Long Terminal Repeat Region Research Articles

CREB and COUP-tF mediate transcriptional activation of the human immunodeficiency virus type 1 genome in jurkat t cells in response to cyclic AMP and dopamine

Infection of lymphocytes by the human immunodeficiency virus type 1 (HIV-1) is associated with an increase in intracellular cAMP levels. Recent studies have shown that lymphocytes are able to synthesize and bind the dopamine, known to affect multiple cellular pathways, such as the cAMP pathway. Here we have investigated the molecular mechanisms by which cAMP and dopamine regulate HIV-1 gene transcription in Jurkat T cells. Transient expression experiments revealed that dopamine and forskolin lead to a synergistic stimulation of long terminal repeat (LTR)-driven transcription. This action is mediated through the cAMP response element binding (CREB) protein and chicken ovalbumin upstream promoter transcription factor (COUP-TF). CREB and COUP-TF act indirectly through the minimal -40/+80 and -68/+80 LTR region, respectively. We have previously demonstrated that COUP-TF stimulates HIV-1 transcription via the -68/+29 LTR region without direct DNA binding. Here, gel supershift experiments show that CREB does not directly bind to the -45/+85 proximal LTR sequences. Moreover, our data reveal novel functional interactions between COUP-TF and CREB, which lead to synergistic cAMP- and dopamine-induced transactivation of the HIV-1 LTR. These findings reveal that dopamine-induced signals and the cAMP pathway stimulate HIV-1 gene transcription in lymphocytes by converging to the minimal -68/+80 LTR region, through the transcription factors CREB and COUP-TF.

Long terminal repeat promoter/enhancer activity of different subtypes of HIV type 1.

Transcription of the HIV-1 provirus genome is regulated by a complex interplay between viral regulatory proteins and cellular transcription factors that interact with the viral long terminal repeat (LTR) region of HIV-1. However, several cellular transcription factors have been identified that can interact with the HIV-1 LTR; the significance of all of these factors is not clearly understood. In this study we have characterized the LTR region of different subtypes of HIV-1 with regard to nucleotide sequence and promoter activity. The LTR regions of HIV-1 from peripheral blood mononuclear cells of 29 infected individuals originating from 10 different geographical regions were sequenced and further analyzed for promoter/enhancer activity in transient transfection of HeLa cells, in the context of a reporter gene and in the context of the complete virus genome. We found several subtype-specific LTR sequences of the various HIV-1 strains, such as an insertion that created a potential third NF-kappaB site in the LTR of the subtype C strains. The USF-binding site in the NRE also contained subtype-specific sequences. Interestingly, the promoter/enhancer activities of the subtype C LTRs were higher than the activities of the other subtypes analyzed here (subtypes A, B, D, E, and G), suggesting that the potential third NF-kappaB site may confer higher LTR activity or that the subtype C NRE may be less potent. Thus, our data suggest that genetic diversity of the LTR may result in HIV-1 subtypes with different replicative properties.

Feline leukemia virus long terminal repeat activates collagenase IV gene expression through AP-1.

Leukemia and lymphoma induced by feline leukemia viruses (FeLVs) are the commonest forms of illness in domestic cats. These viruses do not contain oncogenes, and the source of their pathogenic activity is not clearly understood. Mechanisms involving proto-oncogene activation subsequent to proviral integration and/or development of recombinant viruses with enhanced replication properties are thought to play an important role in their disease pathogenesis. In addition, the long terminal repeat (LTR) regions of these viruses have been shown to be important determinants for pathogenicity and tissue specificity, by virtue of their ability to interact with various transcription factors. Previously, we have shown that, in the case of Moloney murine leukemia virus, the U3 region of the LTR independently induces transcriptional activation of specific cellular genes through an LTR-generated RNA transcript (S. Y. Choi and D. V. Faller, J. Biol. Chem. 269:19691-19694, 1994; S.-Y. Choi and D. V. Faller, J. Virol. 69:7054-7060, 1995). In this report, we show that the U3 region of exogenous FeLV LTRs can induce transcription from collagenase IV (matrix metalloproteinase 9) and monocyte chemotactic protein 1 (MCP-1) promoters up to 12-fold. We also show that AP-1 DNA-binding activity and transcriptional activity are strongly induced in cells expressing FeLV LTRs and that LTR-specific RNA transcripts are generated in those cells. Activation of mitogen-activated protein kinase kinases 1 and 2 (MEK1 and -2) by the LTR is an intermediate step in the FeLV LTR-mediated induction of AP-1 activity. These findings thus suggest that the LTRs of FeLVs can independently activate transcription of specific cellular genes. This LTR-mediated cellular gene transactivation may play an important role in tumorigenesis or preleukemic states and may be a generalizable activity of leukemia-inducing retroviruses.

