Transcription of novel open reading frames of AIDS retrovirus during infection of lymphocytes

CBFβ enhances de novo protein biosynthesis of its binding partners HIV-1 Vif and RUNX1 and potentiates the Vif-induced degradation of APOBEC3G

Vif is a lentiviral accessory protein that regulates viral infectivity in part by inducing proteasomal degradation of APOBEC3G (A3G). Recently, CBFβ was found to facilitate Vif-dependent degradation of A3G. However, the exact role of CBFβ remains unclear. Several studies noted reduced Vif expression in CBFβ knockdown cells while others saw no significant impact of CBFβ on Vif stability. Here, we confirmed that CBFβ increases Vif steady-state levels. CBFβ affected expression of neither viral Gag nor Vpu protein, indicating that CBFβ regulates Vif expression posttranscriptionally. Kinetic studies revealed effects of CBFβ on both metabolic stability and the rate of Vif biosynthesis. These effects were dependent on the ability of CBFβ to interact with Vif. Importantly, at comparable Vif levels, CBFβ further enhanced A3G degradation, suggesting that CBFβ facilitates A3G degradation by increasing the levels of Vif and by independently augmenting the ability of Vif to target A3G for degradation. CBFβ also increased expression of RUNX1 by enhancing RUNX1 biosynthesis. Unlike Vif, however, CBFβ had no detectable effect on RUNX1 metabolic stability. We propose that CBFβ acts as a chaperone to stabilize Vif during and after synthesis and to facilitate interaction of Vif with cellular cofactors required for the efficient degradation of A3G.

IMPORTANCE

In this study, we show that CBFβ has a profound effect on the expression of the HIV-1 infectivity factor Vif and the cellular transcription factor RUNX1, two proteins that physically interact with CBFβ. Kinetic studies revealed that CBFβ increases the rate of Vif and RUNX1 biosynthesis at the level of translation. Mutants of Vif unable to physically interact with CBFβ were nonresponsive to CBFβ. Our data suggest that CBFβ exerts a chaperone-like activity (i) to minimize the production of defective ribosomal products (DRiPs) by binding to nascent protein to prevent premature termination and (ii) to stabilize mature protein conformation to ensure proper function of Vif and RUNX1. Thus, we identified a novel mechanism of protein regulation that affects both viral and cellular factors and thus has broad implications beyond the immediate HIV field.

Application of the hybridization AT-tailing method for detection of human immunodeficiency virus RNA in cells and simian immunodeficiency virus RNA in formalin-fixed and paraffin-embedded tissues

An in situ hybridization (ISH) AT-tailing method (HybrAT) was developed for the detection of viral genomes in infected cells and tissues. The method consists of hybridization with oligonucleotide probe which has a 3' end oligo d(A-T) tag, followed by elongation of the oligo d(A-T) by deltaTth DNA polymerase in the presence of the labeled nucleotide. The in situ HybrAT detected human immunodeficiency virus type 1 (HIV-1) in cells and simian immunodeficiency virus (SIV) in formalin-fixed and paraffin embedded sections with a sensitivity comparable to RNA ISH. The advantage of this method over other methods is discussed.

Replication of HIV type 1 in rabbit cell lines is not limited by deficiencies in tat, rev, or long terminal repeat function

HIV-1 infection has been documented in rabbits, but infection proceeds slowly in this species. Human and rabbit cell lines were compared in order to identify barriers to efficient HIV-1 infection of rabbit cells. A direct comparison of human and rabbit CD4 as receptor for HIV-1 indicated that the rabbit CD4 homolog did not function well even when expressed by human cells. Examination of viral RNA production indicated that the major HIV transcripts were produced in HIV-infected rabbit cells, but were present at levels significantly lower than those found for human cells. Ability of HIV-1 LTRs to direct protein expression in human and rabbit cells was compared using gene constructs with the chloramphenicol acetyltransferase (cat) gene flanked by HIV-1 LTRs. Chloramphenicol acetyltransferase protein expression was equivalent in rabbit and human cell lines transfected with the HIV-1/CAT constructs and cotransfections with the HIV-1 tat gene led to similar increases in CAT expression. Subsequent transfections with an infectious molecular HIV clone yielded approximately equal levels of HIV protein expression in rabbit and human cell lines, suggesting that major barriers to virus production in rabbit lines exist at steps prior to transcription of the viral genome. Because HTLV-I replicates with high efficiency in rabbit cells, a chimeric virus clone was constructed consisting of the 5' portion of HIV-1 through the nef coding sequence followed by the 3' HTLV-I LTR. Transfection of most rabbit cell lines with the chimera produced levels of p24gag protein higher than those transfected with the parent HIV-1 clone. By contrast, the unmodified HIV clone replicated more efficiently in all human cell lines tested.

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.

Alterations in spliced and unspliced HIV-1-specific RNA detection in peripheral blood mononuclear cells of individuals with varying CD4-positive lymphocyte counts

Reverse transcriptase-polymerase chain amplification reactions (RT-PCR) were used to identify transcripts for HIV-1 structural and regulatory proteins in peripheral blood mononuclear cells of a cohort of 48 patients. At least one set of PCR primers was capable of detecting HIV-1 transcripts in 94% of patients. Unspliced gag-pol transcripts were detected with gag or pol primer sets in 60 and 63% of samples, respectively. A significant inverse correlation was noted between transcript identification with the gag primer set and the number of CD4-positive lymphocytes in the blood sample and the clinical stage of infection. Single-spliced env transcripts were identified in 44% of individuals. Multiple-spliced tat or nef transcripts were detected in 6.2 and 53% of individuals, respectively. These findings indicate that viral transcripts are expressed throughout the course of HIV-1 infection.

