A comparitive analysis of RNA coliphages: structural and regulatory features

ABSTRACT

Describes a comparative analysis of RNA coliphages with special emphasis on regulatory and structural features. Phylogenetic phage sequence comparison reveals kinship between different phages and facilitates deduction of their secondary structure. Complete sequences from phage fr and partial sequences from group I phages M12, R17 and f2 were determined. The nucleotide sequence from a serological intermediate JP34 was partially elucidated, Only the fr sequence proved suitable for comparison with MS2 (similarity 77 per cent). A "core" structure (3' terminal region) of phage RNA proposed a certain structural resemblance with tRNA. Comparison of the MS2 and fr nucleotide sequences revealed absence of an AUG initiator codon for the fr lysis (L) gene. However, 4 codons further downstream there is a UUG codon which proved to be the start codon for the fr lysis gene. This UUG start codon proved crucial for L-gene regulation. It is suggested that terminated but not released ribosomes mediate the L-gene activation. A general eubacterial scanning model is proposed. It seems that ribosomes can scan the mRNA in both directions and reinitiate at the first encountered restart site. This eubacterial scanning model parallels the eukaryotic translation initiation mechanism