Phylogenetic Analysis of Simian T Lymphotropic Virus Type I from Kenyan Olive Baboons (Papio anubis), Lowland Sykes Monkeys (Cercopithecus mitis), and Vervet Monkeys (Cercopithecus aethiops pygerythrus)

781 H UM AN T CELL LEU KEM IA/lymphotropic virus type I (HTLVI) strains have a worldwide distribution and are characterized by the genetic stability of their genome and their limited horizontal transmission. Simian T cell leukemia/lymphotropic virus type I (STLV-I) strains have been found in Old World nonhuman primates in Africa and Asia. Together, these two virus groups are referred to as primate T lymphotropic viruses (PTLVs) and have been found in all three Old World African primate families: the Cercopithecidae, 2±4 the Pongidae, and the Hominidae. These viruses cannot be separate d into distinct phyloge netic lineages according to the fam ilies or species of origin, but rather accordi ng to geographical regions , which suggest s multiple interspe cies transm issions in the past. Although uncertain, it is thought that the origina l virus infected nonhu man simian ancesto rs that eventua lly infected humans. 2 Understan ding the sequence diversit y among STLV-I strains may therefor e provide valuable insight into the evolutio n of the PTLV-I group. In this study, we analyze d the HTLV-I sequenc e of 13 nonhum an primates, using HTLV-I cross-r eacting antibod ies provide d with the HTLV-I Serodia particle aggluti nation assay (Fujirebio , Tokyo, Japan). The animals were either colony born (Institu te of Primate Research [IPR], Nairobi, Kenya) or trapped in Kibwezi (eastern Kenya) and in Gilgil and Namanga (Rift Valley Province) . The animals include d four vervet monkeys (Cercopit hecus aethiop s pygerythrus ), two lowland Sykes monkeys (Cercopit hecus mitis), and seven olive baboons (Papio anubis ) (Table 1). We have focused on the diverge nt long terminal repeat (LTR) region because it is more inform ative for sequence analysi s and subtyping, and because of the availab ility of inform ation on other PTLV-I LTR sequenc es. DNA was isolated from peripheral blood mononuclear cells (PBMCs) using a QiaAmp blood kit (Qiagen GmbH, Hilden, Germany). The LTR region was amplified by the polymerase chain reaction (PCR) with primer pairs HFL1/HFL6 and HFL5/HFL6, as described. 11 PCR products were cloned using the PCR-Script SK( 1 ) cloning kit (Stratagene, La Jolla, CA) according to the manufacturer instructions. Sequencing was performed using the Applied Biosystem s model 373 automatic DNA sequencer (Applied Biosystems/Perkin-Elmer , Foster City, CA). Nucleotide sequences were aligned with CLUSTAL V together with reference sequences from the GenBank database. Kimura distance calculation, 13 bootstrap analysis, 14 and tree construction were done with the TREECON software package. Nucleotide sequences were submitted to GenBank under accession numbers AF117282±AF117294. Comparison of the LTR region of the strains revealed that the elements that are critical for viral gene expression were well conserved. No nucleotide changes were observed in the polyadenylation signal (AATAAA), the TATA box (TATAAA), and the splice donor site (TAGGTAA). In the tree containing the LTR sequence (Fig. 1), STLV and HTLV-I clusters were identified as containing sequences representative of many different subtypes.

Nucleotide diversity in three different genomic regions of Venezuelan HIV type 1 isolates: a subtyping update.

