DOCSLIB.ORG

Slip-Sliding the Frame: Programmed −1 Frameshifting on Eukaryotic Transcripts

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Slip-Sliding the Frame: Programmed −1 Frameshifting on Eukaryotic Transcripts Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Insight/Outlook Slip-Sliding the Frame: Programmed −1 Frameshifting on Eukaryotic Transcripts Gerald M. Wilson and Gary Brewer1 Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157-1064 USA -frameshifting Database searches using this com 1מ The basic mechanisms of mRNA tems, some bacterial frameshift sites 1מ translation are ubiquitous among all or- events have also been documented pound algorithm for ganisms, in that the accurate decoding (Blinkowa and Walker 1990; Tsuchiha- yielded a host of potential signals in all of triplet codon sequences programs se- shi and Brown 1992; Chandler and databases tested, including eukaryotic rial amide linkages of amino acid resi- Fayet 1993; Engelberg-Kulka and Schou- sequences, with frequencies signifi- dues by ribosomal complexes. In gen- laker-Schwarz 1994). At present, no ex- cantly higher than found in random se- eral, the fidelity of this process is depen- amples of eukaryotic mRNAs exhibiting quence populations. In a number of frameshift activity have been re- cases, frameshift signals were conserved 1מ dent on both accurate recognition of mRNA codons by aminoacyl tRNAs and ported. However, a number of viruses in- in homologous mRNAs from different maintenance of the corresponding open fecting eukaryotic cells utilize pro- species. A convincing argument for the ribosomal frameshifts, validity of these searches was provided 1מ reading frame. However, in a growing grammed 1מ number of cases, deviations from this demonstrating that the cis elements in- by the functional demonstration of triplet codon rule are observed, indicat- volved in the frameshifting process are frameshifting activity for two selected ing that the information content of an operational in eukaryotes. In viral sys- signals (from Saccharomyces cerevisiae mRNA to encode protein may extend tems, the efficiency of frameshifting is RAS1 and human CCR5 mRNAs) in a re- beyond its primary structure. These an essential determinant of the stoichi- combinant assay system. Furthermore, frameshift 1מ cases, collectively referred to as transla- ometry of synthesized viral protein in four cases, potential tional recoding (for review, see Geste- products, which must be rigidly main- signals colocalized to sites of mutation land and Atkins 1996), present excep- tained for efficient propagation of the linked to heritable diseases in humans, -frame 1מ tions to the venerable genetic code and virus (Brierly 1995 and references raising the possibility that are typically subdivided among three therein; Dinman and Wickner 1995). shift activity may be a physiologically primary mechanisms: (1) frameshifting, In work presented in this issue, relevant component of regulated gene in which translating ribosomes are in- (Hammell et al. 1999), a bioinformatic expression in humans. Modifications of duced to slide one nucleotide forward or approach was used to screen prokaryotic the parameters employed in this search backward at a distinct point in the tran- and eukaryotic DNA sequence databases algorithm may yet reveal additional can- -frameshift signals. Be- didate frameshift signals, as the poten 1מ script, with protein synthesis then con- for potential frame- tial for 3Ј-RNA pseudoknot formation 1מ reading frame, cause of the complexity of 1מ tinuing in the +1 or respectively; (2) alternative codon usage, shift sites and the sequence variability was a constraint placed upon their selec- where stop codons are not interpreted as observed among these elements in na- tion in this study. An RNA pseudoknot frameshifting at 1מ sites of translational termination but, ture, a multicomponent search algo- is not requisite for rather, encode an amino acid residue; rithm was required to identify candidate the gag–pol overlap of HIV-1 (Jacks et al. and (3) translational bypassing, where sites from bulk database entries. This 1988), for example, which only contains the translational machinery traverses a was made possible in part by the a weak 3Ј-stem–loop structure in vivo gap in the mRNA coding sequence yet plethora of information available de- (Parkin et al. 1992). 