TY - JOUR
T1 - Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic modelling
AU - Garcia-Romero, Inma
AU - Nogales, Juan
AU - Díaz, Eduardo
AU - Santero, Eduardo
AU - Floriano, Belén
PY - 2020/5/26
Y1 - 2020/5/26
N2 - 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.
AB - 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.
KW - metabolism, sphingopyxis, TFA, genome-scale, modelling
U2 - 10.1038/s41598-020-65258-9
DO - 10.1038/s41598-020-65258-9
M3 - Article
VL - 10
JO - Nature Scientific Reports
JF - Nature Scientific Reports
SN - 2045-2322
M1 - 8651
ER -