Molecular genetics and structure of the human immunodeficiency virus

Thirty years of the human immunodeficiency virus epidemic and beyond

After more than 30 years of battling a global epidemic, the prospect of eliminating human immunodeficiency virus (HIV) as the most challenging infectious disease of the modern era is within our reach. Major scientific discoveries about the virus responsible for this immunodeficiency disease state, including its pathogenesis, transmission patterns and clinical course, have led to the development of potent antiretroviral drugs that offer great hopes in HIV treatment and prevention. Although these agents and many others still in development and testing are capable of effectively suppressing viral replication and survival, the medical management of HIV infection at the individual and the population levels remains challenging. Timely initiation of antiretroviral drugs, adherence to the appropriate therapeutic regimens, effective use of these agents in the pre and post-exposure prophylaxis contexts, treatment of comorbid conditions and addressing social and psychological factors involved in the care of individuals continue to be important considerations.

Determination of the size of HIV using adenovirus type 2 as an internal length marker

The size of a virion is a key criterion to its proper classification and may have implications in many practical aspects. Size determinations by thin section electron microscopy often result in length aberrations of more than 10% because of a number of preparative and instrumental inaccuracies, e.g. specimen shrinkage or swelling and unreliable calibration. Using adenovirus type 2 as an isometric size marker for internal calibration, we have determined the diameters of mature and immature HIV-1 to be 110 to 128 and 132 to 146 nm, respectively. The marker had been used either as a purified particle suspension added to the HIV producing culture, or adenovirus had been propagated together with HIV by infecting HIV producing cells. Using well characterized isometric markers, e.g. an icosahedral virus, in thin section electron microscopy appears to be a suitable technique for viral size determinations.

Viral gene products and replication of the human immunodeficiency type 1 virus

The acquired immunodeficiency syndrome (AIDS) epidemic represents a modern-day plague that has not only resulted in a tragic loss of people from a wide spectrum of society but has reshaped our viewpoints regarding health care, the treatment of infectious diseases, and social issues regarding sexual behavior. There is little doubt now that the cause of the disease AIDS is a virus known as the human immunodeficiency virus (HIV). The HIV virus is a member of a large family of viruses termed retroviruses, which have as a hallmark the capacity to convert their RNA genome into a DNA form that then undergoes a process of integration into the host cell chromosome, followed by the expression of the viral genome and translation of viral proteins in the infected cell. This review describes the organization of the HIV-1 viral genome, the expression of viral proteins, as well as the functions of the accessory viral proteins in HIV replication. The replication of the viral genome is divided into two phases, the early phase and the late phase. The early phase consists of the interaction of the virus with the cell surface receptor (CD4 molecule in most cases), the uncoating and conversion of the viral RNA genome into a DNA form, and the integration into the host cell chromosome. The late phase consists of the expression of the viral proteins from the integrated viral genome, the translation of viral proteins, and the assembly and release of the virus. Points in the HIV-1 life cycle that are targets for therapeutic intervention are also discussed.

Studies on the substrate specificity of the proteinase of equine infectious anemia virus using oligopeptide substrates

The proteinase of the equine infectious anemia virus (EIAV), a lentivirus closely related to human immunodeficiency virus (HIV), was purified from concentrated virus. The specificity of the enzyme was characterized using oligopeptides representing naturally occurring cleavage sites in the Gag and Gag-Pol polyproteins. The length of the substrate binding pocket was found to be 1-2 residues longer than that of HIV proteinases. Although the EIAV and HIV proteinases cleaved most of the peptides at the same bond, some were hydrolyzed by only the EIAV enzyme. Oligopeptides representing cleavage sites in the nucleocapsid protein were also found to be substrates of the EIAV proteinase. However, these peptides were not hydrolyzed by the HIV proteinases. While peptides representing the corresponding sequences in the first cysteine arrays of the nucleocapsid proteins of HIV-1 and HIV-2 were substrates of the proteinases, peptides representing the homologous sequences in the second Cys arrays were resistant against the proteolytic attack. A three-dimensional model of the EIAV proteinase built on the basis of homology with HIV-1 proteinase was used to interpret the differences. In addition to the oligopeptides representing cleavage sites in the Gag and Gag-Pol polyproteins, the EIAV proteinase was also able to cleave an oligopeptide mimicking a cleavage site in the transmembrane protein. Our results suggest that the specificity of lentiviral proteinases share common characteristics, although substantial differences may exist in hydrolysis of some peptides.

