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Multi-omics analysis revealed the aromatic compound metabolism in marine Roseobacter clade

ABSTRACT:

Here, we selected Roseovarius nubinhibens as the model organism to comprehensively interrogate aromatic compound metabolism in marine Roseobacter clade. First, we preliminarily elucidated the three distinct mechanisms of aromatic compound transmembrane transport in R. nubinhibens. By integrating multi-omics analysis with genetic perturbation techniques, we successfully identified and experimentally validated the previously unidentified genes (pcaB, pcaI and pcaJ) in the β-ketoadipate pathway. Furthermore, we uncovered genetic crosstalk between the β-ketoadipate and β-oxidation pathways. This study represents the first complete elucidation of the β-ketoadipate pathway in marine Roseobacter clade bacteria. We believe that our findings will advance the potential of marine microbes in geochemical element cycling, pollutant degradation and the sustainable exploitation of marine resources.

INSTRUMENT(S): Liquid Chromatography MS - negative - reverse phase, Liquid Chromatography MS - positive - reverse phase

PROVIDER: MTBLS12306 | MetaboLights | 2025-08-09

REPOSITORIES: MetaboLights

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Project description:Rex2013 - Genome scale metabolic model of D.shibae (iDsh827) The aerobic anoxygenic phototroph Dinoroseobacter shibae DFL12T is a representative of an important group of marine bacteria called the Roseobacter clade. To gain insight into the versatile metabolism of this clade, the authors have taken a constraint-based approach and created this genome-scale metabolic model (iDsh827). This model is the first one to account for the energy demand of motility, the light-driven ATP generation and experimentally determined specific biomass composition. This model is described in the article: Swimming in light: a large-scale computational analysis of the metabolism of Dinoroseobacter shibae. Rex R, Bill N, Schmidt-Hohagen K, Schomburg D. PLoS Comput Biol. 2013;9(10):e1003224. Abstract: The Roseobacter clade is a ubiquitous group of marine α-proteobacteria. To gain insight into the versatile metabolism of this clade, we took a constraint-based approach and created a genome-scale metabolic model (iDsh827) of Dinoroseobacter shibae DFL12T. Our model is the first accounting for the energy demand of motility, the light-driven ATP generation and experimentally determined specific biomass composition. To cover a large variety of environmental conditions, as well as plasmid and single gene knock-out mutants, we simulated 391,560 different physiological states using flux balance analysis. We analyzed our results with regard to energy metabolism, validated them experimentally, and revealed a pronounced metabolic response to the availability of light. Furthermore, we introduced the energy demand of motility as an important parameter in genome-scale metabolic models. The results of our simulations also gave insight into the changing usage of the two degradation routes for dimethylsulfoniopropionate, an abundant compound in the ocean. A side product of dimethylsulfoniopropionate degradation is dimethyl sulfide, which seeds cloud formation and thus enhances the reflection of sunlight. By our exhaustive simulations, we were able to identify single-gene knock-out mutants, which show an increased production of dimethyl sulfide. In addition to the single-gene knock-out simulations we studied the effect of plasmid loss on the metabolism. Moreover, we explored the possible use of a functioning phosphofructokinase for D. shibae. This model is hosted on BioModels Database and identified by: MODEL1308180000 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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Multi-omics analysis revealed the aromatic compound metabolism in marine Roseobacter clade

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