1
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Geng A, Ganser L, Roy R, Shi H, Pratihar S, Case DA, Al-Hashimi HM. An RNA excited conformational state at atomic resolution. Nat Commun 2023; 14:8432. [PMID: 38114465 PMCID: PMC10730710 DOI: 10.1038/s41467-023-43673-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/16/2023] [Indexed: 12/21/2023] Open
Abstract
Sparse and short-lived excited RNA conformational states are essential players in cell physiology, disease, and therapeutic development, yet determining their 3D structures remains challenging. Combining mutagenesis, NMR spectroscopy, and computational modeling, we determined the 3D structural ensemble formed by a short-lived (lifetime ~2.1 ms) lowly-populated (~0.4%) conformational state in HIV-1 TAR RNA. Through a strand register shift, the excited conformational state completely remodels the 3D structure of the ground state (RMSD from the ground state = 7.2 ± 0.9 Å), forming a surprisingly more ordered conformational ensemble rich in non-canonical mismatches. The structure impedes the formation of the motifs recognized by Tat and the super elongation complex, explaining why this alternative TAR conformation cannot activate HIV-1 transcription. The ability to determine the 3D structures of fleeting RNA states using the presented methodology holds great promise for our understanding of RNA biology, disease mechanisms, and the development of RNA-targeting therapeutics.
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Affiliation(s)
- Ainan Geng
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Laura Ganser
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Rohit Roy
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, 27708, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
| | - Supriya Pratihar
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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2
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Imperatore JA, Cunningham CL, Pellegrene KA, Brinson R, Marino J, Evanseck J, Mihailescu M. Highly conserved s2m element of SARS-CoV-2 dimerizes via a kissing complex and interacts with host miRNA-1307-3p. Nucleic Acids Res 2021; 50:1017-1032. [PMID: 34908151 PMCID: PMC8789046 DOI: 10.1093/nar/gkab1226] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 01/14/2023] Open
Abstract
The ongoing COVID-19 pandemic highlights the necessity for a more fundamental understanding of the coronavirus life cycle. The causative agent of the disease, SARS-CoV-2, is being studied extensively from a structural standpoint in order to gain insight into key molecular mechanisms required for its survival. Contained within the untranslated regions of the SARS-CoV-2 genome are various conserved stem-loop elements that are believed to function in RNA replication, viral protein translation, and discontinuous transcription. While the majority of these regions are variable in sequence, a 41-nucleotide s2m element within the genome 3' untranslated region is highly conserved among coronaviruses and three other viral families. In this study, we demonstrate that the SARS-CoV-2 s2m element dimerizes by forming an intermediate homodimeric kissing complex structure that is subsequently converted to a thermodynamically stable duplex conformation. This process is aided by the viral nucleocapsid protein, potentially indicating a role in mediating genome dimerization. Furthermore, we demonstrate that the s2m element interacts with multiple copies of host cellular microRNA (miRNA) 1307-3p. Taken together, our results highlight the potential significance of the dimer structures formed by the s2m element in key biological processes and implicate the motif as a possible therapeutic drug target for COVID-19 and other coronavirus-related diseases.