Requirements for incorporation of Pr160gag-pol from human immunodeficiency virus type 1 into virus-like particles

The roles of the human immunodeficiency virus precursor polyproteins Pr55gag and Pr160gag-pol in viral core assembly were studied in CMT3-COS cells. To do this, the precursors were expressed separately by using a simian virus 40 late replacement vector system described previously. Consistent with previously published data, our results show that the Pr55gag precursor, when expressed alone, was able to form particles which had an immature morphology and that particle formation required the presence of a myristate addition signal at the amino terminus of the precursor. In contrast, the Pr160gag-pol precursor was not able to form particles when expressed alone, although it still underwent proteolytic processing. Coexpression of the two precursor polyproteins from separate vectors in the same cell resulted in processing of the Pr55gag in trans by the protease embedded in Pr160gag-pol and the formation of virus-like particles containing the products of both precursors. Proteolytic processing occurred independently of the presence of a functional myristate addition signal on either precursor. On the other hand, removal of myristate from one or the other precursor had nonreciprocal effects on virus particle formation. Cells expressing Pr55gag lacking myristate and Pr160gag-pol containing it did not produce particles. Cells expressing a myristylated Pr55gag and unmyristylated Pr160gag-pol still produced virus-like particles which contained nearly normal amounts of Pr160gag-pol. The results suggest that the incorporation of Pr160gag-pol into particles is largely determined by intermolecular protein-protein interactions between the two precursor polypeptides.

Human T-cell leukemia virus type I infection of monocytes and microglial cells in primary human cultures

The pathogenesis of progressive spastic paraparesis [HTLV-I-associated myelopathy/tropical spastic paraparesis (HAM/TSP)], a serious consequence of human T-cell leukemia virus type I (HTLV-I) infection, is unclear. T and B lymphocytes can be naturally infected by HTLV-I, but the susceptibility to HTLV-I infection of other cell types that could contribute to the pathogenesis of HAM/TSP has not been determined. We found that a human monocyte cell line (THP-1), primary human peripheral blood monocytes, and isolated microglial cells but not astrocytes or oligodendroglial cells derived from adult human brain were infected by HTLV-I in vitro. Infection with HTLV-I enhanced the secretion of interleukin 6 in human microglial cell-enriched cultures but did not stimulate the release of interleukin 1 from monocytes or microglial cells. Tumor necrosis factor alpha production was stimulated by HTLV-I infection of monocytes and microglial cells and could be enhanced by suboptimal amounts of lipopolysaccharide. Since both tumor necrosis factor alpha and interleukin 6 have been implicated in inflammatory demyelination and gliosis, our findings suggest that human microglial cells and monocytes infected with and activated by HTLV-I could play a role in the pathogenesis of HAM/TSP.

Rapid, non-separation electrochemiluminescent DNA hybridization assays for PCR products, using 3'-labelled oligonucleotide probes

Described are rapid assays for the analysis of PCR products in a one step, non-separation assay based on the use of electrochemiluminescence generated from a tris-bipyridine ruthenium (II) label. The assay uses PCR incorporation of a biotinylated oligonucleotide as a primer, with the inclusion of a labelled oligonucleotide. Oligonucleotides were labelled with an N-hydroxy succinimide ester of tris-bipyridine ruthenium (II) dihexafluorophosphate (Origen-label) by modifying the 3' and 3' 5' ends of the oligonucleotide probes. The assay makes use of the inherent thermal stability and absence of polymerase activity on such probes to allow the PCR and probe hybridization to be completed automatically on the thermocycler. The assay is concluded by the addition of PCR samples to streptavidin beads on an electrochemiluminescence analyser for binding and analysis. Target genes evaluated were the HIV-1 gag gene, and cystic fibrosis delta F-508 deletion mutation. The results obtained from these assays demonstrated the detection of 10 copies of the HIV-1 gag gene, and cystic fibrosis delta F-508 mutation in 1 ng of human DNA within 15 min. This assay format allows a rapid and simple determination of specific amplified DNA sequences, reducing the contamination risks due to washes and multiple pipetting.

