The nucleotide sequence and genome organization of the RNA-1 segment in two bromoviruses: broad bean mottle virus and cowpea chlorotic mottle virus.

The complete nucleotide sequences of the RNA-1 segments in broad bean mottle virus (BBMV) and cowpea chlorotic mottle virus (CCMV) were determined. BBMV RNA-1 consists of 3158 nucleotides and CCMV RNA-1 has 3171 nucleotides. Both BBMV and CCMV RNA-1 are capped at the 5' end but, unlike in other tricornaviruses, BBMV RNA-1 initiates with an A residue. Both BBMV and CCMV RNA-1 are monocistronic encoding for highly homologous 1a proteins of 966 and 958 amino acids, respectively. The highest homologies are clustered within two domains: the N-domain that aligns with the nsP1 Sindbis virus protein, a putative methyl transferase, and the C-domain which has a conserved nucleotide binding motif. Previous sequence comparisons suggest that the C-terminal domain may function as an NTP-dependent RNA helicase. In addition, we find that the C-domain has patterns similar to those of the reovirus and vaccinia virus guanylyl transferases. All this implies that 1a protein is a multifunctional polypeptide involved in both RNA capping and RNA polymerization processes.