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Heng X, Herrera AP, Song Z, Boris-Lawrie K. Retroviral PBS-segment sequence and structure: Orchestrating early and late replication events. Retrovirology 2024; 21:12. [PMID: 38886829 PMCID: PMC11181671 DOI: 10.1186/s12977-024-00646-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
An essential regulatory hub for retroviral replication events, the 5' untranslated region (UTR) encodes an ensemble of cis-acting replication elements that overlap in a logical manner to carry out divergent RNA activities in cells and in virions. The primer binding site (PBS) and primer activation sequence initiate the reverse transcription process in virions, yet overlap with structural elements that regulate expression of the complex viral proteome. PBS-segment also encompasses the attachment site for Integrase to cut and paste the 3' long terminal repeat into the host chromosome to form the provirus and purine residues necessary to execute the precise stoichiometry of genome-length transcripts and spliced viral RNAs. Recent genetic mapping, cofactor affinity experiments, NMR and SAXS have elucidated that the HIV-1 PBS-segment folds into a three-way junction structure. The three-way junction structure is recognized by the host's nuclear RNA helicase A/DHX9 (RHA). RHA tethers host trimethyl guanosine synthase 1 to the Rev/Rev responsive element (RRE)-containing RNAs for m7-guanosine Cap hyper methylation that bolsters virion infectivity significantly. The HIV-1 trimethylated (TMG) Cap licenses specialized translation of virion proteins under conditions that repress translation of the regulatory proteins. Clearly host-adaption and RNA shapeshifting comprise the fundamental basis for PBS-segment orchestrating both reverse transcription of virion RNA and the nuclear modification of m7G-Cap for biphasic translation of the complex viral proteome. These recent observations, which have exposed even greater complexity of retroviral RNA biology than previously established, are the impetus for this article. Basic research to fully comprehend the marriage of PBS-segment structures and host RNA binding proteins that carry out retroviral early and late replication events is likely to expose an immutable virus-specific therapeutic target to attenuate retrovirus proliferation.
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Affiliation(s)
- Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA.
| | - Amanda Paz Herrera
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Zhenwei Song
- Department of Veterinary and Biomedical Sciences, Institute for Molecular Virology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, Institute for Molecular Virology, University of Minnesota, Saint Paul, MN, 55108, USA.
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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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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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Uppuladinne MVN, Sonavane UB, Joshi RR. MD simulations of HIV-1 RT primer-template complex: effect of modified nucleosides and antisense PNA oligomer. J Biomol Struct Dyn 2012; 31:539-60. [PMID: 22888964 DOI: 10.1080/07391102.2012.706076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) requires the human tRNA(3)(Lys) as a reverse transcriptase (RT) primer. The annealing of 3' terminal 18 nucleotides of tRNA(3)(Lys) with the primer binding site (PBS) of viral RNA (vRNA) is crucial for reverse transcription. Additional contacts between the A rich (A-loop) region of vRNA and the anticodon domain of tRNA(3)(Lys) are necessary, which show the specific requirement of tRNA(3)(Lys). The importance of modified nucleosides, present in tRNA(3)(Lys), in giving stability to the primer-template complex has been determined in earlier experiments. It has been observed that the PNA oligomer targeted to PBS of vRNA destabilized the crucial interactions between primer and template due to which the reverse transcription is inhibited. Molecular dynamics simulations have been carried out to study the effect of modified nucleosides on the vRNA-tRNA(3)(Lys) complex stability and the destabilization effect of PNA oligomer on the vRNA-tRNA(3)(Lys)-PNA complex. The root-mean-square deviation, hydrogen bonding, tertiary interactions, and free energy calculations of the simulation data support the experimental results. The analyses have revealed the structural changes in PBS region of vRNA which might be another strong reason for the inability of RT binding to 7F helix for its normal functioning of reverse transcription.
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Song M, Balakrishnan M, Gorelick RJ, Bambara RA. A succession of mechanisms stimulate efficient reconstituted HIV-1 minus strand strong stop DNA transfer. Biochemistry 2010; 48:1810-9. [PMID: 19192967 DOI: 10.1021/bi802149j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Donor-acceptor template systems in vitro were designed to test mechanisms of minus strand transfer of human immunodeficiency virus 1 (HIV-1). Donor RNA D199, extending from the 5' end of the HIV-1 genome to the primer binding site (PBS), promoted transfer to only 35% with an acceptor RNA representing the 3' terminal 97 nucleotides, whereas donor RNA D520, including an additional 321 nucleotides 3' of PBS, exhibited 75% transfer. Both donors transferred through an invasion-driven pathway, but transfer was stimulated by the folding structure resulting from the extra segment in D520. In this study, the significance of interaction between the tRNA(lys3) primer and U3 was examined. Measurements utilizing acceptors having or lacking the U3 region complementary with tRNA(lys3) indicated that a tRNA(lys3)-U3 interaction compensated for inefficient acceptor invasion observed with D199. Stimulation presumably occurred because binding to tRNA(lys3) increased the proximity of the acceptor to elongated cDNA, improving transfer to 78% efficiency with D199, and even higher to 85% with D520. The stimulation did not require natural viral sequences but could be achieved by substituting the original U3 sequence with an equal length sequence that binds a different region of tRNA(lys3). Comparison between acceptors sharing the natural region for tRNA(lys3)-U3 interaction but having or lacking the acceptor invasion site demonstrated that tRNA(lys3)-U3 interaction and acceptor invasion cooperate for maximal stimulation. Overall, observations suggest that both proximity and invasion mechanisms are applied successively by HIV-1 for efficient minus strand transfer.
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Affiliation(s)
- Min Song
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA
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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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Pandey VN, Upadhyay A, Chaubey B. Prospects for antisense peptide nucleic acid (PNA) therapies for HIV. Expert Opin Biol Ther 2009; 9:975-89. [PMID: 19534584 DOI: 10.1517/14712590903052877] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Since the discovery and synthesis of a novel DNA mimic, peptide nucleic acid (PNA) in 1991, PNAs have attracted tremendous interest and have shown great promise as potential antisense drugs. They have been used extensively as tools for specific modulation of gene expression by targeting translation or transcription processes. This review discusses the present and future therapeutic potential of this class of compound as anti-HIV-1 drugs.
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Affiliation(s)
- Virendra N Pandey
- University of Medicine and Dentistry, New Jersey-New Jersey Medical School, Department of Biochemistry and Molecular Biology, Newark, NJ 07103, USA.
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Bilbille Y, Vendeix FAP, Guenther R, Malkiewicz A, Ariza X, Vilarrasa J, Agris PF. The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs. Nucleic Acids Res 2009; 37:3342-53. [PMID: 19324888 PMCID: PMC2691828 DOI: 10.1093/nar/gkp187] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Replication of human immunodeficiency virus (HIV) requires base pairing of the reverse transcriptase primer, human tRNALys3, to the viral RNA. Although the major complementary base pairing occurs between the HIV primer binding sequence (PBS) and the tRNA's 3′-terminus, an important discriminatory, secondary contact occurs between the viral A-rich Loop I, 5′-adjacent to the PBS, and the modified, U-rich anticodon domain of tRNALys3. The importance of individual and combined anticodon modifications to the tRNA/HIV-1 Loop I RNA's interaction was determined. The thermal stabilities of variously modified tRNA anticodon region sequences bound to the Loop I of viral sub(sero)types G and B were analyzed and the structure of one duplex containing two modified nucleosides was determined using NMR spectroscopy and restrained molecular dynamics. The modifications 2-thiouridine, s2U34, and pseudouridine, Ψ39, appreciably stabilized the interaction of the anticodon region with the viral subtype G and B RNAs. The structure of the duplex results in two coaxially stacked A-form RNA stems separated by two mismatched base pairs, U162•Ψ39 and G163•A38, that maintained a reasonable A-form helix diameter. The tRNA's s2U34 stabilized the interaction between the A-rich HIV Loop I sequence and the U-rich anticodon, whereas the tRNA's Ψ39 stabilized the adjacent mismatched pairs.
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Affiliation(s)
- Yann Bilbille
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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McCulley A, Morrow CD. Nucleotides within the anticodon stem are important for optimal use of tRNA(Lys,3) as the primer for HIV-1 reverse transcription. Virology 2007; 364:169-77. [PMID: 17368706 PMCID: PMC2080789 DOI: 10.1016/j.virol.2007.02.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Revised: 01/18/2007] [Accepted: 02/09/2007] [Indexed: 11/30/2022]
Abstract
HIV-1 utilizes tRNA(Lys,3) as the primer for initiation of reverse transcription. To further examine the tRNA sequence and structural requirements for primer selection, we developed a complementation system which required tRNA(Lys) to be provided in trans. We constructed an HIV-1 provirus in which the primer-binding site (PBS) was altered to be complementary to the 3' terminal 18-nucleotides of E. coli tRNA(Lys,3), which shares many bases with mammalian tRNA(Lys,3), and demonstrated that infectious virus was obtained only if the provirus was co-transfected with the plasmid encoding E. coli tRNA(Lys,3). In the current study we have mutated E. coli tRNA(Lys,3) so that nucleotides within the stem of the anticodon stem-loop were made identical to mammalian tRNA(Lys,3). Analysis of the complementation revealed that the modified E. coli tRNA(Lys,3) (E. coli tRNA(Lys,3)-MA) complemented 3-5 times more efficiently than E. coli tRNA(Lys,3). Mutation of nucleotides within the anticodon stem region of E. coli tRNA(Lys,3)-MA that differed from E. coli tRNA(Lys,3) revealed the importance of the nucleotide sequence for efficient use in reverse transcription. The results of our studies highlight that multiple regions of mammalian tRNA(Lys,3) are important for the preference of tRNA(Lys,3) as the primer for HIV-1 reverse transcription.
