51
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Baril M, Dulude D, Steinberg SV, Brakier-Gingras L. The frameshift stimulatory signal of human immunodeficiency virus type 1 group O is a pseudoknot. J Mol Biol 2003; 331:571-83. [PMID: 12899829 PMCID: PMC7127721 DOI: 10.1016/s0022-2836(03)00784-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) requires a programmed -1 ribosomal frameshift to produce Gag-Pol, the precursor of its enzymatic activities. This frameshift occurs at a slippery sequence on the viral messenger RNA and is stimulated by a specific structure, downstream of the shift site. While in group M, the most abundant HIV-1 group, the frameshift stimulatory signal is an extended bulged stem-loop, we show here, using a combination of mutagenesis and probing studies, that it is a pseudoknot in group O. The mutagenesis and probing studies coupled to an in silico analysis show that group O pseudoknot is a hairpin-type pseudoknot with two coaxially stacked stems of eight base-pairs (stem 1 and stem 2), connected by single-stranded loops of 2nt (loop 1) and 20nt (loop 2). Mutations impairing formation of stem 1 or stem 2 of the pseudoknot reduce frameshift efficiency, whereas compensatory changes that allow re-formation of these stems restore the frameshift efficiency to near wild-type level. The difference between the frameshift stimulatory signal of group O and group M supports the hypothesis that these groups originate from a different monkey to human transmission.
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Key Words
- human immunodeficiency virus type 1
- hiv-1 group o
- ribosomal frameshifting
- rna structure
- rna pseudoknot
- bwyv, beet western yellow virus
- cmv, cytomegalovirus
- hiv-1, human immunodeficiency virus type 1
- ibv, infectious bronchitis virus
- luc, firefly luciferase
- mmtv, mouse mammary tumor virus
- pcr, polymerase chain reaction
- rrl, rabbit reticulocyte lysate
- rsv, rous sarcoma virus
- srv-1, simian retrovirus-1
- tfp, gag–pol transframe protein
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Affiliation(s)
- Martin Baril
- Département de Biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, Qué., Canada H3T 1J4
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52
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Atkins JF, Baranov PV, Fayet O, Herr AJ, Howard MT, Ivanov IP, Matsufuji S, Miller WA, Moore B, Prère MF, Wills NM, Zhou J, Gesteland RF. Overriding standard decoding: implications of recoding for ribosome function and enrichment of gene expression. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 66:217-32. [PMID: 12762024 DOI: 10.1101/sqb.2001.66.217] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- J F Atkins
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112-5330, USA
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53
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Brierley I, Pennell S. Structure and function of the stimulatory RNAs involved in programmed eukaryotic-1 ribosomal frameshifting. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 66:233-48. [PMID: 12762025 DOI: 10.1101/sqb.2001.66.233] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- I Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
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54
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Plant EP, Jacobs KLM, Harger JW, Meskauskas A, Jacobs JL, Baxter JL, Petrov AN, Dinman JD. The 9-A solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting. RNA (NEW YORK, N.Y.) 2003; 9:168-74. [PMID: 12554858 PMCID: PMC1237042 DOI: 10.1261/rna.2132503] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
There is something special about mRNA pseudoknots that allows them to elicit efficient levels of programmed -1 ribosomal frameshifting. Here, we present a synthesis of recent crystallographic, molecular, biochemical, and genetic studies to explain this property. Movement of 9 A by the anticodon loop of the aminoacyl-tRNA at the accommodation step normally pulls the downstream mRNA a similar distance along with it. We suggest that the downstream mRNA pseudoknot provides resistance to this movement by becoming wedged into the entrance of the ribosomal mRNA tunnel. These two opposing forces result in the creation of a local region of tension in the mRNA between the A-site codon and the mRNA pseudoknot. This can be relieved by one of two mechanisms; unwinding the pseudoknot, allowing the downstream region to move forward, or by slippage of the proximal region of the mRNA backwards by one base. The observed result of the latter mechanism is a net shift of reading frame by one base in the 5' direction, that is, a -1 ribosomal frameshift.
