DOCSLIB.ORG

A Trna Modification Counteracts a +2 Ribosomal Frameshift

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Trna Modification Counteracts a +2 Ribosomal Frameshift Downloaded from genesdev.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Translational misreading: a tRNA modification counteracts a +2 ribosomal frameshift Damien Brégeon,1,4 Vincent Colot,2,3 Miroslav Radman,1 and François Taddei1 1INSERM EPI9916, Faculté de Médecine Necker-Enfants Malades, 75730 Paris Cedex 15, France; 2Institut Jacques Monod, CNRS-Universités Paris 6 et Paris 7, 75251 Paris Cedex 05, France Errors during gene expression from DNA to proteins via transcription and translation may be deleterious for the functional maintenance of cells. In this paper, extensive genetic studies of the misreading of a GA repeat introduced into the lacZ gene of Escherichia coli indicate that in this bacteria, errors occur predominantly by a +2 translational frameshift, which is controlled by a tRNA modification involving the MnmE and GidA proteins. This ribosomal frameshift results from the coincidence of three events: (1) decreased codon– anticodon affinity at the P-site, which is caused by tRNA hypomodification in mnmE− and gidA− strains; (2) a repetitive mRNA sequence predisposing to slippage; and (3) increased translational pausing attributable to the presence of a rare codon at the A-site. Based on genetic analysis, we propose that GidA and MnmE act in the same pathway of tRNA modification, the absence of which is responsible for the +2 translational frameshift. The difference in the impact of the mutant gene on cell growth, however, indicates that GidA has at least one other function. [Key Words: Translational fidelity; 5-methylaminomethyl-2-thio-uridine; gidA; mnmE; thdF; argU] Received May 10, 2001; revised version accepted July 2, 2001. Processes ensuring the fidelity of DNA replication have direct alteration of the mRNA or by misincorporation of been studied extensively, presumably because of the altered mutagenic nucleotides, such as 8-oxo-GTP, by overwhelming importance of gene mutations in evolu- the RNA polymerase (Taddei et al. 1997). The presence tion, hereditary diseases and cancer (Friedberg et al. of 8-oxo-G in cellular RNA was shown to be restricted to 1995). In contrast, less is known about the fidelity of vulnerable neurons in dementia such as Alzheimer’s dis- transcription and translation, which must be crucial for ease (AD) (Nunomura et al. 1999) or Parkinson’s disease the functional maintenance of cells and organisms. (Zhang et al. 1999) and to be correlated with the synthe- Functional degeneration of nondividing cells limits the sis of altered proteins (Dukan et al. 2000). The rate of lifespan of organs such as the heart or brain. Therefore, transcriptional frameshifting is unknown but it was pro- decreasing fidelity of gene expression may be an under- posed that it may lead to some neurodegenerative dis- lying cause of cellular aging, degenerative diseases, and eases (van Leeuwen et al. 1998b). In patients with AD, death. Accurate gene expression is dependent on the fi- the accumulation of aberrant protein species shifted to delity of both transcription of DNA and translation of the +1 frame with no related mutation in the DNA blue- mRNA. print has been reported. The appearance of those proteins Fidelity of transcription depends on proofreading by a was shown to be caused by a molecular misreading of a 3Ј → 5Ј exonuclease activity found in a number of eu- coding GA repeat resulting in the deletion of a dinucleo- karyotic and prokaryotic RNA polymerases (Thomas et tide GA in the mRNA (Hol et al. 1998; van Leeuwen et al. 1998). The Escherichia coli RNA polymerase exhibits al. 1998a,b). error rates ranging from 1 to 10 misincorporations per Translational errors have been characterized in E. coli 105 synthesized nucleotides (for review, see Libby and and measured in vivo and/or in vitro (for review, see Gallant 1991). Aberrant RNAs also include the presence Kurland 1992). These include missense errors resulting of altered nucleotides in the mRNA caused either by in the substitution of one amino acid for another, or incorporation of extra amino acids caused by read- through of termination codons. Overall, translational er- rors occur at a frequency of 10−3 to 10−4 (Loftfield and 3Present address: Unité de Recherches en Génomique Végétale (INRA-CNRS), 91057 Evry cedex, France. Vanderjagt 1972; Edelmann and Gallant 1977; Ellis and 4Corresponding author. Gallant 1982; Parker 1989) and are limited by the ability E-MAIL [email protected]; FAX 33-1-40-61-53-22. Article and publication are at http://www.genesdev.org/cgi/doi/10.1101/ of the ribosome to discriminate between correct and in- gad.207701. correct tRNAs entering the A-site (Thompson 1988; Ni- GENES & DEVELOPMENT 15:2295–2306 © 2001 by Cold Spring Harbor Laboratory Press ISSN 0890-9369/01 $5.00; www.genesdev.org 2295 Downloaded from genesdev.