73 HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) infection continues its rapid global spread. A short time ago a few HIV-1 subtypes based on env sequences were identified, and outside the African continent most HIV-1 isolates belonged to subtype B. However, the rapid genetic diversification of HIV1 is reflected in the current separation of isolates into two groups (M and O), and an increasing number of subtypes within each group. New subtypes are finding their way outside the geographical areas where they were first isolated.1,2 Continuous reports of additional a non-subtype Bo HIV-1 infections around the world underscore the need for surveillance to track HIV-1 variants and to further define the molecular basis of their genetic variation. In the American continent and the Caribbean region, HIV-1 subtype B is dominant. However, the detection of HIV-1 of different subtypes in this area (i.e., subtypes A, C, D, E, and F, the group O) exemplifies the spread of HIV1 clades well beyond their original geographical locations.4±6 In addition, with more than 1.5 million estimated HIV infections, Latin America and the Caribbean follow Africa and southern Asia as the macroregion with the highest number of estimated HIV infections. We have undertaken the first molecular characterization of HIV-1 isolates from Venezuela.3 These initial viruses (VE1 to VE8) were isolated in 1991, and an analysis of pol and env genomic segments identified them as belonging to subtype B. In the present report 20 additional isolates of HIV-1 from Venezuela have been molecularly characterized on the basis of three distinct, noncontiguous genomic regions: the long terminal repeat (LTR), the first exon of the tat gene, and the env region encoding the C2V3 domain of gp120, with the aim of determining the extent of their genetic variation, and to characterize sequence relationships and evolutionary pattern in recent years. Twenty-eight blood samples were obtained in two periods: a first group of 8 samples (VE1 to VE8) was collected in 1991,3 and the second group includes samples from 1995. Epidemiological and clinical data are provided in Table 1. Proviral DNA was extracted as previously described. Three genomic regions were amplified for each DNA sample: 560 nucleotides of the HIV-1 LTR (positions 2 285 to 1 275 from the transcription start site), the first exon of the tat gene (216 bp), and an internal fragment of 1.2 kb spanning the gp120 V1±V5-coding region of env. Nested polymerase chain reaction (PCR) was used for all amplifications. PCR conditions and primers used to amplify the LTR region and the first exon of tat have been previously described.7 To amplify the V1±V5-coding region of env, the primers described in Delwart et al.8 were used. The PCR products of env were compared with those of 14 previously characterized HIV-1 strains1 by a heteroduplex mobility assay (HMA) as previously described. Nucleotide sequencing was performed using the fmol method (Promega, Madison, WI), followed by treatment with terminal deoxynucleotidyl transferase, as described.9 LTR (nucleotides 170 to 730 of the CAM1 genome1) and tat (nucleotides 5832 to 6047 of the CAM1 genome1) were sequenced using the inner primers LTR3/LTR4, and TAT3/TAT4, respectively. The C2V3-coding region (nucleotides 6817 to 7218 of the CAM1 genome) was sequenced as described previously.9 Initial subtyping experiments involved characterization of the new isolates by heteroduplex mobility assay,8 using reference plasmid DNA corresponding to HIV-1 subtypes A to H (heteroduplex mobility analysis HIV-1 env subtyping kit protocol version 3; NIH AIDS Research and Reference Reagent Program). Comparison of 28 Venezuelan samples with standard probes of several subtypes showed unequivocal electrophoretic patterns, corresponding to subtype B (data not shown). The epidemiological relationships of HIV-1 isolates from Venezuela with other HIV-1 isolates were further analyzed by phylogenetic analyses based on nucleotide sequences of the LTR region, the first exon of tat, and the C2V3 domain of the gp120coding region. Venezuelan HIV-1 isolates clustered with subtype B viruses in all cases (Fig. 1).10±14 Nucleotide diversities among Venezuelan samples were similar for the three genomic segments analyzed. Pairwise comparisons showed an average divergence of 6.6% (range of 1.4 to 11.0%), 8.0% (1.2 to 14.9%), and 9.4% (1.5 to 13.8%) for LTR, tat, and env, respectively. Average genetic distances be-

Genetic analysis of the rat leukemia virus: influence of viral sequences in transduction of the c-ras proto-oncogene and expression of its transforming activity.

The rat leukemia virus (RaLV) is an endogenous retrovirus that is spontaneously released by Sprague-Dawley rat embryo cells. The overall structure of the RaLV genome resembles that of other simple, replication-competent retroviruses, but the sequence of the long terminal repeats (LTR) is unique and unrelated to the known retroviruses. Phylogenetically, the RaLV genome appears to be more closely related to the feline leukemia virus group of retroviruses than to the murine leukemia virus group. A remarkable feature of RaLV is that it is capable of transducing a ras proto-oncogene from rat tumor cells in the form of an acutely transforming virus, designated the Rasheed strain of the rat sarcoma virus (RaSV). With the exception of the c-ras sequence, the genomes of both RaLV and RaSV are collinear. The RaSV-encoded oncogene v-Ra-ras expresses a fusion protein with a molecular mass of 29 kDa, and it exhibits a unique structure that has not been described previously for any known virus. The 5' end of this gene is derived from sequences encoding RaLV matrix followed by 20 bp derived from the U5 region of the RaLV LTR (RS-U5 element) which is joined at its 3' end to sequences derived from all six (coding and noncoding) exons of the c-ras proto-oncogene at the 3' end. This recombinational event represents a novel mechanism among the acutely transforming viruses that have been studied.

Interelement selection in the regulatory region of the copia retrotransposon.

