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At least 595 records · Page 33Linked to original sources
PubMed1999

Cyclin T1 domains involved in complex formation with Tat and TAR RNA are critical for tat-activation.

Tat activates transcription from the human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) by increasing the processivity of RNA polymerase II. Recently, it has been demonstrated that the cellular kinase CDK9 and its binding partner cyclin T1 are involved in regulating transcriptional elongation and tat-activation. Cyclin T1, CDK9 and Tat bind as a complex to elements in TAR RNA that are required for tat-activation. Here, we used cyclin T1 mutants to define domains in this protein that bind to both CDK9 and Tat and are involved in stimulating tat-activation. The region of cyclin T1 extending from amino acid residues 1 to 263 is necessary for complex formation with Tat bound to TAR RNA and for stimulation of tat-activation in murine cells that are normally poorly responsive to the actions of Tat. In contrast, a smaller region of cyclin T1 was required to bind to CDK9 and stimulate its kinase activity. Recombinant cyclin T1 and CDK9 stimulated both basal and tat-induced in vitro transcriptional elongation from the HIV-1 LTR. The effects of Tat on transcriptional elongation may be mediated by its ability to increase CDK9 phosphorylation of the RNA polymerase II C-terminal domain. These results demonstrate that cyclin T1 interactions with Tat and TAR RNA are critical for activation of HIV-1 gene expression.

Cyclin T↗
PubMed2002

Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings.

Ground-state dynamics in RNA is a critical precursor for structural adaptation observed ubiquitously in protein-RNA recognition. A tertiary conformational analysis of the stem-loop structural element in the transactivation response element (TAR) from human immunodeficiency virus type 1 (HIV-I) RNA is presented using recently introduced NMR methods that rely on the measurement of residual dipolar couplings (RDC) in partially oriented systems. Order matrix analysis of RDC data provides evidence for inter-helical motions that are of amplitude 46(+/-4) degrees, of random directional character, and that are executed about an average conformation with an inter-helical angle between 44 degrees and 54 degrees. The generated ensemble of TAR conformations have different organizations of functional groups responsible for interaction with the trans-activator protein Tat, including conformations similar to the previously characterized bound-state conformation. These results demonstrate the utility of RDC-NMR for simultaneously characterizing RNA tertiary dynamics and average conformation, and indicate an avenue for TAR complex formation involving tertiary structure capture.

Gene Products, tat↗
PubMed1996

Peptides derived from the interferon-induced PKR prevent activation by HIV-1 TAR RNA.

The double-stranded RNA-dependent protein kinase (PKR) is believed to mediate cellular antiviral responses, function as a tumor suppressor, and regulate cell growth and differentiation. Its activation is dependent on double-stranded RNA (dsRNA) structures but these interactions are not fully understood. The possibility of direct interaction between dsRNA and the arginine and lysine-rich region of PKR (residues 54-74) was examined using synthetic peptides. We found that addition of a synthetic peptide corresponding to residues 54-74 of murine PKR or residues 60-80 of human PKR inhibited the autophosphorylation and activation of the kinase by either poly(I)-poly(C) or the 82-nucleotide-long TAR RNA. Gel-shift analysis indicated that the peptides disrupted the kinase-TAR complex by binding directly to TAR RNA. These findings delineate at least one dsRNA-binding domain in PKR which may be important for its cellular activation.

Amino Acid Sequence↗
PubMed1999

Interactions between Tat and TAR and human immunodeficiency virus replication are facilitated by human cyclin T1 but not cyclins T2a or T2b.

The transcriptional transactivator (Tat) from the human immunodeficiency virus (HIV) does not function efficiently in Chinese hamster ovary (CHO) cells. Only somatic cell hybrids between CHO and human cells and CHO cells containing human chromosome 12 (CHO12) support high levels of Tat transactivation. This restriction was mapped to interactions between Tat and TAR. Recently, human cyclin T1 was found to increase the binding of Tat to TAR and levels of Tat transactivation in rodent cells. By combining individually with CDK9, cyclin T1 or related cyclins T2a and T2b form distinct positive transcription elongation factor b (P-TEFb) complexes. In this report, we found that of these three cyclins, only cyclin T1 is encoded on human chromosome 12 and is responsible for its effects in CHO cells. Moreover, only human cyclin T1, not mouse cyclin T1 or human cyclins T2a or T2b, supported interactions between Tat and TAR in vitro. Finally, after introducing appropriate receptors and human cyclin T1 into CHO cells, they became permissive for infection by and replication of HIV.

