1
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Bowen NE, Oo A, Kim B. Mechanistic Interplay between HIV-1 Reverse Transcriptase Enzyme Kinetics and Host SAMHD1 Protein: Viral Myeloid-Cell Tropism and Genomic Mutagenesis. Viruses 2022; 14:v14081622. [PMID: 35893688 PMCID: PMC9331428 DOI: 10.3390/v14081622] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/23/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) has been the primary interest among studies on antiviral discovery, viral replication kinetics, drug resistance, and viral evolution. Following infection and entry into target cells, the HIV-1 core disassembles, and the viral RT concomitantly converts the viral RNA into double-stranded proviral DNA, which is integrated into the host genome. The successful completion of the viral life cycle highly depends on the enzymatic DNA polymerase activity of RT. Furthermore, HIV-1 RT has long been known as an error-prone DNA polymerase due to its lack of proofreading exonuclease properties. Indeed, the low fidelity of HIV-1 RT has been considered as one of the key factors in the uniquely high rate of mutagenesis of HIV-1, which leads to efficient viral escape from immune and therapeutic antiviral selective pressures. Interestingly, a series of studies on the replication kinetics of HIV-1 in non-dividing myeloid cells and myeloid specific host restriction factor, SAM domain, and HD domain-containing protein, SAMHD1, suggest that the myeloid cell tropism and high rate of mutagenesis of HIV-1 are mechanistically connected. Here, we review not only HIV-1 RT as a key antiviral target, but also potential evolutionary and mechanistic crosstalk among the unique enzymatic features of HIV-1 RT, the replication kinetics of HIV-1, cell tropism, viral genetic mutation, and host SAMHD1 protein.
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Affiliation(s)
- Nicole E. Bowen
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30329, USA; (N.E.B.); (A.O.)
| | - Adrian Oo
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30329, USA; (N.E.B.); (A.O.)
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30329, USA; (N.E.B.); (A.O.)
- Center for Drug Discovery, Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
- Correspondence:
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2
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Song Z, Gremminger T, Singh G, Cheng Y, Li J, Qiu L, Ji J, Lange MJ, Zuo X, Chen SJ, Zou X, Boris-Lawrie K, Heng X. The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity. Nucleic Acids Res 2021; 49:5925-5942. [PMID: 33978756 PMCID: PMC8191761 DOI: 10.1093/nar/gkab342] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/24/2022] Open
Abstract
HIV-1 reverse transcription initiates at the primer binding site (PBS) in the viral genomic RNA (gRNA). Although the structure of the PBS-segment undergoes substantial rearrangement upon tRNALys3 annealing, the proper folding of the PBS-segment during gRNA packaging is important as it ensures loading of beneficial host factors. DHX9/RNA helicase A (RHA) is recruited to gRNA to enhance the processivity of reverse transcriptase. Because the molecular details of the interactions have yet to be defined, we solved the solution structure of the PBS-segment preferentially bound by RHA. Evidence is provided that PBS-segment adopts a previously undefined adenosine-rich three-way junction structure encompassing the primer activation stem (PAS), tRNA-like element (TLE) and tRNA annealing arm. Disruption of the PBS-segment three-way junction structure diminished reverse transcription products and led to reduced viral infectivity. Because of the existence of the tRNA annealing arm, the TLE and PAS form a bent helical structure that undergoes shape-dependent recognition by RHA double-stranded RNA binding domain 1 (dsRBD1). Mutagenesis and phylogenetic analyses provide evidence for conservation of the PBS-segment three-way junction structure that is preferentially bound by RHA in support of efficient reverse transcription, the hallmark step of HIV-1 replication.
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Affiliation(s)
- Zhenwei Song
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Thomas Gremminger
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yi Cheng
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Jun Li
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Liming Qiu
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA
| | - Juan Ji
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Margaret J Lange
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65211, USA
| | - Xiaobing Zuo
- X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Shi-Jie Chen
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Xiaoqin Zou
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
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3
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High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs. Nat Commun 2021; 12:2500. [PMID: 33947853 PMCID: PMC8096811 DOI: 10.1038/s41467-021-22628-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/12/2021] [Indexed: 02/02/2023] Open
Abstract
Reverse transcription of the HIV-1 viral RNA genome (vRNA) is an integral step in virus replication. Upon viral entry, HIV-1 reverse transcriptase (RT) initiates from a host tRNALys3 primer bound to the vRNA genome and is the target of key antivirals, such as non-nucleoside reverse transcriptase inhibitors (NNRTIs). Initiation proceeds slowly with discrete pausing events along the vRNA template. Despite prior medium-resolution structural characterization of reverse transcriptase initiation complexes (RTICs), higher-resolution structures of the RTIC are needed to understand the molecular mechanisms that underlie initiation. Here we report cryo-EM structures of the core RTIC, RTIC-nevirapine, and RTIC-efavirenz complexes at 2.8, 3.1, and 2.9 Å, respectively. In combination with biochemical studies, these data suggest a basis for rapid dissociation kinetics of RT from the vRNA-tRNALys3 initiation complex and reveal a specific structural mechanism of nucleic acid conformational stabilization during initiation. Finally, our results show that NNRTIs inhibit the RTIC and exacerbate discrete pausing during early reverse transcription.