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Brégeon et al. Table 1. Sequences of alleles used and their corresponding ␤-galactosidase activities Stop codon ␤-Galactosidase Allele Sequencea positionb activityc lacZ+ AAT GA A T CA GG C 3073 12400 ± 10 Asn Gl u Se r Gl y lacZ (+GA) AAT GAG AGA G T G G C1603 0.10 ± 0.01 Asn Gl u Ar g Va l lacZ+ revertants AAT GAG AG T GG C3073 12600 ± 240 Asn Gl u Se r Gl y lacZ (+ Arg462) AAT GAG AGA A G T GGC3076 0.01 ± 0.001 Asn Gl u Ar g S e r Gl y aAll sequences are shown from codon 460 of the lacZ gene. bNucleotide number of the first base of the following stop codon. cMiller units ± standard error. erhaus 1990; Czworkowski and Moore 1996). When in- repeat in E. coli. A reporter system for such errors was duced by the addition of some antibiotics (e.g., strepto- constructed using the lacZ gene encoding the ␤-galacto- mycin), translational misreading leads to increased sidase enzyme. concentrations of oxidized proteins (Dukan et al. 2000), The constructed lacZ(+GA) frameshifted allele con- which were found to accumulate in aging cells (Stadt- tains a repetition of the dinucleotide GA starting from man 1992). Other translational errors include premature the first base of codon 461 to the first base of codon 463 termination (Menninger 1977; Kurland et al. 1996) and (Table 1). These codons normally encode amino acids translational frameshifting. The latter generally gives involved in the active site of ␤-galactosidase (Cupples rise to a shorter peptide because of the subsequent en- and Miller 1988). This insertion results in a sequence counter of stop codons in the shifted frame. Spontaneous shifted to the +2 reading frame when compared with the frameshifts resulting from translational errors occur at a wild-type sequence and the emergence of a premature frequency of <10−5 per codon (Kurland 1992), but were stop codon 210 nucleotides downstream, thereby gener- shown to increase in E. coli cells entering stationary ating a mRNA encoding a 534-amino-acid polypeptide. phase (Barak et al. 1996). The ␤-galactosidase activity of NECB1 cells, which carry Basic mechanisms involved in DNA replication, re- this new allele, is 125,000 times lower than the activity combination, transcription, and translation are often of the isogenic lacZ+ cells (Table 1). As a result, NECB1 conserved phylogenetically (Lewin 1994). Therefore, we cells are not able to grow on minimal media containing set out to study in E. coli the source of errors brought lactose as the sole source of carbon, and form white colo- about by the presence of a GA repeat within an engi- nies on LB plates containing X-Gal (5-bromo-4-chloro-3- neered frameshifted allele of the lacZ gene (Table 1). The indolyl-␤-D-galactopyranoside). characterization of E. coli mutants expressing an inter- ␤ mediate level of -galactosidase led to the identification Only deletion of a dinucleotide GA can restore of three genes that are involved in the faithful transla- an active ␤-galactosidase tion of the GA repeat. Two of these genes, mnmE and gidA, are involved in tRNA modification and the third, To study errors on this GA repeat, we first wanted to Arg argU, encodes the tRNAmnm5UCU. The analysis of the establish the spectrum of mutants that could restore par- mechanism of this unusual +2 translational frameshift at tially or totally the ␤-galactosidase activity. This ques- this sequence is consistent with the recently proposed tion was addressed by selecting for spontaneous rever- +1/−1 translational frameshift dual error model (Qian et al. 1998; Björk et al. 1999; Farabaugh and Björk 1999), Table 2. Generation time of strains in various growth media which can be extended to explain larger ribosomal at 40°C