Simian foamy virus type 1 is a retrovirus which encodes a transcriptional transactivator

AZT-resistant foamy virus

Azidothymidine (AZT) is a reverse transcriptase (RT) inhibitor that efficiently blocks the replication of spumaretroviruses or foamy viruses (FVs). To more precisely elucidate the mechanism of action of the FV RT enzyme, we generated an AZT-resistant FV in cell culture. Biologically resistant virus was obtained for simian foamy virus from macaque (SFVmac), which was insensitive to AZT concentrations of 1 mM, but not for FVs derived from chimpanzees. Nucleotide sequencing revealed four non-silent mutations in the pol gene. Introduction of these mutations into an infectious molecular clone identified all changes to be required for the fully AZT-resistant phenotype of SFVmac. The alteration of individual sites showed that AZT resistance in SFVmac was likely acquired by consecutive acquisition of pol mutations in a defined order, because some alterations on their own did not result in an efficiently replicating virus, neither in the presence nor in the absence of AZT. The introduction of the mutations into the RT of the closely related prototypic FV (PFV) did not yield an AZT-resistant virus, instead they significantly impaired the viral fitness.

Primate-to-human retroviral transmission in Asia

We describe the first reported transmission to a human of simian foamy virus (SFV) from a free-ranging population of nonhuman primates in Asia. The transmission of an exogenous retrovirus, SFV, from macaques (Macaca fascicularis) to a human at a monkey temple in Bali, Indonesia, was investigated with molecular and serologic techniques. Antibodies to SFV were detected by Western blotting of serum from 1 of 82 humans tested. SFV DNA was detected by nested polymerase chain reaction (PCR) from the blood of the same person. Cloning and sequencing of PCR products confirmed the virus's close phylogenetic relationship to SFV isolated from macaques at the same temple. This study raises concerns that persons who work at or live around monkey temples are at risk for infection with SFV.

Feline foamy virus genome and replication strategy

Crucial aspects of the foamy virus (FV) replication strategy have so far only been investigated for the prototypic FV (PFV) isolate, which is supposed to be derived from nonhuman primates. To study whether the unusual features of this replication pathway also apply to more-distantly related FVs, we constructed feline FV (FFV) infectious molecular clones and vectors. It is shown by quantitative RNA and DNA PCR analysis that FFV virions contain more RNA than DNA. Full-length linear DNA was found in extracellular FFV by Southern blot analysis. Similar to PFV, azidothymidine inhibition experiments and the transfection of nucleic acids extracted from extracellular FFV indicated that DNA is the functional relevant FFV genome. Unlike PFV, no evidence was found indicating that FFV recycles its DNA into the nucleus.

Foamy virus transactivation and gene expression

An overview of the pattern and mechanisms of spuma or foamy virus (FV) gene expression is presented. FVs are complex retroviruses with respect to their genetic outfit and the elements used to control and regulate expression of the viral genome. The increased insight into transcriptional and posttranscriptional mechanisms has revealed that the FVs are distinct, unconventional retroviruses clearly apart from the orthoretroviruses. Although less characterized than the orthoretroviruses, FVs have several unique features that are important for construction and assembly of FV-based vectors for targeted gene delivery and vaccination purposes. Some of these distinguishing features are directly related to the FV-specific mechanisms of gene expression and include (1) the presence of an internal, functional active second transcription unit for expression of the nonstructural genes, (2) the utilization of a subgenomic, spliced transcript for Pol protein expression, and (3) distinct but not yet understood mechanisms for the nuclear exit of defined transcripts and thus an additional level of posttranscriptional control of gene expression. Finally, the interactions of the viral transactivator not only with both viral promoters but also with regulatory elements controlling the expression of defined cellular genes are an important issue with respect to vector development and the apparent apathogenicity of FVs in their natural hosts.

Low-level expression of functional foamy virus receptor on hematopoietic progenitor cells

Foamy viruses have several qualities favorable for vector development: they are not known to cause disease; they can transduce stationary cells; and the foamy virus receptor is expressed on a wide variety of cells. Here, we analyzed the level of virus receptor expression on hematopoietic progenitor cells. Foamy virus binding was measured by a flow cytometric assay and was found to be considerably reduced in hematopoietic progenitors cell lines as well as in primary CD34(+) cells when compared to fibroblasts. Retroviral vectors based on murine leukemia virus (MLV) pseudotyped with a foamy virus envelope transduced hematopoietic cell lines with a more than 10-fold lower efficiency than fibroblasts. Moreover, less than 1% of primary CD34(+) hematopoietic progenitor cells were transduced with the foamy virus pseudotypes, while gene transfer efficiencies of 8-40% were achieved using pseudotypes with amphotropic envelope or the G protein of vesicular stomatitis virus. In conclusion, the expression of functional foamy virus receptors on hematopoietic progenitors cells was found to be insufficient to achieve high levels of gene transfer into CD34(+) hematopoietic progenitor cells with cell-free vector supernatants using current transduction protocols.

