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Wang Y, Chen SL. Reaction mechanism of the PuDddK dimethylsulfoniopropionate lyase and cofactor effects of various transition metal ions. Dalton Trans 2022; 51:14664-14672. [PMID: 36098064 DOI: 10.1039/d2dt02133a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The microbial cleavage of dimethylsulfoniopropionate (DMSP) produces volatile dimethyl sulfide (DMS) via the lyase pathway, playing a crucial role in the global sulfur cycle. Herein, the DMSP decomposition catalyzed by PuDddK (a DMSP lyase) devised with various transition metal ion cofactors are investigated using density functional calculations. The PuDddK reaction has been demonstrated to employ a concerted β-elimination mechanism, where the substrate α-proton abstraction by the deprotonated Tyr64 occurs simultaneously with the Cβ-S bond cleavage and Cα = Cβ double bond formation. The PuDddK enzymes with diverse divalent metal ions (Ni2+, Mn2+, Fe2+, Co2+, Zn2+, and Cu2+) incorporated prefer DMSP as a monodentate ligand. The cases of Ni2+, Mn2+, Fe2+, Co2+, and Zn2+ with the same 3His-1Glu ligands have close reaction energy barriers, indicating that the lyase activity may be hardly affected by the divalent transition metal type with the same ligand type and number. The coordination loss of one histidine in Cu2+, forming a 2His-1Glu architecture, leads to a lower activity, revealing that the 3His-1Glu ligand set used by DddK appears to be a scaffold capable of more efficiently catalyzing the DMSP decomposition. Further analysis reveals that the inactivation of Fe3+-dependent PuDddK is derived from an electron transfer from the Tyr64 phenolate to Fe3+, with the implication that the PuDddK activity may be primarily affected by the redox effects induced by a strongly oxidizing transition metal ion (like Fe3+).
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Affiliation(s)
- Ying Wang
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China.
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China.
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2
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Shaw DK, Sekar J, Ramalingam PV. Recent insights into oceanic dimethylsulfoniopropionate biosynthesis and catabolism. Environ Microbiol 2022; 24:2669-2700. [PMID: 35611751 DOI: 10.1111/1462-2920.16045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 11/29/2022]
Abstract
Dimethylsulfoniopropionate (DMSP), a globally important organosulfur compound is produced in prodigious amounts (2.0 Pg sulfur) annually in the marine environment by phytoplankton, macroalgae, heterotrophic bacteria, some corals and certain higher plants. It is an important marine osmolyte and a major precursor molecule for the production of climate-active volatile gas dimethyl sulfide (DMS). DMSP synthesis take place via three pathways: a transamination 'pathway-' in some marine bacteria and algae, a Met-methylation 'pathway-' in angiosperms and bacteria and a decarboxylation 'pathway-' in the dinoflagellate, Crypthecodinium. The enzymes DSYB and TpMMT are involved in the DMSP biosynthesis in eukaryotes while marine heterotrophic bacteria engage key enzymes such as DsyB and MmtN. Several marine bacterial communities import DMSP and degrade it via cleavage or demethylation pathways or oxidation pathway, thereby generating DMS, methanethiol, and dimethylsulfoxonium propionate, respectively. DMSP is cleaved through diverse DMSP lyase enzymes in bacteria and via Alma1 enzyme in phytoplankton. The demethylation pathway involves four different enzymes, namely DmdA, DmdB, DmdC and DmdD/AcuH. However, enzymes involved in the oxidation pathway have not been yet identified. We reviewed the recent advances on the synthesis and catabolism of DMSP and enzymes that are involved in these processes.
