The HIV-1 inducer of short transcripts activates the synthesis of 5,6-dichloro-1-beta-D-benzimidazole-resistant short transcripts in vitro

Manipulation of P-TEFb control machinery by HIV: recruitment of P-TEFb from the large form by Tat and binding of HEXIM1 to TAR

Basal transcription of the HIV LTR is highly repressed and requires Tat to recruit the positive transcription elongation factor, P-TEFb, which functions to promote the transition of RNA polymerase II from abortive to productive elongation. P-TEFb is found in two forms in cells, a free, active form and a large, inactive complex that also contains 7SK RNA and HEXIM1 or HEXIM2. Here we show that HIV infection of cells led to the release of P-TEFb from the large form. Consistent with Tat being the cause of this effect, transfection of a FLAG-tagged Tat in 293T cells caused a dramatic shift of P-TEFb out of the large form to a smaller form containing Tat. In vitro, Tat competed with HEXIM1 for binding to 7SK, blocked the formation of the P-TEFb–HEXIM1–7SK complex, and caused the release P-TEFb from a pre-formed P-TEFb–HEXIM1–7SK complex. These findings indicate that Tat can acquire P-TEFb from the large form. In addition, we found that HEXIM1 binds tightly to the HIV 5′ UTR containing TAR and recruits and inhibits P-TEFb activity. This suggests that in the absence of Tat, HEXIM1 may bind to TAR and repress transcription elongation of the HIV LTR.

Mechanism and history of evolution of symbiotic HIV strains into lethal pandemic strains: the key event may have been a 1927 trial of pamaquine in Leopoldville (Kinshasa), Congo

In previous papers, I have rejected both the zoonosis and the serial transfer hypotheses of the origin and evolution of the current lethal pandemic strains of HIV. The hypothesis that fits the critical observations is that all the human and nonhuman primate species in central Africa (an area of hyper-endemic malaria) have shared (through inter-species transfers) a "primate T-cell retrovirus" (PTRV), which has adapted to each host species. This retrovirus is believed to assist primate T-cells attack the liver stage of the malaria infection. Each geographic region has a dominant primate host and a characteristic virus. Starting in 1955 and continuing into the late 1970s, chloroquine was provided by the WHO and used for prophylaxis against malaria. Chloroquine has a number of biochemical activities but two of the most important are blocking transcription of cellular genes and proviruses activated by NF-kappaB and blocking the glycosylation of surface proteins on viruses and cells. Concurrent with the development of resistance of the malaria parasite to chloroquine, HIV strains were quickly selected, which have enhanced transcription rates (by inclusion of multiple kappaB binding sites in their long terminal repeats by recombination) and enhanced infectivity (fusogenicity) (most likely by mutations in multiple viral genes that regulate glycosylation of Env). There also may have been mutations that enhanced activation of NF-kappaB in the host cell. These changes in the retrovirus genome were not manifest in effects of the HIV strains as long as the hosts were under the influence of chloroquine. But, when the virus infects people who are not protected by chloroquine, the virus multiplies more rapidly and is more communicable. Fortunately, most of these strains (i.e., HIV-2 groups, and HIV-1 O and HIV-1 N) self-regulate (i.e., infected cells kill infected cells) well enough that viral loads remain subdued and bystander cells of the immune system are not excessively attrited. In the case of HIV-1 group M, however, there is more going on. Following the work of Korber et al. on the phylogenetics of HIV-1 groups M, I reach the conclusion that the major subgroups giving rise to the worldwide pandemic, were founded in a 1927 clinical trial of pamaquine (plasmoquine) in Leopoldville (Kinshasa). This drug is much more toxic that chloroquine and appears to have strongly selected for resistance to apoptosis in infected cells, which allows these subgroups to attrite bystander cells leading to AIDS.

