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Fulk EM, Gao X, Lu LC, Redeker KR, Masiello CA, Silberg JJ. Nondestructive Chemical Sensing within Bulk Soil Using 1000 Biosensors Per Gram of Matrix. ACS Synth Biol 2022; 11:2372-2383. [PMID: 35715210 DOI: 10.1021/acssynbio.2c00083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gene expression can be monitored in hard-to-image environmental materials using gas-reporting biosensors, but these outputs have only been applied in autoclaved matrices that are hydrated with rich medium. To better understand the compatibility of indicator gas reporting with environmental samples, we evaluated how matrix hydration affects the gas signal of an engineered microbe added to a sieved soil. A gas-reporting microbe presented a gas signal in a forest soil (Alfisol) when hydrated to an environmentally relevant osmotic pressure. When the gas signal was concentrated prior to analysis, a biosensor titer of 103 cells/gram of soil produced a significant signal when soil was supplemented with halides. A signal was also observed without halide amendment, but a higher cell titer (106 cells/gram of soil) was required. A sugar-regulated gas biosensor was able to report with a similar level of sensitivity when added to an unsterilized soil matrix, illustrating how gas concentration enables biosensing within a soil containing environmental microbes. These results establish conditions where engineered microbes can report on gene expression in living environmental matrices with decreased perturbation of the soil environment compared to previously reported approaches, using biosensor titers that are orders of magnitude lower than the number of cells typically observed in a gram of soil.
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Affiliation(s)
- Emily M Fulk
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, MS-180, Houston, Texas 77005, United States
| | - Xiaodong Gao
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States
| | - Li Chieh Lu
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Kelly R Redeker
- Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Caroline A Masiello
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States.,Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States.,Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, Texas 77005, United States
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2
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Fulk EM, Huh D, Atkinson JT, Lie M, Masiello CA, Silberg JJ. A Split Methyl Halide Transferase AND Gate That Reports by Synthesizing an Indicator Gas. ACS Synth Biol 2020; 9:3104-3113. [PMID: 33104325 DOI: 10.1021/acssynbio.0c00355] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Monitoring microbial reactions in highly opaque or autofluorescent environments like soils, seawater, and wastewater remains challenging. To develop a simple approach for observing post-translational reactions within microbes situated in environmental matrices, we designed a methyl halide transferase (MHT) fragment complementation assay that reports by synthesizing an indicator gas. We show that backbone fission within regions of high sequence variability in the Rossmann domain yields split MHT (sMHT) AND gates whose fragments cooperatively associate to synthesize CH3Br. Additionally, we identify a sMHT whose fragments require fusion to pairs of interacting partner proteins for maximal activity. We also show that sMHT fragments fused to FKBP12 and the FKBP-rapamycin binding domain of mTOR display significantly enhanced CH3Br production in the presence of rapamycin. This gas production is reversed in the presence of the competitive inhibitor of FKBP12/FKPB dimerization, indicating that sMHT is a reversible reporter of post-translational reactions. This sMHT represents the first genetic AND gate that reports on protein-protein interactions via an indicator gas. Because indicator gases can be measured in the headspaces of complex environmental samples, this assay should be useful for monitoring the dynamics of diverse molecular interactions within microbes situated in hard-to-image marine and terrestrial matrices.
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Affiliation(s)
- Emily M. Fulk
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, MS-180, Houston, Texas 77005, United States
| | - Dongkuk Huh
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Joshua T. Atkinson
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Margaret Lie
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Caroline A. Masiello
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
- Department of Earth, Environmental and Planetary Sciences, Rice University, MS 126, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Jonathan J. Silberg
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, Texas 77005, United States
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3
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Liao C, Seebeck FP. S-adenosylhomocysteine as a methyl transfer catalyst in biocatalytic methylation reactions. Nat Catal 2019. [DOI: 10.1038/s41929-019-0300-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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4
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Küpper FC, Miller EP, Andrews SJ, Hughes C, Carpenter LJ, Meyer-Klaucke W, Toyama C, Muramatsu Y, Feiters MC, Carrano CJ. Emission of volatile halogenated compounds, speciation and localization of bromine and iodine in the brown algal genome model Ectocarpus siliculosus. J Biol Inorg Chem 2018; 23:1119-1128. [PMID: 29523971 DOI: 10.1007/s00775-018-1539-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/28/2018] [Indexed: 11/25/2022]
Abstract
This study explores key features of bromine and iodine metabolism in the filamentous brown alga and genomics model Ectocarpus siliculosus. Both elements are accumulated in Ectocarpus, albeit at much lower concentration factors (2-3 orders of magnitude for iodine, and < 1 order of magnitude for bromine) than e.g. in the kelp Laminaria digitata. Iodide competitively reduces the accumulation of bromide. Both iodide and bromide are accumulated in the cell wall (apoplast) of Ectocarpus, with minor amounts of bromine also detectable in the cytosol. Ectocarpus emits a range of volatile halogenated compounds, the most prominent of which by far is methyl iodide. Interestingly, biosynthesis of this compound cannot be accounted for by vanadium haloperoxidase since the latter have not been found to catalyze direct halogenation of an unactivated methyl group or hydrocarbon so a methyl halide transferase-type production mechanism is proposed.
