Mutational analysis of the human immunodeficiency virus: the orf-B region down-regulates virus replication

Genetic characterization of simian immunodeficiency virus isolated from an African mandrill

We constructed an infectious molecular clone of simian immunodeficiency virus from an African mandrill (SIVMND). Upon transfection, this clone directed the production of progeny virus particles infectious to and cytopathic for CD4+ human leukemia cells. Thirteen frameshift proviral mutants with an alteration in the eight open reading frames of SIVMND were generated by recombinant DNA techniques, and were analyzed biologically and biochemically. While mutations in the structural genes gag, pol, and env abolished viral growth and induction of cytopathology, mutants of the vif, vpr, and nef genes were fully biologically active. Of the tat and rev mutants, only one rev mutant grew in CD4+ cells with delayed kinetics. In reporter-based transient expression systems, transactivation potentials of the tat and rev mutants were evaluated. A mutant lacking 2nd coding exon of tat gene exhibited tat activity similar to that of the wild type clone. The infectious rev mutant was partially defective for rev gene activity.

Genetic and biological comparisons of pathogenic and nonpathogenic molecular clones of simian immunodeficiency virus (SIVmac)

Simian immunodeficiency virus (SIV) is a designation for a group of related but unique lentiviruses identified in several primate species. A viral isolate from a rhesus macaque (i.e., SIVmac) causes a fatal AIDS-like disease in experimentally infected macaques, and several infectious molecular clones of this virus have been characterized. This report presents the complete nucleotide sequence of molecularly cloned SIVmac1A11, and comparisons are made with the sequence of molecularly cloned SIVmac239. SIVmac1A11 has delayed replication kinetics in lymphoid cells but replicates as well as uncloned SIVmac in macrophage cultures. Macaques infected with virus from the SIVmac1A11 clone develop antiviral antibodies, but virus does not persist in peripheral blood mononuclear cells and no disease signs are observed. SIVmac239 infects lymphoid cells, shows restricted replication in cultured macrophages, and establishes a persistent infection in animals that leads to a fatal AIDS-like disease. Both viruses are about 98% homologous at the nucleotide sequence level. In SIVmac1A11, the vpr gene as well as the transmembrane domain of env are prematurely truncated, whereas the nef gene of SIVmac239 is prematurely truncated. Sequence differences are also noted in variable region 1 (V1) in the surface domain of the env gene. The potential implications of these and other sequence differences are discussed with respect to the phenotypes of both viruses. This animal model is critically important for investigating the roles of specific viral genes in viral/host interactions that cannot be studied in individuals infected with the human immunodeficiency virus (HIV).

HIV with multiple gene deletions as a live attenuated vaccine for AIDS

Most viral vaccines currently in use in humans are live attenuated strains of virus that lack pathogenic potential. In general, such live attenuated vaccines induce the strongest longest-lasting immunity. Live attenuated strains of human immunodeficiency virus type 1 (HIV-1) have not been previously considered as vaccines for acquired immunodeficiency syndrome (AIDS) because of an inability to envision how their safety could be adequately assured. This report describes a means for making live, nonpathogenic strains of SIVmac and HIV-1 that cannot revert to a virulent form and a stepwise scheme for demonstrating their safety. Replication-competent, multiply deleted derivatives that are currently being tested are missing combinations of auxiliary genes (nef, vpr, vif, vpx, vpu) and certain control elements in the negative regulatory element (NRE) of the long terminal repeat (LTR). Since these genomic regions are in large part conserved among the SIVs and HIVs, they are likely to be important for the virus life cycle in vivo. Consistent with this line of reasoning, a replication-competent nef deletion mutant of SIVmac apparently has lost most or all of its pathogenic potential, yet it still induces strong immune responses. Multiply deleted derivatives of SIVmac and HIV-1 will have to be extensively tested in animal models prior to moving a promising HIV-1 candidate to initial trials in high-risk human volunteers. Definitive evidence for safety and general acceptance for this approach can only evolve gradually over a prolonged period of time.

Expression of nef, vpu, CA and CD4 during the infection of lymphoid and monocytic cell lines with HIV-1

The expression of the capsid antigen (CA) and the two regulatory proteins nef and vpu as well as the CD4 cell surface receptor was followed in HIV-infected lymphoid and promonocytic cells. In the lytic phase of infection all three viral proteins were expressed; production of these proteins coincided with the increase of CA antigen and infectious virus in culture supernatants and with prominent cytopathic effects. After selection of persistently infected cells, the number of lymphoid cells expressing detectable levels of nef decreased to zero; the number of cells positive for CA ranged between 40 to 70%. In chronically infected promonocytic cells nef and vpu expression was reduced to undetectable levels, whereas most of the cells accumulated CA intracellularly. Infectious cell free virus and CA in the supernatant of promonocytic cells had low titers. CD4 surface expression declined in all cell lines investigated before cell free virus was detectable.

