1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Shu Y, Wang Y, Wei Z, Gao N, Wang S, Li C, Xing Q, Hu X, Zhang X, Zhang Y, Zhang W, Bao Z, Ding W. A bacterial symbiont in the gill of the marine scallop Argopecten irradians irradians metabolizes dimethylsulfoniopropionate. MLIFE 2023; 2:178-189. [PMID: 38817626 PMCID: PMC10989825 DOI: 10.1002/mlf2.12072] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/23/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2024]
Abstract
Microbial lysis of dimethylsulfoniopropionate (DMSP) is a key step in marine organic sulfur cycling and has been recently demonstrated to play an important role in mediating interactions between bacteria, algae, and zooplankton. To date, microbes that have been found to lyse DMSP are largely confined to free-living and surface-attached bacteria. In this study, we report for the first time that a symbiont (termed "Rhodobiaceae bacterium HWgs001") in the gill of the marine scallop Argopecten irradians irradians can lyse and metabolize DMSP. Analysis of 16S rRNA gene sequences suggested that HWgs001 accounted for up to 93% of the gill microbiota. Microscopic observations suggested that HWgs001 lived within the gill tissue. Unlike symbionts of other bivalves, HWgs001 belongs to Alphaproteobacteria rather than Gammaproteobacteria, and no genes for carbon fixation were identified in its small genome. Moreover, HWgs001 was found to possess a dddP gene, responsible for the lysis of DMSP to acrylate. The enzymatic activity of dddP was confirmed using the heterologous expression, and in situ transcription of the gene in scallop gill tissues was demonstrated using reverse-transcription PCR. Together, these results revealed a taxonomically and functionally unique symbiont, which represents the first-documented DMSP-metabolizing symbiont likely to play significant roles in coastal marine ecosystems.
Collapse
Affiliation(s)
- Yi Shu
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Yongming Wang
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Zhongcheng Wei
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
| | - Ning Gao
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Shuyan Wang
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Chun‐Yang Li
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Xiao‐Hua Zhang
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Yu‐Zhong Zhang
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Weipeng Zhang
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| |
Collapse
|
3
|
Chhalodia AK, Dickschat JS. Discovery of dimethylsulfoxonium propionate lyases - a missing enzyme relevant to the global sulfur cycle. Org Biomol Chem 2023; 21:3083-3089. [PMID: 36943339 DOI: 10.1039/d2ob02288e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Six dimethylsulfoniopropionate (DMSP) lyases have been shown to cleave the marine sulfur metabolite dimethylsulfoxonium propionate (DMSOP) into DMSO and acrylate. This discovery characterises a missing enzyme relevant to the global sulfur cycle.
Collapse
Affiliation(s)
- Anuj K Chhalodia
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
| |
Collapse
|
4
|
Wang SY, Zhang N, Teng ZJ, Wang XD, Todd JD, Zhang YZ, Cao HY, Li CY. A new dimethylsulfoniopropionate lyase of the cupin superfamily in marine bacteria. Environ Microbiol 2023. [PMID: 36808192 DOI: 10.1111/1462-2920.16355] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) is a marine organosulfur compound with important roles in stress protection, marine biogeochemical cycling, chemical signalling and atmospheric chemistry. Diverse marine microorganisms catabolize DMSP via DMSP lyases to generate the climate-cooling gas and info-chemical dimethyl sulphide. Abundant marine heterotrophs of the Roseobacter group (MRG) are well known for their ability to catabolize DMSP via diverse DMSP lyases. Here, a new DMSP lyase DddU within the MRG strain Amylibacter cionae H-12 and other related bacteria was identified. DddU is a cupin superfamily DMSP lyase like DddL, DddQ, DddW, DddK and DddY, but shares <15% amino acid sequence identity with these enzymes. Moreover, DddU proteins forms a distinct clade from these other cupin-containing DMSP lyases. Structural prediction and mutational analyses suggested that a conserved tyrosine residue is the key catalytic amino acid residue in DddU. Bioinformatic analysis indicated that the dddU gene, mainly from Alphaproteobacteria, is widely distributed in the Atlantic, Pacific, Indian and polar oceans. For reference, dddU is less abundant than dddP, dddQ and dddK, but much more frequent than dddW, dddY and dddL in marine environments. This study broadens our knowledge on the diversity of DMSP lyases, and enhances our understanding of marine DMSP biotransformation.
