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Li CY, Cao HY, Wang Q, Carrión O, Zhu X, Miao J, Wang P, Chen XL, Todd JD, Zhang YZ. Aerobic methylation of hydrogen sulfide to dimethylsulfide in diverse microorganisms and environments. THE ISME JOURNAL 2023; 17:1184-1193. [PMID: 37179443 PMCID: PMC10356932 DOI: 10.1038/s41396-023-01430-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
Dimethylsulfide (DMS) is the major biosulfur source emitted to the atmosphere with key roles in global sulfur cycling and potentially climate regulation. The main precursor of DMS is thought to be dimethylsulfoniopropionate. However, hydrogen sulfide (H2S), a widely distributed and abundant volatile in natural environments, can be methylated to DMS. The microorganisms and the enzymes that convert H2S to DMS, and their importance in global sulfur cycling were unknown. Here we demonstrate that the bacterial MddA enzyme, previously known as a methanethiol S-methyltransferase, could methylate inorganic H2S to DMS. We determine key residues involved in MddA catalysis and propose the mechanism for H2S S-methylation. These results enabled subsequent identification of functional MddA enzymes in abundant haloarchaea and a diverse range of algae, thus expanding the significance of MddA mediated H2S methylation to other domains of life. Furthermore, we provide evidence for H2S S-methylation being a detoxification strategy in microorganisms. The mddA gene was abundant in diverse environments including marine sediments, lake sediments, hydrothermal vents and soils. Thus, the significance of MddA-driven methylation of inorganic H2S to global DMS production and sulfur cycling has likely been considerably underestimated.
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Affiliation(s)
- 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
| | - Hai-Yan Cao
- 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.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Qing Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Ornella Carrión
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Xiaoyu Zhu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jie Miao
- 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
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - 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, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, 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.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
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Gribble GW. Naturally Occurring Organohalogen Compounds-A Comprehensive Review. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 121:1-546. [PMID: 37488466 DOI: 10.1007/978-3-031-26629-4_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.
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Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA.
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3
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Lankau T, Ken HC, Chang HM, Yu CH. A Computational Study of the Promiscuity of the SAM-Dependent Methyltransferase AtHTMT1. ACS OMEGA 2022; 7:12753-12764. [PMID: 35474790 PMCID: PMC9026064 DOI: 10.1021/acsomega.1c07327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
A two-pronged computational approach was taken to study the promiscuity of the SAM+-dependent methyl transferase AtHTMT1 from thale cress with several nucleophiles (Cl-, Br-, I-, NCO-, NCS-). First, enzyme-free methyl transfer reactions were studied with M05/6-311+G(2d,p) DFT calculations and electrostatic continuum models (PCM/SMD) for various chemical environments. Second, QM/MM MD simulations with semiempirical Hamiltonians (PM7, PM6-D3, AM1, PM6-D3H4) and the AMBER 14SB force field were used to study the enzyme catalyzed reaction in silico. The combination of the DFT and MD results shows that reactant desolvation generally accelerates the reaction, but it cannot explain the selectivity of the enzyme. The critical position of H2O molecules at the reactive site favors the reaction of NCS- over Cl- and Br- in agreement with experiments, but not observed in the quantum calculations for the cytosol. The addition of selected H2O molecules to the N terminus of NCS- greatly increases its reactivity, while H2O molecules attached to Cl- slow the reaction. The partial solvation of the nucleophiles in the reactive pouch holds the key to understanding the reactivity of AtHTMT1.
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Affiliation(s)
| | | | | | - Chin Hui Yu
- . Phone: +886 (0)3 5162080. Fax: +886 (0)3 5721534
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Liu SS, Yang GP, He Z, Gao XX, Xu F. Oceanic emissions of methyl halides and effect of nutrients concentration on their production: A case of the western Pacific Ocean (2°N to 24°N). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 769:144488. [PMID: 33485203 DOI: 10.1016/j.scitotenv.2020.144488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Methyl halides are important greenhouse gases responsible for the majority of the ozone layer depletion. This study investigated atmospheric and seawater methyl halides (CH3Cl, CH3Br, and CH3I) in the western Pacific Ocean between 2°N and 24°N. Increases in methyl halides in the atmosphere were likely to have originated from Southeast Asian regions. Elevated CH3I concentrations in seawater were mainly produced photochemically from dissolved organic carbon. Maximum methyl halide and chlorophyll a levels in the upper water column (0-200 m) were linked to biological activity and downwelling or upwelling caused by cold and warm eddies. Ship-based incubation experiments showed that nutrient supplementation promoted methyl halide emissions. The elevated methyl halide production was associated with increases in phytoplankton such as diatoms. The mean fluxes of CH3Cl, CH3Br, and CH3I in study area of during the cruise were 82.91, 4.70, and 3.50 nmol m-2 d-1, respectively. The estimated emissions of CH3Cl, CH3Br, and CH3I in the western Pacific Ocean accounted for 0.67%, 0.79% and 0.09% of global oceanic emissions, respectively, indicating that the open sea contribute insignificantly to the global oceanic emissions of these gases.