1מ yields a single polypeptide chain. scribing structural features of frameshift The identification of functional -ribosomal frame- signals, much of which is described in frameshift signals in chromosomally en 1מ Programmed shift signals are among the most exten- Hammell et al. (1999) and elsewhere coded eukaryotic mRNAs raises several sively characterized of these transla- (Brierly 1995; Chen et al. 1996; Marcz- interesting questions for further investi- tional recoding phenomena (for review, inke et al. 1998). This strategy represents gation. First, it will be important to de- see Brierly 1995; Dinman 1995; Far- a marked contrast to many examples of termine if ribosomal frameshifting oc- abaugh 1996). Although current ex- database searching, which typically in- curs in vivo in the context of these tran- amples are largely limited to viral sys- volve a single motif or are limited to pri- scripts. If so, what is the function of the mary structure parameters (Fickett 1996; frameshift event? A ribosomal frame- 1Corresponding author. E-MAIL [email protected]; FAX (336) 716- Altschul et al. 1997; Aravind and Lands- shift may serve to generate alternate 9928. man 1998; O’Neill 1998). protein isoforms, with common amino- 9:393–394 ©1999 by Cold Spring Harbor Laboratory Press ISSN 1054-9803/99 $5.00; www.genome.org Genome Research 393 www.genome.org Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Insight/Outlook terminal sequences but distinct carboxy- Despite the identification of pro- Brierly, I. 1995. J. Gen. Virol. 76: 1885– .ribosomal frameshifting 1892 1מ terminal regions. Protein products con- grammed taining alternatively framed moieties activity associated with human mRNA Chandler, M. and O. Fayet. 1993. Mol. Microbiol. 7: 497–503. may present unique functional features sequences, the possibility of developing Chen, X., H. Kang, L.X. Shen, M. or may be subject to different modes of antiviral therapeutic strategies targeting Chamorro, H.E. Varmus, and I. Tinoco, regulatory control. In other cases, frame- this mechanism remains an intriguing Jr. 1996. J. Mol. Biol. 260: 479–483. shifting events may have more direct possibility (Dinman et al. 1997, 1998; Cui, Y., J.D. Dinman, and S.W. Peltz. 1996. regulatory roles. For example, frame- Hung et al. 1998). For example, com- EMBO J. 15: 5726–5736. shifts could result in premature termina- pounds that modulate the stability of ei- Cui, Y., J.D. Dinman, T.G. Kinzy, and S.W. tion of protein synthesis if the frame- ther the downstream RNA structural Peltz. 1998. Mol. Cell. Biol. 18: 1506–1516. .motif or codon/anticodon interactions Dinman, J.D. 1995. Yeast 11: 1115–1127 1מ shift generates a stop codon in the open reading frame. In this case, the may alter the efficiency of frameshifting Dinman, J.D. and R.B. Wickner. 1995. mRNA may be subject to accelerated events, leading to a change in the ratio Genetics 141: 95–105. turnover by the nonsense-mediated of frameshifted/nonshifted viral pro- Dinman, J.D., M.J. Ruiz-Echevarria, K. mRNA decay pathway (for review, see teins. Because the function of the RNA Czaplinski, and S.W. Peltz. 1997. Proc. Maquat 1995; Jacobson and Peltz 1996; pseudoknot structure may involve re- Natl. Acad. Sci. 94: 6606–6611. Dinman, J.D., M.J. Ruiz-Echevarria, and Ruiz-Echevarria et al. 1996). Another tarding translating ribosomes at the S.W. Peltz. 1998. Trends Biotechnol. question regarding eukaryotic frame- frameshift site (for review, see Brierly 16: 190–196. shifting events is whether their effi- 1995; Farabaugh 1996), compounds Engelberg-Kulka, H. and R. ciency may be regulated in response to modulating the kinetics of translational Schoulaker-Schwarz. 1994. Mol. Microbiol. signaling pathways or other stimuli. elongation may similarly influence 11: 3–8. This is particularly applicable in the con- frameshit efficiency. Obviously, the im- Farabaugh, P.J. 1996. Annu. Rev. Genet. text of multicellular organisms, whose plications for modulation of host gene 30: 507–528. Fickett, J.W. 1996. Trends Genet. control of gene expression is often sub- expression must also be considered in 12: 316–320. ject to a host of endocrine and develop- the development of such therapies, but Gesteland, R.F. and J.F. Atkins. 1996. Annu. mental effects. even modest changes in viral frameshift- Rev. Biochem. 65: 741–768. ribosomal ing efficiency may be sufficient to confer Hammell, A.B., R.C. Taylor, S.W. Peltz, and 1מ If programmed frameshifting does not occur with eu- significant host benefit. This was dem- J.D. Dinman. 1999. Genome Res. (this karyotic mRNAs, it is possible that flank- onstrated using LA virus infection of issue). ing sequences may have evolved to re- yeast, where up- or down-regulation of Hung, M., P. Patel, S. Davis, and S.R. Green. 1998. J. Virol. 72: 4819-4824. press this activity. Alternatively, specific frameshifting efficiency by more than Jacks, T., M.D. Power, F.R. Masiarz, P.A. trans-acting factors may participate in twofold prevented viral propagation Luciw, P.J. Barr, and H.E. Varmus. 1988. the repression of frameshifting events (Dinman and Wickner 1995). Extrapo- Nature 331: 280–283. on eukaryotic transcripts. For example, lating to the possibility that alterations Jacobson, A. and S.W. Peltz. 1996. Annu. .frameshifting may Rev. Biochem. 65: 693–739 1מ the MOF2/SUI1 gene product of S. cerevi- in programmed siae functions as an inhibitor of viral also contribute to human genetic disor- Maquat, L.E. 1995. RNA 1: 453–465. Marczinke, B., R. Fisher, M. Vidakovic, A.J. RNA frameshifting in infected yeast cells ders, similar strategies aimed at modu- Bloys, and I. Brierly. 1998. J. Mol. Biol. (Cui et al. 1998). This function is well lating the frameshift efficiencies of en- 284: 205–225.
