1
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Abstract
The constrained nature of viral genomes has allowed a translational sleight of hand known as −1 Programmed Ribosomal Frameshifting (−1 PRF) to flourish. Numerous studies have sought to tease apart the mechanisms and implications of −1PRF utilizing a few techniques. The dual-luciferase assay and ribosomal profiling have driven the PRF field to make great advances; however, the use of these assays means that the full impact of the genomic and cellular context on −1 PRF is often lost. Here, we discuss how the Minimal Frameshifting Element (MFE) and its constraints can hide contextual effects on −1 PRF. We review how sequence elements proximal to the traditionally defined MFE, such as the coronavirus attenuator sequence, can affect the observed rates of −1 PRF. Further, the MFE-based approach fully obscured −1 PRF in Barley yellow dwarf virus and would render the exploration of −1 PRF difficult in Porcine reproductive and respiratory syndrome virus, Encephalomyocarditis virus, Theiler’s murine encephalomyelitis virus, and Sindbis virus. Finally, we examine how the cellular context of tRNA abundance, miRNAs, and immune response elements can affect −1 PRF. The use of MFE was instrumental in establishing the basic foundations of PRF; however, it has become clear that the contextual impact on −1 PRF is no longer the exception so much as it is the rule and argues for new approaches to study −1PRF that embrace context. We therefore urge our field to expand the strategies and methods used to explore −1 PRF.
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2
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Riegger RJ, Caliskan N. Thinking Outside the Frame: Impacting Genomes Capacity by Programmed Ribosomal Frameshifting. Front Mol Biosci 2022; 9:842261. [PMID: 35281266 PMCID: PMC8915115 DOI: 10.3389/fmolb.2022.842261] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/26/2022] [Indexed: 01/08/2023] Open
Abstract
Translation facilitates the transfer of the genetic information stored in the genome via messenger RNAs to a functional protein and is therefore one of the most fundamental cellular processes. Programmed ribosomal frameshifting is a ubiquitous alternative translation event that is extensively used by viruses to regulate gene expression from overlapping open reading frames in a controlled manner. Recent technical advances in the translation field enabled the identification of precise mechanisms as to how and when ribosomes change the reading frame on mRNAs containing cis-acting signals. Several studies began also to illustrate that trans-acting RNA modulators can adjust the timing and efficiency of frameshifting illuminating that frameshifting can be a dynamically regulated process in cells. Here, we intend to summarize these new findings and emphasize how it fits in our current understanding of PRF mechanisms as previously described.
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Affiliation(s)
- Ricarda J. Riegger
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany
- Graduate School of Life Sciences (GSLS), University of Würzburg, Würzburg, Germany
| | - Neva Caliskan
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
- *Correspondence: Neva Caliskan,
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3
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Penn WD, Harrington HR, Schlebach JP, Mukhopadhyay S. Regulators of Viral Frameshifting: More Than RNA Influences Translation Events. Annu Rev Virol 2020; 7:219-238. [PMID: 32600156 DOI: 10.1146/annurev-virology-012120-101548] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Programmed ribosomal frameshifting (PRF) is a conserved translational recoding mechanism found in all branches of life and viruses. In bacteria, archaea, and eukaryotes PRF is used to downregulate protein production by inducing a premature termination of translation, which triggers messenger RNA (mRNA) decay. In viruses, PRF is used to drive the production of a new protein while downregulating the production of another protein, thus maintaining a stoichiometry optimal for productive infection. Traditionally, PRF motifs have been defined by the characteristics of two cis elements: a slippery heptanucleotide sequence followed by an RNA pseudoknot or stem-loop within the mRNA. Recently, additional cis and new trans elements have been identified that regulate PRF in both host and viral translation. These additional factors suggest PRF is an evolutionarily conserved process whose function and regulation we are just beginning to understand.
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Affiliation(s)
- Wesley D Penn
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Haley R Harrington
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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4
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Thulson E, Hartwick EW, Cooper-Sansone A, Williams MAC, Soliman ME, Robinson LK, Kieft JS, Mouzakis KD. An RNA pseudoknot stimulates HTLV-1 pro-pol programmed -1 ribosomal frameshifting. RNA (NEW YORK, N.Y.) 2020; 26:512-528. [PMID: 31980578 PMCID: PMC7075266 DOI: 10.1261/rna.070490.119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Programmed -1 ribosomal frameshifts (-1 PRFs) are commonly used by viruses to regulate their enzymatic and structural protein levels. Human T-cell leukemia virus type 1 (HTLV-1) is a carcinogenic retrovirus that uses two independent -1 PRFs to express viral enzymes critical to establishing new HTLV-1 infections. How the cis-acting RNA elements in this viral transcript function to induce frameshifting is unknown. The objective of this work was to conclusively define the 3' boundary of and the RNA elements within the HTLV-1 pro-pol frameshift site. We hypothesized that the frameshift site structure was a pseudoknot and that its 3' boundary would be defined by the pseudoknot's 3' end. To test these hypotheses, the in vitro frameshift efficiencies of three HTLV-1 pro-pol frameshift sites with different 3' boundaries were quantified. The results indicated that nucleotides included in the longest construct were essential to highly efficient frameshift stimulation. Interestingly, only this construct could form the putative frameshift site pseudoknot. Next, the secondary structure of this frameshift site was determined. The dominant structure was an H-type pseudoknot which, together with the slippery sequence, stimulated frameshifting to 19.4(±0.3)%. The pseudoknot's critical role in frameshift stimulation was directly revealed by examining the impact of structural changes on HTLV-1 pro-pol -1 PRF. As predicted, mutations that occluded pseudoknot formation drastically reduced the frameshift efficiency. These results are significant because they demonstrate that a pseudoknot is important to HTLV-1 pro-pol -1 PRF and define the frameshift site's 3' boundary.
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Affiliation(s)
- Eliza Thulson
- Department of Chemistry and Biochemistry, Fort Lewis College, Durango, Colorado 81301, USA
| | - Erik W Hartwick
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Andrew Cooper-Sansone
- Department of Chemistry and Biochemistry, Fort Lewis College, Durango, Colorado 81301, USA
| | - Marcus A C Williams
- Department of Chemistry and Biochemistry, Fort Lewis College, Durango, Colorado 81301, USA
| | - Mary E Soliman
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, California 90045, USA
| | - Leila K Robinson
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, California 90045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Kathryn D Mouzakis
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, California 90045, USA
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5
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Korniy N, Goyal A, Hoffmann M, Samatova E, Peske F, Pöhlmann S, Rodnina MV. Modulation of HIV-1 Gag/Gag-Pol frameshifting by tRNA abundance. Nucleic Acids Res 2019; 47:5210-5222. [PMID: 30968122 PMCID: PMC6547452 DOI: 10.1093/nar/gkz202] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/12/2019] [Accepted: 04/08/2019] [Indexed: 12/16/2022] Open
Abstract
A hallmark of translation in human immunodeficiency virus type 1 (HIV-1) is a –1 programmed ribosome frameshifting event that produces the Gag-Pol fusion polyprotein. The constant Gag to Gag-Pol ratio is essential for the virion structure and infectivity. Here we show that the frameshifting efficiency is modulated by Leu-tRNALeu that reads the UUA codon at the mRNA slippery site. This tRNALeu isoacceptor is particularly rare in human cell lines derived from T-lymphocytes, the cells that are targeted by HIV-1. When UUA decoding is delayed, the frameshifting follows an alternative route, which maintains the Gag to Gag-Pol ratio constant. A second potential slippery site downstream of the first one is normally inefficient but can also support –1-frameshifting when altered by a compensatory resistance mutation in response to current antiviral drug therapy. Together these different regimes allow the virus to maintain a constant –1-frameshifting efficiency to ensure successful virus propagation.