frameshifting and short tRNA hopping. Measurements a of the growth rate of strains carrying a mutation in the Media gidA or mnmE genes showed that the impact of tRNA Relevant genotypes LB Mm + 0.4% glucose hypomodification varies with nutritional conditions and is not equivalent for both strains (Table 2). These obser- Wild type (NECB1) 32.9 ± 0.7 75.7 ± 3.7 gidAϻTn10 38.0 ± 1.2b 91.1 ± 3.4e vations suggest that GidA may also be involved in other mnmEϻTn10 38.2 ± 0.4c 77.7 ± 2.5 pathways. gidAϻTn10, mnmEϻkan 45.2 ± 0.7d 95.8 ± 2.0f a Results Numbers represent the average generation time of 5 cultures given in minutes ± SEM. b–f The reporter system Generation times that are significantly different from that of the wild type in the same medium. T-test comparison between We studied the control of error rates of expression (tran- WT and mutants grown in the same media have the following scription or translation) of a gene containing a coding GA P-values: b, 0.0054; c, 0.0002; d, <0.0001; e, 0.0154; f, 0.0013.
Load more

Recommended publications
  • 1 Ribosomal Frameshift Signal of SARS-Cov-2
    bioRxiv preprint doi: https://doi.org/10.1101/2020.03.13.991083; this version posted March 15, 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. Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS-CoV-2 Jamie A. Kelly and Jonathan D. Dinman* Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742 *Corresponding author: Jonathan D. Dinman E-mail: [email protected] Running title: Frameshifting in SARS-CoV-2 Keywords: COVID-19, coronavirus, programmed -1 ribosomal frameshifting (-1 PRF), translation, RNA, structure, virus, (+) ssRNA 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.13.991083; this version posted March 15, 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. Abstract. Introduction 17 years after the SARS-CoV epidemic, the SARS-CoV2, the etiological agent of COVID- world is facing the COVID-19 pandemic. 19, is a member of the coronavirus family (1). COVID-19 is caused by a coronavirus named Coronaviruses have (+) ssRNA genomes that SARS-CoV-2. Given the most optimistic harbor two long open reading frames (ORF) projections estimating that it will take more than which occupy the 5’ ~ two-thirds of the genomic a year to develop a vaccine, our best short term RNA (ORF1 and ORF2), followed by several strategy may lie in identifying virus-specific ORFs that are expressed late in the viral targets for small molecule interventions.
    [Show full text]
  • Ribosomes Slide on Lysine-Encoding Homopolymeric a Stretches
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Crossref RESEARCH ARTICLE elifesciences.org Ribosomes slide on lysine-encoding homopolymeric A stretches Kristin S Koutmou1, Anthony P Schuller1, Julie L Brunelle1,2, Aditya Radhakrishnan1, Sergej Djuranovic3, Rachel Green1,2* 1Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States; 2Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, United States; 3Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, United States Abstract Protein output from synonymous codons is thought to be equivalent if appropriate tRNAs are sufficiently abundant. Here we show that mRNAs encoding iterated lysine codons, AAA or AAG, differentially impact protein synthesis: insertion of iterated AAA codons into an ORF diminishes protein expression more than insertion of synonymous AAG codons. Kinetic studies in E. coli reveal that differential protein production results from pausing on consecutive AAA-lysines followed by ribosome sliding on homopolymeric A sequence. Translation in a cell-free expression system demonstrates that diminished output from AAA-codon-containing reporters results from premature translation termination on out of frame stop codons following ribosome sliding. In eukaryotes, these premature termination events target the mRNAs for Nonsense-Mediated-Decay (NMD). The finding that ribosomes slide on homopolymeric A sequences explains bioinformatic analyses indicating that consecutive AAA codons are under-represented in gene-coding sequences. Ribosome ‘sliding’ represents an unexpected type of ribosome movement possible during translation. DOI: 10.7554/eLife.05534.001 *For correspondence: ragreen@ Introduction jhmi.edu Messenger RNA (mRNA) transcripts can contain errors that result in the production of incorrect protein products.