SIV/HIV recombinants and their use in studying biological properties

A series of chimeric clones between human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency viruses (SIV) were constructed. Viability of the recombinant viruses was dependent on the position of recombination. Infectious chimeric viruses between HIV-1 and SIVAGM (isolated from an African green monkey) and those between HIV-1 and SIVMAC (isolated from a rhesus monkey) were examined for host cell tropism. Viral determinants that restrict the replication of SIVAGM in human MT-4 cells and that of HIV-1 in macaque monkey peripheral blood mononuclear cells (PBMC) mapped to the 5' half of the virus genome. One HIV-1/SIVMAC chimera which contained the HIV-1 env gene was shown to replicate in macaque PBMC in vitro and to infect macaque monkeys in vivo. This HIV-1/SIVMAC chimera will be useful for a variety of AIDS pathogenesis and vaccine studies.

Biological characterization of human immunodeficiency virus type 1 and type 2 mutants in human peripheral blood mononuclear cells

Mutants of human immunodeficiency virus type 1 (HIV-1) and type 2 (HIV-2), which have been shown to be infectious in established cell lines, were tested for ability to replicate and induce syncytium formation in human peripheral blood mononuclear cells (PBMC). The vpu mutant of HIV-1 showed depressed kinetics of replication in an established T cell line, as reported previously, but in PBMC, its replication was similar to that of the wild type virus. The vpx gene of HIV-2 was required for efficient virus propagation in PBMC, but not in an established T cell line, as previously reported. However, the growth rates of the vpx mutant in PBMC preparations from two individuals were different. The results of experiments on infection of PBMC with the vif and vpr mutants of HIV-1 and HIV-2 were essentially consistent with previous results of infection of established T cell lines. No negative effect of the nef gene products of HIV-1 and HIV-2 was observed. The abilities of the wild type virus and the mutants of HIV-1 to induce syncytium formation in both PBMC and established cell lines were similar. In contrast, neither the wild type nor any of the mutants of HIV-2 induced syncytium formation in PBMC. These results suggest that the functions of some genes can be detected only in mixed populations or primary cells such as PBMC. Studies on the roles of these genes in PBMC may provide a better understanding of their functions in vivo.

HIV-1 replication and potential targets for intervention

Intense research into fundamental processes of human immunodeficiency syndrome type 1 (HIV-1) replication has yielded knowledge that in many aspects equals or exceeds that of the oncogenic retroviruses. The availability of sensitive virus detection methods has allowed a more thorough characterization of the biology of virus persistence and latency in vivo and removed the dependence on in vitro models. As a clearer picture of the pattern of HIV-1 replication in vivo evolves, it becomes apparent that HIV-1 biology is distinct from that of the prototypic oncogenic retroviruses in several key aspects, particularly with regard to host cell range and determinants of viral permissiveness. In this respect it may be appropriate to examine the lentivirus, rather than the oncovirus model system to better understand the biology and pathogenesis of HIV-1 infection. This synopsis of recent and ongoing research developments in HIV-1 replication and pathogenesis emphasizes the determinants of host cell permissiveness, early events in virus replication, and underlying features in HIV-1 cytopathogenesis. In addition, basic viral replication processes which can be exploited for therapeutic intervention are discussed.

Allelic variation in the effects of the nef gene on replication of human immunodeficiency virus type 1

The effects of the viral gene nef on human immunodeficiency virus type 1 (HIV-1) replication in culture were investigated using nef alleles of the HIV-1 IIIB and ELI strains. The results demonstrate significant allelic variation in the effect of nef on virus replication in both an established human CD4+ T-cell line and primary human lymphocytes. In the context of the HXB2 virus, the ELI nef allele but not the IIIB nef allele permits initiation of efficient low-multiplicity infection in primary peripheral blood mononuclear cells, including unfractionated peripheral blood lymphocytes, T cells, and monocyte/macrophages. Within the same genetic context, the IIIB nef allele slightly retards replication of the virus in a T-cell line, whereas the ELI nef allele accelerates replication of the virus. Sequences in the IIIB and ELI genomes outside of nef also moderate the effects of nef on HIV-1 replication. nef did not appear to determine the host-cell preference of the virus. These studies may help to reconcile apparently conflicting reports on the role of nef in HIV-1 replication and suggest that HIV-1 nef may play an important role in viral pathogenesis.

The HIV-1 nef protein does not have guanine nucleotide binding, GTPase, or autophosphorylating activities

Recombinant HIV-1 Nef proteins with either thr-15 or ala-15 have been constructed and expressed in the T7 bacterial system. From the soluble portion of bacterial lysates both Nef(thr-15) and Nef(ala-15) have been purified to near homogeneity through 6 nondenaturing chromatographic steps in the presence of MgCl2. Neither purified proteins display the previously reported GTP binding activity. Additionally Nef(thr-15) does not have autophosphorylating activity with either [gamma-32P]GTP or [gamma-32P]ATP. Although GTPase activity is present in the preparations of Nef proteins, it does not increase during purification and is attributed to bacterial contaminations.