The bet gene of feline foamy virus is required for virus replication

Foamy viruses (FV) are complex retroviruses with additional bel genes located between env and the 3' long-terminal repeat. The functions of the bel 2 and bet genes are unknown and both are dispensable for replication of the prototypic human foamy virus in cell cultures. We examined the function(s) of bel 2 and bet of the distantly related feline foamy virus (FFV) in the proviral context. Mutagenesis was used to alter the Bel 2 and Bet or to abrogate their expression. The Bel 2/Bet mutants showed a 1000-fold reduced viral titer in feline kidney cells; in human 293T cells, viral titer was only about 10-fold reduced compared to wild-type FFV. In both cell types, the Bel 2/Bet mutations resulted in a reduced release of FFV particles. The results indicate that FFV Bet is required for efficient virus replication. The functions of the Bel 2 and Bet proteins are discussed.

Expression and molecular characterization of an enzymatically active recombinant human spumaretrovirus protease

The human foamy virus (HFV) protease (PR) was cloned into a modified thioredoxin fusion vector that carried a His-tag in the centrally located surface loop of the E. coli trxA protein, bacterially expressed as a soluble fusion protein, and subsequently purified by affinity chromatography. By using HFV Gag protein substrates, the purified recombinant HFV PR was enzymatically active whereas the corresponding active site PR mutant Asp/Ala was inactive. Incubation of synthetic peptides containing residues that flank the putative cleavage site with the recombinant HFV PR and subsequent matrix-assisted laser desorption ionization mass spectrometry of the cleavage products identified the proteolytic processing site of the HFV Gag precursor p74 and revealed that the peptide sequence RAVNTVTQ was cleaved between the Asn and Thr bond.

A sorting motif localizes the foamy virus glycoprotein to the endoplasmic reticulum

We recently identified an endoplasmic reticulum (ER) retrieval signal-the dilysine motif-in the glycoproteins of all five foamy viruses (FVs) for which sequences were available (P. A. Goepfert, G. Wang, and M. J. Mulligan, Cell 82:543-544, 1995). In the present study, expression of recombinant human FV (HFV) glycoprotein and analyses of oligosaccharide modifications and precursor cleavage indicated that the protein was localized to the ER. HFV glycoproteins encoding seven different dilysine motif mutations were then expressed. The results indicated that disruptions of the dilysine motif resulted in higher levels of forward transport of the HFV glycoprotein from the ER through the Golgi apparatus to the plasma membrane. We conclude that the dilysine motif is responsible for ER sorting of the FV glycoprotein. Signal-mediated ER localization has not previously been described for a retroviral glycoprotein.

Characterization of the spliced pol transcript of feline foamy virus: the splice acceptor site of the pol transcript is located in gag of foamy viruses

Foamy viruses, or spumaviruses, are distinct members of the Retroviridae. Here we have characterized the long terminal repeat of the feline, or cat, foamy virus by determining the locations of the transcriptional start site and the poly(A) addition site. The splice donor and splice acceptor sites of the subgenomic mRNA responsible for Pro-Pol protein expression were identified by nucleotide sequencing of the corresponding cDNAs. The leader exon of the feline foamy virus is 57 nucleotides long. The splice acceptor of the subgenomic pol mRNA was found to be located in gag. The location of the splice acceptor of the human foamy virus pol mRNA was confirmed to map in gag. The pol splice acceptor site in gag of the cat foamy virus is located further downstream than that of human foamy virus.

The human foamy virus internal promoter is required for efficient gene expression and infectivity

The human foamy or spumaretrovirus (HFV) is a complex retrovirus that codes for the three retroviral genes gag, pol, and env and the regulatory and accessory bel genes. A particular feature of HFV gene expression was recently described: not only does the HFV provirus contain the classical retroviral long terminal repeat promoter, a second functionally active promoter is present in the env gene upstream of the bel genes (M. Löchelt, W. Muranyi, and R. M. Flügel, 1993, Proc. Natl. Acad. Sci. USA 90, 7317-7321). Both, the HFV long terminal repeat promoter I and internal promoter II depend upon the HFV transcriptional transactivator Bel 1 for efficient gene expression. The internal promoter directs the synthesis of functionally active Bel 1 transactivator and Bet proteins that are expressed early after HFV infection. In this report, it is shown that mutation of the promoter II TATA box resulted in HFV proviral clones with a reduction in infectivity by a factor of approximately 100. Gene expression by promoter II TATA box mutant HFV proviruses was reduced. HFV proviruses with the mutated promoter II TATA box used cryptic start sites of transcription upstream of the original promoter II TATA box, resulting in an inefficient and less accurate transcriptional initiation. The reduced HFV structural gene expression by the mutated HFV proviruses was relieved by providing Bel 1 protein in trans. This demonstrates that HFV promoter II-directed Bel 1 expression is important for producing the high levels of Bel 1 that increases virus replication.