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Affiliation(s)
| | - Casey D. Morrow
- Corresponding author: Casey D. Morrow, University of Alabama at Birmingham, Department of Cell Biology, 802 Kaul Building, 720 20th Street, South Birmingham, AL 35294-0024, (205) 934-5705: Phone, (205) 934-5733: FAX,
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Palmer MT, Kirkman R, Kosloff BR, Eipers PG, Morrow CD. tRNA isoacceptor preference prior to retrovirus Gag-Pol junction links primer selection and viral translation. J Virol 2007; 81:4397-404. [PMID: 17301132 PMCID: PMC1900135 DOI: 10.1128/jvi.02643-06] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
An essential step in the replication of all retroviruses is the capture of a cellular tRNA that is used as the primer for reverse transcription. The 3'-terminal 18 nucleotides of the tRNA are complementary to the primer binding site (PBS). Moloney murine leukemia virus (MuLV) preferentially captures tRNA(Pro). To investigate the specificity of primer selection, the PBS of MuLV was altered to be complementary to different tRNAs. Analysis of the infectivity of the virus and stability of the PBS following in vitro replication revealed that MuLV prefers to select tRNA(Pro), tRNA(Gly), or tRNA(Arg). Previous studies from our laboratory have suggested that tRNA primer capture is coordinated with translation. Coincidentally, a cluster of proline, arginine, and glycine precedes the Gag-Pol junction of MuLV. Human immunodeficiency virus type 1 (HIV-1), which prefers tRNA(3)(Lys) as the primer, can be forced to utilize tRNA(Met), tRNA(1,2)(Lys), tRNA(His), or tRNA(Glu), although these viruses replicate poorly. Codons for methionine, lysine, histidine, or glutamic acid are found prior to the Gag-Pol frameshift site. HIV-1 was mutated so that the 5 lysine codons prior to the Gag-Pol frameshift region were specific for tRNA(1,2)(Lys). HIV-1 forced to use tRNA(1,2)(Lys) as the primer, with the mutation of codons specific for tRNA(1,2)(Lys) prior to the Gag-Pol junction, had enhanced infectivity and replicated similarly to the wild-type virus. The results demonstrate that codon preference prior to the Gag-Pol junction influences primer selection and suggest a coordination of Gag-Pol synthesis and acquisition of the tRNA primer required for retrovirus replication.
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Affiliation(s)
- Matthew T Palmer
- Department of Cell Biology, University of Alabama at Birmingham, 720 20th Street South, Kaul 802, Birmingham, AL 35294-0024, USA
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Djekic UV, Morrow CD. Analysis of the replication of HIV-1 forced to use tRNAMet(i) supports a link between primer selection, translation and encapsidation. Retrovirology 2007; 4:10. [PMID: 17274824 PMCID: PMC1797187 DOI: 10.1186/1742-4690-4-10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Accepted: 02/02/2007] [Indexed: 11/18/2022] Open
Abstract
Background Previous studies have suggested that the process of HIV-1 tRNA primer selection and encapsidation of genomic RNA might be coupled with viral translation. In order to further investigate this relationship, proviruses were constructed in which the primer-binding site (PBS) was altered to be complementary to elongator tRNAMet (tRNAMet(e)) (HXB2-Met(e)) or initiator tRNAMet (tRNAMet(i)) (HXB2-Met(i)). These tRNAMet not only differ with respect to the 3' terminal 18-nucleotides, but also with respect to interaction with host cell proteins during protein synthesis. Results Consistent with previous studies, HXB2-Met(e) were infectious and maintained this PBS following short-term in vitro culture in SupT1 cells. In contrast, transfection of HBX2-Met(i) produced reduced amounts of virus (as determined by p24) and did not establish a productive infection in SupT1 cells. The low infectivity of the virus with the PBS complementary to tRNAMet(i) was not due to differences in endogenous levels of cellular tRNAMet(i) compared to tRNAMet(e); tRNAMet(i) was also capable of being selected as the primer for reverse transcription as determined by the endogenous reverse transcription reaction. The PBS of HXB2-Met(i) contains an ATG, which could act as an upstream AUG and syphon scanning ribosomes thereby reducing initiation of translation at the authentic AUG of Gag. To investigate this possibility, a provirus with an A to G change was constructed (HXB2-Met(i)AG). Transfection of HXB2-Met(i)AG resulted in increased production of virus, similar to that for the wild type virus. In contrast to HXB2-Met(i), HXB2-Met(i)AG was able to establish a productive infection in SupT1 cells. Analysis of the PBS following replication revealed the virus favored the genome with the repaired PBS (A to G) even though tRNAMet(i) was continuously selected as the primer for reverse transcription. Conclusion The results of these studies suggest that HIV-1 has access to both tRNAMet for selection as the replication primer and supports a co-ordination between primer selection, translation and encapsidation during virus replication.
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Affiliation(s)
- Uros V Djekic
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Casey D Morrow
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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Ni N, Xu W, Morrow CD. Importance of A-loop complementarity with tRNAHis anticodon for continued selection of tRNAHis as the HIV reverse transcription primer. Virol J 2007; 4:4. [PMID: 17214904 PMCID: PMC1785369 DOI: 10.1186/1743-422x-4-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Accepted: 01/10/2007] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus (HIV-1) preferentially selects tRNALys,3 as the primer for reverse transcription. HIV-1 can be forced to select alternative tRNAs through mutation in the primer-binding site (PBS) and a region upstream of the PBS designated as the A-loop. Alteration of the PBS and A-loop to be complementary to the 3' terminal nucleotides and anticodon of tRNAHis results in HIV-1 that can stably utilize this tRNA for replication. RESULTS In the current study, we have investigated the effect that mutations within the A-loop have on the stability of HIV-1 with a PBS complementary to tRNAHis. For these studies, we have altered the A-loop to be complementary to tRNAMet, tRNAGln, tRNAIle, tRNAThr and tRNASer. All substitutions of the A-loops with the PBS complementary to tRNAHis resulted in a reduction of infectious virus obtained following transfection of proviral genomes in the 293T cells. Virus replication in SupT1 cells was also impaired as a result of the alteration of the A-loop. Viruses with the A-loop complementary to tRNALys,3 and tRNASer reverted to utilize tRNALys,3 following in vitro replication. In contrast, viruses with the A-loop complementary to the other tRNAs remained stable and continued to use tRNAHis. RNA modeling of the stem-loop structure revealed that nucleotides were displayed on the loop region that could potentially interact with the anticodon of tRNAHis. To further explore the effects of the A-loop mutations on virus replication, the A-loops complementary to tRNASer or tRNAHis were cloned into the wild type genome with the PBS complementary to tRNALys,3. Transfection of proviral genomes which contained the wild type PBS and A-loops complementary to tRNASer or tRNAHis into 293 T cells did not impact on the production of viruses as measured by p24 antigen ELISA. However, viruses with the A-loop complementary to tRNAHis had greatly reduced infectivity and replicated poorly in SupT1 compared to the wild type or viruses with the A-loop complementary to tRNASer. CONCLUSION These studies demonstrate that complementarity of A-loop region with the anticodon of tRNAHis has a pronounced effect on the capacity of HIV-1 to utilize tRNAHis as the primer for reverse transcription. Complementarity between A-loop and anticodon of the tRNA then is important for the selection of the tRNA primer used for reverse transcription.
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Affiliation(s)
- Na Ni
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Wenqin Xu
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Casey D Morrow
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
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Ni N, Morrow CD. Impact of forced selection of tRNAs on HIV-1 replication and genome stability highlight preferences for selection of certain tRNAs. Virus Res 2006; 124:29-37. [PMID: 17070952 PMCID: PMC1847643 DOI: 10.1016/j.virusres.2006.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Revised: 09/22/2006] [Accepted: 09/25/2006] [Indexed: 01/19/2023]
Abstract
Human immunodeficiency virus (HIV-1) exclusively selects tRNA(Lys,3) as the primer for initiation of reverse transcription. How and why HIV-1 selects the tRNA is unresolved. To address this issue, we have generated HIV-1 in which the PBS was changed to be complementary to alternative tRNAs. In this study, we report on HIV-1 that have the PBS mutated to be complementary to tRNA(Thr), tRNA(Phe), tRNA(Ser) and tRNA(Tyr). Virus with a PBS complementary to tRNA(Thr) grew slightly slower than the wild type virus and maintained the PBS for an extended culture period before finally reverting back to utilize tRNA(Lys,3). In contrast, viruses with a PBS complementary to tRNA(Phe) or tRNA(Ser) rapidly reverted to utilize tRNA(Lys,3) following limited in vitro replication, while a virus with a PBS complementary to tRNA(Tyr) had severely compromised infectivity and did not productively infect a continuous T cell line (SupT1) or human peripheral blood mononuclear cells (PBMC). Modification of the A-loop region to be complementary to tRNA(Thr) with the mutation in the PBS to be complementary to tRNA(Thr) resulted in a virus that could stably utilize this tRNA while the modification of the A-loop to be complementary to the anticodon of tRNA(Ser) did not allow the virus to stably utilize tRNA(Ser). Modification of the A-loop region to be complementary to the anticodon of tRNA(Phe) severely impacted the replication of this virus. Finally, the modification of the A-loop region to be complementary to tRNA(Tyr) did not rescue the virus with a PBS complementary to tRNA(Tyr). The results of these studies demonstrate the diverse effects that alteration of the PBS to force selection of alternative primers have on HIV-1 replication and provide a framework to understand the dynamics of primer selection.
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Affiliation(s)
| | - Casey D. Morrow
- Corresponding author: Casey D. Morrow, University of Alabama at Birmingham, Department of Cell Biology, 802 Kaul Building, 720 20 Street, South Birmingham, AL 35294-0024, (205) 934-5705: Phone (205) 934-5733: FAX
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Li M, Eipers PG, Ni N, Morrow CD. HIV-1 designed to use different tRNAGln isoacceptors prefers to select tRNAThr for replication. Virol J 2006; 3:80. [PMID: 17002807 PMCID: PMC1592299 DOI: 10.1186/1743-422x-3-80] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Accepted: 09/26/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Previous studies have shown that infection with human immunodeficiency virus type 1 (HIV-1) causes acceleration of the synthesis of glutamine tRNA (tRNAGln) in infected cells. To investigate whether this might influence HIV-1 to utilize tRNAGln as a primer for initiation of reverse transcription, we have constructed HIV-1 proviral genomes in which the PBS and the A-loop region upstream of the PBS have been made complementary to either the anticodon region of tRNAGln,1 or tRNAGln,3 and 3' terminal 18 nucleotides of each isoacceptor of tRNAGln. RESULTS Viruses in which the PBS was altered to be complementary to tRNAGln,1 or tRNAGln,3 with or without the A-loop all exhibited a lower infectivity than the wild type virus. Viruses with only the PBS complementary to tRNAGln,1 or tRNAGln,3 reverted to wild type following culture in SupT1 cells. Surprisingly, viruses in which the PBS and A-loop were complementary to tRNAGln,1 did not grow in SupT1 cells, while viruses in which the PBS and A-loop were made complementary to tRNAGln,3 grew slowly in SupT1 cells. Analysis of the PBS of this virus revealed that it had reverted to select tRNAThr as the primer, which shares complementarity in 15 of 18 nucleotides with the PBS complementary to tRNAGln,3. CONCLUSION The results of these studies support the concept that the HIV-1 has preferred tRNAs that can be selected as primers for replication.