Load more

Recommended publications
  • Effects of Single Amino Acid Deficiency on Mrna Translation Are Markedly
    www.nature.com/scientificreports OPEN Efects of single amino acid defciency on mRNA translation are markedly diferent for methionine Received: 12 December 2016 Accepted: 4 May 2018 versus leucine Published: xx xx xxxx Kevin M. Mazor, Leiming Dong, Yuanhui Mao, Robert V. Swanda, Shu-Bing Qian & Martha H. Stipanuk Although amino acids are known regulators of translation, the unique contributions of specifc amino acids are not well understood. We compared efects of culturing HEK293T cells in medium lacking either leucine, methionine, histidine, or arginine on eIF2 and 4EBP1 phosphorylation and measures of mRNA translation. Methionine starvation caused the most drastic decrease in translation as assessed by polysome formation, ribosome profling, and a measure of protein synthesis (puromycin-labeled polypeptides) but had no signifcant efect on eIF2 phosphorylation, 4EBP1 hyperphosphorylation or 4EBP1 binding to eIF4E. Leucine starvation suppressed polysome formation and was the only tested condition that caused a signifcant decrease in 4EBP1 phosphorylation or increase in 4EBP1 binding to eIF4E, but efects of leucine starvation were not replicated by overexpressing nonphosphorylatable 4EBP1. This suggests the binding of 4EBP1 to eIF4E may not by itself explain the suppression of mRNA translation under conditions of leucine starvation. Ribosome profling suggested that leucine deprivation may primarily inhibit ribosome loading, whereas methionine deprivation may primarily impair start site recognition. These data underscore our lack of a full
    [Show full text]
  • Structural Insights Into Mrna Reading Frame Regulation by Trna
    RESEARCH ARTICLE Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon–anticodon pairing Eric D Hoffer1, Samuel Hong1, S Sunita1, Tatsuya Maehigashi1, Ruben L Gonzalez Jnr2, Paul C Whitford3, Christine M Dunham1* 1Department of Biochemistry, Emory University School of Medicine, Atlanta, United States; 2Department of Chemistry, Columbia University, New York, United States; 3Department of Physics, Northeastern University, Boston, United States Abstract Modifications in the tRNA anticodon loop, adjacent to the three-nucleotide anticodon, influence translation fidelity by stabilizing the tRNA to allow for accurate reading of the mRNA genetic code. One example is the N1-methylguanosine modification at guanine nucleotide 37 (m1G37) located in the anticodon loop andimmediately adjacent to the anticodon nucleotides 34, 35, 36. The absence of m1G37 in tRNAPro causes +1 frameshifting on polynucleotide, slippery codons. Here, we report structures of the bacterial ribosome containing tRNAPro bound to either cognate or slippery codons to determine how the m1G37 modification prevents mRNA frameshifting. The structures reveal that certain codon–anticodon contexts and the lack of m1G37 destabilize interactions of tRNAPro with the P site of the ribosome, causing large conformational changes typically only seen during EF-G-mediated translocation of the mRNA-tRNA pairs. These studies provide molecular insights into how m1G37 stabilizes the interactions of tRNAPro with the ribosome in the context of a slippery mRNA codon. *For correspondence: Introduction [email protected] Post-transcriptionally modified RNAs, including ribosomal RNA (rRNA), transfer RNA (tRNA) and messenger RNA (mRNA), stabilize RNA tertiary structures during ribonucleoprotein biogenesis, reg- Competing interests: The ulate mRNA metabolism, and influence other facets of gene expression.