Phylogenesis and genetic complexity of the nonhuman primate retroviridae

The three known groups of nonhuman primate retroviruses (simian immunodeficiency virus, simian T cell lymphotropic/leukemic virus type I, and simian foamy virus) are thought to have equivalent human counterparts. This is clearly the case with human immunodeficiency virus types 1 and 2, the causative agents of acquired immunodeficiency syndrome, and with human T cell lymphotropic/leukemia virus type I (HTLV-I), which causes T cell leukemia and a progressive form of myelopathy (tropical spastic paraparesis/HTLV-I-associated myelopathy), and HTLV-II. However, the presence of spumaviruses (foamy viruses) in humans remains uncertain. Data accumulated in the last 5 years suggest the possibility that the human retroviruses are indeed the result of transmission of simian retroviruses to humans. In this article we attempt to parallel the genetic features of the simian retroviridae with their human counterparts and argue for the possibility of horizontal transmission of these viruses from monkeys to humans.

Structure and function of the long terminal repeat of the chimpanzee foamy virus isolates (SFV-6)

The complete long terminal repeat (LTR) nucleotide sequence of the chimpanzee foamy virus isolate SFV-6 was determined. Its 1761-bp size makes it the longest LTR reported to date among all retroviruses. Since the length of its LTR is similar to that of other simian isolates while its sequence homology is closer to that of HFV, SFV-6 genetic structure appears to be intermediate between simian and human foamy viruses. Transient expression assays demonstrate that SFV-6 encodes a transactivator of viral gene expression directed either by its own LTR or by heterologous promoters like HFV and HIV-1 LTRs. Our data also provide evidence for cross-transactivation between SFV-6 and HFV.

Characterization of the internal promoter of simian foamy viruses

Simian and human foamy viruses (HFV and SFV), genetically related members of the spumavirus genus of retroviruses, have complex genome structures which encode the gag, pol, and env genes for virion proteins as well as additional open reading frames. One of these open reading frames is a viral transactivator, encoded by genes designated taf for SFV and bel-1 for HFV, which augments transcription directed by the long terminal repeat (LTR) through cis-acting targets in the U3 domain of the LTR. Recently, an internal transcriptional promoter has been identified in sequences within the 3' end of the HFV env gene (M. Lochelt, W. Muranyi, and R. M. Flugel, Proc. Natl. Acad. Sci. 90:7317-7321, 1993). We have demonstrated by using transient expression assays in several tissue culture cell lines and by analyzing viral transcripts in infected cells that SFV-1 from a rhesus macaque and SFV-3 from an African green monkey also encode an internal promoter in the env gene. Transcription directed by the internal promoters of SFV-1 and SFV-3 is activated by the taf-1 and taf-3 gene products, respectively, in several cell types. The importance of a TATA box for the SFV-1 internal promoter was established by site-specific mutagenesis, and the 5' ends of transcripts initiating in the internal promoter have been determined. cis-acting sequences in the SFV-1 env gene required for the response to taf-1 are contained within a 121-bp element located 5' to the TATA box in the internal promoter. This taf-1-responsive element in the internal promoter functions in a position- and orientation-independent fashion in a heterologous promoter and thus has the properties of an enhancer which depends on taf-1 activity. Alignments reveal that the SFV-1 internal promoter and the SFV-1 LTR have little sequence relatedness. Cross-transactivation studies show that the transactivators of SFV-1 and HFV function on the internal promoter and LTR of the homologous virus but not on the heterologous virus. In summary, the genomes of simian and human foamy viruses direct viral transcription through both the promoter in the LTR and an internal promoter within the env gene, and each promoter contains unique enhancer-like elements regulated by the viral transactivator.

Identification and characterization of the Bel 3 protein of human foamy virus

The human foamy virus (HFV) is a complex retrovirus that contains several regulatory and auxiliary bel genes besides the gag, pol, and env genes. In contrast to the gene products of bel 1 and bel 2/bet that were identified previously, the Bel 3 protein has not been described to date. Here we report the identification of Bel 3 in HFV-infected cells by immunoprecipitation, indirect immunofluorescence, and expression cloning under the control of a strong heterologous promoter. Bel 3 was immunoprecipitated with an antiserum directed against a bacterially expressed and purified form of recombinant Bel 3 antigen. Bel 3 was found to be expressed in low amounts in the cytoplasm of HFV-infected cells and to migrate with an apparent molecular mass of 19.4 kDa on electrophoresis in SDS-polyacrylamide gels, consistent with the calculated value of 18.2 kDa. Radioimmunoprecipitation of HFV-infected cell lysates with the hyperimmune serum against Bel 3 revealed at least two additional immunoreactive bands of 15.5 and 10.6 kDa. The results indicate that Bel 3 was labile, because it was partially degraded even at early time points after infection. On transfection and expression in transfected COS cells, recombinant Bel 3 was immunoprecipitated and migrated in three polypeptide bands of 18.7, 14.8, and 9.3 kDa under denaturing conditions. In the absence of reducing agents, the bacterially expressed and purified recombinant Bel 3 protein of 16.1 kDa can form homodimers of 30 kDa.

