DOCSLIB.ORG

PNAS-2013-Cantara-1222641110

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
PNAS-2013-Cantara-1222641110 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. In this ternal methionines (15, 16). Using chemical synthesis and 5 5 fi case, a modification of cytidine, 5-formylcytidine (f C), at the wob- incorporation of the f C34 modi cation into the heptadecamer Met Met ble position-34 of human mitochondrial tRNAf5CAU (hmtRNAf5CAU) anticodon stem and loop domain (ASL) of human mitochon- enables expanded decoding of AUA, resulting in a deviation in the Met Met 5 drial tRNAf5CAUðhmASLf5CAUÞ (17), we determined that f C34 genetic code. Visualization of the codon•anticodon interaction by destabilized the hmASLMet by increasing the motional dy- X-ray crystallography revealed that recognition of both A and G at f5CAU namics of the loop residues (17). A further study detailing the third position of the codon occurs in the canonical Watson– BIOCHEMISTRY Crick geometry. A modification-dependent shift in the tautomeric the codon-binding characteristics and solution structure of Met 5 equilibrium toward the rare imino-oxo tautomer of cytidine stabil- hmASLf5CAU agreed with the f C-dependent increase in resi- 5 • izes the f C34 A base pair geometry with two hydrogen bonds. due dynamics (18). Proposed mechanisms for the decoding Met 5 • of AUA by tRNAf5CAU depend on the f C34 A3 base pair modified nucleosides | ribosome crystallography | tautomerism forming a specificgeometry(18–20). Based on molecular dynamics simulations, we suggested that this base pair could he genetic code was initially deemed to be universal and frozen be in a sheared geometry that is supported by a bridging water Tin time (1). However, deviations in sense and nonsense codon molecule (18). To test this hypothesis, the geometry of the use are found in bacteria, archaea, and both nuclear and organ- f5C •A base pair in the decoding center of the ribosomal ellar eukaryotic genomes (2, 3). Use of genetic codes that deviate 34 3 A-site was observed in crystal structures of natively modified from the universal code provides insight into its evolution (4) and Met fi possibilities for investigator-initiated manipulation (synthetic hmASLf5CAU bound to AUA. Here, we show for the rst time fi 5 • biology) (5). In many cases, however, the translation of the de- the modi cation-dependent f C34 A3 base pair within the viant sense codons is facilitated by posttranscriptional modifi- codon•anticodon interaction during ribosomal A-site decod- 5 – cation chemistries that are enzymatically added to nucleosides ing. Surprisingly, f C34 forms a canonical Watson Crick base at the first anticodon position. The modification chemistries and pair with both the G of AUG and the A of AUA, refuting the their impact on anticodon conformation alter the decoding ca- conformation predicted from molecular dynamics simulations pacity of the modified tRNA (6). When first proposed, modifi- 5 • (18). This geometry of the f C34 A3 base pair requires a novel cation-dependent wobble decoding was limited to inosine as the 5 amino-imino tautomerism in f C34 similar to the keto-enol tau- first modified anticodon residue. Inosine, a deaminated adeno- 5 tomerism seen for the two wobble position uridines cmo U34 sine residue, expands the ability of a single isoacceptor tRNA to 5 2 Val3 read three codons by base pairing with either U, C, or A at the and mcm s U34 in Escherichia coli tRNAUAC (21) and human – Lys3 third position of the codon (7). Many other wobble position tRNAUUU (22), respectively. modified residues, mostly pyrimidines, are now known to modulate use of specific codons (8). Although modified uridines constitute a great majority of these modifications, modified cytidines are prevalent in controlling a switch between the universal genetic Author contributions: P.F.A. designed research; W.A.C., F.V.M., and H.D. performed re- code and a deviant code in the shared isoleucine/methionine search; W.A.C., F.V.M., H.D., and P.F.A. analyzed data; and W.A.C., F.V.M., H.D., and P.F.A. fi 4 wrote the paper. codon box (9, 10). The modi cation, 4-acetylcytidine (ac C), fl Met The authors declare no con ict of interest. prevents tRNACAU from reading AUA through wobble geometry (11), and lysidine (k2C) (12) and agmatidine (agm2C) (13, 14) This article is a PNAS Direct Submission. prevent tRNAIle from reading AUG in bacteria and archaea. Freely available online through the PNAS open access option. CAU Met Met Interestingly, a fourth cytidine modification, 5-formylcytidine Data deposition: The atomic coordinates for hmASL f5CAU-AUG and hmASL f5CAU-AUA 5 have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 4GKJ and (f C), facilitates the reading of AUA and AUG as methionine by 4GKK, respectively). Met a single tRNAf5CAU responding to both initiator and elongator 1Present address: Department of Chemistry and Biochemistry, Center for Retroviral Re- codons in yeast and many metazoan mitochondrial genomes (6). search, and Center for RNA Biology, Ohio State University, Columbus, OH 43210. 