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Affiliation(s)
- Frithjof C Küpper
- Oceanlab, University of Aberdeen, Main Street, Newburgh, AB41 6AA, Scotland, UK.
- Dunstaffnage Marine Laboratory, Scottish Association for Marine Science, Oban, Argyll, PA37 1QA, Scotland, UK.
| | - Eric P Miller
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182-1030, USA
| | - Stephen J Andrews
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Claire Hughes
- Environment Department, University of York, York, YO10 5NG, UK
| | - Lucy J Carpenter
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Wolfram Meyer-Klaucke
- Department of Chemistry - Inorganic Chemistry, Faculty of Science, University of Paderborn, Warburger Strasse 100, 33098, Paderborn, Germany
| | - Chiaki Toyama
- Geological Survey of Japan, The National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan
| | - Yasuyuki Muramatsu
- Department of Chemistry, Faculty of Science, Gakushuin University, Toshima-Ku, Tokyo, 171-8588, Japan
| | - Martin C Feiters
- Department of Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Carl J Carrano
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182-1030, USA
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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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6
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Cheng HY, Masiello CA, Del Valle I, Gao X, Bennett GN, Silberg JJ. Ratiometric Gas Reporting: A Nondisruptive Approach To Monitor Gene Expression in Soils. ACS Synth Biol 2018; 7:903-911. [PMID: 29366321 DOI: 10.1021/acssynbio.7b00405] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Fluorescent proteins are ubiquitous tools that are used to monitor the dynamic functions of natural and synthetic genetic circuits. However, these visual reporters can only be used in transparent settings, a limitation that complicates nondisruptive measurements of gene expression within many matrices, such as soils and sediments. We describe a new ratiometric gas reporting method for nondisruptively monitoring gene expression within hard-to-image environmental matrices. With this approach, C2H4 is continuously synthesized by ethylene forming enzyme to provide information on viable cell number, and CH3Br is conditionally synthesized by placing a methyl halide transferase gene under the control of a conditional promoter. We show that ratiometric gas reporting enables the creation of Escherichia coli biosensors that report on acylhomoserine lactone (AHL) autoinducers used for quorum sensing by Gram-negative bacteria. Using these biosensors, we find that an agricultural soil decreases the bioavailable concentration of a long-chain AHL up to 100-fold. We also demonstrate that these biosensors can be used in soil to nondisruptively monitor AHLs synthesized by Rhizobium leguminosarum and degraded by Bacillus thuringiensis. Finally, we show that this new reporting approach can be used in Shewanella oneidensis, a bacterium that lives in sediments.
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7
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Keppler F, Fischer J, Sattler T, Polag D, Jaeger N, Schöler HF, Greule M. Chloromethane emissions in human breath. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 605-606:405-410. [PMID: 28672229 DOI: 10.1016/j.scitotenv.2017.06.202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 06/23/2017] [Accepted: 06/24/2017] [Indexed: 06/07/2023]
Abstract
Chloromethane (CH3Cl), currently the most abundant chlorinated organic compound in the atmosphere at around ~550 parts per trillion by volume (pptv), is considered responsible for approximately 16% of halogen-catalyzed stratospheric ozone destruction. Although emissions of CH3Cl are known to occur from animals such as cattle, formation and release of CH3Cl from humans has not yet been reported. In this study a pre-concentration unit coupled with a gas chromatograph directly linked to a mass spectrometer was used to precisely measure concentrations of CH3Cl at the pptv level in exhaled breath from 31 human subjects with ages ranging from 3 to 87years. We provide analytical evidence that all subjects exhaled CH3Cl in the range of 2.5 to 33 parts per billion by volume, levels which significantly exceed those of inhaled air by a factor of up to 60. If the mean of these emissions was typical for the world's population, then the global source of atmospheric CH3Cl from humans would be around 0.66Ggyr-1 (0.33 to 1.48Ggyr-1), which is less than 0.03% of the total annual global atmospheric source strength. The observed endogenous formation of a chlorinated methyl group in humans might be of interest to biochemists and medical scientists as CH3Cl is also known to be a potent methylating agent and thus, could be an important target compound in future medical research diagnostic programs.