HIV-1 Tat stimulates transcription complex assembly through recruitment of TBP in the absence of TAFs

The human immunodeficiency virus type I (HIV-1) transactivator protein Tat is an unusual transcriptional activator that is thought to act solely by promoting RNA polymerase II processivity. Here we study the mechanism of Tat action by analyzing transcription complex (TC) assembly in vivo using chromatin immunoprecipitation assays. We find, unexpectedly, that like typical activators Tat dramatically stimulates TC assembly. Surprisingly, however, the TC formed on the HIV-1 long terminal repeat is atypical and contains TATA-box-binding protein (TBP) but not TBP-associated factors (TAFs). Tat function involves direct interaction with the cellular cofactor positive transcription elongation factor b (P-TEFb). Artificial tethering of P-TEFb subunits to HIV-1 promoter DNA or nascent RNA indicates that P-TEFb is responsible for directing assembly of a TC containing TBP but not TAFs. On the basis of this finding, we identify P-TEFb-dependent cellular promoters that also recruit TBP in the absence of TAFs. Thus, in mammalian cells transcription of protein-coding genes involves alternative TCs that differ by the presence or absence of TAFs.

Flexible DNA binding of the BTB/POZ-domain protein FBI-1

POZ-domain transcription factors are characterized by the presence of a protein-protein interaction domain called the POZ or BTB domain at their N terminus and zinc fingers at their C terminus. Despite the large number of POZ-domain transcription factors that have been identified to date and the significant insights that have been gained into their cellular functions, relatively little is known about their DNA binding properties. FBI-1 is a BTB/POZ-domain protein that has been shown to modulate HIV-1 Tat trans-activation and to repress transcription of some cellular genes. We have used various viral and cellular FBI-1 binding sites to characterize the interaction of a POZ-domain protein with DNA in detail. We find that FBI-1 binds to inverted sequence repeats downstream of the HIV-1 transcription start site. Remarkably, it binds efficiently to probes carrying these repeats in various orientations and spacings with no particular rotational alignment, indicating that its interaction with DNA is highly flexible. Indeed, FBI-1 binding sites in the adenovirus 2 major late promoter, the c-fos gene, and the c-myc P1 and P2 promoters reveal variously spaced direct, inverted, and everted sequence repeats with the consensus sequence G(A/G)GGG(T/C)(C/T)(T/C)(C/T) for each repeat.

Identification of cleavage sites in the HIV-1 TAR RNA by 10-23 and 8-17 catalytic motif containing DNA enzymes

A quick identification of a cleavage site in the target RNA molecule to obtain sequence-specific cleavage by either catalytic RNA (ribozymes) or DNA (DNA enzymes) is very important for achieving gene-specific suppression. These molecules could also provide important information on the secondary and tertiary structure of the target RNA molecule. We have exploited the use of two kinds of DNA enzymes, namely, the 10-23 and 8-17 catalytic motif containing DNA enzymes, to achieve these objectives. We identified several DNA enzyme cleavage sites in the human immunodeficiency virus type 1 (HIV-1) transactivation response element (TAR) RNA-a structural feature present at the 5' end of all HIV-1 transcripts. Most of the DNA enzymes that cleaved the TAR RNA were targeted to the regions that were single-stranded in the predicted structure. Regions that were predicted to be base-paired (stem) failed to show any detectable cleavage. The DNA enzyme possessing the 8-17 catalytic motif was extremely efficient in cleaving full length, as well as short, HIV-1 specific transcripts. The efficiency of cleavage of the same target RNA by DNA enzymes that possessed the 10-23 catalytic motif was significantly less in comparison, and they failed to cleave the short transcripts. These molecules, in principle, have the potential to down regulate expression of all HIV-1 transcripts from a wide range of isolates because this region is functionally very well conserved.

HIV and hepatitis delta virus: evolution takes different paths to relieve blocks in transcriptional elongation

The elongation step of transcription by RNA polymerase II (RNAPII) is controlled both positively and negatively by over a dozen cellular proteins. Recent findings suggest that two distinct viruses, human immunodeficiency virus type 1 and hepatitis delta virus, encode proteins that facilitate viral replication and transcription by targeting the same cellular transcription elongation machinery.