4 2 2 Therefore, ac C, k C and agm C are restrictive modifications 2Present address: Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo that alter the physicochemical properties of the Watson–Crick Park, CA 94025. 5 edge, whereas f C expands decoding using a modification on the 3To whom correspondence should be addressed. E-mail: [email protected]. www.pnas.org/cgi/doi/10.1073/pnas.1222641110 PNAS Early Edition | 1of6 Met • Fig. 1. hmASLf5CAU secondary structure and A-site codon anticodon interaction. (A) The ASL was synthesized as a heptadecamer containing two mod- fi Met i cations: pseudouridine at position 27 and 5-formylcytidine at position 34. (B) The structure of hmASLf5CAU bound to AUG (Left) showed strong electron density for ASL residues 31–39, whereas when bound to AUA (Right), electron density was strong for only residues 34–39. In both structures, the ASL is in 5 green, the mRNA codon is in blue, and the A-site interacting residues (G530,A1492, and A1493) are in black (2mFO-dFC contoured at 1.5 σ). The f C34 modification is colored red. Results structures. The structure of the 30S ribosomal subunit (including hmASLMet all RNA and protein) was nearly identical to those reported Codon Bound f5CAU Structure. The ASL domain of Met previously (21, 22). The hmASLMet took a conformation hmtRNAf5CAU was chemically synthesized with the wobble f5CAU fi 5 modi cation f C34, the native C33, and a pseudouridine, Ψ27,at nearly identical to that of the ASL of a ribosome-bound tRNA- ′ the 5 terminus (Fig. 1A). C33 is quite rare. The uridine at po- EF-Tu complex (24, 25), demonstrating the biological relevance sition 33 in tRNAs is considered invariant and recognized for its of the present structures. More importantly, the conserved A-site contribution to the “U-turn” structural motif. There are only 21 residues G530,A1492, and A1493 were in the correct orientation to • known instances of C33, 13 of which are found in initiator tRNAs constrain the codon anticodon pair residues into the proper (23). The hmASLMet bound both AUG and AUA codons with geometry for recognition (Fig. 1B) (26, 27). As such, differences f5CAU • significant affinity in the A-site of the bacterial ribosome (17) in the characteristics of the codon anticodon interaction can fi Met and within the A-site of the bovine mitochondrial 55S ribosome be attributed to the speci cconformationofhmASLf5CAU and 5 fi (18). In determining the crystallographic structure of the modi- properties of the f C34 modi cation. fi Met ed hmASLf5CAU bound to the AUG or the AUA codons in the hmASLMet Conformational Characteristics of f5CAU: Nearly the entire ribosomal A-site, native Thermus thermophilus 30S ribosomal Met Met hmASLf5CAU exhibited strong electron density when bound to the subunit crystals were soaked with the hmASLf5CAU and hex- Met americ oligonucleotides, each containing either AUG or AUA cognate AUG codon (Fig. 1B). In the structure of hmASLf5CAU • codons. Under the conditions used, both crystals diffracted bound to the wobble AUA codon, the codon anticodon in- ′ to 3.3-Å resolution (Table 1).
Load more

Recommended publications
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • G+ Biosynthesis
    BIOSYNTHESIS AND PHYSIOLOGICAL ROLE OF ARCHAEOSINE IN THE EXTREME HALOPHILIC ARCHAEON Haloferax volcanii By GABRIELA PHILLIPS A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2011 1 © 2011 Gabriela Phillips 2 To my husband for his love, understanding, patience 3 ACKNOWLEDGMENTS Abundant gratitude belongs to Dr. Valerie de Crécy-Lagard for supervision, support, encouragement throughout all the years we worked together in the field. Her knowledgeable and valuable input stimulated this dissertation from preliminary levels to actualization. I would sincerely like to thank my committee members, James Preston, Nemat Keyhani, Claudio Gonzalez, Nigel Richards for their support, time, and helpful insights that helped me become a better prepared scholar in the field. I would like to express my deep and sincere gratitude to Basma el Yacoubi for her helpful teachings, discussions, understanding; her precious support helped me enormously to cope with the difficulties of my doctoral studies. I am grateful to Marc Bailly for insightful discussions and for developing a better procedure for bulk tRNA extraction and purification as well as setting up the protocol for extraction and purification of E. coli tRNAAsp. I am especially indebted to Sophie Alvarez (Danforth Plant Science Center, Proteomics and Mass Spectrometry Facility, St. Louis, MO.) for her LC-MS/MS analysis on bulk tRNA. I also want to thank to Kirk Gaston (Pat A. Limbach Research Group University of Cincinnati) for his prompt E. coli tRNAAsp sequencing and analysis. I am grateful to Dr.
