DOCSLIB.ORG

A Farnesyltransferase Inhibitor Activates Lysosomes and Reduces

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Farnesyltransferase Inhibitor Activates Lysosomes and Reduces SCIENCE TRANSLATIONAL MEDICINE | RESEARCH ARTICLE NEURODEGENERATIVE DISEASE Copyright © 2019 The Authors, some rights reserved; A farnesyltransferase inhibitor activates lysosomes and exclusive licensee American Association reduces tau pathology in mice with tauopathy for the Advancement Israel Hernandez1*, Gabriel Luna1*, Jennifer N. Rauch1, Surya A. Reis2, Michel Giroux1, of Science. No claim 3 1 1 4 4 to original U.S. Celeste M. Karch , Daniel Boctor , Youssef E. Sibih , Nadia J. Storm , Antonio Diaz , Government Works Susmita Kaushik4, Cezary Zekanowski5, Alexander A. Kang1, Cassidy R. Hinman1, Vesna Cerovac1, Elmer Guzman1, Honjun Zhou1, Stephen J. Haggarty2, Alison M. Goate6, Steven K. Fisher1,7, Ana M. Cuervo4, Kenneth S. Kosik1,7† Tau inclusions are a shared feature of many neurodegenerative diseases, among them frontotemporal dementia caused by tau mutations. Treatment approaches for these conditions include targeting posttranslational modifi- cations of tau proteins, maintaining a steady-state amount of tau, and preventing its tendency to aggregate. We discovered a new regulatory pathway for tau degradation that operates through the farnesylated protein, Rhes, a GTPase in the Ras family. Here, we show that treatment with the farnesyltransferase inhibitor lonafarnib reduced Rhes and decreased brain atrophy, tau inclusions, tau sumoylation, and tau ubiquitination in the rTg4510 mouse model of tauopathy. In addition, lonafarnib treatment attenuated behavioral abnormalities in rTg4510 mice and reduced microgliosis in mouse brain. Direct reduction of Rhes in the rTg4510 mouse by siRNA reproduced the results observed with lonafarnib treatment. The mechanism of lonafarnib action mediated by Rhes to reduce tau pathology was shown to operate through activation of lysosomes. We finally showed in mouse brain and in hu- man induced pluripotent stem cell–derived neurons a normal developmental increase in Rhes that was initially suppressed by tau mutations. The known safety of lonafarnib revealed in human clinical trials for cancer suggests that this drug could be repurposed for treating tauopathies. INTRODUCTION Ras superfamily (14). RASD2 became of interest in HD because it The tauopathies constitute a broad range of neurodegenerative dis- was thought to be expressed mainly in the striatum (15). However, eases, all of which share the hallmark feature of tau inclusions. Al- in humans, Rhes expression is clearly evident in the cerebral cortex though tau-related diseases including Alzheimer’s disease and chronic (16). Rhes activates autophagy independently of mammalian target of traumatic encephalopathy are serious public health problems (1), no rapamycin (mTOR) via interaction with beclin 1 (17). Furthermore, disease-modifying treatment currently exists for these conditions. Rhes has been shown to modulate the aggregation state of mutant Generally, approaches to treatment have directly targeted the tau pro- Huntingtin (mHtt), the protein mutated in HD, by promoting its tein and include tau antibodies (2), antisense oligonucleotides (3), sumoylation and reducing cell survival (18). This toxicity involves caspase cleavage products (4), and anti-aggregation agents (5). How- binding of Rhes to mHtt and requires the Rhes CXXX farnesylated ever, few pharmacologic interventions directed toward tau pathways membrane attachment site (18). We inferred that the induction of have reached clinical trials. Interventions in upstream pathways such autophagy is a pharmacological class effect of farnesyltransferase inhi- as inhibitors of tau phosphorylation (6) or acetylation (7) have shown bition (19) and could be relevant for tauopathies. Therefore, we studied some efficacy in animal models, but none of these approaches has farnesyltransferase as a therapeutic target for the treatment of tauopathies. had success in human clinical trials to date. Rapidly growing inter- We used the farnesyltransferase inhibitor lonafarnib, a drug for which est in autophagy as a downstream pathway that mediates tau clear- there is extensive clinical experience (20–22), and tested it in the rTg4510 ance (8–10) as well as the implication of autophagy and lysosomes mouse