Mutational analysis of the simian immunodeficiency virus SIVmac nef gene

We are using site-directed mutagenesis of single viral genes to identify and analyze the genetic determinants of human and simian immunodeficiency virus pathogenicity. In a first approach, we have constructed a series of simian immunodeficiency virus SIVmac nef mutants by partial deletion and insertions in the nef gene, as this gene is a candidate gene for the establishment and maintenance of latency. nef insertion mutants replicated faster than wild-type SIVmac, suggesting that the nef gene product acts as a negative factor for replication. Surface phenotyping revealed that cultures permanently infected with nef mutants exhibit an enhanced expression of viral proteins on the outer cell surface. We have analyzed the properties of the mutant viruses in cell culture and intend to use rapidly replicating mutants (putatively unable to undergo latency) as model vaccine viruses in the rhesus monkey.

Biological Agents in Infectious Diseases

This article examines the use of classical as well as novel immunological agents to augment the immune system. Strategies to prevent infectious disease using vaccines to prime the immune system are discussed. A prospective overview of acquired immunodeficiency syndrome (AIDS) vaccine development provides insights into the possible agents that may be developed in the near future. The rationale for the use of intravenous immunoglobulin and colony stimulating factors in selected clinical situations is also discussed.

Nef proteins of the human immunodeficiency viruses (HIV-1 and HIV-2) and simian immunodeficiency virus (SIV) are structurally similar to leucine zipper transcriptional activation factors

Analysis of the predicted amino acid sequences of the human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2) and of the related simian immunodeficiency virus (SIV) nef gene products (Nef) reveals the presence of a conserved leucine zipper-like repeat with the characteristic 4,3 arrangement of mainly hydrophobic amino acids in the middle (core) region of the proteins, but lacking the basic (DNA binding) domain characteristic of DNA-binding leucine zipper (bZIP) proteins. Also, at the C-terminus of the Nef proteins is a highly acidic sequence (net charge of -5 to -8) stretched over about 40 amino acids, and contains two predicted alpha-helices separated by a beta-turn linker sequence with sequence homology to known activation domains of acidic transcriptional activation factors. Moreover, within this acidic region of transcriptional activators and the homologous sequence within the second Nef alpha-helix, is a potential transcriptional activation consensus sequence (TACS) bounded by a pair of acidic amino acids (aspartic or glutamic acids) at the N-terminus and a highly invariant phenylalanine (hydrophobic), often followed by an acidic (aspartic) residue, at the C-terminus of the sequence. These findings strongly implicate Nef proteins as belonging to a class of non-DNA-binding leucine zipper acidic transcription factors, and provide a structural basis for new approaches to studying Nef function.

Simian immunodeficiency virus negative factor suppresses the level of viral mRNA in COS cells

The nef gene is conserved among all human and simian lentiviruses. However, the amino acid similarity between simian immunodeficiency virus (SIV) and human immunodeficiency virus type 1 NEF is only 38%. To assess the role of SIV NEF on virus replication and compare its activity with that of its human immunodeficiency virus type 1 counterpart, we examined the activity of an intact nef gene from proviral clone pSIV 102, an isolate from SIV-MAC-251-infected cells. Proviral clone pSIV BA was constructed by introducing a premature termination codon at codon 40 of the nef gene without altering the predicted amino acid sequence of the overlapping env gene. These two clones were transfected into CD4- COS cells, and virus replication was monitored by p27 enzyme-linked immunosorbent assay kits. In seven independent experiments, clone pSIV BA afforded two- to sixfold greater levels of viral antigen compared with those in clone pSIV 102 and two- to sixfold-increased levels of viral mRNAs as indicated with Northern (RNA) blot and S1 nuclease protection analyses. Nuclear run-on assays demonstrated a two- to threefold increased rate of RNA synthesis with nuclei isolated from cells transfected with pSIV BA compared with that from cells transfected with pSIV 102. In contrast, there was no apparent destabilization of SIV mRNAs by NEF, as measured in dactinomycin-treated cells. This study demonstrates that SIV NEF is a negative regulator of virus replication and acts by suppressing the level of mRNA synthesis and accumulation in COS cells.