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Affiliation(s)
- Deepak Kumar Shaw
- Microbiology Lab, Department of Biotechnology, M. S. Swaminathan Research Foundation, Taramani, Chennai, 600113, Tamil Nadu, India
| | - Jegan Sekar
- Microbiology Lab, Department of Biotechnology, M. S. Swaminathan Research Foundation, Taramani, Chennai, 600113, Tamil Nadu, India
| | - Prabavathy Vaiyapuri Ramalingam
- Microbiology Lab, Department of Biotechnology, M. S. Swaminathan Research Foundation, Taramani, Chennai, 600113, Tamil Nadu, India
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Teng ZJ, Qin QL, Zhang W, Li J, Fu HH, Wang P, Lan M, Luo G, He J, McMinn A, Wang M, Chen XL, Zhang YZ, Chen Y, Li CY. Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans. MICROBIOME 2021; 9:207. [PMID: 34654476 PMCID: PMC8520302 DOI: 10.1186/s40168-021-01153-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Dimethyl sulfide (DMS) is the dominant volatile organic sulfur in global oceans. The predominant source of oceanic DMS is the cleavage of dimethylsulfoniopropionate (DMSP), which can be produced by marine bacteria and phytoplankton. Polar oceans, which represent about one fifth of Earth's surface, contribute significantly to the global oceanic DMS sea-air flux. However, a global overview of DMS and DMSP cycling in polar oceans is still lacking and the key genes and the microbial assemblages involved in DMSP/DMS transformation remain to be fully unveiled. RESULTS Here, we systematically investigated the biogeographic traits of 16 key microbial enzymes involved in DMS/DMSP cycling in 60 metagenomic samples from polar waters, together with 174 metagenome and 151 metatranscriptomes from non-polar Tara Ocean dataset. Our analyses suggest that intense DMS/DMSP cycling occurs in the polar oceans. DMSP demethylase (DmdA), DMSP lyases (DddD, DddP, and DddK), and trimethylamine monooxygenase (Tmm, which oxidizes DMS to dimethylsulfoxide) were the most prevalent bacterial genes involved in global DMS/DMSP cycling. Alphaproteobacteria (Pelagibacterales) and Gammaproteobacteria appear to play prominent roles in DMS/DMSP cycling in polar oceans. The phenomenon that multiple DMS/DMSP cycling genes co-occurred in the same bacterial genome was also observed in metagenome assembled genomes (MAGs) from polar oceans. The microbial assemblages from the polar oceans were significantly correlated with water depth rather than geographic distance, suggesting the differences of habitats between surface and deep waters rather than dispersal limitation are the key factors shaping microbial assemblages involved in DMS/DMSP cycling in polar oceans. CONCLUSIONS Overall, this study provides a global overview of the biogeographic traits of known bacterial genes involved in DMS/DMSP cycling from the Arctic and Antarctic oceans, laying a solid foundation for further studies of DMS/DMSP cycling in polar ocean microbiome at the enzymatic, metabolic, and processual levels. Video Abstract.
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Affiliation(s)
- Zhao-Jie Teng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Weipeng Zhang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
| | - Jian Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Hui-Hui Fu
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China
| | - Peng Wang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China
| | - Musheng Lan
- The Key Laboratory for Polar Science MNR, Polar Research Institute of China, Shanghai, 200136, China
| | - Guangfu Luo
- The Key Laboratory for Polar Science MNR, Polar Research Institute of China, Shanghai, 200136, China
| | - Jianfeng He
- The Key Laboratory for Polar Science MNR, Polar Research Institute of China, Shanghai, 200136, China
| | - Andrew McMinn
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Min Wang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
| | - Xiu-Lan Chen
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China
| | - Yin Chen
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.
- School of Life Sciences, University of Warwick, Coventry, UK.
| | - Chun-Yang Li
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China.
