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A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism
Version 2 2024-01-17, 19:11
Version 1 2023-05-15, 17:12
journal contributionposted on 2024-01-17, 19:11 authored by Garrett W. Roell, Christina Schenk, Winston E. Anthony, Rhiannon R. Carr, Aditya Ponukumati, Joonhoon Kim, Elena Akhmatskaya, Marcus Foston, Gautam Dantas, Tae Seok Moon, Yinjie J. Tang, Hector García Martín
Rhodococcus opacus is a bacterium that has a high tolerance to aromatic compounds and can produce significant amounts of triacylglycerol (TAG). Here, we present iGR1773, the first genome-scale model (GSM) of R. opacus PD630 metabolism based on its genomic sequence and associated data. The model includes 1773 genes, 3025 reactions, and 1956 metabolites, was developed in a reproducible manner using CarveMe, and was evaluated through Metabolic Model tests (MEMOTE). We combine the model with two Constraint-Based Reconstruction and Analysis (COBRA) methods that use transcriptomics data to predict growth rates and fluxes: E-Flux2 and SPOT (Simplified Pearson Correlation with Transcriptomic data). Growth rates are best predicted by E-Flux2. Flux profiles are more accurately predicted by E-Flux2 than flux balance analysis (FBA) and parsimonious FBA (pFBA), when compared to 44 central carbon fluxes measured by 13C-Metabolic Flux Analysis (13C-MFA). Under glucose-fed conditions, E-Flux2 presents an R2 value of 0.54, while predictions based on pFBA had an inferior R2 of 0.28. We attribute this improved performance to the extra activity information provided by the transcriptomics data. For phenol-fed metabolism, in which the substrate first enters the TCA cycle, E-Flux2’s flux predictions display a high R2 of 0.96 while pFBA showed an R2 of 0.93. We also show that glucose metabolism and phenol metabolism function with similar relative ATP maintenance costs. These findings demonstrate that iGR1773 can help the metabolic engineering community predict aromatic substrate utilization patterns and perform computational strain design.
simplified pearson correlationproduce significant amountssubstrate first entersflux predictions displayrhodococcus opacus use transcriptomics datapredict growth ratesmetabolic model tests2 sup13 suptranscriptomic data ).flux balance analysispd630 metabolism basedphenol metabolism functionopacus transcriptomics datagrowth ratespredictions basedflux profilesfirst genomeassociated databased reconstructiontag ).mfa ).memote ).>< supfed metabolismr two constrainttca cyclescale modelquality genomeimproved performancegenomic sequencefindings demonstratefed conditionsbest predictedaromatic compoundsalso showaccurately predicted3025 reactions1956 metabolites