    [Show full text]
  • Mrna Stem-Loops Can Pause the Ribosome by Hindering A-Site Trna
    RESEARCH ARTICLE mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding Chen Bao1†, Sarah Loerch2†, Clarence Ling1, Andrei A Korostelev3,4, Nikolaus Grigorieff2,4*, Dmitri N Ermolenko1* 1Department of Biochemistry and Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of Rochester, Rochester, United States; 2Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States; 3Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States; 4RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States Abstract Although the elongating ribosome is an efficient helicase, certain mRNA stem-loop structures are known to impede ribosome movement along mRNA and stimulate programmed ribosome frameshifting via mechanisms that are not well understood. Using biochemical and single- molecule Fo¨ rster resonance energy transfer (smFRET) experiments, we studied how frameshift- inducing stem-loops from E. coli dnaX mRNA and the gag-pol transcript of Human Immunodeficiency Virus (HIV) perturb translation elongation. We find that upon encountering the ribosome, the stem-loops strongly inhibit A-site tRNA binding and ribosome intersubunit rotation *For correspondence: that accompanies translation elongation. Electron cryo-microscopy (cryo-EM) reveals that the HIV [email protected] (NG); stem-loop docks into the A site of the ribosome. Our results suggest that mRNA stem-loops can Dmitri_Ermolenko@urmc. transiently escape the ribosome helicase by binding to the A site. Thus, the stem-loops can rochester.edu (DNE) modulate gene expression by sterically hindering tRNA binding and inhibiting translation †These authors contributed elongation. equally to this work Competing interest: See page 22 Introduction Funding: See page 22 During translation elongation, the ribosome moves along mRNA in a codon-by-codon manner while Received: 06 February 2020 the mRNA is threaded through the mRNA channel of the small ribosomal subunit.
    [Show full text]
  • HIV-1 Virus Cycle Replication: a Review of RNA Polymerase II Transcription, Alternative Splicing and Protein Synthesis Corresponding Autor
    HIV-1 virus cycle replication: a review of RNA polymerase II transcription, alternative splicing and protein synthesis Correspondingautor: MiguelRamos-Pascual Abstract HIV virus replication is a time-related process that includes attachment to host cell and fusion, reverse transcription, integration on host cell DNA, transcription and splicing, multiple mRNA transport, protein synthesis, budding and maturation. Focusing on the core steps, RNA polymerase II transcripts in an early stage pre-mRNA containing regulator proteins (i.e nef,tat,rev,vif,vpr,vpu), which are completely spliced by the spliceosome complex (0.9kb and 1.8kb) and exported to the ribosome for protein synthesis. These splicing and export processes are regulated by tat protein, which binds on Trans-activation response (TAR) element, and by rev protein, which binds to the Rev-responsive Element (RRE). As long as these regulators are synthesized, splicing is progressively inhibited (from 4.0kb to 9.0kb) and mRNAs are translated into structural and enzymatic proteins (env, gag-pol). During this RNAPII scanning and splicing, around 40 different multi-cystronic mRNA have been produced. Long-read sequencing has been applied to the HIV-1 virus genome (type HXB2CG) with the HIV.pro software, a fortran 90 code for simulating the virus replication cycle, specially RNAPII transcription, exon/intron splicing and ribosome protein synthesis, including the frameshift at gag/pol gene and the ribosome pause at env gene. All HIV-1 virus proteins have been identified as far as other ORFs. As observed, tat/rev protein regulators have different length depending on the splicing cleavage site: tat protein varies from 224aa to a final state of 72aa, whereas rev protein from 25aa to 27aa, with a maximum of 119aa.