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Affiliation(s)
- Ewan P Plant
- Department of Cell Biology and Molecular Genetics, Microbiology Building, University of Maryland, College Park, MD 20742, USA
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55
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Wang Y, Wills NM, Du Z, Rangan A, Atkins JF, Gesteland RF, Hoffman DW. Comparative studies of frameshifting and nonframeshifting RNA pseudoknots: a mutational and NMR investigation of pseudoknots derived from the bacteriophage T2 gene 32 mRNA and the retroviral gag-pro frameshift site. RNA (NEW YORK, N.Y.) 2002; 8:981-96. [PMID: 12212853 PMCID: PMC1370320 DOI: 10.1017/s1355838202024044] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Mutational and NMR methods were used to investigate features of sequence, structure, and dynamics that are associated with the ability of a pseudoknot to stimulate a -1 frameshift. In vitro frameshift assays were performed on retroviral gag-pro frameshift-stimulating pseudoknots and their derivatives, a pseudoknot from the gene 32 mRNA of bacteriophage T2 that is not naturally associated with frameshifting, and hybrids of these pseudoknots. Results show that the gag-pro pseudoknot from human endogenous retrovirus-K10 (HERV) stimulates a -1 frameshift with an efficiency similar to that of the closely related retrovirus MMTV. The bacteriophage T2 mRNA pseudoknot was found to be a poor stimulator of frameshifting, supporting a hypothesis that the retroviral pseudoknots have distinctive properties that make them efficient frameshift stimulators. A hybrid, designed by combining features of the bacteriophage and retroviral pseudoknots, was found to stimulate frameshifting while retaining significant structural similarity to the nonframeshifting bacteriophage pseudoknot. Mutational analyses of the retroviral and hybrid pseudoknots were used to evaluate the effects of an unpaired (wedged) adenosine at the junction of the pseudoknot stems, changing the base pairs near the junction of the two stems, and changing the identity of the loop 2 nucleotide nearest the junction of the stems. Pseudoknots both with and without the wedged adenosine can stimulate frameshifting, though the identities of the nucleotides near the stem1/stem2 junction do influence efficiency. NMR data showed that the bacteriophage and hybrid pseudoknots are similar in their local structure at the junction of the stems, indicating that pseudoknots that are similar in this structural feature can differ radically in their ability to stimulate frameshifting. NMR methods were used to compare the internal motions of the bacteriophage T2 pseudoknot and representative frameshifting pseudoknots. The stems of the investigated pseudoknots are similarly well ordered on the time scales to which nitrogen-15 relaxation data are sensitive; however, solvent exchange rates for protons at the junction of the two stems of the nonframeshifting bacteriophage pseudoknot are significantly slower than the analogous protons in the representative frameshifting pseudoknots.
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Affiliation(s)
- Yue Wang
- Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, 78712, USA
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56
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Kontos H, Napthine S, Brierley I. Ribosomal pausing at a frameshifter RNA pseudoknot is sensitive to reading phase but shows little correlation with frameshift efficiency. Mol Cell Biol 2001; 21:8657-70. [PMID: 11713298 PMCID: PMC100026 DOI: 10.1128/mcb.21.24.8657-8670.2001] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here we investigated ribosomal pausing at sites of programmed -1 ribosomal frameshifting, using translational elongation and ribosome heelprint assays. The site of pausing at the frameshift signal of infectious bronchitis virus (IBV) was determined and was consistent with an RNA pseudoknot-induced pause that placed the ribosomal P- and A-sites over the slippery sequence. Similarly, pausing at the simian retrovirus 1 gag/pol signal, which contains a different kind of frameshifter pseudoknot, also placed the ribosome over the slippery sequence, supporting a role for pausing in frameshifting. However, a simple correlation between pausing and frameshifting was lacking. Firstly, a stem-loop structure closely related to the IBV pseudoknot, although unable to stimulate efficient frameshifting, paused ribosomes to a similar extent and at the same place on the mRNA as a parental pseudoknot. Secondly, an identical pausing pattern was induced by two pseudoknots differing only by a single loop 2 nucleotide yet with different functionalities in frameshifting. The final observation arose from an assessment of the impact of reading phase on pausing. Given that ribosomes advance in triplet fashion, we tested whether the reading frame in which ribosomes encounter an RNA structure (the reading phase) would influence pausing. We found that the reading phase did influence pausing but unexpectedly, the mRNA with the pseudoknot in the phase which gave the least pausing was found to promote frameshifting more efficiently than the other variants. Overall, these experiments support the view that pausing alone is insufficient to mediate frameshifting and additional events are required. The phase dependence of pausing may be indicative of an activity in the ribosome that requires an optimal contact with mRNA secondary structures for efficient unwinding.