Analysis of the 5' long terminal repeat of bovine syncytial virus

Four molecular clones of the bovine syncytial virus (BSV) were determined to be replication competent by the initiation of cytopathic infections and production of viable virus following transfection of viral DNA into permissive cells. The nucleotide (nt) sequence of the 5' long terminal repeat (LTR) of the infectious clone, BSV-11, was determined and analyzed to identify regions common to retroviral LTRs and elements with the potential for involvement in transcriptional regulation.

Transcriptional mapping of the 3' end of the bovine syncytial virus genome

The bovine syncytial virus, a member of the retroviral subfamily Spumavirinae, causes a persistent, asymptomatic infection in cattle. Nucleotide sequence analysis of the viral genome revealed two overlapping reading frames in the 3' region, traditionally occupied by accessory-function genes in other complex retroviruses. In order to analyze the transcripts from the accessory-gene region, we designed oligonucleotide primers complementary to sequences within the 5' and 3' long terminal repeats (LTRs) for use with the PCR. Southern blot analysis of amplification products revealed eight major cDNA bands. Eleven distinct cDNA clones were subsequently isolated and characterized. The initial splice donor in each clone is located 49 bp downstream from the mRNA cap site in the 5' LTR. The primary splice acceptor site was located 17 bp upstream from the proximal 3' open reading frame known as BF-ORF1. A second major splice acceptor was localized to a region upstream of the second open reading frame, BF-ORF2. Clones were identified which spliced directly to each of these sites. Additional splice donor and acceptor sites within BF-ORF1 and BF-ORF2 and the 3' LTR were variously used to generate a complex array of multiply spliced transcripts. Each of these transcripts remained in frame and coded for a potential protein product.

The human foamy virus internal promoter directs the expression of the functional Bel 1 transactivator and Bet protein early after infection

The human foamy virus or spumaretrovirus (HFV) is a complex retrovirus that has the capacity to code not only for the three retroviral genes gag, pol, and env but, in addition, for at least three bel genes. The HFV provirus contains two different and functionally active promoters: the classical retroviral promoter in the 5' long terminal repeat and a recently identified second promoter in the env gene upstream of the bel genes. Both promoter/enhancers are strongly dependent on the HFV transcriptional transactivator protein Bel 1. Here we report that the internal promoter directs the synthesis of viral transcripts that code for functionally active Bel 1 and for Bet proteins that appeared early after HFV infection. The viral mRNAs of the internal promoter have a 112-nucleotide-long leader exon and were spliced predominantly at the first splice donor site in the 5' untranslated region. The data were obtained by transient expression assays, transactivation experiments, and RNA analyses of transcripts derived from HFV-infected cells. The results provide strong evidence for the crucial role the internal promoter plays during HFV infection in generating bel-specific transcripts.

Functional domains of the simian foamy virus type 1 transcriptional transactivator (Taf)

The genome of simian foamy virus type 1 encodes a transcriptional transactivator (Taf) that dramatically elevates gene expression directed by the viral long terminal repeat. In this report, we describe the functional domains of simian foamy virus type 1 Taf. Several taf mutants and fusion proteins of Taf and the DNA-binding domain of the Saccharomyces cerevisiae transcriptional transactivator GAL4 were used in this study. Taf contains two potent activation domains. One of the activation domains is located at the amino terminus (positions 1 to 48, with position 1 representing the initiator amino acid methionine) and contains several acidic amino acids. The second activation domain was mapped to a region at the carboxy terminus (positions 277 to 300). These two domains activate gene expression directed by the viral long terminal repeat independently of each other. No significant amino acid sequence homology between the activation domains is noted. Thus, Taf belongs in part to the family of acidic transcriptional transactivators. The activation domain at the carboxy terminus is conserved among foamy virus transactivators but is not related to other known transcriptional activators. Therefore, the mechanism of gene activation by the carboxy terminus of Taf may be novel. In addition, a potential binding domain rich in basic amino acids (positions 179 to 222) and a highly conserved sequence among foamy virus transactivators (positions 93 to 109) were found to be critical for Taf activity.

