Complex Retroviruses Research Articles

Evidence for superantigen activity of the Bel 3 protein of the human foamy virus.

The human foamy virus is a complex retrovirus that codes for several regulatory bel genes in addition to the conventional gag, pol, and env genes. The bel 3 gene is located in the 3' part of the viral genome comparable to that of the superantigen of the mouse mammary tumor virus. Superantigens bound to major histocompatibility complex (MHC) class II molecules have been shown to stimulate T cells in a V beta-specific manner. The recombinant Bel 3 protein purified to near homogeneity was assayed in vitro to determine whether or not it functions as a superantigen that stimulates human T lymphocytes expressing particular V beta T cell receptor (TCR) chains. Therefore, an analysis including all known human V beta elements was performed. The expression of different V beta chains of the TCR was analyzed by reverse transcription of the V beta RNAs and subsequent amplification of the corresponding V beta cDNA elements by polymerase chain reaction in unstimulated, phytohemaggluttinin (PHA)- and Bel 3-stimulated human T lymphocytes. In addition, eight monoclonal antibodies directed against particular V beta family members were used to determine any change in the expression of the remaining known V beta elements upon treatment with PHA and Bel 3. The comparative V beta-specific transcriptional analysis revealed that the in vitro expression of the V beta 18 chain was specifically and strongly expanded in Bel 3-stimulated human T cells, a property characteristic for a superantigen.

Regulation of HIV expression by viral genes and cytokines.

The human immunodeficiency virus (HIV) is the causative agent of the acquired immunodeficiency syndrome (AIDS), a leading cause of death among young individuals. As a complex pathogenic retrovirus, HIV is characterized in vitro and in vivo by the ability to establish either a latent or productive infection of CD4+ T lymphocytes and mononuclear phagocytes (MPs). Viral latency and expression are under the control of both viral genes and several host-related factors. Among these latter, several proinflammatory and immunoregulatory cytokines profoundly affect HIV replication in T lymphocytes and MPs in vitro. Because many of these cytokines have been found to be elevated in HIV-infected individuals, it is likely that they act as regulators of viral expression in vivo. Both viral genes and cytokines regulate transcriptional and posttranscriptional steps in HIV replication. Thus, it is likely that common regulatory pathways between these two distinct classes of regulator molecules will be identified in the near future and will provide potential targets for pharmacologic intervention and treatment of HIV disease.

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.

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.

Identification of the Caprine Arthritis Encephalitis Virus Rev Protein and Its Cis-Acting Ray-Responsive Element

Caprine Arthritis Encephalitis Virus (CAEV) is a lentivirus closely related to visna virus of sheep and more distantly related to the human lentivirus HIV-1. The genomes of lentiviruses contain additional genes that regulate the lentivirus gene expression; one of these is Rev, a protein that regulates the expression of viral proteins via post-transcriptional mechanisms. A cDNA clone was isolated from CAEV infected cells and shown to encode the 18-kDa Rev protein of CAEV. Antibodies against CAEV Rev (Rev-C) demonstrated that the CAEV Ray protein accumulated in the nucleus and in particular in the nucleolus of transiently transfected cells. Mutation of a basic region in the CAEV Rev protein resulted in loss of nucleolar localization. A highly structured RNA element has been identified in the env gene of CAEV (nt 7850-8150); its structure and location suggested that it was analogous to the Ray-responsive element (RRE) of HIV-1 and visna virus. A 300-bp fragment (nt 7850-8150) spanning this region was substituted for the HIV-1 RRE in an HIV-1 Gag expression vector. Expression of the Gag protein was dramatically increased when Rev-C was added in trans, indicating that this fragment contained the cis-acting CAEV Rev Responsive Element. Cross-activation by the Rev/Rex proteins of other lentiviruses and members of the HTLV-I family indicated that this RRE could interact with Rev or Rex proteins of other viruses. This suggests that the highly divergent lentiviruses share similar mechanisms and cofactors regulating post-transcriptional viral gene expression. The Rev/RRE mechanism is thus the most conserved regulatory mechanism in lentiviruses and other complex retroviruses.