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Affiliation(s)
- Joshua A Imperatore
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282, USA
| | - Caylee L Cunningham
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282, USA
| | - Kendy A Pellegrene
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282, USA
| | - Robert G Brinson
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - John P Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Jeffrey D Evanseck
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282, USA
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3
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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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4
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Merriman DK, Yuan J, Shi H, Majumdar A, Herschlag D, Al-Hashimi HM. Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics. RNA (NEW YORK, N.Y.) 2018; 24:1363-1376. [PMID: 30012568 PMCID: PMC6140463 DOI: 10.1261/rna.066258.118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/05/2018] [Indexed: 05/03/2023]
Abstract
Helical elements separated by bulges frequently undergo transitions between unstacked and coaxially stacked conformations during the folding and function of noncoding RNAs. Here, we examine the dynamic properties of poly-pyrimidine bulges of varying length (n = 1-4, 7) across a range of Mg2+ concentrations using HIV-1 TAR RNA as a model system and solution NMR spectroscopy. In the absence of Mg2+, helices linked by bulges with n ≥ 3 residues adopt predominantly unstacked conformations (stacked population <15%), whereas one-bulge and two-bulge motifs adopt predominantly stacked conformations (stacked population >74%). In the presence of 3 mM Mg2+, the helices predominantly coaxially stack (stacked population >84%), regardless of bulge length, and the midpoint for the Mg2+-dependent stacking transition is within threefold regardless of bulge length. In the absence of Mg2+, the difference between free energy of interhelical coaxial stacking across the bulge variants is estimated to be ∼2.9 kcal/mol, based on an NMR chemical shift mapping with stacking being more energetically disfavored for the longer bulges. This difference decreases to ∼0.4 kcal/mol in the presence of Mg2+ NMR RDCs and resonance intensity data show increased dynamics in the stacked state with increasing bulge length in the presence of Mg2+ We propose that Mg2+ helps to neutralize the growing electrostatic repulsion in the stacked state with increasing bulge length thereby increasing the number of coaxial conformations that are sampled. Energetically compensated interhelical stacking dynamics may help to maximize the conformational adaptability of RNA and allow a wide range of conformations to be optimally stabilized by proteins and ligands.
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Affiliation(s)
- Dawn K Merriman
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Jiayi Yuan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Ananya Majumdar
- Biomolecular NMR Facility, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Hashim M Al-Hashimi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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5
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Kharytonchyk S, Brown JD, Stilger K, Yasin S, Iyer AS, Collins J, Summers MF, Telesnitsky A. Influence of gag and RRE Sequences on HIV-1 RNA Packaging Signal Structure and Function. J Mol Biol 2018; 430:2066-2079. [PMID: 29787767 PMCID: PMC6082134 DOI: 10.1016/j.jmb.2018.05.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 12/22/2022]
Abstract
The packaging signal (Ψ) and Rev-responsive element (RRE) enable unspliced HIV-1 RNAs' export from the nucleus and packaging into virions. For some retroviruses, engrafting Ψ onto a heterologous RNA is sufficient to direct encapsidation. In contrast, HIV-1 RNA packaging requires 5' leader Ψ elements plus poorly defined additional features. We previously defined minimal 5' leader sequences competitive with intact Ψ for HIV-1 packaging, and here examined the potential roles of additional downstream elements. The findings confirmed that together, HIV-1 5' leader Ψ sequences plus a nuclear export element are sufficient to specify packaging. However, RNAs trafficked using a heterologous export element did not compete well with RNAs using HIV-1's RRE. Furthermore, some RNA additions to well-packaged minimal vectors rendered them packaging-defective. These defects were rescued by extending gag sequences in their native context. To understand these packaging defects' causes, in vitro dimerization properties of RNAs containing minimal packaging elements were compared to RNAs with sequence extensions that were or were not compatible with packaging. In vitro dimerization was found to correlate with packaging phenotypes, suggesting that HIV-1 evolved to prevent 5' leader residues' base pairing with downstream residues and misfolding of the packaging signal. Our findings explain why gag sequences have been implicated in packaging and show that RRE's packaging contributions appear more specific than nuclear export alone. Paired with recent work showing that sequences upstream of Ψ can dictate RNA folds, the current work explains how genetic context of minimal packaging elements contributes to HIV-1 RNA fate determination.
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Affiliation(s)
- Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109-5620, United States
| | - Joshua D Brown
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Krista Stilger
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109-5620, United States
| | - Saif Yasin
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Aishwarya S Iyer
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - John Collins
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109-5620, United States
| | - Michael F Summers
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109-5620, United States.
