SUBPOPULATIONS OF NONCODING CONTROL REGION VARIANTS WITHIN A CELL CULTURE-PASSAGED STOCK OF BK VIRUS - SEQUENCE COMPARISONS AND BIOLOGICAL CHARACTERISTICS

In the circular DNA genome of the human polyomavirus BK an approximate ly 400 bp non-coding control region (NCCR) separates the early and lat e genes. The NCCR contains the origin of replication as well as the pr omoter/enhancer with a mosaic of cis-acting elements involved in the r egulation of both early and late transcription. The NCCR has been show n to be very heterogeneous between different BK virus (BKV) strains. T his may affect the host cell permissivity and oncogenic potential of a given BKV strain. Our previous studies with BKT-1B, a continuous cell line established from a BKV (Gardner)-induced hamster fibrosarcoma, r evealed that the BKV DNA is integrated in the host genome in multiple copies. The sequence of the integrated BKV NCCR was substantially diff erent from (and even contained sequences not found in) that of the BKV (Gardner) strain supposedly used to establish the BKT-1B cell line. P CR amplification, cloning and subsequent sequencing revealed that the original BKV (Gardner) stock contained at least seven different subpop ulations of viral genomes. None of them had a control region 'anatomy' which was identical to either the BKV (Gardner) strain, the variant f ound integrated in BKT-1B cells or any previously published NCCR. In o rder to study the biological significance of these new BKV NCCR varian ts we developed a simple cassette model allowing the NCCRs of the new variants to be cloned in an identical genomic background of BKV protei n-coding sequences and performed transfection studies with the recombi nant genomes in non-permissive rodent cells and in semi-permissive mon key cells. The results demonstrated that the NCCR variants conferred s triking differences, in both transforming capacity and host cell permi ssivity, to the recombinant BKV genomes. Sequence comparisons suggeste d genetic explanations for these differences, as well as evolutionary relationships between BKV NCCRs.