    [Show full text]
  • Ribosomal Frameshifting and Dual-Target Antiactivation Restrict Quorum-Sensing–Activated Transfer of a Mobile Genetic Element
    Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing–activated transfer of a mobile genetic element Joshua P. Ramsaya,b,1, Laura G. L. Testera, Anthony S. Majora, John T. Sullivana, Christina D. Edgarc, Torsten Kleffmannc, Jackson R. Patterson-Houseb, Drew A. Hallb, Warren P. Tatec, Michael F. Hynesd, and Clive W. Ronsona Departments of aMicrobiology and Immunology and cBiochemistry, University of Otago, Dunedin 9016, New Zealand; bCurtin Health Innovation Research Institute Biosciences Precinct, Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia; and dDepartment of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada Edited by E. Peter Greenberg, University of Washington, Seattle, WA, and approved February 25, 2015 (received for review January 27, 2015) Symbiosis islands are integrative and conjugative mobile genetic excisionase RdfS (9). Several regulatory elements that influence elements that convert nonsymbiotic rhizobia into nitrogen-fixing excision and transfer of ICEMlSymR7A have been identified, symbionts of leguminous plants. Excision of the Mesorhizobium including TraR, a LuxR-family quorum-sensing (QS) regulator R7A loti symbiosis island ICEMlSym is indirectly activated by quorum that activates gene transcription in response to N-acyl-homo- sensing through TraR-dependent activation of the excisionase serine-lactones (AHLs) produced by TraI1 (10, 11). However, rdfS + gene . Here we show that a 1 programmed ribosomal frame- the direct regulators of rdfS expression have not been identified. shift (PRF) fuses the coding sequences of two TraR-activated Two hypothetical ORFs, msi172 and msi171, are primary can- genes, msi172 and msi171, producing an activator of rdfS expres- sion named Frameshifted excision activator (FseA).
    [Show full text]
  • Detection of Frameshifts and Improving Genome Annotation
    DETECTION OF FRAMESHIFTS AND IMPROVING GENOME ANNOTATION A Thesis Presented to The Academic Faculty by Ivan Valentinovich Antonov In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the School of Computational Science and Engineering Georgia Institute of Technology December 2012 DETECTION OF FRAMESHIFTS AND IMPROVING GENOME ANNOTATION Approved by: Professor Mark Borodovsky, Advisor Professor Kostas T. Konstantinidis School of Computational Science and School of Civil and Environment Engineering Engineering Georgia Institute of Technology Georgia Institute of Technology Professor Brian Hammer Professor Le Song School of Biology School of Computational Science and Georgia Institute of Technology Engineering Georgia Institute of Technology Professor King I. Jordan Professor Pavel Baranov School of Biology Biochemistry Department Georgia Institute of Technology University College Cork, Ireland Date Approved: December 2012 To my family back in Russia iii ACKNOWLEDGEMENTS I would like to thank my advisor Dr. Borodovsky for providing me the opportunity to study Bioinformatics at the Georgia Institute of Technology and for his guidance and motivation. I would like to thank Dr. Pavel Baranov and Arthur Coakley for conducting the experiments for the selected programmed frameshift candidates. I would like to thank Alex Lomsadze for many useful discussions. I would like to thank all my soccer friends with whom I played for the last two years. These games gave me a diversion from the challenging journey of the PhD. I am grateful to the members of my committee, Dr. Pavel Baranov, Dr. Brian Hammer, Dr. King Jordan, Dr. Kostas Konstantinidis and Dr. Le Song, for their time and effort reviewing this thesis.