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6
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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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7
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NMR detection of intermolecular interaction sites in the dimeric 5'-leader of the HIV-1 genome. Proc Natl Acad Sci U S A 2016; 113:13033-13038. [PMID: 27791166 DOI: 10.1073/pnas.1614785113] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
HIV type-1 (HIV-1) contains a pseudodiploid RNA genome that is selected for packaging and maintained in virions as a noncovalently linked dimer. Genome dimerization is mediated by conserved elements within the 5'-leader of the RNA, including a palindromic dimer initiation signal (DIS) that has been proposed to form kissing hairpin and/or extended duplex intermolecular contacts. Here, we have applied a 2H-edited NMR approach to directly probe for intermolecular interactions in the full-length, dimeric HIV-1 5'-leader (688 nucleotides; 230 kDa). The interface is extensive and includes DIS:DIS base pairing in an extended duplex state as well as intermolecular pairing between elements of the upstream Unique-5' (U5) sequence and those near the gag start site (AUG). Other pseudopalindromic regions of the leader, including the transcription activation (TAR), polyadenylation (PolyA), and primer binding (PBS) elements, do not participate in intermolecular base pairing. Using a 2H-edited one-dimensional NMR approach, we also show that the extended interface structure forms on a time scale similar to that of overall RNA dimerization. Our studies indicate that a kissing dimer-mediated structure, if formed, exists only transiently and readily converts to the extended interface structure, even in the absence of the HIV-1 nucleocapsid protein or other RNA chaperones.
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8
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Merriman DK, Xue Y, Yang S, Kimsey IJ, Shakya A, Clay M, Al-Hashimi HM. Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales. Biochemistry 2016; 55:4445-56. [PMID: 27232530 DOI: 10.1021/acs.biochem.6b00285] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Helix-junction-helix (HJH) motifs are flexible building blocks of RNA architecture that help define the orientation and dynamics of helical domains. They are also frequently involved in adaptive recognition of proteins and small molecules and in the formation of tertiary contacts. Here, we use a battery of nuclear magnetic resonance techniques to examine how deleting a single bulge residue (C24) from the human immunodeficiency virus type 1 (HIV-1) transactivation response element (TAR) trinucleotide bulge (U23-C24-U25) affects dynamics over a broad range of time scales. Shortening the bulge has an effect on picosecond-to-nanosecond interhelical and local bulge dynamics similar to that casued by increasing the Mg(2+) and Na(+) concentration, whereby a preexisting two-state equilibrium in TAR is shifted away from a bent flexible conformation toward a coaxial conformation, in which all three bulge residues are flipped out and flexible. Surprisingly, the point deletion minimally affects microsecond-to-millisecond conformational exchange directed toward two low-populated and short-lived excited conformational states that form through reshuffling of bases pairs throughout TAR. The mutant does, however, adopt a slightly different excited conformational state on the millisecond time scale, in which U23 is intrahelical, mimicking the expected conformation of residue C24 in the excited conformational state of wild-type TAR. Thus, minor changes in HJH topology preserve motional modes in RNA occurring over the picosecond-to-millisecond time scales but alter the relative populations of the sampled states or cause subtle changes in their conformational features.