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Affiliation(s)
- Natalia Korniy
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Akanksha Goyal
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany.,Faculty of Biology and Psychology, University of Göttingen, Wilhelm-Weber-Str. 2, 37073 Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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6
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Thermodynamic control of -1 programmed ribosomal frameshifting. Nat Commun 2019; 10:4598. [PMID: 31601802 PMCID: PMC6787027 DOI: 10.1038/s41467-019-12648-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/11/2019] [Indexed: 12/18/2022] Open
Abstract
mRNA contexts containing a 'slippery' sequence and a downstream secondary structure element stall the progression of the ribosome along the mRNA and induce its movement into the -1 reading frame. In this study we build a thermodynamic model based on Bayesian statistics to explain how -1 programmed ribosome frameshifting can work. As training sets for the model, we measured frameshifting efficiencies on 64 dnaX mRNA sequence variants in vitro and also used 21 published in vivo efficiencies. With the obtained free-energy difference between mRNA-tRNA base pairs in the 0 and -1 frames, the frameshifting efficiency of a given sequence can be reproduced and predicted from the tRNA-mRNA base pairing in the two frames. Our results further explain how modifications in the tRNA anticodon modulate frameshifting and show how the ribosome tunes the strength of the base-pair interactions.
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7
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Jindal S, Ghosh A, Ismail A, Singh N, Komar AA. Role of the uS9/yS16 C-terminal tail in translation initiation and elongation in Saccharomyces cerevisiae. Nucleic Acids Res 2019; 47:806-823. [PMID: 30481328 PMCID: PMC6344880 DOI: 10.1093/nar/gky1180] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 11/06/2018] [Indexed: 12/18/2022] Open
Abstract
The small ribosomal subunit protein uS9 (formerly called rpS16 in Saccharomyces cerevisiae), has a long protruding C-terminal tail (CTT) that extends towards the mRNA cleft of the ribosome. The last C-terminal residue of uS9 is an invariably conserved, positively charged Arg that is believed to enhance interaction of the negatively charged initiator tRNA with the ribosome when the tRNA is base-paired to the AUG codon in the P-site. In order to more fully characterize the role of the uS9 CTT in eukaryotic translation, we tested how truncations, extensions and substitutions within the CTT affect initiation and elongation processes in Saccharomyces cerevisiae. We found that uS9 C-terminal residues are critical for efficient recruitment of the eIF2•GTP•Met-tRNAiMet ternary complex to the ribosome and for its proper response to the presence of an AUG codon in the P-site during the scanning phase of initiation. These residues also regulate hydrolysis of the GTP in the eIF2•GTP•Met-tRNAiMet complex to GDP and Pi. In addition, our data show that uS9 CTT modulates elongation fidelity. Therefore, we propose that uS9 CTT is critical for proper control of the complex interplay of events surrounding accommodation of initiator and elongator tRNAs in the P- and A-sites of the ribosome.
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Affiliation(s)
- Supriya Jindal
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Arnab Ghosh
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Amra Ismail
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Nishant Singh
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Anton A Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
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8
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Korniy N, Samatova E, Anokhina MM, Peske F, Rodnina MV. Mechanisms and biomedical implications of -1 programmed ribosome frameshifting on viral and bacterial mRNAs. FEBS Lett 2019; 593:1468-1482. [PMID: 31222875 PMCID: PMC6771820 DOI: 10.1002/1873-3468.13478] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/14/2019] [Accepted: 05/26/2019] [Indexed: 12/11/2022]
Abstract
Some proteins are expressed as a result of a ribosome frameshifting event that is facilitated by a slippery site and downstream secondary structure elements in the mRNA. This review summarizes recent progress in understanding mechanisms of –1 frameshifting in several viral genes, including IBV 1a/1b, HIV‐1 gag‐pol, and SFV 6K, and in Escherichia coli dnaX. The exact frameshifting route depends on the availability of aminoacyl‐tRNAs: the ribosome normally slips into the –1‐frame during tRNA translocation, but can also frameshift during decoding at condition when aminoacyl‐tRNA is in limited supply. Different frameshifting routes and additional slippery sites allow viruses to maintain a constant production of their key proteins. The emerging idea that tRNA pools are important for frameshifting provides new direction for developing antiviral therapies.
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Affiliation(s)
- Natalia Korniy
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Maria M Anokhina
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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9
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mRNA-Mediated Duplexes Play Dual Roles in the Regulation of Bidirectional Ribosomal Frameshifting. Int J Mol Sci 2018; 19:ijms19123867. [PMID: 30518074 PMCID: PMC6321510 DOI: 10.3390/ijms19123867] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 11/17/2022] Open
Abstract
In contrast to -1 programmed ribosomal frameshifting (PRF) stimulation by an RNA pseudoknot downstream of frameshifting sites, a refolding upstream RNA hairpin juxtaposing the frameshifting sites attenuates -1 PRF in human cells and stimulates +1 frameshifting in yeast. This eukaryotic functional mimicry of the internal Shine-Dalgarno (SD) sequence-mediated duplex was confirmed directly in the 70S translation system, indicating that both frameshifting regulation activities of upstream hairpin are conserved between 70S and 80S ribosomes. Unexpectedly, a downstream pseudoknot also possessed two opposing hungry codon-mediated frameshifting regulation activities: attenuation of +1 frameshifting and stimulation of a non-canonical -1 frameshifting within the +1 frameshift-prone CUUUGA frameshifting site in the absence of release factor 2 (RF2) in vitro. However, the -1 frameshifting activity of the downstream pseudoknot is not coupled with its +1 frameshifting attenuation ability. Similarly, the +1 frameshifting activity of the upstream hairpin is not required for its -1 frameshifting attenuation function Thus, each of the mRNA duplexes flanking the two ends of a ribosomal mRNA-binding channel possesses two functions in bi-directional ribosomal frameshifting regulation: frameshifting stimulation and counteracting the frameshifting activity of each other.
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10
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Penno C, Kumari R, Baranov PV, van Sinderen D, Atkins JF. Specific reverse transcriptase slippage at the HIV ribosomal frameshift sequence: potential implications for modulation of GagPol synthesis. Nucleic Acids Res 2017; 45:10156-10167. [PMID: 28973470 PMCID: PMC5737442 DOI: 10.1093/nar/gkx690] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/24/2017] [Indexed: 12/28/2022] Open
Abstract
Synthesis of HIV GagPol involves a proportion of ribosomes translating a U6A shift site at the distal end of the gag gene performing a programmed -1 ribosomal frameshift event to enter the overlapping pol gene. In vitro studies here show that at the same shift motif HIV reverse transcriptase generates -1 and +1 indels with their ratio being sensitive to the relative concentration ratio of dNTPs specified by the RNA template slippage-prone sequence and its 5' adjacent base. The GGG sequence 3' adjacent to the U6A shift/slippage site, which is important for ribosomal frameshifting, is shown here to limit reverse transcriptase base substitution and indel 'errors' in the run of A's in the product. The indels characterized here have either 1 more or less A, than the corresponding number of template U's. cDNA with 5 A's may yield novel Gag product(s), while cDNA with an extra base, 7 A's, may only be a minor contributor to GagPol polyprotein. Synthesis of a proportion of non-ribosomal frameshift derived GagPol would be relevant in efforts to identify therapeutically useful compounds that perturb the ratio of GagPol to Gag, and pertinent to the extent in which specific polymerase slippage is utilized in gene expression.
