Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic modelling

Inma Garcia-Romero, Juan Nogales, Eduardo Díaz, Eduardo Santero, Belén Floriano*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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Abstract

Sphingopyxis granuli strain TFA is an α-proteobacterium that belongs to the sphingomonads, a group of bacteria well-known for its degradative capabilities and oligotrophic metabolism. Strain TFA is the only bacterium in which the mineralisation of the aromatic pollutant tetralin has been completely characterized at biochemical, genetic, and regulatory levels and the frst Sphingopyxis characterised as facultative anaerobe. Here we report additional metabolic features of this α-proteobacterium using metabolic modelling and the functional integration of genomic and transcriptomic data. The genomescale metabolic model (GEM) of strain TFA, which has been manually curated, includes information on 743 genes, 1114 metabolites and 1397 reactions. This represents the largest metabolic model for a member of the Sphingomonadales order thus far. The predictive potential of this model was validated against experimentally calculated growth rates on diferent carbon sources and under diferent growth conditions, including both aerobic and anaerobic metabolisms. Moreover, new carbon and nitrogen sources were predicted and experimentally validated. The constructed metabolic model was used as a platform for the incorporation of transcriptomic data, generating a more robust and accurate model. In silico fux analysis under diferent metabolic scenarios highlighted the key role of the glyoxylate cycle in the central metabolism of strain TFA.
Original languageEnglish
Article number8651
Number of pages14
JournalScientific Reports
Volume10
DOIs
Publication statusPublished - 26 May 2020

Keywords

  • metabolism, sphingopyxis, TFA, genome-scale, modelling

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