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4
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Fe(III)-polyuronic acid photochemistry: radical chemistry in natural polysaccharide. Photochem Photobiol Sci 2021; 20:255-263. [DOI: 10.1007/s43630-021-00014-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/19/2021] [Indexed: 12/20/2022]
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Rubredoxin from the green sulfur bacterium Chlorobaculum tepidum donates a redox equivalent to the flavodiiron protein in an NAD(P)H dependent manner via ferredoxin-NAD(P) + oxidoreductase. Arch Microbiol 2020; 203:799-808. [PMID: 33051772 DOI: 10.1007/s00203-020-02079-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/24/2020] [Accepted: 10/01/2020] [Indexed: 10/23/2022]
Abstract
The green sulfur bacterium, Chlorobaculum tepidum, is an anaerobic photoautotroph that performs anoxygenic photosynthesis. Although genes encoding rubredoxin (Rd) and a putative flavodiiron protein (FDP) were reported in the genome, a gene encoding putative NADH-Rd oxidoreductase is not identified. In this work, we expressed and purified the recombinant Rd and FDP and confirmed dioxygen reductase activity in the presence of ferredoxin-NAD(P)+ oxidoreductase (FNR). FNR from C. tepidum and Bacillus subtilis catalyzed the reduction of Rd at rates comparable to those reported for NADH-Rd oxidoreductases. Also, we observed substrate inhibition at high concentrations of NADPH similar to that observed with ferredoxins. In the presence of NADPH, B. subtilis FNR and Rd, FDP promoted dioxygen reduction at rates comparable to those reported for other bacterial FDPs. Taken together, our results suggest that Rd and FDP participate in the reduction of dioxygen in C. tepidum and that FNR can promote the reduction of Rd in this bacterium.
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Zhang XH, Liu J, Liu J, Yang G, Xue CX, Curson ARJ, Todd JD. Biogenic production of DMSP and its degradation to DMS-their roles in the global sulfur cycle. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1296-1319. [PMID: 31231779 DOI: 10.1007/s11427-018-9524-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/16/2019] [Indexed: 01/08/2023]
Abstract
Dimethyl sulfide (DMS) is the most abundant form of volatile sulfur in Earth's oceans, and is mainly produced by the enzymatic clevage of dimethylsulfoniopropionate (DMSP). DMS and DMSP play important roles in driving the global sulfur cycle and may affect climate. DMSP is proposed to serve as an osmolyte, a grazing deterrent, a signaling molecule, an antioxidant, a cryoprotectant and/or as a sink for excess sulfur. It was long believed that only marine eukaryotes such as phytoplankton produce DMSP. However, we recently discovered that marine heterotrophic bacteria can also produce DMSP, making them a potentially important source of DMSP. At present, one prokaryotic and two eukaryotic DMSP synthesis enzymes have been identified. Marine heterotrophic bacteria are likely the major degraders of DMSP, using two known pathways: demethylation and cleavage. Many phytoplankton and some fungi can also cleave DMSP. So far seven different prokaryotic and one eukaryotic DMSP lyases have been identified. This review describes the global distribution pattern of DMSP and DMS, the known genes for biosynthesis and cleavage of DMSP, and the physiological and ecological functions of these important organosulfur molecules, which will improve understanding of the mechanisms of DMSP and DMS production and their roles in the environment.
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Affiliation(s)
- Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Ji Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jingli Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Guipeng Yang
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266071, China
| | - Chun-Xu Xue
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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Abstract
The organosulfur metabolite dimethylsulfoniopropionate (DMSP) and its enzymatic breakdown product dimethyl sulfide (DMS) have important implications in the global sulfur cycle and in marine microbial food webs. Enormous amounts of DMSP are produced in marine environments where microbial communities import and catabolize it via either the demethylation or the cleavage pathways. The enzymes that cleave DMSP are termed "DMSP lyases" and generate acrylate or hydroxypropionate, and ~107tons of DMS annually. An important environmental factor affecting DMS generation by the DMSP lyases is the availability of metal ions as these enzymes use various cofactors for catalysis. This chapter summarizes advances on bacterial DMSP catabolism, with an emphasis on various biochemical methods employed for the isolation and characterization of bacterial DMSP lyases. Strategies are presented for the purification of DMSP lyases expressed in bacterial cells. Specific conditions for the efficient isolation of apoproteins in Escherichia coli are detailed. DMSP cleavage is effectively inferred, utilizing the described HPLC-based acrylate detection assay. Finally, substrate and metal binding interactions are examined using fluorescence and UV-visible assays. Together, these methods are rapid and well suited for the biochemical and structural characterization of DMSP lyases and in the assessment of uncharacterized DMSP catabolic enzymes, and new metalloenzymes in general.