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Affiliation(s)
- H Kontos
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, United Kingdom
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57
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Paul CP, Barry JK, Dinesh-Kumar SP, Brault V, Miller WA. A sequence required for -1 ribosomal frameshifting located four kilobases downstream of the frameshift site. J Mol Biol 2001; 310:987-99. [PMID: 11502008 DOI: 10.1006/jmbi.2001.4801] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Programmed ribosomal frameshifting allows one mRNA to encode regulate expression of, multiple open reading frames (ORFs). The polymerase encoded by ORF 2 of Barley yellow dwarf virus (BYDV) is expressed via minus one (-1) frameshifting from the overlapping ORF 1. Previously, this appeared to be mediated by a 116 nt RNA sequence that contains canonical -1 frameshift signals including a shifty heptanucleotide followed by a highly structured region. However, unlike known -1 frameshift signals, the reporter system required the zero frame stop codon and did not require a consensus shifty site for expression of the -1 ORF. In contrast, full-length viral RNA required a functional shifty site for frameshifting in wheat germ extract, while the stop codon was not required. Increasing translation initiation efficiency by addition of a 5' cap on the naturally uncapped viral RNA, decreased the frameshift rate. Unlike any other known RNA, a region four kilobases downstream of the frameshift site was required for frameshifting. This included an essential 55 base tract followed by a 179 base tract that contributed to full frameshifting. The effects of most mutations on frameshifting correlated with the ability of viral RNA to replicate in oat protoplasts, indicating that the wheat germ extract accurately reflected control of BYDV RNA translation in the infected cell. However, the overall frameshift rate appeared to be higher in infected cells, based on immunodetection of viral proteins. These findings show that use of short recoding sequences out of context in reporter constructs may overlook distant signals. Most importantly, the remarkably long-distance interaction reported here suggests the presence of a novel structure that can facilitate ribosomal frameshifting.
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MESH Headings
- 3' Untranslated Regions/biosynthesis
- 3' Untranslated Regions/chemistry
- 3' Untranslated Regions/genetics
- 3' Untranslated Regions/metabolism
- Avena/cytology
- Avena/virology
- Base Sequence
- Codon, Terminator/genetics
- Conserved Sequence/genetics
- DNA-Directed RNA Polymerases/genetics
- Daucus carota/cytology
- Daucus carota/virology
- Frameshifting, Ribosomal/genetics
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Viral
- Genes, Reporter/genetics
- Genes, Viral/genetics
- Genome, Viral
- Kinetics
- Luteovirus/enzymology
- Luteovirus/genetics
- Molecular Sequence Data
- Mutation/genetics
- Nucleic Acid Conformation
- Open Reading Frames/genetics
- Peptide Chain Initiation, Translational
- RNA, Viral/biosynthesis
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Regulatory Sequences, Nucleic Acid/genetics
- Ribosomes/metabolism
- Virus Replication
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Affiliation(s)
- C P Paul
- Plant Pathology Department, Iowa State University, Ames 50011, USA
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58
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Li Z, Stahl G, Farabaugh PJ. Programmed +1 frameshifting stimulated by complementarity between a downstream mRNA sequence and an error-correcting region of rRNA. RNA (NEW YORK, N.Y.) 2001; 7:275-84. [PMID: 11233984 PMCID: PMC1370085 DOI: 10.1017/s135583820100190x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Like most retroviruses and retrotransposons, the retrotransposon Ty3 expresses its pol gene analog (POL3) as a translational fusion to the upstream gag analog (GAG3). The Gag3-Pol3 fusion occurs by frameshifting during translation of the mRNA that encodes the two separate but overlapping ORFs. We showed previously that the shift occurs by out-of-frame binding of a normal aminoacyl-tRNA in the ribosomal A site caused by an aberrant codonoanticodon interaction in the P site. This event is unlike all previously described