Collapse
Affiliation(s)
- Shu-Yan Wang
- 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.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Nan Zhang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Zhao-Jie Teng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiao-Di Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Yu-Zhong Zhang
- 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.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hai-Yan Cao
- 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
| | - Chun-Yang Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Lin Q, Shang L, Wang X, Hu Z, Du H, Wang H. Different dimethylsulphoniopropionate-producing ability of dinoflagellates could affect the structure of their associated bacterial community. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
7
|
Chhalodia AK, Rinkel J, Konvalinkova D, Petersen J, Dickschat JS. Identification of volatiles from six marine Celeribacter strains. Beilstein J Org Chem 2021; 17:420-430. [PMID: 33633810 PMCID: PMC7884881 DOI: 10.3762/bjoc.17.38] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/02/2021] [Indexed: 01/20/2023] Open
Abstract
The volatiles emitted from six marine Rhodobacteraceae species of the genus Celeribacter were investigated by GC-MS. Besides several known compounds including dimethyl trisulfide and S-methyl methanethiosulfonate, the sulfur-containing compounds ethyl (E)-3-(methylsulfanyl)acrylate and 2-(methyldisulfanyl)benzothiazole were identified and their structures were verified by synthesis. Feeding experiments with [methyl-2H3]methionine, [methyl-13C]methionine and [34S]-3-(dimethylsulfonio)propanoate (DMSP) resulted in the high incorporation into dimethyl trisulfide and S-methyl methanethiosulfonate, and revealed the origin of the methylsulfanyl group of 2-(methyldisulfanyl)benzothiazole from methionine or DMSP, while the biosynthetic origin of the benzothiazol-2-ylsulfanyl portion could not be traced. The heterocyclic moiety of this compound is likely of anthropogenic origin, because 2-mercaptobenzothiazole is used in the sulfur vulcanization of rubber. Also in none of the feeding experiments incorporation into ethyl (E)-3-(methylsulfanyl)acrylate could be observed, questioning its bacterial origin. Our results demonstrate that the Celeribacter strains are capable of methionine and DMSP degradation to widespread sulfur volatiles, but the analysis of trace compounds in natural samples must be taken with care.
Collapse
Affiliation(s)
- Anuj Kumar Chhalodia
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jan Rinkel
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Dorota Konvalinkova
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jörn Petersen
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Jeroen S Dickschat
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
|
10
|
Li S, Chen M, Chen Y, Tong J, Wang L, Xu Y, Hu Z, Chen H. Epibiotic bacterial community composition in red-tide dinoflagellate Akashiwo sanguinea culture under various growth conditions. FEMS Microbiol Ecol 2019; 95:5481520. [DOI: 10.1093/femsec/fiz057] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/25/2019] [Indexed: 12/14/2022] Open
Affiliation(s)
- Shuangfei Li
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Minchun Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yufei Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Jing Tong
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Liyan Wang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Huirong Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| |
Collapse
|
11
|
The metabolite dimethylsulfoxonium propionate extends the marine organosulfur cycle. Nature 2018; 563:412-415. [PMID: 30429546 DOI: 10.1038/s41586-018-0675-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 08/29/2018] [Indexed: 11/09/2022]
Abstract
Algae produce massive amounts of dimethylsulfoniopropionate (DMSP), which fuel the organosulfur cycle1,2. On a global scale, several petagrams of this sulfur species are produced annually, thereby driving fundamental processes and the marine food web1. An important DMSP transformation product is dimethylsulfide, which can be either emitted to the atmosphere3,4 or oxidized to dimethylsulfoxide (DMSO) and other products5. Here we report the discovery of a structurally unusual metabolite, dimethylsulfoxonium propionate (DMSOP), that is synthesized by several DMSP-producing microalgae and marine bacteria. As with DMSP, DMSOP is a low-molecular-weight zwitterionic metabolite that carries both a positively and a negatively charged functional group. Isotope labelling studies demonstrate that DMSOP is produced from DMSP, and is readily metabolized to DMSO by marine bacteria. DMSOP was found in near nanomolar amounts in field samples and in algal culture media, and thus represents-to our knowledge-a previously undescribed biogenic source for DMSO in the marine environment. The estimated annual oceanic production of oxidized sulfur from this pathway is in the teragram range, similar to the calculated dimethylsulfide flux to the atmosphere3. This sulfoxonium metabolite is therefore a key metabolite of a previously undescribed pathway in the marine sulfur cycle. These findings highlight the importance of DMSOP in the marine organosulfur cycle.
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
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.
