The ends on herpesvirus DNA replicative concatemers contain pac2 cis cleavage/packaging elements and their formation is controlled by terminal cis sequences

Herpesviruses have Large double-stranded linear DNA genomes that are formed by site-specific cleavage from complex concatemeric intermediates. In this process, only one of the two genomic ends are formed on the concatemer. Al though the mechanism underlying this asymmetry is not known, one explanatio n is that single genomes are cleaved off of concatemer ends in a preferred direction. This implies that cis elements control the direction of packagin g. Two highly conserved cis elements named pad and pad lie near opposite en ds of herpesvirus genomes and are important for cleavage and packaging. By comparison of published reports and by analysis of two additional herpesvir uses, we found that pac2 elements lie near the ends formed on replicative c oncatemers of four herpesviruses: herpes simplex virus type 1, equine herpe svirus 1, guinea pig cytomegalovirus, and murine cytomegalovirus. Formation of pad ends on concatemers depended on terminal cis sequences, since ectop ic cleavage sites engineered into the murine cytomegalovirus genome mediate d formation of pac2 ends on concatemers regardless of the orientation of th eir insertion. These findings are consistent with a model in which pac2 ele ments at concatemer ends impart a directionality to concatemer packaging by binding proteins that initiate insertion of concatemer ends into empty cap sids.