Edinburgh Napier University

  Of 62 Streptococcus thermophilus bacteriophages isolated from various ecological 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 sequence showed a significantly lower GC content than the
surrounding intron and lysin gene sequences, and the predicted protein shared a motif with endonucleases
found in phages from both gram-positive and gram-negative bacteria. A comparison of the phage lysin genes
revealed a clear 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 genomes. Folding of the intron RNA revealed secondary structure
elements shared with other phage introns: first, a 38-bp insertion between regions P3 and 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 introns); fourth, orf 253, which has sequence
similarity with the H-N-H motif of putative endonuclease genes found in introns from Lactococcus, Lactobacillus,
and Bacillus phages.