Supplementary. Table S1 a Total of Degs Detected in This Study (Gm) No
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Characterization and Phylogeny of the Pfp Gene of Amycolatopsis Methanolica Encoding
JOURNAL OF BACTERIOLOGY, Jan. 1996, p. 149–155 Vol. 178, No. 1 0021-9193/96/$04.0010 Copyright q 1996, American Society for Microbiology Characterization and Phylogeny of the pfp Gene of Amycolatopsis methanolica Encoding PPi-Dependent Phosphofructokinase ALEXANDRA M. C. R. ALVES, WIM G. MEIJER, JAN W. VRIJBLOED, AND LUBBERT DIJKHUIZEN* Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9751 NN Haren, The Netherlands Received 28 July 1995/Accepted 2 November 1995 The actinomycete Amycolatopsis methanolica employs a PPi-dependent phosphofructokinase (PPi-PFK) (EC 2.7.1.90) with biochemical characteristics similar to those of both ATP- and PPi-dependent enzymes during growth on glucose. A 2.3-kb PvuII fragment hybridizing to two oligonucleotides based on the amino-terminal amino acid sequence of PPi-PFK was isolated from a genomic library of A. methanolica. Nucleotide sequence analysis of this fragment revealed the presence of an open reading frame encoding a protein of 340 amino acids with a high degree of similarity to PFK proteins. Heterologous expression of this open reading frame in Escherichia coli gave rise to a unique 45-kDa protein displaying a high level of PPi-PFK activity. The open reading frame was therefore designated pfp, encoding the PPi-PFK of A. methanolica. Upstream and transcribed divergently from pfp, a partial open reading frame (aroA) similar to 3-deoxy-D-arabino-heptulosonate-7- phosphate synthase-encoding genes was identified. The partial open reading frame (chiA) downstream from pfp was similar to chitinase genes from Streptomyces species. A phylogenetic analysis of the ATP- and PPi- dependent proteins showed that PPi-PFK enzymes are monophyletic, suggesting that the two types of PFK evolved from a common ancestor. -
Genome-Wide Transcriptional Changes and Lipid Profile
G C A T T A C G G C A T genes Article Genome-Wide Transcriptional Changes and Lipid Profile Modifications Induced by Medicago truncatula N5 Overexpression at an Early Stage of the Symbiotic Interaction with Sinorhizobium meliloti Chiara Santi 1, Barbara Molesini 1, Flavia Guzzo 1, Youry Pii 2 ID , Nicola Vitulo 1 and Tiziana Pandolfini 1,* ID 1 Department of Biotechnology, University of Verona, 37134 Verona, Italy; [email protected] (C.S.); [email protected] (B.M.); fl[email protected] (F.G.); [email protected] (N.V.) 2 Faculty of Science and Technology, Free University of Bozen-Bolzano, 39100 Bolzano BZ, Italy; [email protected] * Correspondence: tiziana.pandolfi[email protected]; Tel.: +39-045-8027918 Received: 30 October 2017; Accepted: 11 December 2017; Published: 19 December 2017 Abstract: Plant lipid-transfer proteins (LTPs) are small basic secreted proteins, which are characterized by lipid-binding capacity and are putatively involved in lipid trafficking. LTPs play a role in several biological processes, including the root nodule symbiosis. In this regard, the Medicago truncatula nodulin 5 (MtN5) LTP has been proved to positively regulate the nodulation capacity, controlling rhizobial infection and nodule primordia invasion. To better define the lipid transfer protein MtN5 function during the symbiosis, we produced MtN5-downregulated and -overexpressing plants, and we analysed the transcriptomic changes occurring in the roots at an early stage of Sinorhizobium meliloti infection. We also carried out the lipid profile analysis of wild type (WT) and MtN5-overexpressing roots after rhizobia infection. The downregulation of MtN5 increased the root hair curling, an early event of rhizobia infection, and concomitantly induced changes in the expression of defence-related genes. -
