DOCSLIB.ORG

The Cellular and Molecular Dynamics of the Queuosine Modification In

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Cellular and Molecular Dynamics of the Queuosine Modification In Old Dominion University ODU Digital Commons Theses and Dissertations in Biomedical Sciences College of Sciences Summer 1997 The Cellular and Molecular Dynamics of the Queuosine Modification in rT ansfer RNA: Definition, Modulation, Deficiencies and Effect of the Queuosine Modification System Rana C. Morris Old Dominion University Follow this and additional works at: https://digitalcommons.odu.edu/biomedicalsciences_etds Part of the Biochemistry Commons, Biophysics Commons, Molecular Biology Commons, and the Oncology Commons Recommended Citation Morris, Rana C.. "The Cellular and Molecular Dynamics of the Queuosine Modification in rT ansfer RNA: Definition, Modulation, Deficiencies andff E ect of the Queuosine Modification System" (1997). Doctor of Philosophy (PhD), Dissertation, , Old Dominion University, DOI: 10.25777/bwhj-g976 https://digitalcommons.odu.edu/biomedicalsciences_etds/63 This Dissertation is brought to you for free and open access by the College of Sciences at ODU Digital Commons. It has been accepted for inclusion in Theses and Dissertations in Biomedical Sciences by an authorized administrator of ODU Digital Commons. For more information, please contact [email protected]. THE CELLULAR AND MOLECULAR DYNAMICS OF THE QUEUOSINE MODIFICATION IN TRANSFER RNA: DEFINITION, MODULATION, DEFICIENCIES AND EFFECT OF THE QUEUOSINE MODIFICATION SYSTEM by Rana C. Morris B.S. May 1990, the College of William and Mary in Virginia A Dissertation Submitted to the Faculties of Old Dominion University and Eastern Virginia Medical School in Partial Fulfillment of the Requirement for the Degree of DOCTOR OF PHILOSOPHY BIOMEDICAL SCIENCES OLD DOMINION UNIVERSITY and EASTERN VIRGINIA MEDICAL SCHOOL August 1997 Approved by: irk S. Elliott (Chair) rank J. Castora hristophensL^Osgeod Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. ABSTRACT THE CELLULAR AND MOLECULAR DYNAMICS OF THE QUEUOSINE MODIFICATION IN TRANSFER RNA: DEFINITION, MODULATION, DEFICIENCIES, AND EFFECT OF THE QUEUOSINE MODIFICATION SYSTEM Rana C. Morris Old DominioQ University and Eastern Virginia Medical School, 1997 Director Dr. Mark S. Elliott The presence of the queuosine modification in the wobble position of tRNA“ , tRNA*5*, tRNAhIS, and tRNA151* is associated with a decrease in cellular growth rate, an increase in the ability to withstand environmental stress, and differentiation of pleuripotent cells into mature phenotypes. The loss of this normal modification is strongly correlated with neoplastic transformation and tumor progression of a wide variety of cancers. The “normal” system for formation of the queuosine modification in tRNA was studied in human fibroblast cell cultures and in mouse, rat and human liver tissues. The queuosine modification system is shown to be made up of three distinct mechanisms: uptake of the queuine base across the plasma membrane; incorporation of this base into cytoplasmic tRNA; and salvage of the base from products of normal tRNA degradation. The queuine membrane transporter and incorporation enzyme are activated via phosphorylation by protein kinase C and inactivated by the action of a phosphatase. This regulation by phosphorylation integrates the queuosine modification system into a very sensitive eukaryotic cellular switching mechanism already known to produce phenotypic alterations with strong correlations to changes in queuosine levels. A comparative study of two “abnormal” human adenocarcinoma cell-lines (colon and breast) was performed to assess their queuosine levels and determine the malfunctioning system step(s) for the cause of the observed deficiencies. The 100% queuosine-deficient colon tumor cell-line possessed a null mutation for the queuosine incorporation enzyme, while the 50-60% queuosine-deficient breast tumor cell-line exhibited a strong deficiency in the queuine salvage mechanism. These results demonstrate the potential for determination of even multiple sites of lesions in the modification sytem that would yield queuosine- deficient tRNA characteristic of tumors. Computational modeling was utilized to determine the biological function for the queuosine modification. Steric, electrostatic, and structural differences were observed for queuosine, queuosine- analogues and guanosine, the nucleosides incorporated into tRNA“p anticodon stem/loop structures, and in triad complexes of tRNA*sp with mRNA and tRNA1*®. The results of this research identify indistinguishable energetic parameters for complexes of queuosine-modified anticodon loops when paired with an mRNA containing cytosine- or a uridine-ending