    [Show full text]
  • Circular Code Motifs in the Ribosome: a Missing Link in the Evolution of Translation?
    Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Circular code motifs in the ribosome: a missing link in the evolution of translation? Gopal Dila1, Raymond Ripp1, Claudine Mayer1,2,3, Olivier Poch1, Christian J. Michel1,* and Julie D. Thompson1,* 1 Department of Computer Science, ICube, CNRS, University of Strasbourg, Strasbourg, France 2 Unité de Microbiologie Structurale, Institut Pasteur, CNRS, 75724 Paris Cedex 15, France 3 Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France * To whom correspondence should be addressed; Email: [email protected] *Corresponding authors: Names: Christian J. Michel, Julie D. Thompson Address: Department of Computer Science, ICube, Strasbourg, France Phone: (33) 0368853296 Email: [email protected], [email protected] Running title: circular code motifs in the ribosome Keywords: origin of life, genetic code, circular code, translation, ribosome evolution 1 Dila et al. Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract The origin of the genetic code remains enigmatic five decades after it was elucidated, although there is growing evidence that the code co-evolved progressively with the ribosome. A number of primordial codes were proposed as ancestors of the modern genetic code, including comma-free codes such as the RRY, RNY or GNC codes (R = G or A, Y = C or T, N = any nucleotide), and the X circular code, an error-correcting code that also allows identification and maintenance of the reading frame. It was demonstrated previously that motifs of the X circular code are significantly enriched in the protein-coding genes of most organisms, from bacteria to eukaryotes.
    [Show full text]
  • Super-Resolution Ribosome Profiling Reveals Unannotated Translation Events in Arabidopsis
    Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis Polly Yingshan Hsua, Lorenzo Calviellob,c, Hsin-Yen Larry Wud,1, Fay-Wei Lia,e,f,1, Carl J. Rothfelse,f, Uwe Ohlerb,c, and Philip N. Benfeya,g,2 aDepartment of Biology, Duke University, Durham, NC 27708; bBerlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany; cDepartment of Biology, Humboldt Universität zu Berlin, 10099 Berlin, Germany; dBioinformatics Research Center and Department of Statistics, North Carolina State University, Raleigh, NC 27695; eUniversity Herbarium, University of California, Berkeley, CA 94720; fDepartment of Integrative Biology, University of California, Berkeley, CA 94720; and gHoward Hughes Medical Institute, Duke University, Durham, NC 27708 Contributed by Philip N. Benfey, September 13, 2016 (sent for review June 30, 2016; reviewed by Pam J. Green and Albrecht G. von Arnim) Deep sequencing of ribosome footprints (ribosome profiling) maps and contaminants. Several metrics associated with translation have and quantifies mRNA translation. Because ribosomes decode mRNA been exploited (11), for example, the following: (i)ribosomesre- every 3 nt, the periodic property of ribosome footprints could be lease after encountering a stop codon (9), (ii) local enrichment of used to identify novel translated ORFs. However, due to the limited footprints within the predicted ORF (4, 13), (iii) ribosome footprint resolution of existing methods, the 3-nt periodicity is observed length distribution (7), and (iv) 3-nt periodicity displayed by trans- mostly in a global analysis, but not in individual transcripts. Here, we lating ribosomes (2, 6, 10, 14, 15). Among these features, some work report a protocol applied to Arabidopsis that maps over 90% of the well in distinguishing groups of coding vs.