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Affiliation(s)
- Meng Li
- Department of Cell Biology, University of Alabama at Birmingham, 35294-0024 Birmingham, AL, USA
| | - Peter G Eipers
- Department of Cell Biology, University of Alabama at Birmingham, 35294-0024 Birmingham, AL, USA
| | - Na Ni
- Department of Cell Biology, University of Alabama at Birmingham, 35294-0024 Birmingham, AL, USA
| | - Casey D Morrow
- Department of Cell Biology, University of Alabama at Birmingham, 35294-0024 Birmingham, AL, USA
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15
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Xu W, Morrow CD. The G490E mutation in reverse transcriptase does not impact tRNA primer selection by HIV-1 with altered PBS and A-loop. Virology 2006; 352:380-9. [PMID: 16781756 DOI: 10.1016/j.virol.2006.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Revised: 03/29/2006] [Accepted: 04/11/2006] [Indexed: 10/24/2022]
Abstract
The initiation of HIV-1 reverse transcription utilizes a cellular tRNA(Lys,3) as a primer. The 3' terminal 18-nucleotides of the cellular tRNA(Lys,3) are complementary to a region on the viral genome, designated as the primer binding site (PBS). Previous studies have shown that forcing HIV-1 to utilize alternative tRNA primers through alteration of the PBS results in viruses that revert to utilize tRNA(Lys,3) following in vitro replication. In some instances though, HIV-1 has been shown to select alternative tRNAs for initiation of reverse transcription if additional mutations upstream in the U5 region (A-loop) were made to be complementary to these alternative tRNAs. Recently, an HIV-1 has been described in which the U5 region distinct from the A-loop, designated as the primer activation site (PAS), was mutated in conjunction with the PBS to force the virus to use tRNA(Lys1,2) as a primer. An additional mutation in reverse transcriptase (RT), G490E, was found to facilitate the forced use of tRNA(Lys1,2) as the primer. In the current study, we have investigated the impact of the G490E mutation in RT on the selection and use of alternative primers by HIV-1. Viruses were first constructed in which the PBS and A-loop region were made complementary to tRNA(Trp). Previous studies from our laboratory have shown that these viruses are unstable and mutate to select tRNA(Met) or tRNA(Lys1,2). Analysis of the replication of viruses with the U5 and PBS complementary to tRNA(Trp) with or without the G490E mutation revealed no significant differences with respect to infectivity and viral growth in SupT1 or peripheral blood mononuclear cells (PBMC). In addition, the presence of the G490E mutation did not influence the capacity of this virus to revert to utilize tRNA(Met) as the primer for initiation of reverse transcription. In a previous study, we have described an HIV-1 that has been forced to utilize tRNA(Lys1,2) through mutations in the A-loop and PBS. The G490E RT mutation in this virus did not impact on the virus infectivity or growth in SupT1 or PBMC. We did not find a significant fitness advantage to viruses in which the A-loop and PBS were made complementary to tRNA(Lys1,2) that also contained the G490E mutation in RT. The results of these studies then establish that HIV-1 can be forced to use alternative primers through mutations in the U5 (PAS or A-loop) for certain tRNAs. Furthermore, for mutations in the A-loop and PBS, the RT does not play an important role in dictating the selection of the alternative primers to be used for initiation of reverse transcription.
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Affiliation(s)
- Wenqin Xu
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
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16
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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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17
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Wei M, Cen S, Niu M, Guo F, Kleiman L. Defective replication in human immunodeficiency virus type 1 when non-primers are used for reverse transcription. J Virol 2005; 79:9081-7. [PMID: 15994802 PMCID: PMC1168737 DOI: 10.1128/jvi.79.14.9081-9087.2005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
tRNA(3Lys), the primer for reverse transcriptase in human immunodeficiency virus type 1 (HIV-1), anneals to the primer binding site (PBS) in HIV-1 RNA. It has been shown that altering the PBS and U5 regions upstream of the PBS in HIV-1 so as to be complementary to sequences in tRNA(Met) or tRNA(His) will allow these tRNA species to be stably used as primers for reverse transcription. We have examined the replication of these mutant viruses in Sup-T1 cells. When Sup-T1 cells are infected by cocultivation with HIV-1-transfected 293T cells, viruses using tRNA(His) or tRNA(Met) are produced at rates that are approximately 1/10 or 1/100, respectively, of rates for wild-type virions that use tRNA(3Lys). When Sup-T1 cells are directly infected with equal amounts of these different viruses isolated from the culture supernatant of transfected 293T cells, virions using tRNA(Met) are produced at 1/100 the rate of wild-type viruses, and production of virions using tRNA(His) is not detected. Both wild-type and mutant virions selectively package tRNA(Lys) only, and examination of the ability of total viral RNA to prime reverse transcription in vitro indicates a >80% reduction in the annealing of tRNA(His) or tRNA(Met) to the mutant viral RNAs. PCR analysis of which of the three primer tRNAs is used indicates that only tRNA(3Lys) is detected as primer in wild-type virions and only tRNA(His) is detected as primer in virions containing a PBS complementary to tRNA(His), while the mutant viruses containing a PBS complementary to tRNA(Met) use both tRNA(Met) and tRNA(1,2Lys) as primer tRNAs.
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Affiliation(s)
- Min Wei
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Cote Ste-Catherine Road, Montreal, Quebec, Canada H3T 1E2
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18
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Palmer MT, McPherson S, Morrow CD. Murine leukemia virus with a primer-binding site complementary to tRNALys,3 adapts to select new tRNAs for replication following extended in vitro culture. Virology 2005; 333:337-48. [PMID: 15721366 DOI: 10.1016/j.virol.2004.12.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Revised: 11/10/2004] [Accepted: 12/29/2004] [Indexed: 11/20/2022]
Abstract
The preference of MuLV for the selection of tRNA(Pro) as a replication primer was investigated by altering the primer-binding site (PBS) to be complementary to tRNA(Lys,3). MuLV-based vectors with a PBS complementary to tRNA(Lys,3) were found to be approximately 2-fold less infectious than vectors with the wild-type PBS complementary to tRNA(Pro). MuLV with a PBS complementary to tRNA(Lys,3) was replication competent and maintained the PBS during early stages of in vitro culture. Upon extended culture, PBS were isolated which were complementary to tRNA(Arg). A second MuLV was generated in which the region upstream of the PBS which is predicted to form an RNA stem loop structure was altered so that the nucleotide sequence within the loop would be complementary to the anticodon of tRNA(Lys,3). The virus with both the U5 and PBS complementary to tRNA(Lys,3) was also replication competent. Upon extended in vitro culture though, this virus reverted to utilize tRNA(Lys1,2). Analysis of the infectivity and replication of the wild-type and mutant viruses revealed that tRNA(Pro) was the preferred tRNA for high-level replication. Viruses with a PBS complementary to tRNA(Arg) or tRNA(Ly1,2) replicated at levels approximately 30% and 10% as effective as the wild-type virus, while virus with a PBS complementary to tRNA(Lys,3) had the slowest replication kinetics and least infectivity. Comparison of the virion tRNA content of the wild-type and mutant viruses revealed similar ratios with respect to levels of tRNA(Pro), tRNA(Arg) and tRNA(Lys). Modeling of the U5-PBS region revealed that the predicted RNA structure for the virus that selected tRNA(Arg) was more similar to the wild type virus that uses tRNA(Pro) than the virus which use tRNA(Lys1,2) or tRNA(Lys,3); the virus that uses tRNA(Lys,3) had the most profound disruption in the predicted RNA structure. The results of these studies demonstrate that MuLV has evolved to preferentially select tRNA(Pro) for high-level replication and are discussed with respect to common features of the primer selection process between MuLV and other retroviruses.
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Affiliation(s)
- Matthew T Palmer
- Department of Cell Biology, University of Alabama at Birmingham, 720 20th Street, South, Birmingham, AL 35294-0024, USA
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19
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Han W, Wind-Rotolo M, Kirkman RL, Morrow CD. Inhibition of human immunodeficiency virus type 1 replication by siRNA targeted to the highly conserved primer binding site. Virology 2005; 330:221-32. [PMID: 15527848 DOI: 10.1016/j.virol.2004.09.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2004] [Revised: 08/23/2004] [Accepted: 09/20/2004] [Indexed: 11/23/2022]
Abstract
The initiation of HIV-1 reverse transcription occurs at an 18-nucleotide sequence in the viral genome designated as the primer binding site (PBS), which is complementary to the 3' terminal nucleotides of tRNA(Lys,3). Since the PBS is highly conserved among all infectious HIV-1, it represents an attractive target for the development of new therapeutics to inhibit viral replication. In this study, we have evaluated three approaches using small interfering RNA (siRNAs) targeted to the PBS for the capacity to inhibit HIV-1 replication. In the first, transfection of a 21-nucleotide siRNA complementary to the PBS into cells inhibited production of HIV-1 following infection. Control siRNAs of the same length complementary to HIV-1 gag mRNA or to gfp mRNA decreased the production of virus or had no effect on virus replication, respectively. Analysis of the PBS of integrated proviruses derived from viruses that ultimately grew in cultures transfected with siRNA all contained wild-type PBS sequence, demonstrating that HIV-1 did not mutate to escape inhibition by siRNA. In the second approach, hairpin siRNA targeted to the wild-type PBS were expressed using an adeno-associated virus (AAV) vector. HIV-1 replication was inhibited in cells infected with AAV encoding the siRNA to the wild-type PBS, but not in cells infected with AAV encoding an siRNA of the same length targeted to an irrelevant PBS. Finally, studies from this laboratory have shown that alteration of the PBS to be complementary to tRNAHis results in the production of infectious virus that rapidly reverts to utilize tRNALys,3 following in vitro culture. A proviral genome containing a PBS complementary to tRNAHis that encodes an siRNA molecule complementary to the wild-type PBS under control of a U6 promoter within the nef gene was as infectious as the parent HIV-1 genome containing no insert in nef. The virus with the PBS only complementary to tRNAHis reverted to use tRNALys,3, coincident with rapid virus growth, while the virus encoding siRNA grew slower than the virus without siRNA and maintained the PBS complementary to tRNAHis longer in culture. At later times of infection, viruses with the PBS complementary to tRNAHis and the siRNA exhibited a rapid increase in p24 antigen in the culture. Analysis of the PBS revealed that it was now complementary to tRNALys,3. Analysis of the gene encoding the siRNA revealed that the reversion of the PBS coincided with the deletion of the gene encoding siRNA. The results of these studies show that siRNA targeted to the PBS of HIV-1 can inhibit virus replication, supporting the concept that HIV-1 has evolved a strong preference to select tRNALys,3 for high-level replication and establishing the PBS and primer selection as a potential target for new therapeutics.
