Browse > Article
http://dx.doi.org/10.23005/KSMLS.2021.6.1.1

Enzymes and Their Reaction Mechanisms in Dimethylsulfoniopropionate Cleavage and Biosynthesis of Dimethylsulfide by Marine Bacteria  

Do, Hackwon (Research Unit of Cryogenic Novel Material, Korea Polar Research Institute)
Hwang, Jisub (Research Unit of Cryogenic Novel Material, Korea Polar Research Institute)
Lee, Sung Gu (Research Unit of Cryogenic Novel Material, Korea Polar Research Institute)
Lee, Jun Hyuck (Research Unit of Cryogenic Novel Material, Korea Polar Research Institute)
Publication Information
Journal of Marine Life Science / v.6, no.1, 2021 , pp. 1-8 More about this Journal
Abstract
In marine ecosystems, the biosynthesis and catabolism of dimethylsulfoniopropionate (DMSP) by marine bacteria is critical to microbial survival and the ocean food chain. Furthermore, these processes also influence sulfur recycling and climate change. Recent studies using emerging genome sequencing data and extensive bioinformatics analysis have enabled us to identify new DMSP-related genes. Currently, seven bacterial DMSP lyases (DddD, DddP, DddY, DddK, DddL, DddQ and DddW), two acrylate degrading enzymes (DddA and DddC), and four demethylases (DmdA, DmdB, DmdC, and DmdD) have been identified and characterized in diverse marine bacteria. In this review, we focus on the biochemical properties of DMSP cleavage enzymes with special attention to DddD, DddA, and DddC pathways. These three enzymes function in the production of acetyl coenzyme A (CoA) and CO2 from DMSP. DddD is a DMSP lyase that converts DMSP to 3-hydroxypropionate with the release of dimethylsulfide. 3-Hydroxypropionate is then converted to malonate semialdehyde by DddA, an alcohol dehydrogenase. Then, DddC transforms malonate semialdehyde to acetyl-CoA and CO2 gas. DddC is a putative methylmalonate semialdehyde dehydrogenase that requires nicotinamide adenine dinucleotide and CoA cofactors. Here we review recent insights into the structural characteristics of these enzymes and the molecular events of DMSP degradation.
Keywords
Dimethylsulfide; Dimethylsulfoniopropionate; Molecular modeling; Methylmalonate semialdehyde dehydrogenase; Sulfur recycle;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Hehemann J-H, Law A, Redecke L, Boraston AB. 2014. The Structure of Rd DddP from Roseobacter denitrificans Reveals That DMSP Lyases in the DddP-Family Are Metalloenzymes. PloS One 9: e103128.   DOI
2 Tan D, Crabb WM, Whitman WB, Tong L. 2013. Crystal structure of DmdD, a crotonase superfamily enzyme that catalyzes the hydration and hydrolysis of methylthioacryloyl-CoA. PloS One 8: e63870.   DOI
3 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: 1376-1385.   DOI
4 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: 427-438.   DOI
5 Van Boekel J, Stefels W. 1993. Production of DMS from dissolved DMSP in axenic cultures of the marine phytoplankton species Phaeocystis sp. Mar Ecol Prog Ser 97: 11-18.   DOI
6 Howard EC, Sun S, Biers EJ, Moran MA. 2008. Abundant and diverse bacteria involved in DMSP degradation in marine surface waters. Environ Microbiol 10: 2397-2410.   DOI
7 Nevitt GA, Haberman K. 2003. Behavioral attraction of Leach's storm-petrels (Oceanodroma leucorhoa) to dimethyl sulfide. J Exp Biol 206: 1497-1501.   DOI
8 Moran MA, Reisch CR, Kiene RP, Whitman WB. 2012. Genomic insights into bacterial DMSP transformations. Ann Rev Mar Sci 4: 523-542.   DOI
9 Carslaw K, Boucher O, Spracklen D, Mann G, Rae J, Woodward S, Kulmala M. 2010. A review of natural aerosol interactions and feedbacks within the Earth system. Atmos Chem Phys 10: 1701-1737.   DOI
10 Curson AR, Fowler EK, Dickens S, Johnston AW, Todd JD. 2012. Multiple DMSP lyases in the γ-proteobacterium Oceanimonas doudoroffii. Biogeochemistry 110: 109-119.   DOI
11 Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, Snoeyink J, Richardson JS. 2007. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35: W375-W383.   DOI
12 Do H, Lee CW, Lee SG, Kang H, Park CM, Kim HJ, Park H, Park H, Lee JH. 2016. Crystal structure and modeling of the tetrahedral intermediate state of methylmalonate-semialdehyde dehydrogenase (MMSDH) from Oceanimonas doudoroffii. J Microbiol 54: 114-121.   DOI
13 Kiene RP, Linn LJ, Bruton JA. 2000. New and important roles for DMSP in marine microbial communities. J Sea Res 43: 209-224.   DOI
14 Li C-Y, Wei T-D, Zhang S-H, Chen X-L, Gao X, Wang P, Xie B-B, Su H-N, Qin Q-L, Zhang X-Y. 2014. Molecular insight into bacterial cleavage of oceanic dimethylsulfoniopropionate into dimethyl sulfide. Proc Natl Acad Sci 111: 1026-1031.   DOI
15 Peng M, Chen XL, Zhang D, Wang XJ, Wang N, Wang P, Todd JD, Zhang YZ, Li CY. 2019. Structure-Function Analysis Indicates that an Active-Site Water Molecule Participates in Dimethylsulfoniopropionate Cleavage by DddK. Appl Environ Microbio 85: e03127-e03118.
