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Chang KC, Wen JD. Programmed -1 ribosomal frameshifting from the perspective of the conformational dynamics of mRNA and ribosomes. Comput Struct Biotechnol J 2021; 19:3580-3588. [PMID: 34257837 PMCID: PMC8246090 DOI: 10.1016/j.csbj.2021.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 11/01/2022] Open
Abstract
Programmed -1 ribosomal frameshifting (-1 PRF) is a translation mechanism that regulates the relative expression level of two proteins encoded on the same messenger RNA (mRNA). This regulation is commonly used by viruses such as coronaviruses and retroviruses but rarely by host human cells, and for this reason, it has long been considered as a therapeutic target for antiviral drug development. Understanding the molecular mechanism of -1 PRF is one step toward this goal. Minus-one PRF occurs with a certain efficiency when translating ribosomes encounter the specialized mRNA signal consisting of the frameshifting site and a downstream stimulatory structure, which impedes translocation of the ribosome. The impeded ribosome can still undergo profound conformational changes to proceed with translocation; however, some of these changes may be unique and essential to frameshifting. In addition, most stimulatory structures exhibit conformational dynamics and sufficient mechanical strength, which, when under the action of ribosomes, may in turn further promote -1 PRF efficiency. In this review, we discuss how the dynamic features of ribosomes and mRNA stimulatory structures may influence the occurrence of -1 PRF and propose a hypothetical frameshifting model that recapitulates the role of conformational dynamics.
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Affiliation(s)
- Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, CA 94158, United States
| | - Jin-Der Wen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
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Dynamic combinatorial chemistry as a rapid method for discovering sequence-selective RNA-binding compounds. Methods Enzymol 2019; 623:67-84. [PMID: 31239058 DOI: 10.1016/bs.mie.2019.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The ever-growing number of RNA species that are recognized as having a role in human disease is driving a demand for novel molecular probes and therapeutics. Producing sequence-selective RNA-binding molecules remains a substantial challenge, however. One approach that has been successful in producing molecules with high affinity and specificity for disease-relevant RNAs is the use of dynamic combinatorial chemistry, a fragment-based method in which fragments combine reversibly in the presence of the target. We describe methods for the design, synthesis, and screening of dynamic combinatorial libraries targeting RNA.
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Cardno TS, Shimaki Y, Sleebs BE, Lackovic K, Parisot JP, Moss RM, Crowe-McAuliffe C, Mathew SF, Edgar CD, Kleffmann T, Tate WP. HIV-1 and Human PEG10 Frameshift Elements Are Functionally Distinct and Distinguished by Novel Small Molecule Modulators. PLoS One 2015; 10:e0139036. [PMID: 26447468 PMCID: PMC4598141 DOI: 10.1371/journal.pone.0139036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 09/07/2015] [Indexed: 11/19/2022] Open
Abstract
Frameshifting during translation of viral or in rare cases cellular mRNA results in the synthesis of proteins from two overlapping reading frames within the same mRNA. In HIV-1 the protease, reverse transcriptase, and integrase enzymes are in a second reading frame relative to the structural group-specific antigen (gag), and their synthesis is dependent upon frameshifting. This ensures that a strictly regulated ratio of structural proteins and enzymes, which is critical for HIV-1 replication and viral infectivity, is maintained during protein synthesis. The frameshift element in HIV-1 RNA is an attractive target for the development of a new class of anti HIV-1 drugs. However, a number of examples are now emerging of human genes using −1 frameshifting, such as PEG10 and CCR5. In this study we have compared the HIV-1 and PEG10 frameshift elements and shown they have distinct functional characteristics. Frameshifting occurs at several points within each element. Moreover, frameshift modulators that were isolated by high-throughput screening of a library of 114,000 lead-like compounds behaved differently with the PEG10 frameshift element. The most effective compounds affecting the HIV-1 element enhanced frameshifting by 2.5-fold at 10 μM in two different frameshift reporter assay systems. HIV-1 protease:gag protein ratio was affected by a similar amount in a specific assay of virally-infected cultured cell, but the modulation of frameshifting of the first-iteration compounds was not sufficient to show significant effects on viral infectivity. Importantly, two compounds did not affect frameshifting with the human PEG10 element, while one modestly inhibited rather than enhanced frameshifting at the human element. These studies indicate that frameshift elements have unique characteristics that may allow targeting of HIV-1 and of other viruses specifically for development of antiviral therapeutic molecules without effect on human genes like PEG10 that use the same generic mechanism.
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Affiliation(s)
- Tony S. Cardno
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Yosuke Shimaki
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Kurt Lackovic
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - John P. Parisot
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Rebecca M. Moss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | | | - Suneeth F. Mathew
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Torsten Kleffmann
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Centre for Protein Research, University of Otago, Dunedin, New Zealand
| | - Warren P. Tate
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- * E-mail:
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4
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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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Wang QS, Jan E. Switch from cap- to factorless IRES-dependent 0 and +1 frame translation during cellular stress and dicistrovirus infection. PLoS One 2014; 9:e103601. [PMID: 25089704 PMCID: PMC4121135 DOI: 10.1371/journal.pone.0103601] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 07/03/2014] [Indexed: 11/18/2022] Open
Abstract
Internal ribosome entry sites (IRES) are utilized by a subset of cellular and viral mRNAs to initiate translation during cellular stress and virus infection when canonical cap-dependent translation is compromised. The intergenic region (IGR) IRES of the Dicistroviridae uses a streamlined mechanism in which it can directly recruit the ribosome in the absence of initiation factors and initiates translation using a non-AUG codon. A subset of IGR IRESs including that from the honey bee viruses can also direct translation of an overlapping +1 frame gene. In this study, we systematically examined cellular conditions that lead to IGR IRES-mediated 0 and +1 frame translation in Drosophila S2 cells. Towards this, a novel bicistronic reporter that exploits the 2A “stop-go” peptide was developed to allow the detection of IRES-mediated translation in vivo. Both 0 and +1 frame translation by the IGR IRES are stimulated under a number of cellular stresses and in S2 cells infected by cricket paralysis virus, demonstrating a switch from cap-dependent to IRES-dependent translation. The regulation of the IGR IRES mechanism ensures that both 0 frame viral structural proteins and +1 frame ORFx protein are optimally expressed during virus infection.
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Affiliation(s)
- Qing S. Wang
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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Modulation of stop codon read-through efficiency and its effect on the replication of murine leukemia virus. J Virol 2014; 88:10364-76. [PMID: 24991001 PMCID: PMC4178896 DOI: 10.1128/jvi.00898-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Translational readthrough—suppression of termination at a stop codon—is exploited in the replication cycles of several viruses and represents a potential target for antiviral intervention. In the gammaretroviruses, typified by Moloney murine leukemia virus (MuLV), gag and pol are in the same reading frame, separated by a UAG stop codon, and termination codon readthrough is required for expression of the viral Gag-Pol fusion protein. Here, we investigated the effect on MuLV replication of modulating readthrough efficiency. We began by manipulating the readthrough signal in the context of an infectious viral clone to generate a series of MuLV variants in which readthrough was stimulated or reduced. In carefully controlled infectivity assays, it was found that reducing the MuLV readthrough efficiency only 4-fold led to a marked defect and that a 10-fold reduction essentially abolished replication. However, up to an ∼8.5-fold stimulation of readthrough (up to 60% readthrough) was well tolerated by the virus. These high levels of readthrough were achieved using a two-plasmid system, with Gag and Gag-Pol expressed from separate infectious clones. We also modulated readthrough by silencing expression of eukaryotic release factors 1 and 3 (eRF1 and eRF3) or by introducing aminoglycosides into the cells. The data obtained indicate that gammaretroviruses tolerate a substantial excess of viral Gag-Pol synthesis but are very sensitive to a reduction in levels of this polyprotein. Thus, as is also the case for ribosomal frameshifting, antiviral therapies targeting readthrough with inhibitory agents are likely to be the most beneficial. IMPORTANCE Many pathogenic RNA viruses and retroviruses use ribosomal frameshifting or stop codon readthrough to regulate expression of their replicase enzymes. These translational “recoding” processes are potential targets for antiviral intervention, but we have only a limited understanding of the consequences to virus replication of modulating the efficiency of recoding, particularly for those viruses employing readthrough. In this paper, we describe the first systematic analysis of the effect of increasing or decreasing readthrough efficiency on virus replication using the gammaretrovirus MuLV as a model system. We find unexpectedly that MuLV replication is only slightly inhibited by substantial increases in readthrough frequency, but as with other viruses that use recoding strategies, replication is quite sensitive to even modest reductions. These studies provide insights into both the readthrough process and MuLV replication and have implications for the selection of antivirals against gammaretroviruses.