Collapse
Affiliation(s)
- Immo Burkhardt
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
| | | | | | | |
Collapse
|
14
|
|
15
|
Analysis of microbiota of the swimming crab (Portunus trituberculatus) in South Korea to identify risk markers for foodborne illness. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.08.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
16
|
Bullock HA, Luo H, Whitman WB. Evolution of Dimethylsulfoniopropionate Metabolism in Marine Phytoplankton and Bacteria. Front Microbiol 2017; 8:637. [PMID: 28469605 PMCID: PMC5395565 DOI: 10.3389/fmicb.2017.00637] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 03/28/2017] [Indexed: 11/13/2022] Open
Abstract
The elucidation of the pathways for dimethylsulfoniopropionate (DMSP) synthesis and metabolism and the ecological impact of DMSP have been studied for nearly 70 years. Much of this interest stems from the fact that DMSP metabolism produces the climatically active gas dimethyl sulfide (DMS), the primary natural source of sulfur to the atmosphere. DMSP plays many important roles for marine life, including use as an osmolyte, antioxidant, predator deterrent, and cryoprotectant for phytoplankton and as a reduced carbon and sulfur source for marine bacteria. DMSP is hypothesized to have become abundant in oceans approximately 250 million years ago with the diversification of the strong DMSP producers, the dinoflagellates. This event coincides with the first genome expansion of the Roseobacter clade, known DMSP degraders. Structural and mechanistic studies of the enzymes of the bacterial DMSP demethylation and cleavage pathways suggest that exposure to DMSP led to the recruitment of enzymes from preexisting metabolic pathways. In some cases, such as DmdA, DmdD, and DddP, these enzymes appear to have evolved to become more specific for DMSP metabolism. By contrast, many of the other enzymes, DmdB, DmdC, and the acrylate utilization hydratase AcuH, have maintained broad functionality and substrate specificities, allowing them to carry out a range of reactions within the cell. This review will cover the experimental evidence supporting the hypothesis that, as DMSP became more readily available in the marine environment, marine bacteria adapted enzymes already encoded in their genomes to utilize this new compound.
Collapse
Affiliation(s)
- Hannah A Bullock
- Department of Microbiology, University of Georgia, AthensGA, USA
| | - Haiwei Luo
- School of Life Sciences, The Chinese University of Hong KongHong Kong, Hong Kong
| | | |
Collapse
|
17
|
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]
|
18
|
Brummett AE, Dey M. New Mechanistic Insight from Substrate- and Product-Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase DddQ. Biochemistry 2016; 55:6162-6174. [PMID: 27755868 DOI: 10.1021/acs.biochem.6b00585] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The marine microbial catabolism of dimethylsulfoniopropionate (DMSP) by the lyase pathway liberates ∼300 million tons of dimethyl sulfide (DMS) per year, which plays a major role in the biogeochemical cycling of sulfur. Recent biochemical and structural studies of some DMSP lyases, including DddQ, reveal the importance of divalent transition metal ions in assisting DMSP cleavage. While DddQ is believed to be zinc-dependent primarily on the basis of structural studies, excess zinc inhibits the enzyme. We examine the importance of iron in regulating the DMSP β-elimination reaction catalyzed by DddQ as our as-isolated purple-colored enzyme possesses ∼0.5 Fe/subunit. The UV-visible spectrum exhibited a feature at 550 nm, consistent with a tyrosinate-Fe(III) ligand-to-metal charge transfer transition. Incubation of as-isolated DddQ with added iron increases the intensity of the 550 nm peak, whereas addition of dithionite causes a bleaching as Fe(III) is reduced. Both the Fe(III) oxidized and Fe(II) reduced species are active, with similar kcat values and 2-fold differences in their Km values for DMSP. The slow turnover of Fe(III)-bound DddQ allowed us to capture a substrate-bound form of the enzyme. Our DMSP-Fe(III)-DddQ structure reveals conformational changes associated with substrate binding and shows that DMSP is positioned optimally to bind iron and is in the proximity of Tyr 120 that acts as a Lewis base to initiate catalysis. The structures of Tris-, DMSP-, and acrylate-bound forms of Fe(III)-DddQ reported here illustrate various states of the enzyme along the reaction pathway. These results provide new insights into DMSP lyase catalysis and have broader significance for understanding the mechanism of oceanic DMS production.