Animals↗
PubMed1994

Herpes-Simplex-Virus-Infected Cells Produce a Protein that Binds to the TAR DNA Region of the Human Immunodeficiency Virus Type 1 Long Terminal Repeat.

Activation of human immunodeficiency virus type 1 (HIV-1) provirus by herpes simplex virus type 1 (HSV-1) infection is mediated by both HSV-1 gene products and cellular transactivators. Previously, several key factors such as NF-kappaB-specific proteins p55 and p85, HLP-1 protein that binds to the LBP-1 sequences of the HIV-1 long terminal repeat (LTR) and the viral transactivator ICPO were found to play a role in the transcriptional activation of HIV-1 LTR expression. In this report, we describe binding of herpesvirus-specific protein TDP150 to the TAR DNA region of the HIV-1 LTR. Our data suggest that TDP150 may be related to the herpesvirus transactivator protein ICP4; both proteins are 150-kD DNA-binding proteins produced in HSV-infected cells in the presence of an inhibitor of viral DNA replication. However, the appearance of TDP150-binding activity is delayed by several hours compared to that of ICP4 and the DNA-binding specificity of TDP150 differs from that of purified ICP4. These results suggest that TDP150 is not identical to ICP4; whether it is its analogue remains to be determined. TAR DNA alone can confer responsiveness of heterologous promoter to HSV-1 infection, suggesting that this region can function as an enhancer in HSV-1-infected cells. Deletion of the TAR region from the HIV-1 LTR has not changed significantly the HSV-1-mediated stimulation. Copyright 1994 S. Karger AG, Basel

Journal Article↗
PubMed1995

Inhibition of intercellular communication by condensates of high and low tar cigarettes.

Inhibition of gap junctional intercellular communication (GJIC) is a predictive short term test for tumor promoting activity. A new metabolic cooperation assay has been developed, which takes the cytochrome P-450 metabolism into account. In this assay the inhibitory activity of tobacco smoke condensates (CSC) and CSC fractions from high and low tar cigarettes was tested. CSC of both high and low tar cigarettes and fractions thereof contained tumor promoting activity. The tar yield of the cigarettes did not closely reflect the effects in the GJIC assay and the major constituent nicotine had no effect. The effect was only marginally greater in cells expressing different cytochrome P-450 enzymes, indicating that the active substances are not metabolized by these enzymes. The activities of CSC fractions were considerably lower than the activities in the unfractionated CSC. This may indicate that compounds in the CSC act strongly synergistically. Furthermore, CSC and CSC fractions synergistically inhibit GJIC with the tumor promoter 12-O-tetradecanoylphorbol-13-acetate, indicating different mechanisms of action.

Cell Communication↗
PubMed2002

Geochemical and physiological evidence for mixed aerobic and anaerobic field biodegradation of coal tar waste by subsurface microbial communities.

We used geochemical analyses of groundwater and laboratory-incubated microcosms to investigate the physiological responses of naturally occurring microorganisms to coal-tar-waste constituents in a contaminated aquifer. Waters were sampled from wells along a natural hydrologic gradient extending from uncontaminated (1 well) into contaminated (3 wells) zones. Groundwater analyses determined the concentrations of carbon and energy sources (pollutants or total organic carbon), final electron acceptors (oxygen, nitrate, sulfate), and metabolic byproducts (dissolved inorganic carbon [DIC], alkalinity, methane, ferrous iron, sulfide, Mn2+). In the contaminated zone of the study site, concentrations of methane, hydrogen, alkalinity, and DIC were enhanced, while dissolved oxygen and nitrate were depleted. Field-initiated biodegradation assays using headspace-free serum bottle microcosms filled with groundwater examined metabolism of the ambient organic contaminants (naphthalene, 2-methylnaphthalene, benzothiophene, and indene) by the native microbial communities. Unamended microcosms from the contaminated zone demonstrated the simultaneous degradation of several coal-tar-waste constituents at the in situ temperature (10 degrees C). Lag phases prior to the onset of biodegradation indicated the prevalence of both aerobic and anaerobic conditions in situ. Electron acceptor-amended microcosms from the most contaminated well waters demonstrated only aerobic naphthalene degradation. Collectively, the geochemical and microbial evidence show that biodegradation of coal-tar-waste constituents occurs via both aerobic and anaerobic terminal electron accepting processes at this site.

Bacteria, Aerobic↗
PubMed2000

Thrombocytopenia and absent radii (TAR) syndrome associated with horseshoe kidney.