codon. However, guanosine-containing anticodon loops demonstrate much stronger energetic stability with cytosine-ending codons. The difference in codon Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. bias is shown to be due to the restriction of anticodon loop flexibility by a queuosine-induced extended intraloop hydrogen bonding network and only minimally due to a shift in hydrogen bonding pattern produced by an intraresidue hydrogen bond. A key difference in the physiology of normal and neoplastic cells is in the increased expression of oncodevelopmental genes with respect to those housekeeping genes needed for survival. Sequence analysis of several oncodevelopmental and housekeeping transcripts suggests the presence of a contrasting bias in the usage of queuosine*related codons which end in cytosine or either cytosine or uridine, respectively. In combination with the mechanism proposed for tRNA 19 decoding preferences, this codon usage bias suggests a potentially influential role for the queuosine modification system in the translational control of oncodevelopmental gene expression. Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. ‘Turns out not where but who you’re with that really matters. ‘Turns out not where but what you think that really matters. Whatever tears at us, whatever holds us down, if nothing can be done we’U make the best of what’s around. paraphrased from “The Best of What’s Around” by the Dave Matthews Band from their Album Under the Table and Dreaming (1994, The RCA Records Label) Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. ACKNOWLEDGMENTS As much as I've toiled over the preparation of this document, I have procrastinated and postponed writing this “Acknowledgments” section for last because there is no way to adequately compensate the large number of extremely supportive people who have come into my life during my tenure in graduate school. Through the years of agonizing over coursework, written and oral comprehensive exams, research proposals, research itself an oral defense of the research, and the preparation of this enormous document, there have been many people who have contributed to my success, as well as intellectual and emotional survival. I extend my heartfelt gratitude to a large number of people, only some of whom are listed below. Foremost in their tolerance and patience have been my family. To the person who most strongly supported me throughout my tenure in graduate school and in life, I thank Jim for absolutely everything. There is not much else I can say to express my appreciation for your encouragment To the two little rugrats (Jamie and Sean! who showed me that there are truly important things in life, and that distraction, oftimes, can provide perspective that can solve even the most insurmountable of problems, I offer my biggest hugs and kisses. My mother and father (Steve and Louise), sister (Jo) and both sets of grandparents (Naomi & Sim and Ruth & Mannv! have well practiced their heritage of affectionate nagging for tutorials, seminars, reprints and official graduation dates. Even my father-in-law (Jim. Jr.) learned the art of the nag, though not through genetic inheritance. But their love and devotion saw me through the endless reschedulings and postponements. To the only other person who has had to deal with me day in and day out, in coffee and M-n-M surplus and in drought, through boring, incomprehensible seminar and defense, and with new creative ideas that work and that fail, I recognize the tireless, wit-filled, optimistic support from Dr. Mark S. Elliott my research advisor and cohort. However, an additional bucket-o-gratitude must also be extended to his family (Becky. Brent Dave, and Matt..not to mention the three does, rabbit and hamsterl who tolerated his absences and frustrations due to lab problems and successes. My many thanks to my Dissertation Committee (Dr. Frank Castora. Dr. Chris Osgood, and Dr. James Yuan) for their patience, suggestions and guidance, and above all for the time spent reviewing this manuscript. Many faculty members within the Department of Biochemistry and Chemistry aided me not only in my academic education, but also in my professional and personal development. Among these extremely supportive folks are: Dr. Charles Bell. Dr. Ken Brown. Dr. Bob Ake. Dr. Allen Clark. Dr. Pat Pleban. Dr. Laura Moen. Dr. Rov Williams, and Dr. Keith Carson from the Biology Department The large number of students who have come and gone over the years have been encouraging in their willingness to help, provide useful suggestions and criticisms, or just lend a patient ear. I thank a few in particular (soon-to-be! Dr.s Thomas Heard. Miguel Santos and Lester Pretlow. (already) Dr.s Jackie Smith and Sandi Ward, and Julie Patrick.