Collapse
Affiliation(s)
- Adam E Brummett
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Mishtu Dey
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| |
Collapse
|
19
|
Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, Lipton MS, Smith RD, De Leenheer P, Payne SH, Johnston AWB, Davie-Martin CL, Halsey KH, Giovannoni SJ. The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol. Nat Microbiol 2016; 1:16065. [PMID: 27573103 DOI: 10.1038/nmicrobiol.2016.65] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/07/2016] [Indexed: 01/20/2023]
Abstract
Marine phytoplankton produce ∼10(9) tonnes of dimethylsulfoniopropionate (DMSP) per year(1,2), an estimated 10% of which is catabolized by bacteria through the DMSP cleavage pathway to the climatically active gas dimethyl sulfide(3,4). SAR11 Alphaproteobacteria (order Pelagibacterales), the most abundant chemo-organotrophic bacteria in the oceans, have been shown to assimilate DMSP into biomass, thereby supplying this cell's unusual requirement for reduced sulfur(5,6). Here, we report that Pelagibacter HTCC1062 produces the gas methanethiol, and that a second DMSP catabolic pathway, mediated by a cupin-like DMSP lyase, DddK, simultaneously shunts as much as 59% of DMSP uptake to dimethyl sulfide production. We propose a model in which the allocation of DMSP between these pathways is kinetically controlled to release increasing amounts of dimethyl sulfide as the supply of DMSP exceeds cellular sulfur demands for biosynthesis.
Collapse
Affiliation(s)
- Jing Sun
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - J Cameron Thrash
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Yanping Qian
- Department of Food Science, Oregon State University, Corvallis, Oregon 97331, USA
| | - Michael C Qian
- Department of Food Science, Oregon State University, Corvallis, Oregon 97331, USA
| | - Ben Temperton
- Department of Biosciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Jiazhen Guo
- Qingdao Aquarium, Qingdao, Shandong 266003, China
| | - Emily K Fowler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Joshua T Aldrich
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Carrie D Nicora
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Mary S Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Richard D Smith
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Patrick De Leenheer
- Department of Mathematics, Oregon State University, Corvallis, Oregon 97331, USA
| | - Samuel H Payne
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Andrew W B Johnston
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Cleo L Davie-Martin
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Kimberly H Halsey
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Stephen J Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
| |
Collapse
|
20
|
Enzymatic breakage of dimethylsulfoniopropionate — a signature molecule for life at sea. Curr Opin Chem Biol 2016; 31:58-65. [DOI: 10.1016/j.cbpa.2016.01.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 11/18/2022]
|
21
|
Wang P, Chen X, Li C, Gao X, Zhu D, Xie B, Qin Q, Zhang X, Su H, Zhou B, Xun L, Zhang Y. Structural and molecular basis for the novel catalytic mechanism and evolution of
DddP
, an abundant peptidase‐like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold. Mol Microbiol 2015; 98:289-301. [DOI: 10.1111/mmi.13119] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Peng Wang
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Xiu‐Lan Chen
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Chun‐Yang Li
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - De‐yu Zhu
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Bin‐Bin Xie
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Qi‐Long Qin
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Xi‐Ying Zhang
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Hai‐Nan Su
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Bai‐Cheng Zhou
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Lu‐ying Xun
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
| | - Yu‐Zhong Zhang
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| |
Collapse
|
22
|
Brummett AE, Schnicker NJ, Crider A, Todd JD, Dey M. Biochemical, Kinetic, and Spectroscopic Characterization of Ruegeria pomeroyi DddW--A Mononuclear Iron-Dependent DMSP Lyase. PLoS One 2015; 10:e0127288. [PMID: 25993446 PMCID: PMC4437653 DOI: 10.1371/journal.pone.0127288] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/13/2015] [Indexed: 11/19/2022] Open
Abstract
The osmolyte dimethylsulfoniopropionate (DMSP) is a key nutrient in marine environments and its catabolism by bacteria through enzymes known as DMSP lyases generates dimethylsulfide (DMS), a gas of importance in climate regulation, the sulfur cycle, and signaling to higher organisms. Despite the environmental significance of DMSP lyases, little is known about how they function at the mechanistic level. In this study we biochemically characterize DddW, a DMSP lyase from the model roseobacter Ruegeria pomeroyi DSS-3. DddW is a 16.9 kDa enzyme that contains a C-terminal cupin domain and liberates acrylate, a proton, and DMS from the DMSP substrate. Our studies show that as-purified DddW is a metalloenzyme, like the DddQ and DddP DMSP lyases, but contains an iron cofactor. The metal cofactor is essential for DddW DMSP lyase activity since addition of the metal chelator EDTA abolishes its enzymatic activity, as do substitution mutations of key metal-binding residues in the cupin motif (His81, His83, Glu87, and His121). Measurements of metal binding affinity and catalytic activity indicate that Fe(II) is most likely the preferred catalytic metal ion with a nanomolar binding affinity. Stoichiometry studies suggest DddW requires one Fe(II) per monomer. Electronic absorption and electron paramagnetic resonance (EPR) studies show an interaction between NO and Fe(II)-DddW, with NO binding to the EPR silent Fe(II) site giving rise to an EPR active species (g = 4.29, 3.95, 2.00). The change in the rhombicity of the EPR signal is observed in the presence of DMSP, indicating that substrate binds to the iron site without displacing bound NO. This work provides insight into the mechanism of DMSP cleavage catalyzed by DddW.