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Affiliation(s)
- Christophe Penno
- School of Biochemistry, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland.,Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Romika Kumari
- School of Biochemistry, University College Cork, Cork, Ireland
| | - Pavel V Baranov
- School of Biochemistry, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland.,Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - John F Atkins
- School of Biochemistry, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland.,Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
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11
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Caliskan N, Wohlgemuth I, Korniy N, Pearson M, Peske F, Rodnina MV. Conditional Switch between Frameshifting Regimes upon Translation of dnaX mRNA. Mol Cell 2017; 66:558-567.e4. [PMID: 28525745 DOI: 10.1016/j.molcel.2017.04.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 03/07/2017] [Accepted: 04/27/2017] [Indexed: 12/16/2022]
Abstract
Ribosome frameshifting during translation of bacterial dnaX can proceed via different routes, generating a variety of distinct polypeptides. Using kinetic experiments, we show that -1 frameshifting predominantly occurs during translocation of two tRNAs bound to the slippery sequence codons. This pathway depends on a stem-loop mRNA structure downstream of the slippery sequence and operates when aminoacyl-tRNAs are abundant. However, when aminoacyl-tRNAs are in short supply, the ribosome switches to an alternative frameshifting pathway that is independent of a stem-loop. Ribosome stalling at a vacant 0-frame A-site codon results in slippage of the P-site peptidyl-tRNA, allowing for -1-frame decoding. When the -1-frame aminoacyl-tRNA is lacking, the ribosomes switch into -2 frame. Quantitative mass spectrometry shows that the -2-frame product is synthesized in vivo. We suggest that switching between frameshifting routes may enrich gene expression at conditions of aminoacyl-tRNA limitation.
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MESH Headings
- Bacterial Proteins/biosynthesis
- Bacterial Proteins/genetics
- DNA Polymerase III/biosynthesis
- DNA Polymerase III/genetics
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Frameshifting, Ribosomal
- Gene Expression Regulation, Bacterial
- Gene Expression Regulation, Enzymologic
- Kinetics
- Mutation
- Nucleic Acid Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Spectrometry, Mass, Electrospray Ionization
- Structure-Activity Relationship
- Tandem Mass Spectrometry
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Affiliation(s)
- Neva Caliskan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Natalia Korniy
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Pearson
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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12
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Tsai TW, Yang H, Yin H, Xu S, Wang Y. High-Efficiency "-1" and "-2" Ribosomal Frameshiftings Revealed by Force Spectroscopy. ACS Chem Biol 2017; 12:1629-1635. [PMID: 28437082 PMCID: PMC5477775 DOI: 10.1021/acschembio.7b00028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Ribosomal frameshifting is a rare
but ubiquitous process that is
being studied extensively. Meanwhile, frameshifting motifs without
any secondary mRNA structures were identified but rarely studied experimentally.
We report unambiguous observation of highly efficient “–1”
and “–2” frameshiftings on a GA7G
slippery mRNA without the downstream secondary structure, using force-induced
remnant magnetization spectroscopy combined with unique probing schemes.
The result represents the first experimental evidence of multiple
frameshifting steps. It is also one of the rare reports of the “–2”
frameshifting. Our assay removed the ambiguity of transcriptional
slippage involvement in other frameshifting assays. Two significant
insights for the frameshifting mechanism were revealed. First, EF-G·GTP
is indispensable to frameshifting. Although EFG·GDPCP has been
shown to prompt translocation before, we found that it could not induce
frameshifting. This implies that the GTP hydrolysis is responsible
for the codon–anticodon re-pairing in frameshifting, which
corroborates our previous mechanical force measurement of EF-G·GTP.
Second, translation in all three reading frames of the slippery sequence
can be induced by the corresponding in-frame aminoacyl tRNAs. Although
A-site tRNA is known to affect the partition between “0”
and “–1” frameshifting, it has not been reported
that all three reading frames can be translated by their corresponding
tRNAs. The in vitro results were confirmed by toe-printing
assay and protein sequencing.
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13
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Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res 2016; 44:7007-78. [PMID: 27436286 PMCID: PMC5009743 DOI: 10.1093/nar/gkw530] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022] Open
Abstract
Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.
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Affiliation(s)
- John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland School of Microbiology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pramod R Bhatt
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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14
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Xie P. Model of the pathway of -1 frameshifting: Long pausing. Biochem Biophys Rep 2016; 5:408-424. [PMID: 28955849 PMCID: PMC5600365 DOI: 10.1016/j.bbrep.2016.01.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 11/25/2022] Open
Abstract
It has been characterized that the programmed ribosomal -1 frameshifting often occurs at the slippery sequence on the presence of a downstream mRNA pseudoknot. In some prokaryotic cases such as the dnaX gene of Escherichia coli, an additional stimulatory signal-an upstream, internal Shine-Dalgarno (SD) sequence-is also necessary to stimulate the efficient -1 frameshifting. However, the molecular and physical mechanism of the -1 frameshifting is poorly understood. Here, we propose a model of the pathway of the -1 translational frameshifting during ribosome translation of the dnaX -1 frameshift mRNA. With the model, the single-molecule fluorescence data (Chen et al. (2014) [29]) on the dynamics of the shunt either to long pausing or to normal translation, the tRNA transit and sampling dynamics in the long-paused rotated state, the EF-G sampling dynamics, the mean rotated-state lifetimes, etc., are explained quantitatively. Moreover, the model is also consistent with the experimental data (Yan et al. (2015) [30]) on translocation excursions and broad branching of frameshifting pathways. In addition, we present some predicted results, which can be easily tested by future optical trapping experiments.
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15
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Model of the pathway of -1 frameshifting: Kinetics. Biochem Biophys Rep 2016; 5:453-467. [PMID: 28955853 PMCID: PMC5600437 DOI: 10.1016/j.bbrep.2016.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/04/2016] [Accepted: 02/09/2016] [Indexed: 12/20/2022] Open
Abstract
Programmed -1 translational frameshifting is a process where the translating ribosome shifts the reading frame, which is directed by at least two stimulatory elements in the mRNA-a slippery sequence and a downstream secondary structure. Despite a lot of theoretical and experimental studies, the detailed pathway and mechanism of the -1 frameshifting remain unclear. Here, in order to understand the pathway and mechanism we consider two models to study the kinetics of the -1 frameshifting, providing quantitative explanations of the recent biochemical data of Caliskan et al. (Cell 2014, 157, 1619-1631). One model is modified from that proposed by Caliskan et al. and the other is modified from that proposed in the previous work to explain the single-molecule experimental data. It is shown that by adjusting values of some fundamental parameters both models can give quantitative explanations of the biochemical data of Caliskan et al. on the kinetics of EF-G binding and dissociation and on the kinetics of movement of tRNAs inside the ribosome. However, for the former model some adjusted parameter values deviate significantly from those determined from the available single-molecule experiments, while for the latter model all parameter values are consistent with the available biochemical and single-molecule experimental data. Thus, the latter model most likely reflects the pathway and mechanism of the -1 frameshifting.