16 Quaye O, Lountos GT, Fan F, Orville AM, Gadda G. 2008. Role of Glu312 in Binding and Positioning of the Substrate for the Hydride Transfer Reaction in Choline Oxidase. Biochemistry 47: 243-256.   DOI
17 Todd JD, Curson AR, Nikolaidou-Katsaraidou N, Brearley CA, Watmough NJ, Chan Y, Page PC, Sun L, Johnston AW. 2010. Molecular dissection of bacterial acrylate catabolismunexpected links with dimethylsulfoniopropionate catabolism and dimethyl sulfide production. Environ Microbiol 12: 327-343.   DOI
18 Reisch CR, Moran MA, Whitman WB. 2011. Bacterial catabolism of dimethylsulfoniopropionate (DMSP). Front Microbiol 2: 172.   DOI
19 Schnicker NJ, De Silva SM, Todd JD, Dey M. 2017. Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter. Biochemistry 56: 2873-2885.   DOI
20 Schuller DJ, Reisch CR, Moran MA, Whitman WB, Lanzilotta WN. 2012. Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelagabacter ubique. Protein Sci 21: 289-298.   DOI
21 Simo R. 2001. Production of atmospheric sulfur by oceanic plankton: biogeochemical, ecological and evolutionary links. Trends Ecol Evol 16: 287-294.   DOI
22 Song D, Zhang Y, Liu J, Zhong H, Zheng Y, Zhou S, Yu M, Todd JD, Zhang XH. 2020. Metagenomic Insights Into the Cycling of Dimethylsulfoniopropionate and Related Molecules in the Eastern China Marginal Seas. Front Microbiol 11: 157.   DOI
23 Talfournier F, Stines-Chaumeil C, Branlant G. 2011. Methylmalonatesemialdehyde dehydrogenase from Bacillus subtilis substrate specificity and coenzyme A binding. J Biol Chem 286: 21971-21981.   DOI
24 Alcolombri U, Laurino P, Lara-Astiaso P, Vardi A, Tawfik DS. 2014. DddD is a CoA-transferase/lyase producing dimethyl sulfide in the marine environment. Biochemistry 53: 5473-5475.   DOI
25 Anderson D, Cantoni G. 1956. Enzymatic cleavage of dimethylpropiothetin by Polysiphonia lanosa. J Biol Chem 222: 171-177.   DOI
26 Arnold K, Bordoli L, Kopp J, Schwede T. 2006. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22: 195-201.   DOI
27 Bchini R, Dubourg-Gerecke H, Rahuel-Clermont S, Aubry A, Branlant G, Didierjean C, Talfournier F. 2012. Adenine binding mode is a key factor in triggering the early release of NADH in coenzyme A-dependent methylmalonate semialdehyde dehydrogenase. J Biol Chem 287: 31095-31103.   DOI
28 Brummett AE, Schnicker NJ, Crider A, Todd JD, Dey M. 2015. Biochemical, Kinetic, and Spectroscopic Characterization of Ruegeria pomeroyi DddW-A Mononuclear Iron-Dependent DMSP Lyase. PloS One 10: e0127288.   DOI
29 Curson AR, Sullivan MJ, Todd JD, Johnston AW. 2011. DddY, a periplasmic dimethylsulfoniopropionate lyase found in taxonomically diverse species of Proteobacteria. ISME J 5: 1191-1200.   DOI
30 Kirkwood M, Le Brun NE, Todd JD, Johnston AW. 2010. The dddP gene of Roseovarius nubinhibens encodes a novel lyase that cleaves dimethylsulfoniopropionate into acrylate plus dimethyl sulfide. Microbiology 156: 1900-1906.   DOI