Dataset Information

Proteomics and transcriptomics analyses of Methylophaga thiooxydans reveal adaptations for growth on dimethylsulfide in a marine model organism

ABSTRACT: Dimethylsulfide is a volatile organic sulfur compound that provides the largest input of biogenic sulfur from the oceans to the atmosphere, and thence back to land, constituting an important link in the global sulfur cycle. Microorganisms degrading DMS affect fluxes of DMS in the environment, but the underlying metabolic pathways are still poorly understood. Methylophaga thiooxydans is a marine methylotrophic bacterium capable of growth on DMS as sole source of carbon and energy. Using proteomics and transcriptomics we identified genes expressed during growth on dimethylsulfide and methanol to refine our knowledge of the metabolic pathways that are involved in DMS and methanol degradation in this strain. Amongst the most highly expressed genes on DMS were the two methanethiol oxidases driving the oxidation of this reactive and toxic intermediate of DMS metabolism. Growth on DMS also increased expression of the enzymes of the tetrahydrofolate linked pathway of formaldehyde oxidation, in addition to the tetrahydromethanopterin linked pathway. Key enzymes of the inorganic sulfur oxidation pathway included flavocytochrome c sulfide dehydrogenase, sulfide quinone oxidoreductase, and persulfide dioxygenases. A sulP permease was also expressed during growth on DMS. Other enzymes of organic and inorganic sulfur metabolism previously detected in cell extracts of Methylophaga have not been characterised at the genetic level yet; their expression level and regulation could not be analysed. A pan-genome analysis of six available Methylophaga genomes suggests that only two of the six investigated bacteria have the metabolic potential to utilize methanethiol, the degradation product of DMS. These results mirror phenotypic analyses and demonstrate that DMS-utilization and subsequent C1 and sulfur oxidation are not conserved across the entire genus.

INSTRUMENT(S): Orbitrap Fusion ETD

ORGANISM(S): Methylophaga Thiooxydans Dms010

TISSUE(S): Cell Culture

SUBMITTER: Andrew Bottrill

LAB HEAD: Hendrik Schaefer

PROVIDER: PXD011992 | Pride | 2019-11-12

REPOSITORIES: Pride

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Publications

Identification of Proteins and Genes Expressed by <i>Methylophaga thiooxydans</i> During Growth on Dimethylsulfide and Their Presence in Other Members of the Genus.

Kröber Eileen E Schäfer Hendrik H

Frontiers in microbiology 20190529

Dimethylsulfide is a volatile organic sulfur compound that provides the largest input of biogenic sulfur from the oceans to the atmosphere, and thence back to land, constituting an important link in the global sulfur cycle. Microorganisms degrading DMS affect fluxes of DMS in the environment, but the underlying metabolic pathways are still poorly understood. <i>Methylophaga thiooxydans</i> is a marine methylotrophic bacterium capable of growth on DMS as sole source of carbon and energy. Using pr ...[more]

PMID: 31191477

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Project description:The purple sulfur bacterium Allochromatium vinosum DSM 180T is one of the best studied sulfur-oxidizing anoxygenic phototrophic bacteria and has been developed into a model organism for laboratory-based studies of oxidative sulfur metabolism. Here, we took advantage of the organismM-bM-^@M-^Ys high metabolic versatility and performed whole-genome transcriptional profiling to investigate the response of A. vinosum cells upon exposure to sulfide, thiosulfate, elemental sulfur or sulfite as compared to photoorganoheterotrophic growth on malate. Differential expression (at least twofold) of 1149 genes was observed, corresponding to 30% of the A. vinosum genome. A total of 549 genes were identified for which relative transcription increased at least twofold during growth on one of the different sulfur sources while relative transcription of 599 genes decreased. A significant number of genes that were strongly induced have documented sulfur-metabolism-related functions. Among these are the dsr genes including dsrAB for dissimilatory sulfite reductase and the sgp genes for the proteins of the sulfur globule envelope thus confirming former results. In addition we were able to identify new genes encoding proteins with appropriate subcellular localization and properties to participate in oxidative dissimilatory sulfur metabolism. Two of these were chosen for inactivation and phenotypic analyses of the respective mutant strains. This approach verified the importance of the encoded proteins for the oxidation of sulfide and thereby also documented the suitability of comparative transcriptomics for the identification of new sulfur-related genes in anoxygenic phototrophic sulfur bacteria. In this study, the relative genomic expression profiles of A. vinosum DSM 180T growing photolithoautotrophically on different reduced sulfur compounds were determined in comparison to those of cells grown photoorganoheterothrophically on malate (RCV medium) at exactly the same light intensity. The malate-containing medium was supplied with 0.815 mM sulfate in order to satisfy the sulfur-requirement for biosynthesis of sulfur-containing cell constituents. Three independent photolithoautotrophic cultures each, grown on sulfide, thiosulfate or sulfite were harvested 1 h, 2 h or 7 h, respectively, after inoculation. When elemental sulfur was the substrate, four independent cultures were harvested 3 h after inoculation.

Dataset Information

Proteomics and transcriptomics analyses of Methylophaga thiooxydans reveal adaptations for growth on dimethylsulfide in a marine model organism

Publications

Identification of Proteins and Genes Expressed by <i>Methylophaga thiooxydans</i> During Growth on Dimethylsulfide and Their Presence in Other Members of the Genus.

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