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16
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Caliskan N, Peske F, Rodnina MV. Changed in translation: mRNA recoding by -1 programmed ribosomal frameshifting. Trends Biochem Sci 2015; 40:265-74. [PMID: 25850333 PMCID: PMC7126180 DOI: 10.1016/j.tibs.2015.03.006] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/09/2015] [Accepted: 03/09/2015] [Indexed: 12/19/2022]
Abstract
–1PRF occurs when ribosomes move over a slippery sequence. A frameshifting pseudoknot/stem-loop element stalls ribosomes in a metastable state. –1PRF may contribute to the quality-control machinery in eukaryotes. Trans-acting factors (proteins, miRNAs, or antibiotics) can modulate –1PRF.
Programmed −1 ribosomal frameshifting (−1PRF) is an mRNA recoding event commonly utilized by viruses and bacteria to increase the information content of their genomes. Recent results have implicated −1PRF in quality control of mRNA and DNA stability in eukaryotes. Biophysical experiments demonstrated that the ribosome changes the reading frame while attempting to move over a slippery sequence of the mRNA – when a roadblock formed by a folded downstream segment in the mRNA stalls the ribosome in a metastable conformational state. The efficiency of −1PRF is modulated not only by cis-regulatory elements in the mRNA but also by trans-acting factors such as proteins, miRNAs, and antibiotics. These recent results suggest a molecular mechanism and new important cellular roles for −1PRF.
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Affiliation(s)
- Neva Caliskan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany.
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17
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Mathew SF, Crowe-McAuliffe C, Graves R, Cardno TS, McKinney C, Poole ES, Tate WP. The highly conserved codon following the slippery sequence supports -1 frameshift efficiency at the HIV-1 frameshift site. PLoS One 2015; 10:e0122176. [PMID: 25807539 PMCID: PMC4373837 DOI: 10.1371/journal.pone.0122176] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 02/08/2015] [Indexed: 01/18/2023] Open
Abstract
HIV-1 utilises -1 programmed ribosomal frameshifting to translate structural and enzymatic domains in a defined proportion required for replication. A slippery sequence, U UUU UUA, and a stem-loop are well-defined RNA features modulating -1 frameshifting in HIV-1. The GGG glycine codon immediately following the slippery sequence (the 'intercodon') contributes structurally to the start of the stem-loop but has no defined role in current models of the frameshift mechanism, as slippage is inferred to occur before the intercodon has reached the ribosomal decoding site. This GGG codon is highly conserved in natural isolates of HIV. When the natural intercodon was replaced with a stop codon two different decoding molecules-eRF1 protein or a cognate suppressor tRNA-were able to access and decode the intercodon prior to -1 frameshifting. This implies significant slippage occurs when the intercodon is in the (perhaps distorted) ribosomal A site. We accommodate the influence of the intercodon in a model of frame maintenance versus frameshifting in HIV-1.
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Affiliation(s)
- Suneeth F. Mathew
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | | | - Ryan Graves
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Tony S. Cardno
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Cushla McKinney
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Elizabeth S. Poole
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Warren P. Tate
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
- * E-mail:
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18
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Yan S, Wen JD, Bustamante C, Tinoco I. Ribosome excursions during mRNA translocation mediate broad branching of frameshift pathways. Cell 2015; 160:870-881. [PMID: 25703095 PMCID: PMC4344849 DOI: 10.1016/j.cell.2015.02.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/01/2014] [Accepted: 01/28/2015] [Indexed: 11/24/2022]
Abstract
Programmed ribosomal frameshifting produces alternative proteins from a single transcript. -1 frameshifting occurs on Escherichia coli's dnaX mRNA containing a slippery sequence AAAAAAG and peripheral mRNA structural barriers. Here, we reveal hidden aspects of the frameshifting process, including its exact location on the mRNA and its timing within the translation cycle. Mass spectrometry of translated products shows that ribosomes enter the -1 frame from not one specific codon but various codons along the slippery sequence and slip by not just -1 but also -4 or +2 nucleotides. Single-ribosome translation trajectories detect distinctive codon-scale fluctuations in ribosome-mRNA displacement across the slippery sequence, representing multiple ribosomal translocation attempts during frameshifting. Flanking mRNA structural barriers mechanically stimulate the ribosome to undergo back-and-forth translocation excursions, broadly exploring reading frames. Both experiments reveal aborted translation around mutant slippery sequences, indicating that subsequent fidelity checks on newly adopted codon position base pairings lead to either resumed translation or early termination.
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Affiliation(s)
- Shannon Yan
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jin-Der Wen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Carlos Bustamante
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Kavli Energy NanoSciences Institute, Berkeley, CA 94720, USA
| | - Ignacio Tinoco
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.
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19
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Guerrero S, Batisse J, Libre C, Bernacchi S, Marquet R, Paillart JC. HIV-1 replication and the cellular eukaryotic translation apparatus. Viruses 2015; 7:199-218. [PMID: 25606970 PMCID: PMC4306834 DOI: 10.3390/v7010199] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/12/2015] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic translation is a complex process composed of three main steps: initiation, elongation, and termination. During infections by RNA- and DNA-viruses, the eukaryotic translation machinery is used to assure optimal viral protein synthesis. Human immunodeficiency virus type I (HIV-1) uses several non-canonical pathways to translate its own proteins, such as leaky scanning, frameshifting, shunt, and cap-independent mechanisms. Moreover, HIV-1 modulates the host translation machinery by targeting key translation factors and overcomes different cellular obstacles that affect protein translation. In this review, we describe how HIV-1 proteins target several components of the eukaryotic translation machinery, which consequently improves viral translation and replication.
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Affiliation(s)
- Santiago Guerrero
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France.
| | - Julien Batisse
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France.
| | - Camille Libre
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France.
| | - Serena Bernacchi
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France.
| | - Roland Marquet
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France.
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France.
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20
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Musalgaonkar S, Moomau CA, Dinman JD. Ribosomes in the balance: structural equilibrium ensures translational fidelity and proper gene expression. Nucleic Acids Res 2014; 42:13384-92. [PMID: 25389262 PMCID: PMC4245932 DOI: 10.1093/nar/gku1020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
At equilibrium, empty ribosomes freely transit between the rotated and un-rotated states. In the cell, the binding of two translation elongation factors to the same general region of the ribosome stabilizes one state over the other. These stabilized states are resolved by expenditure of energy in the form of GTP hydrolysis. A prior study employing mutants of a late assembling peripheral ribosomal protein suggested that ribosome rotational status determines its affinity for elongation factors, and hence translational fidelity and gene expression. Here, mutants of the early assembling integral ribosomal protein uL2 are used to test the generality of this hypothesis. rRNA structure probing analyses reveal that mutations in the uL2 B7b bridge region shift the equilibrium toward the rotated state, propagating rRNA structural changes to all of the functional centers of ribosome. Structural disequilibrium unbalances ribosome biochemically: rotated ribosomes favor binding of the eEF2 translocase and disfavor that of the elongation ternary complex. This manifests as specific translational fidelity defects, impacting the expression of genes involved in telomere maintenance. A model is presented describing how cyclic intersubunit rotation ensures the unidirectionality of translational elongation, and how perturbation of rotational equilibrium affects specific aspects of translational fidelity and cellular gene expression.
