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MetaCyc Pathway: dimethylsulfoniopropionate degradation I (cleavage)

Enzyme View:

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Synonyms: DMSP degradation

Superclasses: Degradation/Utilization/Assimilation Inorganic Nutrients Metabolism Sulfur Compounds Metabolism Dimethylsulfoniopropionate Degradation

Some taxa known to possess this pathway include ? : Alcaligenes faecalis M3A , Aspergillus sydowii , Crypthecodinium cohnii , Desulfovibrio acrylicus W218 , Dinoroseobacter shibae DFL 12 = DSM 16493 , DSMP-degrading bacterium LFR , Emiliania huxleyi , Fulvimarina pelagi HTCC2506 , Fusarium lateritium , Labrenzia aggregata IAM 12614 , Loktanella vestfoldensis SKA53 , Maritimibacter alkaliphilus HTCC2654 , Oceanicola batsensis HTCC2597 , Oceanimonas doudoroffii , Polysiphonia paniculata , Rhodobacter sphaeroides 2.4.1 , Rhodobacter sphaeroides ATCC 17029 , Roseovarius nubinhibens ISM , Ruegeria pomeroyi DSS-3 , Sulfitobacter sp. EE-36 , Sulfitobacter sp. NAS-14.1 , Ulva curvata , Vertebrata lanosa , [Clostridium] propionicum

Expected Taxonomic Range: Bacteria , Eukaryota

Summary:
General Background

Dimethylsulfoniopropionate (DMSP) is an osmolyte of many marine algae and certain plants [Otte04] (see Dimethylsulfoniopropionate Biosynthesis). Marine phytoplankton synthesize DMSP not only as an osmolyte, but also as a predator deterrent and an antioxidant [Howard06]. DMSP is readily degraded in a variety of biological systems, including bacterial cultures, salt marsh sediments, and seawater samples containing algae and zooplankton [Kiene88].

Two main routes are known for DMSP degradation, one leading to formation of dimethyl sulfide (as described in this pathway and in dimethylsulfoniopropionate degradation II (cleavage)) and the other leading to formation of 3-(methylthio)propanoate (see dimethylsulfoniopropionate degradation III (demethylation)).

Dimethylsulfide, which is very volatile, is exchanged freely between the ocean and the atmosphere, and is the main natural source of sulfur to the atmosphere. Once in the troposphere, DMS is oxidized to sulfuric and methanesulfonic acids, which attract water and promote cloud formation [Charlson87]. However, most of the DMS in the oceanic environment is degraded biologically (see dimethyl sulfide degradation I).

About This Pathway

The bacterial cleavage of DMSP to DMS and acrylate was described already in 1962 [Wagner62]. Since then it has been described in anaerobic bacteria [Wagner62, vanderMaarel06], aerobic bacteria [Ledyard93, deSouza95a, Van96, Visscher92, Gonzalez99], a heterotrophic dinoflagellate [Kadota68], algae [Cantoni56, Stefels93, De96d, Stefels96, Steinke98, Nishiguchi95], and marine fungi, such as Fusarium lateritium [Bacic98].

A dimethylsulfoniopropionate lyase enzyme was initially described from the red alga Vertebrata lanosa [Cantoni56], and subsequently purified from several other organisms, including the microaerophilic bacterium Alcaligenes faecalis M3A [deSouza95a], the red alga Polysiphonia paniculata [Nishiguchi95], the green alga Ulva curvata [De96d] and the anaerobic bacterium Desulfovibrio acrylicus W218 [vanderMaarel06].

The first gene encoding such an enzyme was found only in 2008, in the marine bacterium Sulfitobacter sp. EE-36 [Curson08]. When the dddL gene was cloned and expressed in an Escherichia coli strain, it conferred high levels of DMSP-dependent DMS production on the host. Homologues of DddL were found in the marine bacteria Sulfitobacter sp. NAS-14.1, Loktanella vestfoldensis SKA53, Labrenzia aggregata IAM 12614, Dinoroseobacter shibae DFL 12 = DSM 16493, Oceanicola batsensis HTCC2597, Maritimibacter alkaliphilus HTCC2654, and Fulvimarina pelagi HTCC2506, and in the two Rhodobacter strains Rhodobacter sphaeroides 2.4.1 and Rhodobacter sphaeroides ATCC 17029 [Curson08]. The source of the last two strains is not known, but they may be marine as well.