Load more

Recommended publications
  • (12) United States Patent (10) Patent No.: US 6,822,071 B1 Stephens Et Al
    USOO6822071B1 (12) United States Patent (10) Patent No.: US 6,822,071 B1 Stephens et al. (45) Date of Patent: Nov. 23, 2004 (54) POLYPEPTIDES FROM CHLAMYDIA (56) References Cited PNEUMONIAE AND THEIR USE IN THE DIAGNOSIS, PREVENTION AND FOREIGN PATENT DOCUMENTS TREATMENT OF DISEASE WO 99/27105 * 6/1999 (75) Inventors: Richard S. Stephens, Orinda, CA (US); OTHER PUBLICATIONS Wayne Mitchell, San Francsico, CA Gerhold et al-BioEssays 18(12):973-981, 1996.* (US); Sue S. Kalman, Saratoga, CA Wells et al Journal of Leukocyte Biology 61(5):545-550, (US); Ronald Davis, Palo Alto, CA 1997.* (US) Russell et al Journal of Molecular Biology 244:33-350, 1994.* (73) Assignee: The Regents of the University of Rudinger et al., in “Peptide Hormones' Parsons, TA ets, California, Oakland, CA (US) University Park Press pp. 1–6, 1976.* Burgess et al, The Journal of Cell Biology, 111:2129-2138, Notice: Subject to any disclaimer, the term of this 1990.* patent is extended or adjusted under 35 Lazar et al, Molecular and Cellular Biology U.S.C. 154(b) by 0 days. 8(3):1247–1252, 1988.* Jobling et al, Mol-Microbiol. 5(7): 1755–67, 1991.* (21) Appl. No.: 09/438,185 Pir-68 Database Accession No. E72002 Kalmar et al. Apr. (22) Filed: Nov. 11, 1999 23, 1999.* (Under 37 CFR 1.47) * cited by examiner Primary Examiner Patricia A. Duffy Related U.S. Application Data (74) Attorney, Agent, or Firm Townsend and Townsend (60) Provisional application No. 60/128,606, filed on Apr. 8, and Crew 1999, and provisional application No.
    [Show full text]
  • Prolonging Healthy Aging: Longevity Vitamins and Proteins PERSPECTIVE Bruce N
    PERSPECTIVE Prolonging healthy aging: Longevity vitamins and proteins PERSPECTIVE Bruce N. Amesa,1 Edited by Cynthia Kenyon, Calico Labs, San Francisco, CA, and approved September 13, 2018 (received for review May 30, 2018) It is proposed that proteins/enzymes be classified into two classes according to their essentiality for immediate survival/reproduction and their function in long-term health: that is, survival proteins versus longevity proteins. As proposed by the triage theory, a modest deficiency of one of the nutrients/cofactors triggers a built-in rationing mechanism that favors the proteins needed for immediate survival and reproduction (survival proteins) while sacrificing those needed to protect against future damage (longevity proteins). Impairment of the function of longevity proteins results in an insidious acceleration of the risk of diseases associated with aging. I also propose that nutrients required for the function of longevity proteins constitute a class of vitamins that are here named “longevity vitamins.” I suggest that many such nutrients play a dual role for both survival and longevity. The evidence for classifying taurine as a conditional vitamin, and the following 10 compounds as putative longevity vitamins, is reviewed: the fungal antioxidant ergo- thioneine; the bacterial metabolites pyrroloquinoline quinone (PQQ) and queuine; and the plant antioxidant carotenoids lutein, zeaxanthin, lycopene, α-andβ-carotene, β-cryptoxanthin, and the marine carotenoid astaxanthin. Because nutrient deficiencies are highly prevalent in the United States (and elsewhere), appro- priate supplementation and/or an improved diet could reduce much of the consequent risk of chronic disease and premature aging. vitamins | essential minerals | aging | nutrition I propose that an optimal level of many of the known adverse health effects.