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Affiliation(s)
- Wenlong Han
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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20
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Moore-Rigdon KL, Kosloff BR, Kirkman RL, Morrow CD. Preferences for the selection of unique tRNA primers revealed from analysis of HIV-1 replication in peripheral blood mononuclear cells. Retrovirology 2005; 2:21. [PMID: 15790410 PMCID: PMC1084362 DOI: 10.1186/1742-4690-2-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Accepted: 03/24/2005] [Indexed: 12/23/2022] Open
Abstract
Background All human immunodeficiency virus (HIV-1) uses a host tRNALys,3 as the primer for reverse transcription. The tRNALys,3 is bound to a region on the HIV-1 genome, the primer-binding site (PBS), that is complementary to the 18 terminal nucleotides of tRNALys,3. How HIV-1 selects the tRNA from the intracellular milieu is unresolved. Results HIV-1 tRNA primer selection has been investigated using viruses in which the primer-binding site (PBS) and a sequence within U5 were altered so as to be complementary to tRNAMet, tRNAPro or tRNAIle. Analysis of the replication of these viruses in human peripheral blood mononuclear cells (PBMC) revealed preferences for the selection of certain tRNAs. HIV-1 with the PBS altered to be complementary to tRNAMet, with and without the additional mutation in U5 to be complementary to the anticodon of tRNAMet, stably maintains the PBS complementary to tRNAMet following extended in vitro culture in PBMC. In contrast, viruses with either the PBS or PBS and U5 mutated to be complementary to tRNAIle were unstable during in vitro replication in PBMC and reverted to utilize tRNALys,3. Viruses with the PBS altered to be complementary to tRNAPro replicated in PBMC but reverted to use tRNALys,3; viruses with mutations in both the U5 and PBS complementary to tRNAPro maintained this PBS, yet replicated poorly in PBMC. Conclusion The results of these studies demonstrate that HIV-1 has preferences for selection of certain tRNAs for high-level replication in PBMC.
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MESH Headings
- Binding Sites
- DNA Primers
- HIV Reverse Transcriptase
- HIV-1/genetics
- HIV-1/metabolism
- HIV-1/physiology
- Humans
- Leukocytes, Mononuclear/virology
- Mutation
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- RNA, Transfer, Lys/metabolism
- RNA, Viral/metabolism
- Ribonucleoprotein, U5 Small Nuclear/genetics
- Transcription, Genetic
- Virus Replication
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Affiliation(s)
- Kenda L Moore-Rigdon
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Barry R Kosloff
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Richard L Kirkman
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Casey D Morrow
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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21
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Renda MJ, Bradel-Tretheway B, Planelles V, Bambara RA, Dewhurst S. Inhibition of HIV type 1 replication using lentiviral-mediated delivery of mutant tRNA(Lys3)A58U. AIDS Res Hum Retroviruses 2004; 20:1324-34. [PMID: 15650425 DOI: 10.1089/aid.2004.20.1324] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In previous studies, we showed that residue A58 of cellular tRNALys3 is necessary for appropriate termination of viral plus-strand strong-stop DNA (+SS DNA), and therefore plays a critical role in the life cycle of HIV-1. We also performed proof-of-principle studies that established that a mutant form of this tRNA primer (tRNA(Lys3)A58U, which lacks the M1A58 residue necessary for +SS DNA termination) could inhibit HIV-1 replication. In the present work, we examined whether a third generation lentiviral vector (SIN) could be used to deliver tRNA(Lys3)A58U to CEM cells. Using both viral kinetic studies and limiting dilution assays (LDA), we observed significant impairment of HIV-1 replication, up to 3 logs in the LDA, in CEM sublines expressing mutant tRNA(Lys3)A58U. No inhibition occurred in cells that either expressed wild-type tRNA(Lys3) or were transduced with empty SIN vector. Further, we observed impairment of viral replication using primary isolates of both HIV-1 and HIV-2 in sublines containing tRNA(Lys3)A58U. We also detected "breakthrough" HIV-1 replication in some tRNA(Lys3)A58U-expressing cultures. Interestingly, analyzed breakthrough viruses appeared to be both genetically and phenotypically wild type. One possible explanation for virological breakthrough is that it reflects the gradual accumulation of HIV-1 within the infected cell culture, to a level that ultimately exceeds the containment "threshold" conferred by tRNA(Lys3)A58U. The fact that HIV-1 does not appear to acquire heritable resistance to tRNA(Lys3)A58U-mediated blockade differentiates this antiviral modality from other therapeutic interventions. It also suggests that tRNA-mediated inhibition of viral replication might be a valuable adjunct to other antiviral approaches.
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Affiliation(s)
- Matthew J Renda
- Department of Biochemistry, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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22
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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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23
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Palmer MT, Morrow CD. Analysis of murine leukemia virus replication complemented by yeast tRNA(Phe) reveals inherent preferences for the tRNA primer selected for reverse transcription. Virology 2004; 324:430-8. [PMID: 15207628 DOI: 10.1016/j.virol.2004.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2004] [Revised: 02/13/2004] [Accepted: 03/15/2004] [Indexed: 11/19/2022]
Abstract
The replication of murine leukemia virus (MuLV) requires the capture of a cellular tRNA(Pro) as a primer for reverse transcription. To further study the specificity of primer selection, we have utilized a defective MuLV in which the primer-binding site (PBS) has been altered to be complementary to a nonmammalian tRNA, yeast tRNA(Phe). Infectivity of the defective MuLV is dependent upon co-expression of yeast tRNA(Phe) in the cell. Defective MuLV genomes have been constructed in which the PBS was altered to be complementary to tRNA(Phe) that also encoded the cDNA for tRNA(Phe). Transfection of these defective proviral genomes into cells resulted in the production of infectious MuLV as determined by a single-round assay. The amount of infectious virus produced using this complementation system, though, was approximately 6-fold lower than that produced following transfection of defective proviral genomes with a wild-type PBS complementary to tRNA(Pro). The lower infectivity was not due to reduced expression of tRNA(Phe) in the transfected cells as compared to endogenous tRNA(Pro) or tRNA(Lys,3). Serial passage of the MuLV genome with a PBS complementary to tRNA(Phe) that encoded tRNA(Phe) resulted in amplification of the virus. Using this rescue system, we have passaged the virus for four serial passages, after which time a revertant genome in which the PBS was altered to be complementary to tRNA(Gln) was detected that grew to high titers following subsequent serial passage. The results of these studies suggest that MuLV has preferences for the tRNA primer used in reverse transcription and are discussed with respect to the mechanism of primer selection.
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Affiliation(s)
- Matthew T Palmer
- Department of Cell Biology, University of Alabama at Birmingham, 720 20th Street South, Birmingham, AL 35294, USA
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24
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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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25
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Moore KL, Kosloff BR, Kelly NJ, Kirkman RL, Dupuy LC, McPherson S, Morrow CD. HIV type 1 that select tRNA(His) or tRNA(Lys1,2) as primers for reverse transcription exhibit different infectivities in peripheral blood mononuclear cells. AIDS Res Hum Retroviruses 2004; 20:373-81. [PMID: 15157356 DOI: 10.1089/088922204323048122] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The replication in human peripheral blood mononuclear cells (PBMC) of unique HIV-1 that select tRNA(His) or tRNA(Lys1,2) for reverse transcription was compared to the wild-type virus that uses tRNA(Lys,3). HIV-1 with only the primer-binding site (PBS) changed to be complementary to these alternative tRNAs initially replicated more slowly than the wild-type virus in PBMC, although all viruses eventually reached equivalent growth as measured by p24 antigen. Viruses with only a PBS complementary to the 3' terminal 18 nucleotides of tRNA(His) or tRNA(Lys1,2) reverted to use tRNA(Lys3). HIV-1 with mutations in the U5-PBS to allow selection of tRNA(His) and tRNA(Lys1,2) following long-term growth in SupT1 cells were also evaluated for growth and PBS stability following replication in PBMC. Although both viruses initially grew slower than wild type, they maintained a PBS complementary to the starting tRNA and did not revert to the wild-type PBS after long-term culture in PBMC. Analysis of the U5-PBS regions following long-term culture in PBMC also revealed few changes from the starting sequences. The virus that stably used tRNA(His) was less infectious than the wild type. In contrast, the virus that stably used tRNA(Lys1,2) evolved to be as infectious as wild-type virus following extended culture in PBMC. The results of these studies highlight the impact of the host cell on the tRNA primer selection process and subsequent infectivity of HIV-1.
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Affiliation(s)
- Kenda L Moore
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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26
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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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27
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Kelly NJ, Palmer MT, Morrow CD. Selection of retroviral reverse transcription primer is coordinated with tRNA biogenesis. J Virol 2003; 77:8695-701. [PMID: 12885888 PMCID: PMC167244 DOI: 10.1128/jvi.77.16.8695-8701.2003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Initiation of retrovirus reverse transcription requires the selection of a tRNA primer from the intracellular milieu. To investigate the features of primer selection, a human immunodeficiency virus type 1 (HIV-1) and a murine leukemia virus (MuLV) were created that require yeast tRNA(Phe) to be supplied in trans for infectivity. Wild-type yeast tRNA(Phe) expressed in mammalian cells was transported to the cytoplasm and aminoacylated. In contrast, tRNA(Phe) without the D loop (tRNA(Phe)D(-)) was retained within the nucleus and did not complement infectivity of either HIV-1 or MuLV; however, infectivity was restored when tRNA(Phe)D(-) was directly transfected into the cytoplasm of cells. A tRNA(Phe) mutant (tRNA(Phe)UUA) that did not have the capacity to be aminoacylated was transported to the cytoplasm and did complement infectivity of both HIV-1 and MuLV, albeit at a level less than that with wild-type tRNA(Phe). Collectively, our results demonstrate that the tRNA primer captured by HIV-1 and MuLV occurs after nuclear export of tRNA and supports a model in which primer selection for retroviruses is coordinated with tRNA biogenesis at the intracellular site of protein synthesis.