Vif is crucial for human immunodeficiency virus type 1 proviral DNA synthesis in infected cells

The human immunodeficiency virus type 1 (HIV-1) vif gene encodes a 23-kDa protein of unknown function, also produced by most other known lentiviruses. Vif was found to be essential for the spread of HIV-1 in peripheral blood lymphocytes and in primary macrophages, as well as in some but not all established T-cell lines. Vif was required at the stage of viral particle formation, for cell-to-cell as well as for cell-free transmission of HIV-1. Accordingly, vif-defective viruses could be complemented by the expression of vif in the producer but not in the target cell. vif-defective virions contained wild-type amounts of Gag and Env proteins, reverse transcriptase, integrase, genomic RNA, and partial reverse transcripts. Most importantly, they could enter cells normally, and the vif defect could not be rescued through the use of HIV(MLV [murine leukemia virus]) pseudotypes. Instead, vif-mutant viruses were severely impaired in their ability to complete the synthesis of proviral DNA, once internalized in the target cell. These results suggest that Vif plays a role which is novel for a retroviral protein, in allowing the processing and/or the transport of the internalized HIV core.

Identification of a feline immunodeficiency virus gene which is essential for cell-free virus infectivity

Feline immunodeficiency virus (FIV) contains at least three small open reading frames (ORFs) in the genome, in addition to the three structural genes. Two of these ORFs (putative vif and ORF-A) have unknown functions. Northern (RNA) blot analysis of mRNAs from an FIV-infected cell line showed that the putative-vif-specific mRNA was expressed as a 5.2-kb species. To examine the function of the putative vif gene, we constructed mutants carrying a deletion in either the vif-like gene or the rev gene from an infectious molecular clone of FIV. Although the vif mutant produced virion-associated reverse transcriptase at a normal level upon transfection, cell-free virus prepared from the transfected cells could not infect feline CD4+ cells. The infectivity of the vif mutant, however, was demonstrated in a coculture of the transfected cells and feline CD4+ cells. We conclude that FIV contains the vif gene, which is structurally and functionally similar to that of the primate lentiviruses.

Cell-free transmission of Vif mutants of HIV-1

To determine the phenotype of human immunodeficiency virus type 1 (HIV-1) defective in the production of Vif, mutations were introduced into the vif gene of infectious molecular clones of the LAI, MAL, and ELI strains. Previous results had demonstrated that viruses derived from these wild type clones display different replicative capacities on peripheral blood mononuclear cells (PBMC) and different tropisms for CD4-positive cell lines. Using cell-free infection, Vif mutants of LAI, MAL, and ELI were found to have delayed kinetics and to produce less virus than their corresponding wild type viruses when propagated on most permissive cell lines. An additional mutation in the vpr gene in the LAI strain had no effect on this phenotype. However, on one T cell line, the H9 cell line, two Vif mutants of LAI and a Vif.Vpr double mutant were unable to replicate. Furthermore, Vif mutants from all three strains were only able to establish a productive infection on PBMC by coculture and not by cell-free infection. No defects in the processing of the virion proteins or the release of particles in the Vif mutants were detected.

RNA packaging signal of human immunodeficiency virus type 1

Cells infected with a recombinant vaccinia virus carrying the gag and pol regions of the human immunodeficiency virus type 1 genome (Vac-gag/pol) released human immunodeficiency virus (HIV)-like particles containing HIV-specific RNA. However, cells infected with another recombinant vaccinia, Vac-gag/pol-dP, derived through the deletion of an 85-base region (nucleotide positions 679-763) of the HIV genome between the primer binding site and the gag initiation codon of Vac-gag/pol, produced HIV-like particles devoid of the HIV-specific RNA. This 85-base deletion was suggested to cause the collapse of a stable stem-loop structure of 46 bases (751-796) around the gag initiation codon. To examine the role of the stem-loop structure in the packaging of RNAs, we constructed a vaccinia vector plasmid that carried this 46-base sequence followed by the Sendai virus nucleocapsid (NP) gene. When both Vac-gag/pol-dP and this plasmid were introduced into cells, HIV-like particles released from the cells contained the NP gene RNA. However, another vaccinia vector plasmid, which carried the 46-base sequence in the midst of the NP gene, could not supply RNA for incorporation into HIV-like particles. Computer analysis of this plasmid sequence suggested that the 46-base sequence cannot form the stem-loop structure. These findings suggest that the stem-loop structure formed by the 46-base sequence is crucial as a packaging signal.

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.

