Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process

Abstract

Dimethylsulfoniopropionate (DMSP) is one of the Earth's most abundant organosulfur molecules, a signalling molecule1, a key nutrient for marine microorganisms2,3 and the major precursor for gaseous dimethyl sulfide (DMS). DMS, another infochemical in signalling pathways4, is important in global sulfur cycling2 and affects the Earth's albedo, and potentially climate, via sulfate aerosol and cloud condensation nuclei production5,6. It was thought that only eukaryotes produce significant amounts of DMSP79, but here we demonstrate that many marine heterotrophic bacteria also produce DMSP, probably using the same methionine (Met) transamination pathway as macroalgae and phytoplankton10. We identify the first DMSP synthesis gene in any organism, dsyB, which encodes the key methyltransferase enzyme of this pathway and is a reliable reporter for bacterial DMSP synthesis in marine Alphaproteobacteria. DMSP production and dsyB transcription are upregulated by increased salinity, nitrogen limitation and lower temperatures in our model DMSP-producing bacterium Labrenzia aggregata LZB033. With significant numbers of dsyB homologues in marine metagenomes, we propose that bacteria probably make a significant contribution to oceanic DMSP production. Furthermore, because DMSP production is not solely associated with obligate phototrophs, the process need not be confined to the photic zones of marine environments and, as such, may have been underestimated.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: DMSP biosynthesis pathways and bacterial DMSP production.
Figure 2: Maximum-likelihood phylogenetic tree of DsyB proteins.
Figure 3: DMSP production, dsyB transcription and dddL transcription in L. aggregata LZB033 under different conditions.

References

  1. 1

    Seymour, J. R., Simo, R., Ahmed, T. & Stocker, R. Chemoattraction to dimethylsulfoniopropionate throughout the marine microbial food web. Science 329, 342–345 (2010).

    CAS  Article  Google Scholar 

  2. 2

    Sievert, S. M., Kiene, R. P. & Schulz-Vogt, H. N. The sulfur cycle. Oceanography 20, 117–123 (2007).

    Article  Google Scholar 

  3. 3

    Curson, A. R., Todd, J. D., Sullivan, M. J. & Johnston, A. W. Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes. Nat. Rev. Microbiol. 9, 849–859 (2011).

    CAS  Article  Google Scholar 

  4. 4

    Nevitt, G. A. The neuroecology of dimethyl sulfide: a global-climate regulator turned marine infochemical. Integr. Comp. Biol. 51, 819–825 (2011).

    CAS  Article  Google Scholar 

  5. 5

    Stefels, J., Steinke, M., Turner, S., Malin, G. & Belviso, S. Environmental constraints on the production and removal of the climatically active gas dimethylsulphide (DMS) and implications for ecosystem modelling. Biogeochemistry 83, 245–275 (2007).

    CAS  Article  Google Scholar 

  6. 6

    Vallina, S. M. & Simo, R. Strong relationship between DMS and the solar radiation dose over the global surface ocean. Science 315, 506–508 (2007).

    CAS  Article  Google Scholar 

  7. 7

    Yoch, D. C. Dimethylsulfoniopropionate: its sources, role in the marine food web, and biological degradation to dimethylsulfide. Appl. Environ. Microbiol. 68, 5804–5815 (2002).

    CAS  Article  Google Scholar 

  8. 8

    Van Alstyne, K. L. & Puglisi, M. P. DMSP in marine macroalgae and macroinvertebrates: distribution, function, and ecological impacts. Aquat. Sci. 69, 394–402 (2007).

    CAS  Article  Google Scholar 

  9. 9

    Raina, J. B. et al. DMSP biosynthesis by an animal and its role in coral thermal stress response. Nature 502, 677–680 (2013).

    CAS  Article  Google Scholar 

  10. 10

    Gage, D. A. et al. A new route for synthesis of dimethylsulphoniopropionate in marine algae. Nature 387, 891–894 (1997).

    CAS  Article  Google Scholar 

  11. 11

    Uchida, A., Ooguri, T., Ishida, T., Kitaguchi, H. & Ishida, Y. in Biological and Environmental Chemistry of DMSP and Related Sulfonium Compounds (eds Kiene, R. P., Visscher, P. T., Keller, M. D. & Kirst, G. O. ) Ch. 9, 97–107 (Plenum, 1996).

    Google Scholar 

  12. 12

    Rhodes, D., Gage, D. A., Cooper, A. J. L. & Hanson, A. D. S-methylmethionine conversion to dimethylsulfoniopropionate: evidence for an unusual transamination reaction. Plant Physiol. 115, 1541–1548 (1997).

