zoref-Shani and 0. Sperling Purine Metabolism in Cultured Endothelial Cells 25 S. Nees, A.L. Gerbes, B. Willershausen-Zönnchen, and E. Gerlach Determinants of 5-Phosphoribosyl-l-Pyrophosphate (PRPP) Synthesis in Human Fibroblasts 31 K.0, Raivio, Ch. Lazar, H. Krumholz, and M.A. Becker Xanthine Oxidoreductase Inhibition by NADH as a Regulatory Factor of Purine Metabolism 35 M.M. Jezewska and Z.W. Kaminski vii viii CONTENTS OF PART Β Β. Nucleotide Metabolism Human Placental Adenosine Kinase: Purification and Characterization 41 CM. Andres, T.D. Palella, and I.H. Fox Long-Term Effects of Ribose on Adenine Nucleotide Metabolism in Isoproterenol-Stimulated Hearts .
    [Show full text]
  • The Regulation of Carbamoyl Phosphate Synthetase-Aspartate Transcarbamoylase-Dihydroorotase (Cad) by Phosphorylation and Protein-Protein Interactions
    THE REGULATION OF CARBAMOYL PHOSPHATE SYNTHETASE-ASPARTATE TRANSCARBAMOYLASE-DIHYDROOROTASE (CAD) BY PHOSPHORYLATION AND PROTEIN-PROTEIN INTERACTIONS Eric M. Wauson A dissertation submitted to the faculty of the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Pharmacology. Chapel Hill 2007 Approved by: Lee M. Graves, Ph.D. T. Kendall Harden, Ph.D. Gary L. Johnson, Ph.D. Aziz Sancar M.D., Ph.D. Beverly S. Mitchell, M.D. 2007 Eric M. Wauson ALL RIGHTS RESERVED ii ABSTRACT Eric M. Wauson: The Regulation of Carbamoyl Phosphate Synthetase-Aspartate Transcarbamoylase-Dihydroorotase (CAD) by Phosphorylation and Protein-Protein Interactions (Under the direction of Lee M. Graves, Ph.D.) Pyrimidines have many important roles in cellular physiology, as they are used in the formation of DNA, RNA, phospholipids, and pyrimidine sugars. The first rate- limiting step in the de novo pyrimidine synthesis pathway is catalyzed by the carbamoyl phosphate synthetase II (CPSase II) part of the multienzymatic complex Carbamoyl phosphate synthetase, Aspartate transcarbamoylase, Dihydroorotase (CAD). CAD gene induction is highly correlated to cell proliferation. Additionally, CAD is allosterically inhibited or activated by uridine triphosphate (UTP) or phosphoribosyl pyrophosphate (PRPP), respectively. The phosphorylation of CAD by PKA and ERK has been reported to modulate the response of CAD to allosteric modulators. While there has been much speculation on the identity of CAD phosphorylation sites, no definitive identification of in vivo CAD phosphorylation sites has been performed. Therefore, we sought to determine the specific CAD residues phosphorylated by ERK and PKA in intact cells.
    [Show full text]
  • Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals
    Journal of the American Heart Association ORIGINAL RESEARCH Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals Joonatan Palmu , MD; Aaro Salosensaari , MSc; Aki S. Havulinna , DSc (Tech); Susan Cheng , MD, MPH; Michael Inouye, PhD; Mohit Jain, MD, PhD; Rodolfo A. Salido , BSc; Karenina Sanders , BSc; Caitriona Brennan, BSc; Gregory C. Humphrey, BSc; Jon G. Sanders , PhD; Erkki Vartiainen , MD, PhD; Tiina Laatikainen , MD, PhD; Pekka Jousilahti, MD, PhD; Veikko Salomaa , MD, PhD; Rob Knight , PhD; Leo Lahti , DSc (Tech); Teemu J. Niiranen , MD, PhD BACKGROUND: Several small-scale animal studies have suggested that gut microbiota and blood pressure (BP) are linked. However, results from human studies remain scarce and conflicting. We wanted to elucidate the multivariable-adjusted as- sociation between gut metagenome and BP in a large, representative, well-phenotyped population sample. We performed a focused analysis to examine the previously reported inverse associations between sodium intake and Lactobacillus abun- dance and between Lactobacillus abundance and BP. METHODS AND RESULTS: We studied a population sample of 6953 Finns aged 25 to 74 years (mean age, 49.2±12.9 years; 54.9% women). The participants underwent a health examination, which included BP measurement, stool collection, and 24-hour urine sampling (N=829). Gut microbiota was analyzed using shallow shotgun metagenome sequencing. In age- and sex-adjusted models, the α (within-sample) and β (between-sample) diversities of taxonomic composition were strongly re- lated to BP indexes (P<0.001 for most). In multivariable-adjusted models, β diversity was only associated with diastolic BP (P=0.032).
