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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Hsu HT, Murata A, Dohno C, Nakatani K, Chang K. Premature translation termination mediated non-ER stress induced ATF6 activation by a ligand-dependent ribosomal frameshifting circuit. Nucleic Acids Res 2022; 50:5369-5383. [PMID: 35511080 PMCID: PMC9122530 DOI: 10.1093/nar/gkac257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 03/29/2022] [Accepted: 04/29/2022] [Indexed: 11/14/2022] Open
Abstract
The −1 programmed ribosomal frameshifting (−1 PRF) has been explored as a gene regulatory circuit for synthetic biology applications. The −1 PRF usually uses an RNA pseudoknot structure as the frameshifting stimulator. Finding a ligand-responsive pseudoknot with efficient −1 PRF activity is time consuming and is becoming a bottleneck for its development. Inserting a guanine to guanine (GG)–mismatch pair in the 5′-stem of a small frameshifting pseudoknot could attenuate −1 PRF activity by reducing stem stability. Thus, a ligand-responsive frameshifting pseudoknot can be built using GG-mismatch–targeting small molecules to restore stem stability. Here, a pseudoknot requiring stem–loop tertiary interactions for potent frameshifting activity was used as the engineering template. This considerably amplified the effect of mismatch destabilization, and led to creation of a mammalian −1 PRF riboswitch module capable of mediating premature translation termination as a synthetic regulatory mode. Application of the synthetic circuit allowed ligand-dependent ATF6N mimic formation for the activation of protein folding–related genes involved in the unfolded protein response without an ER-stress inducing agent. With the availability of mismatch-targeting molecules, the tailored module thus paves the way for various mismatch plug-ins to streamline highly efficient orthogonal ligand-dependent −1 PRF stimulator development in the synthetic biology toolbox.
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Affiliation(s)
- Hsiu-Ting Hsu
- Graduate Institute of Biochemistry, National Chung-Hsing University, Taichung 402, Taiwan
| | - Asako Murata
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Chikara Dohno
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - KungYao Chang
- Graduate Institute of Biochemistry, National Chung-Hsing University, Taichung 402, Taiwan
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3
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Houston L, Platten EM, Connelly SM, Wang J, Grayhack EJ. Frameshifting at collided ribosomes is modulated by elongation factor eEF3 and by integrated stress response regulators Gcn1 and Gcn20. RNA (NEW YORK, N.Y.) 2022; 28:320-339. [PMID: 34916334 PMCID: PMC8848926 DOI: 10.1261/rna.078964.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Ribosome stalls can result in ribosome collisions that elicit quality control responses, one function of which is to prevent ribosome frameshifting, an activity that entails the interaction of the conserved yeast protein Mbf1 with uS3 on colliding ribosomes. However, the full spectrum of factors that mediate frameshifting during ribosome collisions is unknown. To delineate such factors in the yeast Saccharomyces cerevisiae, we used genetic selections for mutants that affect frameshifting from a known ribosome stall site, CGA codon repeats. We show that the general translation elongation factor eEF3 and the integrated stress response (ISR) pathway components Gcn1 and Gcn20 modulate frameshifting in opposing manners. We found a mutant form of eEF3 that specifically suppressed frameshifting, but not translation inhibition by CGA codons. Thus, we infer that frameshifting at collided ribosomes requires eEF3, which facilitates tRNA-mRNA translocation and E-site tRNA release in yeast and other single cell organisms. In contrast, we found that removal of either Gcn1 or Gcn20, which bind collided ribosomes with Mbf1, increased frameshifting. Thus, we conclude that frameshifting is suppressed by Gcn1 and Gcn20, although these effects are not mediated primarily through activation of the ISR. Furthermore, we examined the relationship between eEF3-mediated frameshifting and other quality control mechanisms, finding that Mbf1 requires either Hel2 or Gcn1 to suppress frameshifting with wild-type eEF3. Thus, these results provide evidence of a direct link between translation elongation and frameshifting at collided ribosomes, as well as evidence that frameshifting is constrained by quality control mechanisms that act on collided ribosomes.
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Affiliation(s)
- Lisa Houston
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Evan M Platten
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Sara M Connelly
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Jiyu Wang
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Elizabeth J Grayhack
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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4
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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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5
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Bao C, Loerch S, Ling C, Korostelev AA, Grigorieff N, Ermolenko DN. mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding. eLife 2020; 9:e55799. [PMID: 32427100 PMCID: PMC7282821 DOI: 10.7554/elife.55799] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/18/2020] [Indexed: 12/27/2022] Open
Abstract
Although the elongating ribosome is an efficient helicase, certain mRNA stem-loop structures are known to impede ribosome movement along mRNA and stimulate programmed ribosome frameshifting via mechanisms that are not well understood. Using biochemical and single-molecule Förster resonance energy transfer (smFRET) experiments, we studied how frameshift-inducing stem-loops from E. coli dnaX mRNA and the gag-pol transcript of Human Immunodeficiency Virus (HIV) perturb translation elongation. We find that upon encountering the ribosome, the stem-loops strongly inhibit A-site tRNA binding and ribosome intersubunit rotation that accompanies translation elongation. Electron cryo-microscopy (cryo-EM) reveals that the HIV stem-loop docks into the A site of the ribosome. Our results suggest that mRNA stem-loops can transiently escape the ribosome helicase by binding to the A site. Thus, the stem-loops can modulate gene expression by sterically hindering tRNA binding and inhibiting translation elongation.
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Affiliation(s)
- Chen Bao
- Department of Biochemistry and Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of RochesterRochesterUnited States
| | - Sarah Loerch
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Clarence Ling
- Department of Biochemistry and Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of RochesterRochesterUnited States
| | - Andrei A Korostelev
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Dmitri N Ermolenko
- Department of Biochemistry and Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of RochesterRochesterUnited States
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6
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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: 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: 11/05/2018] [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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7
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Dever TE, Dinman JD, Green R. Translation Elongation and Recoding in Eukaryotes. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a032649. [PMID: 29610120 DOI: 10.1101/cshperspect.a032649] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this review, we highlight the current understanding of translation elongation and recoding in eukaryotes. In addition to providing an overview of the process, recent advances in our understanding of the role of the factor eIF5A in both translation elongation and termination are discussed. We also highlight mechanisms of translation recoding with a focus on ribosomal frameshifting during elongation. We see that the balance between the basic steps in elongation and the less common recoding events is determined by the kinetics of the different processes as well as by specific sequence determinants.