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Determinants of Moloney murine leukemia virus Gag-Pol and genomic RNA proportions. J Virol 2014; 88:7267-75. [PMID: 24741085 DOI: 10.1128/jvi.03513-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The Moloney murine leukemia virus (MoMLV) ribonucleoprotein complex is composed of an approximately 20:1 mixture of Gag and Gag-Pol polyproteins plus a single genomic RNA (gRNA) dimer. The mechanisms that regulate these proportions are unknown. Here, we examined whether virion proportions of Gag, Gag-Pol, and gRNA were determined by sampling (that is, if they reflected expression ratios or intracellular concentrations) or more specific recruitment. To this end, MoMLV Gag, Gag-Pol, and gRNA were expressed separately or together in various ratios. Varying the expression ratios of Gag and Gag-Pol revealed that Gag-Pol incorporation was stochastic and that the conserved 20:1 Gag/Gag-Pol ratio coincided with maximal particle production. When skewed expression ratios resulted in excess Gag-Pol, the released virions maintained the intracellular Gag/Gag-Pol ratios and the infectivity per virion was largely maintained, but virion production decreased sharply with high levels of Gag-Pol. The determinants of gRNA proportions were addressed by manipulating the amounts and contexts of functional nucleocapsid (NC) and the ratios of Gag to gRNA. The results showed that the NC domain of either Gag or Gag-Pol could provide gRNA packaging functions equally well. Unlike Gag-Pol, gRNA incorporation was saturable. An upper limit of gRNA incorporation was observed, and particle production was not disrupted by excess gRNA expression. These results indicate that the determinants of Gag/Gag-Pol proportions differ from those for Gag/gRNA. On the basis of the assumption that MoMLV evolved to produce virion components in optimal proportions, these data provide a means of estimating the proportion of unspliced MoMLV RNA that serves as genomic RNA. IMPORTANCE Viruses assemble their progeny from within the cells that they parasitize, where they must sort through a rich milieu of host proteins and nucleic acids to gather together their own building blocks, which are also proteins and nucleic acids. The research described here addresses whether or not the proportions of viral proteins and nucleic acids that are brought together to form a retroviral particle are determined by random sampling from the cell-and thus dictated by the components' availabilities within the cell-or if the amounts of each molecule are specified by the virus replication process. The results indicated that protein components of the murine retrovirus studied here are recruited by chance but that a specific counting mechanism defines the amount of nucleic acid incorporated into each progeny virion.
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Anti-frameshifting ligand reduces the conformational plasticity of the SARS virus pseudoknot. J Am Chem Soc 2014; 136:2196-9. [PMID: 24446874 DOI: 10.1021/ja410344b] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Programmed -1 ribosomal frameshifting (-1 PRF) stimulated by mRNA pseudoknots regulates gene expression in many viruses, making pseudoknots potential targets for anti-viral drugs. The mechanism by which pseudoknots trigger -1 PRF, however, remains controversial, with several competing models. Recent work showed that high -1 PRF efficiency was linked to high pseudoknot conformational plasticity via the formation of alternate conformers. We tested whether pseudoknots bound with an anti-frameshifting ligand exhibited a similar correlation between conformational plasticity and -1 PRF efficiency by measuring the effects of a ligand that was found to inhibit -1 PRF in the SARS coronavirus on the conformational dynamics of the SARS pseudoknot. Using single-molecule force spectroscopy to unfold pseudoknots mechanically, we found that the ligand binding effectively abolished the formation of alternate conformers. This result extends the connection between -1 PRF and conformational dynamics and, moreover, suggests that targeting the conformational dynamics of pseudoknots may be an effective strategy for anti-viral drug design.
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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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Impact of gag genetic determinants on virological outcome to boosted lopinavir-containing regimen in HIV-2-infected patients. AIDS 2013; 27:69-80. [PMID: 23018441 DOI: 10.1097/qad.0b013e32835a10d8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE This study investigated the impact on virological outcome of the gag cleavage sites and the protease-coding region mutations in protease inhibitor-naive and protease inhibitor-experienced patients infected with HIV-2 receiving lopinavir (LPV) containing regimen. METHODS Baseline gag and protease-coding region were sequenced in 46 HIV-2 group A-infected patients receiving lopinavir. Virological response was defined as plasma viral load less than 100 copies/ml at month 3. Associations between virological response and frequencies of mutations in gag [matrix/capsid (CA), CA/p2, p2/nucleocapsid (NC), NC/p1, p1/p6] and gag-pol (NC/p6) cleavage site and protease-coding region, with respect to the HIV-2ROD strain, were tested using Fisher's exact test. RESULTS Virological response occurred in 14 of 17 (82%) protease inhibitor-naive and 17 of 29 (59%) protease inhibitor-experienced patients. Virological failure was associated with higher baseline viral load (median: 6765 versus 1098 copies/ml, P = 0.02). More protease-coding region mutations were observed in protease inhibitor-experienced compared with protease inhibitor-naive patients (median: 8 versus 5, P = 0.003). In protease inhibitor-naive patients, T435A (NC/p6), V447M (p1/p6), and Y14H (protease-coding region) were associated with virological failure (P = 0.011, P = 0.033, P = 0.022, respectively). T435A and V447M were associated with Y14H (P = 0.018, P = 0.039, respectively). In protease inhibitor-experienced patients, D427E (NC/p1) was associated with virological response (P = 0.014). A430V (NC/p1) and I82F (protease-coding region) were associated with virological failure (P = 0.046, P = 0.050, respectively). Mutations at position 430 were associated with a higher number of mutations in protease-coding region (median: 10 versus 7, P = 0.008). CONCLUSION We have demonstrated, for the first time, an association between gag, gag-pol cleavage site and protease-coding region mutations, with distinct profiles between protease inhibitor-naive and protease inhibitor-experienced patients. These mutations might impact the virological outcome of HIV-2-infected patients receiving LPV-containing regimen.
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Ishimaru D, Plant EP, Sims AC, Yount BL, Roth BM, Eldho NV, Pérez-Alvarado GC, Armbruster DW, Baric RS, Dinman JD, Taylor DR, Hennig M. RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus. Nucleic Acids Res 2012; 41:2594-608. [PMID: 23275571 PMCID: PMC3575852 DOI: 10.1093/nar/gks1361] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem–loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further in vitro analysis revealed that SARS-CoV RNA dimers assemble through ‘kissing’ loop–loop interactions. We also show that loop–loop kissing complex formation becomes more efficient at physiological temperature and in the presence of magnesium. When the palindromic sequence was mutated, in vitro RNA dimerization was abolished, and frameshifting was reduced from 15 to 5.7%. Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. These results suggest that the homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that loop–loop kissing interactions involving Stem 3 modulate -1 PRF and play a role in subgenomic and full-length RNA synthesis.
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Affiliation(s)
- Daniella Ishimaru
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
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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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Modulation of ribosomal frameshifting frequency and its effect on the replication of Rous sarcoma virus. J Virol 2012; 86:11581-94. [PMID: 22896611 DOI: 10.1128/jvi.01846-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Programmed -1 ribosomal frameshifting is widely used in the expression of RNA virus replicases and represents a potential target for antiviral intervention. There is interest in determining the extent to which frameshifting efficiency can be modulated before virus replication is compromised, and we have addressed this question using the alpharetrovirus Rous sarcoma virus (RSV) as a model system. In RSV, frameshifting is essential in the production of the Gag-Pol polyprotein from the overlapping gag and pol coding sequences. The frameshift signal is composed of two elements, a heptanucleotide slippery sequence and, just downstream, a stimulatory RNA structure that has been proposed to be an RNA pseudoknot. Point mutations were introduced into the frameshift signal of an infectious RSV clone, and virus replication was monitored following transfection and subsequent infection of susceptible cells. The introduced mutations were designed to generate a range of frameshifting efficiencies, yet with minimal impact on encoded amino acids. Our results reveal that point mutations leading to a 3-fold decrease in frameshifting efficiency noticeably reduce virus replication and that further reduction is severely inhibitory. In contrast, a 3-fold stimulation of frameshifting is well tolerated. These observations suggest that small-molecule inhibitors of frameshifting are likely to have potential as agents for antiviral intervention. During the course of this work, we were able to confirm, for the first time in vivo, that the RSV stimulatory RNA is indeed an RNA pseudoknot but that the pseudoknot per se is not absolutely required for virus viability.
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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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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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16
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Mutational patterns in the frameshift-regulating site of HIV-1 selected by protease inhibitors. Med Microbiol Immunol 2011; 201:213-8. [PMID: 22200908 DOI: 10.1007/s00430-011-0224-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Indexed: 12/29/2022]
Abstract
Sustained suppression of viral replication in HIV-1 infected patients is especially hampered by the emergence of HIV-1 drug resistance. The mechanisms of drug resistance mainly involve mutations directly altering the interaction of viral enzymes and inhibitors. However, protease inhibitors do not only select for mutations in the protease but also for mutations in the precursor Gag and Pol proteins. In this study, we analysed the frameshift-regulating site of HIV-1 subtype B isolates, which also encodes for Gag and Pol proteins, classified as either treatment-naïve (TN) or protease inhibitor resistant (PI-R). HIV-1 Gag cleavage site mutations (G435E, K436N, I437V, L449F/V) especially correlated with protease inhibitor resistance mutations, but also Pol cleavage site mutations (D05G, D05S) could be assigned to specific protease resistance profiles. Additionally, two Gag non-cleavage site mutations (S440F, H441P) were observed more often in HIV-1 isolates carrying protease resistance mutations. However, in dual luciferase assays, the frameshift efficiencies of specific clones did not reveal any effect from these mutations. Nevertheless, two patterns of mutations modestly increased the frameshift rates in vitro, but were not specifically accumulating in PI-resistant HIV-1 isolates. In summary, HIV-1 Gag cleavage site mutations were dominantly selected in PI-resistant HIV-1 isolates but also Pol cleavage site mutations influenced resistance profiles in the protease. Additionally, Gag non-cleavage site mutations accumulated in PI-resistant HIV-1 isolates, but were not related to an increased frameshift efficiency.