Collapse
Affiliation(s)
- Adam E. Brummett
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Nicholas J. Schnicker
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Alexander Crider
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom
| | - Mishtu Dey
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
| |
Collapse
|
23
|
Dickschat JS, Rabe P, Citron CA. The chemical biology of dimethylsulfoniopropionate. Org Biomol Chem 2015; 13:1954-68. [DOI: 10.1039/c4ob02407a] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review addresses synthesis, biosynthesis, transport and degradation of dimethylsulfoniopropionate and its derivatives.
Collapse
Affiliation(s)
- Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
- Institut für Organische Chemie
| | - Patrick Rabe
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
- Institut für Organische Chemie
| | - Christian A. Citron
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
- Institut für Organische Chemie
| |
Collapse
|
24
|
Alcolombri U, Laurino P, Lara-Astiaso P, Vardi A, Tawfik DS. DddD Is a CoA-Transferase/Lyase Producing Dimethyl Sulfide in the Marine Environment. Biochemistry 2014; 53:5473-5. [DOI: 10.1021/bi500853s] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Uria Alcolombri
- Department
of Biological Chemistry and ‡Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Paola Laurino
- Department
of Biological Chemistry and ‡Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Pedro Lara-Astiaso
- Department
of Biological Chemistry and ‡Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Assaf Vardi
- Department
of Biological Chemistry and ‡Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan S. Tawfik
- Department
of Biological Chemistry and ‡Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
25
|
Hehemann JH, Law A, Redecke L, Boraston AB. The structure of RdDddP from Roseobacter denitrificans reveals that DMSP lyases in the DddP-family are metalloenzymes. PLoS One 2014; 9:e103128. [PMID: 25054772 PMCID: PMC4108388 DOI: 10.1371/journal.pone.0103128] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 06/27/2014] [Indexed: 11/19/2022] Open
Abstract
Marine microbes degrade dimethylsulfoniopropionate (DMSP), which is produced in large quantities by marine algae and plants, with DMSP lyases into acrylate and the gas dimethyl sulfide (DMS). Approximately 10% of the DMS vents from the sea into the atmosphere and this emission returns sulfur, which arrives in the sea through rivers and runoff, back to terrestrial systems via clouds and rain. Despite their key role in this sulfur cycle DMSP lyases are poorly understood at the molecular level. Here we report the first X-ray crystal structure of the putative DMSP lyase RdDddP from Roseobacter denitrificans, which belongs to the abundant DddP family. This structure, determined to 2.15 Å resolution, shows that RdDddP is a homodimeric metalloprotein with a binuclear center of two metal ions located 2.7 Å apart in the active site of the enzyme. Consistent with the crystallographic data, inductively coupled plasma mass spectrometry (ICP-MS) and total reflection X-ray fluorescence (TRXF) revealed the bound metal species to be primarily iron. A 3D structure guided analysis of environmental DddP lyase sequences elucidated the critical residues for metal binding are invariant, suggesting all proteins in the DddP family are metalloenzymes.
