Vif Gene Research Articles

Codon optimization of the HIV-1 vpu and vif genes stabilizes their mRNA and allows for highly efficient Rev-independent expression

Two HIV-1 accessory proteins, Vpu and Vif, are notoriously difficult to express autonomously in the absence of the viral Tat and Rev proteins. We examined whether the codon bias observed in the vpu and vif genes relative to highly expressed human genes contributes to the Rev dependence and low expression level outside the context of the viral genome. The entire vpu gene as well as the 5′ half of the vif gene were codon optimized and the resulting open reading frames (ORFs) ( vphu and hvif, respectively) were cloned in autonomous expression vectors under the transcriptional control of the CMV promoter. Codon optimization efficiently removed the expression block observed in the native genes and allowed high levels of Rev- and Tat-independent expression of Vpu and Vif. Most of the higher protein levels detected are accounted for by enhanced steady-state levels of the mRNA encoding the optimized species. Nuclear run-on experiments show for the first time that codon optimization has no effect on the rate of transcriptional initiation or elongation of the vphu mRNA. Instead, optimization of the vpu gene was found to stabilize the vphu mRNA in the nucleus and enhance its export to the cytoplasm. This was achieved by allowing the optimized mRNA to use a new CRM1-independent nuclear export pathway. This work provides a better understanding of the molecular mechanisms underlying the process of codon optimization and introduces novel tools to study the biological functions of the Vpu and Vif proteins independently of other viral proteins.

The vif gene of maedi-visna virus is essential for infectivity in vivo and in vitro

We have investigated the role of vif in maedi-visna virus (MVV), a lentivirus of sheep, by studying in vitro replication of vif-deleted MVV in several cell types, and the effects of vif deletion on in vivo infection. By measuring RT activity, we found that in comparison to wild-type MVV, growth of vif-deleted MVV was similar in fetal ovine synovial (FOS) cells, highly attenuated in sheep choroid plexus (SCP) cells, and not detectable in macrophages, natural target cells of MVV. Productive infection by vif-deleted MVV could not be demonstrated in sheep. An increased mutation frequency was observed in DNA produced by endogenous reverse transcription of viral RNA in vif-deleted virions, indicating the existence of a factor comparable in action to human APOBEC3G. These results suggest that the vif gene of MVV is essential for infectivity and that the Vif protein protects the viral genome from enpackaged mutagenic activities.

Characterization of the caprine arthritis encephalitis virus (CAEV) rev N-terminal elements required for efficient interaction with the RRE

The Caprine Arthritis Encephalitis Virus (CAEV) genome encodes three structural ( gag, pol, and env) and three accessory ( rev, tat, and vif) genes. The Rev-C protein regulates Gag, Pol and Env expression by transporting their mRNAs to the cytoplasm. Rev trans-activation requires binding of Rev to an RNA structure called the Rev Response Element (RRE-C). Previous mutational analyses have shown that two domains of Rev are required for its function. The basic domain mediates RRE binding and multimer formation, and the nuclear export signal (NES) mediates trans-activation. Preliminary experiments demonstrate that Rev-C N-terminal deletion mutants bind the RRE less avidly than does wildtype Rev. As a result, it was hypothesized that an additional domain located in the N-terminal exon of Rev-C was required for optimal RRE binding. To test this hypothesis, Rev-C alanine scanning mutants were generated and in vitro RRE binding assays were performed. Alteration of Rev-C amino acids K13, E14, N15, V19, T20, M21 and R27 dramatically decreased affinity for RRE-C. These data demonstrate that Rev-C N-terminal amino acids are required for optimal RRE-C binding and suggest that a third functional domain exists within the N-terminus of Rev-C.

Mapping of the Bovine Immunodeficiency Virus Packaging Signal and RRE and Incorporation into a Minimal Gene Transfer Vector