C-terminal domain phosphatase sensitivity of RNA polymerase II in early elongation complexes on the HIV-1 and adenovirus 2 major late templates

The fate of RNA polymerase II in early elongation complexes is under the control of factors that regulate and respond to the phosphorylation state of the C-terminal domain (CTD). Phosphorylation of the CTD protects early elongation complexes from negative transcription elongation factors such as NELF, DSIF, and factor 2. To understand the relationship between transcript elongation and the sensitivity of RNA polymerase IIO to dephosphorylation, elongation complexes at defined positions on the Ad2-ML and human immunodeficiency virus type 1 (HIV-1) templates were purified, and their sensitivity to CTD phosphatase was determined. Purified elongation complexes treated with 1% Sarkosyl and paused at U(14)/G(16) on an HIV-1 template and at G(11) on the Ad2-ML template are equally sensitive to dephosphorylation by CTD phosphatase. Multiple elongation complexes paused at more promoter distal sites are more resistant to dephosphorylation than are U(14)/G(16) and G(11) complexes. The HIV-1 long terminal repeat and adenovirus 2 major late promoter do not appear to differentially influence the CTD phosphatase sensitivity of stringently washed complexes. Subsequent elongation by 1% Sarkosyl-washed U(14)/G(16) complexes is unaffected by prior CTD phosphatase treatment. This result is consistent with the hypothesis that CTD phosphatase requires the presence of specific elongation factors to propagate a negative effect on transcript elongation. The action of CTD phosphatase on elongation complexes is inhibited by HIV-1 Tat protein. This observation is consistent with the idea that Tat suppression of CTD phosphatase plays a role in transactivation.

Human immunodeficiency virus gene regulation as a target for antiviral chemotherapy

Inhibitors interfering with human immunodeficiency virus (HIV) gene regulation may have great potential in anti-HIV drug (combination) therapy. They act against different targets to currently used anti-HIV drugs, reduce virus production from acute and chronically infected cells and are anticipated to elicit less virus drug resistance. Several agents have already proven to inhibit HIV gene regulation in vitro. A first class of compounds interacts with cellular factors that bind to the long terminal repeat (LTR) promoter and that are needed for basal level transcription, such as NF-kappa B and Sp1 inhibitors. A second class of compounds specifically inhibits the transactivation of the HIV LTR promoter by the viral Tat protein, such as the peptoid CGP64222. A third class of compounds prevents the accumulation of single and unspliced mRNAs through inhibition of the viral regulator protein Rev, such as the aminoglycosidic antibiotics. Most of these compounds have been tested in specific transactivation assays. Whether they are active at the postulated target in virus replication assays has, for many of them, not been ascertained. Toxicity data are often lacking or insufficient. Yet these data are crucial in view of the toxicity that may be expected for compounds that primarily interact with cellular factors. Although a promising lead, considerable research is still required before gene regulation inhibitors may come of age as clinically useful agents.

Phosphorylation of triciribine is necessary for activity against HIV type 1

Triciribine (TCN) is a tricyclic nucleoside with known antineoplastic and antiviral activity. It is a potent and selective inhibitor of HIV-1 and HIV-2, including strains known to be resistant to AZT or TIBO. TCN is phosphorylated to its 5'-monophosphate (TCN-P) by intracellular adenosine kinase (AK), but is not converted to di- or triphosphates. We now report that 5'-phosphorylation is requisite for the activity of TCN against HIV-1. CEM cells incubated with TCN at concentrations ranging from 0.1 to 330 microM gave intracellular TCN-P concentrations from 27 to 775 microM, respectively. There was no difference in the amount of intracellular TCN-P detected in uninfected compared with HIV-1-infected CEM cells. The antiviral effect of TCN against HIV-1 was strongly antagonized by the AK inhibitor 5-iodotubercidin (ITu). In contrast, TCN and ITu only exhibited additive cytotoxicity. The 5'-deoxy analog of TCN, which cannot be phosphorylated, had no antiviral effect against HIV-1 at a concentration more than 100 times higher than the IC50 of TCN. Similarly, TCN was not active against HIV-1 in an AK-deficient cell line (AA-2) at concentrations shown to inhibit the virus by >95% in CEM cells. Consistent with its AK-deficient phenotype, this cell line phosphorylated TCN to only 3% of the extent observed in CEM cells. We conclude that TCN must be phosphorylated to TCN-P for activity against HIV-1.