The origin of human immunodeficiency virus type-1 rev gene : An evolutionary hypothesis

The Rev protein of human immunodeficiency virus type-1 is an RNA-binding posttranscriptional transregulator encoded by an accessory gene that is distinct from retroviral oncogenes and whose origin is unclear. We hypothesize that the rev gene was generated by duplication of a viral RNA segment having a secondary-structure that evolved into the Rev-responsive element (RRE). This hypothesis is based on the following findings. First, accumulated data on functional mapping of Rev, Tat, and the transmembrane protein of Env suggested that the major coding exon of rev should have been inserted into the transmembrane region of env during the course of its evolution. Experiments with equine infectious anemia virus, another complex retrovirus, also indicate that a large portion of rev is located within the dispensable transmembrane region of env. Second, base usage analysis suggests the same origin for rev and RRE. Our hypothesis may provide a new insight into the evolutionary aspect of RNA0binding transactivators.

Differential effects of ras and jun family members on complex retrovirus promoter activities

Infection by complex retroviruses such as Visna-maedi, HIV1, HTLV-I and HFV is generally not followed by particle production, but rather by a more or less prolonged latency period. Knowledge of the mechanisms triggering an infectious cycle from the latent provirus(es) is of great importance in comprehending the appearance of the disease. It is currently admitted that cellular factors regulate viral expression. In this paper, we report the ability of ras, c-jun, jun-B and jun-D to diversely stimulate the LTR promoter activity of these retroviruses. Transient transfection assays using a luciferase reporter gene linked to LTR show that the Visna-maedi virus LTR, despite high intrinsic activity, is stimulated by Ha-ras and c-jun. The HTLV-I and HIV1 LTR were identically stimulated by ras, but differently by c-jun. In contrast, jun-B and jun-D were weaker activators, since they respectively stimulated only HTLV-I LTR and HIV1 LTR. HFV LTR remains unresponsive to either of these factors.

Lower mutation rate of bovine leukemia virus relative to that of spleen necrosis virus

Genetic variation of the more complex retroviruses in the human T-cell leukemia virus/bovine leukemia virus (HTLV/BLV) group is less than in some other retroviral genera. To test whether reverse transcription of HTLV/BLV group members is less error prone than that of members of other groups, we developed an assay for detecting forward mutations in BLV, similar to that developed for the simpler spleen necrosis virus (SNV). We used this system to study the rates and types of mutations that occur during a single replication cycle. We found that BLV reverse transcription is approximately two and one-half times less error prone than SNV reverse transcription (4.8 x 10(-6) versus 1.2 x 10(-5) mutation per bp per cycle, respectively). The relative numbers of all types of observed mutations (that is, base pair substitutions, frameshifts, deletions, and deletions with insertions) were similar for BLV and SNV.

Identification of the activation domain of equine infectious anemia virus rev

Several members of the lentivirus family of complex retroviruses have been shown to encode proteins that are functionally equivalent to the Rev posttranscriptional regulatory protein of human immunodeficiency virus type 1 (HIV-1). Furthermore, the domain organization of HIV-1 Rev, featuring a highly basic N-terminal RNA binding domain and a leucin-rich C-terminal effector domain, has also been shown to be highly conserved among Rev proteins derived from not only the primate but also the ovine and caprine lentiviruses. Although it has therefore appeared highly probable that the lentivirus equine infectious anemia virus (EIAV) also encodes a Rev, the predicted amino acid sequence of this putative EIAV regulatory protein does not display any evident homology to the basic and leucine-rich motifs characteristic of other known Rev proteins. By fusion of different segments of the proposed EIAV Rev protein to the well-defined RNA binding domain of either HIV-1 or visna virus Rev, we have identified a segment of this EIAV protein that can efficiently substitute in cis for the otherwise essential activation motif. Interestingly, the minimal EIAV Rev activation motif identified in this study comprises approximately 18 amino acids located toward the protein N terminus that lack any evident similarity to the leucine-rich activation domains found in these other lentivirus Rev proteins. It therefore appears that the Rev protein of EIAV, while analogous in function to Rev proteins defined in lentiviruses of primate, ovine, and caprine origin, is nevertheless distinguished by an entirely novel domain organization.

Functional analysis of human foamy virus accessory reading frames

Foamy viruses belong to the retroviruses which possess a complex genome structure. The human foamy virus (HFV) isolate bears three open reading frames (the so-called bel genes) in the 3' region of the genome which have been reported to give rise to possibly six different proteins via alternative splicing (W. Muranyi and R. M. Flügel, J. Virol. 65:727-735, 1991). In order to analyze the requirements of these proteins for HFV replication in vitro, we constructed a set of single and combinatory bel gene mutants of an infectious molecular clone of HFV. The mutant which lacked the transacting activator, bel-1, was found to be replication incompetent. All other mutants replicated equally well and gave rise to comparable titers of infectious cell-free virus. When HFV proviruses were put under the control of a heterologous promoter (simian virus 40), none of the accessory gene products was found to be required for expression of structural (gag) proteins. There was no evidence for a posttranscriptional regulatory protein that is present in other complex retroviruses.

