UpRoi1 - the phage-derived microRNA-size non-coding RNA molecule regulating both phage and its bacterial host development.

The phage Φ24B-encoded small RNA (sRNA), named UpRoi1, was identified following the prophage induction. The UpRoi1 molecule is encoded in the antirepressor region of the phage genome and is notably small, consisting of only 30 nucleotides. This sRNA is comparable in size to microRNAs found in eukaryotic cells, and thus, unusual for prokaryotic sRNAs. Bioinformatic analysis revealed that UpRoi1 has multiple interaction sites within the phage and host genomes, suggesting its complex regulatory role. In turn, RNA-seq analyses confirmed that the UpRoi1 molecule has a broad impact on the host's gene expression and influences numerous biological processes, particularly those involved in bacterial motility. Furthermore, binding assays revealed that the UpRoi1 molecule may directly interact with the 5' UTR of the phage antirepressor Roi mRNA as well as a bacterial transcript of the flgL gene encoding a protein associated with the structural unit of the bacterial flagellum. This affects both phage and host development, facilitating the switch of the phage to the lytic cycle. Besides, the RNA chaperone protein ProQ has been shown to bind the investigated sRNA with its target transcripts. Based on these results, we have found many similarities between UpRoi1 and herpesviral microRNAs, which is of high importance, because it justifies the occurrence of microRNA-type molecules in Shiga toxin-converting phages.