    [Show full text]
  • An Eif4e Allele Confers Resistance to an Uncapped and Non-Polyadenylated RNA Virus in Melon
    The Plant Journal (2006) 48, 452–462 doi: 10.1111/j.1365-313X.2006.02885.x An eIF4E allele confers resistance to an uncapped and non-polyadenylated RNA virus in melon Cristina Nieto1,3,‡, Monica Morales2,3,†,‡, Gisella Orjeda3,‡, Christian Clepet3, Amparo Monfort2, Benedicte Sturbois3, Pere Puigdome` nech4, Michel Pitrat5, Michel Caboche3, Catherine Dogimont5, Jordi Garcia-Mas2, Miguel. A. Aranda1 and Abdelhafid Bendahmane3,* 1Centro de Edafologı´a y Biologı´a Aplicada del Segura (CEBAS)- CSIC, Apdo. correos 164, 30100 Espinardo, Murcia, Spain, 2Departament de Gene` tica Vegetal, Laboratori de Gene` tica Molecular Vegetal CSIC-IRTA, carretera de Cabrils s/n, 08348 Cabrils, Barcelona, Spain, 3Unite´ de Recherche en Ge´ nomique Ve´ ge´ tale, 2, rue Gaston Cre´ mieux CP 5708, 91057 Evry Cedex, France, 4Departament de Gene` tica Molecular, Laboratori de Gene` tica Molecular Vegetal CSIC-IRTA, Jordi Girona 18-26, 08034 Barcelona, Spain, and 5INRA, Unite´ de Ge´ netique et Ame´ lioration des Plantes, BP 94, Montfavet, F-84143, France Received 6 April 2006; revised 5 July 2006; accepted 18 July 2006. *For correspondence (fax þ33 160874510; e-mail [email protected]). †Present address: Department of Disease and Stress Biology and Molecular Microbiology, John Innes Center, Norwich NR4 7UH, UK. ‡These authors contributed equally to this work. Summary The characterization of natural recessive resistance genes and virus-resistant mutants of Arabidopsis have implicated translation initiation factors of the 4E family [eIF4E and eIF(iso)4E] as susceptibility factors required for virus multiplication and resistance expression. To date, viruses controlled by these genes mainly belong to the family Potyviridae.
    [Show full text]
  • Rps3/Us3 Promotes Mrna Binding at the 40S Ribosome Entry Channel and Stabilizes Preinitiation Complexes at Start Codons
    Rps3/uS3 promotes mRNA binding at the 40S ribosome entry channel and stabilizes preinitiation complexes at start codons Jinsheng Donga, Colin Echeverría Aitkenb, Anil Thakura, Byung-Sik Shina, Jon R. Lorschb,1, and Alan G. Hinnebuscha,1 aLaboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892; and bLaboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892 Contributed by Alan G. Hinnebusch, January 24, 2017 (sent for review December 15, 2016; reviewed by Jamie H. D. Cate and Matthew S. Sachs) Met The eukaryotic 43S preinitiation complex (PIC) bearing Met-tRNAi rearrangement to PIN at both near-cognate start codons (e.g., in a ternary complex (TC) with eukaryotic initiation factor (eIF)2-GTP UUG) and cognate (AUG) codons in poor Kozak context; hence scans the mRNA leader for an AUG codon in favorable “Kozak” eIF1 must dissociate from the 40S subunit for start-codon rec- context. AUG recognition provokes rearrangement from an open ognition (Fig. 1A). Consistent with this, structural analyses of PIC conformation with TC bound in a state not fully engaged with partial PICs reveal that eIF1 and eIF1A promote rotation of the “ ” the P site ( POUT ) to a closed, arrested conformation with TC tightly 40S head relative to the body (2, 3), thought to be instrumental bound in the “P ” state. Yeast ribosomal protein Rps3/uS3 resides IN in TC binding in the POUT conformation, but that eIF1 physically in the mRNA entry channel of the 40S subunit and contacts mRNA Met clashes with Met-tRNAi in the PIN state (2, 4), and is both via conserved residues whose functional importance was unknown.
