Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution
Figure 6
Determinants of immunity specificity in Cluster A genomes.
A. Phylogenetic relationship of Cluster A repressors. The neighbor-joining (NJ) tree was drawn by NJPlot using output from an alignment in ClustalW; bootstrap values from 1000 iterations are shown. The repressor clades correspond closely to the subclustering of the genomes as indicated by color shading: Subcluster A1, red: A2, green, A3, yellow, A4, blue. B. The predicted helix-turn-helix motifs of the Cluster A repressor are aligned to show conserved and variant residues. The positions in the second recognition helix of the HTH motif are numbered. The Cluster assignation of the genome encoding the repressors is colored as in A. Bxz2 gp74 and KBG gp73 are included even though both contain frameshift mutations in the repressor gene. In KBG gp73 the mutation lies downstream of the HTH motif. There is a presumed single base deletion in Bxz2 at coordinate 44,987 upstream of the HTH motif, and we have used the ‘corrected’ sequence in the alignment that would results from inclusion of one additional bp at that position. C. Alignment of the consensus stoperator sites in Cluster A genomes. Consensus sequences were derived from alignments of putative operator and stoperator sites (shown in Fig. S4); mixed base consensus positions are indicated as W: A or T, D: A, G or T, V: C, G or T, M: A or C, N: A, C, G or T. Color shading indicates identical consensus positions.