    CAS  Article  Google Scholar 

  13. 13

    Kocsis, M. G. & Hanson, A. D. Biochemical evidence for two novel enzymes in the biosynthesis of 3-dimethylsulfoniopropionate in Spartina alterniflora. Plant Physiol. 123, 1153–1161 (2000).

    CAS  Article  Google Scholar 

  14. 14

    Ferla, M. P. & Patrick, W. M. Bacterial methionine biosynthesis. Microbiology 160, 1571–1584 (2014).

    CAS  Article  Google Scholar 

  15. 15

    Summers, P. S. et al. Identification and stereospecificity of the first three enzymes of 3-dimethylsulfoniopropionate biosynthesis in a chlorophyte alga. Plant Physiol. 116, 369–378 (1998).

    CAS  Article  Google Scholar 

  16. 16

    Ito, T., Asano, Y., Tanaka, Y. & Takabe, T. Regulation of biosynthesis of dimethylsulfoniopropionate and its uptake in sterile mutant of Ulva pertusa (Chlorophyta). J. Phycol. 47, 517–523 (2011).

    CAS  Article  Google Scholar 

  17. 17

    Curson, A. R., Rogers, R., Todd, J. D., Brearley, C. A. & Johnston, A. W. Molecular genetic analysis of a dimethylsulfoniopropionate lyase that liberates the climate-changing gas dimethylsulfide in several marine alpha-proteobacteria and rhodobacter sphaeroides. Environ. Microbiol. 10, 757–767 (2008).

    CAS  Article  Google Scholar 

  18. 18

    Dang, H., Li, T., Chen, M. & Huang, G. Cross-ocean distribution of Rhodobacterales bacteria as primary surface colonizers in temperate coastal marine waters. Appl. Environ. Microbiol. 74, 52–60 (2008).

    CAS  Article  Google Scholar 

  19. 19

    Ayala-Castro, C., Saini, A. & Outten, F. W. Fe–S cluster assembly pathways in bacteria. Microbiol. Mol. Biol. Rev. 72, 110–125 (2008).

    CAS  Article  Google Scholar 

  20. 20

    Dubbs, J. M. & Mongkolsuk, S. Peroxiredoxins in bacterial antioxidant defense. Subcell. Biochem. 44, 143–193 (2007).

    Article  Google Scholar 

  21. 21

    Sunda, W., Kieber, D. J., Kiene, R. P. & Huntsman, S. An antioxidant function for DMSP and DMS in marine algae. Nature 418, 317–320 (2002).

    CAS  Article  Google Scholar 

  22. 22

    Stefels, J. Physiological aspects of the production and conversion of DMSP in marine algae and higher plants. J. Sea Res. 43, 183–197 (2000).

    CAS  Article  Google Scholar 

  23. 23

    Otte, M. L., Wilson, G., Morris, J. T. & Moran, B. M. Dimethylsulphoniopropionate (DMSP) and related compounds in higher plants. J. Exp. Bot. 55, 1919–1925 (2004).

    CAS  Article  Google Scholar 

  24. 24

    Carrion, O. et al. A novel pathway producing dimethylsulphide in bacteria is widespread in soil environments. Nat. Commun. 6, 6579 (2015).

    CAS  Article  Google Scholar 

  25. 25

    Gonzalez, J. M., Whitman, W. B., Hodson, R. E. & Moran, M. A. Identifying numerically abundant culturable bacteria from complex communities: an example from a lignin enrichment culture. Appl. Environ. Microbiol. 62, 4433–4440 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. 26

    Baumann, P. & Baumann, L. in The Prokaryotes: A Handbook on Habitats, Isolation and Identification of Bacteria (eds Starr, M. P., Stolp, H., Trüper, H. G., Balows, A. & Schlegel, H. G. ) 1302–1331 (Springer, 1981).

    Google Scholar 

  27. 27

    Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular Cloning, A Laboratory Manual 2nd edn, Vol. 3 (Cold Spring Harbor Laboratory Press, 1989).

    Google Scholar 

  28. 28

    Beringer, J. E. R factor transfer in Rhizobium leguminosarum. J. Gen. Microbiol. 84, 188–198 (1974).

    CAS  PubMed  Google Scholar 

  29. 29

    Figurski, D. H. & Helinski, D. R. Replication of an origin-containing derivative of plasmid Rk2 dependent on a plasmid function provided in trans. Proc. Natl Acad. Sci. USA 76, 1648–1652 (1979).

