HIV-1 TAT "activates" presynthesized RNA in the nucleus

Molecular characterization of HIV-1 genome in fission yeast Schizosaccharomyces pombe

Background

The human immunodeficiency virus type 1 (HIV-1) genome (~9 kb RNA) is flanked by two long terminal repeats (LTR) promoter regions with nine open reading frames, which encode Gag, Pol and Env polyproteins, four accessory proteins (Vpu, Vif, Vpr, Nef) and two regulatory proteins (Rev, Tat). In this study, we carried out a genome-wide and functional analysis of the HIV-1 genome in fission yeast (Schizosaccharomyces pombe).

Results

Each one of the HIV-1 genes was cloned and expressed individually in fission yeast. Subcellular localization of each viral protein was first examined. The effect of protein expression on cellular proliferation and colony formations, an indication of cytotoxicity, were observed. Overall, there is a general correlation of subcellular localization of each viral protein between fission yeast and mammalian cells. Three viral proteins, viral protein R (Vpr), protease (PR) and regulator of expression of viral protein (Rev), were found to inhibit cellular proliferation. Rev was chosen for further analysis in fission yeast and mammalian cells. Consistent with the observation in fission yeast, expression of HIV-1 rev gene also caused growth retardation in mammalian cells. However, the observed growth delay was neither due to the cytotoxic effect nor due to alterations in cell cycling. Mechanistic testing of the Rev effect suggests it triggers transient induction of cellular oxidative stress.

Conclusions

Some of the behavioral and functional similarities of Rev between fission yeast and mammalian cells suggest fission yeast might be a useful model system for further studies of molecular functions of Rev and other HIV-1 viral proteins.

Curb challenges of the "Trojan Horse" approach: smart strategies in achieving effective yet safe cell-penetrating peptide-based drug delivery

Cell-penetrating peptide (CPP)-mediated intracellular drug delivery system, often specifically termed as "the Trojan horse approach", has become the "holy grail" in achieving effective delivery of macromolecular compounds such as proteins, DNA, siRNAs, and drug carriers. It is characterized by the unique cell- (or receptor-), temperature-, and payload-independent mechanisms, therefore offering potent means to improve poor cellular uptake of a variety of macromolecular drugs. Nevertheless, this "Trojan horse" approach also acts like a double-edged sword, causing serious safety and toxicity concerns to normal tissues or organs for in vivo application, due to lack of target selectivity of the powerful cell penetrating activity. To overcome this problem of potent yet non-selective penetration vs. targeting delivery, a number of "smart" strategies have been developed in recent years, including controllable CPP-based drug delivery systems based on various stimuli-responsive mechanisms. This review article provides a fundamental understanding of these smart systems, as well as a discussion of their real-time in vivo applicability.

Nucleoprotein gene tracking: localization of specific HIV-1 genes to subchromatin nucleoprotein complexes containing endonuclease activity in HIV-1-infected human cells

We developed a technique with which to isolate specific subchromatin deoxyribonucleoprotein/ribonucleoprotein precursor complexes containing discrete genes from intact mammalian nuclei by direct restriction enzyme treatment with MspI. These nucleoprotein complexes can be further fractionated and purified by two-dimensional isoelectric focusing/sodium dodecyl sulfate-polyacrylamide gel electrophoresis. After electroelution and removal of detergent, virtually thousands of nucleoprotein complexes can be examined for the presence of tightly bound genes and enzymatic activities. Nucleoprotein gene tracking procedures were applied to study the acidic nucleoprotein complexes from steady-state human H9 cells uninfected or infected with human immunodeficiency virus type 1 (HIV-1) virus. The purified nucleoprotein complexes were screened for the presence of loosely and tightly associated HIV-1 gene sequences (pol, env, tat, and rev) using a DNA hybridization protocol. In HIV-1-infected cells, four specific nucleoprotein complexes out of several hundred were found to contain tightly bound HIV-1 pol gene sequences after purification. By contrast, the other HIV-1 gene sequences (env, tat, and rev) were not tightly bound to any of the nucleoprotein complexes in HIV-infected cells. The observations suggest that certain HIV-1 genes associate with specific chromatin nucleoprotein complexes, regardless of their pattern of DNA integration into the human genome. At least two of the HIV-1 pol-containing nucleoprotein complexes of apparent M(r) approximately 94,000, pI approximately 6.5, and M(r) approximately 47,000, pI approximately 5.1 contain DNA endonuclease activity. This was confirmed in the present study, using linearized pUC19 plasmid substrate. The technique can be used to study a variety of problems concerning the association of specific genes and enzymes with specific nucleoprotein complexes J. Cell. Biochem. Suppls. 32/33:158-165, 1999.

Tackling Tat

Activation of cellular genes typically involves control of transcription initiation by DNA-binding regulatory proteins. The human immunodeficiency virus transactivator protein, Tat, provides the first example of the regulation of viral gene expression through control of elongation by RNA polymerase II. In the absence of Tat, initiation from the long terminal repeat is efficient, but transcription is impaired because the promoter engages poorly processive polymerases that disengage from the DNA template prematurely. Activation of transcriptional elongation occurs following the recruitment of Tat to the transcription machinery via a specific interaction with an RNA regulatory element called TAR, a 59-residue RNA leader sequence that folds into a specific stem-loop structure. After binding to TAR RNA, Tat stimulates a specific protein kinase called TAK (Tat-associated kinase). This results in hyperphosphorylation of the large subunit of the RNA polymerase II carboxyl- terminal domain. The kinase subunit of TAK, CDK9, is analogous to a component of a positive acting elongation factor isolated from Drosophila called pTEFb. Direct evidence for the role of TAK in transcriptional regulation of the HIV long terminal repeat comes from experiments using inactive mutants of the CDK9 kinase expressed in trans to inhibit transcription. A critical role for TAK in HIV transcription is also demonstrated by selective inhibition of Tat activity by low molecular mass kinase inhibitors. A second link between TAK and transactivation is the observation that the cyclin component of TAK, cyclin T1, also participates in TAR RNA recognition. It has been known for several years that mutations in the apical loop region of TAR RNA abolish Tat activity, yet this region of TAR is not required for binding by recombinant Tat protein in vitro, suggesting that the loop region acts as a binding site for essential cellular co-factors. Tat is able to form a ternary complex with TAR RNA and cyclin T1 only when a functional loop sequence is present on TAR.