Expression of the type 1 human immunodeficiency virus Nef protein in T cells prevents antigen receptor-mediated induction of interleukin 2 mRNA

Stable transformants of the Jurkat T-cell line have been obtained that express either of two distinct forms of the type 1 human immunodeficiency virus nef gene: the nef-1-encoded protein (Nef-1) contains alanine, glycine, and valine at positions 15, 29, and 33, respectively; the protein specified by nef-2 (Nef-2) has threonine, arginine, and alanine at the corresponding positions. When Jurkat cells or their Nef-2-expressing transformants are treated with phorbol 12-myristate 13-acetate (PMA) plus either phytohemagglutinin (PHA) or antibodies against CD3 epsilon, T-cell receptor beta chain, or CD2, there is a prompt increase in interleukin 2 (IL-2) mRNA and intracellular calcium and in the IL-2 receptor alpha chain on the cell surface. Although cells expressing Nef-1 also induce calcium mobilization and the production of IL-2 receptor alpha chain, the formation of IL-2 mRNA is blocked in response to these stimuli. Moreover, Nef-1-expressing cells transfected with a plasmid in which the IL-2 promoter is fused to the chloramphenicol acetyltransferase (CAT) gene fail to induce CAT following treatment with PMA and PHA. By contrast, the parental and Nef-2-containing cells induce CAT normally. Nef-1-expressing cells can produce IL-2 mRNA in response to a combination of PMA and ionomycin, although much less efficiently than the parental Jurkat cells or Nef-2-expressing cells. These findings, and others described herein, suggest that the virally encoded Nef protein interferes with a signal emanating from the T-cell receptor complex that induces IL-2 gene transcription.

Chicken ovalbumin upstream promoter transcription factor binds to a negative regulatory region in the human immunodeficiency virus type 1 long terminal repeat

The human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) contains a negative regulatory element (NRE) which downregulates the rate of LTR-directed transcription and HIV-1 replication. Within the NRE is a GGTCA palindrome, which binds a possible member of the steroid/thyroid hormone receptor superfamily. Mutation of this site leads to an increase in LTR-directed transcriptional activity compared with the wild type, consistent with the element's being a functional part of the NRE. The palindrome contains significant identity to the chicken ovalbumin upstream promoter (COUP) element to which COUP transcription factors (COUP-TFs), members of the steroid/thyroid hormone receptor superfamily, bind. We demonstrate here that human COUP-TFs can bind specifically to this HIV-1 COUP-like element in a manner identical to binding to ovalbumin COUP. We show that the predominant COUP-TF family member synthesized in T cells is the 68-kDa form, which is likely to be responsible for any in vivo function of the HIV-1 COUP-like element in these cells. Finally, we have identified three HIV-1 variant strains that contain mutations in the HIV-1 COUP-like element which affect the binding affinity of COUP-TF for these variant COUP elements.

Kinetics of expression of multiply spliced RNA in early human immunodeficiency virus type 1 infection of lymphocytes and monocytes

The genome of human immunodeficiency virus type 1 (HIV-1) encodes at least six proteins involved in regulation as well as the structural proteins Gag, Pol, and Env. The interplay of the various regulators generates early and late transcriptional phases in the HIV-1 life cycle; the earliest RNA is enriched in subgenomic species, and the genomic transcript appears at the later stage of infection. We investigated the nature of the mRNAs expressed in the early stages of infection when the 2 kilobase subgenomic species predominate. RNA was analyzed in the early phase of a one-step growth cycle of HIV-1 infection in T-lymphoid and monocytic cell lines by using PCR amplification of in vitro-synthesized viral cDNAs. In both cell lines, expression of Tat-, Rev-, and Nef-specific messages appeared simultaneously and could be detected within 8-12 hr of infection but in different amounts with a predominance of Nef-specific message. The Env-specific message could be detected as early as the Rev-specific message, indicating that expression of at least small amounts of the singly spliced message could occur before the accumulation of Rev.

Activation of a diphtheria toxin A gene by expression of human immunodeficiency virus-1 Tat and Rev proteins in transfected cells

Expression of a gene encoding the diphtheria toxin A (DT-A) fragment, controlled by tissue specific regulatory elements, has previously been used to kill selected cell populations. Here, we have examined the feasibility of controlling DT-A expression using regulatory systems from the human immunodeficiency virus (HIV-1) genome. Plasmids were constructed which express either DT-A or, as a model system, the luciferase (luc) reporter gene, under control of HIV-1 long terminal repeat (LTR) sequences (-167 to +80). While trans-activation by expression of the viral protein Tat was demonstrated, significant basal expression was observed. To reduce basal expression, cis-acting negative regulatory elements from the env region of the HIV-1 genome were inserted in the 3' untranslated region of both the luc and DT-A constructs. This dramatically reduced basal expression from the HIV LTR, and now both viral regulatory proteins Tat and Rev were required for maximal trans-activation. Such regulation of DT-A expression might be therapeutically applied to selectively kill HIV-infected cells in acquired immunodeficiency syndrome (AIDS) and AIDS-related complex (ARC).