The foamy virus family: molecular biology, epidemiology and neuropathology

The family of foamy viruses designates a group of retroviruses which share a specific morphology and provoke characteristic cytopathic effects in cultured cells. Like HTLV and HIV, foamy viruses are complex viruses encoding a number of ancillary genes in addition to gag, pol and env, including a transcriptional transactivator. Foamy viruses are endemic in various primate species, and human foamy viruses (HFV) have been isolated from patients with various neoplastic and degenerative diseases. Despite a growing body of knowledge on the biology of foamy viruses, it has not yet been possible to identify a disease specifically caused by foamy virus infection. After reviewing the epidemiology and molecular biology of the various animal foamy viruses, this article focuses on the pathogenic properties of HFV in transgenic mouse systems. HFV transgenes exhibit a striking neurotropism and elicit a progressive degenerative disease of the central nervous system and striated muscle. Similarly to patients with HIV-associated encephalopathy, HFV transgenic mice develop accumulations of syncytial giant cells in their brains. The relevance of these findings for human neuropathology is discussed.

Functional dissection of the human spumaretrovirus transactivator identifies distinct classes of dominant-negative mutants

The bel1 gene of human spumaretrovirus (HSRV) codes for a 300-amino-acid nuclear protein, termed Bel1, that can strongly activate transcription from the cognate long terminal repeat (LTR) by at least 200-fold. Bel1 can also activate human immunodeficiency virus type 1 (HIV-1) LTR expression. By using site-directed mutagenesis, we have identified distinct regions of Bel1 essential for HSRV LTR activation. The amino-terminal 55 residues, which comprise a highly acidic region followed by a short basic stretch, were dispensable for activation. The distribution of functionally defective mutants indicates that two distinct regions between residues 56 and 300 cooperate to confer full activator function. The larger, more amino-terminal region between residues 56 and 227 is sufficient to minimally activate the HSRV LTR. It contains a region between residues 88 and 110 that is strongly conserved between the simian and human spumavirus transactivators but otherwise lacks obvious homology to known transcriptional activators except for an Arg-rich nuclear localization sequence (NLS) between residues 211 and 225 that can be functionally substituted for by the NLS of the simian virus 40 large T antigen. The carboxy-terminal 73 residues contain two functionally redundant regions that can independently augment the activity of the more N-terminal minimal activator domain by 30- to 90-fold. Comparative analysis of the effect of Bel1 mutations on HSRV and HIV-1 LTR expression revealed a similar requirement of Bel1 domains for activation of the two LTRs. Bel1 is phosphorylated in vivo, and a nuclear localization-defective mutant lacking residues 211 to 222 was severely defective for phosphorylation, whereas various deletion mutations in residues 228 to 300 resulted in a four- to eightfold reduction in phosphate incorporation. When functionally defective bel1 mutants were examined for a dominant-negative phenotype, only mutants lacking a proline-rich basic region between residues 194 and 200 or the NLS between residues 211 and 222 that were found to occupy predominantly nuclear and cytoplasmic locations, respectively, could suppress wild-type Bel1 function efficiently. In identifying two classes of dominant-negative mutants with distinct subcellular localization phenotypes, the mutational analysis of Bel1 has revealed a feature unusual for known transcriptional activators.

Bovine immunodeficiency-like virus encodes factors which trans activate the long terminal repeat

Lentiviruses are known to encode factors which trans activate expression from the viral long terminal repeat (LTR); the primary trans activator is the tat gene product. One of the putative accessory genes (tat) of the bovine immunodeficiency-like virus (BIV) bears sequence similarity to other lentivirus tat genes. This finding suggests that BIV may encode a trans-activating protein capable of stimulating LTR-directed gene expression. To test this hypothesis in vitro, BIV LTR-chloramphenicol acetyltransferase (CAT) reporter gene plasmids were constructed and transfected into three cell lines established from canine, bovine, or lapine tissues that are susceptible to BIV infection. The level of BIV LTR-directed CAT gene expression was significantly elevated in BIV-infected cells compared with uninfected cells. The relatively high basal-level expression of BIV LTR-CAT in uninfected canine and bovine cell lines suggests that cellular factors play a role in regulating BIV LTR-directed gene expression. Additionally, by using a clonal canine cell line in which the BIV LTR-CAT plasmid is stably expressed, BIV LTR-directed CAT expression is elevated 15- to 80-fold by cocultivation with BIV-infected cells, supporting the notion that BIV encodes a trans activator. The relative specificity of this viral activation was assessed by coculturing the clonal BIV LTR-CAT cell line with bovine leukemia virus- or bovine syncytial virus-infected cells; these bovine retroviruses increased expression from the BIV LTR only two- to threefold. Thus, BIV LTR regulatory elements in infected cells, like those of human immunodeficiency virus type 1 and other lentiviruses, are trans activated, presumably through the action of a Tat-like protein and cellular factors.