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Affiliation(s)
- Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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8
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Qiao Q, Yan Y, Guo J, Du S, Zhang J, Jia R, Ren H, Qiao Y, Li Q. A review on architecture of the gag-pol ribosomal frameshifting RNA in human immunodeficiency virus: a variability survey of virus genotypes. J Biomol Struct Dyn 2016; 35:1629-1653. [PMID: 27485859 DOI: 10.1080/07391102.2016.1194231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Programmed '-1' ribosomal frameshifting is necessary for expressing the pol gene overlapped from a gag of human immunodeficiency virus. A viral RNA structure that requires base pairing across the overlapping sequence region suggests a mechanism of regulating ribosome and helicase traffic during expression. To get precise roles of an element around the frameshift site, a review on architecture of the frameshifting RNA is performed in combination of reported information with augments of a representative set of 19 viral samples. In spite of a different length for the viral RNAs, a canonical comparison on the element sequence allocation is performed for viewing variability associations between virus genotypes. Additionally, recent and historical insights recognized in frameshifting regulation are looked back as for indel and single nucleotide polymorphism of RNA. As specially noted, structural changes at a frameshift site, the spacer sequence, and a three-helix junction element, as well as two Watson-Crick base pairs near a bulge and a C-G pair close a loop, are the most vital strategies for the virus frameshifting regulations. All of structural changes, which are dependent upon specific sequence variations, facilitate an elucidation about the RNA element conformation-dependent mechanism for frameshifting. These facts on disrupting base pair interactions also allow solving the problem of competition between ribosome and helicase on a same RNA template, common to single-stranded RNA viruses. In a broad perspective, each new insight of frameshifting regulation in the competition systems introduced by the RNA element construct changes will offer a compelling target for antiviral therapy.
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Affiliation(s)
- Qi Qiao
- a School of Pharmaceutical Sciences, Xiamen University , Fujian 361102 , P.R. China
| | - Yanhua Yan
- b Department of Bioscience , Luliang University , Shanxi 033001 , P.R. China
| | - Jinmei Guo
- c Department of Chemistry & Chemical Engineering , Luliang University , Shanxi 033001 , P.R. China
| | - Shuqiang Du
- c Department of Chemistry & Chemical Engineering , Luliang University , Shanxi 033001 , P.R. China
| | - Jiangtao Zhang
- b Department of Bioscience , Luliang University , Shanxi 033001 , P.R. China
| | - Ruyue Jia
- c Department of Chemistry & Chemical Engineering , Luliang University , Shanxi 033001 , P.R. China
| | - Haimin Ren
- c Department of Chemistry & Chemical Engineering , Luliang University , Shanxi 033001 , P.R. China
| | - Yuanbiao Qiao
- d Graduate Institute of Pharmaceutical Chemistry, Luliang University , Shanxi 033001 , P.R. China
| | - Qingshan Li
- e School of Pharmaceutical Sciences , Shanxi Medical University , Shanxi 030001 , P.R. China
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9
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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: 161] [Impact Index Per Article: 20.1] [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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10
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Tinoco I, Kim HK, Yan S. Frameshifting dynamics. Biopolymers 2016; 99:1147-66. [PMID: 23722586 DOI: 10.1002/bip.22293] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/14/2013] [Accepted: 05/20/2013] [Indexed: 01/26/2023]
Abstract
Translation of messenger RNA by a ribosome occurs three nucleotides at a time from start signal to stop. However, a frameshift means that some nucleotides are read twice or some are skipped, and the following sequence of amino acids is completely different from the sequence in the original frame. In some messenger RNAs, including viral RNAs, frameshifting is programmed with RNA signals to produce specific ratios of proteins vital to the replication of the organism. The mechanisms that cause frameshifting have been studied for many years, but there are no definitive conclusions. We review ribosome structure and dynamics in relation to frameshifting dynamics provided by classical ensemble studies, and by new single-molecule methods using optical tweezers and FRET.
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Affiliation(s)
- Ignacio Tinoco
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720-1460
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11
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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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12
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Hagiwara-Komoda Y, Choi SH, Sato M, Atsumi G, Abe J, Fukuda J, Honjo MN, Nagano AJ, Komoda K, Nakahara KS, Uyeda I, Naito S. Truncated yet functional viral protein produced via RNA polymerase slippage implies underestimated coding capacity of RNA viruses. Sci Rep 2016; 6:21411. [PMID: 26898356 PMCID: PMC4761962 DOI: 10.1038/srep21411] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/22/2016] [Indexed: 01/09/2023] Open
Abstract
RNA viruses use various strategies to condense their genetic information into small genomes. Potyviruses not only use the polyprotein strategy, but also embed an open reading frame, pipo, in the P3 cistron in the -1 reading frame. PIPO is expressed as a fusion protein with the N-terminal half of P3 (P3N-PIPO) via transcriptional slippage of viral RNA-dependent RNA polymerase (RdRp). We herein show that clover yellow vein virus (ClYVV) produces a previously unidentified factor, P3N-ALT, in the +1 reading frame via transcriptional slippage at a conserved G(1-2)A(6-7) motif, as is the case for P3N-PIPO. The translation of P3N-ALT terminates soon, and it is considered to be a C-terminal truncated form of P3. In planta experiments indicate that P3N-ALT functions in cell-to-cell movement along with P3N-PIPO. Hence, all three reading frames are used to produce functional proteins. Deep sequencing of ClYVV RNA from infected plants endorses the slippage by viral RdRp. Our findings unveil a virus strategy that optimizes the coding capacity.
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Affiliation(s)
| | - Sun Hee Choi
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Masanao Sato
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Go Atsumi
- Iwate Biotechnology Research Center, Kitakami 024-0003, Japan
- National Institute of Advanced Industrial Science and Technology, Sapporo 062-8517, Japan
| | - Junya Abe
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Junya Fukuda
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Mie N. Honjo
- Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
| | - Atsushi J. Nagano
- Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
- Japan Science and Technology Agency, PRESTO, Kawaguchi 332-0012, Japan
- Faculty of Agriculture, Ryukoku University, Otsu 520-2194, Japan
| | - Keisuke Komoda
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kenji S. Nakahara
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Ichiro Uyeda
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Satoshi Naito
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
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13
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Liu Q, Fredrick K. Intersubunit Bridges of the Bacterial Ribosome. J Mol Biol 2016; 428:2146-64. [PMID: 26880335 DOI: 10.1016/j.jmb.2016.02.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 02/02/2023]
Abstract
The ribosome is a large two-subunit ribonucleoprotein machine that translates the genetic code in all cells, synthesizing proteins according to the sequence of the mRNA template. During translation, the primary substrates, transfer RNAs, pass through binding sites formed between the two subunits. Multiple interactions between the ribosomal subunits, termed intersubunit bridges, keep the ribosome intact and at the same time govern dynamics that facilitate the various steps of translation such as transfer RNA-mRNA movement. Here, we review the molecular nature of these intersubunit bridges, how they change conformation during translation, and their functional roles in the process.