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Affiliation(s)
- Sharmishtha Musalgaonkar
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Christine A Moomau
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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21
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Wojciechowska M, Olejniczak M, Galka-Marciniak P, Jazurek M, Krzyzosiak WJ. RAN translation and frameshifting as translational challenges at simple repeats of human neurodegenerative disorders. Nucleic Acids Res 2014; 42:11849-64. [PMID: 25217582 PMCID: PMC4231732 DOI: 10.1093/nar/gku794] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Repeat-associated disorders caused by expansions of short sequences have been classified as coding and noncoding and are thought to be caused by protein gain-of-function and RNA gain-of-function mechanisms, respectively. The boundary between such classifications has recently been blurred by the discovery of repeat-associated non-AUG (RAN) translation reported in spinocerebellar ataxia type 8, myotonic dystrophy type 1, fragile X tremor/ataxia syndrome and C9ORF72 amyotrophic lateral sclerosis and frontotemporal dementia. This noncanonical translation requires no AUG start codon and can initiate in multiple frames of CAG, CGG and GGGGCC repeats of the sense and antisense strands of disease-relevant transcripts. RNA structures formed by the repeats have been suggested as possible triggers; however, the precise mechanism of the translation initiation remains elusive. Templates containing expansions of microsatellites have also been shown to challenge translation elongation, as frameshifting has been recognized across CAG repeats in spinocerebellar ataxia type 3 and Huntington's disease. Determining the critical requirements for RAN translation and frameshifting is essential to decipher the mechanisms that govern these processes. The contribution of unusual translation products to pathogenesis needs to be better understood. In this review, we present current knowledge regarding RAN translation and frameshifting and discuss the proposed mechanisms of translational challenges imposed by simple repeat expansions.
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Affiliation(s)
- Marzena Wojciechowska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Marta Olejniczak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Paulina Galka-Marciniak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
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22
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Caliskan N, Katunin VI, Belardinelli R, Peske F, Rodnina MV. Programmed -1 frameshifting by kinetic partitioning during impeded translocation. Cell 2014; 157:1619-31. [PMID: 24949973 PMCID: PMC7112342 DOI: 10.1016/j.cell.2014.04.041] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 02/17/2014] [Accepted: 04/10/2014] [Indexed: 02/04/2023]
Abstract
Programmed –1 ribosomal frameshifting (−1PRF) is an mRNA recoding event utilized by cells to enhance the information content of the genome and to regulate gene expression. The mechanism of –1PRF and its timing during translation elongation are unclear. Here, we identified the steps that govern –1PRF by following the stepwise movement of the ribosome through the frameshifting site of a model mRNA derived from the IBV 1a/1b gene in a reconstituted in vitro translation system from Escherichia coli. Frameshifting occurs at a late stage of translocation when the two tRNAs are bound to adjacent slippery sequence codons of the mRNA. The downstream pseudoknot in the mRNA impairs the closing movement of the 30S subunit head, the dissociation of EF-G, and the release of tRNA from the ribosome. The slippage of the ribosome into the –1 frame accelerates the completion of translocation, thereby further favoring translation in the new reading frame. Kinetics of –1 ribosomal frameshifting are monitored at single-codon resolution Frameshifting occurs when the backward movement of the 30S subunit head is impeded Two tRNAs at the XXXYYYZ mRNA sequence are stalled in chimeric POST states The shift to the –1 reading frame occurs prior to EF-G release from the ribosome
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Affiliation(s)
- Neva Caliskan
- Max Planck Institute for Biophysical Chemistry, Department of Physical Biochemistry, 37077 Göttingen, Germany
| | - Vladimir I Katunin
- B.P. Konstantinov Petersburg Nuclear Physics Institute, Department of Molecular and Radiation Biophysics, 188300 Gatchina, Russia
| | - Riccardo Belardinelli
- Max Planck Institute for Biophysical Chemistry, Department of Physical Biochemistry, 37077 Göttingen, Germany
| | - Frank Peske
- Max Planck Institute for Biophysical Chemistry, Department of Physical Biochemistry, 37077 Göttingen, Germany
| | - Marina V Rodnina
- Max Planck Institute for Biophysical Chemistry, Department of Physical Biochemistry, 37077 Göttingen, Germany.
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23
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Single-molecule measurements of the CCR5 mRNA unfolding pathways. Biophys J 2014; 106:244-52. [PMID: 24411256 DOI: 10.1016/j.bpj.2013.09.036] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 08/13/2013] [Accepted: 09/04/2013] [Indexed: 01/07/2023] Open
Abstract
Secondary or tertiary structure in an mRNA, such as a pseudoknot, can create a physical barrier that requires the ribosome to generate additional force to translocate. The presence of such a barrier can dramatically increase the probability that the ribosome will shift into an alternate reading frame, in which a different set of codons is recognized. The detailed biophysical mechanism by which frameshifting is induced remains unknown. Here we employ optical trapping techniques to investigate the structure of a -1 programmed ribosomal frameshift (-1 PRF) sequence element located in the CCR5 mRNA, which encodes a coreceptor for HIV-1 and is, to our knowledge, the first known human -1 PRF signal of nonviral origin. We begin by presenting a set of computationally predicted structures that include pseudoknots. We then employ what we believe to be new analytical techniques for measuring the effective free energy landscapes of biomolecules. We find that the -1 PRF element manifests several distinct unfolding pathways when subject to end-to-end force, one of which is consistent with a proposed pseudoknot conformation, and another of which we have identified as a folding intermediate. The dynamic ensemble of conformations that CCR5 mRNA exhibits in the single-molecule experiments may be a significant feature of the frameshifting mechanism.
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24
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Chen J, Petrov A, Johansson M, Tsai A, O'Leary SE, Puglisi JD. Dynamic pathways of -1 translational frameshifting. Nature 2014; 512:328-32. [PMID: 24919156 PMCID: PMC4472451 DOI: 10.1038/nature13428] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/01/2014] [Indexed: 12/16/2022]
Abstract
Spontaneous changes in the reading frame of translation are rare (frequency of 10−3 – 10−4 per codon)1, but can be induced by specific features in the messenger RNA (mRNA). In the presence of mRNA secondary structures, a heptanucleotide “slippery sequence” usually defined by the motif X XXY YYZ, and (in some prokaryotic cases) mRNA sequences that base pair with the 3′ end of the 16S ribosomal rRNA (internal Shine-Dalgarno (SD) sequences), there is an increased probability that a specific programmed change of frame occurs, wherein the ribosome shifts one nucleotide backwards into an overlapping reading frame (−1 frame) and continues by translating a new sequence of amino acids2,3. Despite extensive biochemical and genetic studies, there is no clear mechanistic description for frameshifting. Here, we apply single-molecule fluorescence to track the compositional and conformational dynamics of the individual ribosomes at each codon during translation of a frameshift-inducing mRNA from the dnaX gene in Escherichia coli. Ribosomes that frameshift into the −1 frame are characterized by a 10-fold longer pause in elongation compared to non-frameshifted ribosomes, which translate through unperturbed. During the pause, interactions of the ribosome with the mRNA stimulatory elements uncouple EF-G catalyzed translocation from normal ribosomal subunit reverse-rotation, leaving the ribosome in a non-canonical intersubunit rotated state with an exposed codon in the aminoacyl-tRNA site (A site). tRNALys sampling and accommodation to the empty A site either lead to the slippage of the tRNAs into the −1 frame or maintain the ribosome into the 0 frame. Our results provide a general mechanistic and conformational framework for −1 frameshifting, highlighting multiple kinetic branchpoints during elongation.