Phosphodiesterase 1B Knock-Out Mice Exhibit Exaggerated Locomotor Hyperactivity and DARPP-32 Phosphorylation in Response to Dopa
The Journal of Neuroscience, June 15, 2002, 22(12):5188–5197 Phosphodiesterase 1B Knock-Out Mice Exhibit Exaggerated Locomotor Hyperactivity and DARPP-32 Phosphorylation in Response to Dopamine Agonists and Display Impaired Spatial Learning Tracy M. Reed,1,3 David R. Repaske,2* Gretchen L. Snyder,4 Paul Greengard,4 and Charles V. Vorhees1* Divisions of 1Developmental Biology and 2Endocrinology, Children’s Hospital Research Foundation, Cincinnati, Ohio 45229, 3Department of Biology, College of Mount St. Joseph, Cincinnati, Ohio 45233, and 4Laboratory of Molecular and Cellular Neuroscience, Rockefeller University, New York, New York 10021 Using homologous recombination, we generated mice lack- maze spatial-learning deficits. These results indicate that en- ing phosphodiesterase-mediated (PDE1B) cyclic nucleotide- hancement of cyclic nucleotide signaling by inactivation of hydrolyzing activity. PDE1B Ϫ/Ϫ mice showed exaggerated PDE1B-mediated cyclic nucleotide hydrolysis plays a signifi- hyperactivity after acute D-methamphetamine administra- cant role in dopaminergic function through the DARPP-32 and tion. Striatal slices from PDE1B Ϫ/Ϫ mice exhibited increased related transduction pathways. levels of phospho-Thr 34 DARPP-32 and phospho-Ser 845 Key words: phosphodiesterases; DARPP-32; dopamine- GluR1 after dopamine D1 receptor agonist or forskolin stimu- stimulated locomotor activity; spatial learning and memory; lation. PDE1B Ϫ/Ϫ and PDE1B ϩ/Ϫ mice demonstrated Morris Morris water maze; methamphetamine; SKF81297; forskolin Calcium/calmodulin-dependent phosphodiesterases (CaM- (CaMKII) and calcineurin and have the potential to activate PDEs) are members of one of 11 families of PDEs (Soderling et CaM-PDEs. Dopamine D1 or D2 receptor activation leads to al., 1999;Yuasa et al., 2001) and comprise the only family that acts adenylyl cyclase activation or inhibition, respectively (Traficante ϩ as a potential point of interaction between the Ca 2 and cyclic et al., 1976; Monsma et al., 1990; Cunningham and Kelley, 1993; nucleotide signaling pathways. -
N-Glycan Trimming in the ER and Calnexin/Calreticulin Cycle
Neurotransmitter receptorsGABA and A postsynapticreceptor activation signal transmission Ligand-gated ion channel transport GABAGABA Areceptor receptor alpha-5 alpha-1/beta-1/gamma-2 subunit GABA A receptor alpha-2/beta-2/gamma-2GABA receptor alpha-4 subunit GABAGABA receptor A receptor beta-3 subunitalpha-6/beta-2/gamma-2 GABA-AGABA receptor; A receptor alpha-1/beta-2/gamma-2GABA receptoralpha-3/beta-2/gamma-2 alpha-3 subunit GABA-A GABAreceptor; receptor benzodiazepine alpha-6 subunit site GABA-AGABA-A receptor; receptor; GABA-A anion site channel (alpha1/beta2 interface) GABA-A receptor;GABA alpha-6/beta-3/gamma-2 receptor beta-2 subunit GABAGABA receptorGABA-A receptor alpha-2receptor; alpha-1 subunit agonist subunit GABA site Serotonin 3a (5-HT3a) receptor GABA receptorGABA-C rho-1 subunitreceptor GlycineSerotonin receptor subunit3 (5-HT3) alpha-1 receptor GABA receptor rho-2 subunit GlycineGlycine receptor receptor subunit subunit alpha-2 alpha-3 Ca2+ activated K+ channels Metabolism of ingested SeMet, Sec, MeSec into H2Se SmallIntermediateSmall conductance conductance conductance calcium-activated calcium-activated calcium-activated potassium potassium potassiumchannel channel protein channel protein 2 protein 1 4 Small conductance calcium-activatedCalcium-activated potassium potassium channel alpha/beta channel 1 protein 3 Calcium-activated potassiumHistamine channel subunit alpha-1 N-methyltransferase Neuraminidase Pyrimidine biosynthesis Nicotinamide N-methyltransferase Adenosylhomocysteinase PolymerasePolymeraseHistidine basic -