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Affiliation(s)
- Qi Liu
- Ohio State Biochemistry Program, Department of Microbiology, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Ohio State Biochemistry Program, Department of Microbiology, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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14
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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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15
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Hu HT, Cho CP, Lin YH, Chang KY. A general strategy to inhibiting viral -1 frameshifting based on upstream attenuation duplex formation. Nucleic Acids Res 2015; 44:256-66. [PMID: 26612863 PMCID: PMC4705660 DOI: 10.1093/nar/gkv1307] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/09/2015] [Indexed: 11/25/2022] Open
Abstract
Viral −1 programmed ribosomal frameshifting (PRF) as a potential antiviral target has attracted interest because many human viral pathogens, including human immunodeficiency virus (HIV) and coronaviruses, rely on −1 PRF for optimal propagation. Efficient eukaryotic −1 PRF requires an optimally placed stimulator structure downstream of the frameshifting site and different strategies targeting viral −1 PRF stimulators have been developed. However, accessing particular −1 PRF stimulator information represents a bottle-neck in combating the emerging epidemic viral pathogens such as Middle East respiratory syndrome coronavirus (MERS-CoV). Recently, an RNA hairpin upstream of frameshifting site was shown to act as a cis-element to attenuate −1 PRF with mechanism unknown. Here, we show that an upstream duplex formed in-trans, by annealing an antisense to its complementary mRNA sequence upstream of frameshifting site, can replace an upstream hairpin to attenuate −1 PRF efficiently. This finding indicates that the formation of a proximal upstream duplex is the main determining factor responsible for −1 PRF attenuation and provides mechanistic insight. Additionally, the antisense-mediated upstream duplex approach downregulates −1 PRF stimulated by distinct −1 PRF stimulators, including those of MERS-CoV, suggesting its general application potential as a robust means to evaluating viral −1 PRF inhibition as soon as the sequence information of an emerging human coronavirus is available.
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Affiliation(s)
- Hao-Teng Hu
- Institute of Biochemistry, National Chung-Hsing University, 250 Kuo-Kung Road, Taichung, 402 Taiwan
| | - Che-Pei Cho
- Institute of Biochemistry, National Chung-Hsing University, 250 Kuo-Kung Road, Taichung, 402 Taiwan
| | - Ya-Hui Lin
- Institute of Biochemistry, National Chung-Hsing University, 250 Kuo-Kung Road, Taichung, 402 Taiwan
| | - Kung-Yao Chang
- Institute of Biochemistry, National Chung-Hsing University, 250 Kuo-Kung Road, Taichung, 402 Taiwan
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16
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Gao F, Simon AE. Multiple Cis-acting elements modulate programmed -1 ribosomal frameshifting in Pea enation mosaic virus. Nucleic Acids Res 2015; 44:878-95. [PMID: 26578603 PMCID: PMC4737148 DOI: 10.1093/nar/gkv1241] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/02/2015] [Indexed: 11/13/2022] Open
Abstract
Programmed -1 ribosomal frameshifting (-1 PRF) is used by many positive-strand RNA viruses for translation of required products. Despite extensive studies, it remains unresolved how cis-elements just downstream of the recoding site promote a precise level of frameshifting. The Umbravirus Pea enation mosaic virus RNA2 expresses its RNA polymerase by -1 PRF of the 5'-proximal ORF (p33). Three hairpins located in the vicinity of the recoding site are phylogenetically conserved among Umbraviruses. The central Recoding Stimulatory Element (RSE), located downstream of the p33 termination codon, is a large hairpin with two asymmetric internal loops. Mutational analyses revealed that sequences throughout the RSE and the RSE lower stem (LS) structure are important for frameshifting. SHAPE probing of mutants indicated the presence of higher order structure, and sequences in the LS may also adapt an alternative conformation. Long-distance pairing between the RSE and a 3' terminal hairpin was less critical when the LS structure was stabilized. A basal level of frameshifting occurring in the absence of the RSE increases to 72% of wild-type when a hairpin upstream of the slippery site is also deleted. These results suggest that suppression of frameshifting may be needed in the absence of an active RSE conformation.
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Affiliation(s)
- Feng Gao
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD 20742, USA
| | - Anne E Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD 20742, USA
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17
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Probing the Translation Dynamics of Ribosomes Using Zero-Mode Waveguides. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 139:1-43. [PMID: 26970189 DOI: 10.1016/bs.pmbts.2015.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In order to coordinate the complex biochemical and structural feat of converting triple-nucleotide codons into their corresponding amino acids, the ribosome must physically manipulate numerous macromolecules including the mRNA, tRNAs, and numerous translation factors. The ribosome choreographs binding, dissociation, physical movements, and structural rearrangements so that they synergistically harness the energy from biochemical processes, including numerous GTP hydrolysis steps and peptide bond formation. Due to the dynamic and complex nature of translation, the large cast of ligands involved, and the large number of possible configurations, tracking the global time evolution or dynamics of the ribosome complex in translation has proven to be challenging for bulk methods. Conventional single-molecule fluorescence experiments on the other hand require low concentrations of fluorescent ligands to reduce background noise. The significantly reduced bimolecular association rates under those conditions limit the number of steps that can be observed within the time window available to a fluorophore. The advent of zero-mode waveguide (ZMW) technology has allowed the study of translation at near-physiological concentrations of labeled ligands, moving single-molecule fluorescence microscopy beyond focused model systems into studying the global dynamics of translation in realistic setups. This chapter reviews the recent works using the ZMW technology to dissect the mechanism of translation initiation and elongation in prokaryotes, including complex processes such as translational stalling and frameshifting. Given the success of the technology, similarly complex biological processes could be studied in near-physiological conditions with the controllability of conventional in vitro experiments.