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Affiliation(s)
- Jin Chen
- 1] Department of Applied Physics, Stanford University, Stanford, California 94305-4090, USA [2] Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Alexey Petrov
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Magnus Johansson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Albert Tsai
- 1] Department of Applied Physics, Stanford University, Stanford, California 94305-4090, USA [2] Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Seán E O'Leary
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
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25
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Advani VM, Belew AT, Dinman JD. Yeast telomere maintenance is globally controlled by programmed ribosomal frameshifting and the nonsense-mediated mRNA decay pathway. ACTA ACUST UNITED AC 2014; 1:e24418. [PMID: 24563826 PMCID: PMC3908577 DOI: 10.4161/trla.24418] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 03/21/2013] [Accepted: 03/22/2013] [Indexed: 11/26/2022]
Abstract
We have previously shown that ~10% of all eukaryotic mRNAs contain potential programmed -1 ribosomal frameshifting (-1 PRF) signals and that some function as mRNA destabilizing elements through the Nonsense-Mediated mRNA Decay (NMD) pathway by directing translating ribosomes to premature termination codons. Here, the connection between -1 PRF, NMD and telomere end maintenance are explored. Functional -1 PRF signals were identified in the mRNAs encoding two components of yeast telomerase, EST1 and EST2, and in mRNAs encoding proteins involved in recruiting telomerase to chromosome ends, STN1 and CDC13. All of these elements responded to mutants and drugs previously known to stimulate or inhibit -1 PRF, further supporting the hypothesis that they promote -1 PRF through the canonical mechanism. All affected the steady-state abundance of a reporter mRNA and the wide range of -1 PRF efficiencies promoted by these elements enabled the determination of an inverse logarithmic relationship between -1 PRF efficiency and mRNA accumulation. Steady-state abundances of the endogenous EST1, EST2, STN1 and CDC13 mRNAs were similarly inversely proportional to changes in -1 PRF efficiency promoted by mutants and drugs, supporting the hypothesis that expression of these genes is post-transcriptionally controlled by -1 PRF under native conditions. Overexpression of EST2 by ablation of -1 PRF signals or inhibition of NMD promoted formation of shorter telomeres and accumulation of large budded cells at the G2/M boundary. A model is presented describing how limitation and maintenance of correct stoichiometries of telomerase components by -1 PRF is used to maintain yeast telomere length.
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Affiliation(s)
- Vivek M Advani
- Department of Cell Biology and Molecular Genetics; University of Maryland; College Park MD, USA
| | - Ashton T Belew
- Department of Cell Biology and Molecular Genetics; University of Maryland; College Park MD, USA
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics; University of Maryland; College Park MD, USA
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26
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Bailey BL, Visscher K, Watkins J. A stochastic model of translation with -1 programmed ribosomal frameshifting. Phys Biol 2014; 11:016009. [PMID: 24501223 DOI: 10.1088/1478-3975/11/1/016009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many viruses produce multiple proteins from a single mRNA sequence by encoding overlapping genes. One mechanism to decode both genes, which reside in alternate reading frames, is -1 programmed ribosomal frameshifting. Although recognized for over 25 years, the molecular and physical mechanism of -1 frameshifting remains poorly understood. We have developed a mathematical model that treats mRNA translation and associated -1 frameshifting as a stochastic process in which the transition probabilities are based on the energetics of local molecular interactions. The model predicts both the location and efficiency of -1 frameshift events in HIV-1. Moreover, we compute -1 frameshift efficiencies upon mutations in the viral mRNA sequence and variations in relative tRNA abundances, predictions that are directly testable in experiment.
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Affiliation(s)
- Brenae L Bailey
- Program in Applied Mathematics, University of Arizona, Tucson, AZ 85721, USA
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27
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Niu S, Cao S, Wong SM. An infectious RNA with a hepta-adenosine stretch responsible for programmed -1 ribosomal frameshift derived from a full-length cDNA clone of Hibiscus latent Singapore virus. Virology 2014; 449:229-34. [PMID: 24418557 PMCID: PMC7127180 DOI: 10.1016/j.virol.2013.11.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 11/09/2013] [Accepted: 11/12/2013] [Indexed: 11/27/2022]
Abstract
Hibiscus latent Singapore virus (HLSV) is a member of Tobamovirus and its full-length cDNA clones were constructed. The in vitro transcripts from two HLSV full-length cDNA clones, which contain a hepta-adenosine stretch (pHLSV-7A) and an octo-adenosine stretch (pHLSV-8A), are both infectious. The replication level of HLSV-7A in Nicotiana benthamiana protoplasts was 5-fold lower, as compared to that of HLSV-8A. The replicase proteins of HLSV-7A were produced through programmed -1 ribosomal frameshift (-1 PRF) and the 7A stretch was a slippery sequence for -1 PRF. Mutations to the downstream pseudoknot of 7A stretch showed that the pseudoknot was not required for the frameshift in vitro. The stretch was found to be extended to 8A after subsequent replication cycles in vivo. It is envisaged that HLSV employs the monotonous runs of A and -1 PRF to convert its 7A to 8A to reach higher replication for its survival in plants.
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Affiliation(s)
- Shengniao Niu
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Lower Kent Ridge Road, Singapore 117543, Singapore
| | - Shishu Cao
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Lower Kent Ridge Road, Singapore 117543, Singapore
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Lower Kent Ridge Road, Singapore 117543, Singapore; Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore; National University of Singapore Suzhou Research Institute, Suzhou, Jiangsu 215123, China.
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28
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Xie P. A dynamical model of programmed −1 ribosomal frameshifting. J Theor Biol 2013; 336:119-31. [DOI: 10.1016/j.jtbi.2013.07.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 07/01/2013] [Accepted: 07/22/2013] [Indexed: 11/29/2022]
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29
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Wills PR. Frameshifted prion proteins as pathological agents: quantitative considerations. J Theor Biol 2013; 325:52-61. [PMID: 23454079 DOI: 10.1016/j.jtbi.2013.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 02/14/2013] [Accepted: 02/18/2013] [Indexed: 11/17/2022]
Abstract
A quantitatively consistent explanation for the titres of infectivity found in a variety of prion-containing preparations is provided on the basis that the ætiological agents of transmissible spongiform encephalopathy comprise a very small population fraction of prion protein (PrP) variants, which contain frameshifted elements in their N-terminal octapeptide-repeat regions. A mechanism for the replication of frameshifted prions is described and calculations are performed to obtain estimates of the concentration of these PrP variants in normal and infected brain, as well as their enrichment in products of protein misfolding cyclic amplification. These calculations resolve the lack of proper quantitative correlation between measures of infectivity and the presence of conformationally-altered, protease-resistant variants of PrP. Experiments, which could confirm or eventually exclude the role of frameshifted variants in the ætiology of prion disease, are suggested.
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Affiliation(s)
- Peter R Wills
- Integrative Transcriptomics, Center for Bioinformatics Tübingen, University of Tübingen, Sand 14, Tübingen 72076, Germany.