A specific inhibitor of cysteine proteases impairs a Vif-dependent modification of human immunodeficiency virus type 1 Env protein

The Vif protein of human immunodeficiency virus type 1 (HIV-1) regulates viral infectivity. Virions produced in cell culture after transfection by a Vif-negative molecular clone show a dramatic decrease in infectivity for susceptible CD4+ cell lines, although the Vif protein does not appear to be a constituent of the viral particle. The exact mechanism by which Vif affects HIV-1 infectivity is so far unknown. We report the existence of structural homologies between Vif and a family of cysteine proteases and present evidence which suggests that one of the targets of Vif is the Env protein and more precisely the cytoplasmic domain of gp41. Vif was found to modify both the processing and conformation of the Env protein. Ethyl(25, 35)- 3[(5)-3-methyl-1-(3-methylbutylcarbamoyl)]oxirane-2-carboxylate, a specific inhibitor of cysteine proteases, inhibits the effect of Vif, as does the mutation of Cys-114 to Leu in Vif. Furthermore, Cys-114 of Vif produced in Escherichia coli, interacts directly with trans-epoxysuccinyl-L-leucylamido-(4-guanidino)butane. These observations suggest that a cysteine protease activity is associated with Vif and that this activity plays a role in Env maturation.

Immunological study of the nef protein from HIV-1 by polyclonal and monoclonal antibodies

We constructed and expressed different overlapping fusion proteins with the nef gene of HIV-1 and generated specific polyclonal rabbit and monoclonal mouse antibodies against these recombinant proteins. The rabbit antisera, one of the monoclonal antibodies as well as a serum from a HIV-1 infected patient recognized the nef protein with Mr 27 kDa in latently HIV-1 infected glioma cells in the immunoblot. In contrast, these antibodies could not detect nef in productively HIV-1 infected Molt-3 cells neither in immunoblot nor in indirect immunofluorescence assays. These results indicate the possible participation of nef in viral latency. The recombinant nef proteins were used as probes for anti-nef antibodies in human sera. We observed in 17 of 57 sera tested specific anti-nef antibodies. All of these anti-nef positive sera also contained antibodies directed against viral structural proteins. The NH2-terminal region of the recombinant nef was shown to be the major immunodominant antigenic site in the immunoblot assay.

Genetic characterization of human immunodeficiency virus type 1 nef gene products translated in vitro and expressed in mammalian cells

Expression of the human immunodeficiency virus type 1 nef gene was studied by in vitro transcription-translation and by transfection into monkey COS cells. Two Nef-related peptides, of 27 and 25 kDa, were identified by immunoprecipitation with anti-Nef antibodies. The relation between these two proteins was determined by metabolically labeling transfected COS cells and by deleting the initiator methionine of nef. We found that the 25-kDa polypeptide is not a cleavage product of 27-kDa Nef but rather is initiated from an internal ATG 57 bases downstream from the Nef initiation site. Myristoylation of the 27-kDa but not of the 25-kDa Nef was demonstrated by the contranslational modification of Nef in an in vitro reticulocyte translation system. The myristoylation pattern of the two Nef polypeptides further implies that the 25-kDa polypeptide lacks the amino terminus of 27-kDa Nef. Cellular localization of the various forms of Nef was studied in transiently transfected COS cells. Myristoylation was found to be necessary for membrane association of Nef. Myristoylation-deficient 27-kDa Nef mutant and 25-kDa Nef were confined to the soluble cytoplasmic fraction of transfected cells, whereas part of the wild-type 27-kDa Nef was membrane attached.

Epitopes of the HIV-1-negative factor (nef) reactive with murine monoclonal antibodies and human HIV-1-positive sera

Murine monoclonal antibodies (MAbs) raised against a recombinant nef protein fragment of human immunodeficiency virus type 1 (HIV-1) strain BH10 were characterized by an epitope mapping system using overlapping decapeptides. Four different immunogenic regions were identified. Ten human HIV-1-positive sera were tested in the same epitope mapping system, seven of these were reactive with four immunogenic regions. Two of the nef-specific epitopes recognized by human sera overlapped with the epitopes defined by the murine monoclonal antibodies. The reactivity of the monoclonal antibodies with the recombinant nef protein and with infected and uninfected cells were investigated in a variety of test systems. The results are discussed with respect to homologous regions of nef and cellular proteins.

Evolution of human immunodeficiency virus type 1 nef and long terminal repeat sequences over 4 years in vivo and in vitro

The evolution of an 851-bp segment of the human immunodeficiency virus type 1 (HIV-1) genome encoding the nef open reading frame and U3/R elements of the long terminal repeat has been followed over a 4-year period in vivo and in vitro. The population of viral sequences at any given time was established by sequencing cloned polymerase chain reaction products. The samples studied were derived from the same man for whom a detailed analysis of the tat gene was previously described (A. Meyerhans, R. Cheynier, J. Albert, M. Seth, S. Kwok, J. Sninsky, L. Morfeldt-Manson, B. Asjö, and S. Wain-Hobson, Cell 58:901-910, 1989). Once again in vitro culture resulted in the selection of minor forms. Over a 4-year period in vivo, there was no obvious selection for, or outgrowth of, any particular nef or U3/R sequence. Few defective nef protein sequences were observed, which argues against nef acting as a negative regulatory factor. Although no functionally defective promoter/trans-activation-responsive elements were identified, the transactivation efficiencies varied between 0.2 and 2 times that of the control. The sequence encoding the most efficient trans-activation-responsive region did not outgrow others. The extreme genetic heterogeneity of the different samples of the locus, either in vivo or in vitro, indicates that there is no such thing as a single, distinct HIV sequence. It is suggested that different HIV-1 loci evolve independently, recombination being responsible for their uncoupling.