BEL-1 Transactivator Responsive Sequences in the Long Terminal Repeat of Human Foamy Virus

Cis-regulatory elements in the long terminal repeat (LTR) of human foamy virus (HFV) were identified by using LTR mutants to transiently express the chloramphenicol acetyl-transferase gene after co-transfection with an expression plasmid for the virus bel-1 (transactivator) gene. The R-U5 region and an element in the 5′ U3 region were found to negatively influence HFV gene expression. The complete BEL-1 responsive region was mapped to extend from nucleotide position -471 to position -93 relative to the start of transcription. Within this region, three elements were identified that in the homologous or a heterologous (SV40) promoter context can, independently and irrespective of their orientation, act as targets for BEL-1. These elements are located between nucleotide positions -413/-378, -361/-291, and 124/-93. The target elements do not share obvious sequence homologies. The mechanism of HFV transactivation appears to be novel among the complex retroviruses and is likely to involve, as yet, undiscovered cellular DNA binding factors.

Human foamy virus genome possesses an internal, Bel-1-dependent and functional promoter.

The human foamy or spumaretrovirus (HSRV) is a complex retrovirus that encodes the three retroviral genes gag, pol, and env and, in addition, at least three bel genes. The HSRV Bel-1 protein was identified as a transcriptional trans-activator. HSRV transcription starts in the 5' long terminal repeat at a defined guanine residue. We report here that a second efficiently utilized start site of transcription is contained within a HSRV env DNA sequence upstream of the bel genes. Bel-specific transcripts that initiate at the internal transcriptional start site at nt 9196 were identified in HSRV-infected cells by primer extension and S1 nuclease analysis, and the intragenic promoter was shown to be constitutively activated by Bel-1 in the HSRV provirus. In transient expression assays with indicator gene constructs, expression by the HSRV intragenic promoter/enhancer is Bel-1 dependent. The data provide evidence for an intragenic start site of transcription in the genome of a complex, exogenous human retrovirus and are discussed in terms of a model for regulating spumaretroviral gene expression.

A proposal for a new approach to a preventive vaccine against human immunodeficiency virus type 1.

Human immunodeficiency virus type 1 (HIV-1) is a more complex retrovirus, coding for several accessory proteins in addition to the structural proteins (Gag, Pol, and Env) that are found in all retroviruses. More complex retroviruses have not been isolated from birds, and simpler retroviruses have not been isolated from humans. However, the proviruses of many endogenous simpler retroviruses are present in the human genome. These observations suggest that humans can mount a successful protective response against simpler retroviruses, whereas birds cannot. Thus, humans might be able to mount a successful protective response to infection with a simpler HIV-1. As a model, a simpler bovine leukemia virus which is capable of replicating has been constructed; a simpler HIV-1 could be constructed in a similar fashion. I suggest that such a simpler HIV-1 would be a safe and effective vaccine against HIV-1.

Increase in the basal transcriptional activity of the human foamy virus internal promoter by the homologous long terminal repeat promoter in cis.

The human foamy or spumaretrovirus HFV is a complex and exogenous retrovirus that encodes several bel genes besides the three classical retroviral genes gag, pol, and env. HFV was recently reported to contain two functionally active promoters that are both strongly trans-activated by the HFV trans-activator protein Bel 1. The occurrence of a second internal cap site underscores the complexity of the HFV genome. We have analysed whether there is interference between the HFV long terminal repeat promoter and the internal promoter located in the 3' end of env upstream of the bel genes. Recombinant clones were constructed that carry two different indicator genes, one under the control of the U3 promoter, the other under the control of the internal promoter. The portion of the basal transcriptional activity of the internal promoter that is not trans-activated by Bel 1 was increased two- to threefold in the presence of the long terminal repeat promoter. The rate of trans-activation by Bel 1 of both HFV promoters was not altered in these constructs.

Mechanism of action of regulatory proteins encoded by complex retroviruses.