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18
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Dunkle JA, Dunham CM. Mechanisms of mRNA frame maintenance and its subversion during translation of the genetic code. Biochimie 2015; 114:90-6. [PMID: 25708857 PMCID: PMC4458409 DOI: 10.1016/j.biochi.2015.02.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/11/2015] [Indexed: 01/26/2023]
Abstract
Important viral and cellular gene products are regulated by stop codon readthrough and mRNA frameshifting, processes whereby the ribosome detours from the reading frame defined by three nucleotide codons after initiation of translation. In the last few years, rapid progress has been made in mechanistically characterizing both processes and also revealing that trans-acting factors play important regulatory roles in frameshifting. Here, we review recent biophysical studies that bring new molecular insights to stop codon readthrough and frameshifting. Lastly, we consider whether there may be common mechanistic themes in -1 and +1 frameshifting based on recent X-ray crystal structures of +1 frameshift-prone tRNAs bound to the ribosome.
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Affiliation(s)
- Jack A Dunkle
- Emory University School of Medicine, Department of Biochemistry, 1510 Clifton Road NE, Suite G223, Atlanta, GA 30322, USA
| | - Christine M Dunham
- Emory University School of Medicine, Department of Biochemistry, 1510 Clifton Road NE, Suite G223, Atlanta, GA 30322, USA.
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19
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Yordanova MM, Wu C, Andreev DE, Sachs MS, Atkins JF. A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA. J Biol Chem 2015; 290:17863-17878. [PMID: 25998126 PMCID: PMC4505036 DOI: 10.1074/jbc.m115.647065] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Indexed: 01/06/2023] Open
Abstract
The protein antizyme is a negative regulator of cellular polyamine concentrations from yeast to mammals. Synthesis of functional antizyme requires programmed +1 ribosomal frameshifting at the 3′ end of the first of two partially overlapping ORFs. The frameshift is the sensor and effector in an autoregulatory circuit. Except for Saccharomyces cerevisiae antizyme mRNA, the frameshift site alone only supports low levels of frameshifting. The high levels usually observed depend on the presence of cis-acting stimulatory elements located 5′ and 3′ of the frameshift site. Antizyme genes from different evolutionary branches have evolved different stimulatory elements. Prior and new multiple alignments of fungal antizyme mRNA sequences from the Agaricomycetes class of Basidiomycota show a distinct pattern of conservation 5′ of the frameshift site consistent with a function at the amino acid level. As shown here when tested in Schizosaccharomyces pombe and mammalian HEK293T cells, the 5′ part of this conserved sequence acts at the nascent peptide level to stimulate the frameshifting, without involving stalling detectable by toe-printing. However, the peptide is only part of the signal. The 3′ part of the stimulator functions largely independently and acts at least mostly at the nucleotide level. When polyamine levels were varied, the stimulatory effect was seen to be especially responsive in the endogenous polyamine concentration range, and this effect may be more general. A conserved RNA secondary structure 3′ of the frameshift site has weaker stimulatory and polyamine sensitizing effects on frameshifting.
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Affiliation(s)
- Martina M Yordanova
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258
| | - Dmitry E Andreev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258
| | - John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112-5330.
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20
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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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21
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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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22
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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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23
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Wang G, Yang Y, Huang X, Du Z. Possible involvement of coaxially stacked double pseudoknots in the regulation of −1 programmed ribosomal frameshifting in RNA viruses. J Biomol Struct Dyn 2014; 33:1547-57. [DOI: 10.1080/07391102.2014.956149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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24
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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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25
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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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26
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Sharma V, Prère MF, Canal I, Firth AE, Atkins JF, Baranov PV, Fayet O. Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli. Nucleic Acids Res 2014; 42:7210-25. [PMID: 24875478 PMCID: PMC4066793 DOI: 10.1093/nar/gku386] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Programmed ribosomal -1 frameshifting is a non-standard decoding process occurring when ribosomes encounter a signal embedded in the mRNA of certain eukaryotic and prokaryotic genes. This signal has a mandatory component, the frameshift motif: it is either a Z_ZZN tetramer or a X_XXZ_ZZN heptamer (where ZZZ and XXX are three identical nucleotides) allowing cognate or near-cognate repairing to the -1 frame of the A site or A and P sites tRNAs. Depending on the signal, the frameshifting frequency can vary over a wide range, from less than 1% to more than 50%. The present study combines experimental and bioinformatics approaches to carry out (i) a systematic analysis of the frameshift propensity of all possible motifs (16 Z_ZZN tetramers and 64 X_XXZ_ZZN heptamers) in Escherichia coli and (ii) the identification of genes potentially using this mode of expression amongst 36 Enterobacteriaceae genomes. While motif efficiency varies widely, a major distinctive rule of bacterial -1 frameshifting is that the most efficient motifs are those allowing cognate re-pairing of the A site tRNA from ZZN to ZZZ. The outcome of the genomic search is a set of 69 gene clusters, 59 of which constitute new candidates for functional utilization of -1 frameshifting.
