Virus Satellites Drive Viral Evolution and Ecology
Fig 3
SaPI-driven phage evolution occurs in vivo.
(A) Partial genetic maps of ϕ55–2 and ϕ55–3 (GenBank accession numbers KR709302 and KR709303, respectively). Arrows indicate predicted ORFs. Coloured arrows indicate the divergent region found in these phages, which include the SaPI1 inducing genes. (B) Lineup of Sri (SaPI1 inducer) protein sequences from phages ϕ55–2 and ϕ55–3, coloured according to relative sequence conservation at each position. Adapted from lineup generated by PRALINE [41]. The scoring scheme works from 0 for the least conserved alignment position, up to 10 (asterisk) for the most conserved alignment position. (C) Lineup of Dut (SaPIbov1 inducer) protein sequences from phages 80α and ϕSaov3 (left) or from phages ϕ11 and ϕB2 (right), coloured according to relative sequence conservation at each position. Adapted from lineup generated by PRALINE [41]. (D) SaPIbov1 excision and replication after induction of cloned dut genes from the natural mutant phages analysed in (C). A non-lysogenic derivative of strain RN4220 carrying SaPIbov1 was complemented with plasmids expressing 3xFlag-tagged Dut proteins, as indicated in Fig 1. The upper panel is a Southern blot probed for SaPIbov1 DNA; the lower panel is a western blot probed with antibody (Sigma) to the Flag tag carried by the proteins.