Complex retroviruses are distinguished by their ability to control the expression of their gene products through the action of virally encoded regulatory proteins. These viral gene products modulate both the quantity and the quality of viral gene expression through regulation at both the transcriptional and posttranscriptional levels. The most intensely studied retroviral regulatory proteins, termed Tat and Rev, are encoded by the prototypic complex retrovirus human immunodeficiency virus type 1. However, considerable information also exists on regulatory proteins encoded by human T-cell leukemia virus type I, as well as several other human and animal complex retroviruses. In general, these data demonstrate that retrovirally encoded transcriptional trans-activators can exert a similar effect by several very different mechanisms. In contrast, posttranscriptional regulation of retroviral gene expression appears to occur via a single pathway that is probably dependent on the recruitment of a highly conserved cellular cofactor. These two shared regulatory pathways are proposed to be critical to the ability of complex retroviruses to establish chronic infections in the face of an ongoing host immune response.

The emergence of simian/human immunodeficiency viruses.

Molecular evolutionary analyses strongly support the hypothesis that human immunodeficiency viruses have recently arisen from a diverse pool of nonhuman primate immunodeficiency viruses. Our understanding of the molecular phylogenetic relationships between primate and nonprimate lentiviruses is less certain, partly because key intermediate forms are still to be discovered. DNA and protein sequence comparisons reveal uncanny dissimilarities, as well as similarities, among the genetic sequences of these complex retroviruses, thereby giving rise to the notion that primate lentiviruses are participants in "fast-forward" evolution.

Mechanism of action of regulatory proteins encoded by complex retroviruses.

Complex retroviruses are distinguished by their ability to control the expression of their gene products through the action of virally encoded regulatory proteins. These viral gene products modulate both the quantity and the quality of viral gene expression through regulation at both the transcriptional and posttranscriptional levels. The most intensely studied retroviral regulatory proteins, termed Tat and Rev, are encoded by the prototypic complex retrovirus human immunodeficiency virus type 1. However, considerable information also exists on regulatory proteins encoded by human T-cell leukemia virus type I, as well as several other human and animal complex retroviruses. In general, these data demonstrate that retrovirally encoded transcriptional trans-activators can exert a similar effect by several very different mechanisms. In contrast, posttranscriptional regulation of retroviral gene expression appears to occur via a single pathway that is probably dependent on the recruitment of a highly conserved cellular cofactor. These two shared regulatory pathways are proposed to be critical to the ability of complex retroviruses to establish chronic infections in the face of an ongoing host immune response.

Effector domains of human immunodeficiency virus type 1 Rev and human T-cell leukemia virus type I Rex are functionally interchangeable and share an essential peptide motif

The human immunodeficiency virus type 1 Rev and human T-cell leukemia virus type I Rex transactivators are posttranscriptional regulatory proteins that promote retroviral gene expression by interacting with specific viral mRNAs. Rev and Rex have markedly dissimilar amino acid sequences and RNA target specificities but are thought to act through the same cellular pathway. In this report, we demonstrate that short peptide domains which are required for effector activity in Rev and Rex are functionally interchangeable. Activity of these effector domains depends upon a previously unrecognized tetrapeptide motif that is present in both Rev and Rex and also in analogous proteins from other complex retroviruses. The conserved effector motif may mediate essential interactions of Rev, Rex, and other transactivators of this type with a common cellular cofactor.

The Human Immunodeficiency Virus

HIV is a complex retrovirus. Like some other viruses it infects host cells for life, but unlike other viruses it appears to do so every time. Its elaborate genetic regulation enables it to remain relatively dormant, replicating steadily but slowly. On appropriate stimulation, it is capable of explosive up-regulation, releasing high numbers of new infectious virus. It replicates in an error-prone way, constantly changing its structure to improve its infectivity while presenting the host's immune system with a constantly moving target.

Molecular biology of the human immunodeficiency virus type 1

The immunodeficiency virus type 1 is a complex retrovirus. In addition to genes that specify the proteins of the virus particle and the replicative enzymes common to all retroviruses, HIV-1 specifies at least six additional proteins that regulate the virus life cycle. Two of these regulatory genes, tat and rev, specify proteins essential for replication. These proteins bind to specific sequences of newly synthesized virus RNA and profoundly affect virus protein expression. Tat and rev appear to be prototypes of novel eukaryotic regulatory proteins. These two genes may play a central role in regulating the rate of virus replication. Three other viral genes, vif, vpu, and vpr, affect the assembly and replication capacity of newly made virus particles. These genes may play a critical role in spread of the virus from tissue to tissue and from person to person. Our understanding of the contribution of each of the virus structural proteins and regulatory genes to the complex life cycle of the virus in natural infections is incomplete. However, enough insight has been gained into the structure and function of each of these components to provide a firm basis for rational antiviral drug development.