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Carrión O, Li CY, Peng M, Wang J, Pohnert G, Azizah M, Zhu XY, Curson ARJ, Wang Q, Walsham KS, Zhang XH, Monaco S, Harvey JM, Chen XL, Gao C, Wang N, Wang XJ, Wang P, Giovanonni SJ, Lee CP, Suffridge CP, Zhang Y, Luo Z, Wang D, Todd JD, Zhang YZ. DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms. Nat Microbiol 2023; 8:2326-2337. [PMID: 38030907 PMCID: PMC10686828 DOI: 10.1038/s41564-023-01526-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Dimethylsulfoxonium propionate (DMSOP) is a recently identified and abundant marine organosulfur compound with roles in oxidative stress protection, global carbon and sulfur cycling and, as shown here, potentially in osmotolerance. Microbial DMSOP cleavage yields dimethyl sulfoxide, a ubiquitous marine metabolite, and acrylate, but the enzymes responsible, and their environmental importance, were unknown. Here we report DMSOP cleavage mechanisms in diverse heterotrophic bacteria, fungi and phototrophic algae not previously known to have this activity, and highlight the unappreciated importance of this process in marine sediment environments. These diverse organisms, including Roseobacter, SAR11 bacteria and Emiliania huxleyi, utilized their dimethylsulfoniopropionate lyase 'Ddd' or 'Alma' enzymes to cleave DMSOP via similar catalytic mechanisms to those for dimethylsulfoniopropionate. Given the annual teragram predictions for DMSOP production and its prevalence in marine sediments, our results highlight that DMSOP cleavage is likely a globally significant process influencing carbon and sulfur fluxes and ecological interactions.
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Affiliation(s)
- Ornella Carrión
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- School of Biological Sciences, University of East Anglia, Norwich, UK.
| | - Chun-Yang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
| | - Ming Peng
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jinyan Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich Schiller University Jena, Jena, Germany
| | - Muhaiminatul Azizah
- Institute of Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich Schiller University Jena, Jena, Germany
| | - Xiao-Yu Zhu
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Qing Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Keanu S Walsham
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Xiao-Hua Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich, UK
| | - James M Harvey
- Department of Chemistry, King's College London, London, UK
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Ning Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Juan Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Peng Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | | | - Chih-Ping Lee
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | | | - Yu Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ziqi Luo
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Jonathan D Todd
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- School of Biological Sciences, University of East Anglia, Norwich, UK.
| | - Yu-Zhong Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Qingdao, China.
- Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China.
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2
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Li J, Todd J, Yu Z. The production of dimethylsulfoniopropionate by bacteria with mmtN linked to non-ribosomal peptide synthase gene. ENVIRONMENTAL TECHNOLOGY 2023:1-9. [PMID: 37970872 DOI: 10.1080/09593330.2023.2283792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/29/2023] [Indexed: 11/19/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) is a vital sulfur-containing compound with worldwide significance, serving as the primary precursor for dimethyl sulfide (DMS), a volatile sulfur compound that plays a role in atmospheric chemistry and influences the Earth's climate on a global scale. The study investigated the ability of four bacterial strains, namely Acidimangrovimonas sediminis MS2-2 (MS2-2), Hartmannibacter diazotrophicus E18T (E18T), Rhizobium lusitanum 22705 (22705), and Nitrospirillum iridis DSM22198 (DSM22198), to produce and degrade DMSP. These strains were assessed for their DMSP synthesis ability with the mmtN linked to non-ribosomal peptide synthase (NRPS) gene. The results showed that MS2-2, and E18T bacteria, which contained the mmtN but not linked to an NRPS gene, increased DMSP production with increasing salinity. The highest production of DMSP was achieved at 25 PSU when either methionine was added or low nitrogen conditions were present, yielding 1656.03 ± 41.04 and 265.59 ± 9.17 nmol/mg protein, respectively, and subsequently under the conditions of methionine addition or low nitrogen, both strains reached their maximum DMSP production at 25 PSU. Furthermore, the strains MS2-2, E18T, and 22705 with the mmtN gene but not linked to an NRPS gene were found to be involved in DMS production. This research contributes to the understanding of the genes involved in DMSP biosynthesis in bacteria that produce DMSP.