The TAR syndrome is an inherited disorder characterized by limb abnormalities, especially absent radii, and hypomegakaryocytic thrombocytopenia. Previous reports have included two infants with genitourinary abnormalities. We report a newborn with bilaterally absent radii and foreshortened ulnae, hypoplastic humeri, a left clubfoot, a ventricular septum defect, and persistent thrombocytopenia. This constellation of abnormalities is consistent with the TAR syndrome. In addition, he had a horseshoe kidney with parenchyma of normal appearance. This is the first report of horseshoe kidney in association with the TAR syndrome.

Abnormalities, Multiple↗
PubMed1995

Tetrahydropyrimidine derivatives inhibit binding of a Tat-like, arginine-containing peptide, to HIV TAR RNA in vitro.

The ability of a small molecule, 2-methyl,4-carboxy,5-hydroxy-3,4,5,6-tetrahydropyrimidine (THP(A)), which accumulates intracellularly in various streptomyces, to inhibit the interaction of Tat peptide (R52) with TAR RNA is presented. Using gel-shift assay, we found that the inhibition constant Ki of THP(A) is 50-100 nM, which is in the range of the binding constants of Tat peptide and protein. THP(A) is approximately 10(6) times more tightly bound than the free L-arginine. The high binding affinity may be attributed to the special delocalized positive charge on the NCN group and the hydroxyl group at the 5 position of this molecule. A model for THP(A)-TAR interaction, analogous to the arginine guanidinum group-TAR interaction, is presented. The relatively high uptake of THP(A) by mammalian cells warrants in vivo Tat/TAR inhibition studies.

Bacterial Proteins↗
PubMed1993

Butter in the initial treatment of hot tar burns.

Hot tar adheres to skin and produces burns of variable depth. Removal of the tar is not essential but it improves patient comfort and allows early assessment of the underlying tissue damage. Butter is readily available and is an effective method of removing the adherent tar.

Accidents, Occupational↗
PubMed1989

Quantitative analysis of the hydrogen peroxide formed in aqueous cigarette tar extracts.

We have established, for the first time, a reliable method to quantitate hydrogen peroxide (H2O2) generated in aqueous extracts of cigarette smoke tar. The aqueous tar extract was passed through a short reverse-phase column and its H2O2 concentration determined by differential pulse polarography using an automatic reference subtraction system. The H2O2 concentration increased with aging, pH and temperature; the presence of superoxide dismutase lead to lower H2O2 concentrations. This method was applied to many kinds of research and commercial cigarettes. With a few exceptions, the amount of H2O2 formed after a fixed time from each cigarette smoke was proportional to its tar yield.

Hydrogen Peroxide↗
PubMed2004

Taste-aversion-prone (TAP) rats and taste-aversion-resistant (TAR) rats differ in ethanol self-administration, but not in ethanol clearance or general consumption.

Taste-aversion (TA)-prone (TAP) rats and TA-resistant (TAR) rats have been developed by means of bidirectional selective breeding on the basis of their behavioral responses to a TA conditioning paradigm. The TA conditioning involved the pairing of an emetic-class agent (cyclophosphamide) with a novel saccharin solution as the conditioned stimulus. Despite the absence of ethanol in the selective breeding process, these rat lines differ widely in ethanol self-administration. In the current study, blood alcohol concentrations (BACs) were determined after 9 days of limited (2 h per day) access to a simultaneous, two-bottle choice of a 10% ethanol in water solution [volume/volume (vol./vol.)] or plain water. The BACs correlated highly with ethanol intake among TAR rats, but an insufficient number of TAP rats yielded measurable BACs to make the same comparison within this rat line. The same rats were subsequently exposed to 24-h access of a two-bottle choice (10% ethanol or plain water) for 8 days. Ethanol consumption during the 24-h access period correlated highly with that seen during limited access. Subsequent TA conditioning with these rats yielded line-typical differences in saccharin preferences. In a separate group of rats, ethanol clearance was determined by measuring BACs at 1, 4, and 7 h after injection of a 2.5-g/kg dose of ethanol. Ethanol clearance was not different between the two lines. Furthermore, the lines did not differ with respect to food and water consumption. Therefore, the TAP rat-TAR rat differences in ethanol consumption cannot be attributed to line differences in ethanol metabolism or in general consummatory behavior. The findings support our contention that the line differences in ethanol consumption are mediated by differences in TA-related mechanisms. The findings are discussed with respect to genetically based differences in the subjective experience of ethanol.

Alcohol Drinking↗
PubMed2004

Inhibition of HIV-1 TAR RNA-Tat peptide complexation using poly(acrylic acid).