Reduction of Pectinesterase Activity in a Commercial Enzyme Preparation
Journal of the Science of Food and Agriculture J Sci Food Agric 85:1613–1621 (2005) DOI: 10.1002/jsfa.2154 Reduction of pectinesterase activity in a commercial enzyme preparation by pulsed electric fields: comparison of inactivation kinetic models Joaquın´ Giner, Pascal Grouberman, Vicente Gimeno and Olga Martın´ ∗ Department of Food Technology, University of Lleida, CeRTA-UTPV, ETSEA, Avda Alcalde Rovira Roure 191, 25198-Lleida, Spain Abstract: The inactivation of pectinesterase (PE) in a commercial enzyme preparation (CEP) under high intensity pulsed electric fields (HIPEF) was studied. After desalting and water dilution of the raw CEP, samples were exposed to exponentially decay waveform pulses for up to 463 µs at electric field intensities ranging from 19 to 38 kV cm−1. Pulses were applied in monopolar mode. Experimental data were fitted to a first-order kinetic model as well as to models based on Fermi, Hulsheger¨ or Weibull equations to describe PE inactivation kinetics. Characteristic parameters for each model were calculated. Relationships between some of the parameters and process variables were obtained. The Weibull model yielded the best accuracy factor. The relationship between residual PE and input of electrical energy density was found to be that of exponential decay. 2005 Society of Chemical Industry Keywords: pulsed electric fields; kinetics; pectinesterase; model; inactivation INTRODUCTION It has become customary to use CEPs in fruit and Pectinesterase (PE; EC 3.1.1.11) is a pectic enzyme vegetable juice technology. Depending -
Regulation of Calmodulin-Stimulated Cyclic Nucleotide Phosphodiesterase (PDE1): Review
95-105 5/6/06 13:44 Page 95 INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 18: 95-105, 2006 95 Regulation of calmodulin-stimulated cyclic nucleotide phosphodiesterase (PDE1): Review RAJENDRA K. SHARMA, SHANKAR B. DAS, ASHAKUMARY LAKSHMIKUTTYAMMA, PONNIAH SELVAKUMAR and ANURAAG SHRIVASTAV Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Cancer Research Division, Saskatchewan Cancer Agency, 20 Campus Drive, Saskatoon SK S7N 4H4, Canada Received January 16, 2006; Accepted March 13, 2006 Abstract. The response of living cells to change in cell 6. Differential inhibition of PDE1 isozymes and its environment depends on the action of second messenger therapeutic applications molecules. The two second messenger molecules cAMP and 7. Role of proteolysis in regulating PDE1A2 Ca2+ regulate a large number of eukaryotic cellular events. 8. Role of PDE1A1 in ischemic-reperfused heart Calmodulin-stimulated cyclic nucleotide phosphodiesterase 9. Conclusion (PDE1) is one of the key enzymes involved in the complex interaction between cAMP and Ca2+ second messenger systems. Some PDE1 isozymes have similar kinetic and 1. Introduction immunological properties but are differentially regulated by Ca2+ and calmodulin. Accumulating evidence suggests that the A variety of cellular activities are regulated through mech- activity of PDE1 is selectively regulated by cross-talk between anisms controlling the level of cyclic nucleotides. These Ca2+ and cAMP signalling pathways. These isozymes are mechanisms include synthesis, degradation, efflux and seque- also further distinguished by various pharmacological agents. stration of cyclic adenosine 3':5'-monophosphate (cAMP) and We have demonstrated a potentially novel regulation of PDE1 cyclic guanosine 3':5'- monophosphate (cGMP) within the by calpain. -
