Domain of Escherichia Coli 16S Ribosomal RNA Using Site-Directed Photoaffinity Crosslinking
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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. -
End Strand of Gene Gene Name Gene Function Starnd of Trascript
Genomic TSS strand Gene starnd of Transcipt relatively to TSS Start End Gene name coordinates relatively TSS type Control_fwd TEX_fwd Control_rev TEX_rev of gene function trascript gene group of TSS to ATG ribosomal 93 854 + rps12 + 1 protein S12 1 1 14.0638317 20.7539794 0 0 93 324 exon 1 + 111 rps12 intron 1 1 13.90756687 18.07149224 0.781323982 0.423550599 829 854 exon 2 + 496 rps12 exon2 2 24.22104343 15.24782157 0 0 30S 904 1371 + gene rps7 ribosomal + 2 protein S7 1303 -209 rps7 inter (ndhB) 2 20.47068832 9.035746118 0.625059185 0.847101199 NADH dehydrogen 1512 3535 + gene ndhB (ndh2) + ase subunit 3 2 1696 ndhB exon 1-inter 2 3.594090315 2.964854195 0.468794389 0.282367066 + 2209 ndhB exon 1-inter 2 46.09811492 4.09432246 0.468794389 0.423550599 1512 2237 exon 1 + 2756 ndhB exon 2 -inter 2 43.28534858 4.800240125 0.312529593 0.282367066 2756 3535 exon 2 + 3090 ndhB exon 2 -inter 2 17.50165719 15.95373924 0.312529593 0 + 3192 ndhB exon 2 -inter 2 140.6383167 117.6058831 2.812766334 1.694202397 - 3462 ndhB exon 2 -inter 3 1.406383167 1.129468265 1.406383167 3.67077186 4 3633 3712 + tRNA tRNA-Leu-CAA + 3610 -23 tRNA-Leu 1 77.19480938 84.85130339 0.625059185 0 + 3633 1 tRNA-Leu 1 359.5652963 649.0207016 0.781323982 0 photosyste 3954 4058 + gene psbM m II protein + 5 M 3775 -179 psbM 2 20.47068832 12.00060031 0 0.141183533 + 3954 psbM-0 2 69.22530477 28.37789015 0.156264796 0 hypothetical 4182 5073 + gene ycf66 6 protein 4182 4287 exon 1 4772 5073 exon 2 7 5202 5113 - gene ycf (ORF29) - 5299 orf29 inter 1 0 0 3.125295926 3.67077186 -
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. -
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. -
Supersized Ribosomal RNA Expansion Segments in Asgard Archaea 2 Authors: Petar I
bioRxiv preprint doi: https://doi.org/10.1101/2019.12.25.888164; this version posted June 13, 2020. 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 Supersized ribosomal RNA expansion segments in Asgard archaea 2 Authors: Petar I. Penev1,2, Sara Fakhretaha-Aval1,3, Vaishnavi J. Patel4, Jamie J. Cannone4, 3 Robin R. Gutell4, Anton S. Petrov1,3*, Loren Dean Williams1,2,3*, Jennifer B. Glass1,2,5* 4 Affiliations: 1NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA 2School of Biological Sciences, Georgia Institute of Technology, North Avenue, Atlanta, GA 30332, USA 3School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr, Atlanta, GA 30332, USA 5 4Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, 6 Austin, TX 78712, USA 7 5School of Earth and Atmospheric Sciences, Georgia Institute of Technology, 311 Ferst Dr, 8 Atlanta, GA 30332, USA 9 *Correspondence to: [email protected]; [email protected]; 10 [email protected] 11 1 bioRxiv preprint doi: https://doi.org/10.1101/2019.12.25.888164; this version posted June 13, 2020. 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. -
A Systematic Rnai Synthetic Interaction Screen Reveals a Link Between P53 and Snornp Assembly
ARTICLES A systematic RNAi synthetic interaction screen reveals a link between p53 and snoRNP assembly Dragomir B. Krastev1,2, Mikolaj Slabicki2, Maciej Paszkowski-Rogacz1,2, Nina C. Hubner3,4, Magno Junqueira2,4, Andrej Shevchenko2, Matthias Mann3, Karla M. Neugebauer2 and Frank Buchholz1,2,5 TP53(tumour protein 53) is one of the most frequently mutated genes in human cancer and its role during cellular transformation has been studied extensively. However, the homeostatic functions of p53 are less well understood. Here, we explore the molecular dependency network of TP53 through an RNAi-mediated synthetic interaction screen employing two HCT116 isogenic cell lines and a genome-scale endoribonuclease-prepared short interfering RNA library. We identify a variety of TP53 synthetic interactions unmasking the complex connections of p53 to cellular physiology and growth control. Molecular dissection of