Generation and characterization of infectious chimeric clones between human immunodeficiency virus type 1 and simian immunodeficiency virus from an African green monkey

A series of chimeric clones of human immunodeficiency virus type 1 and simian immunodeficiency virus isolated from an African green monkey was constructed in vitro. In transient transfection experiments, all clones produced virion-associated reverse transcriptase, gag proteins, and env proteins. Eight out of 10 chimeric viruses clearly grew in the human CD4+ cell line C8166. Susceptibility of other CD4+ cell lines, MT-4, A3.01, and Molt4 clone 8, to infection with these viruses was also demonstrated.

The viral envelope gene is involved in macrophage tropism of a human immunodeficiency virus type 1 strain isolated from brain tissue

Human immunodeficiency virus type 1 (HIV-1) strains isolated from the central nervous system (CNS) may represent a subgroup that displays a host cell tropism different from those isolated from peripheral blood and lymph nodes. One CNS-derived isolate, HIV-1SF128A, which can be propagated efficiently in primary macrophage culture but not in any T-cell lines, was molecularly cloned and characterized. Recombinant viruses between HIV-1SF128A and the peripheral blood isolate HIV-1SF2 were generated in order to map the viral gene(s) responsible for the macrophage tropism. The env gene sequences of the two isolates are about 91.1% homologous, with variations scattered mainly in the hypervariable regions of gp120. Recombinant viruses that have acquired the HIV-1SF128A env gene display HIV-1SF128A tropism for macrophages. Furthermore, the gp120 variable domains, V1, V2, V4, and V5, the CD4-binding domain, and the gp41 fusion domain are not directly involved in determining macrophage tropism.

naf, a trans-regulating negative-acting factor encoded within the mouse mammary tumor virus open reading frame region

The mouse mammary tumor virus (MMTV) long terminal repeat (LTR) open reading frame (ORF) encodes a negative acting factor (naf). In our test system, naf mediates its effect in trans on another MMTV provirus in which the 5' LTR has been replaced by that of Rous sarcoma virus. naf effects are evidenced at the level of transcriptional initiation rather than as reduced mRNA stability. The introduction of a premature termination codon into the MMTV LTR-encoded ORF abolishes the transcriptional down regulation localizing naf within the ORF. In addition, sequences in the gag/pol genes between +320 and +646 and between +3626 and +4590 relative to the site of transcription initiation are also involved in the MMTV-mediated transcriptional down regulation.

Repressive effect of the nef cDNA of human immunodeficiency virus type 1 on the promoter activity of the viral long terminal repeat

The nef gene product of human immunodeficiency virus type 1 (HIV-1) has been implicated as a negative factor for viral replication and is suspected to play an important role in the maintenance of viral latency. However, there seems to be evidence both for and against the negative effect of nef gene product. In the present report, we reevaluated the function of the nef gene by means of transient CAT assays with two human T cell lines. In most of the experiments, carefully controlled triplicate studies were carried out. We observed that not only the nef-expression plasmid, but also an effector plasmid containing the nef cDNA sequence in a reverse orientation, not expressing the Nef protein, showed a similar extent of repression of the HIV-1 promoter activity. We also examined the repressive effect of the nef cDNA with deletion mutants of HIV-1 long terminal repeat and heterologous promoters. The results led us to conclude that the apparent "repressor"-like action of the nef cDNA itself could be explained by competition for certain transcription factors required for HIV-1 gene expression by identical sequences also present in the nef cDNA.

The human immunodeficiency virus type 2 vpr gene is essential for productive infection of human macrophages

The human immunodeficiency virus (HIV) genetic determinant(s) responsible for tropism in human T cells or macrophages are not well defined. We studied the role of the HIV type 2 (HIV-2) nef and vpr genes in viral tropism. HIV-2 mutants, lacking either vpr or nef genes, or both vpr and nef, were obtained by site-specific mutagenesis of a biologically active HIV-2 proviral clone (HIV-2sbl/isy), which is infectious in both human T cells and macrophages. Viral progeny carrying mutations of nef, vpr, or of both nef and vpr genes replicated more efficiently than the parental virus in primary human peripheral blood cells and in the human Hut 78 T-cell line. In contrast, the HIV-2 nef- mutant infected human macrophages as efficiently as the parental virus, whereas viruses lacking the vpr gene either alone or in conjunction with the lack of the nef gene did not replicate in macrophages. Thus, some lack of nef in HIV-2 enhances viral replication in T cells and does not interfere with viral replication in primary macrophages, whereas vpr is essential for replication of HIV-2 in human macrophages. Because the parental HIV-2sbl/isy cloned virus also infects rhesus macaques, the use in animal studies of these HIV-2 mutants with differences in cell tropism and rates of replication will be highly useful in understanding the mechanism of viral infectivity and possibly pathogenicity in vivo.

