A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630

• Published in: Metabolic engineering 2019-09, Vol.55 (C), p.120-130
• Main Authors: Roell, Garrett W., Carr, Rhiannon R., Campbell, Tayte, Shang, Zeyu, Henson, William R., Czajka, Jeffrey J., Martín, Hector García, Zhang, Fuzhong, Foston, Marcus, Dantas, Gautam, Moon, Tae Seok, Tang, Yinjie J.
• Format: Article
• Language: English
• Subjects: 13C-MFA; 13C-pulse-tracing; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Directed Molecular Evolution; Entner–Doudoroff pathway; Escherichia coli - genetics; Escherichia coli - metabolism; Gluconeogenesis; Lignin; Metabolic Networks and Pathways; Phenol - metabolism; Rhodococcus - genetics; Rhodococcus - metabolism; Systems Biology
• ISSN: 1096-7176; 1096-7184
• DOI: 10.1016/j.ymben.2019.06.013

Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branched-chain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, we performed 13C-pathway tracing, 13C-pulse-tracing, transcriptional profiling, biomass composition analysis, and metabolite profiling in conjunction with 13C-metabolic flux analysis (13C-MFA) of phenol metabolism. We found that 1) phenol is metabolized mainly through the ortho–cleavage pathway; 2) phenol utilization requires a highly active TCA cycle; 3) NADPH is generated mainly via NADPH-dependent isocitrate dehydrogenase; 4) active cataplerotic fluxes increase plasticity in the TCA cycle; and 5) gluconeogenesis occurs partially through the reversed Entner–Doudoroff pathway (EDP). We also found that phenol-fed R. opacus PD630 generally has lower sugar phosphate concentrations (e.g., fructose 1,6-bisphosphatase) compared to metabolite pools in 13C-glucose-fed Escherichia coli (set as internal standards), while its TCA metabolites (e.g., malate, succinate, and α-ketoglutarate) accumulate intracellularly with measurable succinate secretion. In addition, we found that phenol utilization was inhibited by benzoate, while catabolite repressions by other tested carbon substrates (e.g., glucose and acetate) were absent in R. opacus PD630. Three adaptively-evolved strains display very different growth rates when fed with phenol as a sole carbon source, but they maintain a conserved flux network. These findings improve our understanding of R. opacus’ metabolism for future lignin valorization. •13C-MFA revealed carbon and energy fluxes in R. opacus when phenol was used as the substrate.•Transcription profiling and metabolite analysis improved genome-to-phenome knowledge of phenol metabolism.•The hierarchy of carbon source co-utilizations by R. opacus was elucidated.•Evolved strains with different growth rates in phenol have a conserved flux network.