    [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]
  • High Coverage Metabolomics Analysis Reveals Phage-Specific Alterations to Pseudomonas Aeruginosa Physiology During Infection
    The ISME Journal (2016) 10, 1823–1835 © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection Jeroen De Smet1, Michael Zimmermann2, Maria Kogadeeva2, Pieter-Jan Ceyssens1,3, Wesley Vermaelen1, Bob Blasdel1, Ho Bin Jang1, Uwe Sauer2 and Rob Lavigne1 1Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Heverlee, Belgium; 2Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland and 3Unit Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium Phage-mediated metabolic changes in bacteria are hypothesized to markedly alter global nutrient and biogeochemical cycles. Despite their theoretic importance, experimental data on the net metabolic impact of phage infection on the bacterial metabolism remains scarce. In this study, we tracked the dynamics of intracellular metabolites using untargeted high coverage metabolomics in Pseudomo- nas aeruginosa cells infected with lytic bacteriophages from six distinct phage genera. Analysis of the metabolomics data indicates an active interference in the host metabolism. In general, phages elicit an increase in pyrimidine and nucleotide sugar metabolism. Furthermore, clear phage-specific and infection stage-specific responses are observed, ranging from extreme metabolite depletion (for example, phage YuA) to complete reorganization of the metabolism (for example, phage phiKZ). As expected, pathways targeted by the phage-encoded auxiliary metabolic genes (AMGs) were enriched among the metabolites changing during infection. The effect on pyrimidine metabolism of phages encoding AMGs capable of host genome degradation (for example, YuA and LUZ19) was distinct from those lacking nuclease-encoding genes (for example, phiKZ), which demonstrates the link between the encoded set of AMGs of a phage and its impact on host physiology.
    [Show full text]
  • SUPPY Liglucosexlmtdh
    US 20100314248A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2010/0314248 A1 Worden et al. (43) Pub. Date: Dec. 16, 2010 (54) RENEWABLE BOELECTRONIC INTERFACE Publication Classification FOR ELECTROBOCATALYTC REACTOR (51) Int. Cl. (76) Inventors: Robert M. Worden, Holt, MI (US); C25B II/06 (2006.01) Brian L. Hassler, Lake Orion, MI C25B II/2 (2006.01) (US); Lawrence T. Drzal, Okemos, GOIN 27/327 (2006.01) MI (US); Ilsoon Lee, Okemo s, MI BSD L/04 (2006.01) (US) C25B 9/00 (2006.01) (52) U.S. Cl. ............... 204/403.14; 204/290.11; 204/400; Correspondence Address: 204/290.07; 427/458; 204/252: 977/734; PRICE HENEVELD COOPER DEWITT & LIT 977/742 TON, LLP 695 KENMOOR, S.E., PO BOX 2567 (57) ABSTRACT GRAND RAPIDS, MI 495.01 (US) An inexpensive, easily renewable bioelectronic device useful for bioreactors, biosensors, and biofuel cells includes an elec (21) Appl. No.: 12/766,169 trically conductive carbon electrode and a bioelectronic inter face bonded to a surface of the electrically conductive carbon (22) Filed: Apr. 23, 2010 electrode, wherein the bioelectronic interface includes cata lytically active material that is electrostatically bound directly Related U.S. Application Data or indirectly to the electrically conductive carbon electrode to (60) Provisional application No. 61/172,337, filed on Apr. facilitate easy removal upon a change in pH, thereby allowing 24, 2009. easy regeneration of the bioelectronic interface. 7\ POWER 1 - SUPPY|- LIGLUCOSEXLMtDH?till pi 6.0 - esses&aaaas-exx-xx-xx-xx-xxxxixax-e- Patent Application Publication Dec. 16, 2010 Sheet 1 of 18 US 2010/0314248 A1 Potential (nV) Patent Application Publication Dec.