programmed translational frameshifts because it does not require tRNA slippage between cognate or near-cognate codons in the mRNA. A sequence of 15 nt distal to the frameshift site stimulates frameshifting 7.5-fold. Here we show that the Ty3 stimulator acts as an unstructured region to stimulate frameshifting. Its function depends on strict spacing from the site of frameshifting. Finally, the stimulator increases frameshifting dependent on sense codon-induced pausing, but has no effect on frameshifting dependent on pauses induced by nonsense codons. Complementarity between the stimulator and a portion of the accuracy center of the ribosome, Helix 18, implies that the stimulator may directly disrupt error correction by the ribosome.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Frameshifting, Ribosomal
- Fusion Proteins, gag-pol/genetics
- Fusion Proteins, gag-pol/metabolism
- Models, Molecular
- Molecular Sequence Data
- Mutation, Missense
- Nucleic Acid Conformation
- Plasmids
- Protein Biosynthesis
- RNA Viruses/physiology
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Retroelements/genetics
- Ribosomes/genetics
- Ribosomes/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
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Affiliation(s)
- Z Li
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore 21250, USA
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59
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Ivanov IP, Gesteland RF, Atkins JF. Antizyme expression: a subversion of triplet decoding, which is remarkably conserved by evolution, is a sensor for an autoregulatory circuit. Nucleic Acids Res 2000; 28:3185-96. [PMID: 10954585 PMCID: PMC110703 DOI: 10.1093/nar/28.17.3185] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2000] [Revised: 06/30/2000] [Accepted: 07/07/2000] [Indexed: 12/11/2022] Open
Abstract
The efficiency of programmed ribosomal frameshifting in decoding antizyme mRNA is the sensor for an autoregulatory circuit that controls cellular polyamine levels in organisms ranging from the yeast Schizosaccharomyces pombe to Drosophila to mammals. Comparison of the frameshift sites and flanking stimulatory signals in many organisms now permits a reconstruction of the likely evolutionary path of the remarkably conserved mRNA sequences involved in the frameshifting.
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Affiliation(s)
- I P Ivanov
- Department of Human Genetics, University of Utah, 15N 2030E, Room 7410, Salt Lake City, UT 84112-5330, USA
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60
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Abstract
In this article, I review how our research on RNA began, how it led us to demonstrate the single-stranded nature of RNA, and the ways in which it differs from double-stranded DNA. It was based on the development of a method for the isolation of undegraded rRNA and the observation that in rRNA preparations due to their viscosity behavior resemble a flexible, contractile coil. In support of this assumption, birefringence of flow measurements showed that rRNA solutions gave moderate positive values, which disappeared upon addition of salt. This is in contrast with DNA solutions where considerable negative birefringence persists even in the presence of salt. Further studies on RNA showed a close correlation of the ionic strength dependencies of optical rotation, optical density and hydrodynamic properties. These early results indicated that rRNA and tRNA possess a significant secondary structure. I then review the basis of the hairpin model for the secondary structure of RNA and finally, summarize current understanding of the tertiary structure of RNA.
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MESH Headings
- History, 20th Century
- Israel
- Nucleic Acid Conformation
- Osmolar Concentration
- RNA/chemistry
- RNA/history
- RNA/isolation & purification
- RNA, Bacterial/chemistry
- RNA, Bacterial/history
- RNA, Bacterial/isolation & purification
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/history
- RNA, Ribosomal/isolation & purification
- RNA, Transfer/chemistry
- RNA, Transfer/history
- RNA, Viral/chemistry
- RNA, Viral/history
- Viscosity
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Affiliation(s)
- U Z Littauer
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel.