Spatial visualization of the maturing HIV-1 core and its linkage to the envelope

The core of late states of maturing human immunodeficiency virus type 1 (HIV-1) has been visualized in three dimensions at approximately 7 nm resolution by electron microscopic tomography. After budding, approximately 25 nm thick precursor material is observed densely assembled inside the viral envelope. Upon proteolysis the core material is transported and condensed in the center of the virion. The core, 100 nm in length, spans the entire diameter of the virion showing a 40-60 nm wide free end and a narrow end approximately 20 nm. A model of the core is derived consisting of two fibers packed into a bilateral, elongated structure. Two ends of the fibers are compacted together, forming one narrow end of the core, while the two other fiber ends are situated more loosely together allowing for flexibility. Structural maturation of the virus could be reflected by the degree of compactness of the core. The narrow end of the core is observed attached to the envelope with a conspicuous core-envelope link (CEL).

The polymerase chain reaction: a new tool for the understanding and diagnosis of HIV-1 infection at the molecular level

The polymerase chain reaction (PCR) is at present the most powerful analytical tool for detection of specific nucleic acid sequences. The method is based on the in vitro amplification of DNA segments before detection with conventional hybridization techniques or visualization following electrophoresis and staining. The current diagnostic methods for HIV-1 do not allow easy identification of subgroups of infected patients including infants born to seropositive mothers, individuals with delayed serological responses to the virus, infected patients with indeterminate serology results, and patients with dual retroviral infections. Furthermore, response to antiviral therapy cannot be evaluated with serological assays. The rationale for applying PCR in those situations is elaborated here. The applications of this technique for HIV-1 as a diagnostic test and for the understanding of the pathogenesis of this retrovirus are described. Potential limitations of this technique for diagnostic purposes include mainly the possibility of false-positive results due to contamination and false-negative reactions caused by Taq polymerase inhibition. Non-isotopic means for detection of amplified products have been described and should allow for a wider application of this technology. Modifications of PCR which make use of internal standards seem promising for quantitative analysis of nucleic acids. PCR has great potential for viral diagnosis but still requires further studies and better characterization.

A western blot assay for the detection of antibodies to bovine immunodeficiency-like virus in experimentally inoculated cattle, sheep, and goats

A cocultivation method was used to establish a cytocidal bovine immunodeficiency-like virus (BIV) infection in primary fetal bovine lung (FBL) cell cultures. Cultures were monitored for virus production using radial immunodiffusion and agar gel immunodiffusion. Pelleted virus and detergent (CHAPS)-solubilized infected cell lysates from BIV-infected cell cultures were compared as sources of antigen for Western blots. Pelleted virus preparations from FBL-BIV cell cultures produced the best antigen for Western blot. Sheep and goats were inoculated with BIV and serum antibody responses were monitored up to 1 year post inoculation (PI). Sera from experimentally infected cattle, sheep, and goats reacted in Western blot assay with BIV viral induced polypeptides gp 110, p 72, p 55, p 50, gp 42, p 38, p 26, p 24, p 18, p 15, and p 13. Antibodies to p 26 were detected as early as 2 weeks PI in cattle, sheep, and goats. Antibodies to gp 110 were detected by 4 to 6 weeks PI in cattle, and by 9 months PI in sheep and goats. Antibodies to BIV proteins were still evident in cattle sera 2 1/2 years PI, and in sheep and goat sera 1 year PI.