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4
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Gremminger T, Song Z, Ji J, Foster A, Weng K, Heng X. Extended Interactions between HIV-1 Viral RNA and tRNA Lys3 Are Important to Maintain Viral RNA Integrity. Int J Mol Sci 2020; 22:ijms22010058. [PMID: 33374603 PMCID: PMC7793103 DOI: 10.3390/ijms22010058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/09/2020] [Accepted: 12/19/2020] [Indexed: 01/19/2023] Open
Abstract
The reverse transcription of the human immunodeficiency virus 1 (HIV-1) initiates upon annealing of the 3′-18-nt of tRNALys3 onto the primer binding site (PBS) in viral RNA (vRNA). Additional intermolecular interactions between tRNALys3 and vRNA have been reported, but their functions remain unclear. Here, we show that abolishing one potential interaction, the A-rich loop: tRNALys3 anticodon interaction in the HIV-1 MAL strain, led to a decrease in viral infectivity and reduced the synthesis of reverse transcription products in newly infected cells. In vitro biophysical and functional experiments revealed that disruption of the extended interaction resulted in an increased affinity for reverse transcriptase (RT) and enhanced primer extension efficiency. In the absence of deoxyribose nucleoside triphosphates (dNTPs), vRNA was degraded by the RNaseH activity of RT, and the degradation rate was slower in the complex with the extended interaction. Consistently, the loss of vRNA integrity was detected in virions containing A-rich loop mutations. Similar results were observed in the HIV-1 NL4.3 strain, and we show that the nucleocapsid (NC) protein is necessary to promote the extended vRNA: tRNALys3 interactions in vitro. In summary, our data revealed that the additional intermolecular interaction between tRNALys3 and vRNA is likely a conserved mechanism among various HIV-1 strains and protects the vRNA from RNaseH degradation in mature virions.
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5
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Identification of the initial nucleocapsid recognition element in the HIV-1 RNA packaging signal. Proc Natl Acad Sci U S A 2020; 117:17737-17746. [PMID: 32647061 PMCID: PMC7395439 DOI: 10.1073/pnas.2008519117] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Understanding the molecular determinants of retroviral genome packaging is important for drug discovery and development of vectors for gene delivery. We show that the HIV-1 leader, which contains the RNA elements necessary for genome packaging, binds approximately two dozen copies of the cognate NC protein with affinities ranging from ∼40 nM to 1.4 µM. Binding to the four highest-affinity “initial” binding sites occurs with endothermic energetics attributed to NC-induced localized RNA melting. Mutations that stabilize these sites inhibit NC binding in vitro and RNA packaging in transfected cells. A small-molecule inhibitor of RNA packaging binds specifically to the initial NC binding sites and stabilizes the RNA structure. Our findings identify a potential RNA Achilles’ heel for HIV therapeutic development. Selective packaging of the HIV-1 genome during virus assembly is mediated by interactions between the dimeric 5ʹ-leader of the unspliced viral RNA and the nucleocapsid (NC) domains of a small number of assembling viral Gag polyproteins. Here, we show that the dimeric 5′-leader contains more than two dozen NC binding sites with affinities ranging from 40 nM to 1.4 μM, and that all high-affinity sites (Kd ≲ 400 nM) reside within a ∼150-nt region of the leader sufficient to promote RNA packaging (core encapsidation signal, ΨCES). The four initial binding sites with highest affinity reside near two symmetrically equivalent three-way junction structures. Unlike the other high-affinity sites, which bind NC with exothermic energetics, binding to these sites occurs endothermically due to concomitant unwinding of a weakly base-paired [UUUU]:[GGAG] helical element. Mutations that stabilize base pairing within this element eliminate NC binding to this site and severely impair RNA packaging into virus-like particles. NMR studies reveal that a recently discovered small-molecule inhibitor of HIV-1 RNA packaging that appears to function by stabilizing the structure of the leader binds directly to the [UUUU]:[GGAG] helix. Our findings suggest a sequential NC binding mechanism for Gag-genome assembly and identify a potential RNA Achilles’ heel to which HIV therapeutics may be targeted.
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6
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Larsen KP, Choi J, Jackson LN, Kappel K, Zhang J, Ha B, Chen DH, Puglisi EV. Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription. J Mol Biol 2020; 432:4499-4522. [PMID: 32512005 DOI: 10.1016/j.jmb.2020.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/21/2020] [Accepted: 06/01/2020] [Indexed: 10/24/2022]
Abstract
A hallmark of the initiation step of HIV-1 reverse transcription, in which viral RNA genome is converted into double-stranded DNA, is that it is slow and non-processive. Biochemical studies have identified specific sites along the viral RNA genomic template in which reverse transcriptase (RT) stalls. These stalling points, which occur after the addition of three and five template dNTPs, may serve as checkpoints to regulate the precise timing of HIV-1 reverse transcription following viral entry. Structural studies of reverse transcriptase initiation complexes (RTICs) have revealed unique conformations that may explain the slow rate of incorporation; however, questions remain about the temporal evolution of the complex and features that contribute to strong pausing during initiation. Here we present cryo-electron microscopy and single-molecule characterization of an RTIC after three rounds of dNTP incorporation (+3), the first major pausing point during reverse transcription initiation. Cryo-electron microscopy structures of a +3 extended RTIC reveal conformational heterogeneity within the RTIC core. Three distinct conformations were identified, two of which adopt unique, likely off-pathway, intermediates in the canonical polymerization cycle. Single-molecule Förster resonance energy transfer experiments confirm that the +3 RTIC is more structurally dynamic than earlier-stage RTICs. These alternative conformations were selectively disrupted through structure-guided point mutations to shift single-molecule Förster resonance energy transfer populations back toward the on-pathway conformation. Our results support the hypothesis that conformational heterogeneity within the HIV-1 RTIC during pausing serves as an additional means of regulating HIV-1 replication.