model of tauopathy. in other neurodegenerative conditions (11–13) suggest therapeutic opportunities. In Huntington’s disease (HD), a pathway linked to autophagy is mediated by the RASD2 gene, which encodes the Rhes RESULTS protein, a small guanosine triphosphatase (GTPase) member of the Farnesylation inhibition attenuates tau pathology in the rTg4510 mouse model of tauopathy 1 Lonafarnib is a potent farnesyltransferase inhibitor with a Ki (inhibi- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, tion constant) in the nanomolar range (23), which crosses the blood- CA 93106, USA. 2Department of Neurology, Massachusetts General Hospital, Chem- ical Neurobiology Lab, and Center for Genomic Medicine, Harvard Medical School, brain barrier and has only a few minor side effects in humans (21). Boston, MA 02114, USA. 3Department of Psychiatry, Washington University School We sought to determine the effects of lonafarnib administration in 4 of Medicine in St. Louis, St. Louis, MO 63110, USA. Department of Developmental the rTg4510 mouse, a widely used model of frontotemporal dementia and Molecular Biology and Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY 10461, USA. 5Laboratory of Neurogenetics, Mossakowski (24). These mice develop tau tangles in the cerebral cortex by 4 months Medical Research Centre, Polish Academy of Sciences, 5 Pawinskiego St., 02-106 of age and in the hippocampus by 5.5 months of age along with the Warsaw, Poland. 6Department of Neuroscience, Icahn School of Medicine at Mount 7 loss of about 60% of their hippocampal CA1 neurons (24). Spatial Sinai, New York, NY 10029, USA. Department of Molecular, Cellular, and Developmen- memory deficits become apparent by 2.5 to 4 months of age, and tal Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA. *These authors contributed equally to this work. electrophysiological properties of cortical neurons are affected before †Corresponding author. Email: [email protected] the accumulation of tau pathology (25, 26). To precisely determine Hernandez et al., Sci. Transl. Med. 11, eaat3005 (2019) 27 March 2019 1 of 17 SCIENCE TRANSLATIONAL MEDICINE | RESEARCH ARTICLE the effects of lonafarnib, we first replicated the time course for the red), which became apparent from ~12 weeks of age and preceded onset of tau pathology in rTg4510 mice (Fig. 1, A to K, and fig. S1). the appearance of MC1-positive neurons (fig. S1). As transgenic mice Similar to the reported data, immunoreactivity for the conforma- aged, anti-GFAP immunoreactivity increased in the cortex but not tional tau antibody MC1, corresponding to neurofibrillary tangles in the hippocampus (Fig. 1, I to K). Lonafarnib treatment decreased throughout the hippocampus, amygdala, entorhinal cortex, and ce- cortical astrocyte immunostaining when compared to vehicle-treated rebral cortex (Fig. 1A, green), was first detected at ~16 weeks of age mice (P = 0.041; Fig. 2, N to R) but displayed no effect on the hippo- (fig. S1D). Immunoreactivity progressed by 20 weeks of age to a mean campus (P = 0.236, ANOVA). of 93.0 ± 13.6 MC1-positive cells/mm2 in the cerebral cortex and 67.6 ± 13.1 MC1-positive cells/mm2 in the hippocampus (Fig. 1, Attenuation of behavioral abnormalities in rTg4510 mice by D and E). Wild-type (WT) mice showed no detectable MC1-positive farnesyltransferase inhibition neurons (Fig. 1C). As rTg4510 transgenic mice age, they display progressive behavioral Lonafarnib treatment was initiated at 10 weeks of age. Lonafarnib impairments. Marble burial and nest shredding behaviors (28, 29) was resuspended in 20% 2-hydroxypropyl-b-cyclodextrin as vehicle, are affected early, and by 30 weeks of age, transgenic animals have and rTg4510 mice were gavaged on an intermittent schedule, with progressed to hyperexcitability and obsessive circling. Using the same 5 days on and 5 days off at 80 mg/kg per day (27). Mice were evalu- lonafarnib treatment protocol (27, 30), beginning at 10 weeks of age, ated at 20 weeks of age (Fig. 2, A to H) and showed that drug treat- we sought to reduce or prevent the behavioral deficits induced by tau ment reduced MC1 immunoreactivity. The MC1 immunoreactivity pathology. Nest building was assessed at 20 weeks. WT littermates in the lonafarnib-treated mouse cortex (88.8 ± 8.1 MC1-positive produced well-rounded nests (Fig. 3A); however, untreated rTg4510 cells/mm2) and hippocampus (27.4 ± 5.2 MC1-positive cells/mm2) mice displayed poor nest shredding and, in some instances, left bed- was significantly reduced compared to either vehicle-treated mice ding material completely undisturbed (Fig. 3B). Lonafarnib treat- (183.3 ± 10.4 MC1-positive cells/mm2 in the cortex and 82.2 ± 6.8 ment rescued nest building (Fig. 3C). At 5 weeks of age, littermate MC1-positive cells/mm2 in the hippocampus; cortex: P = 0.006, controls and transgenic mice produced nests with similar scores hippocampus: P = 0.001; Fig. 2H) or untreated age-matched trans- (control mice, 3.58 ± 0.13; transgenic mice, 3.23 ± 0.12; P = 1.00). genic mice (cortex: P = 0.049, hippocampus: P = 9.6 × 10−6). Compa- Whereas control mice nesting scores did not significantly change with rable results were obtained by immunostaining mouse brain sections time (P = 1.00), transgenic mice nesting scores declined (P =
Load more

Recommended publications
  • Roles of Amino Acids in the <Italic>Escherichia Coli</Italic
    Article pubs.acs.org/biochemistry Roles of Amino Acids in the Escherichia coli Octaprenyl Diphosphate Synthase Active Site Probed by Structure-Guided Site-Directed Mutagenesis † ∥ † ‡ § † ‡ Keng-Ming Chang, Shih-Hsun Chen, Chih-Jung Kuo, , Chi-Kang Chang, Rey-Ting Guo, , ∥ † ‡ § Jinn-Moon Yang, and Po-Huang Liang*, , , † Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan ‡ Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan § Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan ∥ Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan *S Supporting Information ABSTRACT: Octaprenyl diphosphate synthase (OPPS) catalyzes consecutive condensation reactions of farnesyl diphosphate (FPP) with five molecules of isopentenyl diphosphates (IPP) to generate C40 octaprenyl diphosphate, which constitutes the side chain of ubiquinone or menaquinone. To understand the roles of active site amino acids in substrate binding and catalysis, we conducted site- directed mutagenesis studies with Escherichia coli OPPS. In conclusion, D85 is the most important residue in the first DDXXD motif for both FPP and IPP binding through an H-bond network involving R93 and R94, respectively, whereas R94, K45, R48, and H77 are responsible for IPP binding by providing H-bonds and ionic interactions. K170 and T171 may stabilize the farnesyl carbocation intermediate to facilitate the reaction, whereas R93 and K225 may stabilize the catalytic base (MgPPi) for HR proton abstraction after IPP condensation. K225 and K235 in a flexible loop may interact with FPP when the enzyme becomes a closed conformation, which is therefore crucial for catalysis. Q208 is near the hydrophobic part of IPP and is important for IPP binding and catalysis.
    [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]
  • Supplemental Methods
    Supplemental Methods: Sample Collection Duplicate surface samples were collected from the Amazon River plume aboard the R/V Knorr in June 2010 (4 52.71’N, 51 21.59’W) during a period of high river discharge. The collection site (Station 10, 4° 52.71’N, 51° 21.59’W; S = 21.0; T = 29.6°C), located ~ 500 Km to the north of the Amazon River mouth, was characterized by the presence of coastal diatoms in the top 8 m of the water column. Sampling was conducted between 0700 and 0900 local time by gently impeller pumping (modified Rule 1800 submersible sump pump) surface water through 10 m of tygon tubing (3 cm) to the ship's deck where it then flowed through a 156 µm mesh into 20 L carboys. In the lab, cells were partitioned into two size fractions by sequential filtration (using a Masterflex peristaltic pump) of the pre-filtered seawater through a 2.0 µm pore-size, 142 mm diameter polycarbonate (PCTE) membrane filter (Sterlitech Corporation, Kent, CWA) and a 0.22 µm pore-size, 142 mm diameter Supor membrane filter (Pall, Port Washington, NY). Metagenomic and non-selective metatranscriptomic analyses were conducted on both pore-size filters; poly(A)-selected (eukaryote-dominated) metatranscriptomic analyses were conducted only on the larger pore-size filter (2.0 µm pore-size). All filters were immediately submerged in RNAlater (Applied Biosystems, Austin, TX) in sterile 50 mL conical tubes, incubated at room temperature overnight and then stored at -80oC until extraction. Filtration and stabilization of each sample was completed within 30 min of water collection.
