Cloning and functional characterization of the origin of lytic-phase DNA replication of rat cytomegalovirus.

A cis-acting sequence within the rat cytomegalovirus (RCMV) genome (oriLyt) that directs initiation of lytic-phase DNA replication is identified in this report. RCMV oriLyt was localized within a 4.3 kb NcoI fragment that is situated immediately upstream of the gene encoding the major DNA-binding protein. The activity of oriLyt was investigated in a transient replication assay, in which the ability of plasmid constructs to promote DNA replication was tested. Replication of oriLyt-containing plasmids was autonomous and resulted in the generation of high-molecular-mass concatemers of head-to-tail-linked plasmid oligomers. oriLyt-mediated replication was found to depend on viral DNA polymerase activity supplied by RCMV infection. The sequence required for oriLyt function was found to reside within a 3.3 kb HincII-NcoI fragment. The RCMV oriLyt sequence is highly complex, containing 23 direct repeats (DRs) and 16 inverted repeats (IRs) of lengths greater than 10 bp. Two of the DRs (DR21 and DR22) are exceptionally large, being 80 and 88 bp in length, respectively. In addition, two sequence elements (of 127 and 120 bp) with dyad symmetry were identified within oriLyt. Although the sequence similarity of RCMV oriLyt with its human cytomegalovirus counterpart is limited, there is a striking resemblance in the overall organization of several IRs and DRs within both sequences.