Functional annotation of orthologs in metagenomes: a case study of genes for the transformation of oceanic dimethylsulfoniopropionate

González, José M.; Hernández, Laura Esther Castro; Manzano, Iris; Pedrós-Alió, Carlos

doi:10.1038/s41396-019-0347-6

Cited by 22 publications

(28 citation statements)

References 65 publications

(83 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, the enzymes that catalyze DHPS synthesis are still unknown. All cyanobacteria were believed to lack dmdA gene (González et al, 2019), however, they can take up and assimilate DMSP via an as-yet-unidentified pathway (Malmstrom et al, 2005). In addition, the enzymatic or chemical mechanisms of DMSOP synthesis in DMSP and DMS cycling remained unclear (Thume et al, 2018).…”

Section: Characterizations Of Substrates and Specific Enzymesmentioning

confidence: 99%

Chemical Diversity and Biochemical Transformation of Biogenic Organic Sulfur in the Ocean

Tang

2020

Front. Mar. Sci.

View full text Add to dashboard Cite

Organic sulfur compounds are not only essential for organismal survival but also indispensable for the sulfur cycle. Over the past few decades, dimethylsulfoniopropionate (DMSP) and dimethyl sulfide (DMS) cycling in the upper ocean have been well characterized from the genetic to the ecosystem level. Recent advances in the study of marine sulfonate transformation have indicated that phytoplankton and microbes play key roles in oceanic sulfur and carbon fluxes. This review provides biochemical details of the major sulfur metabolites, and presents an interlinked reaction network with genetic information on the microbial transformation and mineralization of sulfur compounds. This review also discusses future prospects for the discovery and characterization of novel substrates and enzymes involved in organosulfur cycling, as well as for investigations of deep sea and sedimentary organic sulfur.

show abstract

Section: Characterizations Of Substrates and Specific Enzymesmentioning

confidence: 99%

Chemical Diversity and Biochemical Transformation of Biogenic Organic Sulfur in the Ocean

Tang

2020

Front. Mar. Sci.

View full text Add to dashboard Cite

show abstract

“…These differences may confound ecological studies which aim to predict functional properties of microbial communities from the presence or absence of specific genes. For instance, the presence of dmdA, the first gene in the pathway, is often used to imply the presence of an active demethylation pathway (31,32). However, the presence of this gene is inherently ambiguous.…”

Section: Discussionmentioning

confidence: 99%

Dimethylsulfoniopropionate Sulfur and Methyl Carbon Assimilation inRuegeriaSpecies

Wirth

Wang

Huang

et al. 2020

mBio

View full text Add to dashboard Cite

Dimethylsulfoniopropionate (DMSP) is abundant in marine environments and an important source of reduced carbon and sulfur for marine bacteria. While both Ruegeria pomeroyi and Ruegeria lacuscaerulensis possessed genes encoding the DMSP demethylation and cleavage pathways, their responses to DMSP differed. A glucose-fed, chemostat culture of R. pomeroyi consumed 99% of the DMSP even when fed a high concentration of 5 mM. At the same time, cultures released 19% and 7.1% of the DMSP as dimethylsulfide (DMS) and methanethiol, respectively. Under the same conditions, R. lacuscaerulensis consumed only 28% of the DMSP and formed one-third of the amount of gases. To examine the pathways of sulfur and methyl C assimilation, glucose-fed chemostats of both species were fed 100 μM mixtures of unlabeled and doubly labeled [dimethyl-13C, 34S]DMSP. Both species derived nearly all of their sulfur from DMSP despite high sulfate availability. In addition, only 33% and 50% of the methionine was biosynthesized from the direct capture of methanethiol in R. pomeroyi and R. lacuscaerulensis, respectively. The remaining methionine was biosynthesized by the random assembly of free sulfide and methyl-tetrahydrofolate derived from DMSP. Thus, although the two species possessed similar genes encoding DMSP metabolism, their growth responses were very different. IMPORTANCE Dimethylsulfoniopropionate (DMSP) is abundant in marine environments and an important source of reduced carbon and sulfur for marine bacteria. DMSP is the precursor for the majority of atmospheric dimethylsulfide (DMS), a climatically active gas that connects the marine and terrestrial sulfur cycles. Although research into the assimilation of DMSP has been conducted for over 20 years, the fate of DMSP in microbial biomass is not well understood. In particular, the biosynthesis of methionine from DMSP has been a focal point, and it has been widely believed that most methionine was synthesized via the direct capture of methanethiol. Using an isotopic labeling strategy, we have demonstrated that the direct capture of methanethiol is not the primary pathway used for methionine biosynthesis in two Ruegeria species, a genus comprised primarily of globally abundant marine bacteria. Furthermore, although the catabolism of DMSP by these species varied greatly, the anabolic pathways were highly conserved.

