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Boyd PS, Brown JB, Brown JD, Catazaro J, Chaudry I, Ding P, Dong X, Marchant J, O’Hern CT, Singh K, Swanson C, Summers MF, Yasin S. NMR Studies of Retroviral Genome Packaging. Viruses 2020; 12:v12101115. [PMID: 33008123 PMCID: PMC7599994 DOI: 10.3390/v12101115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 12/03/2022] Open
Abstract
Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Over the past four decades, combinations of genetic experiments, phylogenetic analyses, nucleotide accessibility mapping, in silico RNA structure predictions, and biophysical experiments were employed to understand how retroviral genomes are selected for packaging. Genetic studies provided early clues regarding the protein and RNA elements required for packaging, and nucleotide accessibility mapping experiments provided insights into the secondary structures of functionally important elements in the genome. Three-dimensional structural determinants of packaging were primarily derived by nuclear magnetic resonance (NMR) spectroscopy. A key advantage of NMR, relative to other methods for determining biomolecular structure (such as X-ray crystallography), is that it is well suited for studies of conformationally dynamic and heterogeneous systems—a hallmark of the retrovirus packaging machinery. Here, we review advances in understanding of the structures, dynamics, and interactions of the proteins and RNA elements involved in retroviral genome selection and packaging that are facilitated by NMR.
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Dubois N, Marquet R, Paillart JC, Bernacchi S. Retroviral RNA Dimerization: From Structure to Functions. Front Microbiol 2018; 9:527. [PMID: 29623074 PMCID: PMC5874298 DOI: 10.3389/fmicb.2018.00527] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/08/2018] [Indexed: 01/18/2023] Open
Abstract
The genome of the retroviruses is a dimer composed by two homologous copies of genomic RNA (gRNA) molecules of positive polarity. The dimerization process allows two gRNA molecules to be non-covalently linked together through intermolecular base-pairing. This step is critical for the viral life cycle and is highly conserved among retroviruses with the exception of spumaretroviruses. Furthermore, packaging of two gRNA copies into viral particles presents an important evolutionary advantage for immune system evasion and drug resistance. Recent studies reported RNA switches models regulating not only gRNA dimerization, but also translation and packaging, and a spatio-temporal characterization of viral gRNA dimerization within cells are now at hand. This review summarizes our current understanding on the structural features of the dimerization signals for a variety of retroviruses (HIVs, MLV, RSV, BLV, MMTV, MPMV…), the mechanisms of RNA dimer formation and functional implications in the retroviral cycle.
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Affiliation(s)
- Noé Dubois
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Roland Marquet
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Serena Bernacchi
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
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3
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Chu W, Weerasekera A, Kim CH. On the conformational stability of the smallest RNA kissing complexes maintained through two G·C base pairs. Biochem Biophys Res Commun 2017; 483:39-44. [PMID: 28063925 DOI: 10.1016/j.bbrc.2017.01.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/03/2017] [Indexed: 11/19/2022]
Abstract
Two identical 5'GACG3' tetra-loop motifs with different stem sequences (called H2 and H3) are found in the 5' end region of Moloney Murine Leukemia Virus (MMLV) genomic RNA. They play important roles in RNA dimerization and encapsidation through two identical tetra-loops (5'GACG3') forming a loop-to-loop kissing complex, the smallest RNA kissing complex ever found in nature. We examined the effects of a loop-closing base pair as well as a stem sequence on the conformational stability of the kissing complex. UV melting analysis and gel electrophoresis were performed on eight RNA sequences mimicking the H2 and H3 hairpin tetra-loops with variation in loop-closing base pairs. Our results show that changing the loop-closing base pair from the wildtype (5'A·U3' for H3, 5'U·A3' for H2) to 5'G·C3'/5'C·G3' has significant effect on the stability of the kissing complexes: the substitution to 5'C·G3' significantly decreases both thermal and mechanical stability, while switching to the 5'G·C3' significantly increases the mechanical stability only. The kissing complexes with the wildtype loop-closing base pairs (5'A·U3' for H3 and 5'U·A3' for H2) show different stability when attached to a different stem sequence (H2 stem vs. H3 stem). This suggests that not only the loop-closing base pair itself, but also the stem sequence, affects the conformational stability of the RNA kissing complex.
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Affiliation(s)
- Wally Chu
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, United States
| | - Akila Weerasekera
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, United States
| | - Chul-Hyun Kim
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, United States.
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4
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Pessel-Vivares L, Houzet L, Lainé S, Mougel M. Insights into the nuclear export of murine leukemia virus intron-containing RNA. RNA Biol 2016; 12:942-9. [PMID: 26158194 DOI: 10.1080/15476286.2015.1065375] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The retroviral genome consists of an intron-containing transcript that has essential cytoplasmic functions in the infected cell. This viral transcript can escape splicing, circumvent the nuclear checkpoint mechanisms and be transported to the cytoplasm by hijacking the host machinery. Once in the cytoplasm, viral unspliced RNA acts as mRNA to be translated and as genomic RNA to be packaged into nascent viruses. The murine leukemia virus (MLV) is among the first retroviruses discovered and is classified as simple Retroviridae due to its minimal encoding capacity. The oncogenic and transduction abilities of MLV are extensively studied, whereas surprisingly the crucial step of its nuclear export has remained unsolved until 2014. Recent work has revealed the recruitment by MLV of the cellular NXF1/Tap-dependent pathway for export. Unconventionally, MLV uses of Tap to export both spliced and unspliced viral RNAs. Unlike other retroviruses, MLV does not harbor a unique RNA signal for export. Indeed, multiple sequences throughout the MLV genome appear to promote export of the unspliced MLV RNA. We review here the current understanding of the export mechanism and highlight the determinants that influence MLV export. As the molecular mechanism of MLV export is elucidated, we will gain insight into the contribution of the export pathway to the cytoplasmic fate of the viral RNA.
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Affiliation(s)
- Lucie Pessel-Vivares
- a CNRS, UM; CPBS ; Montpellier , France.,b Department of Infectious Diseases ; King's College London ; London , UK
| | - Laurent Houzet
- c Inserm U1085-IRSET; Université de Rennes 1; Structure Fédérative Recherche Biosit ; Rennes , France
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5
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Choi J, Kim HM, Yoon JK, Cho Y, Lee HJ, Kim KC, Kim CK, Kim GW, Kim YB. Identification of Porcine Endogenous Retrovirus (PERV) packaging sequence and development of PERV packaging viral vector system. J Microbiol 2015; 53:348-53. [PMID: 25935307 DOI: 10.1007/s12275-015-5134-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/09/2015] [Accepted: 04/13/2015] [Indexed: 12/11/2022]
Abstract
Studies of the retroviruses have focused on the specific interaction of the nucleocapsid protein with a packaging signal in the viral RNA as important for this selectivity, but the packaging signal in porcine endogenous retrovirus (PERV) has not been defined. Herein, we identified and analyzed this packaging signal in PERV and found hairpin structures with conserved tetranucleotides in their loops and nucleocapsid recognition sequences; both of which are key elements in the viral packaging signal of MLV. We evaluated packaging efficiency of sequence variants isolated from viral and proviral integrated genomes. All viral packaging sequences (Ψ) were identical, while five distinct packaging sequences were identified from proviral sources. One proviral sequence (Ψ1) was identical to that of the viral Ψ and had the highest packaging efficiency. Three variants (Ψ2, Ψ3, Ψ4) maintained key elements of the viral packaging signal, but had nucleotide replacements and consequently demonstrated reduced packaging efficiency. Despite of the same overall hairpin structure, the proviral variant (Ψ5) had only one GACG sequence in the hairpin loop and showed the lowest packaging efficiency other than ∆Ψ, in which the essential packaging sequence was removed. This result, thus, defined the packaging sequences in PERV and emphasized the importance of nucleotide sequence and RNA structure in the determination of packaging efficiency. In addition, we demonstrate efficient infection and gene expression from the PERV based viral vector, which may serve as a novel alternative to current retroviral expression systems.
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Affiliation(s)
- Jiwon Choi
- Department of Bioindustrial Technologies, Konkuk University, Seoul, 143-701, Korea
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6
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Jouvenet N, Lainé S, Pessel-Vivares L, Mougel M. Cell biology of retroviral RNA packaging. RNA Biol 2011; 8:572-80. [PMID: 21691151 DOI: 10.4161/rna.8.4.16030] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Generation of infectious retroviral particles rely on the targeting of all structural components to the correct cellular sites at the correct time. Gag, the main structural protein, orchestrates the assembly process and the mechanisms that trigger its targeting to assembly sites are well described. Gag is also responsible for the packaging of the viral genome and the molecular details of the Gag/RNA interaction are well characterized. Until recently, much less was understood about the cell biology of retrovirus RNA packaging. However, novel biochemical and live-cell microscopic approaches have identified where in the cell the initial events of genome recognition by Gag occur. These recent developments have shed light on the role played by the viral genome during virion assembly. Other central issues of the cell biology of RNA packaging, such as how the Gag-RNA complex traffics through the cytoplasm towards assembly sites, await characterization.