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61
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Giedroc DP, Theimer CA, Nixon PL. Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. J Mol Biol 2000; 298:167-85. [PMID: 10764589 PMCID: PMC7126452 DOI: 10.1006/jmbi.2000.3668] [Citation(s) in RCA: 198] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Programmed -1 ribosomal frameshifting has become the subject of increasing interest over the last several years, due in part to the ubiquitous nature of this translational recoding mechanism in pathogenic animal and plant viruses. All cis-acting frameshift signals encoded in mRNAs are minimally composed of two functional elements: a heptanucleotide "slippery sequence" conforming to the general form X XXY YYZ, followed by an RNA structural element, usually an H-type RNA pseudoknot, positioned an optimal number of nucleotides (5 to 9) downstream. The slippery sequence itself promotes a low level ( approximately 1 %) of frameshifting; however, downstream pseudoknots stimulate this process significantly, in some cases up to 30 to 50 %. Although the precise molecular mechanism of stimulation of frameshifting remains poorly understood, significant advances have been made in our knowledge of the three-dimensional structures, thermodynamics of folding, and functional determinants of stimulatory RNA pseudoknots derived from the study of several well-characterized frameshift signals. These studies are summarized here and provide new insights into the structural requirements and mechanism of programmed -1 ribosomal frameshifting.
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MESH Headings
- Base Sequence
- Cations/metabolism
- Cations/pharmacology
- Frameshifting, Ribosomal/genetics
- Infectious bronchitis virus/genetics
- Luteovirus/genetics
- Mammary Tumor Virus, Mouse/genetics
- Models, Genetic
- Nucleic Acid Conformation/drug effects
- RNA Stability/drug effects
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Retroviruses, Simian/genetics
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Affiliation(s)
- D P Giedroc
- Department of Biochemistry and Biophysics, Center for Macromolecular Design, Texas A&M University, TX 77843-2128, USA.
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62
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Theimer CA, Giedroc DP. Contribution of the intercalated adenosine at the helical junction to the stability of the gag-pro frameshifting pseudoknot from mouse mammary tumor virus. RNA (NEW YORK, N.Y.) 2000; 6:409-21. [PMID: 10744025 PMCID: PMC1369923 DOI: 10.1017/s1355838200992057] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The mouse mammary tumor virus (MMTV) gag-pro frameshifting pseudoknot is an H-type RNA pseudoknot that contains an unpaired adenosine (A14) at the junction of the two helical stems required for efficient frameshifting activity. The thermodynamics of folding of the MMTV vpk pseudoknot have been compared with a structurally homologous mutant RNA containing a G x U to G-C substitution at the helical junction (U13C RNA), and an A14 deletion mutation in that context (U13CdeltaA14 RNA). Dual wavelength optical melting and differential scanning calorimetry reveal that the unpaired adenosine contributes 0.7 (+/-0.2) kcal mol(-1) at low salt and 1.4 (+/-0.2) kcal mol(-1) to the stability (deltaG(0)37) at 1 M NaCl. This stability increment derives from a favorable enthalpy contribution to the stability deltadeltaH = 6.6 (+/-2.1) kcal mol(-1) with deltadeltaG(0)37 comparable to that predicted for the stacking of a dangling 3' unpaired adenosine on a G-C or G x U base pair. Group 1A monovalent ions, NH4+, Mg2+, and Co(NH3)6(3+) ions stabilize the A14 and deltaA14 pseudoknots to largely identical extents, revealing that the observed differences in stability in these molecules do not derive from a differential or specific accumulation of ions in the A14 versus deltaA14 pseudoknots. Knowledge of this free energy contribution may facilitate the prediction of RNA pseudoknot formation from primary nucleotide sequence (Gultyaev et al., 1999, RNA 5:609-617).