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Affiliation(s)
- Virag Sharma
- School of Biochemistry and Cell biology, University College Cork, Cork, Ireland
| | - Marie-Françoise Prère
- Laboratoire de Microbiologie et Génétique moléculaire, UMR5100, Centre National de la Recherche Scientifique, Université Paul Sabatier-Toulouse III, 118 route de Narbonne, Toulouse 31062-cedex, France
| | - Isabelle Canal
- Laboratoire de Microbiologie et Génétique moléculaire, UMR5100, Centre National de la Recherche Scientifique, Université Paul Sabatier-Toulouse III, 118 route de Narbonne, Toulouse 31062-cedex, France
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - John F Atkins
- School of Biochemistry and Cell biology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, 15N 2030E, Rm7410, Salt Lake City, UT 84112-5330, USA
| | - Pavel V Baranov
- School of Biochemistry and Cell biology, University College Cork, Cork, Ireland
| | - Olivier Fayet
- Laboratoire de Microbiologie et Génétique moléculaire, UMR5100, Centre National de la Recherche Scientifique, Université Paul Sabatier-Toulouse III, 118 route de Narbonne, Toulouse 31062-cedex, France
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27
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Huang X, Yang Y, Wang G, Cheng Q, Du Z. Highly conserved RNA pseudoknots at the Gag-Pol junction of HIV-1 suggest a novel mechanism of -1 ribosomal frameshifting. RNA (NEW YORK, N.Y.) 2014; 20:587-93. [PMID: 24671765 PMCID: PMC3988561 DOI: 10.1261/rna.042457.113] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
-1 programmed ribosomal frameshifting (PRF) is utilized by many viruses to synthesize their enzymatic (Pol) and structural (Gag) proteins at a defined ratio. For efficient -1 PRF, two cis-acting elements are required: a heptanucleotide frameshift site and a downstream stimulator such as a pseudoknot. We have analyzed the gag-pol junction sequences from 4254 HIV-1 strains. Approximately ninety-five percent of the sequences can form four pseudoknots PK1-PK4 (∼ 97% contain PK1, PK3, and PK4), covering ∼ 72 nt including the frameshift site. Some pseudoknots are mutually excluded due to sequence overlap. PK1 and PK3 arrange tandemly. Their stems form a quasi-continuous helix of ∼ 22 bp. We propose a novel mechanism for possible roles of these pseudoknots. Multiple alternative structures may exist at the gag-pol junction. In most strains, the PK1-PK3 tandem pseudoknots may dominate the structurally heterogeneous pool of RNA due to their greater overall stability. The tandem pseudoknots may function as a breaking system to slow down the ribosome. The ribosome unwinds PK1 and stem 1 of PK3 before it can reach the frameshift site. Then, PK4 can form rapidly because the intact stem 2 of PK3 makes up a large part of the stem 1 of PK4. The newly formed PK4 jams the entrance of the mRNA tunnel. The process then proceeds as in a typical case of -1 PRF. This mechanism incorporates several exquisite new features while still being consistent with the current paradigm of pseudoknot-dependent -1 PRF.
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Affiliation(s)
| | - Yang Yang
- Department of Chemistry and Biochemistry, Southern Illinois University at Carbondale, Carbondale, Illinois 62901, USA
| | - Guan Wang
- Department of Chemistry and Biochemistry, Southern Illinois University at Carbondale, Carbondale, Illinois 62901, USA
| | | | - Zhihua Du
- Department of Chemistry and Biochemistry, Southern Illinois University at Carbondale, Carbondale, Illinois 62901, USA
- Corresponding authorE-mail
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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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Ofori LO, Hilimire TA, Bennett RP, Brown NW, Smith HC, Miller BL. High-affinity recognition of HIV-1 frameshift-stimulating RNA alters frameshifting in vitro and interferes with HIV-1 infectivity. J Med Chem 2014; 57:723-32. [PMID: 24387306 PMCID: PMC3954503 DOI: 10.1021/jm401438g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
life cycle of the human immunodeficiency virus type 1 (HIV-1)
has an absolute requirement for ribosomal frameshifting during protein
translation in order to produce the polyprotein precursor of the viral
enzymes. While an RNA stem-loop structure (the “HIV-1 Frameshift
Stimulating Signal”, or HIV-1 FSS) controls the frameshift
efficiency and has been hypothesized as an attractive therapeutic
target, developing compounds that selectively bind this RNA and interfere
with HIV-1 replication has proven challenging. Building on our prior
discovery of a “hit” molecule able to bind this stem-loop,
we now report the development of compounds displaying high affinity
for the HIV-1 FSS. These compounds are able to enhance frameshifting
more than 50% in a dual-luciferase assay in human embryonic kidney
cells, and they strongly inhibit the infectivity of pseudotyped HIV-1
virions.
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Affiliation(s)
- Leslie O Ofori
- Departments of Chemistry, ‡Biochemistry and Biophysics, and §Dermatology, University of Rochester , Rochester, New York 14642, United States
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30
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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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Role of the ribosomal P-site elements of m²G966, m⁵C967, and the S9 C-terminal tail in maintenance of the reading frame during translational elongation in Escherichia coli. J Bacteriol 2013; 195:3524-30. [PMID: 23729652 DOI: 10.1128/jb.00455-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ribosomal P-site hosts the peptidyl-tRNAs during translation elongation. Which P-site elements support these tRNA species to maintain codon-anticodon interactions has remained unclear. We investigated the effects of P-site features of methylations of G966, C967, and the conserved C-terminal tail sequence of Ser, Lys, and Arg (SKR) of the S9 ribosomal protein in maintenance of the translational reading frame of an mRNA. We generated Escherichia coli strains deleted for the SKR sequence in S9 ribosomal protein, RsmB (which methylates C967), and RsmD (which methylates G966) and used them to translate LacZ from its +1 and -1 out-of-frame constructs. We show that the S9 SKR tail prevents both the +1 and -1 frameshifts and plays a general role in holding the P-site tRNA/peptidyl-tRNA in place. In contrast, the G966 and C967 methylations did not make a direct contribution to the maintenance of the translational frame of an mRNA. However, deletion of rsmB in the S9Δ3 background caused significantly increased -1 frameshifting at 37°C. Interestingly, the effects of the deficiency of C967 methylation were annulled when the E. coli strain was grown at 30°C, supporting its context-dependent role.
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32
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Cho CP, Lin SC, Chou MY, Hsu HT, Chang KY. Regulation of programmed ribosomal frameshifting by co-translational refolding RNA hairpins. PLoS One 2013; 8:e62283. [PMID: 23638024 PMCID: PMC3639245 DOI: 10.1371/journal.pone.0062283] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/19/2013] [Indexed: 01/04/2023] Open
Abstract
RNA structures are unwound for decoding. In the process, they can pause the elongating ribosome for regulation. An example is the stimulation of -1 programmed ribosomal frameshifting, leading to 3′ direction slippage of the reading-frame during elongation, by specific pseudoknot stimulators downstream of the frameshifting site. By investigating a recently identified regulatory element upstream of the SARS coronavirus (SARS-CoV) −1 frameshifting site, it is shown that a minimal functional element with hairpin forming potential is sufficient to down-regulate−1 frameshifting activity. Mutagenesis to disrupt or restore base pairs in the potential hairpin stem reveals that base-pair formation is required for−1 frameshifting attenuation in vitro and in 293T cells. The attenuation efficiency of a hairpin is determined by its stability and proximity to the frameshifting site; however, it is insensitive to E site sequence variation. Additionally, using a dual luciferase assay, it can be shown that a hairpin stimulated +1 frameshifting when placed upstream of a +1 shifty site in yeast. The investigations indicate that the hairpin is indeed a cis-acting programmed reading-frame switch modulator. This result provides insight into mechanisms governing−1 frameshifting stimulation and attenuation. Since the upstream hairpin is unwound (by a marching ribosome) before the downstream stimulator, this study’s findings suggest a new mode of translational regulation that is mediated by the reformed stem of a ribosomal unwound RNA hairpin during elongation.
