A high-resolution map of bacteriophage øX174 transcription

Abstract

Bacteriophage øX174 is a model virus for studies across the fields of structural biology, genetics, gut microbiome, and synthetic biology, but did not have a high-resolution transcriptome until this work. In this study we used next-generation sequencing to measure the RNA produced from øX174 while infecting its host E. coli C. We broadly confirm the past transcriptome model while revealing several interesting deviations from previous knowledge. Additionally, we measure the strength of canonical øX174 promoters and terminators and discover both a putative new promoter that may be activated by heat shock sigma factors, as well as rediscover a controversial Rho-dependent terminator. We also provide evidence for the first antisense transcription observed in the Microviridae family, identify two promoters that may be involved in generating this transcriptional activity, and discuss possible reasons why this RNA may be produced.

Generating complex patterns of gene expression without regulatory circuits

“…Phage genomes are typically small and highly gene dense, which is likely to limit the overall complexity of their native gene expression programs [33,34]. The phage PhiX, for instance, encodes only 11 essential genes on a genome that spans ≈5,000 base-pairs [35,36]. Even with relatively small genomes, phages are nevertheless capable of producing complex gene expression dynamics over the course of an infection cycle.…”