Regulation of TNFalpha and TGFbeta-1 gene transcription by HIV-1 Tat in CNS cells

Tat is a transcription transactivator produced by the human immunodeficiency virus type 1 (HIV-1) at the early phase of infection and plays a critical role in the expression and replication of the viral genome. This 86 amino acid protein, which can be secreted from the infected cells, has the ability to enter uninfected cells and exert its activity upon the responsive genes. Earlier results indicated that in addition to the HIV-1 promoter, Tat has the capacity to induce transcription of a variety of cellular genes. In this study, we demonstrate that exposure of cells from the central nervous system (U-87MG and SK-N-MC) and the lymphoid T cells (Jurkat) to highly purified Tat increases transcriptional activity of the reporter constructs containing the promoters from the transforming growth factor beta-1 (TGFbeta-1), the tumor necrosis factor alpha (TNFalpha), and the HIV-1 LTR. In addition, Tat treatment results in increased levels of TGFbeta-1 and TNFalpha mRNAs in these cells. Activation of the TGFbeta-1 and TNFalpha promoter constructs by Tat in U-87MG and SK-N-MC cells required amino acid residues 2 to 36 which spans the acidic and the cysteine-rich domains of Tat. In both CNS and lymphoid cells, the level of endogenous TGFbeta-1 mRNA was increased by mutant Tat protein containing amino acids 1 to 48 but not with a mutant Tat protein with a deletion between residues 2 to 36. TNFalpha mRNA level was increased by mutant Tat spanning residues 1 to 48 in U-87MG cells, but not in SK-N-MC and Jurkat cells. These observations suggest that activation of cellular and viral genes by Tat in various cells may be mediated by different pathways as evidenced by the requirements of the different regions of Tat. Activation of the TGFbeta-1 and TNFalpha promoters by wild-type Tat was severely affected by the mutant peptides spanning residues 2 to 36 and 1 to 48 suggesting that both truncated Tat peptides may function as dominant negative mutants over TNFalpha and TGFbeta-1 gene transcription. The importance of these findings in Tat-induced regulation of viral and cellular genes in various cell types is discussed.

Individual Cell Analysis of the Cytokine Repertoire in Human Immunodeficiency Virus-1–Infected Monocytes/Macrophages by a Combination of Immunocytochemistry and In Situ Hybridization

The expression of many cytokines is dysregulated in individuals infected with the human immunodeficiency virus-1 (HIV-1). To determine the effects of HIV-1 infection on cytokine expression in individual cells (at the single cell level), we investigated the intracellular levels of proinflammatory cytokines (tumor necrosis factor [TNF]-α, interleukin [IL]-1β, IL-6, and IL-8) and hematopoietic growth factors (granulocyte colony-stimulating factor [G-CSF], granulocyte-macrophage colony-stimulating factor [GM-CSF]) in monocyte-derived macrophages, mock-infected, or infected with HIV-1 by immunocytochemical staining for cytokine protein and compared this with secreted cytokine levels as determined by specific enzyme-linked immunosorbent assay (ELISA). No difference in the frequency or intensity of cell-associated immunocytochemical cytokine staining could be observed between HIV-1 and mock-infected cells even though the level of secreted proinflammatory cytokines increased and the hematopoietic growth factors decreased in HIV-1–infected cultures. Furthermore, equal expression of cytokine mRNA was observed in all cells in the culture regardless of whether the cells were productively infected with HIV-1 as determined by double-labelling immunocytochemical staining for HIV-1 p24 antigen and in situ hybridization for cytokine mRNA expression. These results indicate that HIV-1 infection results in dysregulation of intracellular cytokine mRNA expression and cytokine secretion not only in HIV-1–infected cells, but also through an indirect way(s) affecting cells not producing virus.

Individual Cell Analysis of the Cytokine Repertoire in Human Immunodeficiency Virus-1–Infected Monocytes/Macrophages by a Combination of Immunocytochemistry and In Situ Hybridization

The expression of many cytokines is dysregulated in individuals infected with the human immunodeficiency virus-1 (HIV-1). To determine the effects of HIV-1 infection on cytokine expression in individual cells (at the single cell level), we investigated the intracellular levels of proinflammatory cytokines (tumor necrosis factor [TNF]-α, interleukin [IL]-1β, IL-6, and IL-8) and hematopoietic growth factors (granulocyte colony-stimulating factor [G-CSF], granulocyte-macrophage colony-stimulating factor [GM-CSF]) in monocyte-derived macrophages, mock-infected, or infected with HIV-1 by immunocytochemical staining for cytokine protein and compared this with secreted cytokine levels as determined by specific enzyme-linked immunosorbent assay (ELISA). No difference in the frequency or intensity of cell-associated immunocytochemical cytokine staining could be observed between HIV-1 and mock-infected cells even though the level of secreted proinflammatory cytokines increased and the hematopoietic growth factors decreased in HIV-1–infected cultures. Furthermore, equal expression of cytokine mRNA was observed in all cells in the culture regardless of whether the cells were productively infected with HIV-1 as determined by double-labelling immunocytochemical staining for HIV-1 p24 antigen and in situ hybridization for cytokine mRNA expression. These results indicate that HIV-1 infection results in dysregulation of intracellular cytokine mRNA expression and cytokine secretion not only in HIV-1–infected cells, but also through an indirect way(s) affecting cells not producing virus.