HIV-1 is regulated at the transcriptional level by the interaction of Tat protein with the transactivation responsive region (TAR) RNA, a 59-base stem-loop structure located at the 5'-end of all nascent HIV-1 transcripts. Here, by targeting the Tat peptide, we found that negatively charged poly(acrylic acid) (PAA) had high affinity with Tat peptide and could inhibit the interaction of TAR with Tat. Therefore, PAA could block HIV replication by binding to Tat not to TAR RNA, providing a new thinking for the design of novel anti-HIV drugs.

Acrylic Resins↗
PubMed2004

Binding of hybrid molecules containing pyrrolo [2,1-c][1,4]benzodiazepine (PBD) and oligopyrrole carriers to the human immunodeficiency type 1 virus TAR-RNA.

The binding properties of a set of four hybrids, prepared combining from one to four polypyrrole minor groove binders and pyrrolo [2,1-c][1,4]benzodiazepine (PBD), have been studied using as target molecule the HIV-1 TAR-RNA. We found that these hybrids bind to TAR-RNA and inhibit TAR/protein(s) interactions. The anti-proliferative activity of the hybrids has been tested in vitro on HL3T1 cells and compared to the anti-proliferative effects of the natural product distamycin A and PBD. The effects on HIV-1 LTR directed transcription were studied using the chloramphenicol-acetyltransferase gene reporter system, and structure-activity relationships are discussed. The results obtained demonstrate that the hybrids 22-25 exhibit different TAR-RNA binding activity with respect to both distamycin A and PBD. In addition, a direct relationship was found between number of pyrrole rings present in the hybrids 22-25 and anti-proliferative effects. It was found that increased length of the polypyrrole backbone leads to an increased in vitro anti-proliferative effect, i.e. the hybrid 25, containing the four pyrroles distamycin analogous, is more active than 22, 23 and 24 against cell proliferation. With respect to inhibition of HIV-1 LTR-driven transcription, it was found that the hybrids 23-25 containing two-four pyrroles are active. Therefore, when anti-proliferative effects are considered together with the inhibitory effects of HIV-1 LTR driven transcription, our results suggest that the hybrid 23 is the more interesting, since it exhibits low anti-proliferative activity and inhibits HIV-1 LTR driven transcription both in vitro and in ex vivo experiments.

Antiviral Agents↗
PubMed2006

The design, synthesis, and biological evaluation of novel substituted purines as HIV-1 Tat-TAR inhibitors.

A series of novel substituted purines containing a side chain with a terminal amino or guanidyl group were designed and synthesized as HIV-1 Tat-TAR inhibitors. All the compounds could effectively block the TAR transactivation in human 293T cells with the CAT expression percentage ranging from 34.4% to 65.7% and showed high antiviral effects with low cytotoxicities in inhibiting the formation of SIV-induced syncytium in CEM174 cells. Molecular modeling studies by Auto-dock process suggest that the compounds bind to TAR RNA in two different modes.

Animals↗
PubMed2005

A comparative binding study of BIV Tat peptide against its TAR RNA duplex, RNA-DNA heteroduplex and DNA duplex.

Association between RNA and DNA strands to form RNA-DNA heteroduplex is important in many biological processes such as transcription, DNA replication and reverse transcription. Herein, binding affinities of a 17-mer BIV Tat peptide is compared with TAR DNA duplex, TAR RNA-DNA heteroduplex and TAR RNA duplex. It was observed that binding affinities of Tat peptide is comparable against DNA-RNA heteroduplex and RNA duplex, whereas DNA duplex binding is decidedly poor.

Base Sequence↗
PubMed2005

Neamine dimers targeting the HIV-1 TAR RNA.

Natural aminoglycoside antibiotics, such as neomycin, target bacterial ribosomal RNA. Neomycin also binds strongly to HIV TAR and RRE RNA through the predominant interactions of its neamine core. In the search for antiviral agents targeting multiple binding sites for aminoglycosides in RNA, we report here the synthesis of new neamine dimers and a trimer in which the neamine cores are connected by different linking chains attached at the 4'- and/or 5-positions. Inhibition of TAR-Tat complexation by these oligomers was studied via fluorimetric binding assays performed under two ionic strengths. All dimers strongly inhibit TAR-Tat association, with IC50 values 17-85 times better than the value obtained with neomycin. These results demonstrate that modifying neamine at the 4'- or the 5-position is a promising strategy in the search for antiviral agents.

Aminoglycosides↗