Extracurricular Functions of Trna Modifications in Microorganisms
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The RNA Modification Database, RNAMDB: 2011 Update William A
Published online 10 November 2010 Nucleic Acids Research, 2011, Vol. 39, Database issue D195–D201 doi:10.1093/nar/gkq1028 The RNA modification database, RNAMDB: 2011 update William A. Cantara1, Pamela F. Crain2, Jef Rozenski3, James A. McCloskey2,4, Kimberly A. Harris1, Xiaonong Zhang5, Franck A. P. Vendeix6, Daniele Fabris1,* and Paul F. Agris1,* 1The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, 2Department of Medicinal Chemistry, University of Utah, 30 S. 2000 East, Salt Lake City, UT 84112-5820, USA, 3Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, B 3000 Leuven, Belgium, 4Department of Biochemistry, University of Utah, 30 S. 2000 East, Salt Lake City, UT 84112-5820, 5College of Arts and Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222 and 6Sirga Advanced Biopharma, Inc., 2 Davis Drive, P.O. Box 13169, Research Triangle Park, NC 22709, USA Received September 30, 2010; Revised October 7, 2010; Accepted October 10, 2010 ABSTRACT INTRODUCTION Since its inception in 1994, The RNA Modification The chemical composition of an RNA molecule allows for Database (RNAMDB, http://rna-mdb.cas.albany. its inherent ability to play many roles within biological edu/RNAmods/) has served as a focal point for systems. This ability is further enhanced through the site information pertaining to naturally occurring RNA selected addition of the 109 currently known post- transcriptional modifications catalyzed by specific RNA modifications. In its current state, the database modification enzymes (1). These naturally-occurring modi- employs an easy-to-use, searchable interface fications are found in all three major RNA species (tRNA, for obtaining detailed data on the 109 currently mRNA and rRNA) in all three primary phylogenetic known RNA modifications. -
Identification and Codon Reading Properties of 5
Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Mandal, D., C. Kohrer, D. Su, I. R. Babu, C. T. Y. Chan, Y. Liu, D. Soll, et al. “Identification and Codon Reading Properties of 5- Cyanomethyl Uridine, a New Modified Nucleoside Found in the Anticodon Wobble Position of Mutant Haloarchaeal Isoleucine tRNAs.” RNA 20, no. 2 (December 16, 2013): 177–188. As Published http://dx.doi.org/10.1261/rna.042358.113 Publisher Cold Spring Harbor Laboratory Press/RNA Society Version Final published version Citable link http://hdl.handle.net/1721.1/91989 Terms of Use Creative Commons Attribution-Noncommerical Detailed Terms http://creativecommons.org/licenses/by-nc/3.0/ Downloaded from rnajournal.cshlp.org on April 3, 2014 - Published by Cold Spring Harbor Laboratory Press Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs Debabrata Mandal, Caroline Köhrer, Dan Su, et al. RNA 2014 20: 177-188 originally published online December 16, 2013 Access the most recent version at doi:10.1261/rna.042358.113 Supplemental http://rnajournal.cshlp.org/content/suppl/2013/12/03/rna.042358.113.DC1.html Material References This article cites 38 articles, 17 of which can be accessed free at: http://rnajournal.cshlp.org/content/20/2/177.full.html#ref-list-1 Creative This article is distributed exclusively by the RNA Society for the first 12 months after the Commons full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). -
Identification of the Enzyme Responsible for N1-Methylation of Pseudouridine 54 in Archaeal Trnas