Molecular targets for AIDS therapy

The development of antiretroviral therapy against acquired immunodeficiency syndrome (AIDS) has been an intense research effort since the discovery of the causative agent, human immunodeficiency virus (HIV). A large array of drugs and biologic substances can inhibit HIV replication in vitro. Nucleoside analogs--particularly those belonging to the dideoxynucleoside family--can inhibit reverse transcriptase after anabolic phosphorylation. 3'-Azido-2',3'-dideoxythymidine (AZT) was the first such drug tested in individuals with AIDS, and considerable knowledge of structure-activity relations has emerged for this class of drugs. However, virtually every step in the replication of HIV could serve as a target for a new therapeutic intervention. In the future, non-nucleoside-type drugs will likely become more important in the experimental therapy of AIDS, and antiretroviral therapy will exert major effects against the morbidity and mortality caused by HIV.

Viral determinants of human immunodeficiency virus type 1 T-cell or macrophage tropism, cytopathogenicity, and CD4 antigen modulation

The genome of the human immunodeficiency virus type 1 (HIV-1) is highly heterogeneous. Some of this genomic variability is reflected in the biologic and serologic differences observed among various strains of HIV-1. To map the viral determinants that correlate with pathogenicity of the virus, recombinant viruses were generated between biologically active molecular clones of HIV-1 strains that show differences in T-cell or macrophage tropism, cytopathogenicity, CD4 antigen modulation, and susceptibility to serum neutralization. The results of these studies indicate that the envelope region contains the major determinants of these viral features. Further studies with sequence exchanges within this region should help identify specific domains that contribute to HIV pathogenesis.

Immunogenicity of the human immunodeficiency virus (HIV) recombinant nef gene product. Mapping of T-cell and B-cell epitopes in immunized chimpanzees

The nonstructural nef gene product of human immunodeficiency virus (HIV), p27, is a regulatory "early phase" protein produced by HIV-infected cells. As a possible negative regulator of transcription, it has been suggested that p27 may be involved in the control of HIV proviral latency. Immune reactivity to p27 may result in early destruction of HIV-replicating cells before viral assembly or of latently infected cells. It appeared, thus, of interest to investigate the immunogenicity of the molecule in chimpanzees immunized against HIV antigens. Two of the six chimpanzees that were injected with soluble recombinant p27 in association with other HIV proteins, displayed significant and sustained T-helper lymphocyte proliferative responses to p27 and to the other antigens. Using a set of synthetic peptides spanning the entire p27 sequence, two T-cell epitopes could be located: one within the last 20 amino-acids of the C terminus of the molecule, the other around the region of residues 118-122. Sera from the same animals also reacted to p27 in a radioimmunoassay as well as to some of the peptides in enzyme-linked immunosorbent assay. Sequential B-cell epitopes could thus be determined as being located in the regions of amino acids: 17-35, 52-66, and 185-205. The results obtained with peptides spanning the region between amino acid residues 65 and 172 indicate that at least two additional B-cell epitopes were present in the region comprised between amino acid 65 and 146. Interestingly, the extreme C terminus of the molecule encompasses both immunodominant T- and B-cell epitopes. Taken together, these observations should prove useful for the rational design of a HIV vaccine.

Antibodies to HIV-1 nef(p27): prevalence, significance, and relationship to seroconversion

A sensitive and specific enzyme-linked immunoassay for antibodies to the human immunodeficiency virus type 1 (HIV-1) nef gene product, p27, has been developed using recombinant Escherichia coli-derived protein from the LAV-1-Bru sequence. Of 92 HIV-1 infected hemophiliacs, 72 (78%) produced anti-nef antibodies in this assay; the early appearance of anti-nef prior to full seroconversion was a rare event in this population, occurring in only one subject (approximately 1%). Anti-nef antibodies were not detected in any of 500 sera from 98 repeatedly HIV seronegative subjects who had been exposed to sexually transmitted modes of HIV infection (45 subjects) or through blood products (53 subjects). There was no significant association of titer or anti-nef antibody with protection from disease in HIV infection (p = 0.1). Although the nef protein is relatively immunogenic in natural infection, this study cannot confirm the previously reported high prevalence of anti-nef antibodies prior to seroconversion, nor the finding of anti-nef antibodies in HIV seronegative but exposed subjects.