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8
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Structure-Function Analysis Indicates that an Active-Site Water Molecule Participates in Dimethylsulfoniopropionate Cleavage by DddK. Appl Environ Microbiol 2019; 85:AEM.03127-18. [PMID: 30770407 DOI: 10.1128/aem.03127-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 02/13/2019] [Indexed: 11/20/2022] Open
Abstract
The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram quantities in marine environments and has important roles in global sulfur and carbon cycling. Many marine microorganisms catabolize DMSP via DMSP lyases, generating the climate-active gas dimethyl sulfide (DMS). DMS oxidation products participate in forming cloud condensation nuclei and, thus, may influence weather and climate. SAR11 bacteria are the most abundant marine heterotrophic bacteria; many of them contain the DMSP lyase DddK, and their dddK transcripts are relatively abundant in seawater. In a recently described catalytic mechanism for DddK, Tyr64 is predicted to act as the catalytic base initiating the β-elimination reaction of DMSP. Tyr64 was proposed to be deprotonated by coordination to the metal cofactor or its neighboring His96. To further probe this mechanism, we purified and characterized the DddK protein from Pelagibacter ubique strain HTCC1062 and determined the crystal structures of wild-type DddK and its Y64A and Y122A mutants (bearing a change of Y to A at position 64 or 122, respectively), where the Y122A mutant is complexed with DMSP. The structural and mutational analyses largely support the catalytic role of Tyr64, but not the method of its deprotonation. Our data indicate that an active water molecule in the active site of DddK plays an important role in the deprotonation of Tyr64 and that this is far more likely than coordination to the metal or His96. Sequence alignment and phylogenetic analysis suggest that the proposed catalytic mechanism of DddK has universal significance. Our results provide new mechanistic insights into DddK and enrich our understanding of DMS generation by SAR11 bacteria.IMPORTANCE The climate-active gas dimethyl sulfide (DMS) plays an important role in global sulfur cycling and atmospheric chemistry. DMS is mainly produced through the bacterial cleavage of marine dimethylsulfoniopropionate (DMSP). When released into the atmosphere from the oceans, DMS can be photochemically oxidized into DMSO or sulfate aerosols, which form cloud condensation nuclei that influence the reflectivity of clouds and, thereby, global temperature. SAR11 bacteria are the most abundant marine heterotrophic bacteria, and many of them contain DMSP lyase DddK to cleave DMSP, generating DMS. In this study, based on structural analyses and mutational assays, we revealed the catalytic mechanism of DddK, which has universal significance in SAR11 bacteria. This study provides new insights into the catalytic mechanism of DddK, leading to a better understanding of how SAR11 bacteria generate DMS.
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Cai W, Li Y, Shen Y, Wang C, Wang P, Wang L, Niu L, Zhang W. Vertical distribution and assemblages of microbial communities and their potential effects on sulfur metabolism in a black-odor urban river. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 235:368-376. [PMID: 30708274 DOI: 10.1016/j.jenvman.2019.01.078] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/15/2019] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
Black-odor phenomenon in highly urbanized river is increasingly recognized as a global ecological risk. Biotransformation associated with sulfur cycle is a major contributor to the blank-odor phenomenon. The vertical geochemical gradient in black-odor rivers is likely to alter microbial community assemblages and functions in the sulfur cycle. However, the interactions between geochemical gradients and microbial communities, as well as the changes in the process of sulfur biotransformation under different environmental conditions remain largely unknown. The vertical community assembly patterns and the impacts of microbial communities and genes on the biotransformation in the sulfur cycle were revealed in our study for the first time in a typical urban black-odor river, Jinchuan River, in China. Vertical beta-diversity patterns of microbial communities mainly resulted from species replacement that was largely driven by spatial turnover (βSIM = 0.43) but also influenced by nestedness (βNES = 0.08). MiSeq sequencing and GeoChip 5.0 microarray chip approaches were applied and identify 41 bacterial genera, 8 archaeal genera, and 26 genes involved in the sulfur cycle in Jinchuan River. The vertical beta-diversity patterns of microbial profile mainly resulted from species replacement. Those sulfur-related bacterial and archaeal genera, accounting for 23.15% and 42.65% of the total bacteria and archaea respectively in analysed samples, were mainly responsible for sulfur reduction. According to redundancy analysis, oxidation-reduction potential (r = -0.8662, P < 0.05), S2- concentration (r = -0.6288, P < 0.05), and total nitrogen concentration (r = -0.6782, P < 0.05) were identified as factors that significantly affect sulfur-related microbial communities. The highest reaction potential was detected in the dissimilated sulfate reduction action and experienced an increase with depth increasing in the river system. The results indicated that the sulfur biotransformation in a deeper layer in river sediment could make more contribution to the black-odor phenomenon in urban rivers.