    [Show full text]
  • Transcription and Open Reading Frame
    Transcription The expression of genetic information stored in the DNA sequence starts with synthesis of the RNA copy of the gene in a process called transcription. The RNA copy of the gene is called messenger RNA (mRNA). A special enzyme, RNA polymerase, recognizes a sequence, called promoter, on the DNA double helix upstream from the protein coding sequence. RNA polymerase binds to the promoter and opens it up: separates the complementary strands at about 12-nt-long region of the promoter. Then the enzyme starts the mRNA synthesis using all 4 NTPs. The DNA strand, which is used as a template by RNA polymerase, is called the template or antisense strand. The opposite strand of the gene, which sequence is identical to the sequence of mRNA (except the substitution T U, of course), is called the coding or sense strand. There is also a special sequence after the end of the gene, which signals to RNA polymerase to terminate the mRNA synthesis. Thus synthesized mRNA molecule, which includes the protein coding region flanked by short unrelated sequences from both sides, is either translated by the ribosome into the protein molecule at the spot (in case of prokaryotes) or is transported from the nucleus to the cytoplasm (in case of eukaryotes) and there it is translated by the ribosome. Open Reading Frame (ORF) Since the genetic code is triplet, three reading frames are possible for the same mRNA molecule. For instance, the sequence: …..AUUGCCUAACCCUUAGGG…. can be separated into triplets by three possible ways: ….AUUGCCUAACCCUUAGGG…. ….AUUGCCUAACCCUUAGGG…. ….AUUGCCUAACCCUUAGGG…. The frame, in which no stop codons are encountered, is called the Open Reading Frame (ORF).
    [Show full text]
  • Temperature-Dependent Regulation of Upstream Open
    bioRxiv preprint doi: https://doi.org/10.1101/678409; this version posted June 24, 2019. 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. 1 Temperature-Dependent Regulation of Upstream Open 2 Reading Frame Translation in S. Cerevisiae 3 4 Shardul D. Kulkarni1, Fujun Zhou1, Neelam Dabas Sen2, Hongen Zhang2, Alan G. Hinnebusch2,3, 5 Jon R. Lorsch1,3 6 7 8 1Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver 9 National Institute of Child Health and Human Development, National Institutes of Health, 10 Bethesda, MD USA. 11 12 2Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of 13 Child Health and Human Development, National Institutes of Health, Bethesda, MD USA. 14 15 3To whom correspondence should be addressed ([email protected], [email protected]) 16 17 18 19 20 21 22 1 bioRxiv preprint doi: https://doi.org/10.1101/678409; this version posted June 24, 2019. 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. 23 Abstract 24 Background: Translation of an mRNA in eukaryotes starts at AUG in most cases. Near-cognate 25 codons (NCCs) such as UUG, ACG and AUU are also used as start sites at low levels in S. 26 cerevisiae. Initiation from NCCs or AUGs in the 5’-untranslated regions (UTRs) of mRNAs can 27 lead to translation of upstream open reading frames (uORFs) that might regulate eXpression of 28 the main ORF (mORF).
    [Show full text]
  • The Rnps of Eukaryotic Translation Control
    Trends in Cell & Molecular Biology Vol. 10, 2015 The RNPs of eukaryotic translation control Sarah Fritz and Kathleen Boris-Lawrie*,# Department of Veterinary Biosciences, Center for Retrovirus Research, Center for RNA Biology, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA. ABSTRACT unique RNA binding proteins. The outcome is an Protein synthesis is the essential cellular process enhanced understanding and appreciation for the of translating the genetic code into the major role of RNP biology in the regulation of protein synthesis. structural and functional biomolecule of the cell: the protein. Eukaryotic translation is a dynamic molecular process choreographed by translation KEYWORDS: protein synthesis, eukaryotic translation control, translation RNP (trRNP), CBC ribonucleoprotein (trRNP) complexes that assemble trRNP, eIF4E trRNP, DExH/D-box RNA helicases upon a messenger RNA (mRNA) and regulate its interaction with the bimolecular catalyst of this INTRODUCTION event, the ribosome. From their transcription, mRNAs assemble within dynamic RNA-protein structures Eukaryotic translation occurs in three mechanistic that regulate their stability, processing, localization, stages: initiation, elongation, and termination. Each and ultimately their translation. Ribonucleoprotein stage is coordinated by a set of translation factors, (RNP) complex is a term used to broadly define which are RNA binding and/or scaffolding proteins that assemble upon an mRNA and regulate its these RNA-protein assemblies. trRNP complexes specifically relate to dynamic mRNA-protein engagement with the ribosome. These RNA-protein structures that coordinate the translation process. complexes give rise to the trRNPs of eukaryotic trRNPs are at the core of eukaryotic translation translation control. The integration of distinct RNA binding proteins, such as DExH/D-box control.
