Convergent evolution involving dimeric and trimeric dUTPases in pathogenicity island mobilization
(A) Alignment of dimeric Duts from S. aureus phages ϕNM1, ϕDI, ϕDII, ϕO11, ϕO46, ϕMR25, ϕStauST398-3 (StauST), ϕHKU10-03 (HKU10) and ϕ55 are shown representing the nine different dimeric Dut families identified in the phylogenetic tree described below (Fig 1B). Colours indicate relative sequence conservation at each position, with red being most conserved and blue being least (alignment generated by PRALINE). The five conserved catalytic motifs in dimeric Duts are highlighted in magenta boxes and labeled. The bracket indicates the localization of the extra motif VI. (B) Radial phylogenetic tree of identified staphylococcal and Staphylococcus phage dimeric Duts. Radial tree showing the 9 different groups, constructed using the alignment of protein sequences of the dimeric Duts from staphylococcal phages (including the full sequence, not just the variable region) listed in S1 Table. An NCBI BLAST of the known SaPI inducing ϕNM1 phage encoded dimeric Dut (full sequence) was used to select 59 dimeric Dut sequences that were annotated as staphylococcal phage Duts or as staphylococcal Duts. S.aureus does not encode a genomic Dut so any such annotations would also be phagic. Four trimeric staphylococcal phage Duts were also included in the alignment and tree to provide outliers and show the distance of these proteins from the dimeric Duts. The accession numbers for all sequences are listed in S1 Table. The small box below shows the full tree, including the trimeric Dut outliers (red box), which were hidden for clarity in the more detailed tree above. This detailed tree consists of the area highlighted with the green box in the full depiction. Groups are shown by clustered leaf node names and the name of the representative used in the sequence alignment of panel (A) is highlighted with the same colour of the group. The tree was created using the following parameters; algorithm = Neighbour Joining, distance measure = Jukes-Cantor, bootstrap = 100 Replicates. Proteins are named by NCBI accession number with the exception of the group representative where the name of the corresponding phage is included used (S1 Table).