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Affiliation(s)
- C A Theimer
- Department of Biochemistry and Biophysics, Center for Macromolecular Design, Texas A&M University, College Station 77843-2128, USA
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63
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Marczinke B, Hagervall T, Brierley I. The Q-base of asparaginyl-tRNA is dispensable for efficient -1 ribosomal frameshifting in eukaryotes. J Mol Biol 2000; 295:179-91. [PMID: 10623518 PMCID: PMC7126154 DOI: 10.1006/jmbi.1999.3361] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The frameshift signal of the avian coronavirus infectious bronchitis virus (IBV) contains two cis-acting signals essential for efficient frameshifting, a heptameric slippery sequence (UUUAAAC) and an RNA pseudoknot structure located downstream. The frameshift takes place at the slippery sequence with the two ribosome-bound tRNAs slipping back simultaneously by one nucleotide from the zero phase (U UUA AAC) to the -1 phase (UUU AAA). Asparaginyl-tRNA, which decodes the A-site codon AAC, has the modified base Q at the wobble position of the anticodon (5' QUU 3') and it has been speculated that Q may be required for frameshifting. To test this, we measured frameshifting in cos cells that had been passaged in growth medium containing calf serum or horse serum. Growth in horse serum, which contains no free queuine, eliminates Q from the cellular tRNA population upon repeated passage. Over ten cell passages, however, we found no significant difference in frameshift efficiency between the cell types, arguing against a role for Q in frameshifting. We confirmed that the cells cultured in horse serum were devoid of Q by purifying tRNAs and assessing their Q-content by tRNA transglycosylase assays and coupled HPLC-mass spectroscopy. Supplementation of the growth medium of cells grown either on horse serum or calf serum with free queuine had no effect on frameshifting either. These findings were recapitulated in an in vitro system using rabbit reticulocyte lysates that had been largely depleted of endogenous tRNAs and resupplemented with Q-free or Q-containing tRNA populations. Thus Q-base is not required for frameshifting at the IBV signal and some other explanation is required to account for the slipperiness of eukaryotic asparaginyl-tRNA.
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Key Words
- ribosomal frameshifting
- trna anticodon modification
- q-base
- rna pseudoknot
- asparaginyl-trna
- ibv, infectious bronchitis virus
- rsv, rous sarcoma virus
- hiv, human immunodeficiency virus
- blv, bovine leukaemia virus
- htlv-1, human t-cell leukaemia virus type 1
- tgt, trna transglycosylase
- rrl, rabbit reticulocyte lysate
- hs, horse serum
- fcs, fetal calf serum
- bhk, baby hamster kidney
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Affiliation(s)
- Beate Marczinke
- Division of Virology Department of Pathology University of Cambridge Tennis Court Road, Cambridge CB2 1QP, UK
| | - Tord Hagervall
- Department of Microbiology University of Umeå S-90187 Umeå, Sweden
| | - Ian Brierley
- Division of Virology Department of Pathology University of Cambridge Tennis Court Road, Cambridge CB2 1QP, UK
- Corresponding author
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64
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Alam SL, Atkins JF, Gesteland RF. Programmed ribosomal frameshifting: much ado about knotting! Proc Natl Acad Sci U S A 1999; 96:14177-9. [PMID: 10588670 PMCID: PMC33937 DOI: 10.1073/pnas.96.25.14177] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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65
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Kim YG, Su L, Maas S, O'Neill A, Rich A. Specific mutations in a viral RNA pseudoknot drastically change ribosomal frameshifting efficiency. Proc Natl Acad Sci U S A 1999; 96:14234-9. [PMID: 10588689 PMCID: PMC24420 DOI: 10.1073/pnas.96.25.14234] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many viruses regulate protein synthesis by -1 ribosomal frameshifting using an RNA pseudoknot. Frameshifting is vital for viral reproduction. Using the information gained from the recent high-resolution crystal structure of the beet western yellow virus pseudoknot, a systematic mutational analysis has been carried out in vitro and in vivo. We find that specific nucleotide tertiary interactions at the junction between the two stems of the pseudoknot are crucial. A triplex is found between stem 1 and loop 2, and triplex interactions are required for frameshifting function. For some mutations, loss of one hydrogen bond is sufficient to abolish frameshifting. Furthermore, mutations near the 5' end of the pseudoknot can increase frameshifting by nearly 300%, possibly by modifying ribosomal contacts. It is likely that the selection of suitable mutations can thus allow viruses to adjust frameshifting efficiencies and thereby regulate protein synthesis in response to environmental change.
