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.
Highlights
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
We present a genome-scale metabolic model of another Sphingomonadaceae, Sphingopyxis granuli strain TFA, a small, rod-shaped, facultative anaerobic, streptomycin-resistant bacterium that possesses the capability to grow using tetralin, a volatile toxic compound that consists of an aromatic and an alicyclic ring, as sole carbon and energy source[17]
An initial draft model based on the Escherichia coli K12 model iJO136620 and the Pseudomonas putida KT2440 model iJN141121 was constructed
Summary
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. Oligotrophs show overrepresentation of Clusters of Orthologous Groups (COGs) for lipid transport and metabolism (I) and secondary metabolite biosynthesis, transport, and catabolism (Q) among others[4]. there is a need to better understand the metabolism of these degradative bacteria and to potentially reveal new insights into their degradative capabilities and lifestyle To this end, we set out to establish a GEnome-scale metabolic Network REconstruction (GENRE) for a member of this genus that was likely to prove a powerful tool for future studies[5,6,7,8]. We present a genome-scale metabolic model of another Sphingomonadaceae, Sphingopyxis granuli strain TFA, a small, rod-shaped, facultative anaerobic, streptomycin-resistant bacterium that possesses the capability to grow using tetralin, a volatile toxic compound that consists of an aromatic and an alicyclic ring, as sole carbon and energy source[17]. The model presented here constitutes the first GEM generated for a member of the Sphingopyxis genus and the second within the Sphingomonadales order
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