Genomic organization and expression of simian foamy virus type 3 (SFV-3)

The complete nucleotide sequence of simian foamy virus type 3 (SFV-3) strain LK-3, isolated from an African green monkey, was determined. In addition to translation frames representing the gag, pol, and env genes, two open reading frames are located in the region between the env gene and the 3' long terminal repeat (LTR). Both SFV-3 and SFV-1 encode two open reading frames between env and the 3' LTR, whereas HFV encodes three open reading frames in this region. Northern blot analysis of cell cultures infected with SFV-3 revealed subgenomic RNAs for these open reading frames. The protease of SFV-3 is encoded by the pol gene in contrast to HFV which encodes the protease in the gag gene. Notably, the pol gene of SFV-3 in the +1 translational frame relative to the gag gene; this observation is in agreement with SFV-1, but differs for HFV and all other retrovirus genomes reported. Thus, gag-pol precursors of the SFVs appear to be expressed by a +1 frameshift. Nucleotide and deduced amino acid alignments of SFV-3, SFV-1, and HFV revealed an unexpected homology pattern; highest homologies are observed in the pol and env genes but low homologies are noted in the gag genes and the additional open reading frames. Analysis of phylogenetic trees confirms the classification of foamy viruses as a subfamily of retroviruses, distinct from the lentiviruses and oncoviruses.

cis-acting regulatory regions in the long terminal repeat of simian foamy virus type 1

Simian foamy virus type 1 (SFV-1), a member of the Spumavirinae subfamily of retroviruses, encodes a transcriptional transactivator (taf) that strongly augments gene expression directed by the viral long terminal repeat (LTR) (A. Mergia, K. E. S. Shaw, E. Pratt-Lowe, P. A. Barry, and P. A. Luciw, J. Virol. 65:2903-2909, 1991). This report describes cis-acting regulatory elements in the LTR that control viral gene expression. A series of LTR mutants and hybrid promoter constructs have been analyzed in transient expression assays for responsiveness to Taf. The targets for transactivation have been mapped to two regions of the U3 domain of the LTR, between positions -1196 and -880 and between positions -403 and -125 (+1 represents the transcription initiation site). No significant nucleotide sequence homology between these two regions is noted; thus, the SFV-1 taf gene acts through at least two distinct sequence elements in the LTR. The target contained between positions -403 and -125 acts independently of orientation, in different cell types and species, and in the context of a heterologous promoter. Thus, the target element between positions -403 and -125 has properties of a transcriptional enhancer. The observation that two distinct elements in the SFV-1 LTR are targets for transcriptional transactivation is novel with respect to observations for other retroviral systems. The R-U5 region of the SFV-1 LTR down-regulates transactivation by severalfold. Computer analysis of the R-U5 region revealed a secondary structure with a free-energy level of -74 kcal (ca. -310,000 J); this structural feature may account for the inhibitory effect on gene expression directed by the LTR. Taf of SFV-1 had no effect on gene expression directed by the LTR of the related human foamy virus, whereas Taf transactivates gene expression directed by the LTRs of the human and simian immunodeficiency viruses. Comparative functional analysis of Taf on homologous and heterologous LTRs may facilitate elucidation of the mechanism of transactivation of foamy viruses.

Transcription factor AP-1 modulates the activity of the human foamy virus long terminal repeat

The human foamy virus (HFV) contains within the U3 region of its long terminal repeat (LTR) three perfect consensus sequences for the binding of the inducible transcription factor AP-1. Results of DNase I footprint protection and gel retardation assays demonstrated that proteins in extracts of HeLa and BHK-21 cells as well as bacterially expressed Jun and Fos proteins bind to these AP-1 sites. By conducting transient expression assays using chloramphenicol acetyltransferase plasmids carrying LTR sequences with point-mutated AP-1 sites, it was found that the three AP-1 sites contribute to the optimal activity of the HFV promoter. It is shown that induction of the HFV LTR by 12-O-tetradecanoylphorbol-13-acetate (TPA) and serum factors is mediated through the AP-1 sites.

