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

Journal Article · 02 July 2019 · Metabolic Engineering

DOI: https://doi.org/10.1016/j.ymben.2019.06.013 · OSTI ID:1572523

Roell, Garrett W. ^[1]; Carr, Rhiannon R. ^[1]; Campbell, Tayte ^[1]; Shang, Zeyu ^[1]; Henson, William R. ^[1]; Czajka, Jeffrey J. ^[1]; Martín, Hector García ^[2]; Zhang, Fuzhong ^[1]; Foston, Marcus ^[1]; Dantas, Gautam ^[1]; Moon, Tae Seok ^[1]; Tang, Yinjie J. ^[1]

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1. Washington University, St. Louis, MO (United States)
2. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); BCAM, Basque Center for Applied Mathematics, Bilbao (Spain)

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. In conclusion, 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.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); USDOE
• Grant/Contract Number: SC0018324; DBI-1427621
• OSTI ID: 1572523
• Alternate ID(s): OSTI ID: 1531200
• Journal Information: Metabolic Engineering, Vol. 55, Issue C; ISSN 1096-7176
• Publisher: ElsevierCopyright Statement
• Country of Publication: United States
• Language: English