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

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. Proteomics and transcriptomics also identified a number of highly expressed proteins and gene products whose function is currently not understood. As the identity of some enzymes of organic and inorganic sulfur metabolism previously detected in Methylophaga has not been characterized at the genetic level yet, highly expressed uncharacterized genes provide new targets for further biochemical and genetic analysis. A pan-genome analysis of six available Methylophaga genomes showed that only two of the six investigated strains, M. thiooxydans and M. sulfidovorans have the gene encoding methanethiol oxidase, suggesting that growth on methylated sulfur compounds of M. aminisulfidivorans is likely to involve different enzymes and metabolic intermediates. Hence, the pathways of DMS-utilization and subsequent C 1 and sulfur oxidation are not conserved across Methylophaga isolates that degrade methylated sulfur compounds.

Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater

“…In addition, a Piscirickettsiaceae MAG (MAG 21) containing an mtoX sequence (Table S 5 ) was more abundant in the 13 C-DMSP samples (13C_T; RA 1.5%) compared to the natural (T0) seawater (RA 0.01 ± 0.004%) and was 34-fold more enriched in the 13 C-light (13C_L) than in the 13 C-heavy fraction (13C_H; Table S 5 ), further supporting the notion that members of this family are key bacteria cycling DMS in this coastal seawater. These data are also consistent with previous work showing that mtoX , whose transcription and protein expression is upregulated by growth with DMS in Methylophaga thiooxydans , is the only known reporter gene for carbon assimilation from DMS in the Thiotrichales [ 70 ]. In M .…”

“…This study also provides a new strategy to identify key microorganisms degrading DMS as well as DMSP for carbon assimilation in environmental samples. The use of 13 C-DMSP where only the propionate was 13 C-labelled and not the DMS moiety efficiently identified members of the Piscirickettsiaceae family, especially Methylophaga (well known for their ability to grow on DMS [ 70 ]), as important bacteria likely degrading the DMS generated from DMSP for carbon assimilation in these coastal seawater samples. Thus, it will be interesting to use the SIP strategy applied in this work on more varied marine environments to elucidate the variability in those distinct microorganisms using DMSP and/or DMS primarily for carbon requirements.…”

13C‐chloromethane incubations provide evidence for novel bacterial chloromethane degraders in a living tree fern

“…Genome comparisons within the genus Methylobacterium and the closely related clade Methylorubrum to determine pan, core and dispensable genes and singletons (unique genes) were carried out using EDGAR v2.0 (Blom et al ., 2009) as described previously (Kröber and Schäfer, 2019). The MAG Fern CH 3 Cl SIP LEAF bin s3 was used as a reference and strains of Methylobacterium (including Methylorubrum ) used for this analysis are listed in Supplementary Table S2.…”

Novel bacterial chloromethane degraders of a living tree fern evidenced by 13C-chloromethane incubations

“…was carried out using EDGAR v2.0 [80] as described previously [81]. The MAG Fern CH3Cl SIP LEAF bin s3 was used as a reference and strains of Methylobacterium (including Methylorubrum) used for this analysis are listed in Supplementary Table S2.…”

“…Genome comparisons within the genus Methylobacterium and the closely related clade Methylorubrum to determine pan, core and dispensable genes and singletons (unique genes) was carried out using EDGAR v2.0 [80] as described previously [81]. The MAG Fern CH3Cl SIP LEAF bin s3 was used as a reference and strains of Methylobacterium (including Methylorubrum) used for this analysis are listed in Supplementary Table S2.…”