    [Show full text]
  • Alt-RPL36 Downregulates the PI3K-AKT-Mtor Signaling Pathway by Interacting with TMEM24
    bioRxiv preprint doi: https://doi.org/10.1101/2020.03.04.977314; this version posted March 5, 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. Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24 Xiongwen Cao1,2,5, Alexandra Khitun1,2,5, Zhenkun Na1,2, Thitima Phoodokmai3, Khomkrit Sappakhaw3, Elizabeth Olatunji2, Chayasith Uttamapinant3, Sarah A. Slavoff1,2,4* 1Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States 2Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States 3School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand 4Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06529, United States 5These authors contributed equally *Correspondence: [email protected] Abstract While thousands of previously unannotated small and alternative open reading frames (alt- ORFs) have recently been revealed in the human genome, the functions of only a handful are currently known, and no post-translational modifications of their polypeptide products have yet been reported, leaving open the question of their biological significance as a class. Using a proteomic strategy for discovery of unannotated short open reading frames in human cells, we report the detection of alt-RPL36, a 148-amino acid protein co-encoded with and overlapping human RPL36. Alt-RPL36 interacts with TMEM24, which transports the phosphatidylinositol 4,5- bisphosphate [PI(4,5)P2] precursor phosphatidylinositol from the endoplasmic reticulum to the plasma membrane.
    [Show full text]
  • Gene Expression Regulation by Upstream Open Reading Frames In
    Silva J, Fernandes R, Romão L. J Rare Dis Res Treat. (2017) 2(4): 33-38 Journal of www.rarediseasesjournal.com Rare Diseases Research & Treatment Mini review Open Access Gene expression regulation by upstream open reading frames in rare diseases Joana Silva1,2, Rafael Fernandes1,2, and Luísa Romão1,2* 1Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal 2Gene Expression and Regulation Group, Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal Article Info ABSTRACT Article Notes Upstream open reading frames (uORFs) constitute a class of cis-acting Received: June 19, 2017 elements that regulate translation initiation. Mutations or polymorphisms that Accepted: July 21, 2017 alter, create or disrupt a uORF have been widely associated with several human *Correspondence: disorders, including rare diseases. In this mini-review, we intend to highlight the Dr. Luísa Romão, Department of Human Genetics, Instituto mechanisms associated with the uORF-mediated translational regulation and Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, describe recent examples of their deregulation in the etiology of human rare 1649-016, Lisboa, Portugal; Tel: (+351) 21 750 8155; Fax: diseases. Additionally, we discuss new insights arising from ribosome profiling (+351) 21 752 6410; studies and reporter assays regarding uORF features and their intrinsic role E-mail: [email protected]. in translational regulation. This type of knowledge is of most importance to © 2017 Romão L. This article is distributed under the terms of design and implement new or improved diagnostic and/or treatment strategies the Creative Commons Attribution 4.0 International License.
    [Show full text]
  • Chem 431C-Lecture 8A Central Dogma of Molecular Biology Proteins
    Chem 431c-Lecture 8a Reminder: Wednesday is Test 2 Day Covers Chapters 25 and 26 in toto. 90 points Translation: mRNA directed 6 discussion questions. 15 points each. Work protein synthesis quickly and concisely. Answer the question asked. Some students answer more than is asked. Penalty will be levied. Chapter 27: Will the test be difficult? For some, Yes. Protein Metabolism Study major concepts. Sample Question: Describe Mismatch Repair giving unique enzymes involved and describing when it is used. Copyright © 2004 by W. H. Freeman & Company Central dogma of molecular Proteins biology Typical cell needs 1000’s of proteins. • Proteins =the Protein biosynthesis elucidation-one of greatest endproducts of the challenges in biochemistry; information There are >70 ribosomal proteins; 90% of chem pathways energy used by cell; 15,000 ribosomes; 100,000 molecules of protein factors and enzymes; 200,000 tRNA molecules, Process is complex yet fast: protein of 100 aa’s/5 sec in E.coli. Ribosomes line the endoplasmic reticulum Genetic Code -nucleotide triplet codon/amino acid -non overlapping (overlap would be limiting) -first 2 letters usu. fixed but 3rd may be variable -degenerate: more than 1 codon/amino acid - reading frame determined by initiation codon – AUG; termination codons are UAA, UAG and UGA 1 Crick’s adaptor hypothesis Triplet non-overlapping code Just like assembling a Lego molecule? How many possible unique triplet codons can you have? Reading Frame in genetic code Open reading frame (ORF) In a random sequence of nucleotides, probability of 1/ 20 codons in each reading frame is a termination codon. So if it doesn’t have a termination codon among 50 or more, it’s an “open reading frame”(ORF).
    [Show full text]