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Miyazaki Y, Irobalieva RN, Tolbert BS, Smalls-Mantey A, Iyalla K, Loeliger K, D'Souza V, Khant H, Schmid MF, Garcia EL, Telesnitsky A, Chiu W, Summers MF. Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography. J Mol Biol 2010; 404:751-72. [PMID: 20933521 DOI: 10.1016/j.jmb.2010.09.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 09/07/2010] [Accepted: 09/07/2010] [Indexed: 01/11/2023]
Abstract
The 5'-untranslated regions of all gammaretroviruses contain a conserved "double-hairpin motif" (Ψ(CD)) that is required for genome packaging. Both hairpins (SL-C and SL-D) contain GACG tetraloops that, in isolated RNAs, are capable of forming "kissing" interactions stabilized by two intermolecular G-C base pairs. We have determined the three-dimensional structure of the double hairpin from the Moloney murine leukemia virus ([Ψ(CD)](2), 132 nt, 42.8 kDa) using a (2)H-edited NMR-spectroscopy-based approach. This approach enabled the detection of (1)H-(1)H dipolar interactions that were not observed in previous studies of isolated SL-C and SL-D hairpin RNAs using traditional (1)H-(1)H correlated and (1)H-(13)C-edited NMR methods. The hairpins participate in intermolecular cross-kissing interactions (SL-C to SL-D' and SLC' to SL-D) and stack in an end-to-end manner (SL-C to SL-D and SL-C' to SL-D') that gives rise to an elongated overall shape (ca 95 Å×45 Å×25 Å). The global structure was confirmed by cryo-electron tomography (cryo-ET), making [Ψ(CD)](2) simultaneously the smallest RNA to be structurally characterized to date by cryo-ET and among the largest to be determined by NMR. Our findings suggest that, in addition to promoting dimerization, [Ψ(CD)](2) functions as a scaffold that helps initiate virus assembly by exposing a cluster of conserved UCUG elements for binding to the cognate nucleocapsid domains of assembling viral Gag proteins.
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Affiliation(s)
- Yasuyuki Miyazaki
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
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Gultyaev AP, Fouchier RAM, Olsthoorn RCL. Influenza virus RNA structure: unique and common features. Int Rev Immunol 2010; 29:533-56. [PMID: 20923332 DOI: 10.3109/08830185.2010.507828] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The influenza A virus genome consists of eight negative-sense RNA segments. Here we review the currently available data on structure-function relationships in influenza virus RNAs. Various ideas and hypotheses about the roles of influenza virus RNA folding in the virus replication are also discussed in relation to other viruses.
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9
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Maurel S, Mougel M. Murine leukemia virus RNA dimerization is coupled to transcription and splicing processes. Retrovirology 2010; 7:64. [PMID: 20687923 PMCID: PMC2925334 DOI: 10.1186/1742-4690-7-64] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 08/05/2010] [Indexed: 11/16/2022] Open
Abstract
Most of the cell biological aspects of retroviral genome dimerization remain unknown. Murine leukemia virus (MLV) constitutes a useful model to study when and where dimerization occurs within the cell. For instance, MLV produces a subgenomic RNA (called SD') that is co-packaged with the genomic RNA predominantly as FLSD' heterodimers. This SD' RNA is generated by splicing of the genomic RNA and also by direct transcription of a splice-associated retroelement of MLV (SDARE). We took advantage of these two SD' origins to study the effects of transcription and splicing events on RNA dimerization. Using genetic approaches coupled to capture of RNA heterodimer in virions, we determined heterodimerization frequencies in different cellular contexts. Several cell lines were stably established in which SD' RNA was produced by either splicing or transcription from SDARE. Moreover, SDARE was integrated into the host chromosome either concomitantly or sequentially with the genomic provirus. Our results showed that transcribed genomic and SD' RNAs preferentially formed heterodimers when their respective proviruses were integrated together. In contrast, heterodimerization was strongly affected when the two proviruses were integrated independently. Finally, dimerization was enhanced when the transcription sites were expected to be physically close. For the first time, we report that splicing and RNA dimerization appear to be coupled. Indeed, when the RNAs underwent splicing, the FLSD' dimerization reached a frequency similar to co-transcriptional heterodimerization. Altogether, our results indicate that randomness of heterodimerization increases when RNAs are co-expressed during either transcription or splicing. Our results strongly support the notion that dimerization occurs in the nucleus, at or near the transcription and splicing sites, at areas of high viral RNA concentration.
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Affiliation(s)
- Stéphan Maurel
- Université Montpellier 1, Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS, UMR 5236, 4 Bd Henri IV, 34965 Montpellier, France
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10
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Kharytonchyk S, Pedersen FS. A unique, thermostable dimer linkage structure of RD114 retroviral RNA. RNA (NEW YORK, N.Y.) 2010; 16:572-584. [PMID: 20075164 PMCID: PMC2822922 DOI: 10.1261/rna.1495110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 11/13/2009] [Indexed: 05/28/2023]
Abstract
Retroviruses package their genome as RNA dimers linked together primarily by base-pairing between palindromic stem-loop (psl) sequences at the 5' end of genomic RNA. Retroviral RNA dimers usually melt in the range of 55 degrees C-70 degrees C. However, RNA dimers from virions of the feline endogenous gammaretrovirus RD114 were reported to melt only at 87 degrees C. We here report that the high thermal stability of RD114 RNA dimers generated from in vitro synthesized RNA is an effect of multiple dimerization sites located in the 5' region from the R region to sequences downstream from the splice donor (SD) site. By antisense oligonucleotide probing we were able to map at least five dimerization sites. Computational prediction revealed a possibility to form stems with autocomplementary loops for all of the mapped dimerization sites. Three of them were located upstream of the SD site. Mutant analysis supported a role of all five loop sequences in the formation and thermal stability of RNA dimers. Four of the five psls were also predicted in the RNA of two baboon endogenous retroviruses proposed to be ancestors of RD114. RNA fragments of the 5' R region or prolonged further downstream could be efficiently dimerized in vitro. However, this was not the case for the 3' R region linked to upstream U3 sequences, suggesting a specific mechanism of negative regulation of dimerization at the 3' end of the genome, possibly explained by a long double-stranded RNA region at the U3-R border. Altogether, these data point to determinants of the high thermostability of the dimer linkage structure of the RD114 genome and reveal differences from other retroviruses.
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11
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Miyazaki Y, Garcia EL, King SR, Iyalla K, Loeliger K, Starck P, Syed S, Telesnitsky A, Summers MF. An RNA structural switch regulates diploid genome packaging by Moloney murine leukemia virus. J Mol Biol 2009; 396:141-52. [PMID: 19931283 DOI: 10.1016/j.jmb.2009.11.033] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 11/10/2009] [Accepted: 11/11/2009] [Indexed: 11/26/2022]
Abstract
Retroviruses selectively package two copies of their RNA genomes via mechanisms that have yet to be fully deciphered. Recent studies with small fragments of the Moloney murine leukemia virus (MoMuLV) genome suggested that selection may be mediated by an RNA switch mechanism, in which conserved UCUG elements that are sequestered by base-pairing in the monomeric RNA become exposed upon dimerization to allow binding to the cognate nucleocapsid (NC) domains of the viral Gag proteins. Here we show that a large fragment of the MoMuLV 5' untranslated region that contains all residues necessary for efficient RNA packaging (Psi(WT); residues 147-623) also exhibits a dimerization-dependent affinity for NC, with the native dimer ([Psi(WT)](2)) binding 12+/-2 NC molecules with high affinity (K(d)=17+/-7 nM) and with the monomer, stabilized by substitution of dimer-promoting loop residues with hairpin-stabilizing sequences (Psi(M)), binding 1-2 NC molecules. Identical dimer-inhibiting mutations in MoMuLV-based vectors significantly inhibit genome packaging in vivo (approximately 100-fold decrease), whereas a large deletion of nearly 200 nucleotides just upstream of the gag start codon has minimal effects. Our findings support the proposed RNA switch mechanism and further suggest that virus assembly may be initiated by a complex comprising as few as 12 Gag molecules bound to a dimeric packaging signal.
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Affiliation(s)
- Yasuyuki Miyazaki
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
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12
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Sun X, Li JM, Wartell RM. Conversion of stable RNA hairpin to a metastable dimer in frozen solution. RNA (NEW YORK, N.Y.) 2007; 13:2277-86. [PMID: 17925345 PMCID: PMC2080584 DOI: 10.1261/rna.433307] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Accepted: 08/29/2007] [Indexed: 05/23/2023]
Abstract
Previous studies employing a 79-nucleotide (nt) RNA indicated that this RNA could form two bands in a native polyacrylamide gel while one band was observed in a denaturing gel. This report describes an investigation on the nature of the two corresponding structures and the segment responsible for forming the slower mobility band. Sedimentation equilibrium of the 79-nt RNA was consistent with the two gel bands corresponding to monomer and dimer forms. The portion of the RNA required for dimer formation was explored using a secondary structure prediction algorithm of two 79-nt RNAs linked in a head-to-tail fashion. The predicted structure suggested that the first 21-nt at the 5' end of each RNA formed a self-complementary duplex. A ribonuclease H assay carried out with RNA prepared as monomer (M), or a mixture of monomer and dimer (M/D), gave results consistent with the predicted M and D structures. Gel mobility experiments on 5' and 3' segments of the 79-nt RNA also indicated that dimer formation was due to the 21-nt 5' end. Studies on the 21-nt RNA molecule and sequence variants showed that this sequence can form a hairpin and a dimer complex. Unexpectedly, the hairpin to dimer conversion was shown to occur at high efficiency in frozen solution, although little or no conversion was observed above 0 degrees C. The results indicate that a freezing environment can promote formation of intermolecular RNA complexes from stable RNA hairpins, supporting the notion that this environment could have played a role in the evolution of RNA complexity.