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Affiliation(s)
- Dawn K Merriman
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - Yi Xue
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Shan Yang
- Baxter Health Care (Suzhou) Company, Ltd. , Suzhou, Jiang Su 215028, China
| | - Isaac J Kimsey
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Anisha Shakya
- Department of Chemistry and Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Mary Clay
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Hashim M Al-Hashimi
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States
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9
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van Bel N, Ghabri A, Das AT, Berkhout B. The HIV-1 leader RNA is exquisitely sensitive to structural changes. Virology 2015; 483:236-52. [DOI: 10.1016/j.virol.2015.03.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 03/05/2015] [Accepted: 03/27/2015] [Indexed: 01/14/2023]
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10
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Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Hovorun DM. Phylogenetic study on structural elements of HIV-1 poly(A) region. 2. USE domain and TAR hairpin. ACTA ACUST UNITED AC 2014. [DOI: 10.7124/bc.000879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | | | | | - D. M. Hovorun
- Institute of Molecular Biology and Genetics, NAS of Ukraine
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11
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Abstract
The 5' untranslated leader region of the human immunodeficiency virus type 1 (HIV-1) RNA genome is a strongly conserved sequence that encodes several regulatory motifs important for viral replication. Most of these motifs are exposed as hairpin structures, including the dimerization initiation signal (DIS), the major splice donor site (SD), and the packaging signal (Ψ), which are connected by short single-stranded regions. Mutational analysis revealed many functions of these hairpins, but only a few studies have focused on the single-stranded purine-rich sequences. Using the in vivo SELEX (systematic evolution of ligands by exponential enrichment) approach, we probed the sequence space in these regions that is compatible with efficient HIV-1 replication and analyzed the impact on the RNA secondary structure of the leader RNA. Our results show a strong sequence requirement for the DIS hairpin flanking regions. We postulate that these sequences are important for the binding of specific protein factors that support leader RNA-mediated functions. The sequence between the SD and Ψ hairpins seems to have a less prominent role, despite the strong conservation of the stretch of 5 A residues in natural isolates. We hypothesize that this may reflect the subtle evolutionary pressure on HIV-1 to acquire an A-rich RNA genome. In silico analyses indicate that sequences are avoided in all 3 single-stranded domains that affect the local or overall leader RNA folding. IMPORTANCE Many regulatory RNA sequences are clustered in the untranslated leader domain of the HIV-1 RNA genome. Several RNA hairpin structures in this domain have been proposed to fulfill specific roles, e.g., mediating RNA dimer formation to facilitate HIV-1 recombination. We now focus on the importance of a few well-conserved single-stranded sequences that connect these hairpins. We created libraries of HIV-1 variants in which these segments were randomized and selected the best-replicating variants. For two segments we document the selection of the (nearly) wild-type sequence, thus demonstrating the importance of these primary nucleotide sequences and the power of the in vivo SELEX approach. However, for the third segment a large variety of sequences is compatible with efficient HIV-1 replication. Interestingly, the A-rich sequence of this segment is highly conserved among HIV-1 isolates, which likely reflects the evolutionary tendency of HIV-1 to adopt A-rich sequences.
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12
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Kenyon JC, Prestwood LJ, Le Grice SFJ, Lever AML. In-gel probing of individual RNA conformers within a mixed population reveals a dimerization structural switch in the HIV-1 leader. Nucleic Acids Res 2013; 41:e174. [PMID: 23935074 PMCID: PMC3794615 DOI: 10.1093/nar/gkt690] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Definitive secondary structural mapping of RNAs in vitro can be complicated by the presence of more than one structural conformer or multimerization of some of the molecules. Until now, probing a single structure of conformationally flexible RNA molecules has typically relied on introducing stabilizing mutations or adjusting buffer conditions or RNA concentration. Here, we present an in-gel SHAPE (selective 2'OH acylation analysed by primer extension) approach, where a mixed structural population of RNA molecules is separated by non-denaturing gel electrophoresis and the conformers are individually probed within the gel matrix. Validation of the technique using a well-characterized RNA stem-loop structure, the HIV-1 trans-activation response element, showed that authentic structure was maintained and that the method was accurate and highly reproducible. To further demonstrate the utility of in-gel SHAPE, we separated and examined monomeric and dimeric species of the HIV-1 packaging signal RNA. Extensive differences in acylation sensitivity were seen between monomer and dimer. The results support a recently proposed structural switch model of RNA genomic dimerization and packaging, and demonstrate the discriminatory power of in-gel SHAPE.