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17
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Ghosn J, Delaugerre C, Flandre P, Galimand J, Cohen-Codar I, Raffi F, Delfraissy JF, Rouzioux C, Chaix ML. Polymorphism in Gag gene cleavage sites of HIV-1 non-B subtype and virological outcome of a first-line lopinavir/ritonavir single drug regimen. PLoS One 2011; 6:e24798. [PMID: 21949754 PMCID: PMC3176769 DOI: 10.1371/journal.pone.0024798] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 08/22/2011] [Indexed: 11/18/2022] Open
Abstract
Virological failure on a boosted-protease inhibitor (PI/r) first-line triple combination is usually not associated with the detection of resistance mutations in the protease gene. Thus, other resistance pathways are being investigated. First-line PI/r monotherapy is the best model to investigate in vivo if the presence of mutations in the cleavage sites (CS) of gag gene prior to any antiretroviral treatment might influence PI/r efficacy. 83 patients were assigned to initiate antiretroviral treatment with first-line lopinavir/r monotherapy in the randomised Monark trial. We compared baseline sequence of gag CS between patients harbouring B or non-B HIV-1 subtype, and between those who achieved viral suppression and those who experienced virological failure while on LPV/r monotherapy up to Week 96. Baseline sequence of gag CS was available for 82/83 isolates; 81/82 carried at least one substitution in gag CS compared to HXB2 sequence. At baseline, non-B subtype isolates were significantly more likely to harbour mutations in gag CS than B subtype isolates (p<0.0001). Twenty-three patients experienced virological failure while on lopinavir/r monotherapy. The presence of more than two substitutions in p2/NC site at baseline significantly predicted virological failure (p = 0.0479), non-B subtype isolates being more likely to harbour more than two substitutions in this specific site. In conclusion, gag cleavage site was highly polymorphic in antiretroviral-naive patients harbouring a non-B HIV-1 strain. We show that pre-therapy mutations in gag cleavage site sequence were significantly associated with the virological outcome of a first-line LPV/r single drug regimen in the Monark trial.
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Affiliation(s)
- Jade Ghosn
- Paris Descartes University, EA 3620, Necker University Hospital, Paris, France.
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18
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Marcheschi RJ, Tonelli M, Kumar A, Butcher SE. Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication. ACS Chem Biol 2011; 6:857-64. [PMID: 21648432 DOI: 10.1021/cb200082d] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Programmed -1 translational frameshifting is an essential event in the replication cycle of HIV. Frameshifting is required for expression of the viral Pol proteins, and drug-like molecules that target this process may inhibit HIV replication. A small molecule stimulator of HIV-1 frameshifting and inhibitor of viral replication, DB213 (RG501), was previously discovered from a high-throughput screen. However, the mechanistic basis for this compound's effects was unknown, and to date no structural information exists for small molecule effectors of frameshifting. Here, we investigate the binding of DB213 to the frameshift site RNA and have determined the structure of this complex by NMR. Binding of DB213 stabilizes the RNA and increases its melting temperature by 10 °C. The ligand binds to a primary site on the RNA stem-loop, although nonspecific interactions are also detected. The compound binds in the major groove and spans a distance of 9 base pairs. DB213 hydrogen bonds to phosphate groups on opposite sides of the major groove and alters the conformation of a conserved GGA bulge in the RNA. This study may provide a starting point for structure-based optimization of compounds targeting the HIV-1 frameshift site RNA.
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Affiliation(s)
- Ryan J. Marcheschi
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samuel E. Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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19
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Rakauskaite R, Liao PY, Rhodin MHJ, Lee K, Dinman JD. A rapid, inexpensive yeast-based dual-fluorescence assay of programmed--1 ribosomal frameshifting for high-throughput screening. Nucleic Acids Res 2011; 39:e97. [PMID: 21602263 PMCID: PMC3152369 DOI: 10.1093/nar/gkr382] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Programmed −1 ribosomal frameshifting (−1 PRF) is a mechanism that directs elongating ribosomes to shift-reading frame by 1 base in the 5′ direction that is utilized by many RNA viruses. Importantly, rates of −1 PRF are fine-tuned by viruses, including Retroviruses, Coronaviruses, Flavivriuses and in two endogenous viruses of the yeast Saccharomyces cerevisiae, to deliver the correct ratios of different viral proteins for efficient replication. Thus, −1 PRF presents a novel target for antiviral therapeutics. The underlying molecular mechanism of −1 PRF is conserved from yeast to mammals, enabling yeast to be used as a logical platform for high-throughput screens. Our understanding of the strengths and pitfalls of assays to monitor −1 PRF have evolved since the initial discovery of −1 PRF. These include controlling for the effects of drugs on protein expression and mRNA stability, as well as minimizing costs and the requirement for multiple processing steps. Here we describe the development of an automated yeast-based dual fluorescence assay of −1 PRF that provides a rapid, inexpensive automated pipeline to screen for compounds that alter rates of −1 PRF which will help to pave the way toward the discovery and development of novel antiviral therapeutics.
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Affiliation(s)
- Rasa Rakauskaite
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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20
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Ekström JO, Habayeb MS, Srivastava V, Kieselbach T, Wingsle G, Hultmark D. Drosophila Nora virus capsid proteins differ from those of other picorna-like viruses. Virus Res 2011; 160:51-8. [PMID: 21605604 DOI: 10.1016/j.virusres.2011.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/03/2011] [Accepted: 05/06/2011] [Indexed: 01/29/2023]
Abstract
The recently discovered Nora virus from Drosophila melanogaster is a single-stranded RNA virus. Its published genomic sequence encodes a typical picorna-like cassette of replicative enzymes, but no capsid proteins similar to those in other picorna-like viruses. We have now done additional sequencing at the termini of the viral genome, extending it by 455 nucleotides at the 5' end, but no more coding sequence was found. The completeness of the final 12,333-nucleotide sequence was verified by the production of infectious virus from the cloned genome. To identify the capsid proteins, we purified Nora virus particles and analyzed their proteins by mass spectrometry. Our results show that the capsid is built from three major proteins, VP4A, B and C, encoded in the fourth open reading frame of the viral genome. The viral particles also contain traces of a protein from the third open reading frame, VP3. VP4A and B are not closely related to other picorna-like virus capsid proteins in sequence, but may form similar jelly roll folds. VP4C differs from the others and is predicted to have an essentially α-helical conformation. In a related virus, identified from EST database sequences from Nasonia parasitoid wasps, VP4C is encoded in a separate open reading frame, separated from VP4A and B by a frame-shift. This opens a possibility that VP4C is produced in non-equimolar quantities. Altogether, our results suggest that the Nora virus capsid has a different protein organization compared to the order Picornavirales.
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Affiliation(s)
- Jens-Ola Ekström
- Department of Molecular Biology, Umeå University, S-901 87 Umeå, Sweden.
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21
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Palde PB, Ofori LO, Gareiss PC, Lerea J, Miller BL. Strategies for recognition of stem-loop RNA structures by synthetic ligands: application to the HIV-1 frameshift stimulatory sequence. J Med Chem 2010; 53:6018-27. [PMID: 20672840 DOI: 10.1021/jm100231t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Production of the Gag-Pol polyprotein in human immunodeficiency virus (HIV) requires a -1 ribosomal frameshift, which is directed by a highly conserved RNA stem-loop. Building on our discovery of a set of disulfide-containing peptides that bind this RNA, we describe medicinal chemistry efforts designed to begin to understand the structure-activity relationships and RNA sequence-selectivity relationships associated with these compounds. Additionally, we have prepared analogues incorporating an olefin or saturated hydrocarbon bioisostere of the disulfide moiety, as a first step toward enhancing biostability. The olefin-containing compounds exhibit affinity comparable to the lead disulfide and, importantly, have no discernible toxicity when incubated with human fibroblasts at concentrations up to 1 mM.
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Affiliation(s)
- Prakash B Palde
- Department of Dermatology, University of Rochester, Rochester, NY 14642, USA
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22
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Larrouy L, Chazallon C, Landman R, Capitant C, Peytavin G, Collin G, Charpentier C, Storto A, Pialoux G, Katlama C, Girard PM, Yeni P, Aboulker JP, Brun-Vezinet F, Descamps D. Gag mutations can impact virological response to dual-boosted protease inhibitor combinations in antiretroviral-naïve HIV-infected patients. Antimicrob Agents Chemother 2010; 54:2910-9. [PMID: 20439606 PMCID: PMC2897283 DOI: 10.1128/aac.00194-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 03/23/2010] [Accepted: 04/27/2010] [Indexed: 11/20/2022] Open
Abstract
ANRS 127 was a randomized pilot trial involving naïve patients receiving two dual-boosted protease inhibitor (PI) combinations. Virological response, defined as a plasma HIV RNA level of <50 copies/ml at week 16, occurred in only 41% patients. Low baseline plasma HIV RNA level was the only significant predictor of virological response. The purpose of this study was to investigate the impact on virological response of pretherapy mutations in cleavage sites of gag, gag-pol, and the gag-pol frameshift region. The whole gag gene and protease-coding region were amplified and sequenced at baseline and at week 16 for 48 patients still on the allocated regimen at week 16. No major PI resistance-associated mutations were detected either at baseline or in the 26 patients who did not achieve virological response at week 16. Baseline cleavage site substitutions in the product of the gag open reading frame at positions 128 (p17/p24) (P = 0.04) and 449 (p1/p6(gag)) (P = 0.01) were significantly more frequent in those patients not achieving virological response. Conversely, baseline cleavage site mutation at position 437 (TFP/p6(pol)) was associated with virological response (P = 0.04). In multivariate analysis adjusted for baseline viral load, these 3 substitutions remained independently associated with virological response. We demonstrated here, in vivo, an impact of baseline polymorphic gag mutations on virological response in naïve patients receiving a combination of two protease inhibitors. However, it was not possible to link the substitutions selected under PI selective pressure with virological failure.