    [Show full text]
  • Ribosomal Frameshifting Into an Overlapping Gene in the 2B
    Ribosomal frameshifting into an overlapping gene in PNAS PLUS the 2B-encoding region of the cardiovirus genome Gary Loughrana,1, Andrew E. Firthb,1,2, and John F. Atkinsa,c aBioSciences Institute, University College Cork, Cork, Ireland; bDepartment of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; and cDepartment of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330 AUTHOR SUMMARY −1 Proteins are essential for all −1 frameshift site acaseof frameshifting known life, and the (G GUU UUU) where the frameshift ORF sequences of their constituent 5′UTR 3′UTR is relatively short and, L1A 1B 1C 1D 2A 2B 2C 3AB 3C 3D amino acids are specified by unusually, it is completely the nucleotide sequences of StopGo 2B* transframe protein contained within the non- their template messenger frameshift ORF as an RNAs. Cellular organelles Fig. P1. Map of the EMCV genome, showing the polyprotein L-1ABCD- “overlapping gene” called ribosomes travel along 2ABC-3ABCD, the overlapping gene 2B*, and the site of programmed (Fig. P1). Cardioviruses ribosomal frameshifting. messenger RNAs, reading have an RNA genome that consecutive groups of three contains a single long ORF nucleotides called triplets, or codons, and translating each that is translated as a “polyprotein” (L-1ABCD-2ABC- triplet as an amino acid according to the “genetic code,” 3ABCD) and subsequently cleaved to produce 12 separate until they reach a “stop” codon. However, in response to proteins (3). Like many similar viruses, cardioviruses use an signals in some messenger RNAs, a proportion of ribosomes unusual ribosome-dependent mechanism, termed “StopGo” shift into a different triplet reading frame (a phenomenon or “stop-carry on,” to separate the L-1ABCD-2A segment termed programmed ribosomal frameshifting), which leads to of the polyprotein from the 2BC-3ABCD segment as the a different sequence of amino acids, and thus a different polyprotein is generated (4).
    [Show full text]
  • Hepatitis C Virus Frameshift/Alternate Reading Frame Protein Suppresses Interferon Responses Mediated by Pattern Recognition Receptor Retinoic-Acid-Inducible Gene-I
    RESEARCH ARTICLE Hepatitis C Virus Frameshift/Alternate Reading Frame Protein Suppresses Interferon Responses Mediated by Pattern Recognition Receptor Retinoic-Acid-Inducible Gene-I Seung Bum Park1, Scott Seronello1, Wasima Mayer1, David M. Ojcius1,2* 1 School of Natural Sciences, University of California Merced, Merced, California, United States of America, 2 University of the Pacific, Arthur A. Dugoni School of Dentistry, San Francisco, California, United States of America a11111 * [email protected] Abstract Hepatitis C virus (HCV) actively evades host interferon (IFN) responses but the mechanisms of how it does so are not completely understood. In this study, we present evidence for an HCV OPEN ACCESS factor that contributes to the suppression of retinoic-acid-inducible gene-I (RIG-I)-mediated IFN Citation: Park SB, Seronello S, Mayer W, Ojcius DM induction. Expression of frameshift/alternate reading frame protein (F/ARFP) from HCV -2/+1 (2016) Hepatitis C Virus Frameshift/Alternate Reading Frame Protein Suppresses Interferon frame in Huh7 hepatoma cells suppressed type I IFN responses stimulated by HCV RNA path- Responses Mediated by Pattern Recognition ogen-associated molecular pattern (PAMP) and poly(IC). The suppression occurred indepen- Receptor Retinoic-Acid-Inducible Gene-I. PLoS ONE dently of other HCV factors; and activation of interferon stimulated genes, TNFα,IFN-λ1, and 11(7): e0158419. doi:10.1371/journal.pone.0158419 IFN-λ2/3 was likewise suppressed by HCV F/ARFP. Point mutations in the full-length HCV Editor: Shibo Jiang, Shanghai Medical College, sequence (JFH1 genotype 2a strain) were made to introduce premature termination codons in Fudan University, CHINA the -2/+1 reading frame coding for F/ARFP while preserving the original reading frame, which Received: February 26, 2016 enhanced IFNα and IFNβ induction by HCV.