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Affiliation(s)
- Nathan J Kelly
- Department of Microbiology, University of Alabama at Birmingham, 35294, USA
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28
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Dupuy LC, Kelly NJ, Elgavish TE, Harvey SC, Morrow CD. Probing the importance of tRNA anticodon: human immunodeficiency virus type 1 (HIV-1) RNA genome complementarity with an HIV-1 that selects tRNA(Glu) for replication. J Virol 2003; 77:8756-64. [PMID: 12885895 PMCID: PMC167254 DOI: 10.1128/jvi.77.16.8756-8764.2003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The initiation of human immunodeficiency virus type 1 (HIV-1) reverse transcription occurs at the primer binding site (PBS) that is complementary to the 3'-terminal nucleotides of tRNA(3)(Lys). Why all known strains of HIV-1 select tRNA(3)(Lys) for replication is unknown. Previous studies on the effect of altering the PBS of HIV-1 on replication identified an HIV-1 with a PBS complementary to tRNA(Glu). Since the virus was not initially designed to use tRNA(Glu), the virus had selected tRNA(Glu) from the intracellular pool of tRNA for use in replication. Further characterization of HIV-1 that uses tRNA(Glu) may provide new insights into the preference for tRNA(3)(Lys). HIV-1 constructed with the PBS complementary to tRNA(Glu) was more stable than HIV-1 with the PBS complementary to tRNA(Met) or tRNA(His); however, all of these viruses eventually reverted back to using tRNA(3)(Lys) following growth in SupT1 cells or peripheral blood mononuclear cells (PBMCs). New HIV-1 mutants with nucleotides in U5 complementary to the anticodon of tRNA(Glu) remained stable when grown in SupT1 cells or PBMCs, although the mutants grew more slowly than the wild-type virus. Sequence analysis of the U5 region and the PBS revealed additional mutations predicted to further promote tRNA-viral genome interaction. The results support the importance of the tRNA anticodon-genome interaction in the selection of the tRNA primer and highlight the fact that unique features of tRNA(3)(Lys) are exploited by HIV-1 for selection as the reverse transcription primer.
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Affiliation(s)
- Lesley C Dupuy
- Department of Cell Biology, University of Alabama at Birmingham, 35294, USA
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29
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Wei X, Liang C, Götte M, Wainberg MA. Negative effect of the M184V mutation in HIV-1 reverse transcriptase on initiation of viral DNA synthesis. Virology 2003; 311:202-12. [PMID: 12832217 DOI: 10.1016/s0042-6822(03)00173-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The M184V mutation in HIV reverse transcriptase (RT) is associated with high-level resistance against the nucleoside inhibitor lamivudine as well as diminished viral replication capacity. We have previously demonstrated that HIV variants containing the M184V mutation were relatively unable to successfully undergo compensatory mutagenesis following deletion of an A-rich loop located upstream of the primer binding site (PBS). To understand the mechanisms involved, we synthesized viral RNA templates containing different compensatory mutations that were emergent during the long-term culture of the A-rich loop-deleted viruses. These templates were then used in cell-free reverse transcription initiation assays and in tRNA primer placement assays performed with either recombinant wild-type RT or recombinant RT containing the M184V substitution. The results showed that the RNA template that contained the A-rich loop deletion was impaired in ability to initiate reverse transcription and that the presence of the M184V substitution in RT amplified this effect. Clearance from pausing at position +3 during synthesis of viral DNA was identified as a sensitive step in this reaction that could not be efficiently bypassed with the M184V mutant enzyme. Increased efficiency of initiation was seen with the deleted RNA templates that also contained mutations identified in the revertant viruses, provided that these mutations facilitated formation of a competent binary tRNA/RNA complex. These findings provide biochemical evidence that initiation of tRNA(Lys3)-primed DNA synthesis is an important rate-limiting step in reverse transcription that correlates with viral replication fitness.
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Affiliation(s)
- Xin Wei
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, H3T 1E2, Montréal, Québec, Canada
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30
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Iwatani Y, Rosen AE, Guo J, Musier-Forsyth K, Levin JG. Efficient initiation of HIV-1 reverse transcription in vitro. Requirement for RNA sequences downstream of the primer binding site abrogated by nucleocapsid protein-dependent primer-template interactions. J Biol Chem 2003; 278:14185-95. [PMID: 12560327 DOI: 10.1074/jbc.m211618200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Synthesis of HIV-1 (-) strong-stop DNA is initiated following annealing of the 3' 18 nucleotides (nt) of tRNA(3)(Lys) to the primer binding site (PBS) near the 5' terminus of viral RNA. Here, we have investigated whether sequences downstream of the PBS play a role in promoting efficient (-) strong-stop DNA synthesis. Our findings demonstrate a template requirement for at least 24 bases downstream of the PBS when tRNA(3)(Lys) or an 18-nt RNA complementary to the PBS (R18), but not an 18-nt DNA primer, are used. Additional assays using 18-nt DNA-RNA chimeric primers, as well as melting studies and circular dichroism spectra of 18-nt primer:PBS duplexes, suggest that priming efficiency is correlated with duplex conformation and stability. Interestingly, in the presence of nucleocapsid protein (NC), the 24 downstream bases are dispensable for synthesis primed by tRNA(3)(Lys) but not by R18. We present data supporting the conclusion that NC promotes extended interactions between the anticodon stem and variable loop of tRNA(3)(Lys) and a sequence upstream of the A-rich loop in the template. Taken together, this study leads to new insights into the initiation of HIV-1 reverse transcription and the functional role of NC-facilitated tRNA-template interactions in this process.
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Affiliation(s)
- Yasumasa Iwatani
- Laboratory of Molecular Genetics, National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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31
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Goldschmidt V, Ehresmann C, Ehresmann B, Marquet R. Does the HIV-1 primer activation signal interact with tRNA3(Lys) during the initiation of reverse transcription? Nucleic Acids Res 2003; 31:850-9. [PMID: 12560480 PMCID: PMC149207 DOI: 10.1093/nar/gkg187] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Reverse transcription of HIV-1 RNA is primed by a tRNA3(Lys) molecule bound at the primer binding site (PBS). Complex intermolecular interactions were proposed between tRNA3(Lys) and the RNA of the HIV-1 Mal isolate. Recently, an alternative interaction was proposed between the TPsiC stem of tRNA3(Lys) and a primer activation signal (PAS) of the Lai and Hxb2 RNAs, suggesting major structural variations in the reverse transcription complex of different HIV-1 strains. Here, we analyzed mutants of the Hxb2 RNA that prevent the interaction between the PAS and tRNA3(Lys) or/and a complementary sequence in the viral RNA. We compared the kinetics of reverse transcription of the wild type and mutant Hxb2 RNAs, using either tRNA3(Lys) or an 18mer oligoribonucleotide complementary to the PBS, which cannot interact with the PAS, as primers. We also used chemical probing to test the structure of the mutant and wild type RNAs, as well as the complex formed between the later RNA and tRNA3(Lys). These experiments, together with the analysis of long term replication data of mutant viruses obtained by C. Morrow and coworkers (Birmingham, USA) that use alternate tRNAs as primers, strongly suggest that the interaction between the Hxb2 PAS and tRNA3(Lys) does not exist. Instead, the effects of the vRNA mutations on reverse transcription seem to be linked to incorrect folding of the mutant RNAs.
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MESH Headings
- Base Sequence
- Binding Sites
- DNA Primers
- DNA, Viral/biosynthesis
- Gene Expression Regulation, Viral
- HIV Reverse Transcriptase/metabolism
- HIV-1/genetics
- Kinetics
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Oligoribonucleotides
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Transcription, Genetic
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Affiliation(s)
- Valérie Goldschmidt
- UPR 9002 du CNRS, l'Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France
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32
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Goldschmidt V, Rigourd M, Ehresmann C, Le Grice SFJ, Ehresmann B, Marquet R. Direct and indirect contributions of RNA secondary structure elements to the initiation of HIV-1 reverse transcription. J Biol Chem 2002; 277:43233-42. [PMID: 12194974 DOI: 10.1074/jbc.m205295200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Initiation of human immunodeficiency virus type 1 (HIV-1) reverse transcription requires specific recognition between the viral RNA (vRNA), tRNA(3)(Lys), which acts as primer, and reverse transcriptase (RT). The specificity of this ternary complex is mediated by intricate interactions between the HIV-1 RNA and tRNA(3)(Lys). Here, we compared the relative importance of the secondary structure elements of this complex in the initiation process. To this aim, we used the previously published three-dimensional model of the initiation complex to rationally introduce a series of deletions and substitutions in the vRNA. When necessary, we used chemical probing to check the structure of the tRNA(3)(Lys)-mutant vRNA complexes. For each of them, we measured the binding affinity of RT and the kinetics of initial extension of tRNA(3)(Lys) and of synthesis of the (-) strand strong stop DNA. Our results were overall in keeping with the three-dimensional model of the initiation complex. Surprisingly, we found that disruption of the intermolecular template-primer interactions, which are not directly recognized by RT, more severely affected reverse transcription than deletions or disruption of one of the intramolecular helices to which RT directly binds. Perturbations of the highly constrained junction between the intermolecular helix formed by the primer binding site and the 3' end of tRNA(3)(Lys) and the helix immediately upstream also had dramatic effects on the initiation of reverse transcription. Taken together, our results demonstrate the overwhelming importance of the overall three-dimensional structure of the initiation complex and identify structural elements that constitute promising targets for anti-initiation-specific drugs.
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Affiliation(s)
- Valerie Goldschmidt
- UPR 9002 du CNRS affiliée à l'Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France
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33
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Abstract
RNA loop-loop interactions are frequently used to trigger initial recognition between two RNA molecules. In this review, we present selected well-documented cases that illustrate the diversity of biological processes using RNA loop-loop recognition properties. The first one is related to natural antisense RNAs that play a variety of regulatory functions in bacteria and their extra-chromosomal elements. The second one concerns the dimerization of HIV-1 genomic RNA, which is responsible for the encapsidation of a diploid RNA genome. The third one concerns RNA interactions involving double-loop interactions. These are used by the bicoid mRNA to form dimers, a property that appears to be important for mRNA localization in drosophila embryo, and by bacteriophage phi29 pRNA which forms hexamers that participate in the translocation of the DNA genome through the portal vertex of the capsid. Despite the high diversity of systems and mechanisms, some common features can be highlighted. (1) Efficient recognition requires rapid bi-molecular binding rates, regardless of the RNA pairing scheme. (2) The initial recognition is favored by particular conformations of the loops enabling a proper presentation of nucleotides (generally a restricted number) that initiate the recognition process. (3) The fate of the initial reversible loop-loop complex is dictated by both functional and structural constraints. RNA structures have evolved either to "freeze" the initial complex, or to convert it into a more stable one, which involves propagation of intermolecular interactions along topologically feasible pathways. Stabilization of the initial complex may also be assisted by proteins and/or formation of additional contacts.