    [Show full text]
  • Agmatidine, a Modified Cytidine in the Anticodon of Archaeal Trna , Base
    Agmatidine, a modified cytidine in the anticodon of archaeal tRNAIle, base pairs with adenosine but not with guanosine Debabrata Mandala,1, Caroline Köhrera,1, Dan Sub, Susan P. Russellc, Kady Krivosc, Colette M. Castleberryc, Paul Blumd, Patrick A. Limbachc, Dieter Söllb, and Uttam L. RajBhandarya,2 aDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; bDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; cDepartment of Chemistry, University of Cincinnati, Cincinnati, OH 45221; dGeorge Beadle Center for Genetics, University of Nebraska, Lincoln, NE 68588 Contributed by Dieter Söll, December 24, 2009 (sent for review December 2, 2009) Modification of the cytidine in the first anticodon position of the Eukaryotes, on the other hand, contain a tRNAIle with the anti- Ile Ile AUA decoding tRNA (tRNA2 ) of bacteria and archaea is essential codon IAU (I ¼ inosine), which can read all three isoleucine co- for this tRNA to read the isoleucine codon AUA and to differentiate dons using the wobble pairing rules of Crick. They also contain a between AUA and the methionine codon AUG. To identify the tRNAIle with the anticodon ΨAΨ, which is thought to read only modified cytidine in archaea, we have purified this tRNA species the isoleucine codon AUA but not the methionine codon AUG from Haloarcula marismortui, established its codon reading proper- (8). Given these two distinct mechanisms in bacteria and ties, used liquid chromatography–mass spectrometry (LC-MS) to eukaryotes, a question of much interest is how the archaeal map RNase A and T1 digestion products onto the tRNA, and used tRNAIle accomplishes the task of reading the AUA codon.
    [Show full text]
  • ABSTRACT CANTARA, WILLIAM ANTHONY. Arginyl-Trna Modifications Modulate Anticodon Domain Structure, Function and Dynamics in Esch
    ABSTRACT CANTARA, WILLIAM ANTHONY. Arginyl-tRNA Modifications Modulate Anticodon Domain Structure, Function and Dynamics in Escherichia coli. (Under the direction of Paul F. Agris) During ribosome-mediated protein synthesis, non-initiator tRNAs act as translating chaperones by transferring the correct amino acid to the ribosome through sequence-specific interactions with mRNA codons in the ribosomal A-site. To achieve uniformity in codon recognition ability between different tRNAs, the anticodon domains of all must adopt a singular conformation in the ribosomal decoding center. Since there is a necessary sequence variation for the three anticodon residues, innovative ways of attaining a constant loop structure are required. Nature has resolved this issue by introducing functional groups to the loop residues, changing the chemical environment and, thus, the conformation. In fact, there is a large diversity and number of these modifications found in tRNAs of all known life. Escherichia coli (E.coli) arginyl-tRNAs offer the opportunity to study these modifications in the context of six-fold degenerate codons that vary widely in their cellular usage. A single Arg1 Arg2 set of very similar isoacceptors, tRNA ICG and tRNA ICG, have anticodon domains that 2 differ only in the presence or absence of a very rare modification, 2-thiocytidine (s C32). 2 These tRNAs are particularly interesting not only because of the rare s C32 modification, but also through the wobble position modification I34, they are both responsible for decoding two very common codons CGU and CGC as well as the very rare CGA codon. Typically, the codon usage correlates with the tRNA content of the cell; however, in this instance, the tRNA content is high which does not match what would be expected for an isoacceptor that recognizes a rare codon.