    [Show full text]
  • A Specific Non-Bisphosphonate Inhibitor of the Bifunctional Farnesyl/Geranylgeranyl 2 Diphosphate Synthase in Malaria Parasites 3 4 Jolyn E
    bioRxiv preprint doi: https://doi.org/10.1101/134338; this version posted July 21, 2017. 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. 1 A specific non-bisphosphonate inhibitor of the bifunctional farnesyl/geranylgeranyl 2 diphosphate synthase in malaria parasites 3 4 Jolyn E. Gisselberg1, Zachary Herrera1, Lindsey Orchard4, Manuel Llinás4,5,6, and Ellen Yeh1,2,3* 5 6 1Department of Biochemistry, 2Pathology, and 3Microbiology and Immunology, Stanford 7 Medical School, Stanford University, Stanford, CA 94305, USA 8 9 4Department of Biochemistry & Molecular Biology, 5Department of Chemistry and 6Huck 10 Center for Malaria Research, Pennsylvania State University, University Park, PA 16802 11 12 13 14 15 *Corresponding author and lead contact: [email protected] 16 17 1 bioRxiv preprint doi: https://doi.org/10.1101/134338; this version posted July 21, 2017. 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. 18 Summary 19 Isoprenoid biosynthesis is essential for Plasmodium falciparum (malaria) parasites and contains 20 multiple validated antimalarial drug targets, including a bifunctional farnesyl and geranylgeranyl 21 diphosphate synthase (FPPS/GGPPS). We identified MMV019313 as an inhibitor of 22 PfFPPS/GGPPS. Though PfFPPS/GGPPS is also inhibited by a class of bisphosphonate drugs, 23 MMV019313 has significant advantages for antimalarial drug development.
    [Show full text]
  • (10) Patent No.: US 8119385 B2
    US008119385B2 (12) United States Patent (10) Patent No.: US 8,119,385 B2 Mathur et al. (45) Date of Patent: Feb. 21, 2012 (54) NUCLEICACIDS AND PROTEINS AND (52) U.S. Cl. ........................................ 435/212:530/350 METHODS FOR MAKING AND USING THEMI (58) Field of Classification Search ........................ None (75) Inventors: Eric J. Mathur, San Diego, CA (US); See application file for complete search history. Cathy Chang, San Diego, CA (US) (56) References Cited (73) Assignee: BP Corporation North America Inc., Houston, TX (US) OTHER PUBLICATIONS c Mount, Bioinformatics, Cold Spring Harbor Press, Cold Spring Har (*) Notice: Subject to any disclaimer, the term of this bor New York, 2001, pp. 382-393.* patent is extended or adjusted under 35 Spencer et al., “Whole-Genome Sequence Variation among Multiple U.S.C. 154(b) by 689 days. Isolates of Pseudomonas aeruginosa” J. Bacteriol. (2003) 185: 1316 1325. (21) Appl. No.: 11/817,403 Database Sequence GenBank Accession No. BZ569932 Dec. 17. 1-1. 2002. (22) PCT Fled: Mar. 3, 2006 Omiecinski et al., “Epoxide Hydrolase-Polymorphism and role in (86). PCT No.: PCT/US2OO6/OOT642 toxicology” Toxicol. Lett. (2000) 1.12: 365-370. S371 (c)(1), * cited by examiner (2), (4) Date: May 7, 2008 Primary Examiner — James Martinell (87) PCT Pub. No.: WO2006/096527 (74) Attorney, Agent, or Firm — Kalim S. Fuzail PCT Pub. Date: Sep. 14, 2006 (57) ABSTRACT (65) Prior Publication Data The invention provides polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides US 201O/OO11456A1 Jan. 14, 2010 encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides.