    [Show full text]
  • Transfer RNA Modification Status Influences Retroviral Ribosomal Frameshifting
    Virology 255, 2–8 (1999) Article ID viro.1998.9569, available online at http://www.idealibrary.com on View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector RAPID COMMUNICATION Transfer RNA Modification Status Influences Retroviral Ribosomal Frameshifting Bradley A. Carlson,* So Yeon Kwon,† Mario Chamorro,‡ Stephen Oroszlan,§ Dolph L. Hatfield,* and Byeong Jae Lee†,1 *Section on the Molecular Biology of Selenium, Laboratory of Basic Research and ‡The Varmus Laboratory, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892; †Laboratory of Molecular Genetics, Institute for Molecular Biology and Genetics, Seoul National University, Seoul 151-742, Korea; and §ABL-Basic Research Program, NCI-FCRDC, Frederick, Maryland 21702 Received August 26, 1998; returned to author for revision November 4, 1998; accepted December 11, 1998 The possibility of whether tRNAs with and without a highly modified base in their anticodon loop may influence the level of retroviral ribosomal frameshifting was examined. Rabbit reticulocyte lysates were programmed with mRNA encoding UUU or AAC at the frameshift site and the corresponding Phe tRNA with or without the highly modified wyebutoxine (Y) base on the 39 side of its anticodon or Asn tRNA with or without the highly modified queuine (Q) base in the wobble position of its anticodon added. Phe and Asn tRNAs without the Y or Q base, respectively, stimulated the level of frameshifting, suggesting that the frameshift event is influenced by tRNA modification status. In addition, when AAU occurred immediately upstream of UUU as the penultimate frameshift site codon, addition of tRNAAsn without the Q base reduced the stimulatory effect of tRNAPhe without the Y base, whereas addition of tRNAAsn with the Q base did not alter the stimulatory effect.
    [Show full text]
  • 1 Ribosomal Frameshift in a Double-Stranded RNA Virus of Yeast Forms a Gag-Pol Fusion Protein (RNA Polymerase/Lacz Fusion/L-A Virus) JONATHAN D
    Proc. Nat!. Acad. Sci. USA Vol. 88, pp. 174-178, January 1991 Biochemistry A -1 ribosomal frameshift in a double-stranded RNA virus of yeast forms a gag-pol fusion protein (RNA polymerase/lacZ fusion/L-A virus) JONATHAN D. DINMAN, TATEO ICHO*, AND REED B. WICKNER Section on the Genetics of Simple Eukaryotes, Laboratory of Biochemical Pharmacology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 Communicated by Herbert Tabor, September 20, 1990 (received for review August 3, 1990) ABSTRACT The L-A double-stranded RNA (dsRNA) vi- 9, 23). RNA secondary structure downstream of the slippery rus of Saccharomyces cerevisiae has two open reading frames site may slow or stall ribosomes such that they remain in the (ORFs). ORF1 encodes the 80-kDa major coat protein (gag). slippery site longer, thus promoting frameshifting (4). ORF2, which is expressed only as a 180-kDa fusion protein with The L-A genome (Fig. 1A) has two open reading frames ORF1, encodes a single-stranded RNA-binding domain and has (ORFs). ORF1 encodes the 80-kDa major coat protein (anal- the consensus sequence for RNA-dependent RNA polymerases ogous to retroviral gag). ORF2 has a sequence pattern typical of(+)-strand and double-stranded RNA viruses (pol). We show of the RNA-dependent RNA polymerases of (+) ssRNA that the 180-kDa protein is formed by -1 ribosomal frame- viruses and double-stranded (ds) RNA viruses (analogous to shifting by a mechanism indistinguishable from that of retro- pol) and a ssRNA binding activity thought to be involved in viruses.