    [Show full text]
  • Preferential Import of Queuosine-Modified Trnas Into
    Published online 9 July 2021 Nucleic Acids Research, 2021, Vol. 49, No. 14 8247–8260 https://doi.org/10.1093/nar/gkab567 Preferential import of queuosine-modified tRNAs into Trypanosoma brucei mitochondrion is critical for organellar protein synthesis Sneha Kulkarni1,2, Mary Anne T. Rubio1,3,EvaHegedusov˝ a´ 1, Robert L. Ross4, Patrick A. Limbach 5, Juan D. Alfonzo3 and Zdenekˇ Paris 1,2,* 1Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceskˇ eBud´ ejovice,ˇ Czech Republic, 2Faculty 3 of Science, University of South Bohemia, Ceskˇ eBud´ ejovice,ˇ Czech Republic, Department of Microbiology and The Downloaded from https://academic.oup.com/nar/article/49/14/8247/6318497 by guest on 01 October 2021 Center for RNA Biology, The Ohio State University, Columbus, OH, USA, 4Metabolomics Mass Spectrometry Core, Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA and 5Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA Received November 30, 2020; Revised May 28, 2021; Editorial Decision June 13, 2021; Accepted June 21, 2021 ABSTRACT sine (Q), a hypermodified 7-deaza-guanosine, is one of the most chemically intricate modifications described to date. Transfer RNAs (tRNAs) are key players in protein syn- Q is found at the wobble position 34 of tRNAs that contain thesis. To be fully active, tRNAs undergo extensive a5-GUN-3 anticodon sequence, where N represents any post-transcriptional modifications, including queuo- of the canonical nucleotides, which includes tRNAHisGUG, sine (Q), a hypermodified 7-deaza-guanosine present tRNAAspGUC, tRNAAsnGUU, tRNATyr GUA (3). Q is in the anticodon of several tRNAs in bacteria and eu- found in both bacteria and eukarya, and catalyzed by tRNA karya.
    [Show full text]
  • Discovery of Novel Bacterial Queuine Salvage Enzymes and Pathways in Human Pathogens
    Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens a,1 b,1 c,1 b d a Yifeng Yuan , Rémi Zallot , Tyler L. Grove , Daniel J. Payan , Isabelle Martin-Verstraete , Sara Sepic´ , Seetharamsingh Balamkundue, Ramesh Neelakandane, Vinod K. Gadie, Chuan-Fa Liue, Manal A. Swairjof,g, Peter C. Dedone,h,i, Steven C. Almoc, John A. Gerltb,j,k, and Valérie de Crécy-Lagarda,l,2 aDepartment of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611; bInstitute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801; cDepartment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461; dLaboratoire de Pathogénèse des Bactéries Anaérobies, Institut Pasteur et Université de Paris, F-75015 Paris, France; eSingapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore; fDepartment of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182; gThe Viral Information Institute, San Diego State University, San Diego, CA 92182; hDepartment of Biological Engineering and Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139; iCenter for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139; jDepartment of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801; kDepartment of Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801; and lUniversity of Florida Genetics Institute, Gainesville, FL 32610 Edited by Tina M. Henkin, The Ohio State University, Columbus, OH, and approved August 1, 2019 (received for review June 16, 2019) Queuosine (Q) is a complex tRNA modification widespread in 1A. The TGT enzyme, which is responsible for the base ex- eukaryotes and bacteria that contributes to the efficiency and accuracy change, is the signature enzyme in the Q biosynthesis pathway.
    [Show full text]
  • Synthesis of Tritium Labeled Queuine, Preq1 and Related Azide Probes Toward Examining the Prevalence of Queuine
    Synthesis of Tritium Labeled Queuine, PreQ1 and Related Azide Probes Toward Examining the Prevalence of Queuine by Allen F. Brooks A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Medicinal Chemistry) in the University of Michigan 2012 Doctoral Committee: Research Professor Hollis D. Showalter, Co-Chair Associate Professor George A. Garcia, Co-Chair Professor Hashim M. Al-Hashimi Assistant Professor Garry D. Dotson Assistant Professor Matthew B. Soellner © Allen F. Brooks 2012 In memory of Edward and Lillian Pederson ii Acknowledgements With my remaining time short, it is appropriate to look back and thank those that supported me in my dissertation work either professionally or as a friend. First and foremost, I have to acknowledge my best friend from the program, Adam Lee. If it was not for the trip to the ACS meeting in Chicago, Adam and I likely would have never got to know each other. Luckily, fate arranged such an occurrence. If not for Adam’s friendship and the support of some others, I likely would have left the program in my second year. I also have to thank Jason Witek, an undergraduate who worked in the Showalter lab. We actually met during the Organic Mechanisms course, as he was in an academic program of his own design. The time we worked together in the lab was a productive one, and interestingly an amusing time as well. I also have to thank several other associates for their help in progressing my research as well as making time here more pleasant, those individuals being: Dr.