Collapse
Affiliation(s)
- Jan-Hendrik Hehemann
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Adrienne Law
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Lars Redecke
- Joint Laboratory for Structural Biology of Infection and Inflammation of the Universities of Hamburg and Lübeck, c/o DESY, Hamburg, Germany
| | - Alisdair B. Boraston
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada
| |
Collapse
|
26
|
Reply to Tawfik et al.: DddQ is a dimethylsulfoniopropionate lyase involved in dimethylsulfoniopropionate catabolism in marine bacterial cells. Proc Natl Acad Sci U S A 2014; 111:E2080. [PMID: 24967457 DOI: 10.1073/pnas.1403460111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
27
|
Trimethylamine N-oxide metabolism by abundant marine heterotrophic bacteria. Proc Natl Acad Sci U S A 2014; 111:2710-5. [PMID: 24550299 DOI: 10.1073/pnas.1317834111] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trimethylamine N-oxide (TMAO) is a common osmolyte found in a variety of marine biota and has been detected at nanomolar concentrations in oceanic surface waters. TMAO can serve as an important nutrient for ecologically important marine heterotrophic bacteria, particularly the SAR11 clade and marine Roseobacter clade (MRC). However, the enzymes responsible for TMAO catabolism and the membrane transporter required for TMAO uptake into microbial cells have yet to be identified. We show here that the enzyme TMAO demethylase (Tdm) catalyzes the first step in TMAO degradation. This enzyme represents a large group of proteins with an uncharacterized domain (DUF1989). The function of TMAO demethylase in a representative from the SAR11 clade (strain HIMB59) and in a representative of the MRC (Ruegeria pomeroyi DSS-3) was confirmed by heterologous expression of tdm (the gene encoding Tdm) in Escherichia coli. In R. pomeroyi, mutagenesis experiments confirmed that tdm is essential for growth on TMAO. We also identified a unique ATP-binding cassette transporter (TmoXWV) found in a variety of marine bacteria and experimentally confirmed its specificity for TMAO through marker exchange mutagenesis and lacZ reporter assays of the promoter for genes encoding this transporter. Both Tdm and TmoXWV are particularly abundant in natural seawater assemblages and actively expressed, as indicated by a number of recent metatranscriptomic and metaproteomic studies. These data suggest that TMAO represents a significant, yet overlooked, nutrient for marine bacteria.
Collapse
|
28
|
Molecular insight into bacterial cleavage of oceanic dimethylsulfoniopropionate into dimethyl sulfide. Proc Natl Acad Sci U S A 2014; 111:1026-31. [PMID: 24395783 DOI: 10.1073/pnas.1312354111] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile DMS through the action of DMSP lyases and is important in the global sulfur and carbon cycles. When released into the atmosphere from the oceans, DMS is oxidized, forming cloud condensation nuclei that may influence weather and climate. Six different DMSP lyase genes are found in taxonomically diverse microorganisms, and dddQ is among the most abundant in marine metagenomes. Here, we examine the molecular mechanism of DMSP cleavage by the DMSP lyase, DddQ, from Ruegeria lacuscaerulensis ITI_1157. The structures of DddQ bound to an inhibitory molecule 2-(N-morpholino)ethanesulfonic acid and of DddQ inactivated by a Tyr131Ala mutation and bound to DMSP were solved. DddQ adopts a β-barrel fold structure and contains a Zn(2+) ion and six highly conserved hydrophilic residues (Tyr120, His123, His125, Glu129, Tyr131, and His163) in the active site. Mutational and biochemical analyses indicate that these hydrophilic residues are essential to catalysis. In particular, Tyr131 undergoes a conformational change during catalysis, acting as a base to initiate the β-elimination reaction in DMSP lysis. Moreover, structural analyses and molecular dynamics simulations indicate that two loops over the substrate-binding pocket of DddQ can alternate between "open" and "closed" states, serving as a gate for DMSP entry. We also propose a molecular mechanism for DMS production through DMSP cleavage. Our study provides important insight into the mechanism involved in the conversion of DMSP into DMS, which should lead to a better understanding of this globally important biogeochemical reaction.
Collapse
|
29
|
Reisch CR, Crabb WM, Gifford SM, Teng Q, Stoudemayer MJ, Moran MA, Whitman WB. Metabolism of dimethylsulphoniopropionate byRuegeria pomeroyi DSS-3. Mol Microbiol 2013; 89:774-91. [DOI: 10.1111/mmi.12314] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2013] [Indexed: 11/25/2022]
Affiliation(s)
- Chris R. Reisch
- Department of Microbiology; University of Georgia; Athens; GA; USA
| | - Warren M. Crabb
- Department of Microbiology; University of Georgia; Athens; GA; USA
| | - Scott M. Gifford
- Department of Marine sciences; University of Georgia; Athens; GA; USA
| | - Quincy Teng
- US Environmental Protection Agency; Athens; GA; USA
| | | | - Mary Ann Moran
- Department of Marine sciences; University of Georgia; Athens; GA; USA
| | | |
Collapse
|
30
|
Abstract
The compatible solute dimethylsulphoniopropionate (DMSP) has important roles in marine environments. It is an anti-stress compound made by many single-celled plankton, some seaweeds and a few land plants that live by the shore. Furthermore, in the oceans it is a major source of carbon and sulphur for marine bacteria that break it down to products such as dimethyl sulphide, which are important in their own right and have wide-ranging effects, from altering animal behaviour to seeding cloud formation. In this Review, we describe how recent genetic and genomic work on the ways in which several different bacteria, and some fungi, catabolize DMSP has provided new and surprising insights into the mechanisms, regulation and possible evolution of DMSP catabolism in microorganisms.