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Affiliation(s)
- Xueguang Sun
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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Maurel S, Houzet L, Garcia EL, Telesnitsky A, Mougel M. Characterization of a natural heterodimer between MLV genomic RNA and the SD' retroelement generated by alternative splicing. RNA (NEW YORK, N.Y.) 2007; 13:2266-2276. [PMID: 17928575 PMCID: PMC2080594 DOI: 10.1261/rna.713807] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Accepted: 08/28/2007] [Indexed: 05/25/2023]
Abstract
Murine leukemia virus (MLV) specifically packages both genomic RNA (FL RNA) and a subgenomic RNA, which we call SD'. SD' RNA results from alternative splicing of FL RNA. It is reverse-transcribed, and its DNA copy, integrated into the host genome, constitutes a splice donor-associated retroelement. FL and SD' RNAs share a common 5'-UTR that includes the packaging/dimerization signal (Psi). To investigate whether the mechanism of copackaging of these two RNAs involves RNA heterodimerization, we examined the spontaneous dimerization capacity of the two RNAs as large synthetic RNAs transcribed in vitro. We showed that SD' RNA not only formed homodimers with similar efficiency as the FL RNA, but that FL and SD' RNAs also formed FL/SD' heterodimers via Psi sequences. Comparison of the thermostabilities determined for these different dimeric species and competition experiments with Psi RNA fragments indicate the recruitment of similar dimer-linkage interactions within the Psi region. To validate these results, the dimeric state of the SD' RNA was analyzed in MLV particles. RNA capture assays performed with the FL RNA as bait revealed that SD', and not the host packageable U6 or 7SL RNAs, was associated with the FL RNA in virions. Heterodimerization of SD' RNA with FL RNA may argue for the recent concept of a nuclear dimerization at or near the site of transcription and raises the new hypothesis of RNA dimerization during splicing. Furthermore, FL/SD' heterodimerization may have leukemogenic consequences by influencing the pool of genomic dimers that will undergo recombinogenic template switching by reverse transcriptase.
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Affiliation(s)
- Stéphan Maurel
- Centre d'Etudes d'Agents Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS UMR5236, UMI, UMII, IFR122, CS 69033, 34965 Montpellier, France
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14
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Li PTX, Bustamante C, Tinoco I. Unusual mechanical stability of a minimal RNA kissing complex. Proc Natl Acad Sci U S A 2006; 103:15847-52. [PMID: 17043221 PMCID: PMC1635091 DOI: 10.1073/pnas.0607202103] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
By using optical tweezers, we have investigated the mechanical unfolding of a minimal kissing complex with only two G.C base pairs. The loop-loop interaction is exceptionally stable; it is disrupted at forces ranging from 7 to 30 pN, as compared with 14-20 pN for unfolding hairpins of 7 and 11 bp. By monitoring unfolding/folding trajectories of single molecules, we resolved the intermediates, measured their rate constants, and pinpointed the rate-limiting steps. The two hairpins unfold only after breaking the intramolecular kissing interaction, and the kissing interaction forms only after the folding of the hairpins. At forces that favor the unfolding of the hairpins, the entire RNA structure is kinetically stabilized by the kissing interaction, and extra work is required to unfold the metastable hairpins. The strong mechanical stability of even a minimal kissing complex indicates the importance of such loop-loop interactions in initiating and stabilizing RNA dimers in retroviruses.
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Affiliation(s)
| | - Carlos Bustamante
- Departments of *Chemistry and
- Physics and Molecular and Cell Biology, and
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
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15
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Gherghe C, Weeks KM. The SL1-SL2 (stem-loop) domain is the primary determinant for stability of the gamma retroviral genomic RNA dimer. J Biol Chem 2006; 281:37952-61. [PMID: 16984912 DOI: 10.1074/jbc.m607380200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Retroviral genomes are assembled from two sense-strand RNAs by noncovalent interactions at their 5' ends, forming a dimer. The RNA dimerization domain is a potential target for antiretroviral therapy and represents a compelling RNA folding problem. The fundamental dimerization unit for the Moloney murine sarcoma gamma retrovirus spans a 170-nucleotide minimal dimerization active sequence. In the dimer, two self-complementary sequences, PAL1 and PAL2, form intermolecular duplexes, and an SL1-SL2 (stem-loop) domain forms loop-loop base pairs, mediated by GACG tetraloops, and extensive tertiary interactions. To develop a framework for assembly of the retroviral RNA dimer, we quantified the stability of and established nucleotide resolution secondary structure models for sequence variants in which each motif was compromised. Base pairing and tertiary interactions between SL1-SL2 domains contribute a large free energy increment of -10 kcal/mol. In contrast, even though the PAL1 and PAL2 intermolecular duplexes span 10 and 16 bp in the dimer, respectively, they contribute only -2.5 kcal/mol to stability, roughly equal to a single new base pair. First, these results emphasize that the energetic costs for disrupting interactions in the monomer state nearly balance the PAL1 and PAL2 base pairing interactions that form in the dimer. Second, intermolecular duplex formation plays a biological role distinct from simply stabilizing the structure of the retroviral genomic RNA dimer.
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Affiliation(s)
- Cristina Gherghe
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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16
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Rasmussen SV, Pedersen FS. Co-localization of gammaretroviral RNAs at their transcription site favours co-packaging. J Gen Virol 2006; 87:2279-2289. [PMID: 16847124 DOI: 10.1099/vir.0.81759-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A retroviral vector-rescue system in which co-packaging of the two co-expressed vectors is required for transduction of one of the vectors has been established previously. By using this rescue system, two distinct packaging-cell populations have been generated. One cell population expressed retroviral RNA from co-localized transcription sites, resulting in local and overlapping accumulation of both RNA transcripts. In the other cell population, the two transcription cassettes were introduced separately, leading to distinct transcription sites of the two RNAs and no significant co-localization of the RNAs. Titre measurements from the two distinct cell populations showed large differences in rescue titre, which is an indirect measure of co-packaging efficiency. Thus, the cell populations with overlapping RNA accumulation gave rise to 15-80-fold-higher rescue titres than cell populations with non-overlapping RNA accumulation. These data show that the spatial position of proviral transcription sites affects the level of retroviral RNA co-packaging and suggest that there is already a linkage of RNAs for co-packaging at the transcription site. It is hypothesized that this linkage is due to RNA dimerization taking place at the transcription site.
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Affiliation(s)
- Søren Vestergaard Rasmussen
- Department of Molecular Biology, University of Aarhus, C. F. Møllers Allé, Building 130, DK-8000 Aarhus C, Denmark
| | - Finn Skou Pedersen
- Department of Medical Microbiology and Immunology, University of Aarhus, C. F. Møllers Allé, Building 130, DK-8000 Aarhus C, Denmark
- Department of Molecular Biology, University of Aarhus, C. F. Møllers Allé, Building 130, DK-8000 Aarhus C, Denmark
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17
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Smagulova F, Maurel S, Morichaud Z, Devaux C, Mougel M, Houzet L. The highly structured encapsidation signal of MuLV RNA is involved in the nuclear export of its unspliced RNA. J Mol Biol 2005; 354:1118-28. [PMID: 16289115 DOI: 10.1016/j.jmb.2005.10.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2005] [Revised: 10/03/2005] [Accepted: 10/05/2005] [Indexed: 11/22/2022]
Abstract
The encapsidation signal (Psi) of retroviruses is located in the 5' UTR of the viral genomic unspliced transcript and is highly structured. In the Psi of murine leukaemia virus (MuLV), four stem-loops, called A, B, C and D, promote dimerization and encapsidation of the MuLV unspliced RNA into virions. Through analysis of Psi-deleted transcripts, we found that the AB and CD motifs independently enhanced the cytoplasmic accumulation of RNAs. Furthermore, we showed that over-expression of the Psi sequence in the infected cells led to a competition with the nuclear export of unspliced MuLV transcripts, revealing a new function for these stem-loops in the transport of viral intron-containing RNAs from the nucleus to the cytoplasm.
