Fig. 1.

Sphingobium sp. strain SYK-6 has a number of TBDR genes of unknown function which are specifically induced in the presence of lignin-derived aromatic compounds. a A phylogenetic tree based on the alignment of the deduced amino acid sequences of the 74 putative TBDR genes in SYK-6 with those of the TBDR genes of known function (Supplementary Table 1). Bootstrap values (based on 1000 replicates) are shown at the branch points. b A heat map showing the fold change in the expression of each TBDR gene in cells grown in Wx minimal medium containing SEMP³⁷ with lignin-derived aromatic compounds versus those grown without lignin-derived aromatic compounds, as determined by DNA microarray analysis. Lignin-derived aromatic compounds used for the DNA microarray analysis were: DDVA, 5,5′-dehydrodivanillate (5-5 type); DCA, dehydrodiconiferyl alcohol (β-5 type); HMPPD, 1,2-bis(4-hydroxy-3-methoxyphenyl)-propane-1,3-diol (β-1 type); PR, pinoresinol (β-β type); GGE, guaiacylglycerol-β-guaiacyl ether (β-O-4 type); FA, ferulate; AV, acetovanillone; VN, vanillin; VA, vanillate; SA, syringate; PCA, protocatechuate. The chemical structures of these compounds are shown in Supplementary Fig. 1. Induction ratios were calculated as described in the Methods. The P value of each field without an asterisk, P > 0.05 (one-way ANOVA with Dunnett’s multiple comparisons post-test).