Curiously, several additional genes, dddP, dddQ and dddY, were found to encode unrelated enzymes that possess the same activity [Todd09, Kirkwood10, Todd11, Curson11]. DddP genes were found in many marine bacteria (they are more abundant than the dddL genes in the Global Ocean sampling dataset), as well as some fungi [Kirkwood10a] and marine phages [Raina10], while dddQ appears to be limited to the Roseobacter clade, and dddY is limited to several microaerophilic genera. The remarkable diversity of these enzymes suggests that they have evolved in different environments, to address different needs and conditions, and emphesizes the importance of DMSP in the marine environment.

A second DMSP cleavage pathway, catalyzed by the dddD-encoded dimethylsulfoniopropanoate:acyl-CoA transferase, is described in dimethylsulfoniopropionate degradation II (cleavage).

Variants: dimethylsulfoniopropionate degradation II (cleavage) , dimethylsulfoniopropionate degradation III (demethylation) , superpathway of dimethylsulfoniopropionate degradation

Credits:
Created 18-Sep-2008 by Caspi R , SRI International


References

Bacic98: Bacic MK, Yoch DC (1998). "In Vivo Characterization of Dimethylsulfoniopropionate Lyase in the Fungus Fusarium lateritium." Appl Environ Microbiol 64(1);106-111. PMID: 16349475

Cantoni56: Cantoni GL, Anderson, DG (1956). "Enzymatic cleavage of dimethylpropiothetin by Polysiphonia lanosa." J Biol Chem 222(1);171-7. PMID: 13366990

Charlson87: Charlson, RJ, Lovelock, JE, Andreae, MO, Warren, SG (1987). "Oceanic phytoplankton, atmospheric sulphur, cloud albedo and climate." Nature 326:655-661.

Curson08: Curson AR, Rogers R, Todd JD, Brearley CA, Johnston AW (2008). "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(3);757-67. PMID: 18237308

Curson11: Curson AR, Sullivan MJ, Todd JD, Johnston AW (2011). "DddY, a periplasmic dimethylsulfoniopropionate lyase found in taxonomically diverse species of Proteobacteria." ISME J. PMID: 21248856

De96d: De Souza, M.P., Chen, Y.P., Yoch, D.C. (1996). "Dimethylsulfoniopropionate lyase from the marine macroalga Ulva curvata: purification and characterization of the enzyme." Planta 199, 433-438.

deSouza95a: de Souza MP, Yoch DC (1995). "Purification and Characterization of Dimethylsulfoniopropionate Lyase from an Alcaligenes-Like Dimethyl Sulfide-Producing Marine Isolate." Appl Environ Microbiol 61(1);21-26. PMID: 16534905

Gonzalez99: Gonzalez JM, Kiene RP, Moran MA (1999). "Transformation of sulfur compounds by an abundant lineage of marine bacteria in the alpha-subclass of the class Proteobacteria." Appl Environ Microbiol 65(9);3810-9. PMID: 10473380

Howard06: Howard EC, Henriksen JR, Buchan A, Reisch CR, Burgmann H, Welsh R, Ye W, Gonzalez JM, Mace K, Joye SB, Kiene RP, Whitman WB, Moran MA (2006). "Bacterial taxa that limit sulfur flux from the ocean." Science 314(5799);649-52. PMID: 17068264

Kadota68: Kadota, H., Ishida, Y. (1968). "Effect of salts on enzymatical production of dimethyl sulfide from Gyrodinium cohnii." Bull. Jpn. Soc.Sci. Fish. 34, 512-518.

Kiene88: Kiene RP, Taylor BF (1988). "Demethylation of Dimethylsulfoniopropionate and Production of Thiols in Anoxic Marine Sediments." Appl Environ Microbiol 54(9);2208-2212. PMID: 16347732

Kirkwood10: Kirkwood, M., Le Brun, N. E., Todd, J. D., Johnston, A. W. B. (2010). "The dddP gene of Roseovarius nubinhibens encodes a novel lyase that cleaves dimethylsulfoniopropionate into acrylate plus dimethylsulfide." Microbiology 156(6):1900-1906. PMID: 20378650

Kirkwood10a: Kirkwood M, Todd JD, Rypien KL, Johnston AW (2010). "The opportunistic coral pathogen Aspergillus sydowii contains dddP and makes dimethyl sulfide from dimethylsulfoniopropionate." ISME J 4(1);147-50. PMID: 19776768

Ledyard93: Ledyard, K. M., DeLong, E. F., Dacey, J. W. H. (1993). "Characterization of a DMSP-degrading bacterial isolate from the Sargasso Sea." Archives of Microbiology 160(4): 312-318.