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Affiliation(s)
- Christine Brunel
- UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
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34
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Kaushik N, Basu A, Palumbo P, Myers RL, Pandey VN. Anti-TAR polyamide nucleotide analog conjugated with a membrane-permeating peptide inhibits human immunodeficiency virus type 1 production. J Virol 2002; 76:3881-91. [PMID: 11907228 PMCID: PMC136084 DOI: 10.1128/jvi.76.8.3881-3891.2002] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The emergence of drug-resistant variants has posed a significant setback against effective antiviral treatment for human immunodeficiency virus (HIV) infections. The choice of a nonmutable region of the viral genome such as the conserved transactivation response element (TAR element) in the 5' long terminal repeat (LTR) may potentially be an effective target for drug development. We have earlier demonstrated that a polyamide nucleotide analog (PNA) targeted to the TAR hairpin element, when transfected into cells, can effectively inhibit Tat-mediated transactivation of HIV type 1 (HIV-1) LTR (T. Mayhood et al., Biochemistry 39:11532-11539, 2000). Here we show that this anti-TAR PNA (PNA(TAR)), upon conjugation with a membrane-permeating peptide vector (transportan) retained its affinity for TAR in vitro similar to the unconjugated analog. The conjugate was efficiently internalized into the cells when added to the culture medium. Examination of the functional efficacy of the PNA(TAR)-transportan conjugate in cell culture using luciferase reporter gene constructs resulted in a significant inhibition of Tat-mediated transactivation of HIV-1 LTR. Furthermore, PNA(TAR)-transportan conjugate substantially inhibited HIV-1 production in chronically HIV-1-infected H9 cells. The mechanism of this inhibition appeared to be regulated at the level of transcription. These results demonstrate the efficacy of PNA(TAR)-transportan as a potential anti-HIV agent.
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Affiliation(s)
- Neerja Kaushik
- Center for the Study of Emerging and Re-Emerging Pathogens, UMDNJ-New Jersey Medical School, Newark, New Jersey 07103, USA
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35
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Beerens N, Berkhout B. Switching the in vitro tRNA usage of HIV-1 by simultaneous adaptation of the PBS and PAS. RNA (NEW YORK, N.Y.) 2002; 8:357-369. [PMID: 12003495 PMCID: PMC1370257 DOI: 10.1017/s1355838202028194] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Reverse transcription of the HIV-1 RNA genome is primed by the cellular tRNA(lys3) molecule that anneals to a complementary sequence in the viral genome, the primer-binding site (PBS). Additional interactions between the tRNA primer and the viral RNA were proposed to play a role in reverse transcription. We recently identified an 8-nt element in the U5 region upstream of the PBS that is critical for initiation and processive elongation of reverse transcription. This motif was termed the primer activation signal (PAS), and is proposed to interact with the "antiPAS sequence" in the TphiC arm of tRNA(lys3). In this study, we demonstrate that the efficiency of initiation of reverse transcription can be modulated by PAS mutations that strengthen or weaken the interaction with antiPAS. These results provide further evidence for a direct base-pairing interaction between the PAS in the viral RNA and the antiPAS in the tRNA(lys3) molecule. A broad phylogenetic survey indicated that a PAS element is present in all retroviral RNA genomes, suggesting that the process of reverse transcription is regulated by a common mechanism in all retroviridae. It has proven very difficult to change the identity of the tRNA primer for HIV-1 reverse transcription by changing the PBS sequence. Using in vitro reverse transcription assays, we demonstrate that the identity of the priming tRNA species can be switched by simultaneous alteration of the PBS and PAS motifs to accommodate a new tRNA primer. These results indicate that the PAS-antiPAS interaction is important for both primer selection and efficient reverse transcription.
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MESH Headings
- 5' Untranslated Regions/chemistry
- 5' Untranslated Regions/genetics
- 5' Untranslated Regions/metabolism
- Base Pairing
- Base Sequence
- Gene Expression Regulation, Viral
- Genome, Viral
- HIV Infections/virology
- HIV-1/genetics
- HIV-1/metabolism
- Humans
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- RNA
- RNA, Transfer, Lys/genetics
- RNA, Transfer, Lys/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Templates, Genetic
- Transcription, Genetic/genetics
- Transfection
- Virus Replication/genetics
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Affiliation(s)
- Nancy Beerens
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands
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36
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Muthuswami R, Chen J, Burnett BP, Thimmig RL, Janjic N, McHenry CS. The HIV plus-strand transfer reaction: determination of replication-competent intermediates and identification of a novel lentiviral element, the primer over-extension sequence. J Mol Biol 2002; 315:311-23. [PMID: 11786014 DOI: 10.1006/jmbi.2001.5205] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Current retroviral replication models propose that during (+) strand synthesis, the initial (-) strand tRNA primer is partially replicated to reproduce the 18 nt primer-binding site (PBS). Subsequent removal of the tRNA primer from the (-) strand template exposes the PBS, which anneals to complementary sequences on a DNA acceptor template to enable (+) strand transfer. We used model templates composed of primed (-) strand DNA covalently linked with post-transcriptionally modified tRNA(3)(lys) along with natural sequence human immunodeficiency virus (HIV) acceptor DNA to study the generation of the (+) strand strong stop intermediate and the subsequent (+) strand transfer reaction. The rate of formation of the (+) strand transfer reaction products was modestly increased (threefold) by inclusion of nucleocapsid protein, suggesting an ancillary role for this protein in this stage of retroviral replication. In addition to the well-known stop site opposite G59 of the tRNA primer, we detected two additional stop sites opposite psi55 and at A38. Kinetic analysis showed that only the intermediates formed by stops opposite G59 and psi55 were active in the subsequent (+) strand transfer reaction. The surprising discovery of the longer, viable (+) strand interaction intermediate prompted us to survey retroviral sequences for a region complementary to the additional donor DNA nucleotides involved in this over-extension. Indeed, complementary sequences that could support this over-extension were found. A strong consensus sequence is immediately adjacent to and downstream of the PBS in lentiviruses and spumaviruses. This consensus sequence was not found in other genera of retroviruses. We have named this element the "primer over-extension sequence" (POS), and propose that it provides a complementary sequence for strand transfer reactions proceeding from intermediates that extend beyond the standard 18 nt complement of the PBS.
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MESH Headings
- Base Pairing/genetics
- Base Sequence
- Consensus Sequence/genetics
- DNA, Viral/genetics
- DNA, Viral/metabolism
- HIV/genetics
- Humans
- Kinetics
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA/biosynthesis
- RNA/chemistry
- RNA/genetics
- RNA, Transfer, Lys/chemistry
- RNA, Transfer, Lys/genetics
- RNA, Transfer, Lys/metabolism
- RNA, Viral/biosynthesis
- RNA, Viral/chemistry
- RNA, Viral/genetics
- Regulatory Sequences, Nucleic Acid/genetics
- Spumavirus/genetics
- Templates, Genetic
- Virus Replication/genetics
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Affiliation(s)
- Rohini Muthuswami
- Department of Biochemistry & Molecular Genetics and Molecular Biology Program, University of Colorado Health Sciences Center, 4200 E. Ninth Avenue, B121, Denver, CO 80262, USA
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37
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Brulé F, Marquet R, Rong L, Wainberg MA, Roques BP, Le Grice SFJ, Ehresmann B, Ehresmann C. Structural and functional properties of the HIV-1 RNA-tRNA(Lys)3 primer complex annealed by the nucleocapsid protein: comparison with the heat-annealed complex. RNA (NEW YORK, N.Y.) 2002; 8:8-15. [PMID: 11873759 PMCID: PMC1370235 DOI: 10.1017/s1355838202010981] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The conversion of the single-stranded RNA genome into double-stranded DNA by virus-coded reverse transcriptase (RT) is an essential step of the retrovirus life cycle. In human immunodeficiency virus type 1 (HIV-1), RT uses the cellular tRNA(Lys)3 to initiate the (-) strand DNA synthesis. Placement of the primer tRNA(Lys)3 involves binding of its 3'-terminal 18 nt to a complementary region of genomic RNA termed PBS. However, the PBS sequence is not the unique determinant of primer usage and additional contacts are important. This placement is believed to be achieved in vivo by the nucleocapsid domain of Gag or by the mature protein NCp. Up to now, structural information essentially arose from heat-annealed primer-template complexes (Isel et al., J Mol Biol, 1995, 247:236-250; Isel et al., EMBO J, 1999, 18:1038-1048). Here, we investigated the formation of the primer-template complex mediated by NCp and compared structural and functional properties of heat- and NCp-annealed complexes. We showed that both heat- and NCp-mediated procedures allow comparable high yields of annealing. Then, we investigated structural features of both kinds of complexes by enzymatic probing, and we compared their relative efficiency in (-) strong stop DNA synthesis. We did not find any significant differences between these complexes, suggesting that information derived from the heat-annealed complex can be transposed to the NCp-mediated complex and most likely to complexes formed in vivo.
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MESH Headings
- Base Pairing
- Base Sequence
- DNA/biosynthesis
- DNA Replication
- Electrophoretic Mobility Shift Assay
- HIV-1/genetics
- HIV-1/metabolism
- Hot Temperature
- Humans
- Molecular Sequence Data
- Nucleic Acid Conformation
- Nucleic Acid Hybridization
- Nucleic Acid Probes
- Nucleocapsid Proteins/metabolism
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA, Transfer, Lys/chemistry
- RNA, Transfer, Lys/genetics
- RNA, Transfer, Lys/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Templates, Genetic
- Transcription, Genetic
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Affiliation(s)
- Fabienne Brulé
- Unité Propre de Recherche 9002, Centre Nationale de la Recherche Scientifique, Institut de Biologie Moleculaire et Cellulaire, Strasbourg, France
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38
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Kaushik N, Talele TT, Monel R, Palumbo P, Pandey VN. Destabilization of tRNA3(Lys) from the primer-binding site of HIV-1 genome by anti-A loop polyamide nucleotide analog. Nucleic Acids Res 2001; 29:5099-106. [PMID: 11812842 PMCID: PMC97570 DOI: 10.1093/nar/29.24.5099] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Initiation of human immunodeficiency virus type 1 (HIV-1) reverse transcription occurs by extension of the cellular tRNA3(Lys) which anneals to the primer-binding site (PBS) on the 5' non-translated region of the viral RNA genome. The A-rich sequence (A-loop) upstream of the PBS interacts with the anticodon loop of tRNA3(Lys) and has been proposed to be essential for conferring specificity to tRNA3(Lys) for priming the initiation of HIV-1 reverse transcription. We observed that polyamide nucleic acid targeted to the A-loop sequence (PNAAL) exhibits high binding specificity for its target sequence. The PNAAL pre-bound to the A-loop sequence prevents tRNA3(Lys) priming on the viral RNA consequently blocking in vitro initiation of reverse transcription. Further, PNAAL can efficiently disrupt the preformed [tRNA3(Lys)--viral RNA] complex thereby rendering it non-functional for reverse transcription. The endogenous reverse transcription in disrupted HIV-1 virions containing packaged tRNA3(Lys) and its replicating enzyme RT was significantly inhibited by PNAAL, thus providing direct evidence of the involvement of the A-loop region of viral RNA genome in tRNA3(Lys) priming process. These findings suggest the potential of the A-loop region as a critical target for blocking HIV-1 replication.