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Affiliation(s)
- Kevin P Larsen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Biophysics, Stanford University, Stanford, CA 94305, USA
| | - Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Lynnette N Jackson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kalli Kappel
- Program in Biophysics, Stanford University, Stanford, CA 94305, USA
| | - Jingji Zhang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Betty Ha
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dong-Hua Chen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elisabetta Viani Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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7
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Larsen KP, Choi J, Prabhakar A, Puglisi EV, Puglisi JD. Relating Structure and Dynamics in RNA Biology. Cold Spring Harb Perspect Biol 2019; 11:11/7/a032474. [PMID: 31262948 DOI: 10.1101/cshperspect.a032474] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent advances in structural biology methods have enabled a surge in the number of RNA and RNA-protein assembly structures available at atomic or near-atomic resolution. These complexes are often trapped in discrete conformational states that exist along a mechanistic pathway. Single-molecule fluorescence methods provide temporal resolution to elucidate the dynamic mechanisms of processes involving complex RNA and RNA-protein assemblies, but interpretation of such data often requires previous structural knowledge. Here we highlight how single-molecule tools can directly complement structural approaches for two processes--translation and reverse transcription-to provide a dynamic view of molecular function.
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Affiliation(s)
- Kevin P Larsen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305.,Biophysics Program, Stanford University, Stanford, California 94305
| | - Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305.,Department of Applied Physics, Stanford University, Stanford, California 94305
| | - Arjun Prabhakar
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305.,Biophysics Program, Stanford University, Stanford, California 94305
| | - Elisabetta Viani Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
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8
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Abstract
Here we have directly visualized conformational changes in the 5′UTR of the HIV-1 genome using single-molecule fluorescence techniques. We find that the monomeric 5′UTR can spontaneously transition between two conformations, which have distinct intramolecular base pairing. One of the observed conformations is competent for dimerization with a second 5′UTR molecule. Our results are consistent with a model in which dimerization initiates by way of localized intermolecular kissing-loop base pairing, which is promoted by tRNA primer annealing. The intermolecular interface then extends, giving rise to the putative extended dimer, which is stabilized by HIV-1 NC. Thus, the 5′UTR is intrinsically dynamic, and both viral and host factors play a role in modulating the RNA conformation and dynamics. The highly conserved 5′ untranslated region (5′UTR) of the HIV-1 RNA genome is central to the regulation of virus replication. NMR and biochemical experiments support a model in which the 5′UTR can transition between at least two conformational states. In one state the genome remains a monomer, as the palindromic dimerization initiation site (DIS) is sequestered via base pairing to upstream sequences. In the second state, the DIS is exposed, and the genome is competent for kissing loop dimerization and packaging into assembling virions where an extended dimer is formed. According to this model the conformation of the 5′UTR determines the fate of the genome. In this work, the dynamics of this proposed conformational switch and the factors that regulate it were probed using multiple single-molecule and in-gel ensemble FRET assays. Our results show that the HIV-1 5′UTR intrinsically samples conformations that are stabilized by both viral and host factor binding. Annealing of tRNALys3, the primer for initiation of reverse transcription, can promote the kissing dimer but not the extended dimer. In contrast, HIV-1 nucleocapsid (NC) promotes formation of the extended dimer in both the absence and presence of tRNALys3. Our data are consistent with an ordered series of events that involves primer annealing, genome dimerization, and virion assembly.
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9
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Jin D, Musier-Forsyth K. Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication. J Biol Chem 2019; 294:5352-5364. [PMID: 30700559 DOI: 10.1074/jbc.rev118.002957] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The lifecycle of retroviruses and retrotransposons includes a reverse transcription step, wherein dsDNA is synthesized from genomic RNA for subsequent insertion into the host genome. Retroviruses and retrotransposons commonly appropriate major components of the host cell translational machinery, including cellular tRNAs, which are exploited as reverse transcription primers. Nonpriming functions of tRNAs have also been proposed, such as in HIV-1 virion assembly, and tRNA-derived fragments may also be involved in retrovirus and retrotransposon replication. Moreover, host cellular proteins regulate retroviral replication by binding to tRNAs and thereby affecting various steps in the viral lifecycle. For example, in some cases, tRNA primer selection is facilitated by cognate aminoacyl-tRNA synthetases (ARSs), which bind tRNAs and ligate them to their corresponding amino acids, but also have many known nontranslational functions. Multi-omic studies have revealed that ARSs interact with both viral proteins and RNAs and potentially regulate retroviral replication. Here, we review the currently known roles of tRNAs and their derivatives in retroviral and retrotransposon replication and shed light on the roles of tRNA-binding proteins such as ARSs in this process.