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Affiliation(s)
- Jinmei Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, People's Republic of China
- School of Biological Sciences, University of East Anglia, Norwich, UK
- RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, People's Republic of China
| | - Jonathan Todd
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, People's Republic of China
- RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, People's Republic of China
- Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou City People's Republic of China
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3
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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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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: 3] [Impact Index Per Article: 1.5] [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: 3] [Impact Index Per Article: 1.0] [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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An X, Chen C, Wang T, Huang A, Zhang D, Han MJ, Wang J. Genetic Incorporation of Selenotyrosine Significantly Improves Enzymatic Activity of Agrobacterium radiobacter Phosphotriesterase. Chembiochem 2021; 22:2535-2539. [PMID: 32789938 DOI: 10.1002/cbic.202000460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/11/2020] [Indexed: 12/16/2022]
Abstract
Tyrosine plays important roles in many enzymes. To facilitate enzyme design, mechanistic studies and minimize structural perturbation in the active site, here we report the genetic incorporation of a novel unnatural amino acid selenotyrosine (SeHF), which has single-atom replacement in comparison to tyrosine. The arPTE-(Agrobacterium radiobacter Phosphotriesterase) Tyr309SeHF mutant exhibits a significant 12-fold increase in kcat and 3.2-fold enhancement in kcat /KM at pH 7.0. Molecular dynamics simulations show that the SeHF309 mutation results in a conformational switch which opens up the product release pocket and increases the product release rate, thereby elevating the overall enzyme activity. Significant improvement of the catalytic efficiency at neutral pH by single unnatural amino acid (UAA) mutation broadens the application of this enzyme, and provides valuable insights to the mechanism. Our method represents a new approach for designing enzymes with enhanced activity.
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Affiliation(s)
- Xiaojing An
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Chao Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,University of the Chinese Academy of Sciences (UCAS), Hefei, China
| | - Tianyuan Wang
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Aiping Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Ming-Jie Han
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Jiangyun Wang
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
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Song D, Zhang Y, Liu J, Zhong H, Zheng Y, Zhou S, Yu M, Todd JD, Zhang XH. Metagenomic Insights Into the Cycling of Dimethylsulfoniopropionate and Related Molecules in the Eastern China Marginal Seas. Front Microbiol 2020; 11:157. [PMID: 32132981 PMCID: PMC7039863 DOI: 10.3389/fmicb.2020.00157] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/22/2020] [Indexed: 11/13/2022] Open
Abstract
The microbial cycling of dimethylsulfoniopropionate (DMSP) and its gaseous catabolites dimethylsulfide (DMS) and methanethiol (MeSH) are important processes in the global sulfur cycle, marine microbial food webs, signaling pathways, atmospheric chemistry, and potentially climate regulation. Many functional genes have been identified and used to study the genetic potential of microbes to produce and catabolize these organosulfur compounds in different marine environments. Here, we sampled seawater, marine sediment and hydrothermal sediment, and polymetallic sulfide in the eastern Chinese marginal seas and analyzed their microbial communities for the genetic potential to cycle DMSP, DMS, and MeSH using metagenomics. DMSP was abundant in all sediment samples, but was fivefold less prominent in those from hydrothermal samples. Indeed, Yellow Sea (YS) sediment samples had DMSP concentrations two orders of magnitude higher than in surface water samples. Bacterial genetic potential to synthesize DMSP (mainly in Rhodobacteraceae bacteria) was far higher than for phytoplankton in all samples, but particularly in the sediment where no algal DMSP synthesis genes were detected. Thus, we propose bacteria as important DMSP producers in these marine sediments. DMSP catabolic pathways mediated by the DMSP lyase DddP (prominent in Pseudomonas and Mesorhizobium bacteria) and DMSP demethylase DmdA enzymes (prominent in Rhodobacteraceae bacteria) and MddA-mediated MeSH S-methylation were very abundant in Bohai Sea and Yellow Sea sediments (BYSS) samples. In contrast, the genetic potential for DMSP degradation was very low in the hydrothermal sediment samples-dddP was the only catabolic gene detected and in only one sample. However, the potential for DMS production from MeSH (mddA) and DMS oxidation (dmoA and ddhA) was relatively abundant. This metagenomics study does not provide conclusive evidence for DMSP cycling; however, it does highlight the potential importance of bacteria in the synthesis and catabolism of DMSP and related compounds in diverse sediment environments.
