Figure 7. Reconstruction of L-rhamnose utilization system in bacteria.

A. Occurence and features of genes involved in L-rhamnose utilization. Species in several taxonomic groups of bacteria are shown as rows. the presence of genes for the respective functional roles (columns) is shown by capital letters corresponding to the four identified rhamnose regulons: S, RahS regulon (as in E. coli); R1, R2, R3, and R3’ correspond to the novel regulons of the same names. Other genes that were not identified within the above rhamnose regulons are marked by ‘U’. Genes clustered on the chromosome (operons) are outlined by matching background colors. Tentatively predicted functional roles are marked by asterisks. Functional roles corresponding to the predicted bifunctional enzymes RhaE-RhaW are underlined. The four Rhizobiaceae genomes that have the same set of genes and genome context are Mesorhizobium loti (ML), Agrobacterium tumefaciens (AT), Rhizobium leguminosarum (RL), and Sinorhizobium meliloti (SM).

B. The reconstructed L-rhamnose utilization pathway.

C. Chromosomal clusters of L-rhamnose utilization genes (arrows) and localization of candidate binding sites (circles) for rhamnose-specific TFs. The genes corresponding to the rhamnose-specific regulators RhaS, RhaR, R1, R2, and R3 are shown by black arrows with S, R, R1, R2, and R3 letters, respectively. Other homologous genes are marked by matching colors.

D. Consensus sequence logos for predicted binding sites of rhamnose-specific TFs. The corresponding TF protein family name is given in parenthesis.