    [Show full text]
  • Supplementary Information
    Supplementary information (a) (b) Figure S1. Resistant (a) and sensitive (b) gene scores plotted against subsystems involved in cell regulation. The small circles represent the individual hits and the large circles represent the mean of each subsystem. Each individual score signifies the mean of 12 trials – three biological and four technical. The p-value was calculated as a two-tailed t-test and significance was determined using the Benjamini-Hochberg procedure; false discovery rate was selected to be 0.1. Plots constructed using Pathway Tools, Omics Dashboard. Figure S2. Connectivity map displaying the predicted functional associations between the silver-resistant gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S3. Connectivity map displaying the predicted functional associations between the silver-sensitive gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S4. Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-resistance are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle.
    [Show full text]
  • Farnesyltransferase-Mediated Delivery of a Covalent Inhibitor Overcomes Alternative Prenylation to Mislocalize K‑Ras † ∥ ⊥ † ∥ # ‡ § † # Chris J
    Articles pubs.acs.org/acschemicalbiology Farnesyltransferase-Mediated Delivery of a Covalent Inhibitor Overcomes Alternative Prenylation to Mislocalize K‑Ras † ∥ ⊥ † ∥ # ‡ § † # Chris J. Novotny, , , Gregory L. Hamilton, , , Frank McCormick, , and Kevan M. Shokat*, , † Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States ‡ NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21701, United States § Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, United States *S Supporting Information ABSTRACT: Mutationally activated Ras is one of the most common oncogenic drivers found across all malignancies, and its selective inhibition has long been a goal in both pharma and academia. One of the oldest and most validated methods to inhibit overactive Ras signaling is by interfering with its post-translational processing and subsequent cellular localization. Previous attempts to target Ras processing led to the development of farnesyltransferase inhibitors, which can inhibit H-Ras localization but not K-Ras due to its ability to bypass farnesyltransterase inhibition through alternative prenylation by geranylgeranyltransferase. Here, we present the creation of a neo- substrate for farnesyltransferase that prevents the alternative prenlation by geranylgeranyltransferase and
    [Show full text]
  • For Personal Use. Only Reproduce with Permission from the Lancet
    Correlation to non-HGNT Accesion group 2 Description AA897204 1.479917 ESTs T85111 1.286576 null T60168 | AI821353 1.274487 thyroid transcription factor 1 AA600173 1.183065 ubiquitin-conjugating enzyme E2A (RAD6 homolog) R55745 1.169339 ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D) AA400492 1.114935 ESTs AA864791 1.088826 hypothetical protein FLJ21313 N53758 1.070402 EST AI216628 1.067763 ESTs AI167637 1.058561 ESTs AA478265 1.056331 similar to transmembrane receptor Unc5H1 AA969924 1.039315 EST AI074650 1.039043 hypothetical protein FLJ13842 R20763 1.035807 ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C) AI347081 1.034518 Ca2+-dependent activator protein for secretion R44386 1.028005 ESTs AA976699 1.027227 chromogranin A (parathyroid secretory protein 1) AA634475 1.026766 KIAA1796 protein AA496809 1.02432 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 H16572 1.013059 null H29013 1.002117 seizure related 6 homolog (mouse)-like AI299731 1.001053 Homo sapiens nanos mRNA, partial cds AA400194 0.9950039 EST AI216537 | AI820870 0.9737153 Homo sapiens cDNA FLJ39674 fis, clone SMINT2009505 AA426408 0.9728649 type I transmembrane receptor (seizure-related protein) AA971742 | AI733380 0.9707561 achaete-scute complex-like 1 (Drosophila) R41450 0.9655133 ESTs AA487505 0.9636143 immunoglobulin superfamily, member 4 AA404337 0.957686 thymus high mobility group box protein TOX N68578 0.9552571 ESTs R45008 0.9422938 ELAV (embryonic lethal, abnormal
    [Show full text]
  • Genome-Wide Investigation of Cellular Functions for Trna Nucleus
    Genome-wide Investigation of Cellular Functions for tRNA Nucleus- Cytoplasm Trafficking in the Yeast Saccharomyces cerevisiae DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Hui-Yi Chu Graduate Program in Molecular, Cellular and Developmental Biology The Ohio State University 2012 Dissertation Committee: Anita K. Hopper, Advisor Stephen Osmani Kurt Fredrick Jane Jackman Copyright by Hui-Yi Chu 2012 Abstract In eukaryotic cells tRNAs are transcribed in the nucleus and exported to the cytoplasm for their essential role in protein synthesis. This export event was thought to be unidirectional. Surprisingly, several lines of evidence showed that mature cytoplasmic tRNAs shuttle between nucleus and cytoplasm and their distribution is nutrient-dependent. This newly discovered tRNA retrograde process is conserved from yeast to vertebrates. Although how exactly the tRNA nuclear-cytoplasmic trafficking is regulated is still under investigation, previous studies identified several transporters involved in tRNA subcellular dynamics. At least three members of the β-importin family function in tRNA nuclear-cytoplasmic intracellular movement: (1) Los1 functions in both the tRNA primary export and re-export processes; (2) Mtr10, directly or indirectly, is responsible for the constitutive retrograde import of cytoplasmic tRNA to the nucleus; (3) Msn5 functions solely in the re-export process. In this thesis I focus on the physiological role(s) of the tRNA nuclear retrograde pathway. One possibility is that nuclear accumulation of cytoplasmic tRNA serves to modulate translation of particular transcripts. To test this hypothesis, I compared expression profiles from non-translating mRNAs and polyribosome-bound translating mRNAs collected from msn5Δ and mtr10Δ mutants and wild-type cells, in fed or acute amino acid starvation conditions.