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Affiliation(s)
- Lucile Larrouy
- AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Laboratoire de Virologie, Paris F-75018, France, EA 4409, Université Paris-Diderot, Paris 7, Paris, France, INSERM SC10, Villejuif F-94807, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Service de Maladies Infectieuses et Tropicales, Paris F-75018, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Pharmacie, Paris F-75018, France, Université Pierre et Marie Curie-Paris 6, Paris, France, AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et Tropicales, Paris F-75020, France, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris F-75013, France, INSERM UMR 943, Paris, France, AP-HP, Hôpital Saint-Antoine, Service de Maladies Infectieuses et Tropicales, Paris F-75011, France
| | - C. Chazallon
- AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Laboratoire de Virologie, Paris F-75018, France, EA 4409, Université Paris-Diderot, Paris 7, Paris, France, INSERM SC10, Villejuif F-94807, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Service de Maladies Infectieuses et Tropicales, Paris F-75018, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Pharmacie, Paris F-75018, France, Université Pierre et Marie Curie-Paris 6, Paris, France, AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et Tropicales, Paris F-75020, France, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris F-75013, France, INSERM UMR 943, Paris, France, AP-HP, Hôpital Saint-Antoine, Service de Maladies Infectieuses et Tropicales, Paris F-75011, France
| | - R. Landman
- AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Laboratoire de Virologie, Paris F-75018, France, EA 4409, Université Paris-Diderot, Paris 7, Paris, France, INSERM SC10, Villejuif F-94807, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Service de Maladies Infectieuses et Tropicales, Paris F-75018, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Pharmacie, Paris F-75018, France, Université Pierre et Marie Curie-Paris 6, Paris, France, AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et Tropicales, Paris F-75020, France, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris F-75013, France, INSERM UMR 943, Paris, France, AP-HP, Hôpital Saint-Antoine, Service de Maladies Infectieuses et Tropicales, Paris F-75011, France
| | - C. Capitant
- AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Laboratoire de Virologie, Paris F-75018, France, EA 4409, Université Paris-Diderot, Paris 7, Paris, France, INSERM SC10, Villejuif F-94807, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Service de Maladies Infectieuses et Tropicales, Paris F-75018, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Pharmacie, Paris F-75018, France, Université Pierre et Marie Curie-Paris 6, Paris, France, AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et Tropicales, Paris F-75020, France, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris F-75013, France, INSERM UMR 943, Paris, France, AP-HP, Hôpital Saint-Antoine, Service de Maladies Infectieuses et Tropicales, Paris F-75011, France
| | - G. Peytavin
- AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Laboratoire de Virologie, Paris F-75018, France, EA 4409, Université Paris-Diderot, Paris 7, Paris, France, INSERM SC10, Villejuif F-94807, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Service de Maladies Infectieuses et Tropicales, Paris F-75018, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Pharmacie, Paris F-75018, France, Université Pierre et Marie Curie-Paris 6, Paris, France, AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et Tropicales, Paris F-75020, France, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris F-75013, France, INSERM UMR 943, Paris, France, AP-HP, Hôpital Saint-Antoine, Service de Maladies Infectieuses et Tropicales, Paris F-75011, France
| | - G. Collin
- AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Laboratoire de Virologie, Paris F-75018, France, EA 4409, Université Paris-Diderot, Paris 7, Paris, France, INSERM SC10, Villejuif F-94807, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Service de Maladies Infectieuses et Tropicales, Paris F-75018, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Pharmacie, Paris F-75018, France, Université Pierre et Marie Curie-Paris 6, Paris, France, AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et Tropicales, Paris F-75020, France, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris F-75013, France, INSERM UMR 943, Paris, France, AP-HP, Hôpital Saint-Antoine, Service de Maladies Infectieuses et Tropicales, Paris F-75011, France
| | - C. Charpentier
- AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Laboratoire de Virologie, Paris F-75018, France, EA 4409, Université Paris-Diderot, Paris 7, Paris, France, INSERM SC10, Villejuif F-94807, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Service de Maladies Infectieuses et Tropicales, Paris F-75018, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Pharmacie, Paris F-75018, France, Université Pierre et Marie Curie-Paris 6, Paris, France, AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et Tropicales, Paris F-75020, France, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris F-75013, France, INSERM UMR 943, Paris, France, AP-HP, Hôpital Saint-Antoine, Service de Maladies Infectieuses et Tropicales, Paris F-75011, France
| | - A. Storto
- AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Laboratoire de Virologie, Paris F-75018, France, EA 4409, Université Paris-Diderot, Paris 7, Paris, France, INSERM SC10, Villejuif F-94807, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Service de Maladies Infectieuses et Tropicales, Paris F-75018, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Pharmacie, Paris F-75018, France, Université Pierre et Marie Curie-Paris 6, Paris, France, AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et Tropicales, Paris F-75020, France, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris F-75013, France, INSERM UMR 943, Paris, France, AP-HP, Hôpital Saint-Antoine, Service de Maladies Infectieuses et Tropicales, Paris F-75011, France
| | - G. Pialoux
- AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Laboratoire de Virologie, Paris F-75018, France, EA 4409, Université Paris-Diderot, Paris 7, Paris, France, INSERM SC10, Villejuif F-94807, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Service de Maladies Infectieuses et Tropicales, Paris F-75018, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Pharmacie, Paris F-75018, France, Université Pierre et Marie Curie-Paris 6, Paris, France, AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et Tropicales, Paris F-75020, France, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris F-75013, France, INSERM UMR 943, Paris, France, AP-HP, Hôpital Saint-Antoine, Service de Maladies Infectieuses et Tropicales, Paris F-75011, France
| | - C. Katlama
- AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Laboratoire de Virologie, Paris F-75018, France, EA 4409, Université Paris-Diderot, Paris 7, Paris, France, INSERM SC10, Villejuif F-94807, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Service de Maladies Infectieuses et Tropicales, Paris F-75018, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Pharmacie, Paris F-75018, France, Université Pierre et Marie Curie-Paris 6, Paris, France, AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et Tropicales, Paris F-75020, France, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris F-75013, France, INSERM UMR 943, Paris, France, AP-HP, Hôpital Saint-Antoine, Service de Maladies Infectieuses et Tropicales, Paris F-75011, France
| | - P. M. Girard
- AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Laboratoire de Virologie, Paris F-75018, France, EA 4409, Université Paris-Diderot, Paris 7, Paris, France, INSERM SC10, Villejuif F-94807, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Service de Maladies Infectieuses et Tropicales, Paris F-75018, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Pharmacie, Paris F-75018, France, Université Pierre et Marie Curie-Paris 6, Paris, France, AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et Tropicales, Paris F-75020, France, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris F-75013, France, INSERM UMR 943, Paris, France, AP-HP, Hôpital Saint-Antoine, Service de Maladies Infectieuses et Tropicales, Paris F-75011, France
| | - P. Yeni
- AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Laboratoire de Virologie, Paris F-75018, France, EA 4409, Université Paris-Diderot, Paris 7, Paris, France, INSERM SC10, Villejuif F-94807, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Service de Maladies Infectieuses et Tropicales, Paris F-75018, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Pharmacie, Paris F-75018, France, Université Pierre et Marie Curie-Paris 6, Paris, France, AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et Tropicales, Paris F-75020, France, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris F-75013, France, INSERM UMR 943, Paris, France, AP-HP, Hôpital Saint-Antoine, Service de Maladies Infectieuses et Tropicales, Paris F-75011, France
| | - J. P. Aboulker
- AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Laboratoire de Virologie, Paris F-75018, France, EA 4409, Université Paris-Diderot, Paris 7, Paris, France, INSERM SC10, Villejuif F-94807, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Service de Maladies Infectieuses et Tropicales, Paris F-75018, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Pharmacie, Paris F-75018, France, Université Pierre et Marie Curie-Paris 6, Paris, France, AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et Tropicales, Paris F-75020, France, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris F-75013, France, INSERM UMR 943, Paris, France, AP-HP, Hôpital Saint-Antoine, Service de Maladies Infectieuses et Tropicales, Paris F-75011, France
| | - F. Brun-Vezinet
- AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Laboratoire de Virologie, Paris F-75018, France, EA 4409, Université Paris-Diderot, Paris 7, Paris, France, INSERM SC10, Villejuif F-94807, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Service de Maladies Infectieuses et Tropicales, Paris F-75018, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Pharmacie, Paris F-75018, France, Université Pierre et Marie Curie-Paris 6, Paris, France, AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et Tropicales, Paris F-75020, France, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris F-75013, France, INSERM UMR 943, Paris, France, AP-HP, Hôpital Saint-Antoine, Service de Maladies Infectieuses et Tropicales, Paris F-75011, France
| | - D. Descamps
- AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Laboratoire de Virologie, Paris F-75018, France, EA 4409, Université Paris-Diderot, Paris 7, Paris, France, INSERM SC10, Villejuif F-94807, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Service de Maladies Infectieuses et Tropicales, Paris F-75018, France, AP-HP, Groupe Hospitalier Bichat-Claude Bernard, Pharmacie, Paris F-75018, France, Université Pierre et Marie Curie-Paris 6, Paris, France, AP-HP, Hôpital Tenon, Service de Maladies Infectieuses et Tropicales, Paris F-75020, France, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris F-75013, France, INSERM UMR 943, Paris, France, AP-HP, Hôpital Saint-Antoine, Service de Maladies Infectieuses et Tropicales, Paris F-75011, France
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Kobayashi Y, Zhuang J, Peltz S, Dougherty J. Identification of a cellular factor that modulates HIV-1 programmed ribosomal frameshifting. J Biol Chem 2010; 285:19776-84. [PMID: 20418372 DOI: 10.1074/jbc.m109.085621] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Programmed -1 ribosomal frameshifting (PRF) is a distinctive mode of gene expression utilized by some viruses, including human immunodeficiency virus type 1 (HIV-1), to produce multiple proteins from a single mRNA. -1 PRF induces a subset of elongating ribosomes to shift their translational reading frame by 1 base in the 5' direction. The appropriate ratio of Gag to Gag-Pol synthesis is tightly regulated by the PRF signal which promotes ribosomes to shift frame, and even small changes in PRF efficiency, either up or down, have significant inhibitory effects upon virus production, making PRF essential for HIV-1 replication. Although little has been reported about the cellular factors that modulate HIV-1 PRF, the cis-acting elements regulating PRF have been extensively investigated, and the PRF signal of HIV-1 was shown to include a slippery site and frameshift stimulatory signal. Recently, a genome-wide screen performed to identify cellular factors that affect HIV-1 replication demonstrated that down-regulation of eukaryotic release factor 1 (eRF1) inhibited HIV-1 replication. Because of the eRF1 role in translation, we hypothesized that eRF1 is important for HIV-1 PRF. Using a dual luciferase reporter system harboring a HIV-1 PRF signal, results showed that depletion or inhibition of eRF1 enhanced PRF in yeast, rabbit reticulocyte lysates, and mammalian cells. Consistent with the eRF1 role in modulating HIV PRF, depleting eRF1 increased the Gag-Pol to Gag ratio in cells infected with replication-competent virus. The increase in PRF was independent of a proximal termination codon and did not result from increased ribosomal pausing at the slippery site. This is the first time that a cellular factor has been identified which can promote HIV-1 PRF and highlights HIV-1 PRF as essential for replication and an important but under exploited antiviral drug target.
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Affiliation(s)
- Yoshifumi Kobayashi
- Department of Molecular Genetics, Microbiology and Immunology, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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24
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Hong HS, Kim YG, Hohng SC. Single-Molecule FRET Studies on Frameshifting RNA Structures of Human Immunodeficiency Virus. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.04.1021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Achieving a golden mean: mechanisms by which coronaviruses ensure synthesis of the correct stoichiometric ratios of viral proteins. J Virol 2010; 84:4330-40. [PMID: 20164235 DOI: 10.1128/jvi.02480-09] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
In retroviruses and the double-stranded RNA totiviruses, the efficiency of programmed -1 ribosomal frameshifting is critical for ensuring the proper ratios of upstream-encoded capsid proteins to downstream-encoded replicase enzymes. The genomic organizations of many other frameshifting viruses, including the coronaviruses, are very different, in that their upstream open reading frames encode nonstructural proteins, the frameshift-dependent downstream open reading frames encode enzymes involved in transcription and replication, and their structural proteins are encoded by subgenomic mRNAs. The biological significance of frameshifting efficiency and how the relative ratios of proteins encoded by the upstream and downstream open reading frames affect virus propagation has not been explored before. Here, three different strategies were employed to test the hypothesis that the -1 PRF signals of coronaviruses have evolved to produce the correct ratios of upstream- to downstream-encoded proteins. Specifically, infectious clones of the severe acute respiratory syndrome (SARS)-associated coronavirus harboring mutations that lower frameshift efficiency decreased infectivity by >4 orders of magnitude. Second, a series of frameshift-promoting mRNA pseudoknot mutants was employed to demonstrate that the frameshift signals of the SARS-associated coronavirus and mouse hepatitis virus have evolved to promote optimal frameshift efficiencies. Finally, we show that a previously described frameshift attenuator element does not actually affect frameshifting per se but rather serves to limit the fraction of ribosomes available for frameshifting. The findings of these analyses all support a "golden mean" model in which viruses use both programmed ribosomal frameshifting and translational attenuation to control the relative ratios of their encoded proteins.
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26
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Marcheschi RJ, Mouzakis KD, Butcher SE. Selection and characterization of small molecules that bind the HIV-1 frameshift site RNA. ACS Chem Biol 2009; 4:844-54. [PMID: 19673541 DOI: 10.1021/cb900167m] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV-1 requires a -1 translational frameshift to properly synthesize the viral enzymes required for replication. The frameshift mechanism is dependent upon two RNA elements, a seven-nucleotide slippery sequence (UUUUUUA) and a downstream RNA structure. Frameshifting occurs with a frequency of approximately 5%, and increasing or decreasing this frequency may result in a decrease in viral replication. Here, we report the results of a high-throughput screen designed to find small molecules that bind to the HIV-1 frameshift site RNA. Out of 34,500 compounds screened, 202 were identified as positive hits. We show that one of these compounds, doxorubicin, binds the HIV-1 RNA with low micromolar affinity (K(d) = 2.8 microM). This binding was confirmed and localized to the RNA using NMR. Further analysis revealed that this compound increased the RNA stability by approximately 5 degrees C and decreased translational frameshifting by 28% (+/-14%), as measured in vitro.
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Affiliation(s)
- Ryan J. Marcheschi
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Kathryn D. Mouzakis
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Samuel E. Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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27
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Identification of Structural Motifs of RNA Aptamers Interacting with the Stem-loop Sequence at the Gag-pol Junction of HIV-1 RNA. B KOREAN CHEM SOC 2008. [DOI: 10.5012/bkcs.2008.29.11.2227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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28
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Functional consequences of human immunodeficiency virus escape from an HLA-B*13-restricted CD8+ T-cell epitope in p1 Gag protein. J Virol 2008; 83:1018-25. [PMID: 18945768 DOI: 10.1128/jvi.01882-08] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The observed association between HLA-B*13 and control of human immunodeficiency virus type 1 (HIV-1) infection has been linked to the number of Gag-specific HLA-B*13-restricted cytotoxic T-cell (CTL) responses identified. To date, the Gag escape mutations described that result in an in vitro fitness cost to the virus have been located within structural protein p24 only. Here we investigated the hypothesis that CTL escape mutations within other regions of HIV Gag may also reduce viral fitness and contribute to immune control. We analyzed an HLA-B*13-restricted CTL response toward an epitope in p1 Gag, RQANFLGKI(429-437) (RI9), where amino acid variation at Gag residues 436 and 437 is associated with HLA-B*13 expression. In this work, we assessed the impact of amino acid substitutions at these positions on CTL recognition and on HIV-1 fitness. We demonstrated that substitutions I437L and I437M largely abrogate CTL recognition and reduce viral fitness while variants K436R and I437V have only a marginal effect on recognition and fitness. Examination of the patterns of protein synthesis indicated that the loss of fitness in the I437L and I437M mutants is associated with the accumulation of unprocessed Gag precursors. A significant reduction in ribosomal frameshifting efficiency was observed with I437M, suggesting that this mechanism contributes to the observed reduced fitness of this virus. These studies illustrate the apparent trade-off available to the virus between evasion of CTL recognition in p1 Gag and the functional consequences for viral fitness.
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29
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Dulude D, Théberge-Julien G, Brakier-Gingras L, Heveker N. Selection of peptides interfering with a ribosomal frameshift in the human immunodeficiency virus type 1. RNA (NEW YORK, N.Y.) 2008; 14:981-91. [PMID: 18367719 PMCID: PMC2327360 DOI: 10.1261/rna.887008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 02/04/2008] [Indexed: 05/26/2023]
Abstract
The human immunodeficiency virus of type 1 (HIV-1) uses a programmed -1 ribosomal frameshift to produce the precursor of its enzymes, and changes in frameshift efficiency reduce replicative fitness of the virus. We used a fluorescent two-reporter system to screen for peptides that reduce HIV-1 frameshift in bacteria, knowing that the frameshift can be reproduced in Escherichia coli. Expression of one reporter, the green fluorescent protein (GFP), requires the HIV-1 frameshift, whereas the second reporter, the red fluorescent protein (RFP), is used to assess normal translation. A peptide library biased for RNA binding was inserted into the sequence of the protein thioredoxin and expressed in reporter-containing bacteria, which were then screened by fluorescence-activated cell sorting (FACS). We identified peptide sequences that reduce frameshift efficiency by over 50% without altering normal translation. The identified sequences are also active against different frameshift stimulatory signals, suggesting that they bind a target important for frameshifting in general, probably the ribosome. Successful transfer of active sequences to a different scaffold in a eukaryotic test system demonstrates that the anti-frameshift activity of the peptides is neither due to scaffold-dependent conformation nor effects of the scaffold protein itself on frameshifting. The method we describe identifies peptides that will provide useful tools to further study the mechanism of frameshift and may permit the development of lead compounds of therapeutic interest.
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Affiliation(s)
- Dominic Dulude
- Département de Biochimie, Université de Montréal, Montréal H3T 1J4, Québec, Canada
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30
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Staple DW, Venditti V, Niccolai N, Elson-Schwab L, Tor Y, Butcher SE. Guanidinoneomycin B recognition of an HIV-1 RNA helix. Chembiochem 2008; 9:93-102. [PMID: 18058789 PMCID: PMC2782590 DOI: 10.1002/cbic.200700251] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Indexed: 01/16/2023]
Abstract
Aminoglycoside antibiotics are small-molecule drugs that bind RNA. The affinity and specificity of aminoglycoside binding to RNA can be increased through chemical modification, such as guanidinylation. Here, we report the binding of guanidinoneomycin B (GNB) to an RNA helix from the HIV-1 frameshift site. The binding of GNB increases the melting temperature (T(m)) of the frameshift-site RNA by at least 10 degrees C, to a point at which a melting transition is not even observed in 2 M urea. A structure of the complex was obtained by using multidimensional heteronuclear NMR spectroscopic methods. We also used a novel paramagnetic-probe assay to identify the site of GNB binding to the surface of the RNA. GNB makes major-groove contacts to two sets of Watson-Crick bases and is in van der Waals contact with a highly structured ACAA tetraloop. Rings I and II of GNB fit into the major groove and form the binding interface with the RNA, whereas rings III and IV are exposed to the solvent and disordered. The binding of GNB causes a broadening of the major groove across the binding site.
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Affiliation(s)
- David W. Staple
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706 (USA)
| | - Vincenzo Venditti
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, 53100 Siena (Italy)
| | - Neri Niccolai
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, 53100 Siena (Italy)
| | - Lev Elson-Schwab
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093 (USA)
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093 (USA)
| | - Samuel E. Butcher
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706 (USA)
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31
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McNaughton BR, Gareiss PC, Miller BL. Identification of a selective small-molecule ligand for HIV-1 frameshift-inducing stem-loop RNA from an 11,325 member resin bound dynamic combinatorial library. J Am Chem Soc 2007; 129:11306-7. [PMID: 17722919 DOI: 10.1021/ja072114h] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brian R McNaughton
- Department of Dermatology, University of Rochester, Rochester, New York 14642, USA
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32
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Maisonhaute C, Ogereau D, Hua-Van A, Capy P. Amplification of the 1731 LTR retrotransposon in Drosophila melanogaster cultured cells: Origin of neocopies and impact on the genome. Gene 2007; 393:116-26. [PMID: 17382490 DOI: 10.1016/j.gene.2007.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 01/31/2007] [Accepted: 02/01/2007] [Indexed: 10/23/2022]
Abstract
Transposable elements (TEs), represent a large fraction of the eukaryotic genome. In Drosophila melanogaster, about 20% of the genome corresponds to such middle repetitive DNA dispersed sequences. A fraction of TEs is composed of elements showing a retrovirus-like structure, the LTR-retrotransposons, the first TEs to be described in the Drosophila genome. Interestingly, in D. melanogaster embryonic immortal cell culture genomes the copy number of these LTR-retrotransposons was revealed to be higher than the copy number in the Drosophila genome, presumably as the result of transposition of some copies to new genomic locations [Potter, S.S., Brorein Jr., W.J., Dunsmuir, P., Rubin, G.M., 1979. Transposition of elements of the 412, copia and 297 dispersed repeated gene families in Drosophila. Cell 17, 415-427; Junakovic, N., Di Franco, C., Best-Belpomme, M., Echalier, G., 1988. On the transposition of copia-like nomadic elements in cultured Drosophila cells. Chromosoma 97, 212-218]. This suggests that so many transpositions modified the genome organisation and consequently the expression of targeted genes. To understand what has directed the transposition of TEs in Drosophila cell culture genomes, a search to identify the newly transposed copies was undertaken using 1731, a LTR-retrotransposon. A comparison between 1731 full-length elements found in the fly sequenced genome (y(1); cn(1)bw(1), sp(1) stock) and 1731 full-length elements amplified by PCR in the two cell line was done. The resulting data provide evidence that all 1731 neocopies were derived from a single copy slightly active in the Drosophila genome and subsequently strongly activated in cultured cells; and that this active copy is related to a newly evolved genomic variant (Kalmykova, A.I., et al., 2004. Selective expansion of the newly evolved genomic variants of retrotransposon 1731 in the Drosophila genomes. Mol. Biol. Evol. 21, 2281-2289). Moreover, neocopies are shown to be inserted in different sets of genes in the two cell lines suggesting they might be involved in the biological and physiological differences observed between Kc and S2 cell lines.
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Affiliation(s)
- Claude Maisonhaute
- Laboratoire Evolution Génomes et Spéciation, CNRS Bat.13, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
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33
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Girnary R, King L, Robinson L, Elston R, Brierley I. Structure-function analysis of the ribosomal frameshifting signal of two human immunodeficiency virus type 1 isolates with increased resistance to viral protease inhibitors. J Gen Virol 2007; 88:226-235. [PMID: 17170455 DOI: 10.1099/vir.0.82064-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Expression of the pol-encoded proteins of human immunodeficiency virus type 1 (HIV-1) requires a programmed -1 ribosomal frameshift at the junction of the gag and pol coding sequences. Frameshifting takes place at a heptanucleotide slippery sequence, UUUUUUA, and is enhanced by a stimulatory RNA structure located immediately downstream. In patients undergoing viral protease (PR) inhibitor therapy, a p1/p6(gag) L449F cleavage site (CS) mutation is often observed in resistant isolates and frequently generates, at the nucleotide sequence level, a homopolymeric and potentially slippery sequence (UUUUCUU to UUUUUUU). The mutation is located within the stimulatory RNA downstream of the authentic slippery sequence and could act to augment levels of pol-encoded enzymes to counteract the PR deficit. Here, RNA secondary structure probing was employed to investigate the structure of a CS-containing frameshift signal, and the effect of this mutation on ribosomal frameshift efficiency in vitro and in tissue culture cells was determined. A second mutation, a GGG insertion in the loop of the stimulatory RNA that could conceivably lead to resistance by enhancing the activity of the structure, was also tested. It was found, however, that the CS and GGG mutations had only a very modest effect on the structure and activity of the HIV-1 frameshift signal. Thus the increased resistance to viral protease inhibitors seen with HIV-1 isolates containing mutations in the frameshifting signal is unlikely to be accounted for solely by enhancement of frameshift efficiency.
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Affiliation(s)
- Roseanne Girnary
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Louise King
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Laurence Robinson
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Robert Elston
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
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34
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Tschochner M, Schwingel E, Thein C, Wittmann S, Paatz C, Walter H. Superiority of infectivity-based over particle-based methods for quantitation of drug resistant HIV-1 as inocula for cell cultures. J Virol Methods 2006; 141:87-96. [PMID: 17196267 DOI: 10.1016/j.jviromet.2006.11.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Revised: 11/24/2006] [Accepted: 11/28/2006] [Indexed: 10/01/2022]
Abstract
Performance of phenotypic assays and replication capacity assays require normalization of virus input. Therefore, quantitation of HIV-1 in supernatants to inoculate cell cultures is an important step. Since the gold standard for the determination of infectivity, the tissue culture infectious dose 50% (TCID50) is time-consuming, several other methods are in use. This study evaluated methods for the quantitation of drug resistant viruses in cell culture supernatants. The compared methods were based on the detection of viral structural components like genomic RNA or p24 antigen (CA-p24) (particle-based), the determination of reverse transcriptase (RT) activity, and methods based on the detection of viral infectivity like LTR-induced beta-galactosidase (beta-gal) activity and the TCID50 (infectivity-based). Significant correlations were observed between beta-gal activity and TCID50, and between CA-p24 and viral RNA. RT activity did not correlate with any other method. However, RT activity correlated significantly with infectivity when non-resistant subtype-B isolates were analyzed. In contrast to viral infectivity, CA-p24 exhibited a long half life and accumulated in cell culture, resulting in decreasing ratios of infectious virions to CA-p24 over time. As a consequence, relative replication capacities of drug resistant viruses were only determined reliably if the input virus was normalized according to infectivity. In conclusion, RT activity seems to be feasible for non-resistant subtype-B viruses but may be of limited use for non-B subtypes and for drug resistant viruses. Methods determining infectivity are most suitable for quantitation of cell culture inocula, whereas particle-based assays are more appropriate for quantitation of virus production during an experiment.
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Affiliation(s)
- Monika Tschochner
- Institute of Clinical and Molecular Virology, University of Erlangen-Nuremberg, Schlossgarten 4, D-91054 Erlangen, Germany.
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35
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Dulude D, Brakier-Gingras L. [The structure of the frameshift stimulatory signal in HIV-1 RNA: a potential target for the treatment of patients infected with HIV]. Med Sci (Paris) 2006; 22:969-72. [PMID: 17101099 DOI: 10.1051/medsci/20062211969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ribosomal frameshift is used by HIV-1 to synthesize the precursor of its enzymes. The frameshift stimulator is a peculiar structure in the viral messenger RNA coding for this precursor, which increases the probability that this frameshift occurs. It was proposed to be either a triplex structure or an irregular stem-loop. Recently, two NMR groups independently showed that the frameshift stimulatory signal of HIV-1 is an extended stem-loop, with an internal three-purine bulge separating two helical regions. However, it remains unclear how such a structure promotes frameshifting. It is proposed that frameshifting results from a specific interaction between the stimulatory signal and either a hypothetical protein factor or the ribosome. The characterization of the structure of the frameshift stimulatory signal paves the way to the rational design of novel antiviral drugs, which, by binding to this signal, could interfere with frameshifting and viral replication.
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Affiliation(s)
- Dominic Dulude
- Département de Biochimie, Université de Montréal, 2900, Boulevard Edouard-Montpetit, Montréal (Québec) H3T 1J4, Canada
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36
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Brierley I, Dos Ramos FJ. Programmed ribosomal frameshifting in HIV-1 and the SARS-CoV. Virus Res 2005; 119:29-42. [PMID: 16310880 PMCID: PMC7114087 DOI: 10.1016/j.virusres.2005.10.008] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Revised: 07/31/2005] [Accepted: 10/19/2005] [Indexed: 01/11/2023]
Abstract
Ribosomal frameshifting is a mechanism of gene expression used by several RNA viruses to express replicase enzymes. This article focuses on frameshifting in two human pathogens, the retrovirus human immunodeficiency virus type 1 (HIV-1) and the coronavirus responsible for severe acute respiratory syndrome (SARS). The nature of the frameshift signals of HIV-1 and the SARS–CoV will be described and the impact of this knowledge on models of frameshifting will be considered. The role of frameshifting in the replication cycle of the two pathogens and potential antiviral therapies targeting frameshifting will also be discussed.
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Affiliation(s)
- Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.
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37
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Rachidi M, Lopes C, Benichou JC, Hellio R, Maisonhaute C. Virus-like particle formation in Drosophila melanogaster germ cells suggests a complex translational regulation of the retrotransposon cycle and new mechanisms inhibiting transposition. Cytogenet Genome Res 2005; 111:88-95. [PMID: 16093726 DOI: 10.1159/000085675] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2004] [Accepted: 12/23/2004] [Indexed: 11/19/2022] Open
Abstract
Transposition of 1731, a Drosophila melanogaster LTR retrotransposon, was investigated in reproductive organs by RNA, protein and VLP distribution during its life cycle. We detected 1731 transcription in oogonia but not in spermatogonia; in all cells during oogenesis but only in primary spermatocytes; and in ovarian cytoplasm but both in nuclei and cytoplasm of primary spermatocytes. By confocal scanning, we showed that whereas Gag protein appeared in all cytoplasms during oogenesis, in testes Gag detection began in late premeiotic primary spermatocytes and increased in elongating spermatids suggesting distinct mechanisms of 1731 transcription and translation regulation. By electron microscopy, we did not detect 1731 VLPs in ovaries, suggesting a complex post-translational control blocking VLP assembly and transposition. Interestingly, in testes we discovered VLP aggregates in cystic cytoplasm of maturing partially individualized spermatids. In testes, we observed two delays in 1731 product expressions, suggesting a complex temporal control mechanism. Transcriptional/translational delay may be determined by accumulation of 1731 RNAs in primary spermatocyte nuclei. Translational/VLP assembly delay may be determined by post-transductional mechanisms controlling +1 frameshift and Pol-protein degradation. Our results indicated two differential mechanisms inhibiting 1731 transposition in Drosophila melanogaster ovaries and testes. In addition, we proposed a new mechanism for transposition control at the cell cycle level.
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Affiliation(s)
- M Rachidi
- EA 3508 Université Paris 7-Denis Diderot, Paris, France.
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38
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Dulude D, Berchiche YA, Gendron K, Brakier-Gingras L, Heveker N. Decreasing the frameshift efficiency translates into an equivalent reduction of the replication of the human immunodeficiency virus type 1. Virology 2005; 345:127-36. [PMID: 16256163 DOI: 10.1016/j.virol.2005.08.048] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2005] [Revised: 08/23/2005] [Accepted: 08/31/2005] [Indexed: 10/25/2022]
Abstract
The Gag-Pol polyprotein of the human immunodeficiency virus type 1 (HIV-1) is the precursor of the virus enzymatic activities and is produced via a programmed -1 translational frameshift. In this study, we altered the frameshift efficiency by introducing mutations within the slippery sequence and the frameshift stimulatory signal, the two elements that control the frameshift. These mutations decreased the frameshift efficiency to different degrees, ranging from approximately 0.3% to 70% of the wild-type efficiency. These values were mirrored by a reduced incorporation of Gag-Pol into virus-like particles, as assessed by a decrease in the reverse transcriptase activity associated to these particles. Analysis of Gag processing in infectious mutant virions revealed processing defects to various extents, with no clear correlation with frameshift decrease. Nevertheless, the observed frameshift reductions translated into equivalently reduced viral infectivity and replication kinetics. Our results show that even moderate variations in frameshift efficiency, as obtained with mutations in the frameshift stimulatory signal, reduce viral replication. Therapeutic targeting of this structure may therefore result in the attenuation of virus replication and in clinical benefit.
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Affiliation(s)
- Dominic Dulude
- Département de Biochimie, Université de Montréal, 2900 Boul. Edouard-Montpetit, Montréal, Québec, Canada H3T1J4
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39
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Gendron K, Dulude D, Lemay G, Ferbeyre G, Brakier-Gingras L. The virion-associated Gag-Pol is decreased in chimeric Moloney murine leukemia viruses in which the readthrough region is replaced by the frameshift region of the human immunodeficiency virus type 1. Virology 2005; 334:342-52. [PMID: 15780884 DOI: 10.1016/j.virol.2005.01.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Revised: 01/21/2005] [Accepted: 01/31/2005] [Indexed: 01/15/2023]
Abstract
The human immunodeficiency virus type 1 (HIV-1) requires a programmed -1 translational frameshift event to synthesize the precursor of its enzymes, Gag-Pol, when ribosomes from the infected cells translate the full-length viral messenger RNA. Translation of the same RNA according to conventional translational rules produces Gag, the precursor of the structural proteins of the virus. The efficiency of the frameshift controls the ratio of Gag-Pol to Gag, which is critical for viral infectivity. The Moloney murine leukemia virus (MoMuLV) uses a different strategy, the programmed readthrough of a stop codon, to synthesize Gag-Pol. In this study, we investigated whether different forms of the HIV-1 frameshift region can functionally replace the readthrough signal in MoMuLV. Chimeric proviral DNAs were obtained by inserting into the MoMuLV genome the HIV-1 frameshift region encompassing the slippery sequence where the frameshift occurs, followed by the frameshift stimulatory signal. The inserted signal was either a simple stem-loop, previously considered as the stimulatory signal, or a longer bulged helix, now shown to be the complete stimulatory signal, or a mutated version of the complete signal with a three-nucleotide deletion. Although the three chimeric viruses can propagate essentially as the wild-type virus in NIH 3T3 cells, single-round infectivity assays revealed that the infectivity of the chimeric virions is about three to fivefold lower than that of the wild-type virions, depending upon the nature of the frameshift signal. It was also observed that the Gag-Pol to Gag ratio was decreased about two to threefold in chimeric virions. Comparison of the readthrough efficiency of MoMuLV to the HIV-1 frameshift efficiency, by monitoring the expression of a luciferase reporter in cultured cells, revealed that the frameshift efficiencies were only 30-60% of the readthrough efficiency. Altogether, these observations indicate that replacement of the readthrough region of MoMuLV with the frameshift region of HIV-1 results in virions that are replication competent, although less infectious than wild-type MoMuLV. This type of chimera could provide an interesting tool for in vivo studies of novel drugs targeted against the HIV-1 frameshift event.
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Affiliation(s)
- Karine Gendron
- Département de Biochimie, Université de Montréal, 2900, Boulevard Edouard-Montpetit, D-353, Montréal, Québec, Canada H3T 1J4
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40
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Staple DW, Butcher SE. Solution structure and thermodynamic investigation of the HIV-1 frameshift inducing element. J Mol Biol 2005; 349:1011-23. [PMID: 15927637 DOI: 10.1016/j.jmb.2005.03.038] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2005] [Revised: 03/10/2005] [Accepted: 03/14/2005] [Indexed: 10/25/2022]
Abstract
Expression of the HIV reverse transcriptase and other essential viral enzymes requires a -1 translational frameshift. The frameshift event is induced by two highly conserved RNA elements within the HIV-1 mRNA: a UUUUUUA heptamer known as the slippery sequence, and a downstream RNA structure. Here, we report structural and thermodynamic evidence that the HIV-1 frameshift site RNA forms a stem-loop and lower helix separated by a three-purine bulge. We have determined the structure of the 45 nucleotide frameshift site RNA using multidimensional heteronuclear nuclear magnetic resonance (NMR) methods. The upper helix is highly thermostable (T(m)>90 degrees C), forming 11 Watson-Crick base-pairs capped by a stable ACAA tetraloop. The eight base-pair lower helix was found to be only moderately stable (T(m)=47 degrees C). A three-purine bulge separates the highly stable upper helix from the lower helix. Base stacking in the bulge forms a wedge, introducing a 60 degrees bend between the helices. Interestingly, this bend is similar to those seen in a number of frameshift inducing pseudoknots for which structures have been solved. The lower helix must denature to allow the ribosome access to the slippery site, but likely functions as a positioning element that enhances frameshift efficiency.
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Affiliation(s)
- David W Staple
- Department of Biochemistry, University of Wisconsin-Madison, WI 53706, USA
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41
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Paulus C, Ludwig C, Wagner R. Contribution of the Gag-Pol transframe domain p6* and its coding sequence to morphogenesis and replication of human immunodeficiency virus type 1. Virology 2005; 330:271-83. [PMID: 15527852 DOI: 10.1016/j.virol.2004.09.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2004] [Revised: 08/19/2004] [Accepted: 09/13/2004] [Indexed: 10/26/2022]
Abstract
The human immunodeficiency virus type-1 (HIV-1) transframe domain p6* is located between the nucleocapsid protein (NC) and the protease (PR) within the Gag-Pol precursor. This flexible, 68-amino-acid HIV-1 p6* domain has been suggested to negatively interfere with HIV PR activity in vitro proposing a contribution of either the C-terminal p6* tetrapeptide, internal cryptic PR cleavage sites, or a zymogen-related mechanism to a regulated PR activation. To assess these hypotheses in the viral context, a series of recombinant HX10-based provirus constructs has been established with clustered amino acid substitutions throughout the entire p6* coding sequence. Comparative analysis of the mutant proviral clones in different cell culture systems revealed that mutations within the well-conserved amino-terminal p6* region modified the Gag/Gag-Pol ratio and thus resulted in the release of viruses with impaired infectivity. Clustered amino acid substitutions destroying (i) the predicted cryptic PR cleavage sites or (ii) homologies to the pepsinogen propeptide did not influence viral replication in cell culture, whereas substitutions of the carboxyl-terminal p6* residues 62 to 68 altering proper release of the mature PR from the Gag-Pol precursor drastically reduced viral infectivity. Thus, the critical contribution of p6* and overlapping cis-acting sequence elements to timely regulated virus maturation and infectivity is closely linked to precise ribosomal frameshifting and proper N-terminal release of the viral PR from the Gag-Pol precursor, clearly disproving the hypothesis that sequence motifs in the central part of p6* modulate PR activation and viral infectivity.
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Affiliation(s)
- Christina Paulus
- Institute of Medical Microbiology and Hygiene, D-93053 Regensburg, Germany
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42
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Gao X, Havecker ER, Baranov PV, Atkins JF, Voytas DF. Translational recoding signals between gag and pol in diverse LTR retrotransposons. RNA (NEW YORK, N.Y.) 2003; 9:1422-30. [PMID: 14623998 PMCID: PMC1370496 DOI: 10.1261/rna.5105503] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Because of their compact genomes, retroelements (including retrotransposons and retroviruses) employ a variety of translational recoding mechanisms to express Gag and Pol. To assess the diversity of recoding strategies, we surveyed gag/pol gene organization among retroelements from diverse host species, including elements exhaustively recovered from the genome sequences of Caenorhabditis elegans, Drosophila melanogaster, Schizosaccharomyces pombe, Candida albicans, and Arabidopsis thaliana. In contrast to the retroviruses, which typically encode pol in the -1 frame relative to gag, nearly half of the retroelements surveyed encode a single gag-pol open reading frame. This was particularly true for the Ty1/copia group retroelements. Most animal Ty3/gypsy retroelements, on the other hand, encode gag and pol in separate reading frames, and likely express Pol through +1 or -1 frameshifting. Conserved sequences conforming to slippery sites that specify viral ribosomal frameshifting were identified among retroelements with pol in the -1 frame. None of the plant retroelements encoded pol in the -1 frame relative to gag; however, two closely related plant Ty3/gypsy elements encode pol in the +1 frame. Interestingly, a group of plant Ty1/copia retroelements encode pol either in a +1 frame relative to gag or in two nonoverlapping reading frames. These retroelements have a conserved stem-loop at the end of gag, and likely express pol either by a novel means of internal ribosomal entry or by a bypass mechanism.
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Affiliation(s)
- Xiang Gao
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
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43
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Chen C, Montelaro RC. Characterization of RNA elements that regulate gag-pol ribosomal frameshifting in equine infectious anemia virus. J Virol 2003; 77:10280-7. [PMID: 12970412 PMCID: PMC228510 DOI: 10.1128/jvi.77.19.10280-10287.2003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Synthesis of Gag-Pol polyproteins of retroviruses requires ribosomes to shift translational reading frame once or twice in a -1 direction to read through the stop codon in the gag reading frame. It is generally believed that a slippery sequence and a downstream RNA structure are required for the programmed -1 ribosomal frameshifting. However, the mechanism regulating the Gag-Pol frameshifting remains poorly understood. In this report, we have defined specific mRNA elements required for sufficient ribosomal frameshifting in equine anemia infectious virus (EIAV) by using full-length provirus replication and Gag/Gag-Pol expression systems. The results of these studies revealed that frameshifting efficiency and viral replication were dependent on a characteristic slippery sequence, a five-base-paired GC stretch, and a pseudoknot structure. Heterologous slippery sequences from human immunodeficiency virus type 1 and visna virus were able to substitute for the EIAV slippery sequence in supporting EIAV replication. Disruption of the GC-paired stretch abolished the frameshifting required for viral replication, and disruption of the pseudoknot reduced the frameshifting efficiency by 60%. Our data indicated that maintenance of the essential RNA signals (slippery sequences and structural elements) in this region of the genomic mRNA was critical for sufficient ribosomal frameshifting and EIAV replication, while concomitant alterations in the amino acids translated from the same region of the mRNA could be tolerated during replication. The data further indicated that proviral mutations that reduced frameshifting efficiency by as much as 50% continued to sustain viral replication and that greater reductions in frameshifting efficiency lead to replication defects. These studies define for the first time the RNA sequence and structural determinants of Gag-Pol frameshifting necessary for EIAV replication, reveal novel aspects relative to frameshifting elements described for other retroviruses, and provide new genetic determinants that can be evaluated as potential antiviral targets.
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Affiliation(s)
- Chaoping Chen
- Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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Baril M, Dulude D, Gendron K, Lemay G, Brakier-Gingras L. Efficiency of a programmed -1 ribosomal frameshift in the different subtypes of the human immunodeficiency virus type 1 group M. RNA (NEW YORK, N.Y.) 2003; 9:1246-1253. [PMID: 13130138 PMCID: PMC1370488 DOI: 10.1261/rna.5113603] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2003] [Accepted: 07/16/2003] [Indexed: 05/24/2023]
Abstract
The synthesis of the Gag-Pol polyprotein, the precursor of the enzymes of the human immunodeficiency virus type 1 (HIV-1), requires a programmed -1 ribosomal frameshift. This frameshift has been investigated so far only for subtype B of HIV-1 group M. In this subtype, the frameshift stimulatory signal was found to be a two-stem helix, in which a three-purine bulge interrupts the two stems. In this study, using a luciferase reporter system, we compare, for the first time, the frameshift efficiency of all the subtypes of group M. Mutants of subtype B, including a natural variant were also investigated. Our results with mutants of subtype B confirm that the bulge and the lower stem of the frameshift stimulatory signal contribute to the frameshift in addition to the upper stem-loop considered previously as the sole participant. Our results also show that the frameshift stimulatory signal of all of the other subtypes of group M can be folded into the same structure as in subtype B, despite sequence variations. Moreover, the frameshift efficiency of these subtypes, when assessed in cultured cells, falls within a narrow window (the maximal deviation from the mean value calculated from the experimental values of all the subtypes being approximately 35%), although the predicted thermodynamic stability of the frameshift stimulatory signal differs between the subtypes (from -17.2 kcal/mole to -26.2 kcal/mole). The fact that the frameshift efficiencies fall within a narrow range for all of the subtypes of HIV-1 group M stresses the potential of the frameshift event as an antiviral target.
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Affiliation(s)
- Martin Baril
- Département de Biochimie, Université de Montréal, Montréal, Québec, Canada, H3T 1J4
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45
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Staple DW, Butcher SE. Solution structure of the HIV-1 frameshift inducing stem-loop RNA. Nucleic Acids Res 2003; 31:4326-31. [PMID: 12888491 PMCID: PMC169958 DOI: 10.1093/nar/gkg654] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The translation of reverse transcriptase and other essential viral proteins from the HIV-1 Pol mRNA requires a programmed -1 ribosomal frameshift. This frameshift is induced by two highly conserved elements within the HIV-1 mRNA: a slippery sequence comprised of a UUUUUUA heptamer, and a downstream stem-loop structure. We have determined the structure of the HIV-1 frameshift inducing RNA stem-loop, using multidimensional heteronuclear nuclear magnetic resonance (NMR) methods. The 22 nucleotide RNA solution structure [root mean squared deviation (r.m.s.d.) = 1.2 A] was determined from 475 nuclear Overhauser effect (NOE)-derived distance restrains, 20 residual dipolar couplings and direct detection of hydrogen bonds via scalar couplings. We find that the frameshift inducing stem-loop is an A-form helix capped by a structured ACAA tetraloop. The ACAA tetraloop is stabilized by an equilateral 5' and 3' stacking pattern, a sheared A-A pair and a cross-strand hydrogen bond. Unexpectedly, the ACAA tetraloop structure is nearly identical to a known tetraloop fold, previously identified in the RNase III recognition site from Saccharomyces cerevisiae.
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Affiliation(s)
- David W Staple
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
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Brunelle MN, Brakier-Gingras L, Lemay G. Replacement of murine leukemia virus readthrough mechanism by human immunodeficiency virus frameshift allows synthesis of viral proteins and virus replication. J Virol 2003; 77:3345-50. [PMID: 12584361 PMCID: PMC149774 DOI: 10.1128/jvi.77.5.3345-3350.2003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Retroviruses use unusual recoding strategies to synthesize the Gag-Pol polyprotein precursor of viral enzymes. In human immunodeficiency virus, ribosomes translating full-length viral RNA can shift back by 1 nucleotide at a specific site defined by the presence of both a slippery sequence and a downstream stimulatory element made of an extensive secondary structure. This so-called frameshift mechanism could become a target for the development of novel antiviral strategies. A different recoding strategy is used by other retroviruses, such as murine leukemia viruses, to synthesize the Gag-Pol precursor; in this case, a stop codon is suppressed in a readthrough process, again due to the presence of a specific structure adopted by the mRNA. Development of antiframeshift agents will greatly benefit from the availability of a simple animal and virus model. For this purpose, the murine leukemia virus readthrough region was rendered inactive by mutagenesis and the frameshift region of human immunodeficiency virus was inserted to generate a chimeric provirus. This substitution of readthrough by frameshift allows the synthesis of viral proteins, and the chimeric provirus sequence was found to generate infectious viruses. This system could be a most interesting alternative to study ribosomal frameshift in the context of a virus amenable to the use of a simple animal model.
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Hill MK, Shehu-Xhilaga M, Crowe SM, Mak J. Proline residues within spacer peptide p1 are important for human immunodeficiency virus type 1 infectivity, protein processing, and genomic RNA dimer stability. J Virol 2002; 76:11245-53. [PMID: 12388684 PMCID: PMC136739 DOI: 10.1128/jvi.76.22.11245-11253.2002] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The full-length human immunodeficiency virus type 1 (HIV-1) mRNA encodes two precursor polyproteins, Gag and GagProPol. An infrequent ribosomal frameshifting event allows these proteins to be synthesized from the same mRNA in a predetermined ratio of 20 Gag proteins for each GagProPol. The RNA frameshift signal consists of a slippery sequence and a hairpin stem-loop whose thermodynamic stability has been shown in in vitro translation systems to be critical to frameshifting efficiency. In this study we examined the frameshift region of HIV-1, investigating the effects of altering stem-loop stability in the context of the complete viral genome and assessing the role of the Gag spacer peptide p1 and the GagProPol transframe (TF) protein that are encoded in this region. By creating a series of frameshift region mutants that systematically altered the stability of the frameshift stem-loop and the protein sequences of the p1 spacer peptide and TF protein, we have demonstrated the importance of stem-loop thermodynamic stability in frameshifting efficiency and viral infectivity. Multiple changes to the amino acid sequence of p1 resulted in altered protein processing, reduced genomic RNA dimer stability, and abolished viral infectivity. The role of the two highly conserved proline residues in p1 (position 7 and 13) was also investigated. Replacement of the two proline residues by leucines resulted in mutants with altered protein processing and reduced genomic RNA dimer stability that were also noninfectious. The unique ability of proline to confer conformational constraints on a peptide suggests that the correct folding of p1 may be important for viral function.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Dimerization
- Frameshifting, Ribosomal
- Gene Products, gag/chemistry
- Gene Products, gag/genetics
- Gene Products, gag/metabolism
- Genome, Viral
- HIV Infections/virology
- HIV-1/genetics
- HIV-1/metabolism
- HIV-1/pathogenicity
- Humans
- Leukocytes, Mononuclear/virology
- Molecular Sequence Data
- Mutation
- Peptides/chemistry
- Peptides/genetics
- Peptides/metabolism
- Proline/chemistry
- Protein Processing, Post-Translational
- RNA Stability
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Viral/chemistry
- RNA, Viral/genetics
- Viral Proteins
- gag Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- Melissa K Hill
- AIDS Pathogenesis Research Unit, Macfarlane Burnet Institute for Medical Research and Public Health, Monash University, Melbourne, Victoria, Australia
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