Enzyme DHRS7
Toward the identification of a function of the “orphan” enzyme DHRS7 Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel von Selene Araya, aus Lugano, Tessin Basel, 2018 Originaldokument gespeichert auf dem Dokumentenserver der Universität Basel edoc.unibas.ch Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. Dr. Alex Odermatt (Fakultätsverantwortlicher) und Prof. Dr. Michael Arand (Korreferent) Basel, den 26.6.2018 ________________________ Dekan Prof. Dr. Martin Spiess I. List of Abbreviations 3α/βAdiol 3α/β-Androstanediol (5α-Androstane-3α/β,17β-diol) 3α/βHSD 3α/β-hydroxysteroid dehydrogenase 17β-HSD 17β-Hydroxysteroid Dehydrogenase 17αOHProg 17α-Hydroxyprogesterone 20α/βOHProg 20α/β-Hydroxyprogesterone 17α,20α/βdiOHProg 20α/βdihydroxyprogesterone ADT Androgen deprivation therapy ANOVA Analysis of variance AR Androgen Receptor AKR Aldo-Keto Reductase ATCC American Type Culture Collection CAM Cell Adhesion Molecule CYP Cytochrome P450 CBR1 Carbonyl reductase 1 CRPC Castration resistant prostate cancer Ct-value Cycle threshold-value DHRS7 (B/C) Dehydrogenase/Reductase Short Chain Dehydrogenase Family Member 7 (B/C) DHEA Dehydroepiandrosterone DHP Dehydroprogesterone DHT 5α-Dihydrotestosterone DMEM Dulbecco's Modified Eagle's Medium DMSO Dimethyl Sulfoxide DTT Dithiothreitol E1 Estrone E2 Estradiol ECM Extracellular Membrane EDTA Ethylenediaminetetraacetic acid EMT Epithelial-mesenchymal transition ER Endoplasmic Reticulum ERα/β Estrogen Receptor α/β FBS Fetal Bovine Serum 3 FDR False discovery rate FGF Fibroblast growth factor HEPES 4-(2-Hydroxyethyl)-1-Piperazineethanesulfonic Acid HMDB Human Metabolome Database HPLC High Performance Liquid Chromatography HSD Hydroxysteroid Dehydrogenase IC50 Half-Maximal Inhibitory Concentration LNCaP Lymph node carcinoma of the prostate mRNA Messenger Ribonucleic Acid n.d. -
Analyses of PDE-Regulated Phosphoproteomes Reveal Unique and Specific Camp-Signaling Modules in T Cells
Analyses of PDE-regulated phosphoproteomes reveal unique and specific cAMP-signaling modules in T cells Michael-Claude G. Beltejara, Ho-Tak Laua, Martin G. Golkowskia, Shao-En Onga, and Joseph A. Beavoa,1 aDepartment of Pharmacology, University of Washington, Seattle, WA 98195 Contributed by Joseph A. Beavo, May 28, 2017 (sent for review March 10, 2017; reviewed by Paul M. Epstein, Donald H. Maurice, and Kjetil Tasken) Specific functions for different cyclic nucleotide phosphodiester- to bias T-helper polarization toward Th2, Treg, or Th17 pheno- ases (PDEs) have not yet been identified in most cell types. types (13, 14). In a few cases increased cAMP may even potentiate Conventional approaches to study PDE function typically rely on the T-cell activation signal (15), particularly at early stages of measurements of global cAMP, general increases in cAMP- activation. Recent MS-based proteomic studies have been useful dependent protein kinase (PKA), or the activity of exchange in characterizing changes in the phosphoproteome of T cells under protein activated by cAMP (EPAC). Although newer approaches various stimuli such as T-cell receptor stimulation (16), prosta- using subcellularly targeted FRET reporter sensors have helped glandin signaling (17), and oxidative stress (18), so much of the define more compartmentalized regulation of cAMP, PKA, and total Jurkat phosphoproteome is known. Until now, however, no EPAC, they have limited ability to link this regulation to down- information on the regulation of phosphopeptides by PDEs has stream effector molecules and biological functions. To address this been available in these cells. problem, we have begun to use an unbiased mass spectrometry- Inhibitors of cAMP PDEs are useful tools to study PKA/EPAC- based approach coupled with treatment using PDE isozyme- mediated signaling, and selective inhibitors for each of the 11 PDE – selective inhibitors to characterize the phosphoproteomes of the families have been developed (19 21). -