    [Show full text]
  • B Number Gene Name Strand Orientation Protein Length Mrna
    list list sample) short list predicted B number Operon ID Gene name assignment Protein length mRNA present mRNA intensity Gene description Protein detected - Strand orientation Membrane protein detected (total list) detected (long list) membrane sample Proteins detected - detected (short list) # of tryptic peptides # of tryptic peptides # of tryptic peptides # of tryptic peptides # of tryptic peptides Functional category detected (membrane Protein detected - total Protein detected - long b0001 thrL + 21 1344 P 1 0 0 0 0 thr operon leader peptide Metabolism of small molecules 1 b0002 thrA + 820 13624 P 39 P 18 P 18 P 18 P(m) 2 aspartokinase I, homoserine dehydrogenase I Metabolism of small molecules 1 b0003 thrB + 310 6781 P 9 P 3 3 P 3 0 homoserine kinase Metabolism of small molecules 1 b0004 thrC + 428 15039 P 18 P 10 P 11 P 10 0 threonine synthase Metabolism of small molecules 1 b0005 b0005 + 98 432 A 5 0 0 0 0 orf, hypothetical protein Open reading frames 2 b0006 yaaA - 258 1047 P 11 P 1 2 P 1 0 orf, hypothetical protein Open reading frames 3 b0007 yaaJ - 476 342 P 8 0 0 0 0 MP-GenProt-PHD inner membrane transport protein Miscellaneous 4 b0008 talB + 317 20561 P 20 P 13 P 16 P 13 0 transaldolase B Metabolism of small molecules 5 b0009 mog + 195 1296 P 7 0 0 0 0 required for the efficient incorporation of molybdate into molybdoproteins Metabolism of small molecules 6 b0010 yaaH - 188 407 A 2 0 0 0 0 PHD orf, hypothetical protein Open reading frames 7 b0011 b0011 - 237 338 P 13 0 0 0 0 putative oxidoreductase Miscellaneous 8 b0012 htgA
    [Show full text]
  • Cysteine Farnesyltransferase
    Proc. Nati. Acad. Sci. USA Vol. 87, pp. 7541-7545, October 1990 Biochemistry Identification and preliminary characterization of protein- cysteine farnesyltransferase (ras oncogenes/p21 proteins/CAAX-box motif/farnesyl pyrophosphate) VEERASWAMY MANNE*, DANIEL ROBERTS*, ANDREW TOBIN*, EDWARD O'RoURKE*, MARCIA DE VIRGILIOt, CHESTER MEYERSt, NASHEED AHMEDt, BORIS KuRzf, MARILYN RESHt, HSIANG-FU KUNG§, AND MARIANO BARBACID* Departments of *Molecular Biology and tChemistry, Squibb Institute for Medical Research, P.O. Box 4000, Princeton, NJ 08543-4000; tDepartment of Biology, Princeton University, Princeton, NJ 08540; and §Laboratory of Biochemical Physiology, National Cancer Institute-Frederick Cancer Research Facility, Frederick, MD 21701 Communicated by George J. Todaro, July 16, 1990 ABSTRACT Ras proteins must be isoprenylated at a con- Saccharomyces cerevisiae have shown that deprivation of served cysteine residue near the carboxyl terminus (Cys-186 in mevalonate (a precursor of FPP) in mutants deficient in mammalian Ras p21 proteins) in order to exert their biological 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reduc- activity. Previous studies indicate that an intermediate in the tase, the enzyme responsible for mevalonate synthesis, re- mevalonate pathway, most likely farnesyl pyrophosphate, is stores the normal phenotype to cells that either overexpress the donor of this isoprenyl group. Inhibition of mevalonate the wild-type RAS2 gene or carry a mutated RAS2v"l-9 allele synthesis reverts the abnormal phenotypes induced by the (14). Similarly, inhibitors of HMG-CoA reductase blocked mutant RAS2vW19 gene in Saccharomyces cerevisiae and blocks the maturation ofXenopus oocytes induced by a transforming the maturation ofXenopus oocytes induced by an oncogenic Ras Ha-Rasval-12 protein (14).