Translational repression by a transcriptional elongation factor

One of the classical positive regulators of gene expression is bacteriophage lambda N protein. N regulates the transcription of early phage genes by participating in the formation of a highly processive, terminator-resistant transcription complex and thereby stimulates the expression of genes lying downstream of transcriptional terminators. Also included in this antiterminating transcription complex are an RNA site (NUT) and host proteins (Nus). Here we demonstrate that N has an additional, hitherto unknown regulatory role, as a repressor of the translation of its own gene. N-dependent repression does not occur when NUT is deleted, demonstrating that N-mediated antitermination and translational repression both require the same cis-acting site in the RNA. In addition, we have identified one nut and several host mutations that eliminate antitermination and not translational repression, suggesting the independence of these two N-mediated mechanisms. Finally, the position of nutL with respect to the gene whose expression is repressed is important.

Masking and unmasking maternal mRNA. The role of polyadenylation, transcription, splicing, and nuclear history

We establish that masked mRNAs synthesized from exogenous plasmid templates microinjected into the nuclei of Xenopus oocytes are translationally activated (unmasked) on oocyte maturation concomitant with polyadenylation. Synthetic mRNA injected into the cytoplasm of the oocyte is translated over an order of magnitude more efficiently than is the cognate mRNA synthesized in vivo. Both mRNA synthesized in vivo and mRNA microinjected into the oocyte cytoplasm require a cytoplasmic polyadenylation element in the 3'-untranslated region to activate translation on maturation. Although polyadenylation upon oocyte maturation can relieve the translational repression of mRNA synthesized in vivo, the excision of an intron within the nucleus does not relieve repression. We suggest that the translational repression coupled to the transcription process will more effectively repress inappropriate gene expression in the oocyte and offer the potential to achieve a wider range of gene regulation.

The regulation of human immunodeficiency virus type-1 gene expression

Despite 15 years of intensive research we still do not have an effective treatment for AIDS, the disease caused by human immunodeficiency virus (HIV). Recent research is, however, revealing some of the secrets of the replication cycle of this complex retrovirus, and this may lead to the development of novel antiviral compounds. In particular the virus uses strategies for gene expression that seem to be unique in the eukaryotic world. These involve the use of virally encoded regulatory proteins that mediate their effects through interactions with specific viral target sequences present in the messenger RNA rather than in the proviral DNA. If there are no cellular counterparts of these RNA-dependent gene-regulation pathways then they offer excellent targets for the development of antiviral compounds. The viral promoter is also subject to complex regulation by combinations of cellular factors that may be functional in different cell types and at different cell states. Selective interference of specific cellular factors may also provide a route to inhibiting viral replication without disrupting normal cellular functions. The aim of this review is to discuss the regulation of HIV-1 gene expression and, as far as it is possible, to relate the observations to viral pathogenesis. Some areas of research into the regulation of HIV-1 replication have generated controversy and rather than rehearsing this controversy we have imposed our own bias on the field. To redress the balance and to give a broader view of HIV-1 replication and pathogenesis we refer you to a number of excellent reviews [Cullen, B. R. (1992) Microbiol. Rev. 56, 375-394; Levy, J. A. (1993) Microbiol. Rev. 57, 183-394; Antoni, B. A., Stein, S. & Rabson, A. B. (1994) Adv. Virus Res. 43, 53-145; Rosen, C. A. & Fenyoe, E. M. (1995) AIDS (Phila.) 9, S1-S3].

Conformational heterogeneity in two regions of TAT results in structural variations of this protein as a function of HIV-1 isolates

TAT protein is an essential regulatory protein of the human immunodeficiency virus type 1 (HIV-1). Inhibition of TAT activity blocks the virus cycle, and a drug that blocks TAT is one of the possibilities to cure AIDS. Circular dichroism (CD) was measured for TAT peptides covering the TAT sequence with overlaps. The CD spectrum of each peptide was measured in different solvents to evaluate the ability of each TAT region to form different secondary structures. The most variation or conformational heterogeneity is observed with the two regions adjacent to the TAT basic region. CD data show that the basic region can adopt an extended structure in a full TAT protein, which is not the case for the isolated peptide. TAT sequences from the different HIV-1 isolates were analyzed, and the results showed that the sequences could be gathered into six groups. Molecular modeling was done on the various isolates based on a TAT structure from two-dimensional NMR. After minimization and dynamic steps, the modeled three-dimensional structures were compared. The results showed structural variations of the TAT protein as a function of the HIV-1 isolates. These structural variations were mainly in the two regions adjacent to the basic region, confirming the conformational heterogeneity indicated by the CD measurements. Furthermore, Chou-Fasman analysis shows significant changes in propensities for each secondary structure only for regions III and V. This conformational heterogeneity should be essential for TAT activity and points out that regions III and V are a poor potential target to design a TAT ligand. We propose a target involving TAT structurally conserved regions, accessible whatever the size of the TAT C terminus.