    CAS  Article  Google Scholar 

  30. 30

    Downie, J. A. et al. Cloned nodulation genes of Rhizobium leguminosarum determine host range specificity. Mol. Gen. Genet. 190, 359–365 (1983).

    CAS  Article  Google Scholar 

  31. 31

    Tett, A. J., Rudder, S. J., Bourdes, A., Karunakaran, R. & Poole, P. S. Regulatable vectors for environmental gene expression in Alphaproteobacteria. Appl. Environ. Microb. 78, 7137–7140 (2012).

    CAS  Article  Google Scholar 

  32. 32

    Keen, N. T., Tamaki, S., Kobayashi, D. & Trollinger, D. Improved broad-host-range plasmids for DNA cloning in Gram-negative bacteria. Gene 70, 191–197 (1988).

    CAS  Article  Google Scholar 

  33. 33

    Delcher, A. L., Bratke, K. A., Powers, E. C. & Salzberg, S. L. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673–679 (2007).

    CAS  Article  Google Scholar 

  34. 34

    Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).

    CAS  Article  Google Scholar 

  35. 35

    Pruitt, K. D., Tatusova, T. & Maglott, D. R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35, D61–D65 (2007).

    CAS  Article  Google Scholar 

  36. 36

    Tatusov, R. L., Galperin, M. Y., Natale, D. A. & Koonin, E. V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33–36 (2000).

    CAS  Article  Google Scholar 

  37. 37

    Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y. & Hattori, M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277–D280 (2004).

    CAS  Article  Google Scholar 

  38. 38

    Ashburner, M. et al. Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25–29 (2000).

    CAS  Article  Google Scholar 

  39. 39

    Todd, J. D. et al. DddQ, a novel, cupin-containing, dimethylsulfoniopropionate lyase in marine roseobacters and in uncultured marine bacteria. Environ. Microbiol. 13, 427–438 (2011).

    CAS  Article  Google Scholar 

  40. 40

    Schafer, A. et al. Small mobilizable multipurpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 145, 69–73 (1994).

    CAS  Article  Google Scholar 

  41. 41

    Zhang, Y. H., Tang, K. H., Shi, X. C. & Zhang, X. H. Flaviramulus ichthyoenteri sp nov., an N-acylhomoserine lactone-degrading bacterium isolated from the intestine of a flounder (Paralichthys olivaceus), and emended descriptions of the genus Flaviramulus and Flaviramulus basaltis. Int. J. Syst. Evol. Microbiol. 63, 4477–4483 (2013).

    CAS  Article  Google Scholar 

  42. 42

    Tang, K. H. et al. Evaluation of a new high-throughput method for identifying quorum quenching bacteria. Sci. Rep. 3, 2935 (2013).

    Article  Google Scholar 

  43. 43

    Simon, M. & Azam, F. Protein content and protein synthesis rates of planktonic marine bacteria. Mar. Ecol. Prog. Ser. 51, 201–213 (1989).

    CAS  Article  Google Scholar 

  44. 44

    Uchino, Y., Hirata, A., Yokota, A. & Sugiyama, J. Reclassification of marine Agrobacterium species: proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev. J. Gen. Appl. Microbiol. 44, 201–210 (1998).

    CAS  Article  Google Scholar 

  45. 45

    Cho, J. C. & Giovannoni, S. J. Oceanicola granulosus gen. nov., sp. nov. and Oceanicola batsensis sp. nov., poly-β-hydroxybutyrate-producing marine bacteria in the order ‘Rhodobacterales’. Int. J. Syst. Evol. Microbiol. 54, 1129–1136 (2004).

    CAS  Article  Google Scholar 

  46. 46

    Gonzalez, J. M., Mayer, F., Moran, M. A., Hodson, R. E. & Whitman, W. B. Sagittula stellata gen. nov., sp. nov., a lignin-transforming bacterium from a coastal environment. Int. J. Syst. Bacteriol. 47, 773–780 (1997).

    CAS  Article  Google Scholar 

  47. 47

    Yosef, D. Z. B., Ben-Dov, E. & Kushmaro, A. Amorphus coralli gen. nov., sp. nov., a marine bacterium isolated from coral mucus, belonging to the order Rhizobiales. Int. J. Syst. Evol. Microbiol. 58, 2704–2709 (2008).