    [Show full text]
  • Queuine, a Bacterial Derived Hypermodified Nucleobase, Shows Protection in in Vitro Models of Neurodegeneration
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.20.427538; this version posted January 22, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Queuine, a bacterial derived hypermodified nucleobase, shows protection in in vitro models of neurodegeneration Patricia Richard1*, Xavier Manière2*, Lucie Kozlowski2, Hélène Guillorit2,3, Patrice Garnier2, Antoine Danchin4, Nicole C. McKnight1** 1 Stellate Therapeutics Inc., 101 Avenue of the Americas, JLABS @ NYC, New York, NY 10013 2 Stellate Therapeutics SAS, 47 rue de Montmorency, 75003, Paris, France 3 Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094, Montpellier, France 4 Kodikos Labs, Institut Cochin, 24 rue du Faubourg Saint-Jacques, 75014, Paris, France ** corresponding author Email: [email protected] * These authors contributed equally to this work 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.20.427538; this version posted January 22, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Growing evidence suggests that human gut bacteria, comprising the microbiome that communicates with the brain through the so-called ‘gut-brain-axis’, are linked to neurodegener- ative disorders. Imbalances in the microbiome of Parkinson’s disease (PD) and Alzheimer’s dis- ease (AD) patients have been detected in several studies. Queuine is a hypermodified nucleobase enriched in the brain and exclusively produced by bacteria and salvaged by humans through their gut epithelium. Queuine replaces guanine at the wobble position of tRNAs with GUN anticodons and promotes efficient cytoplasmic and mitochondrial mRNA translation.
    [Show full text]
  • Deficiency of Queuine, a Highly Modified Furine Base, in Transfer Rnas from Primary and Metastatic Ovarian Malignant Tumors in Women1
    [CANCER RESEARCH 54, 446X-4471. August 15, 19<M| Deficiency of Queuine, a Highly Modified Furine Base, in Transfer RNAs from Primary and Metastatic Ovarian Malignant Tumors in Women1 Wlodzimierz Baranowski,2 Guy Dirheimer, Jerzy Andrzej Jakowicki, and GérardKeith Second Clinic of Gynecological Surgery, Academy of Medicine, 8 Jaczewski Street, Lublin 20849. Poland fW. B., J. A. J.J, and Unité"Structure des Macromolécules Biologiques et Mécanismesde Reconnaissance, " Institut de Biologie Moléculaireet Cellulaire du CNRS, 15 rue RenéDescartes, Strasbourg 67084, France [G. D., G. K.] ABSTRACT queuine on their own despite its presence in their queuine family tRNAs. In mammals, queuine is provided by the intestinal flora or as The IUN As from rapidly growing tissues, particularly from neoplasia, a diet factor. Furthermore, in embryonic tissues and regenerating rat often exhibit queuine deficiency. In order to check whether different kinds liver (i.e., in rapidly growing tissues), the queuine family tRNAs are of ovarian tumors display queuine deficiencies we have analyzed tRNA partially queuine deficient (6, 9). Similar observations of queuine samples from 16 ovarian malignancies. The tRNAs from histologically normal myometrium (4 samples) and myoma (6 samples) were taken as deficiency have been made in queuine family tRNAs from placenta healthy tissue and benign tumor references. Queuine deficiency was de tissue despite the presence of a large amount of free queuine in the termined by an exchange assay using (8-'H]guanine and tRNA:guanine amniotic fluid (8, 10). It has in addition been observed that neoplastic transglycosylase from Escherìchiacoli. tissues very often exhibit significant deficiencies in the queuine con The mean values of queuine deficiencies in tRNAs were: 10.95 ±2.21 tent of queuine family tRNAs (9).