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Affiliation(s)
- Che-Pei Cho
- Institute of Biochemistry, National Chung-Hsing University, Taichung, Taiwan, Republic of China
| | - Szu-Chieh Lin
- Institute of Biochemistry, National Chung-Hsing University, Taichung, Taiwan, Republic of China
| | - Ming-Yuan Chou
- Institute of Biochemistry, National Chung-Hsing University, Taichung, Taiwan, Republic of China
| | - Hsiu-Ting Hsu
- Institute of Biochemistry, National Chung-Hsing University, Taichung, Taiwan, Republic of China
| | - Kung-Yao Chang
- Institute of Biochemistry, National Chung-Hsing University, Taichung, Taiwan, Republic of China
- * E-mail:
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33
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Kirilov KT, Golshani A, Ivanov IG. Termination Codons and Stop Codon Context in Bacteria and Mammalian Mitochondria. BIOTECHNOL BIOTEC EQ 2013. [DOI: 10.5504/bbeq.2013.0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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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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35
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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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36
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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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37
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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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38
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Kirilov K, Ivanov I. A Programme for Determination of Codons and Codons Context Frequency of Occurrence in Sequenced Genomes. BIOTECHNOL BIOTEC EQ 2012. [DOI: 10.5504/bbeq.2012.0074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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39
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Allosteric vs. spontaneous exit-site (E-site) tRNA dissociation early in protein synthesis. Proc Natl Acad Sci U S A 2011; 108:16980-5. [PMID: 21969541 DOI: 10.1073/pnas.1106999108] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During protein synthesis, deacylated transfer RNAs leave the ribosome via an exit (E) site after mRNA translocation. How the ribosome regulates tRNA dissociation and whether functional linkages between the aminoacyl (A) and E sites modulate the dynamics of protein synthesis have long been debated. Using single molecule fluorescence resonance energy transfer experiments, we find that, during early cycles of protein elongation, tRNAs are often held in the E site until being allosterically released when the next aminoacyl tRNA binds to the A site. This process is regulated by the length and sequence of the nascent peptide and by the conformational state, detected by tRNA proximity, prior to translocation. In later cycles, E-site tRNA dissociates spontaneously. Our results suggest that the distribution of pretranslocation tRNA states and posttranslocation pathways are correlated within each elongation cycle via communication between distant subdomains in the ribosome, but that this correlation between elongation cycle intermediates does not persist into succeeding cycles.
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40
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Baranov PV, Wills NM, Barriscale KA, Firth AE, Jud MC, Letsou A, Manning G, Atkins JF. Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC). RNA Biol 2011; 8:637-47. [PMID: 21593603 DOI: 10.4161/rna.8.4.15395] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A programmed ribosomal frameshift (PRF) in the decoding of APC (adenomatous polyposis coli) mRNA has been identified and characterized in Caenorhabditis worms, Drosophila and mosquitoes. The frameshift product lacks the C-terminal approximately one-third of the product of standard decoding and instead has a short sequence encoded by the -1 frame which is just 13 residues in C. elegans, but is 125 in D. melanogaster. The frameshift site is A_AA.A_AA.C in Caenorhabditids, fruit flies and the mosquitoes studied while a variant A_AA.A_AA.A is found in some other nematodes. The predicted secondary RNA structure of the downstream stimulators varies considerably in the species studied. In the twelve sequenced Drosophila genomes, it is a long stem with a four-way junction in its loop. In the five sequenced Caenorhabditis species, it is a short RNA pseudoknot with an additional stem in loop 1. The efficiency of frameshifting varies significantly, depending on the particular stimulator within the frameshift cassette, when tested with reporter constructs in rabbit reticulocyte lysates. Phylogenetic analysis of the distribution of APC programmed ribosomal frameshifting cassettes suggests it has an ancient origin and raises questions about a possibility of synthesis of alternative protein products during expression of APC in other organisms such as humans. The origin of APC as a PRF candidate emerged from a prior study of evolutionary signatures derived from comparative analysis of the 12 fly genomes. Three other proposed PRF candidates (Xbp1, CG32736, CG14047) with switches in conservation of reading frames are likely explained by mechanisms other than PRF.
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Affiliation(s)
- Pavel V Baranov
- Biochemistry Department, University College Cork, Cork, Ireland.
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41
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Abstract
Errors occur randomly and at low frequency during the translation of mRNA. However, such errors may also be programmed by the sequence and structure of the mRNA. These programmed events are called ‘recoding’ and are found mostly in viruses, in which they are usually essential for viral replication. Translational errors at a stop codon may also be induced by drugs, raising the possibility of developing new treatment protocols for genetic diseases on the basis of nonsense mutations. Many studies have been carried out, but the molecular mechanisms governing these events remain largely unknown. Studies on the yeast Saccharomyces cerevisiae have contributed to characterization of the HIV‐1 frameshifting site and have demonstrated that frameshifting is conserved from yeast to humans. Yeast has also proved a particularly useful model organism for deciphering the mechanisms of translation termination in eukaryotes and identifying the factors required to obtain a high level of natural suppression. These findings open up new possibilities for large‐scale screening in yeast to identify new drugs for blocking HIV replication by inhibiting frameshifting or restoring production of the full‐length protein from a gene inactivated by a premature termination codon. We explore these two aspects of the contribution of yeast studies to human medicine in this review.
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Affiliation(s)
- Laure Bidou
- Université Paris-Sud, IGM CNRS UMR 8621, Orsay, France
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42
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Liao PY, Choi YS, Dinman JD, Lee KH. The many paths to frameshifting: kinetic modelling and analysis of the effects of different elongation steps on programmed -1 ribosomal frameshifting. Nucleic Acids Res 2010; 39:300-12. [PMID: 20823091 PMCID: PMC3017607 DOI: 10.1093/nar/gkq761] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Several important viruses including the human immunodeficiency virus type 1 (HIV-1) and the SARS-associated Coronavirus (SARS-CoV) employ programmed −1 ribosomal frameshifting (PRF) for their protein expression. Here, a kinetic framework is developed to describe −1 PRF. The model reveals three kinetic pathways to −1 PRF that yield two possible frameshift products: those incorporating zero frame encoded A-site tRNAs in the recoding site, and products incorporating −1 frame encoded A-site tRNAs. Using known kinetic rate constants, the individual contributions of different steps of the translation elongation cycle to −1 PRF and the ratio between two types of frameshift products were evaluated. A dual fluorescence reporter was employed in Escherichia coli to empirically test the model. Additionally, the study applied a novel mass spectrometry approach to quantify the ratios of the two frameshift products. A more detailed understanding of the mechanisms underlying −1 PRF may provide insight into developing antiviral therapeutics.
