Transcriptomics-driven characterization of LUZ100, a T7-like Pseudomonas phage with temperate features

Autographiviridae is a diverse yet distinct family of bacterial viruses markedby a strictly lytic lifestyle and a generally conserved genome organization. Here, wecharacterized Pseudomonas aeruginosa phage LUZ100, a distant relative of type phageT7. LUZ100 is a podovirus with a limited host range which likely uses lipopolysaccharide(LPS) as a phage receptor. Interestingly, infection dynamics of LUZ100 indicatedmoderate adsorption rates and low virulence, hinting at temperate characteristics. Thishypothesis was supported by genomic analysis, which showed that LUZ100 shares theconventional T7-like genome organization yet carries key genes associated with a temperatelifestyle. To unravel the peculiar characteristics of LUZ100, ONT-cappable-seqtranscriptomics analysis was performed. These data provided a bird's-eye view of theLUZ100 transcriptome and enabled the discovery of key regulatory elements, antisenseRNA, and transcriptional unit structures. The transcriptional map of LUZ100also allowed us to identify new RNA polymerase (RNAP)-promoter pairs that canform the basis for biotechnological parts and tools for new synthetic transcriptionregulation circuitry. The ONT-cappable-seq data revealed that the LUZ100 integraseand a MarR-like regulator (proposed to be involved in the lytic/lysogeny decision)are actively cotranscribed in an operon. In addition, the presence of a phage-specificpromoter transcribing the phage-encoded RNA polymerase raises questions on theregulation of this polymerase and suggests that it is interwoven with the MarRbasedregulation. This transcriptomics-driven characterization of LUZ100 supportsrecent evidence that T7-like phages should not automatically be assumed to have astrictly lytic life cycle.