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Affiliation(s)
- Wei Cai
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China; College of Environmental Science and Engineering, Yangzhou University, Huayang West Road #196, Yangzhou, 225009, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China.
| | - Yun Shen
- Department of Civil & Environmental Engineering, University of Michigan, 1351 Beal Ave., 219 EWRE Bldg., Ann Arbor, MI, 48109-2125, USA
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
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Chen Y, Schäfer H. Towards a systematic understanding of structure-function relationship of dimethylsulfoniopropionate-catabolizing enzymes. Mol Microbiol 2019; 111:1399-1403. [PMID: 30802340 DOI: 10.1111/mmi.14230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2019] [Indexed: 11/28/2022]
Abstract
Each year, several million tons of dimethylsulfoniopropionate (DMSP) are produced by marine phytoplankton and bacteria as an important osmolyte to regulate their cellular osmosis. Microbial breakdown of DMSP to the volatile gas dimethylsulfide (DMS) plays an important role in global biogeochemical cycles of the sulphur element between land and the sea. Understanding the enzymes involved in the transformation of DMSP and DMS holds the key to a better understanding of oceanic DMSP cycles. Recent work by Shao et al. (2019) has resolved the crystal structure of two important enzymes, DmdB and DmdC, involved in DMSP transformation through the demethylation pathway. Their work represents an important step towards a systematic understanding of the structure-function relationships of DMSP-catabolizing enzymes in marine microbes.
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Affiliation(s)
- Yin Chen
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, Coventry, UK
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11
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Lei L, Alcolombri U, Tawfik DS. Biochemical Profiling of DMSP Lyases. Methods Enzymol 2018; 605:269-289. [PMID: 29909827 DOI: 10.1016/bs.mie.2018.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Dimethyl sulfide (DMS) is released at rates of >107 tons annually and plays a key role in the oceanic sulfur cycle and ecology. Marine bacteria, algae, and possibly other organisms release DMS via cleavage of dimethylsulfoniopropionate (DMSP). DMSP lyases have been identified in various organisms, including bacteria, coral, and algae, thus comprising a range of gene families putatively assigned as DMSP lyases. Metagenomics may therefore provide insight regarding the presence of DMSP lyases in various marine environments, thereby promoting a better understanding of global DMS emission. However, gene counts, and even mRNA levels, do not necessarily reflect the level of DMSP cleavage activity in a given environmental sample, especially because some of the families assigned as DMSP lyases may merely exhibit promiscuous lyase activity. Here, we describe a range of biochemical profiling methods that can assign an observed DMSP lysis activity to a specific gene family. These methods include selective inhibitors and DMSP substrate analogues. Combined with genomics and metagenomics, biochemical profiling may enable a more reliable identification of the origins of DMS release in specific organisms and in crude environmental samples.