    [Show full text]
  • Metabolomics Identifies Pyrimidine Starvation As the Mechanism of 5-Aminoimidazole-4-Carboxamide-1- Β-Riboside-Induced Apoptosis in Multiple Myeloma Cells
    Published OnlineFirst April 12, 2013; DOI: 10.1158/1535-7163.MCT-12-1042 Molecular Cancer Cancer Therapeutics Insights Therapeutics Metabolomics Identifies Pyrimidine Starvation as the Mechanism of 5-Aminoimidazole-4-Carboxamide-1- b-Riboside-Induced Apoptosis in Multiple Myeloma Cells Carolyne Bardeleben1, Sanjai Sharma1, Joseph R. Reeve3, Sara Bassilian3, Patrick Frost1, Bao Hoang1, Yijiang Shi1, and Alan Lichtenstein1,2 Abstract To investigate the mechanism by which 5-aminoimidazole-4-carboxamide-1-b-riboside (AICAr) induces apoptosis in multiple myeloma cells, we conducted an unbiased metabolomics screen. AICAr had selective effects on nucleotide metabolism, resulting in an increase in purine metabolites and a decrease in pyrimidine metabolites. The most striking abnormality was a 26-fold increase in orotate associated with a decrease in uridine monophosphate (UMP) levels, indicating an inhibition of UMP synthetase (UMPS), the last enzyme in the de novo pyrimidine biosynthetic pathway, which produces UMP from orotate and 5-phosphoribosyl- a-pyrophosphate (PRPP). As all pyrimidine nucleotides can be synthesized from UMP, this suggested that the decrease in UMP would lead to pyrimidine starvation as a possible cause of AICAr-induced apoptosis. Exogenous pyrimidines uridine, cytidine, and thymidine, but not purines adenosine or guanosine, rescued multiple myeloma cells from AICAr-induced apoptosis, supporting this notion. In contrast, exogenous uridine had no protective effect on apoptosis resulting from bortezomib, melphalan, or metformin. Rescue resulting from thymidine add-back indicated apoptosis was induced by limiting DNA synthesis rather than RNA synthesis. DNA replicative stress was identified by associated H2A.X phosphorylation in AICAr-treated cells, which was also prevented by uridine add-back.
    [Show full text]
  • The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
    Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota.
    [Show full text]
  • 1611 REGULATION of PYRIMIDINE METABOLISM in PLANTS Chris
    [Frontiers in Bioscience 9, 1611-1625, May 1, 2004] REGULATION OF PYRIMIDINE METABOLISM IN PLANTS 1, 2 1, 3 1, 4 1, 5 1, 6 1, 7 Chris Kafer , Lan Zhou , Djoko Santoso , Adel Guirgis , Brock Weers , Sanggyu Park and Robert Thornburg 1 1 Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, 2 BASF Plant Science LLC, 2901 South Loop Drive, Ste 3800, Ames, Iowa 50014, 3 Lan Zhou, Pioneer Hi-Bred International, Inc. 7300 NW 62nd Avenue, PO Box 1004, Johnston, Iowa 50131-1004, 4 Indonesian Biotechnology Research Institute for Estate Crops, Jl, Taman Kencana No 1, Bogor 16151 Indonesia, 5 Institute of Genetic Engineering and Biotechnology, Menofiya University, PO Box 79/22857, Sadat City, Egypt, 6 Department of Biochemistry, University of Iowa, 4/511 Bowen Science Building, Iowa City, Iowa 52242-1109, 7 Division of Life and Environment, College of Natural Resources, Daegu University, Gyongsan City, Gyongbuk, Korea 712-714 TABLE OF CONTENTS 1. Abstract 2. Introduction 3. Pyrimidine metabolic pathways 3.1. De novo pyrimidine biosynthesis 3.1.1. CPSase 3.1.2. ATCase 3.1.3. DHOase 3.1.4. DHODH 3.1.5. UMPS 3.1.6. Intracellular Organization of the de novo Pathway 3.2. Pyrimidine Salvage and Recycling 3.2.1. Cytosine deaminase 3.2.2. Cytidine deaminase 3.2.3. UPRTase 3.3. Pyrimidine Modification 3.3.1. UMP/CMP kinase 3.3.2. NDP kinase 3.3.3. CTP synthase, NDP reductase, dUTPase 3.3.4. Thymidylate synthase/Dihydrofolate reductase 3.4. Pyrimidine Catabolism 4. Regulation of pyrimidine metabolism 4.1.