Examination of TAR-independent Trans activation by human immunodeficiency virus type 1 Tat in human glial cells

Astrocytic glial cells derived from central nervous system (CNS) can support human immunodeficiency virus type 1 (HIV-1) replication in cell culture, may be infected in tissue culture, and are thought to be a large HIV-1 reservoir in vivo. The Tat protein of HIV-1 interacts with a cis-acting target sequence referred to as TAR. However, Tat can also stimulate gene expression directed from some heterologous promoters and, in certain circumstances, an HIV-1 long terminal repeat (LTR) that lacks the TAR element. Therefore, we attempted to investigate Tat trans activation of HIV-1 LTR in the astrocytic glial cells. Using transfection of LTR-reporter gene constructs and HIV-1 proviral constructs, we demonstrate TAR-dependent replication in astrocytic cells. We also examined the expression of HIV-1 env gene from an LTR that lacks TAR element. In a previous study (Kim and Panganiban: J Virol 67:3739-3747, 1993), we observed that env expression is trans activated only by the full-length Tat protein through a TAR-independent manner in HeLa cells. However, in astrocytic glial cells, the trans activation of env expression from the LTR-lacking TAR element was mediated by the first exon peptide of Tat as well as the full-length Tat peptide through a post-transcriptional mechanism rather than a transcriptional one. This result suggests that cell type-specific factor(s) is involved in the TAR-independent Tat responsiveness.

Coupling transcription to translation: a novel site for the regulation of eukaryotic gene expression

Recent experiments using Xenopus oocytes demonstrate that the history of a particular mRNA in the nucleus can influence the efficiency with which that mRNA will be utilized by the translational machinery. Individual promoter elements, specific protein-RNA interactions and the splicing process within the nucleus can all influence translational fate within the cytoplasm. Central to the regulatory mechanisms influencing the translation process is the packaging of mRNA by a highly conserved family of Y-box proteins. These Y-box proteins are found in cytoplasmic messenger ribonucleoprotein particles where they have a causal role in restricting the recruitment of mRNA to the translational machinery. Nuclear processes influence the packaging of mRNA by the Y-box proteins in the cytoplasm and in consequence mRNA translation. This functional coupling provides a novel site for the regulation of eukaryotic gene expression.

A Tat-induced auto-up-regulatory loop for superactivation of the human immunodeficiency virus type 1 promoter

The virus-encoded Tat protein strongly activates transcription of human immunodeficiency virus (HIV). A well-recognized mechanism involves interaction of Tat with the nascent RNA transcript of the viral tar gene; mutation of tar greatly decreases activation by Tat. However, Tat still provides a low level of activation, demonstrating that it also has a tar-independent mode of action. We propose that this tar-independent mode of Tat action is through activation of gene transcription to produce tumor necrosis factor alpha. This cytokine and other compounds that activate NF-kappa B up-regulate the HIV promoter at a low level, similarly to the second Tat action. Through this mechanism, they also activate promoters of tumor necrosis factor alpha and other cytokines and thereby establish an auto-up-regulatory loop. Activated NF-kappa B motifs in the HIV promoter synergize with Tat/tar. Mutations of these motifs decrease activation by Tat to a few percent of the wild-type value. In cooperation, the two modes of activation by Tat (tar dependent and cytokine based) set up positive up-regulatory loops which greatly superactivate transcription of HIV. Agents that block these synergistic pathways at three different steps and are more inhibitory in combination than is any one alone have been found. Thereby, multidrug modalities for transcription of HIV are proposed for virus suppression.

Molecular cloning and characterization of a TAR-binding nuclear factor from T cells

The TAt protein of the human immunodeficiency virus type 1 (HIV-1) activates the expression of viral mRNA through a cis-acting element in the LTR termed TAR. TAR RNA forms a stable stem-loop structure. Mutagenesis studies indicate that the stem structure, the primary sequence of the loop, and three unpaired bases in the stem (bulge) are important for Tat activation. Using the in vitro-transcribed TAR RNA as a probe, we have cloned a gene (TARBP-b) that encodes a TAR-binding protein from a cDNA expression library derived from Hut-78 cells. Expression of the 1.4-kb TARBP-b mRNA was observed in all mammalian cell lines tested. TARBP-b binds specifically to the bulge region of TAR RNA and trans-activates the HIV-1 long terminal repeat in the presence of ptat and prev expression plasmids. These results suggest that TARBP-b contributes to tat-mediated trans-activation.

A homologue of the human MSS1 gene, a positive modulator of HIV-1 gene expression, is massively expressed in Xenopus oocytes

Here the nucleotide sequence of a Xenopus homologue of the human MSS1 gene, a positive modulator of the HIV-1 Tat mediated transactivation in mammalian cells, is presented. This gene is highly conserved and almost exclusively expressed in Xenopus oocytes. We speculate about a possible role of this gene in the HIV-1 Tat/TAR mediated transactivation in Xenopus oocytes.

Promoter control of translation in Xenopus oocytes

The HIV-1 promoter directs the high level production of transcripts in Xenopus oocytes. However, despite being exported to the cytoplasm, the transcripts are not translated [M. Braddock, A. M. Thorburn, A. Chambers, G. D. Elliott, G. J. Anderson, A. J. Kingsman and S. M. Kingsman (1990) Cell, 62, 1123-1133]. We have shown previously that this is a function of promoter sequences and is independent of the TAR RNA element that is normally located at the 5' end of all HIV mRNAs. We now show that a three nucleotide substitution at position -340, upstream of the RNA start site, reverses the translation inhibition. This site coincides with a sequence that can bind the haematopoietic transcription factor GATA. The inhibition of translation can also be reversed by treatment with inhibitors of casein kinase II or by injection into the nucleus of antibodies specific for the FRGY2 family of RNP proteins. We suggest that the -340 site influences the quality of the transcription complex such that transcripts are diverted to a nucleus-dependent translation inhibition pathway.

