Ubiquitous occurrence of a dimethylsulfoniopropionate ABC transporter in abundant marine bacteria

Abstract

Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur compound in marine environments with important functions in both microorganisms and global biogeochemical carbon and sulfur cycling. The SAR11 clade and marine Roseobacter group (MRG) represent two major groups of heterotrophic bacteria in Earth's surface oceans, which can accumulate DMSP to high millimolar intracellular concentrations. However, few studies have investigated how SAR11 and MRG bacteria import DMSP. Here, through comparative genomics analyses, genetic manipulations, and biochemical analyses, we identified an ABC (ATP-binding cassette)-type DMSP-specific transporter, DmpXWV, in Ruegeria pomeroyi DSS-3, a model strain of the MRG. Mutagenesis suggested that DmpXWV is a key transporter responsible for DMSP uptake in strain DSS-3. DmpX, the substrate binding protein of DmpXWV, had high specificity and binding affinity towards DMSP. Furthermore, the DmpX DMSP-binding mechanism was elucidated from structural analysis. DmpX proteins are prevalent in the numerous cosmopolitan marine bacteria outside the SAR11 clade and the MRG, and dmpX transcription was consistently high across Earth's entire global ocean. Therefore, DmpXWV likely enables pelagic marine bacteria to efficiently import DMSP from seawater. This study offers a new understanding of DMSP transport into marine bacteria and provides novel insights into the environmental adaption of marine bacteria.

Fig. 1. Phylogeny of all identified SBPs containing the pfam04069 domain in selected marine bacteria related to the MRG (strains Ruegeria pomeroyi DSS-3; Roseovarius nubinhibens ISM) and the SAR11 clade (Pelagibacter sp. HTCC7211), as well as selected bacteria including Escherichia coli (Ec), Pseudomonas syringae (Ps), Sinorhizobium meliloti (Sm) that possess experimentally characterised SBPs with affinity for closely related DMSP analogue.

These include TMAO-TmoX, choline-ChoX, carnitine-CaiX, proline betaine-ProX, glycine betaine-BetX, and histidine-HisX.

Fig. 2. Characterization of the DmpX protein and the genomic position of dmpXWV.

a ITC data for titrations of DMSP into recombinant DmpX from R. pomeroyi DSS-3. b The DMSP transporter gene cluster in the genome of R. pomeroyi DSS-3. c ITC data for titrations of DMSP into recombinant DmpX from Pelagibacter sp. HTCC7211. d The DMSP transporter gene cluster in the genome of Pelagibacter sp. HTCC7211.

Fig. 3. DmpXWV is important for the uptake of DMSP in R. pomeroyi DSS-3.

¹⁴C-DMSP uptake in the WT, ΔdmpXWV::Gm mutant, and complemented mutant (comp. ΔdmpXWV::Gm) at three concentrations by spiking DMSP in the marine broth medium. The error bar represents the standard deviation of triplicate experiments. Small letters indicate significant differences (p < 0.05) between wild-type, mutant and complemented mutant cultures at different DMSP concentrations based on a two-way ANOVA with Tukey’s multiple comparison test.

Fig. 4. Structural analysis of the RnDmpX/DMSP complex.

a Overall structure of the RnDmpX/DMSP complex. Domain I is coloured in pink, and domain II in wheat. The location of the DMSP molecule is indicated by a black arrow. b Residues composing the DMSP-binding pocket. The oxygen, nitrogen and sulfur atoms in the structure are coloured in red, blue and yellow, respectively. The carbon atoms of residues from domain I are shown in pink, and from domain II in wheat. The carbon atoms of the DMSP molecule are shown in cyan. c Structural analysis of the function of residue Tyr200 (carbon atoms coloured in purple) in binding DMSP.

Fig. 5. Environmental distribution and expression of dmpX in the global ocean.

Phylogenetic reconstruction of DmpX based on sequences retrieved from genomes of bacterial isolates, MAGs and SAGs. Blue and Red circles represent Roseobacter and SAR11 DmpX homologues, respectively, that were experimentally validated in this study or those shown in figure S5.

Fig. 6. The distribution, diversity, and expression of dmpX across the global ocean.

dmpX gene (a) and transcript (b) abundance by taxonomic assignment in marine surface waters. Normalized gene and transcript abundance in the Tara Ocean dataset (surface water sites only). Circle radius represents normalized abundance, calculated as a percentage of the median gene abundance or transcript abundance of 10 single-copy marker genes. Relative abundance of different taxa at each site is shown as pie charts, summing taxonomy at the level of Order, or the lowest taxonomic rank above Order. In the figure legend, unclassified is abbreviated to Unc., for clarity of presentation.