Identification of feline immunodeficiency virus rev gene activity

We constructed 16 deletion mutants from an infectious molecular clone of feline immunodeficiency virus (FIV) and a reporter plasmid carrying the bacterial chloramphenicol acetyltransferase (CAT) gene to identify the rev transactivator activity of the virus. Cotransfections of various mutants and the rev reporter clone bearing a portion of FIV env in addition to the CAT gene revealed that the sequence important for the augmentation of CAT production was located in three separate parts of the virus genome. This enhancement was FIV specific in that the human retrovirus rev and rex gene products did not activate the reporter. The phenotypic properties of an FIV proviral mutant containing a small deletion in the genome were similar to those of rev mutants derived from primate immunodeficiency viruses. These results indicate that FIV, like the other lentiviruses, contains the rev gene in its genome.

rev-like transcripts of caprine arthritis encephalitis virus

The pattern of expression of the caprine arthritis encephalitis virus genome (CAEV) in acutely infected tahr lung cells was found to be complex and temporally regulated. Employing Northern analysis, five CAEV-specific transcripts, 9, 6.5, 5.0, 2.5, and 1.4 kb, were detected. Nucleotide sequence analysis established the genetic structure of two species of cDNA, isolated from a library of CAEV-infected tahr cells, and suggested that they represent rev-like transcripts. One of these cDNA species was composed of three exons--the leader, an exon derived from the 5' region of env, and an exon which spanned the 3' orf. The second cDNA species consisted of four exons--three of which were identical with those of the former species. The additional exon (the second) was located at the 3' end of pol. These transcripts could potentially encode three proteins--a Rev-like protein, which is a fusion of 38 amino acids derived from the N-terminus of env and 91 residues from the 3' orf; a truncated form of the env transmembrane protein, and a novel protein, designated X composed of 73 amino acids. Thus, CAEV, like other lentiviruses, displays a complex pattern of gene expression, characterized by alternative splicing and the production of potentially polycistronic transcripts.

Expression of human immunodeficiency virus type 1 vif and vpr mRNAs is Rev-dependent and regulated by splicing

We have analyzed the structure and expression of the HIV-1 vif and vpr mRNAs. The results revealed that the predominant vif and vpr mRNAs belong to the intermediate size class of HIV-1 mRNAs and that their expression is dependent on the presence of Rev protein. In addition, low levels of a small multiply spliced vpr mRNA were produced by HIV-1. cDNA cloning and expression of vpr cDNAs in eucaryotic cells revealed that high levels of Vpr were produced only from the intermediate-size mRNA in the presence of Rev. Thus, as demonstrated for the viral structural proteins, expression of Vif and Vpr is regulated by Rev. The arrangement of the splice sites and the Rev-RRE interaction are responsible for the regulation of viral expression, and especially for the switching from an early stage, producing only or primarily Tat, Rev, and Nef from multiply spliced mRNAs, to a late stage, leading to the production of Gag, Pol, Env, Vpu, Vif, and Vpr from unspliced and partially spliced mRNAs.

Analysis of the transcription pattern and mapping of the putative rev and env splice junctions of bovine immunodeficiency-like virus

The bovine immunodeficiency-like virus (BIV) genome contains the obligatory structural genes of all retroviruses and, in addition, the complex central region of lentiviruses; this novel region may code for at least five nonstructural/regulatory genes in BIV (K.J.Garvey, M.S. Oberste, J.E. Elser, M.J. Braun, and M.A. Gonda, Virology 175:391-409, 1990). As a prelude to determining the function of these novel open reading frames, the transcriptional pattern of BIV was studied by Northern analysis of RNA from BIV-infected cells. Five size classes of BIV-specific RNAs of 8.5, 4.1, 3.8, 1.7, and 1.4 kb were detected. The 8.5-kb RNA contains sequences from all regions of the genome; it is the virion RNA and probably serves as the gag-pol transcript as well. By using gene-specific probes, subgenomic viral RNAs of 3.8, 1.7, and 1.4 kb were tentatively identified as the env, tat, and rev spliced messages, respectively. The 4.1-kb RNA could not be unambiguously identified but may encode vif. The hybridization patterns of the putative tat and rev mRNAs suggest that they are the products of multiple splicing events. Discrete transcripts for the BIV W and Y central region open reading frames were not defined. The characterization of partial cDNA clones has permitted the mapping of the env and putative rev splice junctions.

Rev is necessary for translation but not cytoplasmic accumulation of HIV-1 vif, vpr, and env/vpu 2 RNAs

The effect of Rev on cytoplasmic accumulation of the singly spliced human immunodeficiency virus type 1 (HIV-1) vif, vpr, and env/vpu RNAs was examined by using a quantitative RNA polymerase chain reaction (PCR) analysis following transfection of complete proviral molecular clones into lymphoid cells. Previously published studies using subgenomic env constructs in nonlymphoid cell types concluded that Rev was necessary for cytoplasmic accumulation of high levels of unspliced env RNA and that, by analogy, Rev must be necessary for the cytoplasmic accumulation of all HIV-1 RNAs that contain the Rev-responsive element (RRE). We confirm those results in COS cells. Unexpectedly, in lymphoid cells, we find that although Rev acts somewhat to increase the cytoplasmic level of full-length HIV-1 RNA, Rev has little or no effect on cytoplasmic accumulation of singly spliced HIV-1 RNAs. However, Env protein expression was greatly reduced in the absence of Rev. Analysis of the cytoplasmic RNA revealed that in the absence of Rev or the RRE, the cytoplasmic vif, vpr, and env/vpu 2 RNAs were not associated with polysomes but with a complex of 40S-80S in size. Consequently, efficient expression of the Vif, Vpr, Vpu, and Env proteins from these RNAs is dependent on Rev. These results exclude a mechanism whereby the sole function of Rev is simply to export RNAs from nucleus to cytoplasm. We discuss other models to take into account the dependence on Rev for efficient translation of cytoplasmic HIV-1 RNAs.