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Mouzakis KD, Lang AL, Vander Meulen KA, Easterday PD, Butcher SE. HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome. Nucleic Acids Res 2012; 41:1901-13. [PMID: 23248007 PMCID: PMC3561942 DOI: 10.1093/nar/gks1254] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The human immunodeficiency virus (HIV) requires a programmed −1 ribosomal frameshift for Pol gene expression. The HIV frameshift site consists of a heptanucleotide slippery sequence (UUUUUUA) followed by a spacer region and a downstream RNA stem–loop structure. Here we investigate the role of the RNA structure in promoting the −1 frameshift. The stem–loop was systematically altered to decouple the contributions of local and overall thermodynamic stability towards frameshift efficiency. No correlation between overall stability and frameshift efficiency is observed. In contrast, there is a strong correlation between frameshift efficiency and the local thermodynamic stability of the first 3–4 bp in the stem–loop, which are predicted to reside at the opening of the mRNA entrance channel when the ribosome is paused at the slippery site. Insertion or deletions in the spacer region appear to correspondingly change the identity of the base pairs encountered 8 nt downstream of the slippery site. Finally, the role of the surrounding genomic secondary structure was investigated and found to have a modest impact on frameshift efficiency, consistent with the hypothesis that the genomic secondary structure attenuates frameshifting by affecting the overall rate of translation.
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Affiliation(s)
- Kathryn D Mouzakis
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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31
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Choi YS. Reaching for the deep proteome: recent nano liquid chromatography coupled with tandem mass spectrometry-based studies on the deep proteome. Arch Pharm Res 2012; 35:1861-70. [PMID: 23212627 DOI: 10.1007/s12272-012-1102-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/30/2012] [Accepted: 08/21/2012] [Indexed: 11/24/2022]
Abstract
In the last decade, there has been a dramatic progress in separation techniques, mass spectrometry, and bioinformatics, and this progress has significantly improved the techniques on protein analysis. However, the analysis of low-abundance proteins is still challenging because of the limited performance in the method of choice compared to the complexity and the vast dynamic range of biological samples. Since this issue is a big obstacle in most proteomics investigations, great interest has been paid recently to various techniques, such as multi-dimensional analysis, specific peptide selection, high-abundance protein depletion, ligand library treatment, to address this challenge. Therefore, here, the author reviews recent nano liquid chromatography coupled with tandem mass spectrometry-based studies on the deep proteome, mainly focusing on their methods and perspectives.
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Affiliation(s)
- Yong Seok Choi
- College of Pharmacy, Dankook University, Cheonan 330-714, Korea.
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32
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Brakier-Gingras L, Charbonneau J, Butcher SE. Targeting frameshifting in the human immunodeficiency virus. Expert Opin Ther Targets 2012; 16:249-58. [PMID: 22404160 DOI: 10.1517/14728222.2012.665879] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION HIV-1 uses a programmed –1 ribosomal frameshift to generate Gag-Pol, the precursor of its enzymes, when its full-length mRNA is translated by the ribosomes of the infected cells. This change in the reading frame occurs at a so-called slippery sequence that is followed by a specific secondary structure, the frameshift stimulatory signal. This signal controls the frameshift efficiency. The synthesis of HIV-1 enzymes is critical for virus replication and therefore, the –1 ribosomal frameshift could be the target of novel antiviral drugs. AREAS COVERED Various approaches were used to select drugs interfering with the –1 frameshift of HIV-1. These include the selection and modification of chemical compounds that specifically bind to the frameshift stimulatory signal, the use of antisense oligonucleotides targeting this signal and the selection of compounds that modulate HIV-1 frameshift, by using bicistronic reporters where the expression of the second cistron depends upon HIV-1 frameshift. EXPERT OPINION The most promising approach is the selection and modification of compounds specifically targeting the HIV-1 frameshift stimulatory signal. The use of antisense oligonucleotides binding to the frameshift stimulatory signal is still questionable. The use of bicistronic reporters preferentially selects compounds that modulate the frameshift by targeting the ribosomes, which is less promising.
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Dinman JD. Control of gene expression by translational recoding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 86:129-49. [PMID: 22243583 PMCID: PMC7149833 DOI: 10.1016/b978-0-12-386497-0.00004-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Like all rules, even the genetic code has exceptions: these are generically classified as “translational recoding.” Almost every conceivable mode of recoding has been documented, including signals that redefine translational reading frame and codon assignation. While first described in viruses, it is becoming clear that sequences that program elongating ribosomes to shift translational reading frame are widely used by organisms in all domains of life, thus expanding both the coding capacity of genomes and the modes through which gene expression can be regulated at the posttranscriptional level. Instances of programmed ribosomal frameshifting and stop codon reassignment are opening up new avenues for treatment of numerous inborn errors of metabolism. The implications of these findings on human health are only beginning to emerge.
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Affiliation(s)
- Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
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Dinman JD. Mechanisms and implications of programmed translational frameshifting. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:661-73. [PMID: 22715123 PMCID: PMC3419312 DOI: 10.1002/wrna.1126] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
While ribosomes must maintain translational reading frame in order to translate primary genetic information into polypeptides, cis‐acting signals located in mRNAs represent higher order information content that can be used to fine‐tune gene expression. Classes of signals have been identified that direct a fraction of elongating ribosomes to shift reading frame by one base in the 5′ (−1) or 3′ (+1) direction. This is called programmed ribosomal frameshifting (PRF). Although mechanisms of PRF differ, a common feature is induction of ribosome pausing, which alters kinetic partitioning rates between in‐frame and out‐of‐frame codons at specific ‘slippery’ sequences. Many viruses use PRF to ensure synthesis of the correct ratios of virus‐encoded proteins required for proper viral particle assembly and maturation, thus identifying PRF as an attractive target for antiviral therapeutics. In contrast, recent studies indicate that PRF signals may primarily function as mRNA destabilizing elements in cellular mRNAs. These studies suggest that PRF may be used to fine‐tune gene expression through mRNA decay pathways. The possible regulation of PRF by noncoding RNAs is also discussed. WIREs RNA 2012 doi: 10.1002/wrna.1126 This article is categorized under:
RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Evolution and Genomics > Computational Analyses of RNA Translation > Translation Regulation
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Affiliation(s)
- Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.
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35
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Charbonneau J, Gendron K, Ferbeyre G, Brakier-Gingras L. The 5' UTR of HIV-1 full-length mRNA and the Tat viral protein modulate the programmed -1 ribosomal frameshift that generates HIV-1 enzymes. RNA (NEW YORK, N.Y.) 2012; 18:519-529. [PMID: 22286970 PMCID: PMC3285939 DOI: 10.1261/rna.030346.111] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 12/01/2011] [Indexed: 05/31/2023]
Abstract
Translation of the full-length messenger RNA (mRNA) of the human immunodeficiency virus type 1 (HIV-1) generates the precursor of the viral enzymes via a programmed -1 ribosomal frameshift. Here, using dual-luciferase reporters, we investigated whether the highly structured 5' untranslated region (UTR) of this mRNA, which interferes with translation initiation, can modulate HIV-1 frameshift efficiency. We showed that, when the 5' UTR of HIV-1 mRNA occupies the 5' end of the reporter mRNA, HIV-1 frameshift efficiency is increased about fourfold in Jurkat T-cells, compared with a control dual-luciferase reporter with a short unstructured 5' UTR. This increase was related to an interference with cap-dependent translation initiation by the TAR-Poly(A) region at the 5' end of the messenger. HIV-1 mRNA 5' UTR also contains an internal ribosome entry site (IRES), but we showed that, when the cap-dependent initiation mode is available, the IRES is not used or is weakly used. However, when the ribosomes have to use the IRES to translate the dual-luciferase reporter, the frameshift efficiency is comparable to that of the control dual-luciferase reporter. The decrease in cap-dependent initiation and the accompanying increase in frameshift efficiency caused by the 5' UTR of HIV-1 mRNA is antagonized, in a dose-dependent way, by the Tat viral protein. Tat also stimulates the IRES-dependent initiation and decreases the corresponding frameshift efficiency. A model is presented that accounts for the variations in frameshift efficiency depending on the 5' UTR and the presence of Tat, and it is proposed that a range of frameshift efficiencies is compatible with the virus replication.