Collapse
|
31
|
Reisch CR, Moran MA, Whitman WB. Bacterial Catabolism of Dimethylsulfoniopropionate (DMSP). Front Microbiol 2011; 2:172. [PMID: 21886640 PMCID: PMC3155054 DOI: 10.3389/fmicb.2011.00172] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 07/28/2011] [Indexed: 11/13/2022] Open
Abstract
Dimethylsulfoniopropionate (DMSP) is a metabolite produced primarily by marine phytoplankton and is the main precursor to the climatically important gas dimethylsulfide (DMS). DMS is released upon bacterial catabolism of DMSP, but it is not the only possible fate of DMSP sulfur. An alternative demethylation/demethiolation pathway results in the eventual release of methanethiol, a highly reactive volatile sulfur compound that contributes little to the atmospheric sulfur flux. The activity of these pathways control the natural flux of sulfur released to the atmosphere. Although these biochemical pathways and the factors that regulate them are of great interest, they are poorly understood. Only recently have some of the genes and pathways responsible for DMSP catabolism been elucidated. Thus far, six different enzymes have been identified that catalyze the cleavage of DMSP, resulting in the release of DMS. In addition, five of these enzymes appear to produce acrylate, while one produces 3-hydroxypropionate. In contrast, only one enzyme, designated DmdA, has been identified that catalyzes the demethylation reaction producing methylmercaptopropionate (MMPA). The metabolism of MMPA is performed by a series of three coenzyme-A mediated reactions catalyzed by DmdB, DmdC, and DmdD. Interestingly, CandidatusPelagibacter ubique, a member of the SAR11 clade of Alphaproteobacteria that is highly abundant in marine surface waters, possessed functional DmdA, DmdB, and DmdC enzymes. Microbially mediated transformations of both DMS and methanethiol are also possible, although many of the biochemical and molecular genetic details are still unknown. This review will focus on the recent discoveries in the biochemical pathways that mineralize and assimilate DMSP carbon and sulfur, as well as the areas for which a comprehensive understanding is still lacking.
Collapse
Affiliation(s)
- Chris R Reisch
- Department of Microbiology, University of Georgia Athens, GA, USA
| | | | | |
Collapse
|
32
|
Todd JD, Kirkwood M, Newton-Payne S, Johnston AWB. DddW, a third DMSP lyase in a model Roseobacter marine bacterium, Ruegeria pomeroyi DSS-3. ISME JOURNAL 2011; 6:223-6. [PMID: 21677693 DOI: 10.1038/ismej.2011.79] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ruegeria pomeroyi DSS-3 is a model Roseobacter marine bacterium, particularly regarding its catabolism of dimethylsulfoniopropionate (DMSP), an abundant anti-stress molecule made by marine phytoplankton. We found a novel gene, dddW, which encodes a DMSP lyase that cleaves DMSP into acrylate plus the environmentally important volatile dimethyl sulfide (DMS). Mutations in dddW reduced, but did not abolish DMS production. Transcription of dddW was greatly enhanced by pre-growth of cells with DMSP, via a LysR-type regulator. Close DddW homologs occur in only one other Roseobacter species, and there are no close homologs and only a few related sequences in metagenomes of marine bacteria. In addition to DddW, R. pomeroyi DSS-3 had been shown to have two other, different, DMSP lyases, DddP and DddQ, plus an enzyme that demethylates DMSP, emphasizing the importance of this substrate for this model bacterium.
Collapse
Affiliation(s)
- Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
| | | | | | | |
Collapse
|
33
|
Curson ARJ, Sullivan MJ, Todd JD, Johnston AWB. DddY, a periplasmic dimethylsulfoniopropionate lyase found in taxonomically diverse species of Proteobacteria. ISME JOURNAL 2011; 5:1191-200. [PMID: 21248856 DOI: 10.1038/ismej.2010.203] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The abundant compatible solute dimethylsulfoniopropionate (DMSP) is made by many marine algae. Different marine bacteria catabolise DMSP by various mechanisms, some of which liberate the environmentally important gas dimethyl sulfide (DMS). We describe an enzyme, DddY, which cleaves DMSP into DMS plus acrylate and is located in the bacterial periplasm, unlike other DMSP lyases that catalyse this reaction. There are dddY-like genes in strains of Alcaligenes, Arcobacter and Shewanella, in the β-, ɛ- and γ-proteobacteria, respectively. In Alcaligenes, dddY is in a cluster of ddd and acu genes that resemble, but also have significant differences to, those in other bacteria that catabolise both DMSP and acrylate. Although production of DMS and transcription of Alcaligenes dddY are both apparently inducible by pre-growth of cells with DMSP, this substrate must be catabolised to form acrylate, the bona fide coinducer.