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Affiliation(s)
- Lei Lei
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Uria Alcolombri
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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12
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Burkhardt I, Lauterbach L, Brock NL, Dickschat JS. Chemical differentiation of three DMSP lyases from the marine Roseobacter group. Org Biomol Chem 2018; 15:4432-4439. [PMID: 28485454 DOI: 10.1039/c7ob00913e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) catabolism of marine bacteria plays an important role in marine and global ecology. The genome of Ruegeria pomeroyi DSS-3, a model organism from the Roseobacter group, harbours no less than three genes for different DMSP lyases (DddW, DddP and DddQ) that catalyse the degradation of DMSP to dimethyl sulfide (DMS) and acrylate. Despite their apparent similar function these enzymes show no significant overall sequence identity. In this work DddQ and DddW from R. pomeroyi and the DddP homolog from Phaeobacter inhibens DSM 17395 were functionally characterised and their substrate scope was tested using several synthetic DMSP analogues. Comparative kinetic assays revealed differences in the conversion of DMSP and its analogues in terms of selectivity and overall velocity, giving additional insights into the molecular mechanisms of DMSP lyases and into their putatively different biological functions.
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Affiliation(s)
- Immo Burkhardt
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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13
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Lei L, Cherukuri KP, Alcolombri U, Meltzer D, Tawfik DS. The Dimethylsulfoniopropionate (DMSP) Lyase and Lyase-Like Cupin Family Consists of Bona Fide DMSP lyases as Well as Other Enzymes with Unknown Function. Biochemistry 2018; 57:3364-3377. [DOI: 10.1021/acs.biochem.8b00097] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lei Lei
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Uria Alcolombri
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Diana Meltzer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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14
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Wang P, Cao HY, Chen XL, Li CY, Li PY, Zhang XY, Qin QL, Todd JD, Zhang YZ. Mechanistic insight into acrylate metabolism and detoxification in marine dimethylsulfoniopropionate-catabolizing bacteria. Mol Microbiol 2017; 105:674-688. [PMID: 28598523 DOI: 10.1111/mmi.13727] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2017] [Indexed: 12/24/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) cleavage, yielding dimethyl sulfide (DMS) and acrylate, provides vital carbon sources to marine bacteria, is a key component of the global sulfur cycle and effects atmospheric chemistry and potentially climate. Acrylate and its metabolite acryloyl-CoA are toxic if allowed to accumulate within cells. Thus, organisms cleaving DMSP require effective systems for both the utilization and detoxification of acrylate. Here, we examine the mechanism of acrylate utilization and detoxification in Roseobacters. We propose propionate-CoA ligase (PrpE) and acryloyl-CoA reductase (AcuI) as the key enzymes involved and through structural and mutagenesis analyses, provide explanations of their catalytic mechanisms. In most cases, DMSP lyases and DMSP demethylases (DmdAs) have low substrate affinities, but AcuIs have very high substrate affinities, suggesting that an effective detoxification system for acylate catabolism exists in DMSP-catabolizing Roseobacters. This study provides insight on acrylate metabolism and detoxification and a possible explanation for the high Km values that have been noted for some DMSP lyases. Since acrylate/acryloyl-CoA is probably produced by other metabolism, and AcuI and PrpE are conserved in many organisms across all domains of life, the detoxification system is likely relevant to many metabolic processes and environments beyond DMSP catabolism.
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Affiliation(s)
- Peng Wang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Hai-Yan Cao
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Chun-Yang Li
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Ping-Yi Li
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Xi-Ying Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Qi-Long Qin
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Yu-Zhong Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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15
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Schnicker NJ, De Silva SM, Todd JD, Dey M. Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter. Biochemistry 2017; 56:2873-2885. [DOI: 10.1021/acs.biochem.7b00099] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Nicholas J. Schnicker
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Saumya M. De Silva
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Jonathan D. Todd
- School
of Biological Sciences, University of East Anglia, Norwich Research
Park, Norwich NR4 7TJ, United Kingdom
| | - Mishtu Dey
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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16
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Enzymology of Microbial Dimethylsulfoniopropionate Catabolism. STRUCTURAL AND MECHANISTIC ENZYMOLOGY 2017; 109:195-222. [DOI: 10.1016/bs.apcsb.2017.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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