Rev activates expression of the human immunodeficiency virus type 1 vif and vpr gene products

The proteins encoded by human immunodeficiency virus type 1 (HIV-1) can be divided into two temporally regulated classes. Early gene products are encoded by multiply spliced mRNA species and are expressed constitutively. In contrast, late proteins are encoded by a class of unspliced or singly spliced viral transcripts whose cytoplasmic expression is induced by the viral Rev trans activator. Here, we demonstrate that the viral Vif and Vpr proteins are encoded by singly spliced viral mRNAs whose expression is activated by Rev. This activation is shown to result from the reduced utilization of splice sites adjacent to or within the vif and vpr coding sequences. Vif and Vpr therefore belong to the class of late HIV-1 gene products.

Inhibition of human immunodeficiency virus forward and reverse transcription by PC6, a natural product from cones of pine trees

We have previously shown that PC6, a natural product extracted from cones of Pinus parviflora Sieb et Zucc, can inhibit the replication of human immunodeficiency virus type 1 (HIV-1) in CD4+ T cells and in monocyte/macrophage cell lines. Here, we show by immunoprecipitation of HIV-1 proteins with a specific pooled serum that PC6 inhibited the expression of all HIV-1 proteins in CEM cells. PC6 did not affect the posttranslational processing of the HIV-1 proteins. Northern, Southern, and kinetics analyses revealed that PC6 inhibited HIV-1 reverse and forward transcription in CEM cells. Transient transfection of CEM cells with HIV-1 long terminal repeat (LTR) linked CAT DNA also showed that PC6 inhibited LTR-driven gene expression at the transcriptional level.

Functional comparison of transactivation by human retrovirus rev and rex genes

The effect of rev-responsive element deletion on human immunodeficiency virus type 1 (HIV-1) and type 2 (HIV-2) gene expression was examined. The phenotypes of HIV-1 and HIV-2 provirus DNAs lacking the rev-responsive element, as determined by transfection experiments, were indistinguishable from those of virus DNAs carrying rev gene mutations. By using rev-response elements derived from these two viruses, we developed two monitoring systems to evaluate the functionality of HIV-1 rev, HIV-2 rev, and human T-lymphotropic virus type I rex. In both systems, HIV-1 rev and human T-lymphotropic virus type I rex transactivated HIV-2 very efficiently. On the contrary, HIV-2 rev and human T-lymphotropic virus type I rex were poor activators of HIV-1. No functional replacement of rex by HIV-2 rev was observed.

Characterization and expression of novel singly spliced RNA species of human immunodeficiency virus type 1

Human immunodeficiency virus type 1 (HIV-1) expresses the Vif, Vpr, Vpu, and Env proteins through complex differential splicing of a single full-length RNA precursor. We used HIV-1-specific oligonucleotide primer pairs in a quantitative polymerase chain reaction procedure on RNA from fresh peripheral blood lymphocytes infected with HIV-1JR-CSF to detect and characterize the singly spliced RNA species which might encode these proteins. The nucleotide sequences at the junctions of splice donor and acceptor sites of these RNAs were determined. One of these RNAs, which has not been previously described, appears to be a novel HIV-1 RNA encoding Env and/or Vpu proteins.

Comparative studies on tat mutants of three primate lentiviruses

A frame-shift tat gene mutant of human immunodeficiency virus type 1 (HIV-1), which showed no detectable trans-activation potential, was constructed in vitro. Upon transfection, this clone directed the synthesis of virus mRNAs, gag proteins and virion-associated reverse transcriptase (RT) at a low level as was observed with the tat mutants of HIV-2 and simian immunodeficiency virus isolated from African green monkey (SIVAGM). Using these mutant viruses, trans-activation efficiency of viral gene expression by tat was compared among HIV-1, HIV-2, and SIVAGM. SIVAGM seemed to be less dependent on tat for RT production than HIV-1 and HIV-2.

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.

Pattern of transcription of the genome of equine infectious anemia virus

The pattern of expression of the equine infectious anemia virus (EIAV) genome in a persistently infected canine cell line was determined. Five EIAV-specific transcripts (8.2, 5.0, 4.0, 2, and 1.8 kilobases [kb]) were detected by using subgenomic restriction enzyme fragments of EIAV DNA and EIAV-specific oligonucleotides as probes. The 8.2-kb mRNA could be shown to represent viral genomic RNA, whereas the smaller transcripts were generated by splicing events. Evidence was obtained that indicated that each subgenomic RNA species shared a common 5'-splice donor. The 5.0-kb mRNA was found to be expressed at relatively low levels, was difficult to detect consistently, and appeared to be generated by a single splicing event which linked the 5' exon to the 3' region of pol. The 4.0-kb transcript was concluded to be the env mRNA on the basis of its hybridization pattern with the various probes and its abundance. The 2-kb species was found to be multiply spliced and was encoded by sequences derived from orf2 but was not detected by probes representing 3'-env/3'-orf sequences. The 1.8-kb species was shown to consist of sequences representing orf1, part of orf2, and the 3'-orf/env and may represent the message for the EIAV trans-activator gene.