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MESH Headings
- 5' Untranslated Regions
- Active Transport, Cell Nucleus
- Animals
- Capsid/metabolism
- Cell Fractionation
- Cell Nucleus/metabolism
- Cytoplasm/metabolism
- Dimerization
- Fluorescent Dyes
- In Situ Hybridization, Fluorescence
- Indoles
- Introns
- Mice
- Microscopy, Fluorescence
- Moloney murine leukemia virus/chemistry
- Moloney murine leukemia virus/genetics
- Mutation
- NIH 3T3 Cells
- Nucleic Acid Conformation
- RNA Splicing
- RNA, Ribosomal/analysis
- RNA, Ribosomal/chemistry
- RNA, Small Nucleolar/analysis
- RNA, Small Nucleolar/metabolism
- RNA, Transfer/analysis
- RNA, Transfer/chemistry
- RNA, Viral/analysis
- RNA, Viral/chemistry
- RNA, Viral/isolation & purification
- RNA, Viral/metabolism
- Transfection
- Virion/chemistry
- Virion/genetics
- Virus Replication/genetics
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Affiliation(s)
- Fatima Smagulova
- CNRS UMR5121-UM1, IFR122, Institut de Biologie, 34960 Montpellier, France
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18
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Basyuk E, Boulon S, Skou Pedersen F, Bertrand E, Vestergaard Rasmussen S. The packaging signal of MLV is an integrated module that mediates intracellular transport of genomic RNAs. J Mol Biol 2005; 354:330-9. [PMID: 16253274 DOI: 10.1016/j.jmb.2005.09.071] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Revised: 09/19/2005] [Accepted: 09/21/2005] [Indexed: 12/22/2022]
Abstract
Packaging of MLV genomes requires four cis-acting stem-loops. Stem-loops A and B are self-complementary and bind Gag in their dimeric form, while the C and D elements mediate loop-loop interactions that facilitate RNA dimerization. Packaging also requires nuclear export of viral genomes, and their cytoplasmic transport toward the plasma membrane. For MLV, this is mediated by Gag and Env, and occurs on endosomal vesicles. Here, we report that MLV Psi acts at several steps during the transport of genomic RNAs. First, deletion of stem-loop B or C leads to the accumulation of genomic RNAs in the nucleus, suggesting that these elements are involved in export. Second, in chronically infected cells, mutation of the C and D loops impairs endosomal transport. This suggests that RNA dimerization is essential for vesicular transport, consistent with its proposed requirement for Gag binding. Surprisingly, deletion of stem-loop A blocks vesicular transport, whereas removal of stem-loop B has no effects. This suggests that stem-loop A has unique functions in packaging, not predicted from previous in vitro analyses. Finally, in packaging cells that do not express any Psi-containing RNA, endosomal RNA transport becomes sequence-independent. This non-specific activity of Gag likely promotes packaging of cellular mRNAs.
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Affiliation(s)
- Eugenia Basyuk
- IGMM-CNRS UMR5535, IFR 24, 1919, route de Mende 34293 Montpellier Cedex 5, France
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19
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Abstract
As retroviruses assemble in infected cells, two copies of their full-length, unspliced RNA genomes are selected for packaging from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Understanding the molecular details of genome packaging is important for the development of new antiviral strategies and to enhance the efficacy of retroviral vectors used in human gene therapy. Recent studies of viral RNA structure in vitro and in vivo and high-resolution studies of RNA fragments and protein-RNA complexes are helping to unravel the mechanism of genome packaging and providing the first glimpses of the initial stages of retrovirus assembly.
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Affiliation(s)
- Victoria D'Souza
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
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20
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Badorrek CS, Weeks KM. RNA flexibility in the dimerization domain of a gamma retrovirus. Nat Chem Biol 2005; 1:104-11. [PMID: 16408007 DOI: 10.1038/nchembio712] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2005] [Accepted: 05/16/2005] [Indexed: 11/08/2022]
Abstract
Retroviruses are the causative agents of serious diseases, such as acquired immunodeficiency syndromes and several cancers, and are also useful gene therapy vectors. Retroviruses contain two sense-strand RNA genomes, which become linked at their 5' ends to form an RNA dimer. Understanding the molecular basis for dimerization may yield new approaches for controlling viral infectivity. Because this RNA domain is highly conserved within retrovirus groups, it has not been possible to define a consensus structure for the 5' dimerization domain by comparative sequence analysis. Here, we defined a 170-nucleotide minimal dimerization active sequence (MiDAS) for a representative gamma retrovirus, the Moloney murine sarcoma virus, by stringent competitive dimerization. We then analyzed the structure at every nucleotide in the MiDAS monomeric starting state with quantitative selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry. Notably, SHAPE analysis demonstrated that the RNA monomer contains an extensive flexible domain spanning 50 nucleotides. These findings support a structural model in which RNA flexibility directly facilitates retroviral genome dimerization by reducing the energetic cost of disrupting pre-existing base pairings in the monomer.
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Affiliation(s)
- Christopher S Badorrek
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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21
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Rasmussen S, Pedersen FS. Complementarity between RNA dimerization elements favors formation of functional heterozygous murine leukemia viruses. Virology 2005; 329:440-53. [PMID: 15518822 DOI: 10.1016/j.virol.2004.08.027] [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: 05/10/2004] [Revised: 08/06/2004] [Accepted: 08/12/2004] [Indexed: 11/16/2022]
Abstract
The cis-elements that direct packaging and dimerization of retroviral RNAs overlap, and it has been suggested that dimerization is required for RNA packaging. This also implies that heterodimerization would be necessary for co-packaging and recombination. Moreover, co-packaging of distinct RNAs may be reduced if incapable of heterodimerizing. In this study, we have designed a novel two-vector rescue system in which co-packaging and interstrand transfer are necessary for transduction. Thus, the rescue titer is a measure of the ability of a given vector combination to co-package and subsequently generate a provirus. In the current MLV-based set-up, we explored Akv- and MLV-like-endogenous virus (MLEV)-derived vectors with modulated dimerization signals. Results show that rescue is influenced by competition at the level of RNA packaging, as well as complementarity between dimerization elements. Altogether, the results support the hypothesis that complementarity between dimerization elements may favor co-packaging of distinct retroviral RNAs.
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22
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Hibbert CS, Mirro J, Rein A. mRNA molecules containing murine leukemia virus packaging signals are encapsidated as dimers. J Virol 2004; 78:10927-38. [PMID: 15452213 PMCID: PMC521861 DOI: 10.1128/jvi.78.20.10927-10938.2004] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prior work by others has shown that insertion of psi (i.e., leader) sequences from the Moloney murine leukemia virus (MLV) genome into the 3' untranslated region of a nonviral mRNA leads to the specific encapsidation of this RNA in MLV particles. We now report that these RNAs are, like genomic RNAs, encapsidated as dimers. These dimers have the same thermostability as MLV genomic RNA dimers; like them, these dimers are more stable if isolated from mature virions than from immature virions. We characterized encapsidated mRNAs containing deletions or truncations of MLV psi or with psi sequences from MLV-related acute transforming viruses. The results indicate that the dimeric linkage in genomic RNA can be completely attributed to the psi region of the genome. While this conclusion agrees with earlier electron microscopic studies on mature MLV dimers, it is the first evidence as to the site of the linkage in immature dimers for any retrovirus. Since the Psi(+) mRNA is not encapsidated as well as genomic RNA, it is only present in a minority of virions. The fact that it is nevertheless dimeric argues strongly that two of these molecules are packaged into particles together. We also found that the kissing loop is unnecessary for this coencapsidation or for the stability of mature dimers but makes a major contribution to the stability of immature dimers. Our results are consistent with the hypothesis that the packaging signal involves a dimeric structure in which the RNAs are joined by intermolecular interactions between GACG loops.
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Affiliation(s)
- Catherine S Hibbert
- HIV Drug Resistance Program, National Cancer Institute-Frederick, P. O. Box B, Frederick, MD 21702-1201, USA
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23
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Flynn JA, An W, King SR, Telesnitsky A. Nonrandom dimerization of murine leukemia virus genomic RNAs. J Virol 2004; 78:12129-39. [PMID: 15507599 PMCID: PMC525042 DOI: 10.1128/jvi.78.22.12129-12139.2004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2004] [Accepted: 07/07/2004] [Indexed: 11/20/2022] Open
Abstract
Retroviral genomes consist of two unspliced RNAs linked noncovalently in a dimer. Although these two RNAs are generally identical, two different RNAs can be copackaged when virions are produced by coinfected cells. It has been assumed, but not tested, that copackaging results from random RNA associations in the cytoplasm to yield encapsidated RNA homodimers and heterodimers in Hardy-Weinberg proportions. Here, virion RNA homo- and heterodimerization were examined for Moloney murine leukemia virus (MLV) using nondenaturing Northern blotting and a novel RNA dimer capture assay. The results demonstrated that coexpressed MLV RNAs preferentially self-associated, even when RNAs were identical in known packaging and dimerization sequences or when they differed overall by less than 0.1%. In contrast, HIV-1 RNAs formed homo- and heterodimers in random proportions. We speculate that these species-specific differences in RNA dimer partner selection may at least partially explain the higher frequency of genetic recombination observed for human immunodeficiency virus type 1 than for MLV.
