Precise Transcription Control Drives Optimized Catabolism of β-5-Type Lignin-Derived Dimers in <i>Sphingobium lignivorans</i> SYK-6

<i>Sphingobium lignivorans</i> SYK-6, a promising platform for lignin valorization, can degrade dehydrodiconiferyl alcohol (DCA), which is a β-5-type dimer. We found that <i>phcR</i> (a gene encoding a MarR-type transcriptional regulator) negatively regulates the transcription of DCA catabolism genes. Furthermore, the previously identified DesR was observed to be involved in the regulation of a specific DCA catabolism gene. The effector molecule of PhcR was identified as a DCA metabolite: 5-(2-carboxyvinyl)-2-(4-hydroxy-3-methoxyphenyl)-7-methoxy-2,3-dihydrobenzofuran-3-carboxylic acid. The disruption of <i>phcR</i> was hypothesized to increase the production rate of a metabolite as a polymer building block (2-pyrone-4,6-dicarboxylic acid [PDC]) from DCA. However, PDC production from DCA using a <i>phcR</i>-disrupted PDC-producing strain led to the accumulation of a metabolite from the activated minor DCA catabolic pathway, thereby resulting in a significant decrease in the rate of PDC production. These findings underscore the critical importance of a precise regulatory system for DCA catabolism genes in ensuring efficient catabolism.