A window into lysogeny: Revealing temperate phage biology with transcriptomics [article]

Siân V. Owen, Rocío Canals, Nicolas Wenner, Disa L. Hammarlöf, Carsten Kröger, Jay C. D. Hinton
2019 bioRxiv   pre-print
ABSTRACTIntegrated phage elements, known as prophages, are a pervasive feature of bacterial genomes. Prophages can enhance the fitness of their bacterial hosts by conferring beneficial functions, such as virulence, stress tolerance or phage resistance, which are encoded by accessory loci. Whilst the majority of phage-encoded genes are repressed during lysogeny, accessory loci are often highly expressed. However, novel prophage accessory loci are challenging to identify based on DNA sequence
more » ... on DNA sequence data alone. Here, we use bacterial RNA-seq data to examine the transcriptional landscapes of five Salmonella prophages. We show that transcriptomic data can be used to heuristically enrich for prophage features that are highly expressed within bacterial cells and often represent functionally-important accessory loci. Using this approach we identify a novel anti-sense RNA species in prophage BTP1, STnc6030, which mediates superinfection exclusion of phage BTP1 and immunity to closely-related phages. Bacterial transcriptomic datasets are a powerful tool to explore the molecular biology of temperate phages.
doi:10.1101/787010 fatcat:qfvm2d67yvfx7f4ovjezitfiae