    [Show full text]
  • Synthetic Ligands for Preq1 Riboswitches Provide Structural and Mechanistic Insights Into Targeting RNA Tertiary Structure
    ARTICLE https://doi.org/10.1038/s41467-019-09493-3 OPEN Synthetic ligands for PreQ1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure Colleen M. Connelly1, Tomoyuki Numata2,3, Robert E. Boer1, Michelle H. Moon1, Ranu S. Sinniah1, Joseph J. Barchi1, Adrian R. Ferré-D’Amaré 2 & John S. Schneekloth Jr. 1 1234567890():,; Riboswitches are naturally occurring RNA aptamers that regulate gene expression by binding to specific small molecules. Riboswitches control the expression of essential bacterial genes and are important models for RNA-small molecule recognition. Here, we report the discovery of a class of synthetic small molecules that bind to PreQ1 riboswitch aptamers. These molecules bind specifically and reversibly to the aptamers with high affinity and induce a conformational change. Furthermore, the ligands modulate riboswitch activity through tran- scriptional termination despite no obvious chemical similarity to the cognate ligand. X-ray crystallographic studies reveal that the ligands share a binding site with the cognate ligand but make different contacts. Finally, alteration of the chemical structure of the ligand causes changes in the mode of RNA binding and affects regulatory function. Thus, target- and structure-based approaches can be used to identify and understand the mechanism of synthetic ligands that bind to and regulate complex, folded RNAs. 1 Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21701, USA. 2 Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA. 3 Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan. These authors contributed equally: Colleen M.
    [Show full text]
  • Protection of the Queuosine Biosynthesis Enzyme Quef from Irreversible Oxidation by a Conserved Intramolecular Disulfide
    biomolecules Article Protection of the Queuosine Biosynthesis Enzyme QueF from Irreversible Oxidation by a Conserved Intramolecular Disulfide Adeba Mohammad 1, Adriana Bon Ramos 2, Bobby W. K. Lee 2, Spencer W. Cohen 2, Maryam K. Kiani 1, Dirk Iwata-Reuyl 2, Boguslaw Stec 3 and Manal A. Swairjo 1,3,* 1 Graduate College of Biomedical Sciences, Western University of Health Sciences, 309 E. Second Street, Pomona, CA 91766, USA; [email protected] (A.M.); [email protected] (M.K.K.) 2 Department of Chemistry, Portland State University, P.O. Box 751, Portland, OR 97207, USA; [email protected] (A.B.R.); [email protected] (B.W.K.L.); [email protected] (S.W.C.); [email protected] (D.I.-R.) 3 Department of Chemistry and Biochemistry, San Diego State University 5500 Campanile Drive, San Diego, CA 92182, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-619-206-3864 Academic Editor: Jürg Bähler Received: 10 January 2017; Accepted: 10 March 2017; Published: 16 March 2017 Abstract: QueF enzymes catalyze the nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) in the biosynthetic pathway to the tRNA modified nucleoside queuosine. The QueF-catalyzed reaction includes formation of a covalent thioimide intermediate with a conserved active site cysteine that is prone to oxidation in vivo. Here, we report the crystal structure of a mutant of Bacillus subtilis QueF, which reveals an unanticipated intramolecular disulfide formed between the catalytic Cys55 and a conserved Cys99 located near the active site.
    [Show full text]
  • Prokaryotic Transcription Regulation by the Nascent RNA Elements
    pISSN 2288-6982 l eISSN 2288-7105 Biodesign https://doi.org/10.34184/kssb.2020.8.2.33 MINI REVIEW P 33-40 Prokaryotic transcription regulation by the nascent RNA elements Seungha Hwang†, Jimin Lee† and Jin Young Kang* Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea *Correspondence: [email protected] †These authors contributed equally to this work. Transcription regulation by cis-acting elements such as DNA and RNA has not been investigated much compared to that of trans-acting elements like transcription factors because most cis-elements are much larger and more flexible than protein factors. Consequently, it was challenging to recapitulate the function of cis-elements in a reduced system for in vitro assays. However, the recent cryo-electron microscopy (cryo-EM) made it possible to study the effect of nascent RNA elements to the transcription in combination with biochemical experiments as cryo-EM does not require crystallization and tolerates heterogeneity to an extent. In this review, we briefly described the current model on prokaryotic transcriptional pausing based on the crystal and cryo-EM structures of RNA polymerases in different contexts, including an RNA hairpin pause. We then introduced two other nascent RNA elements that modulate transcription – preQ1 riboswitch and HK022 put RNA. Understanding the function of the RNA elements to transcription will deepen our understanding of the fundamental mechanism transcription and provide the structural basis for drug discovery as well as bioresearch tool development. INTRODUCTION synthesis is initiated (Tomsic et al., 2001). As the nascent RNA Transcription is an essential cellular process that transfers the is elongated, the 3’-end of the transcript makes clashes with a genetic information engraved in DNA to RNA transcripts to make loop (named “σ finger”) from the σ factor.
