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Domain of Escherichia Coli 16S Ribosomal RNA Using Site-Directed Photoaffinity Crosslinking
Downloaded from rnajournal.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press RNA (1998), 4:1455–1466+ Cambridge University Press+ Printed in the USA+ Copyright © 1998 RNA Society+ Analysis of the conformation of the 39 major domain of Escherichia coli 16S ribosomal RNA using site-directed photoaffinity crosslinking ALEXANDRE MONTPETIT,1 CATHERINE PAYANT,1 JAMES M. NOLAN,2 and LÉA BRAKIER-GINGRAS1 1Département de Biochimie, Université de Montréal, Montréal, Québec H3T 1J4, Canada 2Department of Biochemistry, Tulane University Medical Center, New Orleans, Louisiana 70112, USA ABSTRACT The 39 major domain of Escherichia coli 16S rRNA, which occupies the head of the small ribosomal subunit, is involved in several functions of the ribosome. We have used a site-specific crosslinking procedure to gain further insights into the higher-order structure of this domain. Circularly permuted RNAs were used to introduce an azi- dophenacyl group at specific positions within the 39 major domain. Crosslinks were generated in a high-ionic strength buffer that has been used for ribosome reconstitution studies and so enables the RNA to adopt a structure recognized by ribosomal proteins. The crosslinking sites were identified by primer extension and confirmed by assessing the mobility of the crosslinked RNA lariats in denaturing polyacrylamide gels. Eight crosslinks were characterized. Among them, one crosslink demonstrates that helix 28 is proximal to the top of helix 34, and two others show that the 1337 region, located in an internal loop at the junction of helices 29, 30, 41, and 42, is proximal to the center of helix 30 and to a segment connecting helix 28 to helix 29. -
Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6
Research Collection Doctoral Thesis Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6 Author(s): Voigts-Hoffmann, Felix Publication Date: 2012 Permanent Link: https://doi.org/10.3929/ethz-a-007303759 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library ETH Zurich Dissertation No. 20189 Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6 A dissertation submitted to ETH ZÜRICH for the degree of Doctor of Sciences (Dr. sc. ETH Zurich) presented by Felix Voigts-Hoffmann MSc Molecular Biotechnology, Universität Heidelberg born April 11, 1981 citizen of Göttingen, Germany accepted on recommendation of Prof. Dr. Nenad Ban (Examiner) Prof. Dr. Raimund Dutzler (Co-examiner) Prof. Dr. Rudolf Glockshuber (Co-examiner) 2012 blank page ii Summary Ribosomes are large complexes of several ribosomal RNAs and dozens of proteins, which catalyze the synthesis of proteins according to the sequence encoded in messenger RNA. Over the last decade, prokaryotic ribosome structures have provided the basis for a mechanistic understanding of protein synthesis. While the core functional centers are conserved in all kingdoms, eukaryotic ribosomes are much larger than archaeal or bacterial ribosomes. Eukaryotic ribosomal rRNA and proteins contain extensions or insertions to the prokaryotic core, and many eukaryotic proteins do not have prokaryotic counterparts. Furthermore, translation regulation and ribosome biogenesis is much more complex in eukaryotes, and defects in components of the translation machinery are associated with human diseases and cancer. -
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. -
Intimate Relations—Mitochondria and Ageing
International Journal of Molecular Sciences Review Intimate Relations—Mitochondria and Ageing Michael Webb and Dionisia P. Sideris * Mitobridge Inc., an Astellas Company, 1030 Massachusetts Ave, Cambridge, MA 02138, USA; [email protected] * Correspondence: [email protected] Received: 29 August 2020; Accepted: 6 October 2020; Published: 14 October 2020 Abstract: Mitochondrial dysfunction is associated with ageing, but the detailed causal relationship between the two is still unclear. Wereview the major phenomenological manifestations of mitochondrial age-related dysfunction including biochemical, regulatory and energetic features. We conclude that the complexity of these processes and their inter-relationships are still not fully understood and at this point it seems unlikely that a single linear cause and effect relationship between any specific aspect of mitochondrial biology and ageing can be established in either direction. Keywords: mitochondria; ageing; energetics; ROS; gene regulation 1. Introduction The last two decades have witnessed a dramatic transformation in our view of mitochondria, their basic biology and functions. While still regarded as functioning primarily as the eukaryotic cell’s generator of energy in the form of adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide (reduced form; NADH), mitochondria are now recognized as having a plethora of functions, including control of apoptosis, regulation of calcium, forming a signaling hub and the synthesis of various bioactive molecules. Their biochemical functions beyond ATP supply include biosynthesis of lipids and amino acids, formation of iron sulphur complexes and some stages of haem biosynthesis and the urea cycle. They exist as a dynamic network of organelles that under normal circumstances undergo a constant series of fission and fusion events in which structural, functional and encoding (mtDNA) elements are subject to redistribution throughout the network. -