Humoral immune response to the bovine immunodeficiency-like virus in experimentally and naturally infected cattle

Calves inoculated with bovine immunodeficiency-like virus (BIV) produced virus-specific antibodies that could be detected from 2 weeks to 2.5 years postinoculation by using both indirect fluorescent-antibody and Western immunoblot assays. Antibodies were primarily to p26. Virus and BIV-specific antibodies were isolated from calves given BIV-infected blood. Antibodies to BIV proteins were found in sera from naturally infected cattle.

Human immunodeficiency virus type 1 Pr55gag and Pr160gag-pol expressed from a simian virus 40 late replacement vector are efficiently processed and assembled into viruslike particles

Human immunodeficiency virus type 1 (HIV-1) gag and pol genes were expressed by using fragments of the BH10 clone of HIV inserted into a simian virus 40 late replacement vector. An initial construct containing the entire coding regions of gag, pol, and vif produced only minute amounts of the gag precursor, Pr55gag. However, high-level expression was obtained when an additional sequence from the env gene (the rev-responsive element) was inserted 3' of vif in the correct orientation, and rev was provided in trans from a second vector. Western immunoblot analysis of transfected cells showed the presence of large amounts of both Pr55gag and Pr160gag-pol as well as all of the expected cleavage products. Electron microscopy of thin sections of transfected cells showed a multitude of viruslike particles. Both immature particles in the process of budding and particles containing the condensed core characteristic of HIV were observed. Analysis of the released viruslike particles showed the presence of active reverse transcriptase. Sucrose gradient analysis of particles produced from [3H]uridine-labeled cells indicated a peak of radioactivity which cosedimented with a peak of p24, suggesting that the particles contained RNA.

Negative regulation of human immune deficiency virus replication in monocytes. Distinctions between restricted and latent expression in THP-1 cells

In THP-1 monocytoid cells infected with HIV, viral expression can be regulated in several ways: (a) latency (no viral expression); (b) restricted expression (chronic low-level viral expression with little or no detectable virus released); and (c) continuous production. In cells with restricted HIV expression, nuclear factor(s) were found that blocked tat-associated DNA binding complex formation, suggesting that initiation of transcription was negatively regulated. Also, viral particles were seen budding into and accumulating within intracytoplasmic vacuoles with little virus released, suggesting multiple levels of regulation. These cells with restricted expression had no detectable viral antigens on the cell surface and were not lysed by IL-2-activated large granular lymphocytes. However, they could cause viral-mediated T cell cytolysis in cell-cell assays, suggesting viral transmission through cell contact. In addition, cells with latent HIV were identified and could still produce infectious virus after 5-azacytidine exposure 10 mo later. LPS and other treatments could increase viral production in cells with restricted but not latent expression, suggesting they occur by distinct mechanisms. These infected cells provide a reservoir for viral transmission to uninfected T cells that itself is not detected by immune surveillance mechanisms.

Nucleotide composition bias and CpG dinucleotide content in the genomes of HIV and HTLV 1/2

Nucleotide compositions of the HIV subfamily and HTLV 1/2 genomes are strongly biased in a remarkably opposite way; HIV is adenine-rich and cytosine-poor while HTLV 1/2 is cytosine-rich and adenine-poor. In addition, the CpG dinucleotides are underrepresented in HIV but abundant in HTLV 1/2. By these two properties the genomes of HIV and HTLV 1/2 mimic an (A + T)-rich and (G + C)-rich segment of the host genome, respectively. These dramatic differences between the two human retroviruses might have evolved to direct integration of the retroviral genomes into specific segments of the human chromosomes.

The preparation and biochemical characterization of intact capsids of equine infectious anemia virus

Capsids of equine infectious anemia virus have been isolated as cone-shaped particles 60 x 120 nm in size. Detergent treatment of whole virus followed by two cycles of rate-zonal centrifugation in Ficoll produces these capsids in a yield of approximately 10%. The major protein components are the gag-encoded p11 nucleocapsid protein and p26 capsid protein, which are present in equimolar amounts. Substantial cleavage of p11 to p6 and p4 can be observed under conditions where the viral protease packaged in the capsid is enzymatically active.

