Sequences within the feline immunodeficiency virus long terminal repeat that regulate gene expression and respond to activation by feline herpesvirus type 1.

We constructed a series of deletion mutants of feline immunodeficiency virus (FIV) long terminal repeat (LTR) to identify the regions that regulate gene expression and are responsive to trans-activation of FIV LTR by feline herpes-virus type 1 (FHV-1). We demonstrated that sequences between -124 and -79, and between -21 and -32 (relative to the cap site) are essential for gene expression of FIV in Felis catus whole fetus 4 (fcwf-4) cells. Further, we demonstrated that the sequence between -63 and -23 responds to trans-activation of FIV LTR by FHV-1 in fcwf-4 cells.     

Evolution of the long terminal repeat and accessory genes of feline immunodeficiency virus genomes from naturally infected cougars

FIVpco is a member of the feline immunodeficiency virus family that is endemic in wild cougar populations. Virus replication is robust in FIVpco-infected cougars but there are no consequences of infection to cougar survival, fecundity or susceptibility to other infections. Unlike pathogenic lentiviruses, there is no evidence for positive selection on FIVpco gag or env. To better understand how lentivirus genomes evolve in natural infections, we evaluated the regulatory region and accessory genes from fourteen full-length FIVpco genomes, which represent the FIVpco diversity in the Northern Rockies Ecosystem. Our data demonstrate that the two sister groups of FIVpco have each acquired binding sites for different interferon response factors (IRF). The most variable gene in the FIVpco genome encodes OrfA, although there is no indication that it, or any other accessory gene, is under positive selection. There is a single-splice acceptor site for vif expression, which is conserved among all FIVpco genomes. However, there are several putative means to express rev and orfA, which differ between the phylogenetic groups of FIVpco. Our comparative study on divergent FIVpco genomes indicates that variation in potential gene regulation mechanisms, not changes in structural proteins, characterize the evolution of FIVpco in natural infections.     

Functional analysis of simian immunodeficiency virus SIVAGM long terminal repeat

We have previously shown that long terminal repeats (LTRs) derived from various isolates of SIV_AGM share a unique functional property. In the absence of viral Tat, all SIV_AGM LTRs act as much more efficient promoters than any of the other LTRs derived from representative primate immunodeficiency viruses. In the presence of Tat, however, SIV_AGM LTRs are activated relatively inefficiently. To map the elements that confer these features on the SIV_AGM LTR, a number of deletion mutants were constructed, and their promoter activities were determined using a bacterial CAT gene as a marker. The results obtained indicated that various elements located in the U3 region may contribute to the high basal promoter activity and that no negative elements are present in the region. The Tat-responsive sequence TAR was localized to the R region as observed for the other LTRs. A mutant carrying a single nucleotide deletion in this region completely lost responsiveness to Tat protein.     

Phylogenetic analysis of the long terminal repeat of feline immunodeficiency viruses from Japan,Argentina and Australia

Summary The nucleotide sequences of the long terminal repeat of five Japanese, five Argentine and three Australian isolates of feline immunodeficiency virus (FIV) were determined and compared with those of isolates previously described. The results revealed that the Japanese isolates were found to cluster with nucleotide sequence similarity of 95.6%–99.4%. The Australian isolates also clustered with nucleotide sequence similarity of 97.2%–99.4%. The Argentine isolates formed two groups; the LP9 isolate is closely related to the Japanese isolates, whereas the LP1, LP3, LP20 and LP24 isolates are distant from both the Japanese and Australian isolates. From these results, FIV can be divided into three groups, namely: (I) the Californian, Australian and British isolates; (II) the Japanese isolates and one Argentine LP9 isolate; (III) the other Argentine isolates.     

Sequence and repeat structure variants in the long terminal repeat of maedi-visna virus EV1

Diversity in the LTR of maedi-visna virus strain EV1 has been examined by PCR-based gene amplification using DNA from infected cells both in vitro and in experimentally infected animals. In vitro, several variant structures were found in the U3 regions of the LTR which contained repeats of sequences including presumed AP-1 and AP-4 binding sites. Although these repeat variants formed a minor fraction of the LTRs present in the proviral population, they were neither produced nor lost at a significant rate when PCR was performed on cloned viral DNA and so were unlikely to be artefacts of the isolation procedure. When LTRs were isolated from two experimentally EV1 infected sheep, repeat variant structures were found to be present in efferent lymph by 14 days postinfection (p.i.) (although not seen at 9 days p.i.). They were also present at later times and in blood. Overall sequence diversity at 9 days p.i. was reduced compared both with the infecting virus and with later times of infection. When a number of the variant LTR structures were used to drive CAT reporter gene constructs in chondrocytes, all were found to be active, although consistent differences of up to fourfold in activity were seen. However, there is no evidence from these data for strong selective pressure operating on the LTR in vivo.     

Functional mapping of the activity of the R region in the human T-cell leukemia virus type I long terminal repeat to increase gene expression

We previously demonstrated the activity of the R fragment in the long terminal repeat of human T-cell leukemia virus type I for elevation of the level of gene expression. In this study, the fragment was deleted with BAL31 nuclease to determine its functional domain. Series of the shortened R fragments were linked to the simian virus 40 promoter unit, which regulated expression of a reporter gene. Examination with the R fragments deleted from the 5 and 3 ends showed that borders of the functional domain were mapped within nucleotide positions 458 to 473 for the 5 end and nucleotide positions 559 to 594 for the 3 end, respectively. Thus we conclude that a 136-base-pair fragment corresponding to the second half of the R region was sufficient to allow elevation of the level of gene expression.     

Characterization of a solitary long terminal repeat of avian endogenous virus origin

A recombinant lambda phage library constructed with a partial EcoR1 digest of DNA from a normal RPRL line 15B chicken was screened using 32P-labeled plasmid containing Rous-associated virus (pRAV-2). Nucleotide sequence analyses of a fragment of one subclone revealed the presence of a solitary long terminal repeat (LTR) that is similar to the LTRs of avian endogenous retroviruses ev1 and ev2. This LTR is flanked by unique 6 bp direct repeats characteristic of the target site for duplication of avian leukosis viruses.