Organization and Evolution of 5S Ribosomal Dna in the Fish Genome
In: Focus on Genome Research ISSN 1-59033-960-6 Editor: Clyde R. Williams, pp335-363 ©2004 Nova Science Publishers, Inc. Chapter X ORGANIZATION AND EVOLUTION OF 5S RIBOSOMAL DNA IN THE FISH GENOME Cesar Martins 1 and Adriane Pinto Wasko 2 Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, CEP 18618-000, Botucatu, SP, Brazil. Phone/Fax +55 14 38116264, 1e-mail [email protected]; 2e-mail: [email protected] ABSTRACT In higher eukaryotes, the 5S ribosomal multigene family (5S rDNA) is tandemly organized in repeat units composed of a coding region (5S rRNA gene) and a non-transcribed spacer sequence (NTS). Although the 5S rDNA organization has been investigated in several vertebrate species, present data are concentrated in mammals and amphibians, whereas other groups, such as fishes, have been poorly studied. To further the understanding on the dynamics and evolution of 5S rDNA arrays in the vertebrate genome, recent studies have focused on the genome organization of these sequences in fish species, which represent the base group of vertebrate evolution. It was evidenced that the chromosome distribution of the 5S rDNA is quite conserved among related fish species occupying an interstitial position in the chromosomes. Although the 5S rDNA clusters have been maintained conserved in the chromosomes, changes in the nucleotide sequences and organization of the repeat units have occurred in fish species, as demonstrated by the presence of 5S rDNA variant types within and between genomes clustered in distinct chromosome environments. These variants are distributed in two major classes, suggesting that such pattern could represent a primitive condition for the fish genome, as well as for vertebrates. -
WO 2016/200987 Al 15 December 2016 (15.12.2016) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2016/200987 Al 15 December 2016 (15.12.2016) P O P C T (51) International Patent Classification: Trudi, A.; Indigo Agriculture, Inc., 500 Rutherford Aven A01N 63/02 (2006.01) A01C 1/00 (2006.01) ue, North Building, Boston, MA 02129 (US). A01N 63/00 (2006.01) A01C 1/06 (2006.01) (74) Agents: HUBL, Susan, T. et al; Fenwick & West LLP, (21) International Application Number: Silicon Valley Center, 801 California Street, Mountain PCT/US20 16/036504 View, CA 94041 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 8 June 2016 (08.06.2016) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (25) Filing Language: English BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (26) Publication Language: English DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, N , IR, IS, JP, KE, KG, KN, KP, KR, (30) Priority Data: KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, 62/172,748 8 June 2015 (08.06.2015) US MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, 62/172,750 8 June 2015 (08.06.2015) US PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, 62/172,755 8 June 2015 (08.06.2015) us SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 62/3 16,386 31 March 2016 (3 1.03.2016) us TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. -
HUMAN RIBOSOME BIOGENESIS and the REGULATION of the TUMOUR SUPPRESSOR P53
HUMAN RIBOSOME BIOGENESIS AND THE REGULATION OF THE TUMOUR SUPPRESSOR p53 Andria Pelava Submitted for Doctor of Philosophy Final submission: December 2016 Institute of Cell and Molecular Biosciences Faculty of Medical Sciences Newcastle University ii Abstract Ribosome production is an energetically expensive and, therefore, highly regulated process. Defects in ribosome biogenesis lead to genetic diseases called Ribosomopathies, such as Dyskeratosis Congenita (DC), and mutations in ribosomal proteins and ribosome biogenesis factors are linked to multiple types of cancer. During ribosome biogenesis, the ribosomal RNAs (rRNAs) are processed and modified, and defects in ribosome biogenesis lead to the activation of p53. This project aimed to investigate the functions of Dyskerin, mutated in X-linked DC, in human ribosome biogenesis and p53 regulation, and to explore the link between ribosome production and p53 homeostasis. Dyskerin is an rRNA pseudouridine synthase and required