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MESH Headings
- Base Sequence
- Binding Sites
- DNA, Antisense/chemistry
- DNA, Antisense/metabolism
- DNA, Antisense/pharmacology
- Dose-Response Relationship, Drug
- Genome, Viral
- HIV-1/drug effects
- HIV-1/genetics
- HIV-1/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Nylons/chemistry
- Peptide Nucleic Acids/chemistry
- Peptide Nucleic Acids/metabolism
- Peptide Nucleic Acids/pharmacology
- RNA, Transfer, Lys/chemistry
- RNA, Transfer, Lys/genetics
- RNA, Transfer, Lys/metabolism
- RNA, Viral/chemistry
- RNA, Viral/drug effects
- RNA, Viral/genetics
- Transcription, Genetic/drug effects
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Affiliation(s)
- N Kaushik
- Department of Biochemistry and Molecular Biology, Center for the Study of Emerging and Re-Emerging Pathogens UMDNJ-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
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39
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Freund F, Boulmé F, Litvak S, Tarrago-Litvak L. Initiation of HIV-2 reverse transcription: a secondary structure model of the RNA-tRNA(Lys3) duplex. Nucleic Acids Res 2001; 29:2757-65. [PMID: 11433020 PMCID: PMC55777 DOI: 10.1093/nar/29.13.2757] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Human immunodeficiency virus type 2 (HIV-2) reverse transcription is initiated from cellular tRNA(Lys3) partially annealed to the RNA viral genome at the primer binding site (PBS). This annealing involves interactions between two highly structured RNA molecules. In contrast to HIV-1, in which the reverse transcription initiation complex has been thoroughly studied, there is still little information regarding a possible model to describe the secondary structure of the template-primer complex in HIV-2. To determine whether HIV-2 RNA sequences flanking the PBS may specifically interact with the natural primer tRNA, we performed site-directed mutagenesis and enzymatic footprinting. An RNA fragment corresponding to the HIV-2 U5 RNA domain and tRNA(Lys3) were probed either in their free form or in the binary complex. Important reactivity changes to nucleases were obtained upon complex formation. In addition to the canonical contacts between the viral PBS and the 3' end acceptor stem of tRNA(Lys3), we identified two additional interacting domains: (i) the U-rich region of the anticodon loop with the A-rich sequence of the internal loop within the U5-prePBS region; (ii) nucleotides 48-54 from the TPsiC domain of tRNA(Lys3) and the 240-247 region of viral U5-RNA. In view of these experimental data and sequence comparison between different HIV-2 isolates, we propose a model for the secondary structure of the HIV-2 template-primer initiation complex.
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MESH Headings
- Anticodon/genetics
- Base Pairing
- Base Sequence
- HIV Long Terminal Repeat/genetics
- HIV-2/genetics
- Molecular Sequence Data
- Mutation/genetics
- Nuclease Protection Assays
- Nucleic Acid Conformation
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA, Transfer, Lys/chemistry
- RNA, Transfer, Lys/genetics
- RNA, Transfer, Lys/metabolism
- RNA, Viral/biosynthesis
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Sequence Alignment
- Templates, Genetic
- Transcription, Genetic/genetics
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Affiliation(s)
- F Freund
- UMR-5097, CNRS-Université Victor Segalen Bordeaux 2, Case 103, 146 rue Léo Saignat, 33076 Bordeaux cedex, France. IFR 66 'Pathologies Infectieuses', Bordeaux
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40
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Hansen AC, Grunwald T, Lund AH, Schmitz A, Duch M, Uberla K, Pedersen FS. Transfer of primer binding site-mutated simian immunodeficiency virus vectors by genetically engineered artificial and hybrid tRNA-like primers. J Virol 2001; 75:4922-8. [PMID: 11312366 PMCID: PMC114249 DOI: 10.1128/jvi.75.10.4922-4928.2001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Simian immunodeficiency viruses (SIV) harbor primer binding sites (PBS) matching tRNA or tRNA. To study determinants of primer usage in SIV, a SIVmac239-based vector was impaired by mutating the PBS to a sequence (PBS-X2) with no match to any tRNA. By cotransfection of a synthetic gene encoding a tRNA(Pro)-like RNA with a match to PBS-X2, the activity of this vector could be restored to a transduction efficiency slightly lower than that of the wild-type vector. A vector with a PBS matching tRNA(Pro) was functional at a level slightly below that of the wild-type vector, but higher transduction efficiency could be obtained by cotransfection of a gene for an engineered tRNA(Pro)-tRNA hybrid with a match to PBS-Pro. The importance of tRNA backbone identity was further analyzed by complementing the PBS-X2 vector with a gene for a matching x2 primer with a tRNA backbone, which led to three- to fourfold-higher titers than those observed for the x2 primer with the tRNA(Pro) backbone. In summary, our results demonstrate flexibility in PBS and primer usage for SIVmac239, with PBS-primer complementarity being the major determinant, in analogy with previous findings for murine leukemia viruses and human immunodeficiency virus type 1.
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Affiliation(s)
- A C Hansen
- Department of Molecular and Structural Biology, Aarhus University, DK-8000 Aarhus, Denmark
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41
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Abstract
Human immunodeficiency virus (HIV), like all retroviruses, requires a cellular tRNA as a primer for initiation of reverse transcription. In a previous study, we demonstrated that an HIV-1 with a primer binding site complementary to yeast tRNA(Phe) (psHIV-Phe) was not infectious unless yeast tRNA(Phe) was supplied in trans. This unique in vivo complementation system has now been used to define the elements of the tRNA required for HIV-1 replication. Mutant tRNA(Phe) with deletions in TPsiC stem-loop, anticodon stem-loop or D stem-loop of the tRNA were generated and assessed for the capacity to rescue psHIV-Phe. Mutant tRNA(Phe) with disrupted TPsiC stem-loop did not rescue psHIV-Phe. In contrast, a mutant tRNA(Phe) without the D stem-loop was fully functional for the rescue. The tRNA anticodon stem-loop region was found to be important for efficient complementation. The results of our studies demonstrate for the first time the importance of specific structural and sequence elements of the tRNA primer for HIV-1 reverse transcription and define new targets for interruption of HIV-1 replication.
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MESH Headings
- Base Sequence
- Cell Line
- DNA, Recombinant
- Genetic Complementation Test
- HIV-1/genetics
- HeLa Cells
- Humans
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Plasmids/genetics
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer, Lys/chemistry
- RNA, Transfer, Lys/genetics
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/genetics
- RNA, Viral/chemistry
- RNA, Viral/genetics
- Saccharomyces cerevisiae/genetics
- Sequence Homology, Nucleic Acid
- Virus Replication/genetics
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Affiliation(s)
- Q Yu
- Department of Microbiology, University of Alabama at Birmingham, 701 South 19th Street, LHRB 619, Birmingham, AL 35294, USA
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42
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43
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Wei X, Götte M, Wainberg MA. Human immunodeficiency virus type-1 reverse transcription can be inhibited in vitro by oligonucleotides that target both natural and synthetic tRNA primers. Nucleic Acids Res 2000; 28:3065-74. [PMID: 10931921 PMCID: PMC108450 DOI: 10.1093/nar/28.16.3065] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Reverse transcription of human immunodeficiency virus type-1 is primed by cellular tRNA(Lys3), which is selectively packaged into viral particles where it is bound at its 3' terminus to a complementary sequence of viral RNA termed the primer binding site (PBS). Since cellular tRNA(Lys3) is highly conserved, it might conceivably serve as a good target for novel antagonists to block reverse transcriptase (RT) activity. In this study, we have examined a number of antisense oligodeoxyribonucleotides (ODNs) that are complementary to different parts of the tRNA primer and, therefore, may interfere with the initiation of RT-mediated DNA synthesis. We found that the stability of complexes between synthetic tRNA(Lys3 )and ODNs was significantly increased when binding occurred via sequences involved in tertiary interactions of the tRNA. In particular, ODNs with complementarity to both the variable and TPsiC stem-loop of tRNA(Lys3 )bound with high affinity to both free tRNA(Lys3 )as well as to the binary tRNA(Lys3)/RNA complex. As a result, the initiation of DNA synthesis was severely compromised under these conditions. Moreover, RT-associated RNase H activity recognized the tRNA within this ternary tRNA(Lys3)/RNA/ODN complex as an RNA template and initiated its degradation. Both this RNase H degradation of tRNA(Lys3 )as well as the altered structure of the tRNA/RNA complex, due to the binding of the ODN, contributed to the inhibition of synthesis of viral DNA. The initiation of RT activity was almost completely blocked when using ODNs that interfered with intermolecular tRNA/RNA interactions that involved both the PBS and sequences outside the PBS. Similar findings were obtained with natural preparation of tRNA(Lys3).
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Affiliation(s)
- X Wei
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, 3755, chemin Côte-Ste-Catherine, Montréal, Québec H3T 1E2, Canada
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44
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Beerens N, Berkhout B. In vitro studies on tRNA annealing and reverse transcription with mutant HIV-1 RNA templates. J Biol Chem 2000; 275:15474-81. [PMID: 10809779 DOI: 10.1074/jbc.275.20.15474] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) RNA genome encodes a semistable stem-loop structure, the U5-PBS hairpin, which occludes part of the tRNA primer binding site (PBS). In previous studies, we demonstrated that mutations that alter the stability of the U5-PBS hairpin inhibit virus replication. A reverse transcription defect was measured in assays with the virion-extracted RNA-tRNA complexes. We now extend these studies with in vitro synthesized wild-type and mutant RNA templates that were tested in primer annealing and reverse transcription assays. The effect of annealing temperature and the presence of the viral nucleocapsid protein on reverse transcription was analyzed for the templates with a stabilized or destabilized U5-PBS hairpin, and in reactions initiated by tRNA or DNA primers. The results of this in vitro assay are consistent with the in vivo findings, in that both tRNA annealing and initiation of reverse transcription are sensitive to stable template RNA structure. Reverse transcription initiated by a DNA primer is less hindered by secondary structure in the RNA template than tRNA primed reactions. The inhibitory effect of template structure on tRNA-primed reverse transcription is more pronounced in this in vitro assay compared with the in vivo material, indicating that the heat-annealed RNA-tRNA complex differs from the virion-extracted viral RNA-tRNA complex.