We report the results of an analysis of naturally occurring cis-regulatory variation within and between two families of the copia Drosophila long terminal repeat (LTR) retrotransposon. The copia 5' LTR and adjacent untranslated leader region (ULR) consists of a number of well-characterized sequence motifs which play a role in regulating expression of the element. In order to understand the evolutionary forces which may be responsible for generating and maintaining copia regulatory sequence variation, we have quantified levels of naturally occurring copia LTR-ULR nucleotide variation and subjected the data to a series of tests of neutrality. Our analysis indicates that the copia LTR-ULR has been subject to negative purifying selection within families and positive adaptive selection between families. We discuss these findings with respect to the regulatory evolution of retrotransposons and the phenomenon of interelement selection.

High resolution mapping DNAs by R-loop atomic force microscopy.

R-loops formed by short RNA transcripts have been imaged by atomic force microscopy (AFM) at a constant force in the height mode. The technique was applied to mapping the human endogenous retrovirus K10 family (HERV-K10) long terminal repeats (LTR) within individual plasmids and cosmids. RNA probes specific for the U3 (384 nt) and U5 (375 nt) LTR regions separated by a span of 200 bp were used for R-loop formation with LTRs located within plasmid (3.8 kb) or cosmid ( approximately 40 kb) DNAs. R-loops stabilized by glyoxal treatment and adsorbed onto the mica surface in the presence of magnesium ions looked like looped out segments of RNA:DNA hybrids. The total yield of R-loops was usually approximately 95%. The RNA:DNA hybrids were found to be 12-15% shorter than the corresponding DNA:DNA duplex. The two regions of the LTR could be easily discerned in the AFM images as clearly separated loops. R-loop positions determined on cosmids by AFM were accurate to approximately 0.5% of the cosmid length. This technique might be easily adapted for mapping various sequences such as gene exons or regulatory regions and for detecting insertions, deletions and rearrangements that cause human genetic diseases.

An exposed KID-like domain in human T-cell lymphotropic virus type 1 Tax is responsible for the recruitment of coactivators CBP/p300.

Human T-cell lymphotropic virus type 1 (HTLV-1) transcriptional activation is mediated by the viral transactivator, Tax, and three 21-bp repeats (Tax response element [TxRE]) located in the U3 region of the viral long terminal repeat (LTR). Each TxRE contains a core cyclic AMP response element (CRE) flanked by 5' G-rich and 3' C-rich sequences. The TxRE binds CREB (CRE-binding protein) and Tax to form a ternary complex and confers Tax-dependent transactivation. Recent data indicate that Tax functions as a specific link to connect CREB-binding protein (CBP)/p300 in a phosphorylation-independent manner to CREB/ATF-1 assembled on the viral 21-bp repeats. Glutathione S-transferase pull-down performed with Tax deletion mutants and peptide competition have localized the site in Tax critical for binding CBP/p300 to a highly protease-sensitive region around amino acid residues 81 to 95 (81QRTSKTLKVLTPPIT95) which lies between the domains previously proposed to be important for CREB binding and Tax subunit dimerization. Amino acid residues around the trypsin- and chymotrypsin-sensitive sites (88KVL90) of Tax bear resemblance to those in the kinase-inducible domain of CREB (129SRRPSYRKILNE140) surrounding Ser-133, which undergoes signal-induced phosphorylation to recruit CBP/p300. Site-directed mutagenesis of residues in this domain (R82A, K85A, K88A, and V89A) resulted in proteins which failed to transactivate from the HTLV-1 LTR in vivo. These mutants (K85A, K88A, and V89A) bind CREB with similar affinities as wild-type Tax, yet interaction with CBP/p300 is abrogated in various biochemical assays, indicating that the recruitment of CBP/p300 is crucial for Tax transactivation. A Tax mutant, M47, defective in the COOH-terminal transactivation domain, continued to interact with CBP/p300, suggesting that interactions with additional cellular factors are required for proper Tax function.

Surveillance using molecular tools: examples from Brazil.