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Affiliation(s)
- Frank Keppler
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 234-236, 69120 Heidelberg, Germany; Heidelberg Center for the Environment (HCE), Heidelberg University, D-69120 Heidelberg, Germany.
| | - Jan Fischer
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 234-236, 69120 Heidelberg, Germany
| | - Tobias Sattler
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 234-236, 69120 Heidelberg, Germany
| | - Daniela Polag
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 234-236, 69120 Heidelberg, Germany
| | - Nicole Jaeger
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 234-236, 69120 Heidelberg, Germany
| | - Heinz Friedrich Schöler
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 234-236, 69120 Heidelberg, Germany
| | - Markus Greule
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 234-236, 69120 Heidelberg, Germany
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8
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Cheng HY, Masiello CA, Bennett GN, Silberg JJ. Volatile Gas Production by Methyl Halide Transferase: An In Situ Reporter Of Microbial Gene Expression In Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:8750-8759. [PMID: 27415416 DOI: 10.1021/acs.est.6b01415] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Traditional visual reporters of gene expression have only very limited use in soils because their outputs are challenging to detect through the soil matrix. This severely restricts our ability to study time-dependent microbial gene expression in one of the Earth's largest, most complex habitats. Here we describe an approach to report on dynamic gene expression within a microbial population in a soil under natural water levels (at and below water holding capacity) via production of methyl halides using a methyl halide transferase. As a proof-of-concept application, we couple the expression of this gas reporter to the conjugative transfer of a bacterial plasmid in a soil matrix and show that gas released from the matrix displays a strong correlation with the number of transconjugant bacteria that formed. Gas reporting of gene expression will make possible dynamic studies of natural and engineered microbes within many hard-to-image environmental matrices (soils, sediments, sludge, and biomass) at sample scales exceeding those used for traditional visual reporting.
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Affiliation(s)
- Hsiao-Ying Cheng
- Department of Bioengineering, Rice University , 6100 Main Street, MS 142, Houston, Texas 77005, United States
| | - Caroline A Masiello
- Department of Earth Science, Rice University , 6100 Main Street, MS 126, Houston, Texas 77005, United States
- Department of Biosciences, Rice University , 6100 Main Street, MS 140, Houston, Texas 77005, United States
| | - George N Bennett
- Department of Biosciences, Rice University , 6100 Main Street, MS 140, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University , 6100 Main Street, MS 362, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of Bioengineering, Rice University , 6100 Main Street, MS 142, Houston, Texas 77005, United States
- Department of Biosciences, Rice University , 6100 Main Street, MS 140, Houston, Texas 77005, United States
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9
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Yang G, Ding Y. Recent advances in biocatalyst discovery, development and applications. Bioorg Med Chem 2014; 22:5604-12. [DOI: 10.1016/j.bmc.2014.06.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/13/2014] [Accepted: 06/17/2014] [Indexed: 12/25/2022]
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Straathof AJJ. Transformation of Biomass into Commodity Chemicals Using Enzymes or Cells. Chem Rev 2013; 114:1871-908. [DOI: 10.1021/cr400309c] [Citation(s) in RCA: 315] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Adrie J. J. Straathof
- Department of Biotechnology, Delft University of Technology, Julianalaan
67, 2628
BC Delft, The Netherlands
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11
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Toda H, Itoh N. Isolation and characterization of a gene encoding a S-adenosyl-l-methionine-dependent halide/thiol methyltransferase (HTMT) from the marine diatom Phaeodactylum tricornutum: Biogenic mechanism of CH(3)I emissions in oceans. PHYTOCHEMISTRY 2011; 72:337-343. [PMID: 21227473 DOI: 10.1016/j.phytochem.2010.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 11/19/2010] [Accepted: 12/03/2010] [Indexed: 05/27/2023]
Abstract
Several marine algae including diatoms exhibit S-adenosyl-l-methionine (SAM) halide/thiol methyltransferase (HTMT) activity, which is involved in the emission of methyl halides. In this study, the in vivo biogenic emission of methyl iodide from the diatom Phaeodactylum tricornutum was found to be clearly correlated with iodide concentration in the incubation media. The gene encoding HTMT (Pthtmt) was isolated from P. tricornutum CCAP 1055/1, and expressed in Escherichia coli. The molecular weight of the enzyme was 29.7kDa including a histidine tag, and the optimal pH was around pH 7.0. The kinetic properties of recombinant PtHTMT towards Cl(-), Br(-), I(-), [SH](-), [SCN](-), and SAM were 637.88mM, 72.83mM, 8.60mM, 9.92mM, 7.9mM, and 0.016mM, respectively, and were similar to those of higher-plant HTMTs, except that the activity towards thiocyanate was lower. The biogenic emission of methyl halides from the cultured cells and the enzymatic properties of HTMT suggest that the HMT/HTMT reaction is key to understanding the biogenesis of methyl halides in oceanic environments as well as terrestrial ones.