Nishiguchi95: Nishiguchi, M. K., Goff, L. J. (1995). "Isolation, purification, and characterization of DMSP lyase (dimethylpropiothetin dethiomethylase (4.4.1.3)) from the red alga Polysiphonia paniculata." Journal of Phycology 31(4): 567 - 574.

Otte04: Otte ML, Wilson G, Morris JT, Moran BM (2004). "Dimethylsulphoniopropionate (DMSP) and related compounds in higher plants." J Exp Bot 55(404);1919-25. PMID: 15181109

Raina10: Raina JB, Dinsdale EA, Willis BL, Bourne DG (2010). "Do the organic sulfur compounds DMSP and DMS drive coral microbial associations?." Trends Microbiol 18(3);101-8. PMID: 20045332

Stefels93: Stefels, J., Van Boekel, W.H.M. (1993). "Production of DMS from dissolved DMSP in axenic cultures of the marine phytoplankton species Phaeocystis sp." Mar. Ecol. Prog. Ser. 97, 11-18.

Stefels96: Stefels, J., Dijkhuizen, L. (1996). "Characteristics of DMSP-lyase in Phaeocystis sp. (Prymnesiophyceae)." Mar. Ecol. Prog. Ser. 131:307-313.

Steinke98: Steinke, M., Wolfe, G.V., Kirst, G.O. (1998). "Partial characterisation of dimethylsulfoniopropionate (DMSP) lyase isozymes in 6 strains of Emiliania huxleyi." Mar. Ecol. Prog. Ser. 175, 215-225.

Todd09: Todd JD, Curson AR, Dupont CL, Nicholson P, Johnston AW (2009). "The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi." Environ Microbiol 11(6);1376-85. PMID: 19220400

Todd11: Todd JD, Curson AR, Kirkwood M, Sullivan MJ, Green RT, Johnston AW (2011). "DddQ, a novel, cupin-containing, dimethylsulfoniopropionate lyase in marine roseobacters and in uncultured marine bacteria." Environ Microbiol 13(2);427-38. PMID: 20880330

Van96: Van der Maarel, M.J.E.C., Aukema, W., Hansen, T.A. (1996). "Purification and characterization of a dimethylsulfoniopropionate cleaving enzyme from Desulfovibrio acrylicus." FEMS Microbiol Lett. 143:241-245.

vanderMaarel06: van der Maarel, M.J.E.C., Aukema, W., Hansen, T.A. (2006). "Purification and characterization of a dimethylsulfoniopropionate cleaving enzyme from Desulfovibrio acrylicus." FEMS Microbiology Letters 143(2-3): 241 - 245.

Visscher92: Visscher, P. T., Diaz, M. R., Taylor, B. F. (1992). "Enumeration of bacteria which cleave or demethylate dimethylsulfoniopropionate in the Caribbean Sea." Marine ecology progress series 89:293-296.

Wagner62: Wagner, C, Stadtman, ER (1962). "Bacterial fermentation of dimethyl-beta-propiothetin." Arch Biochem Biophys 98;331-6. PMID: 14004329

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

deSouza95b: de Souza MP, Yoch DC (1995). "Comparative Physiology of Dimethyl Sulfide Production by Dimethylsulfoniopropionate Lyase in Pseudomonas doudoroffii and Alcaligenes sp. Strain M3A." Appl Environ Microbiol 61(11);3986-3991. PMID: 16535162

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Reisch08: Reisch CR, Moran MA, Whitman WB (2008). "Dimethylsulfoniopropionate-dependent demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi." J Bacteriol 190(24);8018-24. PMID: 18849431

Yoch02: Yoch DC (2002). "Dimethylsulfoniopropionate: its sources, role in the marine food web, and biological degradation to dimethylsulfide." Appl Environ Microbiol 68(12);5804-15. PMID: 12450799


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Wed Dec 17, 2014, biocyc13.