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Affiliation(s)
- Jessica A Flynn
- Department of Microbiology and Immunology, 1150 W. Medical Center Drive, Room 5641, University of Michigan Medical School, Ann Arbor, MI 48109-0620, USA
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24
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Russell RS, Liang C, Wainberg MA. Is HIV-1 RNA dimerization a prerequisite for packaging? Yes, no, probably? Retrovirology 2004; 1:23. [PMID: 15345057 PMCID: PMC516451 DOI: 10.1186/1742-4690-1-23] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Accepted: 09/02/2004] [Indexed: 01/14/2023] Open
Abstract
During virus assembly, all retroviruses specifically encapsidate two copies of full-length viral genomic RNA in the form of a non-covalently linked RNA dimer. The absolute conservation of this unique genome structure within the Retroviridae family is strong evidence that a dimerized genome is of critical importance to the viral life cycle. An obvious hypothesis is that retroviruses have evolved to preferentially package two copies of genomic RNA, and that dimerization ensures the proper packaging specificity for such a genome. However, this implies that dimerization must be a prerequisite for genome encapsidation, a notion that has been debated for many years. In this article, we review retroviral RNA dimerization and packaging, highlighting the research that has attempted to dissect the intricate relationship between these two processes in the context of HIV-1, and discuss the therapeutic potential of these putative antiretroviral targets.
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Affiliation(s)
- Rodney S Russell
- McGill AIDS Centre, Lady Davis Institute, Jewish General Hospital, 3755 Cote Ste-Catherine Road Montreal, Quebec, Canada H3T 1E2
- Department of Microbiology & Immunology Montreal, Quebec, Canada H3A 2B4
| | - Chen Liang
- McGill AIDS Centre, Lady Davis Institute, Jewish General Hospital, 3755 Cote Ste-Catherine Road Montreal, Quebec, Canada H3T 1E2
- Department of Medicine, McGill University, Montreal, Quebec, Canada H3A 2B4
| | - Mark A Wainberg
- McGill AIDS Centre, Lady Davis Institute, Jewish General Hospital, 3755 Cote Ste-Catherine Road Montreal, Quebec, Canada H3T 1E2
- Department of Microbiology & Immunology Montreal, Quebec, Canada H3A 2B4
- Department of Medicine, McGill University, Montreal, Quebec, Canada H3A 2B4
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25
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Greatorex J. The retroviral RNA dimer linkage: different structures may reflect different roles. Retrovirology 2004; 1:22. [PMID: 15317659 PMCID: PMC516450 DOI: 10.1186/1742-4690-1-22] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2004] [Accepted: 08/18/2004] [Indexed: 11/16/2022] Open
Abstract
Retroviruses are unique among virus families in having dimeric genomes. The RNA sequences and structures that link the two RNA molecules vary, and these differences provide clues as to the role of this feature in the viral lifecycles. This review draws upon examples from different retroviral families. Differences and similarities in both secondary and tertiary structure are discussed. The implication of varying roles for the dimer linkage in related viruses is considered.
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Affiliation(s)
- Jane Greatorex
- Division of Infectious Diseases, Dept. of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 2QQ, UK.
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26
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Evans MJ, Bacharach E, Goff SP. RNA sequences in the Moloney murine leukemia virus genome bound by the Gag precursor protein in the yeast three-hybrid system. J Virol 2004; 78:7677-84. [PMID: 15220442 PMCID: PMC434088 DOI: 10.1128/jvi.78.14.7677-7684.2004] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Encapsidation of the Moloney murine leukemia virus (MMLV) genome is mediated through a specific interaction between the major viral structural protein, Gag, and an RNA packaging signal, Psi. Many studies have investigated this process in vivo, although the specific examination of the Gag-RNA interaction in this context is difficult due to the variety of other viral functions involved in virion assembly in vivo. The Saccharomyces cerevisiae three-hybrid assay was used to directly examine the interaction between MMLV Gag and Psi. In this system, MMLV RNA regions exhibiting high-affinity Gag binding were mapped. All Gag-binding regions were located 3' to the viral splice donor sequence of the viral RNA transcript. No single short RNA sequence within Psi supported strong Gag interaction. Instead, an RNA comprised of nearly the entire Psi region was necessary to demonstrate an appreciable Gag interaction in the yeast three-hybrid system. These finding support the notion that two stem-loops (C and D) are not sufficient to form a core MMLV encapsidation signal.
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Affiliation(s)
- Matthew J Evans
- Department of Biochemistry and Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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27
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Réblová K, Spacková N, Sponer JE, Koca J, Sponer J. Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Res 2004; 31:6942-52. [PMID: 14627827 PMCID: PMC290250 DOI: 10.1093/nar/gkg880] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Explicit solvent molecular dynamics (MD) simulations were carried out for three RNA kissing-loop complexes. The theoretical structure of two base pairs (2 bp) complex of H3 stem-loop of Moloney murine leukemia virus agrees with the NMR structure with modest violations of few NMR restraints comparable to violations present in the NMR structure. In contrast to the NMR structure, however, MD shows relaxed intermolecular G-C base pairs. The core region of the kissing complex forms a cation-binding pocket with highly negative electrostatic potential. The pocket shows nanosecond-scale breathing motions coupled with oscillations of the whole molecule. Additional simulations were carried out for 6 bp kissing complexes of the DIS HIV-1 subtypes A and B. The simulated structures agree well with the X-ray data. The subtype B forms a novel four-base stack of bulged-out adenines. Both 6 bp kissing complexes have extended cation-binding pockets in their central parts. While the pocket of subtype A interacts with two hexacoordinated Mg2+ ions and one sodium ion, pocket of subtype B is filled with a string of three delocalized Na+ ions with residency times of individual cations 1-2 ns. The 6 bp complexes show breathing motions of the cation-binding pockets and loop major grooves.
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Affiliation(s)
- Kamila Réblová
- National Center for Biomolecular Research, Masaryk University, Kotlárská 2, 611 37 Brno, Czech Republic
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28
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Paillart JC, Shehu-Xhilaga M, Marquet R, Mak J. Dimerization of retroviral RNA genomes: an inseparable pair. Nat Rev Microbiol 2004; 2:461-72. [PMID: 15152202 DOI: 10.1038/nrmicro903] [Citation(s) in RCA: 232] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Jean-Christophe Paillart
- UPR 9002 du CNRS affiliée à l'Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France
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29
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D'Souza V, Dey A, Habib D, Summers MF. NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus. J Mol Biol 2004; 337:427-42. [PMID: 15003457 DOI: 10.1016/j.jmb.2004.01.037] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2004] [Revised: 01/19/2004] [Accepted: 01/20/2004] [Indexed: 10/26/2022]
Abstract
The full length, positive-strand genome of the Moloney Murine Leukemia Virus contains a "core encapsidation signal" that is essential for efficient genome packaging during virus assembly. We have determined the structure of a 101-nucleotide RNA that contains this signal (called mPsi) using a novel isotope-edited NMR approach. The method is robust and should be generally applicable to larger RNAs. mPsi folds into three stem loops, two of which (SL-C and SL-D) co-stack to form an extended helix. The third stem loop (SL-B) is connected to SL-C by a flexible, four-nucleotide linker. The structure contains five mismatched base-pairs, an unusual C.CG base-triple platform, and a novel "A-minor K-turn," in which unpaired adenosine bases A340 and A341 of a GGAA bulge pack in the minor groove of a proximal stem, and a bulged distal uridine (U319) forms a hydrogen bond with the phosphodiester of A341. Phylogenetic analyses indicate that these essential structural elements are conserved among the murine C-type retroviruses.
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Affiliation(s)
- Victoria D'Souza
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
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30
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Aagaard L, Rasmussen SV, Mikkelsen JG, Pedersen FS. Efficient replication of full-length murine leukemia viruses modified at the dimer initiation site regions. Virology 2004; 318:360-70. [PMID: 14972561 DOI: 10.1016/j.virol.2003.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2003] [Revised: 09/08/2003] [Accepted: 09/11/2003] [Indexed: 11/29/2022]
Abstract
Retroviruses encapsidate two copies of full-length viral RNA molecules linked together as a dimeric genome. RNA stem loop structures harboring palindromic (or "kissing") loop sequences constitute important cis-elements for viral dimerization known as dimer initiation sites (DIS). In murine leukemia virus (MLV), a 10-mer and a 16-mer palindrome (DIS-1 and DIS-2, respectively) located in the viral leader region mediate dimerization in vitro and affect dimer stability of vector RNA in vivo. We have investigated the effect on viral replication of introducing deletions or nucleotide substitutions within these palindromes in a full-length MLV genome. Our results demonstrate that viruses modified at the dimer initiation site regions are viable and show wild-type levels of RNA encapsidation. One mutant lacking the DIS-1 palindrome was severely impaired and displayed an increased cellular ratio of spliced versus genomic RNA that most likely contributes to the inefficient replication. The implications for development of DIS-modified retrovirus-based vectors are discussed.