Construction of an infectious DNA clone of the full-length human spumaretrovirus genome and mutagenesis of the bel 1 gene

An infectious and full-length molecular clone of genomic human spumaretrovirus (HSRV) DNA was constructed. The infectivity of the pHSRV13 clone was demonstrated after transfection into susceptible cells by passage of HSRV-specific cytopathic effects as a cell-free culture supernatant, by electron microscopy of HSRV particles in pHSRV13 DNA-transfected cells, by detection of HSRV transcripts, and by identification of HSRV-encoded proteins with Env- and Bel-specific antisera in indirect immunofluorescence assays and in protein blotting. The predominant HSRV protein detected in immunoblots by both Bel 1- and Bel 2-specific antisera had an apparent molecular weight of 56 kDa and corresponds to Bet. The amino-terminus of Bet is encoded by part of a Bel 1-specific RNA and the larger Bet domain by an RNA species from the bel 2 gene (Muranyi, W., and Flügel, R. M. J. Virology 65, 727-735, 1991). HSRV-specific proteins of 36 and 43 kDa reacted with Bel 1 and Bel 2 antisera, consistent with the values calculated for the bel 1 and bel 2 gene products, respectively. Deletion mutagenesis of the transcriptional HSRV-specific trans-activator bel 1 and the bet genes completely abolished the infectivity of the pHSRV13 clone. The defect in RNA, protein, and virion synthesis was trans-complemented by cotransfection of an expression clone harboring the complete bel coding region. This result demonstrates that the bel 1 gene is required for viral replication. It remains to be determined whether other HSRV gene products, like bet that share a common region with bel 1, contributed to the defect observed.

Distinct cis-acting regions in U3 regulate trans-activation of the human spumaretrovirus long terminal repeat by the viral bel1 gene product

The human spumaretrovirus (HSRV) genome contains, in addition to coding information for the structural proteins, open reading frames (ORFs) for at least three additional genes termed bel1, bel2 and bel3. We report here the localization of the transcriptional activator of HSRV to the bel1 ORF. In reporter-based transient expression assays in COS cells utilizing the bacterial CAT gene linked to HSRV LTR sequences between -710 and +309 with respect to the transcriptional initiation site, co-expression of the bel1 gene product alone caused an over 100 to 300-fold increase in the level of LTR activity. High-level trans-activation by bel1 was specific for the HSRV LTR, as relatively minor positive and negative regulatory effects were observed on HIV-1 LTR and RSV LTR expression, respectively, whereas HTLV-1 LTR activity remained unaffected. Distinct regions of the HSRV LTR were found to be involved in bel1-induced trans-activation. Specifically, deletions between -500 and -389 and between -136 and -62 in the U3 region resulted in a 4- and 30 to 35-fold decline, respectively, in the response to bel1. Limited mutagenesis of the bel1 ORF indicated that most of the bel1 coding region, except for the carboxy-terminal 27 residues, is essential for the activation function.

Identification of the simian foamy virus transcriptional transactivator gene (taf)

Simian foamy virus type 1 (SFV-1), a member of spumavirus subfamily of retroviruses, encodes a transcriptional transactivator that functions to strongly augment gene expression directed by the viral long terminal repeat (LTR). The objective of this study was to identify the viral gene responsible for transactivation. Nucleotide sequences between the env gene and the LTR of SFV-1 were determined. The predicted amino acid sequence revealed two large open reading frames (ORFs), designated ORF-1 (311 amino acids) and ORF-2 (422 amino acids). In the corresponding region of the human foamy virus, three ORFs (bel-1, bel-2, and bel-3) have been identified (R. M. Flugel, A. Rethwilm, B. Maurer, and G. Darai, EMBO J. 6:2077-2084, 1987). Pairwise comparisons of the ORF-1 and ORF-2 with bel-1 and bel-2 show small clusters of homology; less than 39% overall homology of conserved amino acids is observed. A counterpart for human foamy virus bel-3 is not present in the SFV-1 sequence. Three species of viral RNA have been identified in cells infected with SFV-1; an 11.5-kb RNA representing full-length transcripts, a 6.5-kb RNA representing the env message, and a 2.8-kb RNA from the ORF region. Analysis of a cDNA clone encoding the ORF region of SFV-1 reveals that the 2.8-kb message is generated by complex splicing events involving the 3' end of the env gene. In transient expression assays in cell lines representing several species. ORF-1 was shown to be necessary and sufficient for transactivating viral gene expression directed by the SFV-1 LTR. The target for transactivation is located in the U3 domain of the LTR, upstream from position - 125 (+ 1 represents the transcription initiation site). We propose that OFF-1 of SFV-1 be designated the transcriptional transactivator of foamy virus (taf).

Sequence analysis of the simian foamy virus type 1 genome

We have cloned the simian foamy virus type 1 genome (SFV1) and determined its nucleotide sequence. Analysis of this genome reveals, in addition to the usual genes encoding retroviral capsid, reverse transcriptase, and envelope protein (respectively, gag, pol, and env), two open reading frames (ORFs) between env and the long terminal repeat with partial homology to the human foamy virus (HFV) bel1 and bel2 genes. The first ORF could code for a polypeptide of 312 amino acids (aa) showing 40% homology with the HFV bel1 putative gene product. A more detailed analysis showed that the protein encoded by this ORF would have features characteristic of known trans-activating proteins. The second ORF could code for a polypeptide of 403 aa showing 38% homology with the putative HFV bel2 gene product. Moreover, the 5' extremity of the RNA genome can be folded into a secondary structure identical to the Tat-response element of human immunodeficiency viruses. A phylogenetic tree of retroviruses, including SFV1 and HFV, was constructed. It showed at the molecular level that Spumavirinae, previously classified on the basis of their morphology and their biological properties, constitute a separate group. The homology between SFV1 and HFV reaches 89% in the reverse transcriptase domain of the pol gene. but is much smaller in other parts of the genome.