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Affiliation(s)
- Julia C Kenyon
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, Cambridgeshire, CB2 0QQ, UK and HIV-Drug Resistance Program, Centre for Cancer Research, National Cancer Institute, P.O. Box B, Building 535, Frederick, MD 21702-1201, USA
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13
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Parkash B, Ranjan A, Tiwari V, Gupta SK, Kaur N, Tandon V. Inhibition of 5'-UTR RNA conformational switching in HIV-1 using antisense PNAs. PLoS One 2012; 7:e49310. [PMID: 23152893 PMCID: PMC3495914 DOI: 10.1371/journal.pone.0049310] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Accepted: 10/08/2012] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The genome of retroviruses, including HIV-1, is packaged as two homologous (+) strand RNA molecules, noncovalently associated close to their 5'-end in a region called dimer linkage structure (DLS). Retroviral HIV-1 genomic RNAs dimerize through complex interactions between dimerization initiation sites (DIS) within the (5'-UTR). Dimer formation is prevented by so calledLong Distance Interaction (LDI) conformation, whereas Branched Multiple Hairpin (BMH) conformation leads to spontaneous dimerization. METHODS AND RESULTS We evaluated the role of SL1 (DIS), PolyA Hairpin signal and a long distance U5-AUG interaction by in-vitro dimerization, conformer assay and coupled dimerization and template-switching assays using antisense PNAs. Our data suggests evidence that PNAs targeted against SL1 produced severe inhibitory effect on dimerization and template-switching processes while PNAs targeted against U5 region do not show significant effect on dimerization and template switching, while PNAs targeted against AUG region showed strong inhibition of dimerization and template switching processes. CONCLUSIONS Our results demonstrate that PNA can be used successfully as an antisense to inhibit dimerization and template switching process in HIV -1 and both of the processes are closely linked to each other. Different PNA oligomers have ability of switching between two thermodynamically stable forms. PNA targeted against DIS and SL1 switch, LDI conformer to more dimerization friendly BMH form. PNAs targeted against PolyA haipin configuration did not show a significant change in dimerization and template switching process. The PNA oligomer directed against the AUG strand of U5-AUG duplex structure also showed a significant reduction in RNA dimerization as well as template- switching efficiency.The antisense PNA oligomers can be used to regulate the shift in the LDI/BMH equilibrium.
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Affiliation(s)
- Braham Parkash
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Atul Ranjan
- Department of Chemistry, University of Delhi, Delhi, India
| | - Vinod Tiwari
- Department of Chemistry, University of Delhi, Delhi, India
| | - Sharad Kumar Gupta
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Navrinder Kaur
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Vibha Tandon
- Department of Chemistry, University of Delhi, Delhi, India
- * E-mail:
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14
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Das AT, Vrolijk MM, Harwig A, Berkhout B. Opening of the TAR hairpin in the HIV-1 genome causes aberrant RNA dimerization and packaging. Retrovirology 2012; 9:59. [PMID: 22828074 PMCID: PMC3432602 DOI: 10.1186/1742-4690-9-59] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 07/04/2012] [Indexed: 01/29/2023] Open
Abstract
Background The TAR hairpin is present at both the 5′ and 3′ end of the HIV-1 RNA genome. The 5′ element binds the viral Tat protein and is essential for Tat-mediated activation of transcription. We recently observed that complete TAR deletion is allowed in the context of an HIV-1 variant that does not depend on this Tat-TAR axis for transcription. Mutations that open the 5′ stem-loop structure did however affect the leader RNA conformation and resulted in a severe replication defect. In this study, we set out to analyze which step of the HIV-1 replication cycle is affected by this conformational change of the leader RNA. Results We demonstrate that opening the 5′ TAR structure through a deletion in either side of the stem region caused aberrant dimerization and reduced packaging of the unspliced viral RNA genome. In contrast, truncation of the TAR hairpin through deletions in both sides of the stem did not affect RNA dimer formation and packaging. Conclusions These results demonstrate that, although the TAR hairpin is not essential for RNA dimerization and packaging, mutations in TAR can significantly affect these processes through misfolding of the relevant RNA signals.
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Affiliation(s)
- Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
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