Figure 1.
Methionine metabolism and its conserved regulation in Proteobacteria.
Genes encoding enzymes for respective reactions are shown in boxes. The Enzyme Commission numbers (EC numbers) of these reactions are shown. Genes encoding transporters of methionine, methylmethionine, and methylthioribose are shown in rounded boxes. Alternative isoenzymes or transporters are shown in different boxes attached to the same arrow. Core regulon members for TFs and riboswitches are shown by colored circles and squares, respectively. The taxonomic distributions of these regulatory interactions are shown in Figure 7.
Table 1.
Statistics of reconstructed methionine regulons in Proteobacteria.
Figure 2.
Conservation of regulatory interactions in the reconstructed MetJ regulons.
The core regulon, taxon- and genome-specific regulon members are highlighted and listed along with their average conservation scores and functional annotations in Table S2.
Figure 3.
Conservation of regulatory interactions in the reconstructed MetR regulons.
The core regulon, taxon- and genome-specific regulon members are highlighted and listed along with their average conservation scores and functional annotations in Table S2.
Figure 4.
Conservation of regulatory interactions in the reconstructed SahR regulons.
The core regulon, taxon- and genome-specific regulon members are highlighted and listed along with their average conservation scores and functional annotations in Table S2.
Figure 5.
Conservation of regulatory interactions in the reconstructed SAH riboswitch regulons.
The core regulon, taxon- and genome-specific regulon members are highlighted and listed along with their average conservation scores and functional annotations in Table S2.
Figure 6.
Conservation of regulatory interactions in the reconstructed SAM_alpha riboswitch regulons.
The core regulon, taxon- and genome-specific regulon members are highlighted and listed along with their average conservation scores and functional annotations in Table S2.
Figure 7.
Distribution of regulatory interactions for core members of methionine regulons in Proteobacteria.
The presence or absence of gene orthologs in at least one studied genome in a taxonomic group is shown by light green or gray background, respectively. Regulation of at least one gene ortholog within each taxonomic group is shown by colored circles and squares as in Figure 1.
Figure 8.
Alternative secondary structures of candidate metXZ RNA element.
Regions 1–6 shown in yellow boxes are conserved sequences found in the multiple alignment of leader regions of 34 metX and metZ genes from β-proteobacteria (Figure S2). In the consensus RNA sequence, N denotes any nucleotide, and M stands for A or C. Possible secondary structures formed by the interaction between the conserved regions are shown by yellow lines.