Nucleotide sequence and genome organization of biologically active proviruses of the bovine immunodeficiency-like virus

The complete nucleotide sequences and translations of major open reading frames (ORF) of two distinct, infectious, proviral molecular clones (106 and 127) of the bovine immunodeficiency-like virus (BIV), obtained from a single virus isolation, were determined and compared. The genomes of BIV 127 and 106 are 8482 and 8391 nucleotides (nt), respectively, in the form predicted for the viral RNA. The structural organization of the genomes of BIV 127 and 106 are identical to one another and most similar to that of the lentivirus subfamily of retroviruses. In addition to gag, pol, and env genes, the BIV genome contains five short ORFs between and overlapping pol and env in the "central region," a hallmark of the lentiviruses which is believed to play an important role in their pathogenesis. Three of the short ORFs in the central region of BIV have been identified by location and structural similarity to the nonstructural/regulatory genes (vif, tat, and rev) of other lentiviruses; we also discovered two unique ORFs, termed W and Y, which may serve as exons for novel genes. BIV does not have the nef gene found in primate lentivirus genomes. The proviral LTR of BIV 127 is 589 nt, contains regulatory signals for initiation, enhancement, and termination of viral transcription, and has sequences related to the Sp1 and NF-kappa B binding sites. A major deletion (87 nt) in the env gene and 2 minor deletions (2 nt each) in the R regions of the LTRs account for the smaller size of clone 106. Numerous point mutations were also present; some caused coding substitutions that were most prevalent in the env encoding ORF. These data suggest that, within a single virus isolate, BIV displays extensive genomic variation. These infectious clones of BIV represent well-defined tools with which to analyze the function of the various ORFs and to dissect the molecular mechanisms of replication and pathogenesis.

Epitope mapping of the HIV-1 gag region by analysis of gag gene deletion fragments expressed in Escherichia coli defines eight antigenic determinants

Immune response to HIV infection is generally characterized by appearance of antibodies to the gag protein p24 early in infection, and by apparent loss of p24 antibodies accompanied by increases in p24 antigen levels with disease progression. Precise definition of the immunodominant epitopes present in gag gene proteins has potential clinical significance. Seventeen anti-gag monoclonal antibodies (MAb) were used in enzyme-linked immunosorbent assays (ELISA) with antigens expressed by nine recombinant clones to define epitopes on HIV gag proteins which elicit an immune response. All of the MAbs tested, except two anti-p17, reacted with a clone which expresses the carboxyl terminal 13 amino acids of p17 and all of p24 and p15. All anti-p24 MAbs reacted with clones containing all of p24. MAbs reacted differentially with clones containing deleted regions depending on the antigenic portion expressed. Of thirteen potential identifiably different genomic regions which could be predicted from the genomic structure of the clones, eight different antigen epitopes were defined: two on p17, five on p24, and one on p15 (in the region corresponding to the carboxyl terminal protein p6). Six regions did not appear to react with any of the monoclonal antibodies available. Identification of the epitopes present in the cloned antigens should allow their use to evaluate sera from HIV-infected donors at different clinical stages of progression to AIDS.

Mutational analysis of the human immunodeficiency virus type 2 (HIV-2) genome in relation to HIV-1 and simian immunodeficiency virus SIV (AGM)

We constructed an infectious molecular clone of the human immunodeficiency virus type 2 (HIV-2) and generated nine frameshift mutants corresponding to nine open reading frames identified so far. Three structural (gag, pol, env) and two regulative (tat, rev) gene mutants were not infectious, whereas vif, vpx, vpr, and nef genes were dispensable for infectivity. All of the mutants except env and rev were cytopathic in CD4+ human leukemia cells. In transfection assays, the expression of HIV-2 long terminal repeat was activated by infectious clones of HIV-1, HIV-2, and simian immunodeficiency virus from African green monkey but not by the tat mutants. However, an HIV-2 tat mutant could produce small amounts of virus proteins and particles in contrast to a rev mutant, which directed no detectable synthesis of virus proteins and virions.

Various regulatory sequences are deprived of their uniqueness by the universal rule of TA/CG deficiency and TG/CT excess

The universal rule of TA/CG deficiency-TG/CT excess endures the extremely high mutation rate of a retrovirus (human immunodeficiency virus type 1) as well as methylation of CAG rather than CG in a plant (maize). Among the consistently abundant nucleotide oligomers, there are two complementary pairs of palindromic nucleotide pentamers containing TG and CA. Out of the CAGTG and CACTG pair emerged the heptameric pair for the long-distance recombination of immunoglobulin genes, CACAGTG and CACTGTG. Reflecting their origin, these heptamers are found everywhere in all DNA, and a substantial fraction of them are accompanied by nonameric components properly spaced from them. It appears that, were the recombination event not confined to B cells, results of illegitimate recombinations might be disastrous. The other pentameric pair is TGCAT and ATGCA. Out of this pair emerged the complementary pair of transcription enhancer decamers: TNATTTGCAT for immunoglobulin light chains and ATGCAAATNA for immunoglobulin heavy chains. Again reflecting their origin, these decamers are found everywhere in all DNA and some genes--for example, in the 3' flanking region of immunoglobulin heavy chain constant region--are accompanied by a downstream "TATA box." It seems that even with regard to the productively recombined immunoglobulin genes, misinitiation of enhanced transcription is a real possibility.