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Affiliation(s)
- Danni Jin
- From the Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
| | - Karin Musier-Forsyth
- From the Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
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10
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Coey AT, Larsen KP, Choi J, Barrero DJ, Puglisi JD, Puglisi EV. Dynamic Interplay of RNA and Protein in the Human Immunodeficiency Virus-1 Reverse Transcription Initiation Complex. J Mol Biol 2018; 430:5137-5150. [PMID: 30201267 DOI: 10.1016/j.jmb.2018.08.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/26/2018] [Accepted: 08/27/2018] [Indexed: 10/28/2022]
Abstract
The initiation of reverse transcription in human immunodeficiency virus-1 is a key early step in the virus replication cycle. During this process, the viral enzyme reverse transcriptase (RT) copies the single-stranded viral RNA (vRNA) genome into double-stranded DNA using human tRNALys3 as a primer for initiation. The tRNA primer and vRNA genome contain several complementary sequences that are important for regulating reverse transcription initiation kinetics. Using single-molecule Förster resonance energy transfer spectroscopy, we demonstrate that the vRNA-tRNA initiation complex is conformationally heterogeneous and dynamic in the absence of RT. As shown previously, nucleic acid-RT interaction is characterized by rapid dissociation constants. We show that extension of the vRNA-tRNA primer binding site helix from 18 base pairs to 22 base pairs stabilizes RT binding to the complex and that the tRNA 5' end has a role in modulating RT binding. RT occupancy on the complex stabilizes helix 1 formation and reduces global structural heterogeneity. The stabilization of helix 1 upon RT binding may serve to destabilize helix 2, the first pause site for RT during initiation, during later steps of reverse transcription initiation.
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Affiliation(s)
- Aaron T Coey
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 943055126, USA; Biophysics Program Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Kevin P Larsen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 943055126, USA; Biophysics Program Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 943055126, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305-5126, USA
| | - Daniel J Barrero
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 943055126, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 943055126, USA
| | - Elisabetta Viani Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 943055126, USA.
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11
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Larsen KP, Mathiharan YK, Kappel K, Coey AT, Chen DH, Barrero D, Madigan L, Puglisi JD, Skiniotis G, Puglisi EV. Architecture of an HIV-1 reverse transcriptase initiation complex. Nature 2018; 557:118-122. [PMID: 29695867 PMCID: PMC5934294 DOI: 10.1038/s41586-018-0055-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/19/2018] [Indexed: 11/29/2022]
Abstract
Reverse transcription of the HIV-1 RNA genome into double-stranded DNA is a central step in infection1 and a common target of antiretrovirals2. The reaction is catalyzed by viral reverse transcriptase (RT)3,4 that is packaged in an infectious virion along with 2 copies of dimeric viral genomic RNA5 and host tRNALys3, which acts as a primer for initiation of reverse transcription6,7. Upon viral entry, initiation is slow and non-processive compared to elongation8,9. Despite extensive efforts, the structural basis for RT function during initiation has remained a mystery. Here we apply cryo-electron microscopy (cryo-EM) to determine a three-dimensional structure of the HIV-1 RT initiation complex. RT is in an inactive polymerase conformation with open fingers and thumb and with the nucleic acid primer-template complex shifted away from the active site. The primer binding site (PBS) helix formed between tRNALys3 and HIV-1 RNA lies in the cleft of RT and is extended by additional pairing interactions. The 5′ end of the tRNA refolds and stacks on the PBS to create a long helical structure, while the remaining viral RNA forms two helical stems positioned above the RT active site, with a linker that connects these helices to the RNase H region of the PBS. Our results illustrate how RNA structure in the initiation complex alters RT conformation to decrease activity, highlighting a potential target for drug action.
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Affiliation(s)
- Kevin P Larsen
- Program in Biophysics, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yamuna Kalyani Mathiharan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kalli Kappel
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Aaron T Coey
- Program in Biophysics, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dong-Hua Chen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Barrero
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lauren Madigan
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Georgios Skiniotis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
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12
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Coey A, Larsen K, Puglisi JD, Viani Puglisi E. Heterogeneous structures formed by conserved RNA sequences within the HIV reverse transcription initiation site. RNA (NEW YORK, N.Y.) 2016; 22:1689-1698. [PMID: 27613581 PMCID: PMC5066621 DOI: 10.1261/rna.056804.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/03/2016] [Indexed: 06/06/2023]
Abstract
Reverse transcription is a key process in the early steps of HIV infection. This process initiates within a specific complex formed by the 5' UTR of the HIV genomic RNA (vRNA) and a host primer tRNALys3 Using nuclear magnetic resonance (NMR) spectroscopy and single-molecule fluorescence spectroscopy, we detect two distinct conformers adopted by the tRNA/vRNA initiation complex. We directly show that an interaction between the conserved 8-nucleotide viral RNA primer activation signal (PAS) and the primer tRNA occurs in one of these conformers. This intermolecular PAS interaction likely induces strain on a vRNA intramolecular helix, which must be broken for reverse transcription to initiate. We propose a mechanism by which this vRNA/tRNA conformer relieves the kinetic block formed by the vRNA intramolecular helix to initiate reverse transcription.
