Structure of the rat cytomegalovirus genome termini

The lytic replication cycle of herpesviruses can be divided into the following three steps: (i) circularization, in which, after infection, the termini of the linear double-stranded viral genome are fused; (ii) replication, in which the circular DNA serves as template for DNA replication, which generates large DNA concatemers; and (iii) maturation, in which the concatemeric viral DNA is processed into unit-length genomes, which are packaged into capsids. Sequences at the termini of the linear virion DNA are thought to play a key role in both genome circularization and maturation. To investigate the mechanism of these processes in the replication of rat cytomegalovirus (RCMV), we cloned, sequenced, and characterized the genomic termini of this betaherpesvirus. Both RCMV genomic termini were found to contain a single copy of a direct terminal repeat (TR). The TR sequence is 504 bp in length, has a high GC content (76%), and is not repeated at internal sites within the RCMV genome. The TR comprises Several small internal direct repeats as well as two sequences which are homologous to herpesvirus pac-1 and pac-2 sites, respectively. The organization of the RCMV TR is unique among cytomegaloviruses with respect to the position of the pac sequences: pac-1 is located near the left end of the TR, whereas pac-2 is present near the right end. Both RCMV DNA termini carry an extension of a single nucleotide at the 3' end. Since these nucleotides are complementary, circularization of the viral genome is likely to occur via a simple ligation reaction.