Characterization of the transcriptional trans activator of human foamy retrovirus

The human foamy viruses, or spumaviruses, a distinct subfamily of complex human retroviruses, remain poorly understood both in terms of their pathogenic potential and in terms of the regulatory mechanisms that govern their replication. Here, we demonstrate that the human spumaretrovirus shares with other complex human retroviruses the property of encoding a transcriptional trans activator of the homologous viral long terminal repeat. This regulatory protein is encoded by the viral Bel-1 open reading frame and is localized to the nucleus of expressing cells. The Bel-1 trans activator is shown to function effectively in cell lines derived from human, simian, murine, and avian sources. The viral target sequence for Bel-1 has been mapped 5' to the start of viral transcription and is therefore likely to be recognized as a DNA sequence. Our results further suggest that the mechanism of action of the Bel-1 protein may be distinct from those reported for the transcriptional trans activators encoded by members of the other human retroviral subfamilies.

Cellular factors regulate transactivation of human immunodeficiency virus type 1

It is hypothesized that the immediate-early (IE) gene products of human cytomegalovirus (CMV) and the transactivator (TAT) of human immunodeficiency virus type 1 (HIV-1) regulate HIV-1 gene expression through mechanisms involving host cell factors. By using transient transfection assays with the gene for chloramphenicol acetyltransferase (CAT) under the transcriptional control of the HIV-1 long terminal repeat (LTR), we examined transactivation of the LTR by plasmids that express either the HIV-1 gene for TAT or human CMV IE. The ratio of the level of transactivation by CMV IE to the level of transactivation by TAT varied up to 1,000-fold between cell types. The difference in the activities of these transactivators in various cell types was not a consequence of differential expression of the transactivator gene. Analysis of RNA species initiated in the HIV-1 LTR supports the conclusion that cellular factors regulate the level of elongation of the transcription complex on the LTR. Furthermore, evidence that in some cell types the predominant mechanism of transactivation by HIV-1 TAT involves posttranscriptional processes is presented.

The transcriptional transactivator of human foamy virus maps to the bel 1 genomic region

The human foamy virus (HFV) genome possesses three open reading frames (bel 1, 2, and 3) located between env and the 3' long terminal repeat. By analogy to other human retroviruses this region was selected as the most likely candidate to encode the viral transactivator. Results presented here confirmed this and showed further that a deletion introduced only into the bel 1 open reading frame of a plasmid derived from an infectious molecular clone of HFV abolished transactivation. In contrast, deletions in bel 2 and bel 3 had only minor effects on the ability to transactivate. The role of the bel 1 genomic region as a transactivator was further investigated by eukaryotic expression of a genome fragment of HFV spanning the bel 1 open reading frame. A construct expressing bel 1 under control of a heterologous promoter was found to transactivate the HFV long terminal repeat in a dose-dependent fashion. Furthermore, it is shown that the U3 region of the HFV long terminal repeat is sufficient to respond to the HFV transactivator.

Analysis of splicing patterns of human spumaretrovirus by polymerase chain reaction reveals complex RNA structures

Mapping of transcripts of the human foamy virus genome was carried out in permissive human embryonic fibroblast cells by Northern blot hybridization and S1 nuclease analysis. Since several splice sites that are localized within a relatively narrow genomic region were detected, the polymerase chain reaction (PCR) was employed, and cloning and sequencing of the splice site junctions of the corresponding viral cDNAs were subsequently performed. All spumavirus transcripts have a common but relatively short leader RNA. Genomic, singly spliced env mRNAs and several singly and multiply spliced subgenomic transcripts were identified. The multiply spliced viral mRNAs consist of various exons located in the central or 3' part of the viral genome. At least four novel gene products, termed Bet, Bes, Beo, and Bel3, are predicted to exist. The poly(A) addition site that defines the boundary of the R and U5 region in the 3' long terminal repeat was determined. The pattern of spumavirus splicing is more complex than that of oncoviruses and more similar to that of lentiviruses. One of the characteristic features of spumavirus transcription is the existence of singly spliced bel1 and bel2 mRNAs that alternatively are multiply spliced, thereby generating a complexity comparable to, but different from, that of lentiviruses and from that of other known retroviruses. The complex spumavirus transcriptional pattern of human spumavirus and the coding potential of the 10 exons identified are discussed.