    [Show full text]
  • A Covalent Approach for Sitespecific RNA Labeling in Mammalian Cells
    Angewandte Chemie International Edition:DOI:10.1002/anie.201410433 RNA Labeling Very Important Paper German Edition:DOI:10.1002/ange.201410433 ACovalent Approach for Site-Specific RNALabeling in Mammalian Cells** Fahui Li, Jianshu Dong, Xiaosong Hu, Weimin Gong,Jiasong Li, Jing Shen, Huifang Tian, and Jiangyun Wang* Abstract: Advances in RNAresearch and RNAnanotechnol- approaches,[2] bioorthogonal chemistry[3] relies upon the ogy depend on the ability to manipulate and probe RNAwith specific and covalent attachment of probe molecules to the high precision through chemical approaches,both in vitro and biomacromolecule of interest (BOI). As aresult, it offers in mammalian cells.However,covalent RNAlabeling methods several advantages:1)the affinity can be considered to be with scope and versatility comparable to those of current infinity,therefore stringent wash conditions can be applied to protein labeling strategies are underdeveloped. Amethod is rigorously purify the BOI;2)the high affinity allows for the reported for the site- and sequence-specific covalent labeling of visualization of low-abundance BOIs,which is particularly RNAs in mammalian cells by using tRNAIle2-agmatidine important for non-coding RNAs;[1a] 3) this method is synthetase (Tias) and click chemistry.The crystal structure of extremely versatile;probe molecules harboring fluorescence, Tias in complex with an azide-bearing agmatine analogue was NMR, IR, or EPR functional groups can be conveniently solved to unravel the structural basis for Tias/substrate conjugated to
    [Show full text]
  • Chaos, Order and Systematics in Evolution of the Genetic Code
    Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 October 2020 doi:10.20944/preprints202009.0162.v2 Review Chaos, order and systematics in evolution of the genetic code Lei Lei 1 and Zachary F. Burton 2 * 1 Department of Biology, University of New England, ME, USA; [email protected] 2 Department of Biochemistry and Molecular Biology, Michigan State University; [email protected] * Correspondence: [email protected]; Tel.: +01-517-881-2243 Abstract: The genetic code evolved by parallel tracks of chaotic and ordered processes. Liquid- liquid phase separation (hydrogels), a chaotic process, constructs diverse membraneless compartments within cells, resulting in regulated hydration and sequestration and concentration of reaction components. Hydrogels relate to chaotic amyloid fiber production. We propose that polyglycine and related hydrogels (i.e. GADV; G is glycine), phase separations, membraneless droplets and amyloid accretions organized protocell domains to drive the earliest evolution of the genetic code and the pre-life to cellular life transition. By contrast, evolution of tRNA, tRNAomes, aminoacyl-tRNA synthetases and translation systems followed highly ordered and systematic pathways, described by well-defined mechanisms and rules. The pathway of evolution of aminoacyl-tRNA synthetases, which tracked evolution of the genetic code, is clarified. Hydrogels and amyloids form a chaotic component, therefore, that complemented otherwise systematic processes. We describe with detail a pre-life world in which hydrogels and amyloids provided the selections of the first life. Keywords: amyloids; frozen accident; genetic code; hydrogels; liquid-liquid phase separation; mRNA; polyglycine; rRNA; ribosomes; translational fidelity; tRNA. 1. Introduction Eukaryotic cells divide into compartments. Some compartments are set aside by membranes but others are membraneless and divided instead by regulation of liquid phases [1-5].
    [Show full text]
  • Agmatidine, a Modified Cytidine in the Anticodon of Archaeal Trna(Ile), Base Pairs with Adenosine but Not with Guanosine
    Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Mandal, D. et al. “Agmatidine, a modified cytidine in the anticodon of archaeal tRNAIle, base pairs with adenosine but not with guanosine.” Proceedings of the National Academy of Sciences 107.7 (2010): 2872-2877. Copyright ©2011 by the National Academy of Sciences As Published http://dx.doi.org/10.1073/pnas.0914869107 Publisher National Academy of Sciences (U.S.) Version Final published version Citable link http://hdl.handle.net/1721.1/61373 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. Biochemistry Agmatidine, a modified cytidine in the anticodon of archaeal tRNAIle, base pairs with adenosine but not with guanosine. Debabrata Mandal*║, Caroline Köhrer*║, Dan Su†, Susan P. Russell‡, Kady Krivos‡, Colette M. Castleberry‡, Paul Blum§, Patrick A. Limbach‡, Dieter Söll†, Uttam L. RajBhandary*¶ ║ contributed equally to the work *Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA †Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA ‡Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA §George Beadle Center for Genetics, University of Nebraska, Lincoln, NE 68588, USA ¶Corresponding author: Department of Biology Room 68-671 M.I.T., Cambridge, MA 02139, USA Tel.: 617-253-4702 FAX: 617-252-1556 E-mail: [email protected] 1 Ile Modification of the cytidine in the first anticodon position of the AUA decoding tRNA Ile (tRNA2 ) of bacteria and archaea is essential for this tRNA to read the isoleucine codon AUA and to differentiate between AUA and the methionine codon AUG.