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Affiliation(s)
- Lars Aagaard
- Department of Molecular Biology, University of Aarhus, DK-8000 Aarhus, Denmark
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31
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Mikkelsen JG, Rasmussen SV, Pedersen FS. Complementarity-directed RNA dimer-linkage promotes retroviral recombination in vivo. Nucleic Acids Res 2004; 32:102-14. [PMID: 14715920 PMCID: PMC373270 DOI: 10.1093/nar/gkh159] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Retroviral particles contain a dimeric RNA genome, which serves as template for the generation of double-stranded DNA by reverse transcription. Transfer between RNA strands during DNA synthesis is governed by both sequence similarity between templates and structural features of the dimeric RNA. A kissing hairpin, believed to facilitate intermolecular recognition and dimer formation, was previously found to be a preferred site for recombination. To investigate if hairpin loop-loop-complementarity is the primary determinant for this recombination preference, we have devised a novel 5' leader recombination assay based upon co-packaging of two wild-type or loop-modified murine leukemia virus vector RNAs. We found that insertion of an alternative palindromic loop in one of the two vectors disrupted site-directed template switching, whereas site-specificity was restored between vectors with complementary non-wild-type palindromes. By pairing vector RNAs that contained identical non-palindromic loop motifs and that were unlikely to interact by loop-loop kissing, we found no preference for recombination at the kissing hairpin site. Of vector pairs designed to interact through base pairing of non-palindromic loop motifs, we could in one case restore hairpin-directed template switching, in spite of the reduced sequence identity, whereas another pair failed to support hairpin- directed recombination. However, analyses of in vitro RNA dimerization of all studied vector combinations showed a good correlation between efficient dimer formation between loop-modified viral RNAs and in vivo cDNA transfer at the kissing hairpin. Our findings demonstrate that complementarity between wild-type or non-wild-type hairpin kissing loops is essential but not sufficient for site-specific 5' leader recombination and lend further support to the hypothesis that a specific 'kissing' loop-loop interaction is guided by complementary sequences and maintained within the mature dimeric RNA of retroviruses.
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32
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Rasmussen SV, Mikkelsen JG, Pedersen FS. Modulation of homo- and heterodimerization of Harvey sarcoma virus RNA by GACG tetraloops and point mutations in palindromic sequences. J Mol Biol 2002; 323:613-28. [PMID: 12419254 DOI: 10.1016/s0022-2836(02)00966-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Retroviruses harbour a diploid genome of two plus-strand RNAs linked non-covalently at the dimer linkage structure. Co-packaging of two parental RNAs is a prerequisite for recombination in retroviruses, but formation of heterodimers has not been demonstrated directly in vivo. Here, we explore elements in Harvey sarcoma virus (HaSV) RNA involved in homodimerization and heterodimerization with RNA of Moloney (Mo) and Akv murine leukemia viruses (MLV). By an in vitro assay, we found that HaSV dimerization specificity could be modulated by mutations in a decanucleotide palindrome (Pal) probably folded into a kissing-loop. Autocomplementary and non-autocomplementary sequences introduced into the putative loop directed the specificity towards formation of homodimers and heterodimers, respectively. Two stem-loop (SL) structures, both exposing a GACG tetraloop, enhanced the formation of stable HaSV dimers.A similar decanucleotide palindrome has been implicated in homodimerization of MLVs. Heterodimers between HaSV RNA and Mo- or Akv MLV were unstable, but could be stabilized by introduction of two point mutations in the putative HaSV kissing-loop, creating exact complementarity with Mo/Akv MLV palindromes. Moreover, such changes increased the HaSV RNA affinity for the two MLV RNAs. Similar to HaSV RNA homodimers, formation of heterodimers with Mo- or Akv MLV RNAs was induced by the presence of GACG loops. On the basis of these results, we propose that palindromic sequences act as variable determinants of specificity and GACG tetraloops as conserved determinants in the formation of homodimers and heterodimers of gamma-retrovirus retroviral RNAs in vivo. The complementarity of loop sequences in the packaging signal upstream of the GACG tetraloops might therefore determine homo- and heterodimerization specificity and recombination activity of these viruses.
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33
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Abstract
RNA loop-loop interactions are frequently used to trigger initial recognition between two RNA molecules. In this review, we present selected well-documented cases that illustrate the diversity of biological processes using RNA loop-loop recognition properties. The first one is related to natural antisense RNAs that play a variety of regulatory functions in bacteria and their extra-chromosomal elements. The second one concerns the dimerization of HIV-1 genomic RNA, which is responsible for the encapsidation of a diploid RNA genome. The third one concerns RNA interactions involving double-loop interactions. These are used by the bicoid mRNA to form dimers, a property that appears to be important for mRNA localization in drosophila embryo, and by bacteriophage phi29 pRNA which forms hexamers that participate in the translocation of the DNA genome through the portal vertex of the capsid. Despite the high diversity of systems and mechanisms, some common features can be highlighted. (1) Efficient recognition requires rapid bi-molecular binding rates, regardless of the RNA pairing scheme. (2) The initial recognition is favored by particular conformations of the loops enabling a proper presentation of nucleotides (generally a restricted number) that initiate the recognition process. (3) The fate of the initial reversible loop-loop complex is dictated by both functional and structural constraints. RNA structures have evolved either to "freeze" the initial complex, or to convert it into a more stable one, which involves propagation of intermolecular interactions along topologically feasible pathways. Stabilization of the initial complex may also be assisted by proteins and/or formation of additional contacts.
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Affiliation(s)
- Christine Brunel
- UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
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Owens GC, Mistry S, Edelman GM, Crossin KL. Efficient marking of neural stem cell-derived neurons with a modified murine embryonic stem cell virus, MESV2. Gene Ther 2002; 9:1044-8. [PMID: 12101436 DOI: 10.1038/sj.gt.3301780] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2001] [Accepted: 04/04/2002] [Indexed: 11/09/2022]
Abstract
Treatments for nervous system disorders that involve transplanting genetically modified neural stem cells may ultimately be feasible. As a step towards this therapeutic approach, a novel murine embryonic stem cell gammaretroviral vector was developed with features designed to optimize transgene expression in neural stem cells and to increase vector safety. All potential start sites of translation in the 5' leader were removed. These sites may compete with an inserted transgene for translation initiation, and also produce potentially immunogenic peptides. Further, all of the gag gene sequences were replaced with a well-defined constitutive transport element from avian leukemia virus to promote nuclear export of viral RNA, and to eliminate any homology between the vector and a murine leukemia virus-derived gag-pol packaging plasmid. Two versions of the virus were made in which EGFP expression was driven either by the Rous sarcoma virus U3 enhancer or by a combination of sequences from the Syn1 and Pgk-1 promoters. Both of these viruses efficiently transduced neural stem cells isolated from embryonic rat hippocampus, and robust EGFP expression was observed in neurons derived from these cells following differentiation in vitro.
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Affiliation(s)
- G C Owens
- The Neurosciences Institute, San Diego, CA 92121, USA
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35
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Abstract
An essential step in the replication cycle of all retroviruses is the dimerization of genomic RNA prior to or during encapsidation and budding. In HIV-1, a stem-loop structure in the genomic RNA called the dimerization initiation site, or DIS, has been well characterized. However, the identification of the structure(s) necessary for dimerization of HIV-2 genomic RNA has been less straightforward, as reflected by recent conflicting reports. Here, using a variety of mutant and wild-type RNA constructs and a systematic analysis of experimental conditions, we demonstrate that two dimerization sites in HIV-2 RNA are clearly discernible under different experimental conditions. A short sequence overlapping the primer binding site acts as the default dimerization site for wild-type viral RNA transcripts of several lengths provided that dimerization incubation conditions do not include a high heat step (>50 degrees C), and electrophoresis is carried out under mild conditions that do not deplete the RNA of magnesium. However, some RNA constructs are able to dimerize through stem-loop 1 (SL1), which is the structure homologous to the HIV-1 DIS, under certain experimental conditions. Interestingly, deletion or mutation of the default PBS dimerization site leads to efficient usage of the SL1 dimerization site. This study defines conditions under which each site may be used for dimerization and demonstrates, furthermore, the facility with which the two sites can substitute for each other. This is suggestive of a switching mechanism that may be used in the viral replication cycle.
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Affiliation(s)
- Jean-Marc Lanchy
- Division of Biological Sciences, The University of Montana, Science Complex Room 202, Missoula, MT 59812-1002, USA
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36
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Abstract
We investigated the features of the Moloney murine sarcoma virus leader sequence necessary for RNA packaging function by using a deletion analysis approach. We found that sequences that extend beyond those characterized genetically in previous reports are important for optimal packaging efficiency. A fragment covering a minimum of four potential stem-loop structures is required for the shortest packaging element compatible with gene transfer. Our results reveal the extent to which each of the segments of the packaging sequence contribute to packaging efficiency.
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Affiliation(s)
- Elena Izmailova
- Department of Medicine, Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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37
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Abstract
Retroviral virions each contain two identical genomic RNA strands that are stably but noncovalently joined in parallel near their 5' ends. For certain viruses, this dimerization has been shown to depend on a unique RNA stem-loop locus, called the dimer initiation site (DIS), that efficiently homodimerizes through a palindromic base sequence in its loop. Previous studies with Moloney murine leukemia virus (Mo-MuLV) identified two alternative DIS loci that can each independently support RNA dimerization in vitro but whose relative contributions are unknown. We now report that both of these loci contribute to the assembly of the Mo-MuLV dimer. Using targeted deletions, point mutagenesis, and antisense oligonucleotides, we found that each of the two stem-loops forms as predicted and contributes independently to dimerization in vitro through a mechanism involving autocomplementary interactions of its loop. Disruption of either DIS locus individually reduced both the yield and the thermal stability of the in vitro dimers, whereas disruption of both eliminated dimerization altogether. Similarly, the thermal stability of virion-derived dimers was impaired by deletion of both DIS elements, and point mutations in either element produced defects in viral replication that correlated with their effects on in vitro RNA dimerization. These findings support the view that in some retroviruses, dimer initiation and stability involve two or more closely linked DIS loci which together align the nascent dimer strands in parallel and in register.