Proviral DNA integration and transcriptional patterns of equine infectious anemia virus during persistent and cytopathic infections

The structure and integration patterns of equine infectious anemia virus (EIAV) proviral DNA and the patterns of viral transcription were examined in persistent and cytopathic infections of cultured cells. The results of Southern blot analyses indicated that, in persistently infected cells, about 30% of the EIAV provirus exists as randomly integrated DNA, while the remaining 70% is equally divided between unintegrated linear and closed circular forms. The cytopathic infection, in contrast, is characterized by levels of integrated provirus ranging from 65 to more than 90% of the total proviral DNA, depending on the extent of cytopathology exhibited by the virus strain employed. In both persistent and cytopathic infections, extensive Northern (RNA) blot analyses have revealed the presence of two major virus-specific transcripts, an 8.2-kilobase (kb) full-length genomic mRNA and a 3.5-kb single-spliced mRNA. A low-abundance 1.5-kb mRNA, presumably formed by a double-splicing event of the full-length RNA, was also detected in the cytopathic EIAV infection. The two major viral transcripts are present in approximately equal quantities in persistently infected cells, while the cytopathic infection reveals nearly a 30-fold higher level of viral transcripts in which the 3.5-kb species constitutes over 75% of the total viral mRNA. The relatively high proportion of proviral DNA integration and the simple pattern of viral transcription observed during EIAV infections appeared to be different from the generally observed patterns of predominantly unintegrated proviral DNA and multi-spliced viral mRNAs in cells infected with other lentiviruses such as visna virus or human immunodeficiency virus type 1. Moreover, the data suggested that the cytopathology of EIAV may be correlated in part with the degree of proviral DNA integration and levels of viral mRNA in infected cells, particularly that of the spliced 3.5-kb mRNA.

Construction and characterization of an infectious DNA clone and of mutants of simian immunodeficiency virus isolated from the African green monkey

We constructed a full-length molecular clone of simian immunodeficiency virus from an African green monkey. Upon transfection, this clone directed the production of virus particles cytopathic and infectious to human CD4+ leukemia cell lines. Mutations were introduced by recombinant DNA techniques into eight open reading frames of simian immunodeficiency virus from the African green monkey thus far identified. The phenotypes of mutant viruses, i.e., infectivity, cytopathogenicity, transactivation of gene expression controlled by a long terminal repeat, and viral RNA and protein syntheses, were examined by transfection and infection experiments. Three structural (gag, pol, and env) and two regulatory (tat and rev) gene mutants were not infectious, whereas vif, vpx, and nef were dispensable for infectivity and mutant viruses were highly cytopathic. In transient transfection assays, a rev mutant produced mainly small mRNA species and no detectable virus protein and particles. The transactivation potential of a tat mutant was about 10-fold less than that of wild-type DNA, generating small amounts of virus.

Characterization of a cDNA clone encoding the visna virus transactivating protein

The unique pathogenesis of lentiviral infections in humans and ruminant animals may be explained, in part, by the complex mechanisms regulating transcription and translation of their viral genes. This report demonstrates that a visna virus-encoded protein transactivates viral gene expression. A 1.4-kilobase cDNA clone encodes two distinct proteins with apparent molecular masses of 21.5 and 10 kDa. We demonstrate that the 10-kDa species is the visna virus transactivating (Tat) protein; the other species may be analogous to the rev (formerly art or trs) gene product of human immunodeficiency virus.

Infection of rabbit T-cell and macrophage lines with human immunodeficiency virus

We report the successful infection of two rabbit T-cell lines and one rabbit macrophage line with human immunodeficiency virus 1 (HIV-1). One T-cell line was a herpesvirus ateles transformant, the other T-cell line was a human T-cell leukemia virus I transformant, and the macrophage line was a simian virus 40 transformant. After infection with a high-titered HIV-1 stock, the rabbit cultures exhibited properties that closely mimic those of HIV-1-infected human cells. Productive infection was evident in cultures 7-14 days after infection, as shown by an increase in reverse transcriptase activity, a concomitant increase in positive cells detected by indirect immunofluorescence using serum from a patient with acquired immunodeficiency syndrome, and a decrease in cell viability. RNA gel blot hybridization and protein immunoblot analyses of infected cells indicated that all predicted viral transcripts and proteins were synthesized during the course of the infection. Proof that cell-free culture supernatants of the infected rabbit cell lines contained infectious virus was given by successful passage onto a susceptible human T-cell line. The ability of HIV-1 to infect transformed rabbit cell lines in vitro suggests that, with appropriate manipulation, the rabbit may provide a model for infection with HIV-1.