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Affiliation(s)
- Y G Kim
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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66
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Sundararajan A, Michaud WA, Qian Q, Stahl G, Farabaugh PJ. Near-cognate peptidyl-tRNAs promote +1 programmed translational frameshifting in yeast. Mol Cell 1999; 4:1005-15. [PMID: 10635325 DOI: 10.1016/s1097-2765(00)80229-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Translational frameshifting is a ubiquitous, if rare, form of alternative decoding in which ribosomes spontaneously shift reading frames during translation elongation. In studying +1 frameshifting in Ty retrotransposons of the yeast S. cerevisiae, we previously showed that unusual P site tRNAs induce frameshifting. The frameshift-inducing tRNAs we show here are near-cognates for the P site codon. Their abnormal decoding induces frameshifting in either of two ways: weak codon-anticodon pairing allows the tRNA to disengage from the mRNA and slip +1, or an unusual codon-anticodon structure interferes with cognate in-frame decoding allowing out-of-frame decoding in the A site. We draw parallels between this mechanism and a proposed mechanism of frameshift suppression by mutant tRNAs.
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Affiliation(s)
- A Sundararajan
- Department of Biological Sciences, University of Maryland, Baltimore County 21250, USA
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Liphardt J, Napthine S, Kontos H, Brierley I. Evidence for an RNA pseudoknot loop-helix interaction essential for efficient -1 ribosomal frameshifting. J Mol Biol 1999; 288:321-35. [PMID: 10329145 PMCID: PMC7141562 DOI: 10.1006/jmbi.1999.2689] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
RNA pseudoknots are structural elements that participate in a variety of biological processes. At -1 ribosomal frameshifting sites, several types of pseudoknot have been identified which differ in their organisation and functionality. The pseudoknot found in infectious bronchitis virus (IBV) is typical of those that possess a long stem 1 of 11-12 bp and a long loop 2 (30-164 nt). A second group of pseudoknots are distinguishable that contain stems of only 5 to 7 bp and shorter loops. The NMR structure of one such pseudoknot, that of mouse mammary tumor virus (MMTV), has revealed that it is kinked at the stem 1-stem 2 junction, and that this kinked conformation is essential for efficient frameshifting. We recently investigated the effect on frameshifting of modulating stem 1 length and stability in IBV-based pseudoknots, and found that a stem 1 with at least 11 bp was needed for efficient frameshifting. Here, we describe the sequence manipulations that are necessary to bypass the requirement for an 11 bp stem 1 and to convert a short non-functional IBV-derived pseudoknot into a highly efficient, kinked frameshifter pseudoknot. Simple insertion of an adenine residue at the stem 1-stem 2 junction (an essential feature of a kinked pseudoknot) was not sufficient to create a functional pseudoknot. An additional change was needed: efficient frameshifting was recovered only when the last nucleotide of loop 2 was changed from a G to an A. The requirement for an A at the end of loop 2 is consistent with a loop-helix contact similar to those described in other RNA tertiary structures. A mutational analysis of both partners of the proposed interaction, the loop 2 terminal adenine residue and two G.C pairs near the top of stem 1, revealed that the interaction was essential for efficient frameshifting. The specific requirement for a 3'-terminal A residue was lost when loop 2 was increased from 8 to 14 nt, suggesting that the loop-helix contact may be required only in those pseudoknots with a short loop 2.
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Affiliation(s)
- Jan Liphardt
- Division of Virology Department of Pathology University of Cambridge Tennis Court Road, Cambridge CB2 1QP, UK
| | - Sawsan Napthine
- Division of Virology Department of Pathology University of Cambridge Tennis Court Road, Cambridge CB2 1QP, UK
| | - Harry Kontos
- Division of Virology Department of Pathology University of Cambridge Tennis Court Road, Cambridge CB2 1QP, UK
| | - Ian Brierley
- Division of Virology Department of Pathology University of Cambridge Tennis Court Road, Cambridge CB2 1QP, UK
- Corresponding author
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