the TP53 synthetic interaction with UNRIP indicates an enhanced dependency of TP53-negative cells on small nucleolar ribonucleoprotein (snoRNP) assembly. This dependency is mediated by the snoRNP chaperone gene NOLC1 (also known as NOPP140), which we identify as a physiological p53 target gene. This unanticipated function of TP53 in snoRNP assembly highlights the potential of RNAi-mediated synthetic interaction screens to dissect molecular pathways of tumour suppressor genes. More than 30 years of intense research on the tumour suppressor to different chemical drugs14,15. Several synthetic interactions with gene TP53 has revealed its relevance in many aspects of tumour tumour suppressor genes have also been published11,16, but to our biology (reviewed in ref. 1). It is now well established that p53 knowledge a genome-scale survey for synthetic interactions of a (the protein product of TP53) activation leads to the execution of a tumour suppressor gene has not been reported. -
Characterization of R-Protein Variants in Saccharomyces Cerevisiae
Characterization of r-protein variants in Saccharomyces cerevisiae DISSERTATION ZUR ERLANGUNG DES DOKTORGRADES DER NATURWISSENSCHAFTEN (DR. RER. NAT.) DER NATURWISSENSCHAFTLICHEN FAKULTÄT III BIOLOGIE UND VORKLINISCHE MEDIZIN DER UNIVERSITÄT REGENSBURG vorgelegt von Andreas Neueder aus Bogen Regensburg, 2010 Promotionsgesuch eingereicht am: 13.04.2010 Prüfungausschuss: Vorsitzender: Prof. Dr. A. Kurtz 1. Gutachter: Prof. Dr. H. Tschochner 2. Gutachter: Prof. Dr. R. Sterner 3. Prüfer: Prof. Dr. W. Seufert Ersatzprüfer: Prof. Dr. T. Dresselhaus Diese Arbeit wurde unter der Anleitung von Prof. Dr. Herbert Tschochner und Dr. Philipp Milkereit am Lehrstuhl für Biochemie III des Instituts für Mikrobiologie, Genetik und Biochemie der Universität Regensburg erstellt. Ich erkläre hiermit, dass ich die vorliegende Arbeit ohne unzulässige Hilfe Dritter und ohne Benutzung anderer als der angegebenen Hilfsmittel angefertigt habe. Die aus anderen Quellen direkt oder indirekt übernommenen Daten und Konzepte sind unter Angabe der Quelle gekennzeichnet. Insbesondere habe ich nicht die entgeltliche Hilfe von Vermittlungs- bzw. Beratungsdiensten (Promotionsberater oder andere Personen) in Anspruch genommen. Niemand hat von mir unmittelbar oder mittelbar geldwerte Leistungen für Arbeit erhalten, die im Zusammenhang mit dem Inhalt der vorgelegten Dissertation stehen. Die Arbeit wurde bisher weder im In- noch im Ausland in gleicher oder ähnlicher Form einer anderen Prüfungsbehörde vorgelegt. Regensburg, den Table of contents Table of contents 1 Introduction -
S6:S18 Ribosomal Protein Complex Interacts with a Structural Motif Present in Its Own Mrna
Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press BIOINFORMATICS S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA DOROTA MATELSKA,1 ELZBIETA PURTA,1 SYLWIA PANEK,1 MICHAL J. BONIECKI,1 JANUSZ M. BUJNICKI,1,2,3 and STANISLAW DUNIN-HORKAWICZ1,3 1Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland 2Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan´,61-614, Poland ABSTRACT Prokaryotic ribosomal protein genes are typically grouped within highly conserved operons. In many cases, one or more of the encoded proteins not only bind to a specific site in the ribosomal RNA, but also to a motif localized within their own mRNA, and thereby regulate expression of the operon. In this study, we computationally predicted an RNA motif present in many bacterial phyla within the 5′ untranslated region of operons encoding ribosomal proteins S6 and S18. We demonstrated that the S6:S18 complex binds to this motif, which we hereafter refer to as the S6:S18 complex-binding motif (S6S18CBM). This motif is a conserved CCG sequence presented in a bulge flanked by a stem and a hairpin structure. A similar structure containing a CCG trinucleotide forms the S6:S18 complex binding site in 16S ribosomal RNA. We have constructed a 3D structural model of a S6:S18 complex with S6S18CBM, which suggests that the CCG trinucleotide in a specific structural context may be specifically recognized by the S18 protein.