Intron-less RNA injected into the nucleus of Xenopus oocytes accesses a regulated translation control pathway

The translation of a capped, polyadenylated RNA after injection into the nucleus of Xenopus oocytes occurs only if the RNA contains an intron. A single point mutation in the splice donor site prevents translation. Intron-less RNA is exported efficiently to the cytoplasm and is held, undegraded, in a translationally inert state for several days. Translation can be activated by treating the oocytes with progesterone or by injecting antibodies that bind the FRGY2 class of messenger RNA binding proteins, p56 and p60, but these antibodies are only effective if delivered to the nucleus. Inhibitors of casein kinase II also activate translation whereas phosphatase inhibitors block progesterone-mediated activation of translation. These data suggest the presence of an RNA handling pathway in the nucleus of Xenopus oocytes which is regulated by casein kinase type II phosphorylation and which directs transcripts to be sequestered by p56/p60 or by closely related proteins. This pathway can be bypassed if the RNA contains an intron and it can be reversed by progesterone treatment. These data may have implications for understanding translational control during early development.

Industrial production of heterologous proteins by fed-batch cultures of the yeast Saccharomyces cerevisiae

This review concerns the issues involved in the industrial development of fed-batch culture processes with Saccharomyces cerevisiae strains producing heterologous proteins. Most of process development considerations with fed-batch recombinant cultures are linked to the reliability and reproducibility of the process for manufacturing environments where quality assurance and quality control aspects are paramount. In this respect, the quality, safety and efficacy of complex biologically active molecules produced by recombinant techniques are strongly influenced by the genetic background of the host strain, genetic stability of the transformed strain and production process factors. An overview of the recent literature of these culture-related factors is coupled with our experience in yeast fed-batch process development for producing various therapeutic grade proteins. The discussion is based around three principal topics: genetics, microbial physiology and fed-batch process design. It includes the fundamental aspects of yeast strain physiology, the nature of the recombinant product, quality control aspects of the biological product, features of yeast expression vectors, expression and localization of recombinant products in transformed cells and fed-batch process considerations for the industrial production of Saccharomyces cerevisiae recombinant proteins. It is our purpose that this review will provide a comprehensive understanding of the fed-batch recombinant production processes and challenges commonly encountered during process development.

Identification of a novel HIV-1 TAR RNA bulge binding protein

The Tat protein binds to TAR RNA to stimulate the expression of the human immunodeficiency virus type 1 (HIV-1) genome. Tat is an 86 amino acid protein that contains a short region of basic residues (aa49-aa57) that are required for RNA binding and TAR is a 59 nucleotide stem-loop with a tripyrimidine bulge in the upper stem. TAR is located at the 5' end of all viral RNAs. In vitro, Tat specifically interacts with TAR by recognising the sequence of the bulge and upper stem, with no requirement for the loop. However, in vivo the loop sequence is critical for activation, implying a requirement for accessory cellular TAR RNA binding factors. A number of TAR binding cellular factors have been identified in cell extracts and various models for the function of these factors have been suggested, including roles as coactivators and inhibitors. We have now identified a novel 38 kD cellular factor that has little general, single-stranded or double-stranded RNA binding activity, but that specifically recognises the bulge and upper stem region of TAR. The protein, referred to as BBP (bulge binding protein), is conserved in mammalian and amphibian cells and in Schizosaccharomyces pombe but is not found in Saccharomyces cerevisiae. BBP is an effective competitive inhibitor of Tat binding to TAR in vitro. Our data suggest that the bulge-stem recognition motif in TAR is used to mediate cellular factor/RNA interactions and indicates that Tat action might be inhibited by such competing reactions in vivo.

Effects of the Tat basic domain on human immunodeficiency virus type 1 transactivation, using chemically synthesized Tat protein and Tat peptides

To study the structure relationship of different Tat domains, the full-length Tat protein Tat1-86, the gene product of the first exon Tat1-72 which retains full activity of the protein, and a panel of shorter peptides mimicking different regions of the primary structure of the Tat protein were chemically synthesized by the solid-phase method, using an efficient protocol. Synthetic Tat1-86 and Tat1-72 transactivated beta-galactosidase activity in HeLa cells containing the lacZ gene under the control of the human immunodeficiency virus type 1 long terminal repeat. Analyses of the activity of Tat1-86 and Tat1-72 with the sulfhydryl of cysteine residues free or protected by the acetamidomethyl group showed that only the Tat fragments with deprotected cysteine residues retain transactivation ability. In contrast, peptide Tat1-48 was inactive, with cysteine residues either free or protected. Similarly, other shorter synthetic peptides covering the different Tat domains were inactive. Interestingly, when peptides Tat1-48 and Tat38-60 were used simultaneously, a significant transactivation was obtained. This result suggests that both peptide domains are implicated in transactivation, probably by acting at two different sites. This permits us to propose a fundamentally new step in the understanding of the molecular mechanism of Tat transactivation.

Production and purification of hybrid Ty-VLPs

This article describes how pure Ty-VLPs (virus-like particles) can be prepared from hybrid Ty-VLPs. Many different hybrid Ty-VLPs have been produced and may be easily purified. Since the sedimentation properties of different hybrid Ty-VLPs are similar, a simple purification process can be used for any VLP. This fast, versatile, and easy process allows for the production of a variety of recombinant proteins.

Expression vectors for the construction of hybrid Ty-VLPs

Purification of expressed proteins can be facilitated by expressing the recombinant protein as a fusion with a carrier protein that assembles into particulate structures. This article describes the use of expression vectors in producing a hybrid of the yeast retrotransposon Ty, which self-assembles into virus-like particles (VLPs). Hybrid VLPs can be used in such laboratory applications as the production of polyclonal and monoclonal antibodies, structure/function analyses, the detection of important antigenic determinants, and epitope mapping of monoclonal antibodies.

Hybrid Ty virus-like particles

Vaccines need to activate antigen presenting cells, overcome genetic restriction in T-cell responses and elicit both T and B memory cells. In order to produce recombinant vaccines which can do this, considerable effort has been put into developing particulate antigen presentation systems to generate polyvalent, high molecular weight antigens which should maximally stimulate the immune system. One such antigen-carrier system is based on the ability of a protein encoded by the yeast retrotransposon, Ty, to self-assemble into virus-like particles (VLPs). Ty-fusion proteins retain this ability to form particles and a range of hybrid VLPs carrying a variety of heterologous antigens have been produced and shown to elicit potent immune responses. Hybrid VLPs carrying human immunodeficiency virus (HIV) antigens stimulate the three main components of the immune system, namely antibody synthesis, T-cell proliferative responses and cytotoxic T-lymphocyte (CTL) responses.

