A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630
| Autor: | Rhiannon R. Carr, William R. Henson, Jeffrey J. Czajka, Yinjie J. Tang, Tae Seok Moon, Fuzhong Zhang, Hector Garcia Martin, Marcus Foston, Gautam Dantas, Tayte Campbell, Zeyu Shang, Garrett W. Roell |
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| Rok vydání: | 2019 |
| Předmět: |
0106 biological sciences
Metabolite Catabolite repression Bioengineering 01 natural sciences Applied Microbiology and Biotechnology 03 medical and health sciences chemistry.chemical_compound Rhodococcus opacus Bacterial Proteins 010608 biotechnology Escherichia coli Rhodococcus Entner–Doudoroff pathway 030304 developmental biology chemistry.chemical_classification 0303 health sciences Sugar phosphates Phenol Systems Biology Fructose Metabolism Citric acid cycle chemistry Biochemistry Directed Molecular Evolution Metabolic Networks and Pathways Biotechnology |
| Zdroj: | BIRD: BCAM's Institutional Repository Data instname |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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