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Affiliation(s)
- Hinh Ly
- Department of Pathology, University of California, San Francisco, California 94143-0511, USA
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D'Souza V, Melamed J, Habib D, Pullen K, Wallace K, Summers MF. Identification of a high affinity nucleocapsid protein binding element within the Moloney murine leukemia virus Psi-RNA packaging signal: implications for genome recognition. J Mol Biol 2001; 314:217-32. [PMID: 11718556 DOI: 10.1006/jmbi.2001.5139] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Murine leukemia virus (MLV) is currently the most widely used gene delivery system in gene therapy trials. The simple retrovirus packages two copies of its RNA genome by a mechanism that involves interactions between the nucleocapsid (NC) domain of a virally-encoded Gag polyprotein and a segment of the RNA genome located just upstream of the Gag initiation codon, known as the Psi-site. Previous studies indicated that the MLV Psi-site contains three stem loops (SLB-SLD), and that stem loops SLC and SLD play prominent roles in packaging. We have developed a method for the preparation and purification of large quantities of recombinant Moloney MLV NC protein, and have studied its interactions with a series of oligoribonucleotides that contain one or more of the Psi-RNA stem loops. At RNA concentrations above approximately 0.3 mM, isolated stem loop SLB forms a duplex and stem loops SL-C and SL-D form kissing complexes, as expected from previous studies. However, neither the monomeric nor the dimeric forms of these isolated stem loops binds NC with significant affinity. Longer constructs containing two stem loops (SL-BC and SL-CD) also exhibit low affinities for NC. However, NC binds with high affinity and stoichiometrically to both the monomeric and dimeric forms of an RNA construct that contains all three stem loops (SL-BCD; K(d)=132(+/-55) nM). Titration of SL-BCD with NC also shifts monomer-dimer equilibrium toward the dimer. Mutagenesis experiments demonstrate that the conserved GACG tetraloops of stem loops C and D do not influence the monomer-dimer equilibrium of SL-BCD, that the tetraloop of stem loop B does not participate directly in NC binding, and that the tetraloops of stem loops C and D probably also do not bind to NC. These surprising results differ considerably from those observed for HIV-1, where NC binds to individual stem loops with high affinity via interactions with exposed residues of the tetraloops. The present results indicate that MLV NC binds to a pocket or surface that only exists in the presence of all three stem loops.
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Affiliation(s)
- V D'Souza
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
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39
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Monie T, Greatorex J, Lever AM. Oligonucleotide mapping of the core genomic RNA dimer linkage in human T-cell leukaemia virus type-1. Virus Res 2001; 78:45-56. [PMID: 11520579 DOI: 10.1016/s0168-1702(01)00283-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have previously mapped the sequences required for dimerisation of the 5' leader of the human T-cell leukaemia virus type-1 (HTLV-1) genome. The smallest sequence necessary and sufficient for dimer formation, in vitro, was ascertained to be a 37 nucleotide (nt) region downstream of the splice donor and just upstream of the primer binding site. Deletion of a 32 base-pair sequence encompassing this region within the provirus was associated with a minor decrease in infectivity of the virus in an in vitro system. To further map and help elucidate the nature of the dimer linkage, we used RNA and DNA oligonucleotide competition assays to define the nucleotides involved. These experiments revealed that a 14 nt sequence containing a potential stem loop structure, formed from a palindromic sequence, is important for dimer formation. This was confirmed by the ability of this RNA sequence to form heterodimers with larger RNA transcripts from the same region, while sequences lacking this motif could not. RNA transcripts containing the reverse sequence, the same nucleotides in a random arrangement, and complementary DNA oligos, all failed to form heterodimers with the 14 nt sequence. The primary dimer initiation site of HTLV-1 has thus been located to a 14 nt palindrome containing sequence, and dimerisation is shown to be dependent on specific sense-sense RNA interactions.
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Affiliation(s)
- T Monie
- Department of Medicine, University of Cambridge, Level 5, Addenbrooke's Hospital, Hills Road, CB2 2QQ, Cambridge, UK
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40
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Sakuragi J, Shioda T, Panganiban AT. Duplication of the primary encapsidation and dimer linkage region of human immunodeficiency virus type 1 RNA results in the appearance of monomeric RNA in virions. J Virol 2001; 75:2557-65. [PMID: 11222678 PMCID: PMC115878 DOI: 10.1128/jvi.75.6.2557-2565.2001] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The dimerization initiation site (DIS) and the dimer linkage sequences (DLS) of human immunodeficiency virus type 1 have been shown to mediate in vitro dimerization of genomic RNA. However, the precise role of the DIS-DLS region in virion assembly and RNA dimerization in virus particles has not been fully elucidated, since deletion or mutation of the DIS-DLS region also abolishes the packaging ability of genomic RNA. To characterize the DIS-DLS region without altering packaging ability, we generated mutant constructs carrying a duplication of approximately 1,000 bases including the encapsidation signal and DIS-DLS (E/DLS) region. We found that duplication of the E/DLS region resulted in the appearance of monomeric RNA in virus particles. No monomers were observed in virions of mutants carrying the E/DLS region only at ectopic positions. Monomers were not observed when pol or env regions were duplicated, indicating an absolute need for two intact E/DLS regions on the same RNA for generating particles with monomeric RNA. These monomeric RNAs were most likely generated by intramolecular interaction between two E/DLS regions on one genome. Moreover, incomplete genome dimerization did not affect RNA packaging and virion formation. Examination of intramolecular interaction between E/DLS regions could be a convenient tool for characterizing the E/DLS region in virion assembly and RNA dimerization within virus particles.
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Affiliation(s)
- J Sakuragi
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
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41
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Jossinet F, Lodmell JS, Ehresmann C, Ehresmann B, Marquet R. Identification of the in vitro HIV-2/SIV RNA dimerization site reveals striking differences with HIV-1. J Biol Chem 2001; 276:5598-604. [PMID: 11092889 DOI: 10.1074/jbc.m008642200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Although their genomes cannot be aligned at the nucleotide level, the HIV-1/SIVcpz and the HIV-2/SIVsm viruses are closely related lentiviruses that contain homologous functional and structural RNA elements in their 5'-untranslated regions. In both groups, the domains containing the trans-activating region, the 5'-copy of the polyadenylation signal, and the primer binding site (PBS) are followed by a short stem-loop (SL1) containing a six-nucleotide self-complementary sequence in the loop, flanked by unpaired purines. In HIV-1, SL1 is involved in the dimerization of the viral RNA, in vitro and in vivo. Here, we tested whether SL1 has the same function in HIV-2 and SIVsm RNA. Surprisingly, we found that SL1 is neither required nor involved in the dimerization of HIV-2 and SIV RNA. We identified the NarI sequence located in the PBS as the main site of HIV-2 RNA dimerization. cis and trans complementation of point mutations indicated that this self-complementary sequence forms symmetrical intermolecular interactions in the RNA dimer and suggested that HIV-2 and SIV RNA dimerization proceeds through a kissing loop mechanism, as previously shown for HIV-1. Furthermore, annealing of tRNA(3)(Lys) to the PBS strongly inhibited in vitro RNA dimerization, indicating that, in vivo, the intermolecular interaction involving the NarI sequence must be dissociated to allow annealing of the primer tRNA.
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Affiliation(s)
- F Jossinet
- Institut de Biologie Moléculaire et Cellulaire, UPR 9002 du CNRS, 15 rue René Descartes, 67084 Strasbourg, France
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42
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Ly H, Nierlich DP, Olsen JC, Kaplan AH. Functional characterization of the dimer linkage structure RNA of Moloney murine sarcoma virus. J Virol 2000; 74:9937-45. [PMID: 11024121 PMCID: PMC102031 DOI: 10.1128/jvi.74.21.9937-9945.2000] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several determinants that appear to promote the dimerization of murine retroviral genomic RNA have been identified. The interaction between these determinants has not been extensively examined. Previously, we proposed that dimerization of the Moloney murine sarcoma virus genomic RNAs relies upon the concentration-dependent interactions of a conserved palindrome that is initiated by separate G-rich stretches (H. Ly, D. P. Nierlich, J. C. Olsen, and A. H. Kaplan, J. Virol. 73:7255-7261, 1999). The cooperative action of these two elements was examined using a combination of genetic and antisense approaches. Dimerization of RNA molecules carrying both the palindrome and G-rich sequences was completely inhibited by an oligonucleotide complementary to the palindrome; molecules lacking the palindrome could not dimerize in the presence of oligomers that hybridize to two G-rich sequences. The results of spontaneous dimerization experiments also demonstrated that RNA molecules lacking either of the two stretches of guanines dimerized much more slowly than the full-length molecule which includes the dimer linkage structure (DLS). However, the addition of an oligonucleotide complementary to the remaining stretch of guanines restored the kinetics of dimerization to wild-type levels. The ability of this oligomer to rescue the kinetics of dimerization was dependent on the presence of the palindrome, suggesting that interactions within the G-rich regions produce changes in the palindrome that allow dimerization to proceed with maximum efficiency. Further, unsuccessful attempts to produce heterodimers between constructs lacking various combinations of these elements indicate that the G-rich regions and the palindrome do not interact directly. Finally, we demonstrate that both of these elements are important in maintaining efficient viral replication. Modified antisense oligonucleotides targeting the DLS were found to reduce the level of viral vector titer production. The reduction in viral titer is due to a decrease in the efficiency of viral genomic RNA encapsidation. Overall, our data support a dynamic model of retroviral RNA dimerization in which discrete dimerization elements act in a concerted fashion.