Gene transfer systems based on lentiviruses have emerged as promising gene delivery vehicles for human gene therapy due to their ability to efficiently transduce nondividing target cells. Both primate and nonprimate lentiviruses have been used for construction of lentiviral vectors. An early generation of gene transfer system based on bovine immunodeficiency virus (BIV) has been developed (R. D. Berkowitz, H. Ilves, W. Y. Lin, K. Eckert, A. Coward, S. Tamaki, G. Veres, and I. Plavec, 2001, J. Virol. 75, 3371–3382). In this study, we mapped the BIV Rev response element (RRE) to 312 bp of the Env coding region. Furthermore, we compared transduction efficiencies of vectors containing different portions of the BIV Gag coding region and found that the first 104 bp of gag contains a functional part of the BIV packaging signal. These findings enabled the generation of a minimal BIV-based lentiviral vector. The minimal transfer vector construct consists of a self-inactivating long terminal repeats (LTR), minimal packaging sequence, putative central polypurine tract, minimal RRE, an internal promoter driving the gene of interest, and a woodchuck hepatitis posttranscriptional regulatory element. In addition, we constructed a BIV packaging construct containing gag/pol, minimal Rev/RRE, and the accessory gene vpy. The regulatory gene tat and the accessory genes vif and vpw have been inactivated or truncated. The current system has significantly reduced regions of homologies between the transfer vector and the packaging constructs. The vectors generated from this system achieved a titer of greater than 1 × 10 6 transducing units per milliliter and are fully functional as indicated by their ability to efficiently transduce both dividing and nondividing cells. These modifications should provide improved safety features for the BIV-based gene transfer system.

Down regulation of human immunodeficiency virus type-1 (HIV-1) expression by Vif antisense RNA expression vectors in transfected cells.

The HIV-1 vif gene is a potential candidate in the quest for anti-retroviral interventions, due to its unique role in the target cell infection. We employed the antisense RNA strategy to determine the antiviral activity of intracellularly expressed anti-sense RNAs of various lengths complementary to the targeted HIV-1 vif gene. Expression vectors mediating the delivery of the vif-ORF, 5'-Vif, M-vif, and 3'-vif antisense RNAs under the CMV promoter were constructed using pcDNA 3.1. The COS cells transfected with the antisense vectors showed a steady-state of antisense RNA expression levels. In contrast, those co-transfected with the Infectious molecular clone, pNL-E, exhibited a significant reduction in the steady-state antisense RNA levels, which correlated with a significant reduction in p24 antigen production. Thus, this expression method for these antisense RNAs provides a promising gene therapy strategy for HIV-1.

Inhibition of human immunodeficiency virus type 1 (HIV-1) replication by a two-amino-acid insertion in HIV-1 Vif from a nonprogressing mother and child.

We studied a 15-year-old girl, patient X, who has maintained consistently low plasma loads of human immunodeficiency virus type 1 (HIV-1) RNA, as well as normal and stable CD4(+) T-cell concentrations. She has presented no clinical manifestations of AIDS, despite having only received zidovudine monotherapy for a part of her life. Patient X's HIV-positive mother (patient Y) has also not progressed to AIDS and has never been treated with antiretroviral agents. HIV-1 isolated from patient X replicated poorly in human peripheral blood mononuclear cells (PBMC). In order to map the determinant of the poor growth of patient X's isolate, viral sequences from patient X were determined and examined for insertion or deletion mutations. These sequences contained a two-amino-acid insertion mutation in the Vif gene, which was also observed in uncultured PBMC acquired at different times. Furthermore, Vif sequences harbored by patient Y contained the identical mutation. These observations suggest that polymorphic HIV-1 was transmitted to patient X perinatally 15 years previously and has been maintained since that time. Recombinant HIV-1, engineered with Vif sequences from patient X, replicated in PBMC to levels approximately 20-fold lower than that of wild type. Removal of the insertion mutation from this recombinant restored replication efficiency to wild-type levels, while introduction of the insertion mutation into wild-type Vif sequences resulted in greatly decreased replication. Furthermore, Vif protein from patient X's HIV-1 was aberrantly cleaved, suggesting a mechanism for loss of Vif function. Since HIV-1 containing these sequences replicates poorly, the implication is that the two-amino-acid insertion mutation in Vif contributes significantly to the nonprogressor status of this mother and child. Further studies of these sequences might provide information regarding contributions of Vif structure and/or function to HIV-1 virulence.

Characterization of pol, vif, vpr, and vpu genes of HIV type 1 in AIDS patients with high viral load and stable CD4+ T cell counts on combination therapy.

The success of combination therapy has also led to AIDS patients who exhibit elevated viral load without a corresponding decline in CD4+ T cells. In this study, we characterized changes in the pol gene and accessory genes vif, vpr, and vpu of HIV-1 isolated from the plasma of patients receiving highly active antiretroviral therapy. From each patient three sequences were obtained and compared with the sequence of HIV-1 from nontreated patients, revealing many substitutions that were similar in most cases. Protease and reverse transcriptase genes showed many mutations that were due to antiviral drugs. Premature termination was observed in the vif gene of one patient, leading to a protein truncated after 187 amino acids. In another patient the entire vpr open reading frame was missing, with no synthesis of Vpu protein because the 5' end of the gene was missing, including the start codon. In the same patient, the Vif protein was also truncated because of the deletion of 100 nucleotides at the 3' end of the vif gene.