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Affiliation(s)
- Aaron Coey
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
- Biophysics Program, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Kevin Larsen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
- Biophysics Program, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Elisabetta Viani Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
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13
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Sleiman D, Barraud P, Brachet F, Tisne C. The Interaction between tRNA(Lys) 3 and the primer activation signal deciphered by NMR spectroscopy. PLoS One 2013; 8:e64700. [PMID: 23762248 PMCID: PMC3675109 DOI: 10.1371/journal.pone.0064700] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/17/2013] [Indexed: 11/23/2022] Open
Abstract
The initiation of reverse transcription of the human immunodeficiency virus type 1 (HIV-1) requires the opening of the three-dimensional structure of the primer tRNALys3 for its annealing to the viral RNA at the primer binding site (PBS). Despite the fact that the result of this rearrangement is thermodynamically more stable, there is a high-energy barrier that requires the chaperoning activity of the viral nucleocapsid protein. In addition to the nucleotide complementarity to the PBS, several regions of tRNALys3 have been described as interacting with the viral genomic RNA. Among these sequences, a sequence of the viral genome called PAS for “primer activation signal” was proposed to interact with the T-arm of tRNALys3, this interaction stimulating the initiation of reverse transcription. In this report, we investigate the formation of this additional interaction with NMR spectroscopy, using a simple system composed of the primer tRNALys3, the 18 nucleotides of the PBS, the PAS (8 nucleotides) encompassed or not in a hairpin structure, and the nucleocapsid protein. Our NMR study provides molecular evidence of the existence of this interaction and highlights the role of the nucleocapsid protein in promoting this additional RNA-RNA annealing. This study presents the first direct observation at a single base-pair resolution of the PAS/anti-PAS association, which has been proposed to be involved in the chronological regulation of the reverse transcription.
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Affiliation(s)
- Dona Sleiman
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris Sorbonne Cité, Paris, France
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14
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Sleiman D, Goldschmidt V, Barraud P, Marquet R, Paillart JC, Tisné C. Initiation of HIV-1 reverse transcription and functional role of nucleocapsid-mediated tRNA/viral genome interactions. Virus Res 2012; 169:324-39. [PMID: 22721779 DOI: 10.1016/j.virusres.2012.06.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 06/05/2012] [Accepted: 06/06/2012] [Indexed: 12/28/2022]
Abstract
HIV-1 reverse transcription is initiated from a tRNA(Lys)(3) molecule annealed to the viral RNA at the primer binding site (PBS). The annealing of tRNA(Lys)(3) requires the opening of its three-dimensional structure and RNA rearrangements to form an efficient initiation complex recognized by the reverse transcriptase. This annealing is mediated by the nucleocapsid protein (NC). In this paper, we first review the actual knowledge about HIV-1 viral RNA and tRNA(Lys)(3) structures. Then, we summarize the studies explaining how NC chaperones the formation of the tRNA(Lys)(3)/PBS binary complex. Additional NMR data that investigated the NC interaction with tRNA(Lys)(3) D-loop are presented. Lastly, we focused on the additional interactions occurring between tRNA(Lys)(3) and the viral RNA and showed that they are dependent on HIV-1 isolates, i.e. the sequence and the structure of the viral RNA.
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Affiliation(s)
- Dona Sleiman
- Laboratoire de Cristallographie et RMN biologiques, Université Paris-Descartes, CNRS UMR 8015, 4 avenue de l'Observatoire, 75006 Paris, France
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15
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Puglisi EV, Puglisi JD. Secondary structure of the HIV reverse transcription initiation complex by NMR. J Mol Biol 2011; 410:863-74. [PMID: 21763492 DOI: 10.1016/j.jmb.2011.04.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/06/2011] [Accepted: 04/11/2011] [Indexed: 01/11/2023]
Abstract
Initiation of reverse transcription of genomic RNA is a key early step in replication of the human immunodeficiency virus (HIV) upon infection of a host cell. Viral reverse transcriptase initiates from a specific RNA-RNA complex formed between a host transfer RNA (tRNA(Lys)(3)) and a region at the 5' end of genomic RNA; the 3' end of the tRNA acts as a primer for reverse transcription of genomic RNA. We report here the secondary structure of the HIV genomic RNA-human tRNA(Lys)(3) initiation complex using heteronuclear nuclear magnetic resonance methods. We show that both RNAs undergo large-scale conformational changes upon complex formation. Formation of the 18-bp primer helix with the 3' end of tRNA(Lys)(3) drives large conformational rearrangements of the tRNA at the 5' end while maintaining the anticodon loop for potential loop-loop interactions. HIV RNA forms an intramolecular helix adjacent to the intermolecular primer helix. This helix, which must be broken by reverse transcription, likely acts as a kinetic block to reverse transcription.