Downloaded from rnajournal.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press REPORT Identification of the enzyme responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs JAN PHILIP WURM,1 MARCO GRIESE,1 UTE BAHR,2 MARTIN HELD,2,3 ALEXANDER HECKEL,2,3,4 MICHAEL KARAS,2,4 JO¨ RG SOPPA,1 and JENS WO¨ HNERT1,4,5,6 1Institut fu¨r Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universita¨t, 60438 Frankfurt/M., Germany 2Institut fu¨r Pharmazeutische Chemie, Johann-Wolfgang-Goethe-Universita¨t, 60438 Frankfurt/M., Germany 3Institut fu¨r Organische Chemie und Chemische Biologie, Johann-Wolfgang-Goethe-Universita¨t, 60438 Frankfurt/M., Germany 4Cluster of Excellence ‘‘Macromolecular complexes,’’ Johann-Wolfgang-Goethe-Universita¨t, 60438 Frankfurt/M., Germany 5Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-Universita¨t, 60438 Frankfurt/M., Germany ABSTRACT tRNAs from all three kingdoms of life contain a variety of modified nucleotides required for their stability, proper folding, and accurate decoding. One prominent example is the eponymous ribothymidine (rT) modification at position 54 in the T-arm of eukaryotic and bacterial tRNAs. In contrast, in most archaea this position is occupied by another hypermodified nucleotide: the isosteric N1-methylated pseudouridine. While the enzyme catalyzing pseudouridine formation at this position is known, the pseudouridine N1-specific methyltransferase responsible for this modification has not yet been experimentally identified. Here, we present biochemical and genetic evidence that the two homologous proteins, Mja_1640 (COG 1901, Pfam DUF358) and Hvo_1989 (Pfam DUF358) from Methanocaldococcus jannaschii and Haloferax volcanii, respectively, are representatives of the methyltransferase responsible for this modification. -
Characterization of a B. Subtilis Minor Isoleucine Trna Deduced from Tdna Having a Methionine Anticodon CAT1
J. Biochem. 119, 811-816 (1996) Characterization of a B. subtilis Minor Isoleucine tRNA Deduced from tDNA Having a Methionine Anticodon CAT1 Jitsuhiro Matsugi,2 Katsutoshi Murao, and Hisayuki Ishikura Laboratory of Chemistry, Jichi Medical School, 3311-1 Minamikawachi-machi, Tochigi 329-04 Received for publication, December 1, 1995 Bacillus subtilis, which belongs to Gram-positive eubacteria, has been predicted to have a minor isoleucine tRNA transcribed from the gene possessing the CAT anticodon, which corresponds to methionine. We isolated this tRNA and determined its sequence including modified nucleotides. Modified nucleotide analyses using TLC, UV, and FAB mass spectros copy revealed that the first letter of the anticodon is modified to lysidine [4-amino-2-(N6 - lysino)-1-ƒÀ-D-ribofuranosyl pyrimidine]. As a result, this tRNA agrees with the minor one predicted from the DNA sequence and is thought to decode the isoleucine codon AUA. Key words: Bacillus subtilis, FAB mass spectroscopy, lysidine, modified nucleotide, tRNA. In the codon table, isoleucine is assigned to three codons, lysidine in the wobble position can form a base pair only AUU, AUC, and AUA, but theoretically two kinds of with adenosine, not with guanosine, and consequently the anticodon (GAU and UAU) are sufficient to decode these minor tRNA11e can read only the AUA codon. At the same three codons. To decode the AUA codon, some organisms time, lysidine contributes to a change in charging specificity utilize a minor species of tRNA11e whose first letter of the from methionine to isoleucine (7). anticodon is a unique or an unknown modified nucleotide. In B. -
Us 2018 / 0353618 A1
