Analysis of phage and PAI excision and TEM of phage. A. Excision and circularization of the PAI and prophage elements were confirmed by amplification of the attP site by PCR using primers (black arrows) that faced out of the 5′ and 3′ ends of the genomic islands (data not shown). The PAI and prophage are both inserted between a tRNA gene at the 3′ end and partially duplicated copy at the 5′ end. B. qPCR analysis of genomic DNA samples showed that the frequency of excision of the PAI and prophage is higher in the rsmA mutant compared to WT. Copy number of pigB was included as a negative control. or1483 and or4140 are cargo genes on the PAI and prophage, respectively. Copy number was determined as the percentage of cells containing the gene or attP site relative to the copy number of the internal reference gene gyrB. Values represent average gene expression ± SD from three independent experiments. C. TEM image of a putative podoviridae-like phage particle (65–70 nm in diameter) isolated from the culture supernatant of the rsmA mutant. The arrow indicates what may be a very short tail at the apex.