for telomere maintenance. There is some debate as to whether DC is the result of telomere maintenance or ribosome biogenesis defects. It is shown here that human Dyskerin is required for the production of both LSU and SSU, and knockdown of Dyskerin leads to p53 activation via inhibition of MDM2 via the 5S RNP, an LSU assembly intermediate which accumulates after ribosome biogenesis defects. My data indicate that p53 activation, due to defects in ribosome biogenesis, may contribute to the clinical symptoms seen in patients suffering with DC. In addition, it is shown that defects in early or late stages of SSU or LSU biogenesis, result in activation of p53 via the 5S RNP-MDM2 pathway, and that p53 is induced in less than 12 hours after ribosome biogenesis defects. -
Selenoprotein H Is an Essential Regulator of Redox Homeostasis That
Selenoprotein H is an essential regulator of redox PNAS PLUS homeostasis that cooperates with p53 in development and tumorigenesis Andrew G. Coxa, Allison Tsomidesa, Andrew J. Kima, Diane Saundersa, Katie L. Hwanga, Kimberley J. Evasonb, Jerry Heidelc, Kristin K. Brownd, Min Yuand, Evan C. Liend, Byung Cheon Leea,e, Sahar Nissima, Bryan Dickinsonf, Sagar Chhangawalag, Christopher J. Changh,i, John M. Asarad, Yariv Houvrasg, Vadim N. Gladysheva,j, and Wolfram Goesslinga,j,k,l,1 aBrigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115; bUniversity of Utah, Salt Lake City, UT 84112; cOregon State University, Corvallis, OR 97331; dBeth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115; eKorea University, 02841 Seoul, Republic of Korea; fUniversity of Chicago, Chicago, IL 60637; gWeill Cornell Medical College and New York Presbyterian Hospital, New York, NY 10065; hHoward Hughes Medical Institute, Bethesda, MD 20815; iUniversity of California, Berkeley, CA 20815; jBroad Institute of MIT and Harvard, Cambridge, MA 02142; kHarvard Stem Cell Institute, Cambridge, MA 02138; and lDana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115 Edited by Leonard I. Zon, Howard Hughes Medical Institute, Boston Children’s Hospital, Harvard Medical School, Boston, MA, and accepted by Editorial Board Member Carol Prives July 18, 2016 (received for review January 7, 2016) Selenium, an essential micronutrient known for its cancer preven- mice exhibit impaired selenium transport from the liver to pe- tion properties, is incorporated into a class of selenocysteine- ripheral tissues and show growth retardation and impaired motor containing proteins (selenoproteins). Selenoprotein H (SepH) is a coordination (13, 14). -
Transcriptomic Regulation of Alternative Phenotypic Trajectories in Embryos of the Annual Killifish Austrofundulus Limnaeus
Portland State University PDXScholar Dissertations and Theses Dissertations and Theses Fall 11-30-2017 Transcriptomic Regulation of Alternative Phenotypic Trajectories in Embryos of the Annual Killifish Austrofundulus limnaeus Amie L. Romney Portland State University Follow this and additional works at: https://pdxscholar.library.pdx.edu/open_access_etds Part of the Biology Commons, and the Genetics and Genomics Commons Let us know how access to this document benefits ou.y Recommended Citation Romney, Amie L., "Transcriptomic Regulation of Alternative Phenotypic Trajectories in Embryos of the Annual Killifish Austrofundulus limnaeus" (2017). Dissertations and Theses. Paper 4033. https://doi.org/10.15760/etd.5917 This Dissertation is brought to you for free and open access. It has been accepted for inclusion in Dissertations and Theses by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. Transcriptomic Regulation of Alternative Phenotypic Trajectories in embryos of the Annual Killifish Austrofundulus limnaeus by Amie Lynn Thomas Romney A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology Dissertation Committee Jason Podrabsky, Chair Suzanne Estes Bradley Buckley Todd Rosenstiel Dirk Iwata-Reuyl Portland State University 2017 © 2017 Amie Lynn Thomas Romney ABSTRACT The Annual Killifish, Austrofundulus limnaeus, survives the seasonal drying of their pond habitat in the form of embryos entering diapause midway through development. The diapause trajectory is one of two developmental phenotypes. Alternatively, individuals can “escape” entry into diapause and develop continuously until hatching. The alternative phenotypes of A. limnaeus are a form of developmental plasticity that provides this species with a physiological adaption for surviving stressful environments. -
Ribosomal RNA
Ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits. rRNA is the physical and mechanical factor of the ribosome that forces transfer RNA (tRNA) and messenger RNA (mRNA) to process and translate the latter into proteins.[1] Ribosomal RNA Three-dimensional views of the ribosome, showing rRNA in dark blue (small subunit) is the predominant form of RNA found in most cells; it makes and dark red (large subunit). Lighter colors up about 80% of cellular RNA despite never being translated represent ribosomal proteins. into proteins itself. Ribosomes are composed of approximately 60% rRNA and 40% ribosomal proteins by mass. Contents Structure Assembly Function Subunits and associated ribosomal RNA In prokaryotes In eukaryotes Biosynthesis In eukaryotes Eukaryotic regulation In prokaryotes Prokaryotic regulation Degradation In eukaryotes In prokaryotes Sequence conservation and stability Significance Human genes See also References External links Structure Although the primary structure of rRNA sequences can vary across organisms, base-pairing within these sequences commonly forms stem-loop configurations. The length and position of these rRNA stem-loops allow them to create three-dimensional rRNA structures that are similar across species.[2] Because of these configurations, rRNA can form tight and specific interactions with ribosomal proteins to form ribosomal subunits. These ribosomal proteins contain basic residues (as opposed to acidic residues) and aromatic residues (i.e. -
Open FINAL GRAD SCHOOL.Pdf
The Pennsylvania State University The Graduate School Eberly College of Science PHOSPHOPROTEOMIC ANALYSIS OF RIBOSOMAL PROTEINS: IMPLICATIONS IN TRANSLATION AND APOPTOSIS A Dissertation in Biochemistry, Microbiology, and Molecular Biology by Jennifer Lynn Miller © 2009 Jennifer Lynn Miller Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2009 The dissertation of Jennifer Lynn Miller was reviewed and approved* by the following: Emine C. Koc Assistant Professor Biochemistry and Molecular Biology Dissertation Advisor Chair of Committee Robert A. Schlegel Professor of Biochemistry and Molecular Biology Wendy Hanna-Rose Assistant Professor Biochemistry and Molecular Biology Ming Tien Professor of Biochemistry Erin D. Sheets Assistant Professor of Chemistry Richard J. Frisque Professor of Molecular Virology Head of the Department of Biochemistry and Molecular Biology *Signatures are on file in the Graduate School. ABSTRACT Mammalian mitochondrial ribosomes synthesize thirteen proteins that are essential for oxidative phosphorylation. Besides having a major role in ATP synthesis, mitochondria also contribute to biochemical processes coordinating apoptosis, mitochondrial diseases, and aging in eukaryotic cells. This unique class of ribosomes is protein-rich and distinct from cytoplasmic ribosomes. However, mitochondrial ribosomes (55S) share a significant homology to bacterial ribosomes (70S), particularly in size, the general mechanism of translation, and ribosomal protein content. Due to the overall resemblance between the two systems and the earlier reports of post-translational modifications, we investigated how phosphorylation of ribosomal proteins from bacteria and mitochondria regulates translation and other acquired roles. Identification of twenty- four phosphorylated 70S and 55S ribosomal proteins as well as the potential endogenous kinase was achieved using 2D-gel electrophoresis and tandem mass spectrometry. -
UC Riverside Electronic Theses and Dissertations
UC Riverside UC Riverside Electronic Theses and Dissertations Title Characterization of AtRAP Function in Plant Immunity and in RNA Transportation Permalink https://escholarship.org/uc/item/8pk9k169 Author Wang, Huan Publication Date 2017 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA RIVERSIDE Characterization of AtRAP Function in Plant Immunity and in RNA Transportation A Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Plant Pathology by Huan Wang December 2017 Dissertation Committee: Dr. Hailing Jin, Chairperson Dr. Julia Bailey-Serres Dr. Isgouhi Kaloshian Copyright by Huan Wang 2017 The Dissertation of Huan Wang is approved: Committee Chairperson University of California, Riverside ACKNOWLEDGEMENTS I would like to express my sincere gratitude and appreciation to all those who helped and encouraged me during my graduate study. My deepest gratitude goes first and foremost to Dr. Hailing Jin, my supervisor, for her patient and constant guidance and encouragement. No matter what the difficulty is, she always stands with me to give me very timely, experienced and smart advice to help me solve it quickly and efficiently. Her creative ideas, intelligent analysis, hardworking attitude and generous personality inspire and teach me a lot not only on my research but also on my philosophy of life. Secondly, I would like to express my heartfelt gratitude to my dissertation committee members, Dr. Julia Bailey-Serres and Dr. Isgouhi Kaloshian. I really appreciate your valuable suggestions and kindly help to my study. Dr. Julia Bailey-Serres continuously helps my study to be my guidance committee member, qualifying exam committee member, and dissertation committee member.