Changes in cellular proteins associated with the expression of human immunodeficiency virus type 1 trans-activator protein Tat

Earlier studies have revealed a distinct class of regulatory proteins known as trans-activator proteins in diverse biological systems. These proteins have been shown to act on both homologous and heterologous promoter targets. Activation of heterologous targets is speculated to be an integral part of virus-induced pathogenesis. To verify this hypothesis, stable Tat-producing human rhabdomyosarcoma (RD) cell lines were generated. These cell lines produced significant levels of functional Tat, as measured by transfection with the reporter plasmid pLTR-CAT. Tat-producing cells, although morphologically similar to the control, exhibited a slower growth rate. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of the cellular proteins from control (tat-) and tat+ cells revealed increased quantities of 34- and 40-kD proteins along with the appearance of a new 74-kD protein in tat+ cells. Subsequent two-dimensional gel analysis revealed several additional differences. Tat+ cell lines produced two proteins of M(r) 19.5 and 44 kD anew, while proteins with M(r) 14.5, 42, and 52.5 kD were in greater abundance. Interestingly, a 26-kD protein that was originally present in the G418+/tat- (control) sample disappeared in the presence of Tat. These data support a possible modulator role for Tat in cellular gene expression.

Inhibition of type 1 human immunodeficiency virus replication by a tat antagonist to which the virus remains sensitive after prolonged exposure in vitro

The transactivator of transcription, Tat, of human immunodeficiency virus type 1 (HIV-1) is required for viral replication. Inhibition of Tat function could have the potential to keep integrated provirus in dormancy. In the presence of Tat, Ro 24-7429, an analog of Ro 5-3335, inhibited expression of indicator genes controlled by the HIV-1 long terminal repeat promoter in transient transfection assays and in a constitutive cell line at noncytotoxic concentrations. Reduction of steady-state mRNA of the indicator gene by the compound correlated with reduction of the gene product in the constitutive cell line. Ro 24-7429 has broad activity against several strains of HIV-1 in different cell lines, peripheral blood lymphocytes, and macrophages (IC90 = 1-3 microM). Importantly, Ro 24-7429 inhibited viral replication in both acute and chronic infection in vitro, a characteristic expected of a Tat antagonist and not shared by viral reverse transcriptase inhibitors. Consistent with this, the compound reduced cell-associated viral RNA and proteins and partially restored cell-surface CD4 in chronically infected cells. After 2 years of continued weekly passage of the virus in fresh CEM cells grown in the presence of the compound at 1 or 10 microM, the virus did not develop resistance to the drug. These results indicate that the compound's action might involve a cellular factor.

Two strains of SIVmac show differential transactivation mediated by sequences in the promoter

Two infectious molecular clones of simian immunodeficiency virus, SIVmac251 and SIVmac239, have very different in vivo properties, SIVmac239 being much more pathogenic than SIVmac251. To assess whether the in vivo differences between the two viruses would be reflected in transcriptional rates in vitro, transcriptional activity in the presence of the transactivation protein tat was analyzed by transient transfection assays in HUT-78 and U937 cells. Whereas the two promoters had similar basal activities (Anderson and Clements, 1991, J. Virol. 65, 51-60) the promoter of SIVmac239 was transactivated to a greater extent. Removal of sequences 5' to -225 and 3' to +18 maintained the basal activity, yet made the promoter unresponsive to tat. Addition of bases +19 to +149 reconstituted transactivation and decreased basal activity. Analysis of deletion mutants with reconstituted transactivation response region determined that differences between the two strains were maintained even when only the proximal sequences, -225 to +18 of the U3 and R region were placed upstream of the TAR sequences. This region contains four nucleotide differences and the potential Sp-1-binding sites, where there are an additional 11 bases in SIVmac239 that create a third potential Sp-1 site, compared to only 2 in SIVmac251. Transactivation in this assay system was found to correlate better to RNA differences shortly after transfection (12 hr) than later (46 hr).

Circular dichroism and molecular modeling yield a structure for the complex of human immunodeficiency virus type 1 trans-activation response RNA and the binding region of Tat, the trans-acting transcriptional activator

Transcription in the human immunodeficiency virus type 1 (HIV-1) retrovirus is regulated by binding the viral Tat protein (trans-acting transcriptional activator) to the trans-activation response (TAR) RNA sequence. Here, vacuum UV circular dichroism (VUV-CD) is used to study the structure of TAR and its complex with two peptide fragments that are important for Tat binding to TAR. The VUV-CD spectrum of TAR is typical of A-form RNA and is minimally perturbed when bound to either the short or the long Tat peptide. The CD spectra of the complexes indicate an extended structure in the arginine-rich region of Tat from amino acid residue 47 through residue 58 and a short alpha-helix within the adjacent 59-72 region. Models of TAR and its peptide complexes are constructed to integrate these spectroscopic results with current biochemical data. The model suggests that (i) the arginine-rich 49-58 region is primarily responsible for electrostatic interactions with the phosphates of the RNA, (ii) the arginine side chains can additionally interact with substituent groups of the nucleotide bases to confer base recognition in the complex, (iii) the recognition of uracil-23 in TAR is facilitated by the peptide backbone, and (iv) the glutamine-rich face of an alpha-helix within the 59-72 region pairs to bases UGG at nucleotide positions 31-33 in the TAR loop and thus provides an additional motif in the Tat trans-activating protein to recognize TAR RNA.

