DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms

Abstract

Dimethylsulfoxonium propionate (DMSOP) is a recently identified and abundant marine organosulfur compound with roles in oxidative stress protection, global carbon and sulfur cycling and, as shown here, potentially in osmotolerance. Microbial DMSOP cleavage yields dimethyl sulfoxide, a ubiquitous marine metabolite, and acrylate, but the enzymes responsible, and their environmental importance, were unknown. Here we report DMSOP cleavage mechanisms in diverse heterotrophic bacteria, fungi and phototrophic algae not previously known to have this activity, and highlight the unappreciated importance of this process in marine sediment environments. These diverse organisms, including Roseobacter, SAR11 bacteria and Emiliania huxleyi, utilized their dimethylsulfoniopropionate lyase 'Ddd' or 'Alma' enzymes to cleave DMSOP via similar catalytic mechanisms to those for dimethylsulfoniopropionate. Given the annual teragram predictions for DMSOP production and its prevalence in marine sediments, our results highlight that DMSOP cleavage is likely a globally significant process influencing carbon and sulfur fluxes and ecological interactions.

Fig. 1. DMSP and DMSOP cleavage pathways.

The three distinct pathways for DMSP and DMSOP cleavage are indicated, as are the key catabolic enzymes. DMSP and DMSOP-specific products are shown in pink and lilac shading, respectively. Dotted lines represent unconfirmed steps of the DddX DMSP cleavage pathway. 3-HP, 3-hydroxypropionate; ATP, adenosine triphosphate; ADP, adenosine diphosphate; AMP, adenosine monophosphate; Pi, inorganic phosphate; PPi, pyrophosphate; NADPH, nicotinamide adenine dinucleotide phosphate. Source data

Fig. 2. In vivo DMSP and DMSOP lyase assays with DMSP and DMSOP simultaneously added at equimolar levels.

a, DMSP and DMSOP lyase activities from model organisms with known DMSP lyases. The complement of ddd genes found in tested bacteria are indicated in parentheses. b, DMSP and DMSOP lyase activities of Ddd and Alma enzymes expressed in E. coli BL21. Data are presented as mean ± s.d. (n = 3). Source data

Fig. 3. Growth curve of A. faecalis WT and dddY⁻ strains on succinate, DMSP, DMSOP, DMSO or acrylate as sole carbon source (2 mM).

Growth curves with no carbon sources were performed as negative control. Data are presented as mean ± s.d. (n = 3).

Fig. 4. Analysis of DMSOP cleavage by key bacterial strains.

a, Growth of Halomonas sp. HTNK1 WT and dddD⁻ strains on succinate, DMSP or DMSOP as sole carbon source (2 mM). b, RT–qPCR analysis of Halomonas sp. HTNK1 dddD in cells incubated with succinate (control) and succinate plus DMSP, DMSOP or acrylate (5 mM). Transcription of dddD was normalized to recA and rpoD. c, Growth curves of P. ubique HTCC1062 with 100 µM of pyruvate, acrylate, DMSP or DMSOP as carbon source and 25 µM of DMSP, DMSOP, DMSO or methionine (Met) as sulfur source. d, RT–qPCR analysis of P. ubique HTCC1062 dddK in cells grown with pyruvate and Met only (control) or amended with 100 µM DMSOP and DMSP (Methods). Expression of dddK was normalized to recA. Data are presented as mean ± s.d. (n = 3).

Fig. 5. Structural and mutational analyses of DddK.

a, DMSOP lyase activity of purified site-directed DddK mutant proteins where residues potentially involved in DMSOP catabolism were substituted as indicated. The enzymatic activity of WT DddK was defined as 100%. Results represent the mean of three independent experiments with error bars showing the respective s.d. b, Overall structure of the DddK–DMSOP complex. There are two DddK molecules arranged as a dimer in an asymmetric unit, which are coloured in green and cyan, respectively. The metal ion in DddK is shown as a purple sphere. The DMSOP molecule is shown in magenta sticks. c, Structural alignment of the DddK–DMSOP complex and WT DddK (PDB code: 6A53). The structure of DddK–DMSOP complex is shown in magenta, and the structure of WT DddK complex is shown in cyan. d, Residues and molecules involved in coordinating Mn²⁺ in DddK. The 2Fo-Fc densities for DMSOP and Mn²⁺ are contoured in blue meshes at 1.0σ. e, Residues involved in binding DMSOP. f, Structural alignment of important residues from DddK–DMSOP complex and DddK–DMSP complex (PDB code: 6A55). The structure of DddK–DMSOP complex is coloured in magenta, and the structure of DddK–DMSP complex in yellow.

Fig. 6. Distribution of genes encoding prokaryotic and eukaryotic DMSP lyases in Tara Oceans datasets OM-RGC-v2 (0.22–3 μm) and MATOU (0.8–20 μm), respectively.

a, Relative abundance of eukaryotic Alma genes in 153 of 174 MATOU metagenomes and 174 of 176 metatranscriptomes from SRF water layers (0–10 m) and DCM layers (10–200 m). b, Relative abundance of the nine prokaryotic ddd genes and the DMSP demethylation gene dmdA in OM-RGC-v2 metagenomes and metatranscriptomes from SRF, DCM and MES water layers (200–1,000 m). c, Taxonomic assignment of Alma genes in the MATOU dataset. d, Taxonomic assignment of ddd genes in the OM-RGC-v2 dataset. Letters denote genes or transcripts that are significantly different (P < 0.05) between water layers determined by two-sided Wilcoxon test; a shared letter means no significant differences. Boxplots show median (centre line), upper and lower quartiles (box limits), the interquartile range (whiskers) and outliers (black dots). MetaG, metagenome; MetaT, metatranscriptome.