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Affiliation(s)
- Elisabetta Viani Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
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16
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Isel C, Ehresmann C, Marquet R. Initiation of HIV Reverse Transcription. Viruses 2010; 2:213-243. [PMID: 21994608 PMCID: PMC3185550 DOI: 10.3390/v2010213] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 01/08/2010] [Accepted: 01/13/2010] [Indexed: 12/01/2022] Open
Abstract
Reverse transcription of retroviral genomes into double stranded DNA is a key event for viral replication. The very first stage of HIV reverse transcription, the initiation step, involves viral and cellular partners that are selectively packaged into the viral particle, leading to an RNA/protein complex with very specific structural and functional features, some of which being, in the case of HIV-1, linked to particular isolates. Recent understanding of the tight spatio-temporal regulation of reverse transcription and its importance for viral infectivity further points toward reverse transcription and potentially its initiation step as an important drug target.
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Affiliation(s)
- Catherine Isel
- Authors to whom correspondence should be addressed; E-Mail: ; Tel.: +33-388-417-040; Fax: +33-388-602-218 (C.I.); E-Mail: ; Tel.: +33-388-417-054; Fax: +33-388-602-218 (R.M.)
| | | | - Roland Marquet
- Authors to whom correspondence should be addressed; E-Mail: ; Tel.: +33-388-417-040; Fax: +33-388-602-218 (C.I.); E-Mail: ; Tel.: +33-388-417-054; Fax: +33-388-602-218 (R.M.)
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17
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Abbink TEM, Berkhout B. HIV-1 reverse transcription: close encounters between the viral genome and a cellular tRNA. ADVANCES IN PHARMACOLOGY 2007; 55:99-135. [PMID: 17586313 DOI: 10.1016/s1054-3589(07)55003-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2023]
Affiliation(s)
- Truus E M Abbink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center of the University of Amsterdam, Meibergdreef 15, Amsterdam, The Netherlands
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18
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Ooms M, Cupac D, Abbink TEM, Huthoff H, Berkhout B. The availability of the primer activation signal (PAS) affects the efficiency of HIV-1 reverse transcription initiation. Nucleic Acids Res 2007; 35:1649-59. [PMID: 17308346 PMCID: PMC1865047 DOI: 10.1093/nar/gkm046] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Initiation of reverse transcription of a retroviral RNA genome is strictly regulated. The tRNA primer binds to the primer binding site (PBS), and subsequent priming is triggered by the primer activation signal (PAS) that also pairs with the tRNA. We observed that in vitro reverse transcription initiation of the HIV-1 leader RNA varies in efficiency among 3′-end truncated transcripts, despite the presence of both PBS and PAS motifs. As the HIV-1 leader RNA can adopt two different foldings, we investigated if the conformational state of the transcripts did influence the efficiency of reverse transcription initiation. However, mutant transcripts that exclusively fold one or the other structure were similarly active, thereby excluding the possibility of regulation of reverse transcription initiation by the structure riboswitch. We next set out to determine the availability of the PAS element. This sequence motif enhances the efficiency of reverse transcription initiation, but its activity is regulated because the PAS motif is initially base paired within the wild-type template. We measured that the initiation efficiency on different templates correlates directly with accessibility of the PAS motif. Furthermore, changes in PAS are critical to facilitate a primer-switch to a new tRNA species, demonstrating the importance of this enhancer element.
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Affiliation(s)
| | | | | | | | - Ben Berkhout
- *To whom correspondence should be addressed. +31 205 664 822+31 206 916 531
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19
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Levin JG, Guo J, Rouzina I, Musier-Forsyth K. Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism. ACTA ACUST UNITED AC 2006; 80:217-86. [PMID: 16164976 DOI: 10.1016/s0079-6603(05)80006-6] [Citation(s) in RCA: 256] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Judith G Levin
- Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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20
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Abbink TEM, Beerens N, Berkhout B. Forced selection of a human immunodeficiency virus type 1 variant that uses a non-self tRNA primer for reverse transcription: involvement of viral RNA sequences and the reverse transcriptase enzyme. J Virol 2004; 78:10706-14. [PMID: 15367637 PMCID: PMC516392 DOI: 10.1128/jvi.78.19.10706-10714.2004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 uses the tRNA(3)(Lys) molecule as a selective primer for reverse transcription. This primer specificity is imposed by sequence complementarity between the tRNA primer and two motifs in the viral RNA genome: the primer-binding site (PBS) and the primer activation signal (PAS). In addition, there may be specific interactions between the tRNA primer and viral proteins, such as the reverse transcriptase (RT) enzyme. We constructed viruses with mutations in the PAS and PBS that were designed to employ the nonself primer tRNA(Pro) or tRNA(1,2)(Lys). These mutants exhibited a severe replication defect, indicating that additional adaptation of the mutant virus is required to accommodate the new tRNA primer. Multiple independent virus evolution experiments were performed to select for fast-replicating variants. Reversion to the wild-type PBS-lys3 sequence was the most frequent escape route. However, we identified one culture in which the virus gained replication capacity without reversion of the PBS. This revertant virus eventually optimized the PAS motif for interaction with the nonself primer. Interestingly, earlier evolution samples revealed a single amino acid change of an otherwise well-conserved residue in the RNase H domain of the RT enzyme, implicating this domain in selective primer usage. We demonstrate that both the PAS and RT mutations improve the replication capacity of the tRNA(1,2)(Lys)-using virus.