Brazil presents particular problems for surveil-lance of infectious diseases. These include its con-tinental size, uneven distribution of resources, dif-ficulty of communication and access in some ofthe more remote areas, as well as large areas cov-ered by tropical rain-forests. Surveillance for in-fectious diseases in Brazil has traditionally beencarried out in a passive manner by government au-thorities or as individual initiatives. Most effort hasbeen directed in the collecting and tabulating ofdata on notifiable infections. A limited amount oflaboratory support has been available for the iso-lation and identification of the etiological agents.More recently molecular methods have been in-troduced in the analysis of these data.Here we present some practical examples ofthe use of different molecular tools for diagnosisand in the analysis of infectious diseases and inepidemiological monitoring of outbreaks. The ex-amples are taken from work carried out in our In-stitute.HIV-2, the second AIDS-causing virus, wasoriginally identified and found to be quite commonin West Africa. With a more restricted geographicspread than HIV-1, this virus has also been isolatedin countries with socioeconomic links to West Af-rica (R Marlink 1996 AIDS 10:689-699). Some earlyreports analyzing the seroprevalence of HIV-1 andHIV-2 were contradictory about the presence ofHIV-2 in Brazil (L Oyafuso et al. 1989 New Engl JMed 320: 953-958, RM Hendry et al. J Acq ImmDef Synd 4: 623-627). At that time they concludedthat there was some cross-reactivity between HIV-2 and HIV-1 which resulted in misinterpretation.Using polymerase chain reaction (PCR) and spe-cific internal probes to HIV-2, Pieniazek et al . (1991AIDS 5: 1293-1299), identified mixed HIV-1/HIV-2 infections in Rio de Janeiro, Brazil. In order tovalidate the World Health Organization strategy forHIV testing, sera from 9,885 blood donors from SaoPaulo were screened by HIV enzyme-linkedimmunosorbent assays (ELISA) and Western blotand the results did not support the evidence of HIV-2 circulation in Brazil (MB Carvalho et al. 1996AIDS 10: 1135-1140).We have applied molecular tools in surveillancefor the detection of HIV-2 in HIV-1 positivesamples (possible dual infections) as well as insamples with undetermined Western blots. Morethan 200 samples from different parts of the coun-try were screened for the presence of HIV-2 provi-ral DNA using nested PCR targeting the long ter-minal repeat (LTR), protease and gag regions. Inthree samples only PCR products corresponding tothe LTR region were amplified. These products weresequenced and the nucleotide sequence was differ-ent from that of HIV-2 LTR. They matched withhuman genome sequence, probably a rare allelepresent in few people. At present we have failed todetect and confirm the circulation of HIV-2 in Bra-zil. We have shown that the use of LTR diagnosticprimers to HIV-2 has to be carefully analyzed.Vibrio cholerae occurs naturally in aquatic sys-tems where it may constitute part of the normalmicroflora of zooplankton and larger animals. V.cholerae is a heterogeneous species with more than140 serotypes, only a few of which are associatedwith biotypes causing human cholera and epidem-ics. The ongoing cholera pandemic (7th) is causedby the El Tor biotype, serotype O1. In 1991 chol-era re-emerged in Brazil after being absent for acentury, the previous pandemic involved V.cholerae classical biotype. The present situation isdifferent in that not only is there a new V. choleraebiotype, but also there is now detailed knowledgeabout the bacterial virulence factors determiningthis disease and the molecular tools available forcharacterization of the isolates. In 1993 a new V.cholerae strain was identified in the State ofAmazonas during surveillance using AP-PCR formolecular characterization of cholera vibrios. TheV. cholerae amazonia variant is of the O1 sero-type; it has distinct multilocus enzyme electro-phoresis and AP-PCR profiles from other patho-genic O1 V. cholerae. About 50 isolates have beenmade from cases of diarrhea in the upper Amazon

In vivo protein binding and functional analysis of cis-acting elements in the U3 region of the bovine leukemia virus long terminal repeat.

Bovine leukemia virus (BLV) is a member of the human T-cell leukemia virus (HTLV)/BLV group of retroviruses. These viruses regulate their own transcription by producing Tax, a protein which activates the virus promoter region, the long terminal repeat (LTR). To explore the molecular mechanisms involved in the transactivation, we identified protein binding elements by in vivo footprinting and analyzed their function by site- directed mutagenesis. We used in vivo dimethyl sulfate footprinting by ligation-mediated PCR to detect constitutive in vivo protein-DNA interactions in a BLV-producing cell line, Bat2Cl6. The U3 region and part of the R region of the LTR were footprinted. In addition to the cis-acting elements (three cyclic AMP-responsive elements [CREs] and two AP4 sites) reported by others to be important for Tax-mediated activation of the BLV LTR, we found footprints in regions flanking these elements and in the core promoter region. The importance of these sites for transcriptional activation was studied by site-directed mutagenesis followed by promoter function analysis of the mutants with a chloramphenicol acetyltransferase reporter system. Our data corroborate those of others showing that the CREs are necessary for transactivation of the LTR, and they identify two new functional sites not previously reported by others. We show that the middle region of the BLV U3 contains multiple dual-functioning cis-acting elements which act as either positive or negative regulatory elements depending on the cell type tested. This is the first report of a functional mapping of the cis-acting elements of a virus of the HTLV/BLV group.