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Affiliation(s)
- Shan-Shan Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Gui-Peng Yang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Institute of Marine Chemistry, Ocean University of China, Qingdao 266100, China
| | - Zhen He
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Xu-Xu Gao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Feng Xu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
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Jaeger N, Besaury L, Röhling AN, Koch F, Delort AM, Gasc C, Greule M, Kolb S, Nadalig T, Peyret P, Vuilleumier S, Amato P, Bringel F, Keppler F. Chloromethane formation and degradation in the fern phyllosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 634:1278-1287. [PMID: 29660879 DOI: 10.1016/j.scitotenv.2018.03.316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 03/25/2018] [Accepted: 03/25/2018] [Indexed: 06/08/2023]
Abstract
Chloromethane (CH3Cl) is the most abundant halogenated trace gas in the atmosphere. It plays an important role in natural stratospheric ozone destruction. Current estimates of the global CH3Cl budget are approximate. The strength of the CH3Cl global sink by microbial degradation in soils and plants is under discussion. Some plants, particularly ferns, have been identified as substantial emitters of CH3Cl. Their ability to degrade CH3Cl remains uncertain. In this study, we investigated the potential of leaves from 3 abundant ferns (Osmunda regalis, Cyathea cooperi, Dryopteris filix-mas) to produce and degrade CH3Cl by measuring their production and consumption rates and their stable carbon and hydrogen isotope signatures. Investigated ferns are able to degrade CH3Cl at rates from 2.1 to 17 and 0.3 to 0.9μggdw-1day-1 for C. cooperi and D. filix-mas respectively, depending on CH3Cl supplementation and temperature. The stable carbon isotope enrichment factor of remaining CH3Cl was -39±13‰, whereas negligible isotope fractionation was observed for hydrogen (-8±19‰). In contrast, O. regalis did not consume CH3Cl, but produced it at rates ranging from 0.6 to 128μggdw-1day-1, with stable isotope values of -97±8‰ for carbon and -202±10‰ for hydrogen, respectively. Even though the 3 ferns showed clearly different formation and consumption patterns, their leaf-associated bacterial diversity was not notably different. Moreover, we did not detect genes associated with the only known chloromethane utilization pathway "cmu" in the microbial phyllosphere of the investigated ferns. Our study suggests that still unknown CH3Cl biodegradation processes on plants play an important role in global cycling of atmospheric CH3Cl.
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Affiliation(s)
- Nicole Jaeger
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 236, Heidelberg, Germany.
| | - Ludovic Besaury
- Institut de Chimie de Clermont-Ferrand (ICCF), UMR6096 CNRS-UCA-Sigma, Clermont-Ferrand, France; Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France; UMR FARE, Université de Reims Champagne Ardenne, INRA, Reims, France
| | - Amelie Ninja Röhling
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 236, Heidelberg, Germany
| | - Fabien Koch
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 236, Heidelberg, Germany
| | - Anne-Marie Delort
- Institut de Chimie de Clermont-Ferrand (ICCF), UMR6096 CNRS-UCA-Sigma, Clermont-Ferrand, France
| | - Cyrielle Gasc
- Université Clermont Auvergne, INRA, MEDIS, Clermont-Ferrand, France
| | - Markus Greule
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 236, Heidelberg, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Thierry Nadalig
- Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRA, MEDIS, Clermont-Ferrand, France
| | - Stéphane Vuilleumier
- Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France
| | - Pierre Amato
- Institut de Chimie de Clermont-Ferrand (ICCF), UMR6096 CNRS-UCA-Sigma, Clermont-Ferrand, France
| | - Françoise Bringel
- Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France
| | - Frank Keppler
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 236, Heidelberg, Germany; Heidelberg Center for the Environment HCE, Heidelberg University, Heidelberg, Germany.