show abstract

“…We know that there are likely other DMSP lyases to be identified in bacteria, since Liu et al (2016) identified bacteria from East China Sea seawater with DMSP lyase activity, but which lack known ddd and Alma1 genes (Liu et al, 2018). In contrast, González et al (2019) considered it would be highly unlikely to find an environmentally significant alternative enzyme to DmdA that would carry out the DMSP demethylation reaction. Further work involving process measurements from hydrothermal samples is required to determine if DMSP cleavage and/or demethylation is an important process in this environment, but these data indicate they are not.…”

Section: The Okinawa Trough Hydrothermal Field Has Its Own Specific Dmentioning

confidence: 99%

Metagenomic Insights Into the Cycling of Dimethylsulfoniopropionate and Related Molecules in the Eastern China Marginal Seas

et al. 2020

View full text Add to dashboard Cite

The microbial cycling of dimethylsulfoniopropionate (DMSP) and its gaseous catabolites dimethylsulfide (DMS) and methanethiol (MeSH) are important processes in the global sulfur cycle, marine microbial food webs, signaling pathways, atmospheric chemistry, and potentially climate regulation. Many functional genes have been identified and used to study the genetic potential of microbes to produce and catabolize these organosulfur compounds in different marine environments. Here, we sampled seawater, marine sediment and hydrothermal sediment, and polymetallic sulfide in the eastern Chinese marginal seas and analyzed their microbial communities for the genetic potential to cycle DMSP, DMS, and MeSH using metagenomics. DMSP was abundant in all sediment samples, but was fivefold less prominent in those from hydrothermal samples. Indeed, Yellow Sea (YS) sediment samples had DMSP concentrations two orders of magnitude higher than in surface water samples. Bacterial genetic potential to synthesize DMSP (mainly in Rhodobacteraceae bacteria) was far higher than for phytoplankton in all samples, but particularly in the sediment where no algal DMSP synthesis genes were detected. Thus, we propose bacteria as important DMSP producers in these marine sediments. DMSP catabolic pathways mediated by the DMSP lyase DddP (prominent in Pseudomonas and Mesorhizobium bacteria) and DMSP demethylase DmdA enzymes (prominent in Rhodobacteraceae bacteria) and MddA-mediated MeSH S-methylation were very abundant in Bohai Sea and Yellow Sea sediments (BYSS) samples. In contrast, the genetic potential for DMSP degradation was very low in the hydrothermal sediment samples-dddP was the only catabolic gene detected and in only one sample. However, the potential for DMS production from MeSH (mddA) and DMS oxidation (dmoA and ddhA) was relatively abundant. This metagenomics study does not provide conclusive evidence for DMSP cycling; however, it does highlight the potential importance of bacteria in the synthesis and catabolism of DMSP and related compounds in diverse sediment environments.

show abstract

Functional annotation of orthologs in metagenomes: a case study of genes for the transformation of oceanic dimethylsulfoniopropionate

Cited by 22 publications

References 65 publications

Chemical Diversity and Biochemical Transformation of Biogenic Organic Sulfur in the Ocean

Chemical Diversity and Biochemical Transformation of Biogenic Organic Sulfur in the Ocean

Dimethylsulfoniopropionate Sulfur and Methyl Carbon Assimilation inRuegeriaSpecies

Metagenomic Insights Into the Cycling of Dimethylsulfoniopropionate and Related Molecules in the Eastern China Marginal Seas

Contact Info

Product

Resources

About