Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic modelling.
Sci Rep
; 10(1): 8651, 2020 05 26.
Article
en En
| MEDLINE
| ID: mdl-32457330
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 first 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 genome-scale 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 different carbon sources and under different 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 flux analysis under different metabolic scenarios highlighted the key role of the glyoxylate cycle in the central metabolism of strain TFA.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Genoma Bacteriano
/
Sphingomonadaceae
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Metabolismo Energético
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Redes y Vías Metabólicas
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
Sci Rep
Año:
2020
Tipo del documento:
Article
País de afiliación:
España