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Affiliation(s)
- Pei-Yu Liao
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
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43
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Olsthoorn RCL, Reumerman R, Hilbers CW, Pleij CWA, Heus HA. Functional analysis of the SRV-1 RNA frameshifting pseudoknot. Nucleic Acids Res 2010; 38:7665-72. [PMID: 20639537 PMCID: PMC2995055 DOI: 10.1093/nar/gkq629] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Simian retrovirus type-1 uses programmed ribosomal frameshifting to control expression of the Gag-Pol polyprotein from overlapping gag and pol open-reading frames. The frameshifting signal consists of a heptanucleotide slippery sequence and a downstream-located 12-base pair pseudoknot. The solution structure of this pseudoknot, previously solved by NMR [Michiels,P.J., Versleijen,A.A., Verlaan,P.W., Pleij,C.W., Hilbers,C.W. and Heus,H.A. (2001) Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting. J. Mol. Biol., 310, 1109-1123] has a classical H-type fold and forms an extended triple helix by interactions between loop 2 and the minor groove of stem 1 involving base-base and base-sugar contacts. A mutational analysis was performed to test the functional importance of the triple helix for -1 frameshifting in vitro. Changing bases in L2 or base pairs in S1 involved in a base triple resulted in a 2- to 5-fold decrease in frameshifting efficiency. Alterations in the length of L2 had adverse effects on frameshifting. The in vitro effects were well reproduced in vivo, although the effect of enlarging L2 was more dramatic in vivo. The putative role of refolding kinetics of frameshifter pseudoknots is discussed. Overall, the data emphasize the role of the triple helix in -1 frameshifting.
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Affiliation(s)
- René C L Olsthoorn
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
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44
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Frameshifting in alphaviruses: a diversity of 3' stimulatory structures. J Mol Biol 2010; 397:448-56. [PMID: 20114053 DOI: 10.1016/j.jmb.2010.01.044] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2009] [Accepted: 01/19/2010] [Indexed: 11/27/2022]
Abstract
Programmed ribosomal frameshifting allows the synthesis of alternative, N-terminally coincident, C-terminally distinct proteins from the same RNA. Many viruses utilize frameshifting to optimize the coding potential of compact genomes, to circumvent the host cell's canonical rule of one functional protein per mRNA, or to express alternative proteins in a fixed ratio. Programmed frameshifting is also used in the decoding of a small number of cellular genes. Recently, specific ribosomal -1 frameshifting was discovered at a conserved U_UUU_UUA motif within the sequence encoding the alphavirus 6K protein. In this case, frameshifting results in the synthesis of an additional protein, termed TF (TransFrame). This new case of frameshifting is unusual in that the -1 frame ORF is very short and completely embedded within the sequence encoding the overlapping polyprotein. The present work shows that there is remarkable diversity in the 3' sequences that are functionally important for efficient frameshifting at the U_UUU_UUA motif. While many alphavirus species utilize a 3' RNA structure such as a hairpin or pseudoknot, some species (such as Semliki Forest virus) apparently lack any intra-mRNA stimulatory structure, yet just 20 nt 3'-adjacent to the shift site stimulates up to 10% frameshifting. The analysis, both experimental and bioinformatic, significantly expands the known repertoire of -1 frameshifting stimulators in mammalian and insect systems.
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45
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Huang Y, Koonin EV, Lipman DJ, Przytycka TM. Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage. Nucleic Acids Res 2009; 37:6799-810. [PMID: 19745054 PMCID: PMC2777431 DOI: 10.1093/nar/gkp712] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In a wide range of genomes, it was observed that the usage of synonymous codons is biased toward specific codons and codon patterns. Factors that are implicated in the selection for codon usage include facilitation of fast and accurate translation. There are two types of translational errors: missense errors and processivity errors. There is considerable evidence in support of the hypothesis that codon usage is optimized to minimize missense errors. In contrast, little is known about the relationship between codon usage and frameshifting errors, an important form of processivity errors, which appear to occur at frequencies comparable to the frequencies of missense errors. Based on the recently proposed pause-and-slip model of frameshifting, we developed Frameshifting Robustness Score (FRS). We used this measure to test if the pattern of codon usage indicates optimization against frameshifting errors. We found that the FRS values of protein-coding sequences from four analyzed genomes (the bacteria Bacillus subtilis and Escherichia coli, and the yeasts Saccharomyces cerevisiae and Schizosaccharomyce pombe) were typically higher than expected by chance. Other properties of FRS patterns observed in B. subtilis, S. cerevisiae and S. pombe, such as the tendency of FRS to increase from the 5′- to 3′-end of protein-coding sequences, were also consistent with the hypothesis of optimization against frameshifting errors in translation. For E. coli, the results of different tests were less consistent, suggestive of a much weaker optimization, if any. Collectively, the results fit the concept of selection against mistranslation-induced protein misfolding being one of the factors shaping the evolution of both coding and non-coding sequences.
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Affiliation(s)
- Yang Huang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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46
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Abstract
In coronaviruses such as the SARS coronavirus (SARS-CoV), programmed −1 ribosomal frameshifting (−1 PRF) is used to direct the synthesis of immediate early proteins, e.g., RNA-dependent RNA polymerase (RDRP) and proteases, that are thought to prepare the infected cell for takeover by the virus. Unlike other RNA viruses which make their structural proteins first, this class of proteins is synthesized after −1 PRF, from subgenomic mRNAs produced subsequent to production of RDRP. Also unique among the coronaviruses is the inclusion of mRNA structural elements that do not appear to be essential for frameshifting. Understanding the differences between –1 PRF signals from coronaviruses and other viruses will enhance our understanding of –1 PRF in general, and will be instructive in designing new classes of antiviral therapeutics. In this chapter we summarize current knowledge and add additional insight to the function of the programmed –1 ribosomal frameshift signal present in the SARS-associated coronavirus.