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MESH Headings
- Amino Acid Substitution
- Base Sequence
- Directed Molecular Evolution
- HIV Long Terminal Repeat
- HIV Reverse Transcriptase/genetics
- HIV Reverse Transcriptase/metabolism
- HIV-1/genetics
- HIV-1/growth & development
- Models, Molecular
- Molecular Sequence Data
- Molecular Structure
- Mutation, Missense
- Nucleic Acid Conformation
- Protein Structure, Tertiary
- RNA/metabolism
- RNA, Transfer/metabolism
- RNA, Transfer, Lys/metabolism
- RNA, Transfer, Pro/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Ribonuclease H/genetics
- Ribonuclease H/physiology
- Selection, Genetic
- Transcription, Genetic
- Virus Replication
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Affiliation(s)
- Truus E M Abbink
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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21
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Paillart JC, Dettenhofer M, Yu XF, Ehresmann C, Ehresmann B, Marquet R. First snapshots of the HIV-1 RNA structure in infected cells and in virions. J Biol Chem 2004; 279:48397-403. [PMID: 15355993 DOI: 10.1074/jbc.m408294200] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
With the increasing interest of RNAs in regulating a range of cell biological processes, very little is known about the structure of RNAs in tissue culture cells. We focused on the 5'-untranslated region of the human immunodeficiency virus type 1 RNA genome, a highly conserved RNA region, which contains structural domains that regulate key steps in the viral replication cycle. Up until now, structural information only came from in vitro studies. Here, we developed chemical modification assays to test nucleotide accessibility directly in infected cells and viral particles, thus circumventing possible biases and artifacts linked to in vitro assays. The secondary structure of the 5'-untranslated region in infected cells points to the existence of the various stem-loop motifs associated to distinct functions, proposed from in vitro probing, mutagenesis, and phylogeny. However, compared with in vitro data, subtle differences were observed in the dimerization initiation site hairpin, and none of the proposed long range interactions were observed between the functional domains. Moreover, no global RNA rearrangement was observed; structural differences between infected cells and viral particles were limited to the primer binding site, which became protected against chemical modification upon tRNA(3) (Lys) annealing in virions and to the main packaging signal. In addition, our data suggested that the genomic RNA could already dimerize in the cytoplasm of infected cells. Taken together, our results provided the first analysis of the dynamic of RNA structure of the human immunodeficiency virus type 1 RNA genome during virus assembly ex vivo.
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Affiliation(s)
- Jean-Christophe Paillart
- Unité Propre de Recherche 9002 du CNRS conventionnée à l'Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France.
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22
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Goldschmidt V, Paillart JC, Rigourd M, Ehresmann B, Aubertin AM, Ehresmann C, Marquet R. Structural variability of the initiation complex of HIV-1 reverse transcription. J Biol Chem 2004; 279:35923-31. [PMID: 15194685 DOI: 10.1074/jbc.m404473200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
HIV-1 reverse transcription is initiated from a tRNA(3)(Lys) molecule annealed to the viral RNA at the primer binding site (PBS), but the structure of the initiation complex of reverse transcription remains controversial. Here, we performed in situ structural probing, as well as in vitro structural and functional studies, of the initiation complexes formed by highly divergent isolates (MAL and NL4.3/HXB2). Our results show that the structure of the initiation complex is not conserved. In MAL, and according to sequence analysis in 14% of HIV-1 isolates, formation of the initiation complex is accompanied by complex rearrangements of the viral RNA, and extensive interactions with tRNA(3)(Lys) are required for efficient initiation of reverse transcription. In NL4.3, HXB2, and most isolates, tRNA(3)(Lys) annealing minimally affects the viral RNA structure and no interaction outside the PBS is required for optimal initiation of reverse transcription. We suggest that in MAL, extensive interactions with tRNA(3)(Lys) are required to drive the structural rearrangements generating the structural elements ultimately recognized by reverse transcriptase. In NL4.3 and HXB2, these elements are already present in the viral RNA prior to tRNA(3)(Lys) annealing, thus explaining that extensive interactions with the primer are not required. Interestingly, such interactions are required in HXB2 mutants designed to use a non-cognate tRNA as primer (tRNA(His)). In the latter case, the extended interactions are required to counteract a negative contribution associate with the alternate primer.