    [Show full text]
  • Ribosomal Frameshifting in the CCR5 Mrna Is Regulated by Mirnas and the NMD Pathway
    ARTICLE doi:10.1038/nature13429 Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway Ashton Trey Belew1*, Arturas Meskauskas1,2*, Sharmishtha Musalgaonkar1, Vivek M. Advani1, Sergey O. Sulima1{, Wojciech K. Kasprzak3, Bruce A. Shapiro4 & Jonathan D. Dinman1 Programmed 21 ribosomal frameshift (21 PRF) signals redirect translating ribosomes to slip back one base on messenger RNAs. Although well characterized in viruses, how these elements may regulate cellulargene expression is not understood. Here we describe a 21 PRF signal in the human mRNA encoding CCR5, the HIV-1 co-receptor. CCR5 mRNA-mediated 21 PRF is directed by an mRNA pseudoknot, and is stimulated by at least two microRNAs. Mapping the mRNA–miRNA interaction suggests that formation of a triplex RNA structure stimulates 21 PRF. A 21 PRF event on the CCR5 mRNA directs translating ribosomes to a premature termination codon, destabilizing it through the nonsense-mediated mRNA decay pathway. At least one additional mRNA decay pathway is also involved. Functional 21 PRF signals that seem to be regulated by miRNAs are also demonstrated in mRNAs encoding six other cytokine receptors, suggesting a novel mode through which immune responses may be fine-tuned in mammalian cells. Viral programmed ribosomal frameshift events typically produce purified CCR5–b-gal fusion protein (Extended Data Fig. 2c) unam- carboxy-terminally extended fusion proteins. However, computational biguously identified the predicted 21 frameshift peptide harbouring analyses predict that .95% of 21 PRF events on cellular mRNAs direct the junction between the 02 and 21 frame encoded CCR5 sequence ribosomes to premature termination codons (PTC), suggesting that 21 (Fig.
    [Show full text]
  • Transactivation of Programmed Ribosomal Frameshifting by a Viral
    Transactivation of programmed ribosomal PNAS PLUS frameshifting by a viral protein Yanhua Lia,b,1, Emmely E. Treffersc,d, Sawsan Napthinee, Ali Tasc, Longchao Zhua,b,1, Zhi Suna, Susanne Belle, Brian L. Markf, Peter A. van Veelend, Martijn J. van Hemertc, Andrew E. Firthe, Ian Brierleye,2, Eric J. Snijderc,2, and Ying Fanga,b,1,2 aDepartment of Veterinary and Biomedical Sciences and Department of Biology/Microbiology, South Dakota State University, Brookings, SD 57007; bDepartment of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506; cMolecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands; dDepartment of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands; eDivision of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; and fDepartment of Microbiology, University of Manitoba, Winnipeg, MB, Canada R3T 2N2 Edited by Ian Mohr, New York University School of Medicine, New York, NY, and accepted by the Editorial Board April 17, 2014 (received for review November 22, 2013) Programmed −1 ribosomal frameshifting (−1 PRF) is a widely used replicating elements, such as insertion sequences and trans- translational mechanism facilitating the expression of two poly- posons (12). peptides from a single mRNA. Commonly, the ribosome interacts Recently, we identified an unusual −2 programmed ribosomal with an mRNA secondary structure that promotes −1 frameshift- frameshifting (−2 PRF) event that operates during the trans- ing on a homopolymeric slippery sequence. Recently, we described lation of the genome of porcine reproductive and respiratory an unusual −2 frameshifting (−2 PRF) signal directing efficient syndrome virus (PRRSV), a member of the arterivirus family in expression of a transframe protein [nonstructural protein 2TF the order Nidovirales (13).
    [Show full text]