Figure 6

The evolutionary relationship between some T-boxes. (A) shows a putative phylogeny of the branched-chain amino acid tRNA ligases of B. anthracis Ames, B. subtilis 168, C. acetobutylicum ATCC824D, L. acidophilus NCFM, L. plantarum WCFS1, L. mesenteroides ATCC8293 and S. aureus Mu50. (B) shows the Neighbor-Joining tree for the related T-boxes. The underlying alignments were made with the complete 200 – 300 nucleotides of the identified T-boxes. These alignments were homogeneous in the sense that the fully conserved motifs aligned perfectly and that between those conserved elements there were little gaps. Nevertheless, the low bootstrap support for the various branches indicates that this tree is unlikely to reflect the true phylogeny of the regulatory elements. (C) shows the Neighbor-Joining tree for various T-boxes found in B. anthracis Ames. Next to the tree, the part of the corresponding multiple sequence alignment containing the specifier codon (indicated in white letters) is depicted. The amino acid specificity of the specifier codon is color-coded: Red and orange relate to Ile, green to Leu, light blue to Phe, beige to Pro or Gln, pink to Ser, brown to Thr, turquoise to Trp, purple to Tyr and dark blue to Val. The family of the protein encoded by the regulated gene is indicated by the letters that follow the amino acid code. These protein families included the APC, LIVCS, MFS, NhaC and NSS transporter protein families and various tRNA-ligase families (S or Smr for mupirocin resistant tRNA ligase). The NSS-family transport proteins regulated by a Leu, Phe and Trp T-box are in-paralogs characteristic for the species of the Bacillus cereus group. The purple numbers between brackets indicate the bootstrap support for the displayed clusters (out of 1000).