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Affiliation(s)
- Valérie Goldschmidt
- Unité Propre de Recherche 9002 du CNRS conventionnée à l'Université Louis Pasteur, IBMC, 15 rue René Descartes, 67084 Strasbourg cedex, France
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23
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Damgaard CK, Andersen ES, Knudsen B, Gorodkin J, Kjems J. RNA interactions in the 5' region of the HIV-1 genome. J Mol Biol 2004; 336:369-79. [PMID: 14757051 DOI: 10.1016/j.jmb.2003.12.010] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The untranslated leader of the dimeric HIV-1 RNA genome is folded into a complex structure that plays multiple and essential roles in the viral replication cycle. Here, we have investigated secondary and tertiary structural elements within the 5' 744 nucleotides of the HIV-1 genome using a combination of bioinformatics, enzymatic probing, native gel electrophoresis, and UV-crosslinking experiments. We used a recently developed RNA folding algorithm (Pfold) to predict the common secondary structure of an alignment of 20 divergent HIV-1 sequences. Combining this analysis with biochemical data, we present a secondary structure model for the entire 744 nucleotide fragment, which incorporates previously recognized and novel structural elements. In particular, our data provided strong evidence for a long-distance interaction between the region encompassing the AUG Gag initiation codon and an upstream region and we demonstrate that this feature is highly conserved in distantly related human and animal retroviruses. To obtain information about tertiary interactions we applied an intramolecular UV-crosslinking strategy and identified a novel tertiary interaction within the PBS hairpin structure.
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Affiliation(s)
- Christian Kroun Damgaard
- Department of Molecular Biology, University of Aarhus, C.F. Møllers Allé, Building 130, DK-8000 C, Arhus, Denmark
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24
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Rigourd M, Goldschmidt V, Brulé F, Morrow CD, Ehresmann B, Ehresmann C, Marquet R. Structure-function relationships of the initiation complex of HIV-1 reverse transcription: the case of mutant viruses using tRNA(His) as primer. Nucleic Acids Res 2003; 31:5764-75. [PMID: 14500840 PMCID: PMC206454 DOI: 10.1093/nar/gkg754] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Reverse transcription of HIV-1 RNA is initiated from the 3' end of a tRNA3Lys molecule annealed to the primer binding site (PBS). An additional interaction between the anticodon loop of tRNA3Lys and a viral A-rich loop is required for efficient initiation of reverse transcription of the HIV-1 MAL isolate. In the HIV-1 HXB2 isolate, simultaneous mutations of the PBS and the A-rich loop (mutant His-AC), but not of the PBS alone (mutant His) allows the virus to stably utilize tRNA(His) as primer. However, mutant His-AC selects additional mutations during cell culture, generating successively His-AC-GAC and His-AC-AT-GAC. Here, we wanted to establish direct relationships between the evolution of these mutants in cell culture, their efficiency in initiating reverse transcription and the structure of the primer/template complexes in vitro. The initiation of reverse transcription of His and His-AC RNAs was dramatically reduced. However, His-AC-GAC RNA, which incorporated three adaptative point mutations, was reverse transcribed more efficiently than the wild type RNA. Incorporation of two additional mutations decreased the efficiency of the initiation of reverse transcription, which remained at the wild type level. Structural probing showed that even though both His-AC and His-AC-GAC RNAs can potentially interact with the anticodon loop of tRNA(His), only the latter template formed a stable interaction. Thus, our results showed that the selection of adaptative mutations by HIV-1 mutants utilizing tRNA(His) as primer was initially dictated by the efficiency of the initiation of reverse transcription, which relied on the existence of a stable interaction between the mutated A-rich loop and the anticodon loop of tRNA(His).
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Affiliation(s)
- Mickaël Rigourd
- Unité Propre de Recherche 9002 du CNRS conventionnée à l'Université Louis Pasteur, IBMC, 15 rue René Descartes, 67084 Strasbourg cedex, France
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25
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Huthoff H, Bugala K, Barciszewski J, Berkhout B. On the importance of the primer activation signal for initiation of tRNA(lys3)-primed reverse transcription of the HIV-1 RNA genome. Nucleic Acids Res 2003; 31:5186-94. [PMID: 12930970 PMCID: PMC212812 DOI: 10.1093/nar/gkg714] [Citation(s) in RCA: 13] [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
Initiation of reverse transcription is a complex and regulated process in all retroviruses. Several base pairing interactions have been proposed to occur between the HIV-1 RNA genome and the specific tRNA(lys3) primer. The tRNA primer can form up to 21 bp with the primer binding site (PBS), and an additional 8 bp interaction may form between the primer activation signal (PAS) in the HIV-1 RNA and sequences within the T(Psi)C arm of the tRNA. The latter interaction is further analyzed in this in vitro study with mutant RNA transcripts that were designed to preclude the PAS interaction. These mutant transcripts are able to efficiently bind the tRNA primer, but they exhibit a profound defect at initiating reverse transcription. This defect is specific for the tRNA primer because it is not observed for PBS-bound DNA oligonucleotide primers. These results reinforce the model of regulated reverse transcription in which the PAS-mediated interaction is critical for efficient initiation.
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MESH Headings
- Base Sequence
- Binding Sites/genetics
- DNA Primers/genetics
- DNA Primers/metabolism
- Genome, Viral
- HIV Reverse Transcriptase/metabolism
- HIV-1/genetics
- HIV-1/metabolism
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Nucleic Acid Hybridization
- Oligoribonucleotides/genetics
- Oligoribonucleotides/metabolism
- RNA, Transfer, Lys/chemistry
- RNA, Transfer, Lys/genetics
- RNA, Transfer, Lys/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Temperature
- Transcription, Genetic/genetics
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Affiliation(s)
- Hendrik Huthoff
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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