Molecular pathogenesis of human immunodeficiency virus infection

Molecular studies of the pathogenesis of human immunodeficiency virus (HIV) infections have proceeded rapidly following the molecular cloning and nucleotide sequence analysis of the HIV genome. Correlation of biochemical and functional studies of HIV-infected cells with the HIV nucleotide sequence has allowed the identification and preliminary functional characterization of many HIV proteins. These include structural proteins (gag), viral enzymes (pol), and viral regulatory proteins (tat, art). Cloned HIV DNA segments have been utilized as probes for in situ nucleic acid hybridization to study the distribution of HIV-infected cells in acquired immunodeficiency syndrome (AIDS) and AIDS-related complex (ARC) patients. These studies have demonstrated the infection of macrophages as an important component of HIV-induced neurologic disease. Only very low numbers of HIV-infected lymphocytes can be identified in the peripheral blood of infected individuals. Thus, the mechanism of CD4 cell depletion in the pathogenesis of AIDS remain obscure.

Intragenic cis-acting art gene-responsive sequences of the human immunodeficiency virus

The art gene product of the human immunodeficiency virus is required for the expression of virion capsid and envelope gene proteins. The experiments presented here show that sequences located within the coding region of the envelope gene exert a negative effect on the expression of heterologous genes and that the negative effect of these sequences can be relieved by the art gene product. This region in the env gene contains negative regulatory sequences that inhibit gene expression, as well as a sequence necessary for the art gene product-dependent relief of repression. The experiments define the cis- and trans-acting components of a regulatory system that permits differential expression of human immunodeficiency virus virion structural and regulatory proteins.

Human immunodeficiency virus may encode a novel protein on the genomic DNA plus strand

The genome of the human immunodeficiency virus (HIV) is known to contain eight open reading frames (ORFs) on the minus strand of the double-stranded DNA replicative intermediate. Data presented here indicate that the DNA plus strand of HIV contains a previously unidentified ORF in a region complementary to the envelope gene sequence. This ORF could encode a protein of approximately 190 amino acid residues with a relative molecular mass of 20 kilodaltons if translation began from the first initiation codon. The predicted protein is highly hydrophobic and thus could be membrane associated. It is possible, therefore, that the HIV genome encodes a protein on antisense messenger RNA.

Reactivity of an HIV gag gene polypeptide expressed in E. coli with sera from AIDS patients and monoclonal antibodies to gag

A segment of the gag gene of the human immunodeficiency virus (HIV) (HTLV-IIIB strain), the virus which causes acquired immunodeficiency syndrome (AIDS), has been cloned into the bacterial expression vector, pCQV2, and mapped to the right-hand portion of the gag gene containing the carboxyl-terminal portion of p24 and the amino-terminal portion of p15. Nucleic-acid sequencing of the insert-vector junctions further defined the 5'-terminal nucleotide of HIV sequence as nucleotide 997 and the 3'-terminal nucleotide as 1696. When used in an enzyme-linked immunosorbent assay (ELISA) with sera from HIV-infected patients, the cloned antigen reacted with a subset of sera which were positive on a standard ELISA using whole virus as antigen. Western-blot screening of these sera with whole virus indicated that all p24-positive sera were positive with the clone, suggesting that the carboxyl-terminal portion of p24 contains a highly antigenic epitope(s). A serum which was p24-negative p15-positive by Western blot analysis was also highly reactive, indicating that a p15 epitope is present in the cloned antigen. Epitope mapping with a series of monoclonal antibodies to gag resulted in positive ELISA with 2 of 3 anti-p24, 0 of 1 anti-p15, and 0 of 1 anti-p17 Western-blot-positive monoclonal antibodies, suggesting that one of the anti-p24 monoclonal antibodies reacts with epitopes amino-terminal to those coded from nucleotide 997, two anti-p24 monoclonals react with epitopes carboxyl-terminal to those coded from nucleotide 997, and the anti-p15 monoclonal reacts with epitopes carboxyl-terminal to those coded from nucleotide 1696.

Transcription of visna virus during its lytic cycle: evidence for a sequential early and late gene expression

Visna lentivirus persists in sheep under a restricted form. Following induction events not yet defined at the molecular level, visna virus is activated to replicate productively through a short lytic cycle, the usual expression of visna virus in tissue culture. In an attempt to understand the relationship between latency and lytic replication, we characterized the transcripts of visna virus during its lytic growth by Northern blotting and S1 mapping analyses. The viral transcription pattern is relatively complex with a sequential expression in two steps: (i) an early (24 hr postinfection) expression of two multispliced mRNAs of 1.6 and 1.2 kb, which contain sequences from the 5' end of the genome, sequences from the central part of the genome from the 3' end of pol to the 5' end of env, and 3'-terminal sequences, and (ii) a late (72 hr postinfection) expression of both small mRNAs plus that of four large mRNAs of 9.4, 4.8, 4.3, and 3.7 kb. Except for the 9.4-kb RNA which is the genomic transcript, the three other large transcripts arise by a single splicing event joining 5'-terminal sequences to sequences located at positions 3' to the pol gene. This two-step expression of early and late genes of visna virus represents a novel important feature of the replicative cycle of lentiviruses.

Visna virus exhibits a complex transcriptional pattern: one aspect of gene expression shared with the acquired immunodeficiency syndrome retrovirus

A complex pattern of gene expression was found for visna virus in a highly permissive cell culture system in vitro. In addition to the genomic RNA (9.4 kilobases [kb]), five other mRNAs were detected. The three large RNA transcripts (5.0 kb and a doublet at 4.3 kb) arise by a single splicing event joining 5' sequences to sequences located at positions 3' to the pol gene. The two smallest transcripts (1.8 and 1.5 kb) are at least doubly spliced mRNAs which contain sequences derived from the 5' end of the genome, the region between the pol and env genes, and 3' terminal sequences. In addition to this complex pattern of transcription, the mRNAs appear to be regulated temporally. The 1.5-kb mRNA appears 6 h later than the other transcripts. The significance of this complex pattern of gene expression in the unique aspects of the lentivirus life cycle and pathogenesis is considered.