US 20180353618A1 ( 19) United States (12 ) Patent Application Publication ( 10) Pub . No. : US 2018 /0353618 A1 Burkhardt et al. (43 ) Pub . Date : Dec . 13 , 2018 (54 ) HETEROLOGOUS UTR SEQUENCES FOR Publication Classification ENHANCED MRNA EXPRESSION (51 ) Int. Cl. A61K 48 / 00 ( 2006 .01 ) (71 ) Applicant : Moderna TX , Inc ., Cambridge , MA C12N 15 / 10 (2006 .01 ) (US ) C12N 15 /67 ( 2006 .01 ) (72 ) Inventors : David H . Burkhardt , Somerville , MA A61K 31 / 7115 ( 2006 .01 ) (US ) ; Romesh R . Subramanian , A61K 31 /712 ( 2006 .01 ) A61K 31 / 7125 (2006 . 01 ) Framingham , MA (US ) ; Christian A61P 1 / 16 ( 2006 .01 ) Cobaugh , Newton Highlands , MA (US ) A61P 31/ 14 (2006 .01 ) (52 ) U . S . CI. (73 ) Assignee : Moderna TX , Inc. , Cambridge , MA CPC . .. A61K 48 /0058 ( 2013 .01 ) ; C12N 15 / 1086 (US ) ( 2013 . 01 ) ; A61K 48 / 0066 ( 2013 .01 ) ; C12N 15 /67 ( 2013 .01 ) ; A61P 31 / 14 ( 2018 . 01 ) ; A61K ( 21 ) Appl . No . : 15 / 781, 827 31/ 712 (2013 .01 ) ; A61K 31/ 7125 ( 2013 .01 ) ; A61P 1 / 16 ( 2018 .01 ) ; A61K 31/ 7115 ( 22 ) PCT Filed : Dec . 9 , 2016 ( 2013 .01 ) ( 86 ) PCT No. : PCT/ US2016 / 065796 (57 ) ABSTRACT $ 371 ( c ) ( 1 ) , mRNAs containing an exogenous open reading frame (ORF ) ( 2 ) Date : flanked by a 5 ' untranslated region (UTR ) and a 3 ' UTR is Jun . 6 , 2018 provided , wherein the 5 ' and 3 ' UTRs are derived from a naturally abundant mRNA in a tissue . Also provided are Related U . S . Application Data methods for identifying the 5 ' and 3 ' UTRs, and methods for (60 ) Provisional application No . 62 / 265 , 233 , filed on Dec. making and using the mRNAs . -
WO 2017/112943 Al 29 June 2017 (29.06.2017) W 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 2017/112943 Al 29 June 2017 (29.06.2017) W P O P C T (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, C07K 14/705 (2006.01) A61K 31/7088 (2006.01) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, C12N 15/12 (2006.01) DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KH, KN, (21) International Application Number: KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, PCT/US2016/068552 MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, (22) International Filing Date: NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, 23 December 2016 (23. 12.2016) RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, (25) Filing Language: English ZA, ZM, ZW. (26) Publication Language: English 4 Designated States (unless otherwise indicated, for every (30) Priority Data: kind of regional protection available): ARIPO (BW, GH, 62/387,168 23 December 201 5 (23. 12.2015) US GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, 62/290,413 2 February 2016 (02.02.2016) US TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, (71) Applicant: MODERNATX, INC. -
Expanded Use of Sense Codons Is Regulated by Modified Cytidines in Trna
Expanded use of sense codons is regulated by modified cytidines in tRNA William A. Cantaraa,b,1, Frank V. Murphy IVc, Hasan Demircid,2, and Paul F. Agrisa,3 aThe RNA Institute, Department of Biological Sciences, University at Albany–State University of New York, Albany, NY 12222; bDepartment of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622; cNortheastern Collaborative Access Team, Argonne National Laboratory, Argonne, IL 60439; and dDepartment of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912 Edited by Dieter Söll, Yale University, New Haven, CT, and approved May 23, 2013 (received for review December 26, 2012) Codon use among the three domains of life is not confined to the C-H edge at the C5 position. It is evident that the many post- universal genetic code. With only 22 tRNA genes in mammalian transcriptional modifications of the Watson–Crick edge alter base mitochondria, exceptions from the universal code are necessary pairing abilities, but a clear mechanism of decoding expansion for proper translation. A particularly interesting deviation is the by C5 modifications remains poorly understood, especially mod- decoding of the isoleucine AUA codon as methionine by the one fi Met i cations of cytidine. mitochondrial-encoded tRNA . This tRNA decodes AUA and AUG The mitochondrion’s decoding of AUA as methionine is in both the A- and P-sites of the metazoan mitochondrial ribo- important for proper translation. In humans, this codon con- some. Enrichment of posttranscriptional modifications is a com- monly appropriated mechanism for modulating decoding rules, stitutes 20% of mRNA initiator methionines and 80% of in- enabling some tRNA functions while restraining others. -
