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

ABSTRACT: Sphingopyxis granuli strain TFA is an ?-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 ?-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.

SUBMITTER: Garcia-Romero I

PROVIDER: S-EPMC7250832 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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

García-Romero Inmaculada I Nogales Juan J Díaz Eduardo E Santero Eduardo E Floriano Belén B

Scientific reports 20200526 1

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 us ...[more]

PMID: 32457330

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Project description:BackgroundSphingomonads are Alphaproteobacteria that belong to the Sphingomonas, Novosphingobium, Sphingopyxis or Sphingobium genera, They are physiologically diverse and broadly distributed in nature, playing important roles in oligotrophic environments and in the degradation of recalcitrant polyaromatic compounds, Sphingopyxis is a poorly studied genus of which only one representative (S. alaskensis RB2256) has been deeply characterized. In this paper we analyze the genomic features of S. granuli strain TFA (formerly Sphingomonas macrogoltabida) in comparison with the available Sphingopyxis sequenced genomes, to describe common characteristics of this genus and to highlight unique characteristics of strain TFA.ResultsThe TFA genome has been assembled in a single circular chromosome of 4.7 Mb. Genomic sequence analysis and proteome comparison re-assigned the TFA strain to the Sphingopyxis genus and the S. granuli species. Some regions of the TFA genome show high similarity (ca. 100%) to other bacteria and several genomic islands have been detected. Pathways for aromatic compound degradation have been predicted but no growth of TFA has been detected using these as carbon or nitrogen sources. Genes for nitrate respiration have been identified as TFA exclusive. Experimental data on anaerobic growth of TFA using nitrate as a terminal electron acceptor are also provided.ConclusionsSphingopyxis representatives form a compact phylogenetic group (with the exception of S. baekryungensis DSM 16222) that share several characteristics, such as being naturally resistant to streptomycin, having only one ribosomal operon, a low number of prophages and CRISPR sequences, absence of selenoproteins and presence of ectoin and other biosynthesis pathways for secondary metabolites. Moreover, the TFA genome organization shows evidence of the presence of putative integrative and conjugative elements (ICE) responsible for the acquisition of several characteristics by horizontal transfer mechanisms. Sphingopyxis representatives have been described as strict aerobes but anaerobic growth using nitrate as a terminal electron acceptor might confer an environmental advantage to the first S. granuli strain characterized at genomic level.

Dataset Information

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

Publications

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

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