Genome organization and transactivation of the human immunodeficiency virus type 2

Analysis of the nucleotide sequence of the human retrovirus associated with AIDS in West Africa, HIV-2, shows that it is evolutionarily distant from the previously characterized HIV-1. We suggest that these viruses existed long before the current AIDS epidemics. Their biological properties are conserved in spite of limited sequence homology; this may help the determination of the structure-function relationships of the different viral elements.

Productive, persistent infection of human colorectal cell lines with human immunodeficiency virus

Thirteen adherent human non-lymphocyte cell lines were tested for their susceptibility to infection by human immunodeficiency virus. Productive infection could be demonstrated in three of five colorectal carcinoma cell lines examined; the other eight human non-lymphocyte cell lines were uninfectible. A susceptible colon carcinoma cell line (HT29), as well as normal colonic mucosa, was shown to contain a 3.0-kilobase species of poly(A)+ CD4 RNA, whereas uninfectible colon carcinoma and rhabdomyosarcoma cell lines synthesized no detectable T4 RNA. A persistently infected colon carcinoma cell line was established that continued to produce progeny human immunodeficiency virus for more than 10 weeks postinfection.

Alterations in T4 (CD4) protein and mRNA synthesis in cells infected with HIV

Cells infected with the human immunodeficiency virus (HIV) show decreased expression of the 58-kilodalton T4 (CD4) antigen on their surface. In this study, the effect of HIV infection on the synthesis of T4 messenger RNA (mRNA) and protein products was evaluated in T-cell lines. Metabolically labeled lysates from the T4+ cell line Sup-T1 were immunoprecipitated with monoclonal antibodies to T4. Compared with uninfected cells, HIV-infected Sup-T1 cells showed decreased amounts of T4 that coprecipitated with both the 120-kilodalton viral envelope and the 150-kilodalton envelope precursor molecules. In four of five HIV-producing T-cell lines studied, the steady-state levels of T4 mRNA were also reduced. Thus, the decreased T4 antigen on HIV-infected cells is due to at least three factors: reduced steady-state levels of T4-specific mRNA, reduced amounts of immunoprecipitable T4 antigen, and the complexing of available T4 antigen with viral envelope gene products. The data suggested that the T4 protein produced after infection may be complexed with viral envelope gene products within infected cells. Retroviral envelope-receptor complexes may thus participate in a general mechanism by which receptors for retroviruses are down-modulated and alterations in cellular function develop after infection.

Structural characterization of reverse transcriptase and endonuclease polypeptides of the acquired immunodeficiency syndrome retrovirus

Automated N-terminal microsequencing of immune affinity-purified acquired immunodeficiency syndrome retrovirus polypeptides from infected cells was used to locate the N termini of 64-, 51-, and 34-kilodalton (kDa) polypeptides within the pol open reading frame (ORF) of the proviral DNA. The 64- and 51-kDa proteins had identical N termini (Pro-Ile-Ser-Pro-IIe-Glu-Thr-Val-) positioned 156 residues from the beginning of the pol ORF. The N terminus of the 34-kDa pol gene product, Phe-Leu-Asp-Gly-Ile-Asp-Lys-, mapped 716 residues into the pol ORF. These polypeptides were absent in an RT-negative, CD4-negative, persistently infected cell line (8E5) carrying a single defective copy of a constitutively expressed, integrated proviral DNA.

HTLV-III expression and production involve complex regulation at the levels of splicing and translation of viral RNA

The African green monkey nonlymphoid cell line cos-1 produces infectious HTLV-III virus following transfection with biologically active molecular clones of HTLV-III. Transfected cos-1 cells produce large amounts of viral RNA and protein. We have used this rapid transfection system to study the regulatory functions and synthetic capacity of the HTLV-III genome, as well as mutants derived from it. Analysis of transfected lymphoid and nonlymphoid cell lines suggests that tat-III-mediated trans-activation of viral gene expression is operative predominantly, if not exclusively, at a posttranscriptional level. We have also identified an additional HTLV-III-encoded gene that controls viral gene expression through regulation of the relative proportions of the various viral RNA transcripts and is required for viral replication.

Biological and biochemical characterization of a cloned Leu-3- cell surviving infection with the acquired immune deficiency syndrome retrovirus

Leu-3- cells that survive infection with the acquired immune deficiency syndrome (AIDS) retrovirus can be induced with IUdR to express infectious virus. A cellular clone (8E5), isolated by limiting dilution of a mass culture of survivor cells, was found to contain a single, integrated provirus that was constitutively expressed. Although IUdR treatment of 8E5 cells failed to induce infectious virus, cocultivation with Leu-3+ cells generated the characteristic syncytia associated with acute AIDS retrovirus infection. The single integrated copy of proviral DNA directs the synthesis of all major viral structural proteins except p64, as monitored by immunoblotting. The relationship of the 8E5 clone to viral latency and persistence is discussed.