Widespread distribution of a group I intron and its three deletion derivatives in the lysin gene of Streptococcus thermophilus bacteriophages

Of 62 Streptococcus thermophilus bacteriophages isolated from various ecolo gical settings, half contain a lysin gene interrupted by a group IA2 intron , Phage mRNA splicing was demonstrated. Five phages possess a variant form of the intron resulting from three distinct deletion events located in the intron-harbored open reading frame (orf 253), The predicted orf 253 gene se quence showed a significantly lower GC content than the surrounding intron and lysin gene sequences, and the predicted protein shared a motif with end onucleases found in phages from both gram-positive and gram-negative bacter ia. A comparison of the phage lysin genes revealed a dear division between intron-containing and intron-free alleles, leading to the establishment of a 14-bp consensus sequence associated with intron possession. The conserved intron was not found elsewhere in the phage or S, thermophilus bacterial g enomes. Folding of the intron RNA revealed secondary structure elements sha red with other phage introns: first, a 38-bp insertion between regions P3 a nd P4 that can be folded into two stem-loop structures (shared with introns from Bacillus phage SPO1 and relatives); second, a conserved P7.2 region ( shared with all phage introns); third, the location of the stop codon from orf 253 in the P8 stem (shared with coliphage T4 and Bacillus phage SPO1 in trons); fourth, orf 253, which has sequence similarity with the H-N-H motif of putative endonuclease genes found in introns from Lactococcus, Lactobac illus, and Bacillus phages.