Alternative splice acceptor utilization during human immunodeficiency virus type 1 infection of cultured cells

The utilization of alternative splice acceptors for excision of the 5' major intron of human immunodeficiency virus type 1 RNA was observed after infection in vitro. Specific splice events were monitored by a cDNA-polymerase chain reaction. These splice events shared a common splice donor but utilized several alternative splice acceptors. In addition to identifying the previously documented splice acceptors for tat and nef (S. K. Arya, C. Guo, S. F. Josephs, and F. Wong-Staal, Science 229:69-73, 1985), nucleotide sequence analysis of cDNA-polymerase chain reaction fragments also revealed the following: (i) two splice acceptors 15 and 9 nucleotides upstream from the rev start codon, which are utilized to create transcripts suitable for specific rev expression; and (ii) use of the splice acceptor previously attributed to nef to generate a singly spliced, env-encoding transcript. Hybridization signals representing the nef/env, tat, and rev splice events increased in intensity between 6 and 12 h after infection of CEM cells with the LAV-1BRU strain of human immunodeficiency virus type 1. In contrast, the signal for utilization of the nef/env splice acceptor for the singly spliced env transcript appeared first at 12 h and increased to maximum intensity by 24 h. The nef/env splice acceptor was dominant at all time points examined. We propose that this dominance ensures efficient downstream splicing proximal to the env initiation codon in singly spliced transcripts. However, early after infection, the dominance of the nef/env splice acceptor appears to divert primary transcripts away from tat- and rev-specific processing paths. The relative proportions of hybridization signals representing these alternative splice events remained constant throughout the viral replicative cycle. This result suggests that trans-acting factors that might influence splice choices are not induced during infection, but rather that cis-acting, sequence-specific splice preferences determine the relative efficiency of alternative acceptor utilization.

Differences in the basal activity of the long terminal repeat determine different replicative capacities of two closely related human immunodeficiency virus type 1 isolates

Two human immunodeficiency virus type 1 (HIV-1) variants derived from a single parental isolate were found to differ substantially in their ability to replicate in CD4-positive cells. Using transient chloramphenicol acetyltransferase expression assays, we show that the long terminal repeat (LTR) of the better-replicating virus has significantly higher capacity than that of the companion virus to direct gene expression in T cells. Sequence data and site-specific mutagenesis experiments demonstrate that the higher LTR activity of the better-replicating HIV-1 is due to a combined effect of two mutations: (i) a point mutation in position -94 (relative to the transcriptional start site), which is located between the two subunits of the HIV-1 enhancer, and (ii) a duplication of 24 base pairs in positions -128 to -151, which was not previously known to be involved in any regulatory function. The presence of these mutations increases the basal level of the LTR-driven gene expression and does not influence the degree of induction caused by the viral tat gene product or by cell activation. Reciprocal exchange of LTRs between the respective viral DNAs results in a change of a recombinant virus replication pattern consistent with the activity of the particular LTR. These experiments suggest that the HIV-1 LTR is one of the sites which determines the functional heterogeneity of HIV-1.

Feedback regulation of human immunodeficiency virus type 1 expression by the Rev protein

Rev is an essential regulatory protein of the human immunodeficiency virus type 1 (HIV-1) that affects the transport and half-life of certain viral mRNAs. Rev exerts its function via a unique element, the Rev-responsive element (RRE), located within the env region of HIV-1. It has been previously demonstrated that Rev affects the relative levels of RRE-containing and RRE-lacking mRNAs. We have studied the effects of Rev on the expression of the three different groups of small, multiply spliced mRNAs that lack the RRE sequence and encode the regulatory proteins Tat, Rev, and Nef. To monitor the tat, rev, and nef mRNAs we generated specific S1 nuclease mapping probes that distinguish among them. Analysis of all the mRNA species producing Tat, Rev, and Nef revealed that their levels are coordinately regulated by Rev. They are increased in the absence of Rev protein and are down regulated in the presence of Rev. The corresponding proteins were measured by immunoprecipitations, and their levels are in agreement with the RNA levels. These results verify the model proposing that Rev is a general regulator indirectly affecting all the multiply spliced mRNAs to a similar extent. Therefore, Rev down regulates its own expression and the expression of Tat and Nef.

Human immunodeficiency virus type 1 cellular host range, replication, and cytopathicity are linked to the envelope region of the viral genome

Human immunodeficiency virus type 1 (HIV-1) isolates vary in their in vitro biologic characteristics such as cellular host range, replication kinetics, and cytopathicity. In this study, we molecularly exchanged equivalent regions between two cloned HIV-1 isolates with differing replicative and cytopathic properties. To facilitate generation of recombinant viruses, we used a method involving cotransfection of human monolayer cells with plasmid constructs containing half of the biologically active viral genome. The two halves of the genome were subsequently ligated by intracellular processes to form the complete proviral genome. This method simplifies plasmid construction, since new infectious virus particles can be produced easily from the individual constructs that are correctly ligated in vivo. Results obtained by using recombinant viruses generated in this manner indicate that the ability of HIV to replicate in specific cell types and cytopathicity segregate with the env region of the viral genome.