    Article  Google Scholar 

  48. 48

    Cho, J. C. & Giovannoni, S. J. Pelagibaca bermudensis gen. nov., sp. nov., a novel marine bacterium within the Roseobacter clade in the order Rhodobacterales. Int. J. Syst. Evol. Microbiol. 56, 855–859 (2006).

    CAS  Article  Google Scholar 

  49. 49

    Urios, L., Michotey, V., Intertaglia, L., Lesongeur, F. & Lebaron, P. Thalassobaculum salexigens sp. nov., a new member of the family Rhodospirillaceae from the NW Mediterranean Sea, and emended description of the genus Thalassobaculum. Int. J. Syst. Evol. Microbiol. 60, 209–213 (2010).

    Article  Google Scholar 

  50. 50

    Wang, Y. X. et al. Sediminimonas qiaohouensis gen. nov., sp nov., a member of the Roseobacter clade in the order Rhodobacterales. Int. J. Syst. Evol. Microbiol. 59, 1561–1567 (2009).

    CAS  Article  Google Scholar 

  51. 51

    Dong, J., Signo, K. S. L., Vanderlinde, E. M., Yost, C. K. & Dahms, T. E. S. Atomic force microscopy of a ctpA mutant in Rhizobium leguminosarum reveals surface defects linking CtpA function to biofilm formation. Microbiology 157, 3049–3058 (2011).

    CAS  Article  Google Scholar 

  52. 52

    Todd, J. D. et al. Molecular dissection of bacterial acrylate catabolism—unexpected links with dimethylsulfoniopropionate catabolism and dimethyl sulfide production. Environ. Microbiol. 12, 327–343 (2010).

    CAS  Article  Google Scholar 

  53. 53

    Koressaar, T. & Remm, M. Enhancements and modifications of primer design program Primer3. Bioinformatics 23, 1289–1291 (2007).

    CAS  Article  Google Scholar 

  54. 54

    Untergasser, A. et al. Primer3—new capabilities and interfaces. Nucleic Acids Res. 40, e115 (2012).

    CAS  Article  Google Scholar 

  55. 55

    Pfaffl, M. W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29, e45 (2001).

    CAS  Article  Google Scholar 

  56. 56

    Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729 (2013).

    CAS  Article  Google Scholar 

  57. 57

    Le, S. Q. & Gascuel, O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25, 1307–1320 (2008).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

Funding from the Natural Environmental Research Council (NE/J01138X, NE/M004449 and NE/N002385) supported work in J.D.T.'s laboratory, and funding from the National Natural Science Foundation of China (41521064, 41476112 and 41276141) supported the research in X.-H.Z.'s laboratory. The authors thank L. Hill of the John Innes Centre Metabolite Services for technical support with LC–MS experiments and P. Wells for general technical support. The authors thank C. Brearley, E. Mercadé, C. Murrell and L. Sims for advice and discussion of results. The authors also acknowledge the Tara Oceans Consortium for providing metagenomic sequence data.

Author information

Affiliations

Authors

Contributions

J.D.T. wrote the paper, designed all the experiments and performed experiments (genomic library screening, gene cloning and enzyme assays) and analysed data. A.R.J.C. wrote the paper, performed experiments (genomic library construction, gene cloning, enzyme assays, mutant construction, GC experiments to quantify DMSP and DMS production, growth experiments to measure DMSP production under different environmental conditions, mutant phenotyping, bioinformatics analysis to identify homologues in bacterial genomes, and phylogenetic trees), analysed data and prepared figures/tables. A.B.M. performed experiments (sample preparation, method development and operation of LC–MS, RNA isolation, and RT–qPCR experiments) and analysed data. X.-H.Z. and J.L. performed experiments (isolation of LZB033 and generation of a draft genome sequence, identification of DMS production in LZB033, mutant phenotyping) and analysed data. R.T.G. performed bioinformatic analysis of metagenomes and prepared figures/tables. Y.C. and P.C.B.P. performed chemical syntheses. O.C. and B.T.W. performed GC experiments and discussed results. S.-H.Z. and G.-P.Y. performed preliminary GC experiments on DMS production in LZB033. All authors reviewed the manuscript before submission.

Corresponding authors

Correspondence to Xiao-Hua Zhang or Jonathan D. Todd.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Figures 1 and 2; Supplementary Tables 1–5; Supplementary References. (PDF 538 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Curson, A., Liu, J., Bermejo Martínez, A. et al. Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process. Nat Microbiol 2, 17009 (2017). https://doi.org/10.1038/nmicrobiol.2017.9

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing