Self-splicing introns in genes of Bastillevirinae bacteriophages

Abstract

Group I introns are self-splicing ribozymes that can be found in eukaryotes, prokaryotes, and quite often in their viruses. The distribution, structure, and splicing of group I introns in genes of some phage taxa like the Tevenvirinae or Twortwirinae was extensively studied. On the other hand, the prevalence of intervening sequences in most other clades of bacterial viruses remains mostly unexplored. In this paper, we describe group I autocatalytic introns in genes of phages from the Bastillevirinae subfamily. This taxon belongs to the Herelleviridae family and consists of 15 genera and 37 species, including viruses with strong antimicrobial potential. A bioinformatic search for intron-related RNA structures revealed the presence of 45 intervening sequences within 37 genes that belong to four gene families. Eight of the nine genes selected for experimental validation were spliced—four only in an infected bacteria but additional four self-spliced in vitro. Interestingly, one of the studied genes undergoes alternative splicing. To sum up, our findings expand the knowledge on the distribution and diversity of group I introns and shed new light on this neglected aspect of phage transcriptomics. Additionally, in the course of our study, we demonstrated the effectiveness of nanopore sequencing in elucidating prokaryotic splicing mechanisms.