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Affiliation(s)
- N Beerens
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam 1100 DE, The Netherlands
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45
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Lanchy JM, Isel C, Keith G, Le Grice SF, Ehresmann C, Ehresmann B, Marquet R. Dynamics of the HIV-1 reverse transcription complex during initiation of DNA synthesis. J Biol Chem 2000; 275:12306-12. [PMID: 10766870 DOI: 10.1074/jbc.275.16.12306] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Initiation of human immunodeficiency virus-1 (HIV-1) reverse transcription requires formation of a complex containing the viral RNA (vRNA), tRNA(3)(Lys) and reverse transcriptase (RT). The vRNA and the primer tRNA(3)(Lys) form several intermolecular interactions in addition to annealing of the primer 3' end to the primer binding site (PBS). These interactions are crucial for the efficiency and the specificity of the initiation of reverse transcription. However, as they are located upstream of the PBS, they must unwind as DNA synthesis proceeds. Here, the dynamics of the complex during initiation of reverse transcription was followed by enzymatic probing. Our data revealed reciprocal effects of the tertiary structure of the vRNA.tRNA(3)(Lys) complex and reverse transcriptase (RT) at a distance from the polymerization site. The structure of the initiation complex allowed RT to interact with the template strand up to 20 nucleotides upstream from the polymerization site. Conversely, nucleotide addition by RT modified the tertiary structure of the complex at 10-14 nucleotides from the catalytic site. The viral sequences became exposed at the surface of the complex as they dissociated from the tRNA following primer extension. However, the counterpart tRNA sequences became buried inside the complex. Surprisingly, they became exposed when mutations prevented the intermolecular interactions in the initial complex, indicating that the fate of the tRNA depended on the tertiary structure of the initial complex.
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Affiliation(s)
- J M Lanchy
- UPR 9002 du CNRS, IBMC, 67084 Strasbourg cedex, France
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46
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Beerens N, Klaver B, Berkhout B. A structured RNA motif is involved in correct placement of the tRNA(3)(Lys) primer onto the human immunodeficiency virus genome. J Virol 2000; 74:2227-38. [PMID: 10666253 PMCID: PMC111704 DOI: 10.1128/jvi.74.5.2227-2238.2000] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [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 (HIV-1) reverse transcription is primed by the cellular tRNA(3)(Lys) molecule that binds with its 3'-terminal 18 nucleotides to the fully complementary primer-binding site (PBS) on the viral RNA genome. Besides this complementarity, annealing of the primer may be stimulated by additional base-pairing interactions between other parts of the tRNA molecule and viral sequences flanking the PBS. According to the RNA secondary structure model of the HIV-1 leader region, part of the PBS sequence is involved in base pairing to form a small stem-loop structure, termed the U5-PBS hairpin. This hairpin may be involved in the process of reverse transcription. To study the role of the U5-PBS hairpin in the viral replication cycle, we introduced mutations in the U5 region that affect the stability of this structured RNA motif. Stabilization and destabilization of the hairpin significantly inhibited virus replication. Upon prolonged culturing of the virus mutant with the stabilized hairpin, revertant viruses were obtained with additional mutations that restore the thermodynamic stability of the U5-PBS hairpin. The thermodynamic stability of the U5-PBS hairpin apparently has to stay within narrow limits for efficient HIV-1 replication. Transient transfection experiments demonstrated that transcription of the proviral genomes, translation of the viral mRNAs, and assembly of the virions with a normal RNA content is not affected by the mutations within the U5-PBS hairpin. We show that stabilization of the hairpin reduced the amount of tRNA primer that is annealed to the PBS. Destabilization of the hairpin did not affect tRNA annealing, but the viral RNA-tRNA complex was less stable. These results suggest that the U5-PBS hairpin is involved in correct placement of the tRNA primer on the viral genome. The analysis of virus mutants and revertants and the RNA structure probing experiments presented in this study are consistent with the existence of the U5-PBS hairpin as predicted in the RNA secondary structure model.
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Affiliation(s)
- N Beerens
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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47
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Smith CM, Smith JS, Roth MJ. RNase H requirements for the second strand transfer reaction of human immunodeficiency virus type 1 reverse transcription. J Virol 1999; 73:6573-81. [PMID: 10400754 PMCID: PMC112741 DOI: 10.1128/jvi.73.8.6573-6581.1999] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Retroviral reverse transcriptase (RT) enzymes are responsible for transcribing viral RNA into double-stranded DNA. An in vitro assay to analyze the second strand transfer event during human immunodeficiency virus type 1 (HIV-1) reverse transcription has been developed. Model substrates were constructed which mimic the viral intermediate found during plus-strand strong-stop synthesis. Utilizing wild-type HIV-1 RT and a mutant E478Q RT, the requirement for RNase H activity in this strand transfer event was analyzed. In the presence of Mg2+, HIV-1 RT was able to fully support the second strand transfer reaction in vitro. However, in the presence of Mg2+, the E478Q RT mutant had no detectable RNase H activity and was unable to support strand transfer. In the presence of Mn2+, the E478Q RT yields the initial endoribonucleolytic cleavage at the penultimate C residue of the tRNA primer yet does not support strand transfer. This suggests that subsequent degradation of the RNA primer by the RNase H domain was required for strand transfer. In reactions in which the E478Q RT was complemented with exogenous RNase H enzymes, strand transfer was supported. Additionally, we have shown that HIV-1 RT is capable of supporting strand transfer with substrates that mimic tRNAHis as well as the authentic tRNA3Lys.
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Affiliation(s)
- C M Smith
- Department of Biochemistry, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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48
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Morris S, Leis J. Changes in Rous sarcoma virus RNA secondary structure near the primer binding site upon tRNATrp primer annealing. J Virol 1999; 73:6307-18. [PMID: 10400722 PMCID: PMC112709 DOI: 10.1128/jvi.73.8.6307-6318.1999] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Predicted secondary-structure elements encompassing the primer binding site in the 5' untranslated region of Rous sarcoma virus (RSV) RNA play an integral role in multiple viral replications steps including reverse transcription, DNA integration, and RNA packaging (A. Aiyar, D. Cobrinik, Z. Ge, H. J. Kung, and J. Leis, J. Virol. 66:2464-2472, 1992; D. Cobrinik, A. Aiyar, Z. Ge, M. Katzman, H. Huang, and J. Leis, J. Virol. 65:3864-3872, 1991; J. T. Miller, Z. Ge, S. Morris, K. Das, and J. Leis, J. Virol. 71:7648-7656, 1997). These elements include the U5-Leader stem, U5-IR stem-loop, and U5-TPsiC interaction region. Limited digestion of the 5' untranslated region of wild-type and mutant RSV RNAs with structure- and/or sequence-specific RNases detects the presence of the U5-Leader stem and the U5-IR stem-loop. When a tRNATrp primer is annealed to wild-type RNAs in vitro, limited nuclease mapping indicates that the U5-IR stem becomes partially unwound. This is not observed when mutant RNAs with altered U5-IR stem-loop structures are substituted for wild-type RNAs. The U5-Leader stem also becomes destabilized when the tRNA primer is annealed to either wild-type or mutant RNA fragments. Nuclease mapping studies of tRNATrp, as well as the viral RNA, indicate that the U5-TPsiC helix does form in vitro upon primer annealing. Collectively, these data suggest that the various structural elements near the RSV primer binding site undergo significant changes during the process of primer annealing.
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Affiliation(s)
- S Morris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106-4935, USA
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49
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Götte M, Li X, Wainberg MA. HIV-1 reverse transcription: a brief overview focused on structure-function relationships among molecules involved in initiation of the reaction. Arch Biochem Biophys 1999; 365:199-210. [PMID: 10328813 DOI: 10.1006/abbi.1999.1209] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An early step in the life cycle of the human immunodeficiency virus type 1 (HIV-1) is reverse transcription of viral RNA into proviral DNA, which can then be integrated into the host cell genome. Reverse transcription is a discontinuous process carried out by the viral encoded reverse transcriptase that displays DNA polymerase activities on RNA and DNA templates as well as an RNase H activity that degrades transcribed RNA. DNA synthesis is initiated by cellular tRNALys3 that binds at its 3'-terminus to the complementary primer binding site of the genomic RNA. The initiation of reverse transcription is itself a complex reaction that requires tRNA placement onto viral RNA and the formation of a specific primer/template complex that is recognized by reverse transcriptase. After initiation takes place, the enzyme translocates from the initially bound RNA/RNA duplex into chimeric replication intermediates and finally accommodates newly synthesized DNA/RNA hybrids. This review focuses on structure-function relationships among these various molecules that are involved in the initiation of HIV-1 reverse transcription.
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Affiliation(s)
- M Götte
- McGill AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montréal, Québec, H3T 1E2, Canada
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50
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Kang SM, Zhang Z, Morrow CD. Identification of a human immunodeficiency virus type 1 that stably uses tRNALys1,2 rather than tRNALys,3 for initiation of reverse transcription. Virology 1999; 257:95-105. [PMID: 10208924 DOI: 10.1006/viro.1999.9615] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
HIV-1 virions contain approximately equal amounts of tRNALys,3 and tRNALys1,2, yet tRNALys,3 has been found to be exclusively used for initiation of reverse transcription. Since previous studies have shown that even if the primer binding site (PBS) was mutated to be complementary to tRNALys1,2, the virus did not stably use tRNALys1,2 to initiate reverse transcription, the virus must have evolved a mechanism for the exclusive use of tRNALys,3 to initiate reverse transcription. To investigate how HIV-1 discriminates tRNALys1,2 from tRNALys,3 for initiation of reverse transcription, two proviral genomes that contain nucleotide changes in U5 and a PBS to be complementary to regions of tRNALys1,2 were constructed. One genome contains 5 [HXB2(L12-AC)] nucleotides while another contains 15 [HXB2(L12-ACgg)] nucleotides in U5 complementary to the anticodon region of tRNALys1,2. Viruses derived from the transfection of the proviral genomes were infectious in SupT1 cells. Analysis of the endogenous reverse transcription reactions from viruses derived from HXB2 (L12-AC) and HXB2 (L12-ACgg) obtained from transfection revealed that both exclusively used tRNALys1,2 to initiate reverse transcription. Following extensive in vitro culture, though, sequence analysis of proviral genomes revealed that while the virus derived from HXB2(L12-AC) stably maintained a PBS complementary to tRNALys1,2, the virus derived from HXB2 (L12-ACgg) had reverted back to contain a PBS complementary to tRNALys,3. RNA modeling of the U5-PBS of the genome from HXB2(L12-AC) supports the conclusion that the fine specificity for discrimination between tRNALys,3 and tRNALys1,2 for use as a primer for HIV-1 reverse transcription resides in the structure of the U5-PBS region of the viral genome.
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Affiliation(s)
- S M Kang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
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