    [Show full text]
  • 27Th Trna Conference-Abstractsbook-3
    P1.1 The protein-only RNase P PRORP1 interacts with the nuclease MNU2 in Arabidopsis mitochondria G. Bonnard, M. Arrivé, A. Bouchoucha, A. Gobert, C. Schelcher, F. Waltz, P. Giegé Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France The essential endonuclease activity that removes 5’ leader sequences from transfer RNA precursors is called RNase P. While ribonucleoprotein RNase P enzymes containing a ribozyme are found in all domains of life, another type of RNase P called “PRORP”, for “PROtein-only RNase P”, only composed of protein occurs in a wide variety of eukaryotes, in organelles and the nucleus. Although PRORP proteins function as single subunit enzymes in vitro, we find that PRORP1 occurs in protein complexes and is present in polysome fractions in Arabidopsis mitochondria. The analysis of immuno- precipitated protein complexes identifies proteins involved in mitochondrial gene expression processes. In particular, direct interaction is established between PRORP1 and MNU2 another mitochondrial nuclease involved in RNA 5’ processing. A specific domain of MNU2 and a conserved signature of PRORP1 are found to be directly accountable for this protein interaction. Altogether, results reveal the existence of an RNA 5’ maturation complex in Arabidopsis mitochondria and suggest that PRORP proteins might cooperate with other gene expression regulators for RNA maturation in vivo. 111 P1.2 CytoRP, a cytosolic RNase P to target TLS-RNA phytoviruses 1 1 2 1 A. Gobert , Y. Quan , I. Jupin , P. Giegé 1Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France 1Institut Jacques Monod, CNRS, Université Paris Diderot, Paris, France In plants, PRORP enzymes are responsible for RNase P activity that involves the removal of the 5’ extremity of tRNA precursors.
    [Show full text]
  • MODOMICS: a Database of RNA Modification Pathways. 2017 Update
    Published online 2 November 2017 Nucleic Acids Research, 2018, Vol. 46, Database issue D303–D307 doi: 10.1093/nar/gkx1030 MODOMICS: a database of RNA modification pathways. 2017 update Pietro Boccaletto1,†, Magdalena A. Machnicka1,2,†, Elzbieta Purta1,Pawe-lPiatkowski˛ 1, B-lazej˙ Baginski´ 1, Tomasz K. Wirecki1,Valerie´ de Crecy-Lagard´ 3, Robert Ross4,Patrick A. Limbach4, Annika Kotter5, Mark Helm5 and Janusz M. Bujnicki1,6,* 1Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland, 2Institute of Informatics, University of Warsaw, Banacha 2, PL-02-097 Warsaw, Poland, 3Microbiology and Cell Science Department, University of Florida, Gainesville, FL 32611, USA, 4Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH 45221, USA, 5Institut fur¨ Pharmazie und Biochemie, Johannes Gutenberg-Universitat,¨ Staudinger Weg 5, D-55128 Mainz, Germany and 6Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, PL-61-614 Poznan, Poland Received September 15, 2017; Revised October 15, 2017; Editorial Decision October 16, 2017; Accepted October 18, 2017 ABSTRACT for basic biological processes [review: (1)]. Now we know that 163 post-transcriptional modifications of RNA intro- MODOMICS is a database of RNA modifications duce a functional diversity that allows the four basic ribonu- that provides comprehensive information concern- cleotide residues to gain diverse functions, akin to those of ing the chemical structures of modified ribonucleo- side chains of amino acid residues, which may be e.g., po- sides, their biosynthetic pathways, the location of lar, charged, aliphatic or aromatic. Modifications can di- modified residues in RNA sequences, and RNA- rectly influence RNA structure, by promoting or disrupt- modifying enzymes.
    [Show full text]