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Atkins JF, Gesteland RF. Ribosomal Frameshifting in Decoding Plant Viral RNAs. RECODING: EXPANSION OF DECODING RULES ENRICHES GENE EXPRESSION 2009; 24. [PMCID: PMC7122378 DOI: 10.1007/978-0-387-89382-2_9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Frameshifting provides an elegant mechanism by which viral RNA both encodes overlapping genes and controls expression levels of those genes. As in animal viruses, the −1 ribosomal frameshift site in the viral mRNA consists of a canonical shifty heptanucleotide followed by a highly structured frameshift stimulatory element, and the gene translated as a result of frameshifting usually encodes the RNA-dependent RNA polymerase. In plant viruses, the −1 frameshift stimulatory element consists of either (i) a small pseudoknot stabilized by many triple-stranded regions and a triple base pair containing a protonated cytidine at the helical junction, (ii) an unusual apical loop–internal loop interaction in which a stem-loop in the 3′ untranslated region 4 kb downstream base pairs to a bulged stem-loop at the frameshift site, or (iii) a potential simple stem-loop. Other less well-characterized changes in reading frame occur on plant viral RNAs, including a possible +1 frameshift, and net −1 reading frame changes that do not utilize canonical frameshift signals. All these studies reveal the remarkable ways in which plant viral RNAs interact with ribosomes to precisely control protein expression at the ratios needed to sustain virus replication.
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Affiliation(s)
- John F. Atkins
- grid.223827.e0000000121930096Molecular Biology Program, University of Utah, N. 2030 E. 15, Salt Late City, 84112-5330 U.S.A.
| | - Raymond F. Gesteland
- grid.223827.e0000000121930096Dept. Bioengineering, University of Utah, Salt Lake City, 84112 U.S.A.
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Atkins JF, Gesteland RF, Pennell S. Pseudoknot-Dependent Programmed —1 Ribosomal Frameshifting: Structures, Mechanisms and Models. RECODING: EXPANSION OF DECODING RULES ENRICHES GENE EXPRESSION 2009; 24. [PMCID: PMC7119991 DOI: 10.1007/978-0-387-89382-2_7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Programmed —1 ribosomal frameshifting is a translational recoding strategy that takes place during the elongation phase of protein biosynthesis. Frameshifting occurs in response to specific signals in the mRNA; a slippery sequence, where the ribosome changes frame, and a stimulatory RNA secondary structure, usually a pseudoknot, located immediately downstream. During the frameshift the ribosome slips backwards by a single nucleotide (in the 5′-wards/—1 direction) and continues translation in the new, overlapping reading frame, generating a fusion protein composed of the products of both the original and the —1 frame coding regions. In eukaryotes, frameshifting is largely a phenomenon of virus gene expression and associated predominantly with the expression of viral replicases. Research on frameshifting impacts upon diverse topics, including the ribosomal elongation cycle, RNA structure and function, tRNA modification, virus replication, antiviral intervention, evolution and bioinformatics. This chapter focuses on the structure and function of frameshift-stimulatory RNA pseudoknots and mechanistic aspects of ribosomal frameshifting. A variety of models of the frameshifting process are discussed in the light of recent advances in our understanding of ribosome structure and the elongation cycle.
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Affiliation(s)
- John F. Atkins
- grid.223827.e0000000121930096Molecular Biology Program, University of Utah, N. 2030 E. 15, Salt Late City, 84112-5330 U.S.A.
| | - Raymond F. Gesteland
- grid.223827.e0000000121930096Dept. Bioengineering, University of Utah, Salt Lake City, 84112 U.S.A.
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Mechanisms employed by retroviruses to exploit host factors for translational control of a complicated proteome. Retrovirology 2009; 6:8. [PMID: 19166625 PMCID: PMC2657110 DOI: 10.1186/1742-4690-6-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Accepted: 01/24/2009] [Indexed: 12/14/2022] Open
Abstract
Retroviruses have evolved multiple strategies to direct the synthesis of a complex proteome from a single primary transcript. Their mechanisms are modulated by a breadth of virus-host interactions, which are of significant fundamental interest because they ultimately affect the efficiency of virus replication and disease pathogenesis. Motifs located within the untranslated region (UTR) of the retroviral RNA have established roles in transcriptional trans-activation, RNA packaging, and genome reverse transcription; and a growing literature has revealed a necessary role of the UTR in modulating the efficiency of viral protein synthesis. Examples include a 5' UTR post-transcriptional control element (PCE), present in at least eight retroviruses, that interacts with cellular RNA helicase A to facilitate cap-dependent polyribosome association; and 3' UTR constitutive transport element (CTE) of Mason-Pfizer monkey virus that interacts with Tap/NXF1 and SR protein 9G8 to facilitate RNA export and translational utilization. By contrast, nuclear protein hnRNP E1 negatively modulates HIV-1 Gag, Env, and Rev protein synthesis. Alternative initiation strategies by ribosomal frameshifting and leaky scanning enable polycistronic translation of the cap-dependent viral transcript. Other studies posit cap-independent translation initiation by internal ribosome entry at structural features of the 5' UTR of selected retroviruses. The retroviral armamentarium also commands mechanisms to counter cellular post-transcriptional innate defenses, including protein kinase R, 2',5'-oligoadenylate synthetase and the small RNA pathway. This review will discuss recent and historically-recognized insights into retrovirus translational control. The expanding knowledge of retroviral post-transcriptional control is vital to understanding the biology of the retroviral proteome. In a broad perspective, each new insight offers a prospective target for antiviral therapy and strategic improvement of gene transfer vectors.
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Theis C, Reeder J, Giegerich R. KnotInFrame: prediction of -1 ribosomal frameshift events. Nucleic Acids Res 2008; 36:6013-20. [PMID: 18820303 PMCID: PMC2566878 DOI: 10.1093/nar/gkn578] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Programmed −1 ribosomal frameshift (−1 PRF) allows for alternative reading frames within one mRNA. First found in several viruses, it is now believed to exist in all kingdoms of life. Strong stimulators for −1 PRF are a heptameric slippery site and an RNA pseudoknot. Here, we present a new algorithm KnotInFrame, for the automatic detection of −1 PRF signals from genomic sequences. It finds the frameshifting stimulators by means of a specialized RNA-pseudoknot folding program, fast enough for genome-wide analyses. Evaluations on known −1 PRF signals demonstrate a high sensitivity.
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Affiliation(s)
- Corinna Theis
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
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