Life Without Trna[Superscript Ile]-Lysidine Synthetase: Translation of the Isoleucine Codon AUA in Bacillus Subtilis Lacking the Canonical Trna[Ile Over 2]
Life without tRNA[superscript Ile]-lysidine synthetase: translation of the isoleucine codon AUA in Bacillus subtilis lacking the canonical tRNA[Ile over 2] The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Kohrer, C., D. Mandal, K. W. Gaston, H. Grosjean, P. A. Limbach, and U. L. RajBhandary. “Life without tRNAIle-lysidine synthetase: translation of the isoleucine codon AUA in Bacillus subtilis lacking the canonical tRNA2Ile.” Nucleic Acids Research (November 4, 2013). As Published http://dx.doi.org/10.1093/nar/gkt1009 Publisher Oxford University Press Version Final published version Citable link http://hdl.handle.net/1721.1/83245 Detailed Terms http://creativecommons.org/licenses/by-nc/3.0/ Nucleic Acids Research Advance Access published November 14, 2013 Nucleic Acids Research, 2013, 1–12 doi:10.1093/nar/gkt1009 Life without tRNAIle-lysidine synthetase: translation of the isoleucine codon AUA in Bacillus subtilis Ile lacking the canonical tRNA2 Caroline Ko¨ hrer1, Debabrata Mandal1, Kirk W. Gaston2, Henri Grosjean3, Patrick A. Limbach2 and Uttam L. RajBhandary1,* 1Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, 2Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH 45221, USA and 3Centre de Ge´ ne´ tique Mole´ culaire, CNRS, Gif-sur-Yvette, F-91198, France Received August 29, 2013; Revised October 3, 2013; Accepted October 5, 2013 Downloaded from ABSTRACT Crick proposes how a single tRNA with G in the first position of the anticodon (also called the wobble base) Translation of the isoleucine codon AUA in most can read codons ending in U or C and how a tRNA prokaryotes requires a modified C (lysidine or with U (or a modified U) can read codons ending in A Ile http://nar.oxfordjournals.org/ agmatidine) at the wobble position of tRNA2 to or G (3–5). -
Discovery and Characterization of Trnaile Lysidine Synthetase (Tils)
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 584 (2010) 272–277 journal homepage: www.FEBSLetters.org Review Discovery and characterization of tRNAIle lysidine synthetase (TilS) Tsutomu Suzuki *, Kenjyo Miyauchi Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan article info abstract Article history: In the bacterial decoding system, the AUA codon is deciphered as isoleucine by tRNAIle bearing lysi- Received 12 November 2009 dine (L, 2-lysyl-cytidine) at the wobble position. Lysidine is an essential modification that deter- Revised 21 November 2009 mines both the codon and amino acid specificities of tRNAIle. We identified an enzyme named Accepted 24 November 2009 tRNAIle lysidine synthetase (TilS) that catalyzes lysidine formation by using lysine and ATP as sub- Available online 26 November 2009 strates. Biochemical studies revealed a molecular mechanism of lysidine formation that consists Edited by Manuel Santos of two consecutive reactions involving the adenylated tRNA intermediate. In addition, we deci- phered how Escherichia coli TilS specifically discriminates between tRNAIle and the structurally sim- ilar tRNAMet, which bears the same anticodon loop. Recent structural studies unveiled tRNA Keywords: tRNA recognition by TilS, and a molecular basis of lysidine formation at atomic resolution. Lysidine Ó 2009 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. TilS AUA codon Wobble modification Anticodon 1. Lysidine plays a critical role in decoding the AUA codon as Ile tRNAIle bearing the CAU anticodon was switched to Met, and this tRNA translates the AUG codon as Met [4]. -