Nucleotide substitutions in the long terminal repeat are not required for development of neurovirulence by simian immunodeficiency virus strain mac.

The question of whether consensus nucleotide substitutions in the long terminal repeat (LTR) region of simian immunodeficiency virus strain mac (SIVmac) are important for neurovirulence was investigated in this report. Brains and lymph nodes from two macaques that developed AIDS and encephalitis following inoculation with two strains of neurovirulent SIVmac, and from one animal with AIDS but no neurological disease after inoculation with non-neurovirulent SIVmac239 were used. The 5' LTR regions from neurovirulent SIVmacR71/17E and SIVmac7F-Lu were amplified, cloned and sequenced and these sequences were compared to the LTRs amplified from three regions of the respective encephalitic brains and lymph nodes from macaques inoculated with each virus. The SIVmac7F-Lu and SIVmacR71/17E viruses had zero and three consensus substitutions, respectively, in the U3, R and U5 regions of the LTR compared to that of SIVmac239. The only consensus substitution in the LTR-gag region of the genome was a T to C change at position 829 within the tRNA binding site. The sequences amplified from the brain and lymph nodes of the two animals with AIDS and encephalitis were identical. This single common substitution in this region of the virus genome, the T to C substitution at position 829, was also found in the LTRs isolated from the brain and lymphoid organs from the macaque inoculated with SIVmac239. The virtual identity in nucleotide sequences in the LTR of the neurovirulent and non-neurovirulent viruses and in CNS and lymph tissues of animals inoculated with the viruses suggests that the LTR has no effect on the tissue tropisms of the viruses.

Expression of the human immunodeficiency virus type 1 primer binding sequence inhibits HIV-1 replication.

Optimal targets for anti-human immunodeficiency virus (HIV) moieties are those regions of the viral genome that are greatly conserved. The primer binding site (PBS) of HIV is an 18-nucleotide sequence complementary to the 3' end of tRNA(Lys3) that serves as the primer for HIV-1 reverse transcription. All HIV-1 isolates analyzed to date contain a PBS complementary to tRNA(Lys3) illustrating the conservation of this sequence. We investigated the activity of a hammerhead ribozyme targeting the PBS of HIV-1. CEMss cells transduced with retroviral vectors containing either the PBS hammerhead ribozyme or its complementary sequence (as a control) in the R region of the vector long terminal repeat (LTR) were challenged with HIV-1NL4-3. Surprisingly >80% inhibition of HIV-1 production was observed with the vector containing the (control) sequence complementary to the PBS ribozyme. We propose that the LTR-driven vector transcript containing 18 nucleotides identical to the HIV-1 PBS may act like an RNA decoy to titrate viral proteins such as reverse transcriptase and nucleocapsid away from genuine viral transcripts, thus compromising virus replication.

Identification of Genetic Determinants Responsible for the Rapid Immunosuppressive Activity and the Low Leukemogenic Potential of a Variant of Friend Leukemia Virus, FIS-2

An immunosuppressive variant of Friend murine leukemia virus (F-MuLV), FIS-2, induces suppression of the primary antibody response against sheep erythrocytes (SRBC) in adult NMRI mice more efficiently than the prototype F-MuLV clone 57 (cl.57). It is, however, less potent than F-MuLV cl.57 in inducing erythroleukemia upon inoculation into newborn NMRI mice. Nucleotide sequence analysis shows a high degree of homology between the two viruses. Single point mutations are scattered over both the gag and the env encoding regions. The most notable mutations are the deletion of one direct repeat and a few single point mutations occurring in the binding sites for cellular transcriptional factors in the FIS-2 long terminal repeat region (LTR). To define the genetic determinants responsible for the pathogenic properties of FIS-2, we constructed six chimeras between FIS-2 and F-MuLV cl.57. Adult mice were infected with the chimeras, and their primary antibody responses against SRBC were investigated. The results showed that the fragment encompassing the FIS-2 env encoding region SU is responsible for the increased immunosuppressive activity in adult mice. A leukemogenicity assay was also performed by infecting newborn mice with the chimeras. Consistent with the previous studies, it showed that the deletion of one direct repeat in the FIS-2 LTR is responsible for the long latent period of erythroleukemia induced by FIS-2 in newborn-inoculated mice. However, studies of cell type-specific transcriptional activities of FIS-2 and F-MuLV cl.57 LTRs using LTR-chloramphenicol acetyltransferase constructs showed that the deletion of one direct repeat does not reduce the transcriptional activity of the FIS-2 LTR. The activity is either comparable to or higher than the transcriptional activity of the F-MuLV cl.57 LTR in the different cell lines that we used, even in an erythroleukemia cell line. It seems that the high transcriptional strength of the FIS-2 LTR is not sufficient to give FIS-2 a high leukemogenic effect. This suggestion is inconsistent with the previous suggestion that the transcriptional strength of an LTR in a given cell type is correlated with the leukemogenic potential in the corresponding tissue. In other words, these data indicate that the direct repeats in the F-MuLV LTR may play other roles besides transcriptional enhancer in the leukemogenesis of F-MuLV.