Structure of the gene encoding the beta-subunit of chicken prolyl 4-hydroxylase

Prolyl 4-hydroxylase (EC 1.14.11.2) converts peptidyl proline to peptidyl hydroxyproline in procollagen polypeptides during collagen biosynthesis. The active enzyme is a tetramer which is composed of two pairs of non-identical subunits in a molecular form of alpha 2 beta 2. In addition to the tetrameric prolyl 4-hydroxylase (alpha 2 beta 2), the free beta-subunit is also found inside cells. Recently it was shown that the beta-subunit of prolyl 4-hydroxylase is identical to the protein disulfide isomerase and cellular thyroid hormone-binding protein. We previously isolated and characterized cDNAs of the beta-subunit of chicken prolyl 4-hydroxylase. The cDNA of beta-subunit was used to screen a chicken genomic DNA library constructed with the lambda EMBL-3 vector. Two clones, lambda gCPH beta-22 and beta-50, were isolated and characterized by restriction enzyme analysis, heteroduplex analysis, and nucleotide sequencing. The results showed that the 2.5-kb mRNA of the beta-subunit is divided into eleven exons and that the gene is 9.0 kb long. The gene contains consensus sequence for TATA at -24 bp and four CAAT at -57, -157, -194 and -223 bp in the 5' end flanking sequence of the transcription start point. In addition, there are three GC boxes upstream from the TATA box and four GC boxes in the first intron. This is similar to the structure of the alpha 1(I) collagen coding gene (COL1A1). These elements may interact with nuclear factors and play important roles in expression regulation of the beta-subunit gene as has been described in COL1A1.

Genetic locus, primary structure, and chemical synthesis of human immunodeficiency virus protease

The genetic locus and primary structure of the human immunodeficiency virus (HIV) protease was determined by comparing the data of protein analyses with the published data of the gene analysis. The complete sequence of HIV-1 and HIV-2 protease was synthesized by solid-phase peptide synthesis. The synthetic protease was capable of accurately cleaving synthetic peptide substrates corresponding to known cleavage sites in gag polyproteins of HIV-1, HIV-2, and murine leukemia virus. The chemical synthesis of protease confirms the DNA sequence and provides a means of rapidly producing active protease in substantial quantities for biochemical and physical studies.

A recombinase from Drosophila melanogaster embryos

We have partially purified a DNA strand-exchange activity (recombinase) from nuclear extracts of Drosophila melanogaster embryos. The protein fraction forms a joint molecule between a circular single-strand DNA and a homologous linear duplex DNA that is resolved from the substrates by agarose gel electrophoresis. A strand-exchange activity can be obtained from nuclear extracts from embryos as old as 24 hr. The activity is similar to that partially purified from human cells [Hsieh, P., Meyn, S.M. & Camerini-Otero, R.D. (1986) Cell 44, 885-894]. It is homology-dependent, requires Mg2+, appears to be directional in that it prefers to displace the 3' end of the noncomplementary strand, and does not require exogenous ATP. Forty nanograms of protein in the partially purified DNA strand-exchange fraction from D. melanogaster embryos can completely convert 50 ng of substrate single-strand DNA into joint molecules in 10 min. In the electron microscope, joint molecules are seen to consist of a circular single-strand DNA molecule attached to only one end of a linear duplex DNA molecule; a displaced strand is also seen. The region of heteroduplex formation can be as long as 600 base pairs. The demonstration of a strand-exchange activity from wild-type D. melanogaster embryos invites analysis of recombination-defective mutants to explore the role of DNA strand exchange in homologous recombination.

Viral infections in the acquired immunodeficiency syndrome

The following communication is a tripartite synopsis of the role of viral infection in the acquired immunodeficiency syndrome (AIDS). The first section describes the impact of viral opportunistic infection in AIDS; for each virus, clinical presentation and diagnosis, laboratory diagnostic approaches (with emphasis on electron microscopy), and therapeutic interventions attempted to date are discussed. The second segment explores current theories on the pathogenesis of AIDS, and describes diagnostic and therapeutic approaches to the syndrome itself. The final section catalogues ultrastructural anomalies in the cells of AIDS patients, many of which have been mistakenly identified as etiologic agents.