A new cellular system opposing HIV infection: implications for gene transfer?

One of the longest-standing mysteries in HIV research has been the function of the viral-encoded VIF protein. VIF is required for efficient viral infection in vivo [1–4], apparently because it overcomes the action of a host-encoded antiviral system [5,6]. A recent report in Nature describes a major breakthrough in understanding the cellular defense machinery that is overcome by HIV VIF [7]. In addition to its importance for HIV research, this discovery raises a variety of questions about whether manipulating this system might be helpful in optimizing gene transfer. The vif gene is one of the “auxiliary” genes of HIV, which are defined as being dispensable for efficient replication in at least some settings in cell culture. In vivo, however, vif is clearly required, as indicated, for example, by the finding that simian immunodeficiency viruses (primate relatives of HIVs) lacking vif are greatly attenuated [1]. The outcome of infections with vif-negative viruses in different cell lines was intriguing and ultimately quite informative. In vif-permissive cells, HIV derivatives mutated for vif grow as well as wild-type virus. In vif-nonpermissive cells, growth is greatly abrogated, but in a selective fashion. The nonpermissive phenotype is only seen when vif-negative virus is produced from nonpermissive cells. When vif-negative virus is produced from permissive cells, then used to infect nonpermissive cells, the virus infection proceeds normally. Tests of primary human cells revealed that they were vif nonpermissive, suggesting that VIF acts against this system normally during HIV infection. Elegant experiments from the laboratories of Malim and Kabat established that this could be explained by VIF overcoming a host-encoded antiviral system in virus producer cells. Both labs fused permissive cells with nonpermissive cells and asked whether or not the hybrid cells restricted growth of VIF-mutant HIV. They reasoned that if nonpermissive cells encoded an antiviral system, the fused cells should be nonpermissive because they would contain the interfering factor. The alternative was that nonpermissive cells might lack a factor required for efficient viral replication, in which case the fused cells would be permissive because the factor would be present. The experiments revealed that the fused cells were in fact nonpermissive, supporting the conjecture that restrictive cells express an antiviral system.

Apparent lack of trans-dominant negative effects of various vif mutants on the replication of HIV-1

The vif gene of human immunodeficiency virus type 1 (HIV-1) is essential for virus growth in non-permissive cells such as H9. To elucidate the mechanism of action of the Vif protein, vif mutants, which show trans-dominant negative effects on the replication of HIV-1, would be useful tools. In this study, a new assay system to identify the mutants of this category was established. For this new system, various reporter clones carrying both mutant and authentic vif sequences were generated. By determining the growth ability of the viruses derived from the reporter constructs, the potential negative effect of the mutant vif sequence was readily and sensitively monitored. Ten vif mutant sequences tested were found not to exert the trans-dominant negative effect on the replication of HIV-1.

Silence is golden for HIV-1 siRNA

The use of RNA interference as a mechanism to induce gene silencing is being exploited by an exponentially growing number of investigators. The technique involves the introduction of synthetic short interfering RNA (siRNA) duplexes comprising 21–23 nucleotides into cells. The siRNAs then promote sequence-specific mRNA degradation, essentially enabling the investigator to'knock-out' a gene of choice. Two recent papers [ 1. Novina C.D. et al. siRNA-directed inhibition of HIV-1 infection. Nat. Med. 2002; 8: 681-686 Crossref PubMed Scopus (731) Google Scholar , 2. Jacque J. et al. Modulation of HIV-1 replication by RNA interference. Nature. 2002; 418: 435-438 Crossref PubMed Scopus (763) Google Scholar ] now report the use of the siRNA technique to inhibit HIV-1 replication. The siRNA targets include the genes for CD4 (the cellular receptor for HIV-1), the viral long terminal repeat (LTR) and the viral gag, vif and nef genes. Approximately 20- to 50-times reductions in viral particle production were observed, and the effects were attributed to sequence-specific degradation of viral RNAs.

