Deciphering the transcriptional regulation of the catabolism of lignin-derived aromatics in Rhodococcus opacus PD630

Rhodococcus opacus PD630 has considerable potential as a platform for valorizing lignin due to its innate biological funneling pathways. However, the transcriptional regulation of the aromatic catabolic pathways and the mechanisms controlling aromatic catabolic operons in response to different aromatic mixtures are still underexplored. Here, we identified and studied the transcription factors for aromatic degradation using GFP-based sensors and comprehensive deletion analyses. Our results demonstrate that the funneling pathways for phenol, guaiacol, 4-hydroxybenzoate, and vanillate are controlled by transcriptional activators. The two different branches of the beta-ketoadipate pathway, however, are controlled by transcriptional repressors. Additionally, promoter activity assays revealed that the substrate hierarchy in R. opacus may be ascribed to the transcriptional cross-regulation of the individual aromatic funneling pathways. These results provide clues to clarify the molecule-level mechanisms underlying the complex regulation of aromatic catabolism, which facilitates the development of R. opacus as a promising chassis for valorizing lignin. Gene knockout studies with analysis of aromatic sensors identify transcription factors involved in regulating aromatic degradation pathways in Rhodococcus opacus and substrate hierarchy in aromatic mixtures for applications in lignin valorization.

Automated summary

In this study, we identified and studied the transcription factors involved in aromatic degradation in Rhodococcus opacus using GFP-based sensors and comprehensive deletion analyses. Our results indicate that the funneling pathways for different aromatic compounds are regulated by transcriptional activators or repressors. Additionally, the substrate hierarchy in R. opacus may be due to the transcriptional cross-regulation of different aromatic funneling pathways.