Variable inhibition of cell-free translation by HIV-1 transcript leader sequences

The 5' ends of all human immunodeficiency virus type I (HIV-1) transcripts have the potential to coordinately regulate translation of HIV-1 mRNAs. Conflicting observations of the translational impact of these sequences in various systems stimulated these analyses of translation in reticulocyte lysates. We report a sensitive, rapid, quantitative, and inexpensive cell-free translation assay in which translational efficiency is monitored by enzymatic assay of the translation products. Using this assay and conventional radiolabeling assays, we demonstrate that the HIV-1 transcript leader inhibits downstream translation and that the stem-loop structure is required. Under our assay conditions, this inhibition occurs predominantly in cis and is not mediated by the 68 kD, interferon-induced, double-stranded RNA-activated kinase (p68). However, under other assay conditions the HIV-1 leader may activate p68 and inhibit translation in trans. We show that variation between individual preparations of cell-free extracts can dramatically alter the magnitude of the translational inhibition by the HIV-1 leader. Further, we provide evidence that a heat-labile factor is required for efficient translation of transcripts containing the HIV-1 leader. These observations provide a foundation for identifying factors required for translation of HIV-1 transcripts.

Transcriptional activation of the tat-defective human immunodeficiency virus type-1 provirus: effect of interferon

The effect of human interferon-alpha 2 (HuIFN-alpha 2) on the activation of HIV-1 provirus was studied in cell lines containing either an integrated tat-defective HIV-1 provirus (HIV-1 (-tat)) (HNHIVdt4 cells) or the HIV-1 (-tat) provirus and a plasmid in which the expression of HuIFN-alpha 2 was under the control of HIV LTR (HNHIV alpha 1 cells). In both cell lines, the expression of HIV-1 RNA was below the limit of detection, but transcription of the HIV-1 (-tat) provirus could be induced either by transfection with Tat-expressing plasmid or by treatment with TPA and cycloheximide (CHX). By contrast, stimulation with TPA alone induced HIV-1 transcription only in HNHIVdt4 cells, but not in HNHIV alpha 1 cells that produced low levels of IFN-alpha constitutively. Similarly in a transient expression assay, TPA upregulated transcription of the transfected HIV-1 CAT plasmid only in HNHIVdt4 cells, but not in HNHIV alpha 1 cells. UV-crosslinking analysis of NF-kappa B-specific proteins induced in TPA-treated cells showed the presence of 45 and 55 kDa NF-kappa B-binding protein in TPA-induced HNHIVdt4 cells while, in HNHIV alpha 1 cells, we detected only 55-, 110-, and 200-kDa proteins, but no 45-kDa protein. The transcriptional effects of IFN could not, however, be seen in the presence of Tat protein, suggesting that the virus developed a mechanism to overcome the IFN-mediated restrictions.

Intranuclear topological distribution of HIV-1 trans-activators

Subcellular localization of human immunodeficiency virus type I (HIV-1) Tat and Rev was examined using a confocal laser scanning microscope (CLSM). In transfected COS-7 cells, Tat resided exclusively in the perinocleolar region, while Rev infiltrated fully into the nucleoli. The chimeric Tat in which the nucleolar targeting signal was replaced by that of Rev, which retains trans-acting activity of Tat, remained still in the perinucleolar region as wild-type Tat. Perinucleolar distribution of Tat protein suggests the existence of a novel nucleolar architecture that affects transcription.

Expression of maedi-visna virus major core protein, p25: development of a sensitive p25 antigen detection assay

The gene for the major core protein, p25, of maedi-visna virus (MVV) was cloned using a PCR (polymerase chain reaction) strategy employing primers designed for the insertion of the gene directly into yeast Ty-VLP expression vectors. In this system p25 is expressed as a fusion protein which self-assembles into virus-like particles (VLPs) due to interaction of the Ty A fusion partner. High levels (50-60 mg/l) of p25 fusion protein were produced, and p25 was recovered in soluble and highly pure form following cleavage from the Ty particle by Factor Xa protease digestion. The p25 protein produced in yeast is antigenically authentic, as defined by its reactivity with p25-specific antisera and its ability to elicit antibodies reactive with native viral p25 protein; although the cleaved, soluble form of p25 was found to be considerably more antigenic than the hybrid Ty-p25 VLP. Using this reagent anti-p25 monoclonal and polyclonal antibodies were generated. These sera and the p25 protein have been used to develop a sensitive MVV p25 detection assay. These reagents and assays will facilitate further studies of viral replication and immune response to the virus.

HIV regulatory proteins: potential targets for therapeutic intervention

With the incidence of HIV infection on the rise worldwide, it is obvious that new approaches must be taken to halt the spread of disease. Unfortunately, this is no easy task; of all retroviruses studied to date HIV remains the most complex in terms of genomic organization, regulation of gene expression, and replication. However, as the mechanism of action of the unique viral regulatory proteins is deciphered, new windows of opportunity for attacking the virus like cycle are opened. The essential regulatory function served by both Tat and Rev transacting regulatory proteins makes them attractive targets for prophylactic and therapeutic intervention. This review will focus on our current understanding of Tat and Rev function.

Transactivation of heterologous promoters by HIV-1 tat

To determine whether HIV-1 tat can transactivate a heterologous promoter lacking HIV sequences other than the TAR element, TAR was placed downstream of the chicken beta-actin promoter. Tat increased expression directed by the actin-TAR promoter to a degree equal to tat induction of the HIV-1 LTR. Optimal transactivation was observed when TAR was positioned downstream of the actin promoter such that the expected cap site of transcripts from this promoter would be the same as in transcripts directed by the HIV-1 LTR. Tat was able to transactivate, though to a lesser extent, a promoter consisting solely of a TATA element fused to TAR. Thus, tat induction does not require HIV-1 LTR promoter sequences other than TAR. Tat, when fused to the DNA binding domain of BPV-1 E2, was able to transactivate a truncated SV40 promoter containing upstream E2 binding sites, indicating that tat may be capable of transactivation when directed by a DNA binding protein to an upstream site in a heterologous promoter lacking all HIV sequences. Substitution of Ala for Lys at position 41 of tat in the tat-E2 fusion, a mutation which dramatically decreases tat transactivation of the HIV-1 LTR, eliminated this transactivation.