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Affiliation(s)
- Delei Song
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunhui Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ji Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Haohui Zhong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yanfen Zheng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shun Zhou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Min Yu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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8
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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: 53] [Impact Index Per Article: 10.6] [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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9
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Zeng YX, Qiao ZY. Diversity of Dimethylsulfoniopropionate Degradation Genes Reveals the Significance of Marine Roseobacter Clade in Sulfur Metabolism in Coastal Areas of Antarctic Maxwell Bay. Curr Microbiol 2019; 76:967-974. [DOI: 10.1007/s00284-019-01709-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/21/2019] [Indexed: 11/24/2022]
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10
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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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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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12
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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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13
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Illuminating the catalytic core of ectoine synthase through structural and biochemical analysis. Sci Rep 2019; 9:364. [PMID: 30674920 PMCID: PMC6344544 DOI: 10.1038/s41598-018-36247-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/16/2018] [Indexed: 11/26/2022] Open
Abstract
Ectoine synthase (EctC) is the signature enzyme for the production of ectoine, a compatible solute and chemical chaperone widely synthesized by bacteria as a cellular defense against the detrimental effects of osmotic stress. EctC catalyzes the last step in ectoine synthesis through cyclo-condensation of the EctA-formed substrate N-gamma-acetyl-L-2,4-diaminobutyric acid via a water elimination reaction. We have biochemically and structurally characterized the EctC enzyme from the thermo-tolerant bacterium Paenibacillus lautus (Pl). EctC is a member of the cupin superfamily and forms dimers, both in solution and in crystals. We obtained high-resolution crystal structures of the (Pl)EctC protein in forms that contain (i) the catalytically important iron, (ii) iron and the substrate N-gamma-acetyl-L-2,4-diaminobutyric acid, and (iii) iron and the enzyme reaction product ectoine. These crystal structures lay the framework for a proposal for the EctC-mediated water-elimination reaction mechanism. Residues involved in coordinating the metal, the substrate, or the product within the active site of ectoine synthase are highly conserved among a large group of EctC-type proteins. Collectively, the biochemical, mutational, and structural data reported here yielded detailed insight into the structure-function relationship of the (Pl)EctC enzyme and are relevant for a deeper understanding of the ectoine synthase family as a whole.
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14
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Hu Z, Awakawa T, Ma Z, Abe I. Aminoacyl sulfonamide assembly in SB-203208 biosynthesis. Nat Commun 2019; 10:184. [PMID: 30643149 PMCID: PMC6331615 DOI: 10.1038/s41467-018-08093-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/12/2018] [Indexed: 12/14/2022] Open
Abstract
Sulfonamide is present in many important drugs, due to its unique chemical and biological properties. In contrast, naturally occurring sulfonamides are rare, and their biosynthetic knowledge are scarce. Here we identify the biosynthetic gene cluster of sulfonamide antibiotics, altemicidin, SB-203207, and SB-203208, from Streptomyces sp. NCIMB40513. The heterologous gene expression and biochemical analyses reveal unique aminoacyl transfer reactions, including the tRNA synthetase-like enzyme SbzA-catalyzed L-isoleucine transfer and the GNAT enzyme SbzC-catalyzed β-methylphenylalanine transfer. Furthermore, we elucidate the biogenesis of 2-sulfamoylacetic acid from L-cysteine, by the collaboration of the cupin dioxygenase SbzM and the aldehyde dehydrogenase SbzJ. Remarkably, SbzM catalyzes the two-step oxidation and decarboxylation of L-cysteine, and the subsequent intramolecular amino group rearrangement leads to N-S bond formation. This detailed analysis of the aminoacyl sulfonamide antibiotics biosynthetic machineries paves the way toward investigations of sulfonamide biosynthesis and its engineering.
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Affiliation(s)
- Zhijuan Hu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Zhongjun Ma
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
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15
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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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16
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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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17
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Li CY, Zhang D, Chen XL, Wang P, Shi WL, Li PY, Zhang XY, Qin QL, Todd JD, Zhang YZ. Mechanistic Insights into Dimethylsulfoniopropionate Lyase DddY, a New Member of the Cupin Superfamily. J Mol Biol 2017; 429:3850-3862. [DOI: 10.1016/j.jmb.2017.10.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/08/2017] [Accepted: 10/19/2017] [Indexed: 12/28/2022]
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18
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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: 12] [Impact Index Per Article: 1.7] [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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