Mapping of mRNA transcripts in the genome of molluscum contagiosum virus: Transcriptional analysis of the viral slam gene family

Molluscum contagiosum virus (MCV) is a member of the poxvirus family and ca uses benign skin tumors in children and immunocompromised individuals. The primary structure and coding capacity of MCV was previously determined by D NA nucleotide sequencing (Senkevich et al., Science 273, 813-816, 1996). Hy pothetical genes were predicted based on (i) amino acid homologies with kno wn genes, (ii) presence or absence of conserved transcription regulation si gnals, and (iii) algorithms based on learning sets of coding sequences. The se methods provide a rational basis for the prediction of MCV coding sequen ces. However, the existence and exact size of MCV open reading frames and t he precise position of transcription regulation signals can only be determi ned by MCV mRNA transcript mapping experiments. We developed methods for th e characterization of the mRNA transcripts of MCV genes in infected skin ti ssue and abortively infected human fibroblast cell cultures. Using these me thods the properties of the mRNA transcripts of the MCV SLAM (signaling lym phocytic activating molecule) gene family (mc002L, mc161R, and mc162R) were analyzed. The mRNA start site found for the mc161R transcript suggests tha t a second start codon is used leading to a mc161R open reading frame that is nine amino acid residues shorter than predicted.