Pyruvate-Phosphate Dikinase of Oxymonads and Parabasalia and the Evolution of Pyrophosphate-Dependent Glycolysis in Anaerobic Eukaryotes† Claudio H
EUKARYOTIC CELL, Jan. 2006, p. 148–154 Vol. 5, No. 1 1535-9778/06/$08.00ϩ0 doi:10.1128/EC.5.1.148–154.2006 Copyright © 2006, American Society for Microbiology. All Rights Reserved. Pyruvate-Phosphate Dikinase of Oxymonads and Parabasalia and the Evolution of Pyrophosphate-Dependent Glycolysis in Anaerobic Eukaryotes† Claudio H. Slamovits and Patrick J. Keeling* Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada Received 29 September 2005/Accepted 8 November 2005 In pyrophosphate-dependent glycolysis, the ATP/ADP-dependent enzymes phosphofructokinase (PFK) and pyruvate kinase are replaced by the pyrophosphate-dependent PFK and pyruvate phosphate dikinase (PPDK), respectively. This variant of glycolysis is widespread among bacteria, but it also occurs in a few parasitic anaerobic eukaryotes such as Giardia and Entamoeba spp. We sequenced two genes for PPDK from the amitochondriate oxymonad Streblomastix strix and found evidence for PPDK in Trichomonas vaginalis and other parabasalia, where this enzyme was thought to be absent. The Streblomastix and Giardia genes may be related to one another, but those of Entamoeba and perhaps Trichomonas are distinct and more closely related to bacterial homologues. These findings suggest that pyrophosphate-dependent glycolysis is more widespread in eukaryotes than previously thought, enzymes from the pathway coexists with ATP-dependent more often than previously thought and may be spread by lateral transfer of genes for pyrophosphate-dependent enzymes from bacteria. Adaptation to anaerobic metabolism is a complex process (PPDK), respectively (for a comparison of these reactions, see involving changes to many proteins and pathways of critical reference 21). -
Open Matthew R Moreau Ph.D. Dissertation Finalfinal.Pdf
The Pennsylvania State University The Graduate School Department of Veterinary and Biomedical Sciences Pathobiology Program PATHOGENOMICS AND SOURCE DYNAMICS OF SALMONELLA ENTERICA SEROVAR ENTERITIDIS A Dissertation in Pathobiology by Matthew Raymond Moreau 2015 Matthew R. Moreau Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2015 The Dissertation of Matthew R. Moreau was reviewed and approved* by the following: Subhashinie Kariyawasam Associate Professor, Veterinary and Biomedical Sciences Dissertation Adviser Co-Chair of Committee Bhushan M. Jayarao Professor, Veterinary and Biomedical Sciences Dissertation Adviser Co-Chair of Committee Mary J. Kennett Professor, Veterinary and Biomedical Sciences Vijay Kumar Assistant Professor, Department of Nutritional Sciences Anthony Schmitt Associate Professor, Veterinary and Biomedical Sciences Head of the Pathobiology Graduate Program *Signatures are on file in the Graduate School iii ABSTRACT Salmonella enterica serovar Enteritidis (SE) is one of the most frequent common causes of morbidity and mortality in humans due to consumption of contaminated eggs and egg products. The association between egg contamination and foodborne outbreaks of SE suggests egg derived SE might be more adept to cause human illness than SE from other sources. Therefore, there is a need to understand the molecular mechanisms underlying the ability of egg- derived SE to colonize the chicken intestinal and reproductive tracts and cause disease in the human host. To this end, the present study was carried out in three objectives. The first objective was to sequence two egg-derived SE isolates belonging to the PFGE type JEGX01.0004 to identify the genes that might be involved in SE colonization and/or pathogenesis. -