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Affiliation(s)
- Johanie Charbonneau
- Département de biochimie, Université de Montréal, Montréal, Québec, Canada, H3T 1J4
| | - Karine Gendron
- Département de biochimie, Université de Montréal, Montréal, Québec, Canada, H3T 1J4
- Centre de recherche, Hôpital Ste-Justine, Montréal, Québec, Canada, H3T 1C5
| | - Gerardo Ferbeyre
- Département de biochimie, Université de Montréal, Montréal, Québec, Canada, H3T 1J4
| | - Léa Brakier-Gingras
- Département de biochimie, Université de Montréal, Montréal, Québec, Canada, H3T 1J4
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36
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Jack K, Bellodi C, Landry DM, Niederer RO, Meskauskas A, Musalgaonkar S, Kopmar N, Krasnykh O, Dean AM, Thompson SR, Ruggero D, Dinman JD. rRNA pseudouridylation defects affect ribosomal ligand binding and translational fidelity from yeast to human cells. Mol Cell 2012; 44:660-6. [PMID: 22099312 DOI: 10.1016/j.molcel.2011.09.017] [Citation(s) in RCA: 230] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 05/17/2011] [Accepted: 09/01/2011] [Indexed: 01/04/2023]
Abstract
How pseudouridylation (Ψ), the most common and evolutionarily conserved modification of rRNA, regulates ribosome activity is poorly understood. Medically, Ψ is important because the rRNA Ψ synthase, DKC1, is mutated in X-linked dyskeratosis congenita (X-DC) and Hoyeraal-Hreidarsson (HH) syndrome. Here, we characterize ribosomes isolated from a yeast strain in which Cbf5p, the yeast homolog of DKC1, is catalytically impaired through a D95A mutation (cbf5-D95A). Ribosomes from cbf5-D95A cells display decreased affinities for tRNA binding to the A and P sites as well as the cricket paralysis virus internal ribosome entry site (IRES), which interacts with both the P and the E sites of the ribosome. This biochemical impairment in ribosome activity manifests as decreased translational fidelity and IRES-dependent translational initiation, which are also evident in mouse and human cells deficient for DKC1 activity. These findings uncover specific roles for Ψ modification in ribosome-ligand interactions that are conserved in yeast, mouse, and humans.
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Affiliation(s)
- Karen Jack
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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Kim YG, Chi JS, Lee SM, Kwon NS, Baek KJ, Yun HY. Efficient Ribosomal Frameshifitng Can Occur at the Beginning of the Translation. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.9.3489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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38
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Rhodin MHJ, Dinman JD. An extensive network of information flow through the B1b/c intersubunit bridge of the yeast ribosome. PLoS One 2011; 6:e20048. [PMID: 21625514 PMCID: PMC3098278 DOI: 10.1371/journal.pone.0020048] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Accepted: 04/11/2011] [Indexed: 12/31/2022] Open
Abstract
Yeast ribosomal proteins L11 and S18 form a dynamic intersubunit interaction called the B1b/c bridge. Recent high resolution images of the ribosome have enabled targeting of specific residues in this bridge to address how distantly separated regions within the large and small subunits of the ribosome communicate with each other. Mutations were generated in the L11 side of the B1b/c bridge with a particular focus on disrupting the opposing charge motifs that have previously been proposed to be involved in subunit ratcheting. Mutants had wide-ranging effects on cellular viability and translational fidelity, with the most pronounced phenotypes corresponding to amino acid changes resulting in alterations of local charge properties. Chemical protection studies of selected mutants revealed rRNA structural changes in both the large and small subunits. In the large subunit rRNA, structural changes mapped to Helices 39, 80, 82, 83, 84, and the peptidyltransferase center. In the small subunit rRNA, structural changes were identified in helices 30 and 42, located between S18 and the decoding center. The rRNA structural changes correlated with charge-specific alterations to the L11 side of the B1b/c bridge. These analyses underscore the importance of the opposing charge mechanism in mediating B1b/c bridge interactions and suggest an extensive network of information exchange between distinct regions of the large and small subunits.
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Affiliation(s)
- Michael H. J. Rhodin
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Jonathan D. Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
- * E-mail:
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39
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Rhodin MHJ, Rakauskaitė R, Dinman JD. The central core region of yeast ribosomal protein L11 is important for subunit joining and translational fidelity. Mol Genet Genomics 2011; 285:505-16. [PMID: 21519857 DOI: 10.1007/s00438-011-0623-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 04/11/2011] [Indexed: 12/11/2022]
Abstract
Yeast ribosomal protein L11 is positioned at the intersubunit cleft of the large subunit central protuberance, forming an intersubunit bridge with the small subunit protein S18. Mutants were engineered in the central core region of L11 which interacts with Helix 84 of the 25S rRNA. Numerous mutants in this region conferred 60S subunit biogenesis defects. Specifically, many mutations of F96 and the A66D mutant promoted formation of halfmers as assayed by sucrose density ultracentrifugation. Halfmer formation was not due to deficiency in 60S subunit production, suggesting that the mutants affected subunit-joining. Chemical modification analyses indicated that the A66D mutant, but not the F96 mutants, promoted changes in 25S rRNA structure, suggesting at least two modalities for subunit joining defects. 25S rRNA structural changes were located both adjacent to A66D (in H84), and more distant (in H96-7). While none of the mutants significantly affected ribosome/tRNA binding constants, they did have strong effects on cellular growth at both high and low temperatures, in the presence of translational inhibitors, and promoted changes in translational fidelity. Two distinct mechanisms are proposed by which L11 mutants may affect subunit joining, and identification of the amino acids associated with each of these processes are presented. These findings may have implications for our understanding of multifaceted diseases such as Diamond--Blackfan anemia which have been linked in part with mutations in L11.
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Affiliation(s)
- Michael H J Rhodin
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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The interplay of mRNA stimulatory signals required for AUU-mediated initiation and programmed -1 ribosomal frameshifting in decoding of transposable element IS911. J Bacteriol 2011; 193:2735-44. [PMID: 21478364 DOI: 10.1128/jb.00115-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The IS911 bacterial transposable element uses -1 programmed translational frameshifting to generate the protein required for its mobility: translation initiated in one gene (orfA) shifts to the -1 frame and continues in a second overlapping gene (orfB), thus generating the OrfAB transposase. The A-AAA-AAG frameshift site of IS911 is flanked by two stimulatory elements, an upstream Shine-Dalgarno sequence and a downstream stem-loop. We show here that, while they can act independently, these stimulators have a synergistic effect when combined. Mutagenic analyses revealed features of the complex stem-loop that make it a low-efficiency stimulator. They also revealed the dual role of the upstream Shine-Dalgarno sequence as (i) a stimulator of frameshifting, by itself more potent than the stem-loop, and (ii) a mandatory determinant of initiation of OrfB protein synthesis on an AUU codon directly preceding the A6G motif. Both roles rely on transient base pairing of the Shine-Dalgarno sequence with the 3' end of 16S rRNA. Because of its effect on frameshifting, the Shine-Dalgarno sequence is an important determinant of the level of transposase in IS911-containing cells, and hence of the frequency of transposition.
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