Expanding the Toolkit of Protein Engineering: Towards Multiple Simultaneous in Vivo Incorporation of Noncanonical Amino Acids
TECHNISCHE UNIVERSITÄT MÜNCHEN Max-Planck-Institut für Biochemie Expanding the Toolkit of Protein Engineering: Towards Multiple Simultaneous In Vivo Incorporation of Noncanonical Amino Acids Michael G. Hösl Vollständiger Abdruck der von der Fakultät für Chemie der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Univ.-Prof. Dr. Michael Groll Prüfer der Dissertation: 1. Univ.-Prof. Dr. Nediljko Budisa, Technische Universität Berlin 2. Univ.-Prof. Dr. Thomas Kiefhaber 3. Univ.-Prof. Dr. Johannes Buchner Die Dissertation wurde am 01.02.11 bei der Technischen Universität München eingereicht und durch die Fakultät für Chemie am 03.03.11 angenommen. To Teresa Ariadna García-Grajalva Lucas who influenced the idea of TAG → AGG switch just by the existence of her name Sleeping is giving in, no matter what the time is. Sleeping is giving in, so lift those heavy eyelids. People say that you'll die faster than without water. But we know it's just a lie, scare your son, scare your daughter. People say that your dreams are the only things that save ya. Come on baby in our dreams, we can live on misbehavior. The Arcade Fire Parts of this work were published as listed below: Hoesl, MG, Budisa, N. Expanding and engineering the genetic code in a single expression experiment. ChemBioChem 2011, 12, 552-555. Further publications: Hoesl, MG*, Staudt, H*, Dreuw, A, Budisa, N, Grininger, M, Oesterhelt, D, Wachtveitl, J. Manipulating the eletron transfer in Dodecin by isostructual noncanonical Trp analogs. 2011, [in preparation]. *authors contributed equally to this work Nehring, S*, Hoesl, MG*, Acevedo-Rocha, CG*, Royter, M, Wolschner, C, Wiltschi, B, Budisa, N, Antranikian, G. -
Broad and Adaptable RNA Structure Recognition by the Human Interferon-Induced Tetratricopeptide Repeat Protein IFIT5
Broad and adaptable RNA structure recognition by the human interferon-induced tetratricopeptide repeat protein IFIT5 George E. Katibaha, Yidan Qinb, David J. Sidoteb, Jun Yaob, Alan M. Lambowitzb,1, and Kathleen Collinsa,1 aDepartment of Molecular and Cell Biology, University of California, Berkeley, CA 94720; and bInstitute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712 Contributed by Alan M. Lambowitz, July 8, 2014 (sent for review April 29, 2014; reviewed by Sandra L. Wolin, Eric Phizicky, and Michael Gale, Jr.) Interferon (IFN) responses play key roles in cellular defense against copy numbers and combinations of four distinct IFIT proteins pathogens. Highly expressed IFN-induced proteins with tetratrico- (IFIT1, 2, 3, and 5) even within mammals, generated by paralog peptide repeats (IFITs) are proposed to function as RNA binding expansions and/or gene deletions, including the loss of IFIT5 in proteins, but the RNA binding and discrimination specificities of IFIT mice and rats (14). Human IFIT1, IFIT2, and IFIT3 coassemble proteins remain unclear. Here we show that human IFIT5 has in cells into poorly characterized multimeric complexes that ex- comparable affinity for RNAs with diverse phosphate-containing 5′- clude IFIT5 (15, 16). Recombinant IFIT family proteins range ends, excluding the higher eukaryotic mRNA cap. Systematic muta- from monomer to multimer, with crystal structures solved for genesis revealed that sequence substitutions in IFIT5 can alternatively a human IFIT2 homodimer (17), the human IFIT5 monomer expand or introduce bias in protein binding to RNAs with 5′ mono- (16, 18, 19), and an N-terminal fragment of human IFIT1 (18). -
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.