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Yeager CM, Amachi S, Grandbois R, Kaplan DI, Xu C, Schwehr KA, Santschi PH. Microbial Transformation of Iodine: From Radioisotopes to Iodine Deficiency. ADVANCES IN APPLIED MICROBIOLOGY 2017; 101:83-136. [PMID: 29050668 DOI: 10.1016/bs.aambs.2017.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Iodine is a biophilic element that is important for human health, both as an essential component of several thyroid hormones and, on the other hand, as a potential carcinogen in the form of radioiodine generated by anthropogenic nuclear activity. Iodine exists in multiple oxidation states (-1, 0, +1, +3, +5, and +7), primarily as molecular iodine (I2), iodide (I-), iodate [Formula: see text] , or organic iodine (org-I). The mobility of iodine in the environment is dependent on its speciation and a series of redox, complexation, sorption, precipitation, and microbial reactions. Over the last 15years, there have been significant advances in iodine biogeochemistry, largely spurred by renewed interest in the fate of radioiodine in the environment. We review the biogeochemistry of iodine, with particular emphasis on the microbial processes responsible for volatilization, accumulation, oxidation, and reduction of iodine, as well as the exciting technological potential of these fascinating microorganisms and enzymes.
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Liscombe DK, Louie GV, Noel JP. Architectures, mechanisms and molecular evolution of natural product methyltransferases. Nat Prod Rep 2012; 29:1238-50. [PMID: 22850796 DOI: 10.1039/c2np20029e] [Citation(s) in RCA: 208] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The addition of a methyl moiety to a small chemical is a common transformation in the biosynthesis of natural products across all three domains of life. These methylation reactions are most often catalysed by S-adenosyl-L-methionine (SAM)-dependent methyltransferases (MTs). MTs are categorized based on the electron-rich, methyl accepting atom, usually O, N, C, or S. SAM-dependent natural product MTs (NPMTs) are responsible for the modification of a wide array of structurally distinct substrates, including signalling and host defense compounds, pigments, prosthetic groups, cofactors, cell membrane and cell wall components, and xenobiotics. Most notably, methylation modulates the bioavailability, bioactivity, and reactivity of acceptor molecules, and thus exerts a central role on the functional output of many metabolic pathways. Our current understanding of the structural enzymology of NPMTs groups these phylogenetically diverse enzymes into two MT-superfamily fold classes (class I and class III). Structural biology has also shed light on the catalytic mechanisms and molecular bases for substrate specificity for over fifty NPMTs. These biophysical-based approaches have contributed to our understanding of NPMT evolution, demonstrating how a widespread protein fold evolved to accommodate chemically diverse methyl acceptors and to catalyse disparate mechanisms suited to the physiochemical properties of the target substrates. This evolutionary diversity suggests that NPMTs may serve as starting points for generating new biocatalysts.
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Affiliation(s)
- David K Liscombe
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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Glaser R, Prugger K. Iodine bonding stabilizes iodomethane in MIDAS pesticide. Theoretical study of intermolecular interactions between iodomethane and chloropicrin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:1776-1787. [PMID: 22313191 DOI: 10.1021/jf2037906] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The results are reported of a theoretical study of iodomethane (H(3)C-I, 1) and chloropicrin (Cl(3)C-NO(2), 2), of the heterodimers 3-6 formed by aggregation of 1 and 2, and of their addition products 7 and 8 and their possible fragmentation reactions to 9-18. Mixtures of iodomethane and chloropicrin are not expected to show chemistry resulting from their reactions with each other. The structures and stabilities are discussed of the iodine-bonded molecular aggregates (IBMA) 3 and 4 and of the hydrogen- and iodine-bonded molecular aggregates (IHBMA) 5 and 6. The mixed aggregates 3-5 are bound on the free enthalpy surface relative to the homodimers of 1 and 2, and the IBMA structures 3 and 4 are most stable. This result suggests that the mixture of chloropicrin and iodomethane in the pesticide Midas is a good choice to reduce the volatility of iodomethane because of thermodynamically stabilizing iodine bonding.
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Affiliation(s)
- Rainer Glaser
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States.
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