Human immunodeficiency virus type 1 Vif binds the viral protease by interaction with its N-terminal region

The vif gene, one of the six auxiliary genes of human immunodeficiency virus (HIV), is essential for virus propagation in peripheral blood lymphocytes and macrophages and in certain T-cell lines. Previously, it was demonstrated that Vif inhibits the autoprocessing of truncated HIV type 1 (HIV-1) Gag-Pol polyproteins expressed in bacterial cells, as well as the protease-mediated cleavage of synthetic peptides in vitro. Peptides derived from the aa 78-98 region in the Vif molecule specifically inhibit and bind the HIV-1 protease in vitro and arrest the production of infectious viruses in HIV-1-infected cells. This study demonstrates that (i) purified recombinant Vif protein and HIV-1 but not avian sarcoma leukaemia virus protease specifically bind each other and (ii) the interaction between these two proteins takes place at the N terminus of the protease (aa 1-9) and the central part of Vif (aa 78-98). The data presented in this report suggest a model in which Vif interacts with the dimerization sites of the viral protease.

Induction of Secreted Human Immunodeficiency Virus Type 1 (HIV-1) Resistance Factors in CD4-Positive T Lymphocytes by Attenuated HIV-1 Infection

This report describes induction of HIV-1 resistance and synthesis of resistance factors in immortal CD4-positive T lymphocytes. SupT1 cells were infected by NL4-3 attenuated by a defect in the vif gene through coculture with infected primary lymphocytes. Cell lines from this infection, termed R1, expressed CD4 and CXCR4, carried low levels of HIV-1 DNA, but expressed no other detectable viral products and were resistant to infection by wild-type HIV-1. Investigation of challenge infection in resistant R1 lines demonstrated entry, reverse transcription, and integration by incoming HIV-1 but no synthesis of viral RNA. By assay of marker gene expression, we found that Tat was unable to activate LTR-driven transcription in R1 lines. HIV-1-resistant R1 lines secreted soluble factors that inhibited productive infection of primary lymphocytes by several strains of HIV-1 and blocked viral RNA synthesis in newly infected cells. Resistance factors also blocked the induction of HIV-1 transcription in ACH-2 cells as assayed by viral antigen expression and Northern blot of viral RNA. Soluble factors produced by HIV-1-resistant, immortal R1 cells may form the basis of new approaches to control HIV-1 infection.

Viral and cellular specificities of caprine arthritis encephalitis virus Vif protein.

The caprine arthritis encephalitis virus (CAEV) Vif protein is necessary for a productive infection of susceptible goat cells. The vif gene is conserved among all primate and most nonprimate lentiviruses. However, previous reports demonstrated that, in their respective host cells, primate Vif deleted lentiviruses could not be complemented by nonprimate Vif proteins, suggesting that species-specific restrictions between Vif and the virus-producing cells may modulate the Vif function on viral infectivity. Here we bring further support to this hypothesis since we show that CAEV Vif, when expressed in goat cells, is able to increase the infectivity of Vif deleted human immunodeficiency type-1 virus and of murine leukemia virus. Moreover, we demonstrate in vitro interactions between different Vif proteins and NC domains of heterologous Gag precursors, supporting the notion that species specificity of lentiviral infection is not due to molecular interactions between Vif and viral components.

Virology: Overview

Virology: Overview

Advances in HIV molecular biology

Advances in HIV molecular biology

A retroviral DNA vaccine vector.

A versatile DNA vaccine (pdIV3) was constructed by replacing the integrase, vif, vpx, and vpr genes of a pathogenic simian immunodeficiency virus (SIV) molecular clone with a linker containing unique cloning sites. The 5' long terminal repeat (LTR) is truncated and transcription is controlled by a cytomegalovirus (CMV) promoter. The construct expresses Gag and Env in vitro and noninfectious virus particles are produced from transfected cells. The ability of pdIV3 to promote cellular and humoral immune responses, along with the flexibility of the linker design to allow insertion of immunostimulatory genes in future constructs, makes this a useful base vector for immunization against primate lentiviruses. We present the construction of a retroviral plasmid designed to serve as a template for the development of safe and effective vaccines against primate immunodeficiency retroviruses. This vaccine component should facilitate the simultaneous induction of cellular and humoral immune responses that protect primates against infection with SIV and human immunodeficiency virus (HIV) and the development of acquired immune deficiency syndrome (AIDS). This plasmid could induce the appropriate immune response required to attack both cell-free and cell-associated viruses. The lack of infectivity, the inability to integrate, and the SIV origin make this construct a safe alternative to attenuated vaccines based on HIV. In addition, we intend to develop this construct as an immunotherapeutic approach to lower the viremia in AIDS patients.