    [Show full text]
  • O O2 Enzymes Available from Sigma Enzymes Available from Sigma
    COO 2.7.1.15 Ribokinase OXIDOREDUCTASES CONH2 COO 2.7.1.16 Ribulokinase 1.1.1.1 Alcohol dehydrogenase BLOOD GROUP + O O + O O 1.1.1.3 Homoserine dehydrogenase HYALURONIC ACID DERMATAN ALGINATES O-ANTIGENS STARCH GLYCOGEN CH COO N COO 2.7.1.17 Xylulokinase P GLYCOPROTEINS SUBSTANCES 2 OH N + COO 1.1.1.8 Glycerol-3-phosphate dehydrogenase Ribose -O - P - O - P - O- Adenosine(P) Ribose - O - P - O - P - O -Adenosine NICOTINATE 2.7.1.19 Phosphoribulokinase GANGLIOSIDES PEPTIDO- CH OH CH OH N 1 + COO 1.1.1.9 D-Xylulose reductase 2 2 NH .2.1 2.7.1.24 Dephospho-CoA kinase O CHITIN CHONDROITIN PECTIN INULIN CELLULOSE O O NH O O O O Ribose- P 2.4 N N RP 1.1.1.10 l-Xylulose reductase MUCINS GLYCAN 6.3.5.1 2.7.7.18 2.7.1.25 Adenylylsulfate kinase CH2OH HO Indoleacetate Indoxyl + 1.1.1.14 l-Iditol dehydrogenase L O O O Desamino-NAD Nicotinate- Quinolinate- A 2.7.1.28 Triokinase O O 1.1.1.132 HO (Auxin) NAD(P) 6.3.1.5 2.4.2.19 1.1.1.19 Glucuronate reductase CHOH - 2.4.1.68 CH3 OH OH OH nucleotide 2.7.1.30 Glycerol kinase Y - COO nucleotide 2.7.1.31 Glycerate kinase 1.1.1.21 Aldehyde reductase AcNH CHOH COO 6.3.2.7-10 2.4.1.69 O 1.2.3.7 2.4.2.19 R OPPT OH OH + 1.1.1.22 UDPglucose dehydrogenase 2.4.99.7 HO O OPPU HO 2.7.1.32 Choline kinase S CH2OH 6.3.2.13 OH OPPU CH HO CH2CH(NH3)COO HO CH CH NH HO CH2CH2NHCOCH3 CH O CH CH NHCOCH COO 1.1.1.23 Histidinol dehydrogenase OPC 2.4.1.17 3 2.4.1.29 CH CHO 2 2 2 3 2 2 3 O 2.7.1.33 Pantothenate kinase CH3CH NHAC OH OH OH LACTOSE 2 COO 1.1.1.25 Shikimate dehydrogenase A HO HO OPPG CH OH 2.7.1.34 Pantetheine kinase UDP- TDP-Rhamnose 2 NH NH NH NH N M 2.7.1.36 Mevalonate kinase 1.1.1.27 Lactate dehydrogenase HO COO- GDP- 2.4.1.21 O NH NH 4.1.1.28 2.3.1.5 2.1.1.4 1.1.1.29 Glycerate dehydrogenase C UDP-N-Ac-Muramate Iduronate OH 2.4.1.1 2.4.1.11 HO 5-Hydroxy- 5-Hydroxytryptamine N-Acetyl-serotonin N-Acetyl-5-O-methyl-serotonin Quinolinate 2.7.1.39 Homoserine kinase Mannuronate CH3 etc.
    [Show full text]