Transcriptional initiation and postinitiation effects of murine leukemia virus long terminal repeat R-region sequences

Sequences within the R components of the long terminal repeats (LTRs) of several retroviruses are known to be involved at various steps in expression of the viral genomes. A series of experiments was performed to test whether sequences within the R regions of the murine leukemia viruses Akv and SL3-3 affect viral expression. By using plasmid clones of the viral LTRs linked to a reporter gene, deletion of the R region was found to decrease expression to variable extents in a series of mammalian cell lines, with the largest effects being detected in murine fibroblasts. R-region sequences from the human immunodeficiency virus type 1 LTR or a random sequence were unable to substitute for the murine leukemia virus sequences. Transcripts from the R-region-deleted templates were initiated at the proper site in the LTR, but their levels were decreased at least 10-fold. Nuclear run-on assays showed that the decrease caused by the R-region deletions was due, in part, to an effect on RNA polymerase loading, suggesting an effect on transcriptional initiation. The remainder of the activity was presumably due to a posttranscriptional effect. Analysis of the R-region sequences of murine leukemia viruses and related retroviruses led to the prediction of a conserved secondary structure in the transcribed RNA that might have a role in activity. We conclude that R-region sequences are of importance for the expression of a variety of retroviruses.

tat regulates binding of the human immunodeficiency virus trans-activating region RNA loop-binding protein TRP-185

The TAR element extending from -17 to +80 in the human immunodeficiency virus long terminal repeat (HIV LTR) is required for activation of gene expression by the tat trans-activator protein. TAR RNA forms a stable stem-loop structure, and mutagenesis studies indicate that the stem structure, the primary sequence of the loop, and the bulge element are the major determinants for tat activation. RNA gel retardation analysis demonstrates that both tat and cellular proteins bind to TAR RNA, but the mechanism by which these proteins increase HIV gene expression is unknown. We have fractionated HeLa cell nuclear extracts in an attempt to identify cellular proteins that bind to TAR RNA and are involved in regulating HIV gene expression. RNA gel retardation and UV cross-linking reveal that a cellular protein of 185 kD, which we designate TAR RNA-binding protein 185 (TRP-185), binds with both high affinity and marked specificity to TAR RNA. RNA gel retardation and competition analyses indicate that TRP-185 binding is strongly dependent on the TAR RNA loop sequences. The binding of TRP-185 is modulated by both a set of cellular cofactors and the tat protein. Highly purified preparations of TRP-185 are capable of activating in vitro transcription of wild-type, but not mutated, HIV LTR chloramphenicol acetyltransferase (CAT) constructs. These results characterize a positively acting cellular RNA-binding factor, TRP-185, which is involved in the regulation of HIV gene expression.

Tat-dependent adenosine-to-inosine modification of wild-type transactivation response RNA

Tat is a potent activator of gene expression in human immunodeficiency virus type 1 (HIV-1). Activation by Tat requires a cis-acting element, the transactivation response (TAR) site, located in the viral long terminal repeat and the 5' end of all viral mRNAs. Sequences in TAR RNA can fold into a specific stem-loop structure, and certain features of the stem-loop are essential for Tat-mediated transactivation. In Xenopus oocytes, TAR sequences can inhibit the translation of 3' cis-linked mRNAs. However, coinjection of Tat and the TAR-containing RNA into oocyte nuclei relieves this translational inhibition [Braddock, M., Chambers, A., Wilson, W., Esnout, M. A., Adams, S.E. & Kingsman, S.M. (1989) Cell 58, 269-279]. We report here that the intramolecular TAR stem-loop structure is a substrate for the double-stranded RNA (dsRNA)-modifying activity, which converts adenosines to inosines. This activity is located in the nuclei of Xenopus oocytes. The specificity and extent of modification of adenosines in TAR is dependent on Tat. We propose that the dsRNA-modifying activity may be one of the cellular proteins that interacts with TAR in the nucleus. The possible role of TAR RNA modification in the expression of HIV-1 is discussed.

Inhibition of HIV-LTR gene expression by oligonucleotides targeted to the TAR element

All human immunodeficiency virus mRNAs contain a sequence known as TAR (trans-activating responsive sequence). The TAR element forms a stable RNA stem-loop structure which binds the HIV tat (trans-activator) protein and mediates increased viral gene expression. In principle, molecules which bind to the TAR RNA structure would inhibit trans-activation by perturbing the native RNA secondary structure. We have constructed a series of phosphodiester and phosphorothioate antisense oligonucleotides which specifically bind to the HIV TAR element. Specific binding to the TAR element was demonstrated in vitro with enzymatically synthesized TAR RNA. The TAR-directed phosphorothioates inhibited trans-activation in a sequence-dependent fashion in a cell culture model using an HIV LTR/human placental alkaline phosphatase gene fusion and tat protein supplied in trans. The molecules also inhibited HIV replication in both acute and chronically infected viral assays, but without sequence specificity. We have constructed a series of vectors consisting of the MMTV promoter and 5'-untranslated region of four different mRNAs, including the TAR region, to study the effect of TAR on gene expression in heterologous systems. The results suggest that, in the absence of the HIV LTR, the TAR element has a repressive effect on gene expression, which is relieved by tat.