The use of immunohistochemistry and the polymerase chain reaction for detection of feline leukemia virus and feline sarcoma virus in six cases of feline ocular sarcoma.

Ocular sarcoma was diagnosed by light microscopic examination in enucleated globes (n = 4), orbital tissue biopsy (n = 1) and ocular evisceration contents (n = 1) from six cats. To determine if feline leukemia virus (FeLV) or a replication-defective FeLV, feline sarcoma virus (FeSV), was present in these ocular sarcomas, immunohistochemistry (IHC) and polymerase chain reaction (PCR) for FeLV were utilized. Immunohistochemical staining for FeLV glycoprotein 70 (gp70) was performed on all six formalin-fixed, paraffin-embedded tumors using an avidin-biotin complex technique. DNA was extracted from each specimen and a 166 bp region of the FeLV long-terminal repeat (LTR) was amplified by PCR. All tumors were composed primarily of spindle cells; two neoplasms had PAS-positive basement membrane enveloping areas of spindle cells. All tumors involved the uvea and five of six tumors showed transcleral extension, one of which invaded the optic nerve. Immunohistochemical staining for FeLV gp 70 was negative. PCR to amplify a portion of the FeLV LTR was negative. Based on these findings of these limited number of cases, FeLV/FeSV may not play a role in the tumorigenesis of feline ocular sarcomas. However, additional tumors representing all morphological subtypes should be investigated for the presence of viral antigen and DNA. It is important to determine the etiology and pathogenesis of these malignant ocular sarcomas. If the cell of origin and pathogenesis involve ocular and lenticular injury, and FeLV/FeSV is not present, then the clinical management of cases of feline ocular trauma, uveitis and glaucoma may prevent the development of this tumor.

Repression of human immunodeficiency virus type 1 through the novel cooperation of human factors YY1 and LSF.

A subpopulation of stably infected CD4+ cells capable of producing virus upon stimulation has been identified in human immunodeficiency virus (HIV)-positive individuals (T.-W. Chun, D. Finzi, J. Margolick, K. Chadwick, D. Schwartz, and R. F. Siliciano, Nat. Med. 1:1284-1290, 1995). Few host factors that directly limit HIV-1 transcription and could support this state of nonproductive HIV-1 infection have been described. YY1, a widely distributed human transcription factor, is known to inhibit HIV-1 long terminal repeat (LTR) transcription and virus production. LSF (also known as LBP-1, UBP, and CP-2) has been shown to repress LTR transcription in vitro, but transient expression of LSF has no effect on LTR activity in vivo. We report that both YY1 and LSF participate in the formation of a complex that recognizes the initiation region of the HIV-1 LTR. Further, we have found that these factors cooperate in the repression of LTR expression and viral replication. This cooperative function may account for the divergent effects of LSF previously observed in vitro and in vivo. Thus, the cooperation of two general cellular transcription factors may allow for the selective downregulation of HIV transcription. Through this mechanism of gene regulation, YY1 and LSF could contribute to the establishment and maintenance of a population of cells stably but nonproductively infected with HIV-1.

TNFα Cooperates with the Protein Kinase A Pathway to Synergistically Increase HIV-1 LTR Transcription via Downstream TRE-like cAMP Response Elements