    [Show full text]
  • TITLE Adenylate Kinase 2 Deficiency Causes NAD+ Depletion and Impaired Purine Metabolism During Myelopoiesis
    bioRxiv preprint doi: https://doi.org/10.1101/2021.07.05.450633; this version posted July 6, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. TITLE Adenylate Kinase 2 deficiency causes NAD+ depletion and impaired purine metabolism during myelopoiesis AUTHORS Wenqing Wang1, Andew DeVilbiss2, Martin Arreola1, Thomas Mathews2, Misty Martin-Sandoval2, Zhiyu Zhao2, Avni Awani1, Daniel Dever1, Waleed Al-Herz3, Luigi Noratangelo4, Matthew H. Porteus1, Sean J. Morrison2, Katja G. Weinacht1, * 1. Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305 USA 2. Children’s Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA 3. Department of Pediatrics, Faculty of Medicine, Kuwait University, Safat, 13110 Kuwait 4. Laboratory of Clinical Immunology and Microbiology, National Institute of Health, BETHESDA MD 20814 USA * Corresponding author ABSTRACT Reticular Dysgenesis is a particularly grave from of severe combined immunodeficiency (SCID) that presents with severe congenital neutropenia and a maturation arrest of most cells of the lymphoid lineage. The disease is caused by biallelic loss of function mutations in the mitochondrial enzyme Adenylate Kinase 2 (AK2). AK2 mediates the phosphorylation of adenosine monophosphate (AMP) to adenosine diphosphate (ADP) as substrate for adenosine triphosphate (ATP) synthesis in the mitochondria. Accordingly, it has long been hypothesized that a decline in OXPHOS metabolism is the driver of the disease. The mechanistic basis for Reticular Dysgenesis, however, remained incompletely understood, largely due to lack of appropriate model systems to phenocopy the human disease.
    [Show full text]
  • Download Download
    Robyn A Lindley. Medical Research Archives vol 8 issue 8. Medical Research Archives REVIEW ARTICLE Review of the mutational role of deaminases and the generation of a cognate molecular model to explain cancer mutation spectra Author Robyn A Lindley1,2 1Department of Clinical Pathology 2GMDx Genomics Ltd, The Victorian Comprehensive Cancer Centre Level 3 162 Collins Street, Faculty of Medicine, Dentistry & Health Sciences Melbourne VIC3000, AUSTRALIA University of Melbourne, Email: [email protected] 305 Gratton Street, Melbourne, VIC 3000, AUSTRALIA Email: [email protected] Correspondence: Robyn A Lindley, Department of Clinical Pathology, Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne, 305 Gratton Street, Melbourne VIC 3000 AUSTRALIA Mobile: +61 (0) 414209132 Email: [email protected] Abstract Recent developments in somatic mutation analyses have led to the discovery of codon-context targeted somatic mutation (TSM) signatures in cancer genomes: it is now known that deaminase mutation target sites are far more specific than previously thought. As this research provides novel insights into the deaminase origin of most of the somatic point mutations arising in cancer, a clear understanding of the mechanisms and processes involved will be valuable for molecular scientists as well as oncologists and cancer specialists in the clinic. This review will describe the basic research into the mechanism of antigen-driven somatic hypermutation of immunoglobulin variable genes (Ig SHM) that lead to the discovery of TSM signatures, and it will show that an Ig SHM-like signature is ubiquitous in the cancer exome. Most importantly, the data discussed in this review show that Ig SHM-like cancer-associated signatures are highly targeted to cytosine (C) and adenosine (A) nucleotides in a characteristic codon-context fashion.
    [Show full text]