    [Show full text]
  • WO 2019/067979 Al 04 April 2019 (04.04.2019) W 1P O PCT
    (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 2019/067979 Al 04 April 2019 (04.04.2019) W 1P O PCT (51) International Patent Classification: B 14202, Cambridge, Massachusetts 02139 (US). NI¬ A61K 31/166 (2006.01) A61K 45/06 (2006.01) CHOLS, Andrew J.; c/o CATABASIS PHARMACEUTI¬ A61K 31/7125 (2006.01) A61P 21/00 (2006.01) CALS, INC., One Kendall Square, Suite B 14202, Cam¬ bridge, Massachusetts 02139 (US). (21) International Application Number: PCT/US20 18/053 543 (74) Agent: ROSE GILLENTINE, Marsha et al; STERNE, KESSLER, GOLDSTEIN & FOX P.L.L.C, 1100 New York (22) International Filing Date: Avenue, NW, Washington, District of Columbia 20005 28 September 2018 (28.09.2018) (US). (25) Filing Language: English (81) Designated States (unless otherwise indicated, for every (26) Publication Language: English kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, (30) Priority Data: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, 62/565,016 28 September 2017 (28.09.2017) US DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, 62/737,750 27 September 2018 (27.09.2018) US HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, (71) Applicants: SAREPTA THERAPEUTICS, INC. KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, [US/US]; 215 First Street, Cambridge, Massachusetts MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 02142 (US).
    [Show full text]
  • Agmatidine, a Modified Cytidine in the Anticodon of Archaeal Trna , Base Pairs with Adenosine but Not with Guanosine
    Agmatidine, a modified cytidine in the anticodon of archaeal tRNAIle, base pairs with adenosine but not with guanosine Debabrata Mandala,1, Caroline Köhrera,1, Dan Sub, Susan P. Russellc, Kady Krivosc, Colette M. Castleberryc, Paul Blumd, Patrick A. Limbachc, Dieter Söllb, and Uttam L. RajBhandarya,2 aDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; bDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; cDepartment of Chemistry, University of Cincinnati, Cincinnati, OH 45221; dGeorge Beadle Center for Genetics, University of Nebraska, Lincoln, NE 68588 Contributed by Dieter Söll, December 24, 2009 (sent for review December 2, 2009) Modification of the cytidine in the first anticodon position of the Eukaryotes, on the other hand, contain a tRNAIle with the anti- Ile Ile AUA decoding tRNA (tRNA2 ) of bacteria and archaea is essential codon IAU (I ¼ inosine), which can read all three isoleucine co- for this tRNA to read the isoleucine codon AUA and to differentiate dons using the wobble pairing rules of Crick. They also contain a between AUA and the methionine codon AUG. To identify the tRNAIle with the anticodon ΨAΨ, which is thought to read only modified cytidine in archaea, we have purified this tRNA species the isoleucine codon AUA but not the methionine codon AUG from Haloarcula marismortui, established its codon reading proper- (8). Given these two distinct mechanisms in bacteria and ties, used liquid chromatography–mass spectrometry (LC-MS) to eukaryotes, a question of much interest is how the archaeal map RNase A and T1 digestion products onto the tRNA, and used tRNAIle accomplishes the task of reading the AUA codon.
    [Show full text]
  • A Novel Nuclear Genetic Code Alteration in Yeasts and the Evolution of Codon Reassignment in Eukaryotes
    bioRxiv preprint doi: https://doi.org/10.1101/037226; this version posted January 19, 2016. 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. A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes Stefanie Mühlhausen1, Peggy Findeisen1, Uwe Plessmann2, Henning Urlaub2,3 and Martin Kollmar1§ 1 Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany 2 Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany 3 Bioanalytics Group, Department of Clinical Chemistry, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany §Corresponding author, Tel.: +49-551-2012260, Fax: +49-551-2012202 Email addresses: SM: [email protected] PM: [email protected] UP: [email protected] HU: [email protected] MK: [email protected] Running title A novel nuclear genetic code alteration in yeasts Keywords Genetic code, codon reassignment, tRNA, yeast, proteomics - 1 - bioRxiv preprint doi: https://doi.org/10.1101/037226; this version posted January 19, 2016. 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 The genetic code is the universal cellular translation table to convert nucleotide into amino acid sequences. Changes to sense codons are expected to be highly detrimental. However, reassignments of single or multiple codons in mitochondria and nuclear genomes demonstrated that the code can evolve.
    [Show full text]