Human Lysosomal Sulphate Transport
Human Lysosomal Sulphate Transport Martin David LEWIS B.Sc. (Hons) Thesis Submitted For the Degree Of Doctor of PhilosoPhY rn The University of Adelaide (Faculty of Medicine) May 2001 Lysosomal Diseases Research Unit and Department of P aediatrics PathologY Faculty of Medicine Department of Chemical 'Women's Women's and Children's HosPital and Children's HosPital South Australia South Australia 11 Elliot, Sømuel and Millie Table of Gontents Abstract xl1 Declaration xiv Acknowledgments XV Abbreviations xvi List of Figures xxi List of Tables xxiii 1. INTRODUGTION. """""""" 1 1.1.1 1,1.2 Membrane proteins. """"""""2 1.1.3 Types oftransporters. """"""'4 5 t.t.4 Carrier transport mechanisms. 1.1.5 1.2 Sutphate metabolism. 8 1.2.1 Phosphoadenosinephosphosulphatesynthesis"" I 1 1.2.2 The roles of sulphate within the cell' ' "" " " 1.2.2.1 A structuralrole of sulphation. ..""""' """""""""""' 11 t2 1.2.2.2 Metabolic and regulatory roles of sulphate' """""" 1.2.3 Intracellular sulphate pools...'........ """"""12 12 1.2.3.1 The origins of intracellular sulphate pools"" 1.2.3.2 Metabolism of sulphate from cysteine """""""""""" 15 1.2.3.3 Regulation of sulphate pools 1.3 The definition and function of the lysosome' """""""""""'19 1.3.1 Structure of the lysosome. ....'......... """""'20 1.3.1.1 Lysosomal hydrolysis of glycosaminoglycans"""' """"""""""""'21 25 1.3.1.1.1 Sulphatases 1.3 .2 Lysosomal biogenesis. 1.3.2.1 Targeting of lysosomal luminal proterns' 27 1V t.3.2.2 Targeting of lysosomal membrane proteins. """""""28 28 1.3.2.3 Lysosomal membrane Proteins 30 1.3.3 Lysosomal transporters 32 1.3.3.1 Proton pump (H*-ATPase) 33 1.3.3.2 Lysosomal cystine üansport............ -
Multi-Enzymatic Cascades in the Synthesis of Modified Nucleosides
biomolecules Article Multi-Enzymatic Cascades in the Synthesis of Modified Nucleosides: Comparison of the Thermophilic and Mesophilic Pathways Ilja V. Fateev , Maria A. Kostromina, Yuliya A. Abramchik, Barbara Z. Eletskaya , Olga O. Mikheeva, Dmitry D. Lukoshin, Evgeniy A. Zayats , Maria Ya. Berzina, Elena V. Dorofeeva, Alexander S. Paramonov , Alexey L. Kayushin, Irina D. Konstantinova * and Roman S. Esipov Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 GSP, B-437 Moscow, Russia; [email protected] (I.V.F.); [email protected] (M.A.K.); [email protected] (Y.A.A.); [email protected] (B.Z.E.); [email protected] (O.O.M.); [email protected] (D.D.L.); [email protected] (E.A.Z.); [email protected] (M.Y.B.); [email protected] (E.V.D.); [email protected] (A.S.P.); [email protected] (A.L.K.); [email protected] (R.S.E.) * Correspondence: [email protected]; Tel.: +7-905-791-1719 ! Abstract: A comparative study of the possibilities of using ribokinase phosphopentomutase ! nucleoside phosphorylase cascades in the synthesis of modified nucleosides was carried out. Citation: Fateev, I.V.; Kostromina, Recombinant phosphopentomutase from Thermus thermophilus HB27 was obtained for the first time: M.A.; Abramchik, Y.A.; Eletskaya, a strain producing a soluble form of the enzyme was created, and a method for its isolation and B.Z.; Mikheeva, O.O.; Lukoshin, D.D.; chromatographic purification was developed. It was shown that cascade syntheses of modified nu- Zayats, E.A.; Berzina, M.Y..; cleosides can be carried out both by the mesophilic and thermophilic routes from D-pentoses: ribose, Dorofeeva, E.V.; Paramonov, A.S.; 2-deoxyribose, arabinose, xylose, and 2-deoxy-2-fluoroarabinose.