Analysis of the cell-dependent replication potentials of human immunodeficiency virus type 1 vif mutants

Eleven in-frame vif gene mutants of HIV type 1 produced in non-permissive cells were examined for their replication potentials in various CD4-positive and -negative cell lines. Virus replication for each mutant was monitored by using several single- and multiple-cycle infectivity assays. Except for a mutant with wild-type phenotype, most mutants were severely defective for replication in all the cell lines as expected from the producer cell-dependent functioning of Vif so far reported. In contrast, two mutants, which have mutations in the hydrophilic or effector regions of Vif were found to have target cell-dependent replication potentials. These results demonstrate the presence of a novel category of the vif mutants important for elucidation of the Vif function.

Fully functional, naturally occurring and C-terminally truncated variant human immunodeficiency virus (HIV) Vif does not bind to HIV Gag but influences intermediate filament structure.

A variant human immunodeficiency virus type 1 (HIV-1) vif gene, vifA45-2, which encodes a protein lacking 19 amino acids at the C terminus but which is fully functional in supporting HIV replication in non-permissive cells has been described previously. By employing newly generated anti-VifA45 serum, further properties of VifA45 and its full-length counterpart, VifA45open, in comparison to Vif from HIV strain BH10 are reported in permissive HeLa and COS-7 cells. The results obtained using confocal microscopic localization studies and in vitro binding assays do not support a requirement for the direct interaction of HIV Gag with Vif. Furthermore and in contrast to previous conclusions, detergent solubility analyses do not demonstrate a role for the C terminus of Vif in mediating localization to the fraction containing cellular membrane proteins. Localization of Vif from HIV strain BH10 to perinuclear aggregates in a small fraction (about 10%) of transfected HeLa cells has been previously reported. The intermediate filament protein vimentin colocalizes to these structures. In contrast, VifA45 and VifA45open form perinuclear aggregates in nearly all transfected HeLa cells; vimentin as well as the cytoskeletal-bridging protein plectin, but not the microtubular protein tubulin, become relocalized to these structures. Interestingly, in COS-7 cells, all of the functional Vif proteins tested (Vif from strain BH10, VifA45 and VifA45open) predominantly localize in the cytoplasm but still induce dramatic aggregation of vimentin and plectin, i.e. in these cells the respective Vif proteins are influencing intermediate filament structure in the absence of colocalization.

Tryptophan 95, an Amino Acid Residue of the Caprine Arthritis Encephalitis Virus Vif Protein Which Is Essential for Virus Replication

The Caprine arthritis encephalitis virus (CAEV) vif gene was demonstrated to be essential for efficient virus replication. CAEV Vif deletion mutants demonstrated an attenuated replication phenotype in primary goat cell cultures and resulted in abortive infection when inoculated into goats. In this study, we determined the in vitro replication phenotype of five CAEV Vif point mutant infectious molecular clones and the ability of the corresponding in vitro translated Vif proteins to interact with the CAEV Pr55gag in the glutathione S–transferase (GST) binding assay. Here we show that (i) three of the mutants (S170E, S170G, S197G) behaved as the wild-type CAEV according to virus replication and Vif–Gag interactions; (ii) one mutant (Vif 6mut) was replication incompetent and bound weakly to GST–Gag fusion proteins; and (iii) one mutant (Vif RG) was impaired for replication while retaining its interaction properties. This mutant points out the critical importance of the CAEV Vif tryptophan residue at position 95 for efficient virus replication, defining for this lentivirus a functional domain unrelated to the Gag binding region.

Characterization of Human Immunodeficiency Virus Type 1 vif Gene in Long-Term Asymptomatic Individuals

We have determined the sequence of the human immunodeficiency virus type 1 (HIV-1) vif genes from a cohort of 42 long-term nonprogressors (LTNP) and compared these sequences to those of 8 late progressors. The coding potential of the vif open reading frame directly derived by nested PCR from uncultured peripheral blood mononuclear cell DNA was conserved in all 50 individuals. The nucleotide distances between vif sequences were not significantly different between LTNP and late progressors, indicating similar selections of viruses within both types of long-term HIV-1-infected subjects. However, a statistically significant correlation between an amino acid signature at position 132 of Vif and the viral load was found within LTNP. Namely, amino acid Ser was associated with low viral load and amino acid Arg with high viral load. This signature was also observed when LTNP with low viral load were compared to progressors. The Ser132 signature was introduced in place of Arg132 present in the HIV-1 YU-2 Vif prototype into chimeric viruses to assess the impact of Vif signature on the virus. While the replication properties in the SupT1 cell line were unmodified, the mutagenized virus revealed a fivefold decreased replication in activated PBMC, suggesting a possible role of this Vif signature for viral production in vivo.