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Affiliation(s)
- H Ly
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, North Carolina, USA
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43
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Kim CH, Tinoco I. A retroviral RNA kissing complex containing only two G.C base pairs. Proc Natl Acad Sci U S A 2000; 97:9396-401. [PMID: 10931958 PMCID: PMC16875 DOI: 10.1073/pnas.170283697] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The dimerization of viral RNA through noncovalent interactions at their 5' ends is a key step in the life cycle of retroviruses. In Moloney murine leukemia virus, three stem-loops are important in this process. One is a self-complementary tetraloop (H1), but the other two stem-loops (H2, H3) contain highly conserved GACG tetraloops that are not self-complementary sequences. Using two-dimensional NMR, we determined the structure of the H3 stem-loop. Surprisingly, it forms a stable, homodimeric kissing complex through only two intermolecular G small middle dotC base pairs. Cross-strand interactions of the adenines adjacent to the intermolecular G small middle dotC base pairs, plus unusual strong electrostatic interactions around the base pairs, contribute to the unexpected stability. This structure shows how even stem-loops without self-complementary sequences can facilitate the intermolecular recognition between two identical RNAs, and thus initiate dimerization and encapsidation of retroviral RNAs.
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Affiliation(s)
- C H Kim
- Department of Chemistry, University of California, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley 94720-1460, USA
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44
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Polge E, Darlix JL, Paoletti J, Fossé P. Characterization of loose and tight dimer forms of avian leukosis virus RNA. J Mol Biol 2000; 300:41-56. [PMID: 10864497 DOI: 10.1006/jmbi.2000.3832] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Retroviral genomes consist of two identical RNA molecules joined non-covalently near their 5'-ends. Recently, we showed that an imperfect autocomplementary sequence, located in the L3 domain, plays an essential role in avian sarcoma-leukosis virus (ASLV) RNA dimerization in vitro. This sequence can adopt a stem-loop structure and is involved in ASLV replication. Here, we found that in the absence of nucleocapsid protein, RNA transcripts of avian leukosis virus (ALV) were able to form two types of dimers in vitro that differ in their stability: a loose dimer, formed at a physiological temperature, and a tight dimer, formed at a high temperature. A mutational analysis was performed to define the features of these dimers. The results of this analysis unambiguously confirm that the two L3 stem-loops interact directly in both types of dimers. A loop-loop interaction is the main linkage in the loose dimer. In contrast, in the tight dimer, the stem and the loop of the L3 hairpin form an extended duplex. Surprisingly, we also found that the dimerization properties defined for our ALV strain (type SR-A) differ from those found in other ASLV strains.
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Affiliation(s)
- E Polge
- LBPA-Alembert, Ecole Normale Supérieure de Cachan, Unité Mixte de Recherche 8532 du CNRS, Cachan cedex, 94235, France
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45
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Mikkelsen JG, Lund AH, Duch M, Pedersen FS. Mutations of the kissing-loop dimerization sequence influence the site specificity of murine leukemia virus recombination in vivo. J Virol 2000; 74:600-10. [PMID: 10623721 PMCID: PMC111579 DOI: 10.1128/jvi.74.2.600-610.2000] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genetic information of retroviruses is retained within a dimeric RNA genome held together by intermolecular RNA-RNA interactions near the 5' ends. Coencapsidation of retrovirus-derived RNA molecules allows frequent template switching of the virus-encoded reverse transcriptase during DNA synthesis in newly infected cells. We have previously shown that template shifts within the 5' leader of murine leukemia viruses occur preferentially within the kissing stem-loop motif, a cis element crucial for in vitro RNA dimer formation. By use of a forced recombination approach based on single-cycle transfer of Akv murine leukemia virus-based vectors harboring defective primer binding site sequences, we now report that modifications of the kissing-loop structure, ranging from a deletion of the entire sequence to introduction of a single point mutation in the loop motif, significantly disturb site specificity of recombination within the highly structured 5' leader region. In addition, we find that an intact kissing-loop sequence favors optimal RNA encapsidation and vector transduction. Our data are consistent with the kissing-loop dimerization model and suggest that a direct intermolecular RNA-RNA interaction, here mediated by palindromic loop sequences within the mature genomic RNA dimer, facilitates hotspot template switching during retroviral cDNA synthesis in vivo.
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Affiliation(s)
- J G Mikkelsen
- Department of Molecular and Structural Biology, University of Aarhus, DK-8000 Aarhus, Denmark
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46
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Banks JD, Kealoha BO, Linial ML. An Mpsi-containing heterologous RNA, but not env mRNA, is efficiently packaged into avian retroviral particles. J Virol 1999; 73:8926-33. [PMID: 10515997 PMCID: PMC112923 DOI: 10.1128/jvi.73.11.8926-8933.1999] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/1999] [Accepted: 07/20/1999] [Indexed: 11/20/2022] Open
Abstract
Retroviruses preferentially package full-length genomic RNA over spliced viral messages. For most retroviruses, this preference is likely due to the absence of all or part of the packaging signal on subgenomic RNAs. In avian leukosis-sarcoma virus, however, we have shown that the minimal packaging signal, MPsi, is located upstream of the 5' splice site and therefore is present on both genomic and spliced RNAs. We now show that an MPsi-containing heterologous RNA is packaged only 2.6-fold less efficiently than genomic Rous sarcoma virus RNA. Thus, few additional packaging sequences and/or structures exist outside of MPsi. In contrast, we found that env mRNA is not efficiently packaged. These results indicate that either MPsi is not functional on this RNA or the RNA is somehow segregated from the packaging machinery. Finally, deletion of sequences from the 3' end of MPsi was found to reduce the packaging efficiency of heterologous RNAs.
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Affiliation(s)
- J D Banks
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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47
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Ly H, Nierlich DP, Olsen JC, Kaplan AH. Moloney murine sarcoma virus genomic RNAs dimerize via a two-step process: a concentration-dependent kissing-loop interaction is driven by initial contact between consecutive guanines. J Virol 1999; 73:7255-61. [PMID: 10438813 PMCID: PMC104250 DOI: 10.1128/jvi.73.9.7255-7261.1999] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Retroviruses contain two plus-strand genomic RNAs, which are stably but noncovalently joined in their 5' regions by a dimer linkage structure (DLS). Two models have been put forward to explain the mechanisms by which the RNAs dimerize; each model emphasizes the role of specific molecular determinants. The kissing-loop model implicates interactions between palindromic sequences in the DLS region. The second model proposes that purine-rich stretches in the region form purine quartet structures. Here, we present an examination of the in vitro dimerization of Moloney murine sarcoma virus (MuSV) RNA in the context of these two models. Dimers were found to form spontaneously in a temperature-, time-, concentration-, and salt-dependent manner. In contrast to earlier reports, we found that deletion of neither the palindrome nor the consensus purine motifs (PuGGAPuA) affected the level of dimer formation at low concentrations of RNA. Rather, different purine-rich sequences, i.e., consecutive stretches of guanines, were found to enhance both in vitro RNA dimerization and in vivo viral replication. Biochemical evidence further suggests that these guanine-rich (G-rich) stretches form guanine quartet structures. We also found that the palindromic sequences could support dimerization at significantly higher RNA concentrations. In addition, the G-rich stretches were as important as the palindromic sequence for maintaining efficient viral replication. Overall, our data support a model that entails contributions from both of the previously proposed mechanisms of retroviral RNA dimerization.
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Affiliation(s)
- H Ly
- Departments of Microbiology & Immunology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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48
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Oroudjev EM, Kang PC, Kohlstaedt LA. An additional dimer linkage structure in Moloney murine leukemia virus RNA. J Mol Biol 1999; 291:603-13. [PMID: 10448040 DOI: 10.1006/jmbi.1999.2984] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have identified an additional dimerization linkage structure in the genome of Moloney murine leukemia virus (MoMLV). Retroviral genomes have long been known to be linked at their 5' ends to form dimers. In MoMLV, a hairpin loop functioning as a dimer linkage structure (DLS) has previously been identified at nucleotides 278-303. Here, we describe RNA dimers formed from sections of the MoMLV 5' untranslated region that do not contain the previously described MoMLV DLS. These dimers exhibit the distinctive characteristics previously described for whole genome dimers. We have mapped this novel region to nucleotides 199-243. This sequence contains a stem-loop structure (nucleotides 204-227) much like the 278-303 region. We describe the chemical and thermal stability of dimers containing the 204-227 stem-loop as well as kinetics and salt-dependence of dimer formation. Our results show that dimerization of MoMLV RNA can be nucleated at multiple sites and suggest that the 5' untranslated region may contain separately folding and dimerizing domains.
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Affiliation(s)
- E M Oroudjev
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
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