Collapse
Affiliation(s)
- Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | | | | | | |
Collapse
|
34
|
Sullivan MJ, Curson ARJ, Shearer N, Todd JD, Green RT, Johnston AWB. Unusual regulation of a leaderless operon involved in the catabolism of dimethylsulfoniopropionate in Rhodobacter sphaeroides. PLoS One 2011; 6:e15972. [PMID: 21249136 PMCID: PMC3017554 DOI: 10.1371/journal.pone.0015972] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 12/01/2010] [Indexed: 11/20/2022] Open
Abstract
Rhodobacter sphaeroides strain 2.4.1 is a widely studied bacterium that has recently been shown to cleave the abundant marine anti-stress molecule dimethylsulfoniopropionate (DMSP) into acrylate plus gaseous dimethyl sulfide. It does so by using a lyase encoded by dddL, the promoter-distal gene of a three-gene operon, acuR-acuI-dddL. Transcription of the operon was enhanced when cells were pre-grown with the substrate DMSP, but this induction is indirect, and requires the conversion of DMSP to the product acrylate, the bona fide co-inducer. This regulation is mediated by the product of the promoter-proximal gene acuR, a transcriptional regulator in the TetR family. AcuR represses the operon in the absence of acrylate, but this is relieved by the presence of the co-inducer. Another unusual regulatory feature is that the acuR-acuI-dddL mRNA transcript is leaderless, such that acuR lacks a Shine-Dalgarno ribosomal binding site and 5′-UTR, and is translated at a lower level compared to the downstream genes. This regulatory unit may be quite widespread in bacteria, since several other taxonomically diverse lineages have adjacent acuR-like and acuI-like genes; these operons also have no 5′ leader sequences or ribosomal binding sites and their predicted cis-acting regulatory sequences resemble those of R. sphaeroides acuR-acuI-dddL.
Collapse
Affiliation(s)
- Matthew J. Sullivan
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrew R. J. Curson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Neil Shearer
- Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Robert T. Green
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Andrew W. B. Johnston
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
| |
Collapse
|
35
|
Todd JD, Curson ARJ, Kirkwood M, Sullivan MJ, Green RT, Johnston AWB. DddQ, a novel, cupin-containing, dimethylsulfoniopropionate lyase in marine roseobacters and in uncultured marine bacteria. Environ Microbiol 2010; 13:427-38. [PMID: 20880330 DOI: 10.1111/j.1462-2920.2010.02348.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ruegeria (previously Silicibacter) pomeroyi DSS-3, a marine roseobacter, can catabolize dimethylsulfoniopropionate (DMSP), a compatible solute that is made in large amounts by marine plankton and algae. This strain was known to demethylate DMSP via a demethylase, encoded by the dmdA gene, and it can also cleave DMSP, releasing the environmentally important volatile dimethyl sulfide (DMS) in the process. We found that this strain has two different genes, dddP and dddQ, which encode enzymes that cleave DMSP, generating DMS plus acrylate. DddP had earlier been found in other roseobacters and is a member of the M24 family of peptidases. The newly discovered DddQ polypeptide contains a predicted cupin metal-binding pocket, but has no other similarity to any other polypeptide with known function. DddP(-) and DddQ(-) mutants each produced DMS at significantly reduced levels compared with wild-type R. pomeroyi DSS-3, and transcription of the corresponding ddd genes was enhanced when cells were pre-grown with DMSP. Ruegeria pomeroyi DSS-3 also has a gene product that is homologous to DddD, a previously identified enzyme that cleaves DMSP, but which forms DMS plus 3-OH-propionate as the initial catabolites. However, mutations in this dddD-like gene did not affect DMS production, and it was not transcribed under our conditions. Another roseobacter strain, Roseovarius nubinhibens ISM, also contains dddP and has two functional copies of dddQ, encoded by adjacent genes. Judged by their frequencies in the Global Ocean Sampling metagenomic databases, DddP and DddQ are relatively abundant among marine bacteria compared with the previously identified DddL and DddD enzymes.
Collapse
Affiliation(s)
- Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | | | | | | | | | | |
Collapse
|