Activating protein-1 (AP-1) binding TPA responsive elements (TRE) are located downstream of the transcription initiation site in the U5 region of the HIV-1 long terminal repeat (LTR). These downstream sequence elements, termed DSE, can bind both AP-1 and CREB/ATF transcription factors. Recently, we demonstrated that the DSE are also cAMP-responsive elements (CRE), since they mediated activation signals elicited by cholera toxin (Ctx), a potent activator of the cAMP-dependent protein kinase A (PKA) signal transduction pathway. In the present study, we demonstrate that the HIV-1 DSE can mediate the transcriptional synergy elicited by the combination of Ctx and TNFα. Ctx combined with TNFα or IL-1β to produce a synergistic increase in p24 antigen production in U1 promonocytic cells. Transfection studies of LTR reporter constructs indicated that mutation of the DSE sites abrogated the LTR-mediated synergy induced by Ctx and TNFα, whereas the synergy induced by Ctx and IL-1β was unaffected, suggesting TNFα and IL-1β cooperate differently with the cAMP/PKA activation pathway to induce HIV-1 expression in U1 cells. Because the DSE are also TRE sites, we assessed the effect of the agonist combinations on AP-1-dependent transcription. TNFα as well as IL-1β cooperated with Ctx to produce a synergistic activation of AP-1-mediated transcription. These data indicate that the TRE-like cAMP-responsive DSE sites within the 5′-untranslated leader can mediate the transcriptional cooperativity between TNFα and the cAMP/PKA pathway. Since the DSE and TRE sites cannot bind CREB/ATF homodimers, we propose a mechanism in which the HIV-1 DSE bind heterodimers composed of both AP-1 and CREB/ATF proteins.

Positioning of 72 potentially full size LTRs of human endogenous retroviruses HERV-K on the human chromosome 19 map. Occurrences of the LTRs in human gene sites

Seventy-two near full size long terminal repeats (LTRs) of human endogenous retrovirus of K-family (HERV-K) have been precisely located on the metric map of human chromosome 19. The LTR-related sequences were identified and assigned to cosmids by hybridization with two independent chromosome 19 specific cDNA clones corresponding to different parts of U3 region of LTR of HERV-K. The presence of full-size LTR sequences in a cosmid was further verified by PCR assay with a pair of primers complementary to the termini of the LTR. Coincidences of the LTR and the known genes positions are discussed.

Structure and genomic organization of a novel human endogenous retrovirus family: HERV-K (HML-6).

Prototypic elements of a novel human endogenous retrovirus (HERV) family were identified and cloned from a human genomic library by the use of a pol fragment, HML-6, related to type A and type B retroviruses and class II HERVs. Out of 39 polhybridizing clones, five contained structures of full-length retroviral proviruses, with regions showing similarity to gag, pol and env, flanked by long terminal repeats (LTRs). Restriction mapping and partial sequence analysis of each full-length clone revealed few conserved restriction sites among HML-6 genomes, and about 20% sequence divergence over the reverse transcriptase region sequenced, suggesting that HML-6 constitutes a heterogeneous, but distinct family of elements belonging to the HERV-K superfamily. Sequence analysis of two clones, HML-6p and HML-6.17, revealed a lysine (K) tRNA UUU primer-binding site, and 40-68% nucleotide sequence similarity to LTR, gag, pro, pol and env regions of type B retroviruses and class II HERVs. HERV-K (HML-6) elements are present at about 30-40 copies per haploid genome. The HML-6 LTRs contain putative progesterone-responsive elements, which may be involved in the regulation of HML-6 expression. Furthermore, there are about 50 additional solitary HML-6 LTRs per haploid genome. Such LTRs were integrated within the pol region of two clones belonging to the same HML-6 family, indicating that some site preference may be involved in HERV integration.

Transmission of HIV-1 in infants born to seropositive mothers: PCR-amplified proviral DNA detected by flow cytometric analysis of immunoreactive beads.

The diagnosis of HIV infection in newborns is established by amplification of proviral DNA using the polymerase chain reaction (PCR). We developed a nonisotopic method for heminested PCR using a biotinylated primer among sets of three oligonucleotides, each selected from the HIV long terminal repeat (LTR) and gag sequences. An internal probe incorporating digoxigenin-dUTP was also synthesized by PCR. The PCR products, hybridized with LTR region or gag region probes, were captured with streptavidin-coated magnetic beads and detected by fluorescein isothiocyanate-labeled antidigoxigenin in flow cytometric analysis. This immunoreactive bead assay (PCR-IRB) detected about three copies of HIV proviral DNA. A panel of 50 coded DNA specimens of infants previously assayed by conventional PCR and with known clinical results revealed that the PCR-IRB findings using LTR, but not gag, were in agreement. A double-blind prospective study of blood samples from 14 mother-infant pairs using the PCR-IRB amplification of LTR gave results similar to the commercial Amplicor HIV-1 PCR test and were consistent with the clinical outcomes. PCR-IRB results were positive for 11 mothers and three infants, one at birth, one at 2 weeks after birth, and one at 8 weeks after birth. PCR-IRB is a simple, reliable, specific, and automatable assay useful in the early diagnosis of perinatal HIV infection in clinical practice and regional screening programs.