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Affiliation(s)
- Hiroshi Toda
- Department of Biotechnology, Faculty of Engineering, Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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12
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Paul C, Pohnert G. Production and role of volatile halogenated compounds from marine algae. Nat Prod Rep 2010; 28:186-95. [PMID: 21125112 DOI: 10.1039/c0np00043d] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Carsten Paul
- Friedrich Schiller University Jena, Department for Bioorganic Analytics, Lessingstraße 8, 07743, Jena, Germany
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Schmidberger JW, James AB, Edwards R, Naismith JH, O’Hagan D. Halomethane biosynthesis: structure of a SAM-dependent halide methyltransferase from Arabidopsis thaliana. Angew Chem Int Ed Engl 2010; 49:3646-8. [PMID: 20376845 PMCID: PMC3386781 DOI: 10.1002/anie.201000119] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A product structure of the halomethane producing enzyme in plants (Arabidopsis thaliana ) is reported and a model for presentation of chloride/bromide ion to the methyl group of S-adenosyl-L-methionine (SAM) is presented to rationalise nucleophilic halide attack for halomethane production, gaseous natural products that are produced globally.
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Affiliation(s)
- Jason W. Schmidberger
- University of St Andrews, Department of Chemistry, Centre for Biomolecular Sciences, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | | | - Robert Edwards
- University of Durham, School of Biological & Medical Sciences, South Road, Durham, DH1 3LE, UK Fax: (+44) 191 3341201
| | - James H. Naismith
- University of St Andrews, Department of Chemistry, Centre for Biomolecular Sciences, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - David O’Hagan
- University of St Andrews, Department of Chemistry, Centre for Biomolecular Sciences, North Haugh, St Andrews, Fife, KY16 9ST, UK
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14
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Schmidberger J, James A, Edwards R, Naismith J, O'Hagan D. Halomethane Biosynthesis: Structure of a SAM-Dependent Halide Methyltransferase from Arabidopsis thaliana. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000119] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Affiliation(s)
- Lowell P Hager
- Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
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16
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Itoh N, Toda H, Matsuda M, Negishi T, Taniguchi T, Ohsawa N. Involvement of S-adenosylmethionine-dependent halide/thiol methyltransferase (HTMT) in methyl halide emissions from agricultural plants: isolation and characterization of an HTMT-coding gene from Raphanus sativus (daikon radish). BMC PLANT BIOLOGY 2009; 9:116. [PMID: 19723322 PMCID: PMC2752461 DOI: 10.1186/1471-2229-9-116] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 09/01/2009] [Indexed: 05/20/2023]
Abstract
BACKGROUND Biogenic emissions of methyl halides (CH3Cl, CH3Br and CH3I) are the major source of these compounds in the atmosphere; however, there are few reports about the halide profiles and strengths of these emissions. Halide ion methyltransferase (HMT) and halide/thiol methyltransferase (HTMT) enzymes concerning these emissions have been purified and characterized from several organisms including marine algae, fungi, and higher plants; however, the correlation between emission profiles of methyl halides and the enzymatic properties of HMT/HTMT, and their role in vivo remains unclear. RESULTS Thirty-five higher plant species were screened, and high CH3I emissions and HMT/HTMT activities were found in higher plants belonging to the Poaceae family, including wheat (Triticum aestivum L.) and paddy rice (Oryza sativa L.), as well as the Brassicaceae family, including daikon radish (Raphanus sativus). The in vivo emission of CH3I clearly correlated with HMT/HTMT activity. The emission of CH3I from the sprouting leaves of R. sativus, T. aestivum and O. sativa grown hydroponically increased with increasing concentrations of supplied iodide. A gene encoding an S-adenosylmethionine halide/thiol methyltransferase (HTMT) was cloned from R. sativus and expressed in Escherichia coli as a soluble protein. The recombinant R. sativus HTMT (RsHTMT) was revealed to possess high specificity for iodide (I-), bisulfide ([SH]-), and thiocyanate ([SCN]-) ions. CONCLUSION The present findings suggest that HMT/HTMT activity is present in several families of higher plants including Poaceae and Brassicaceae, and is involved in the formation of methyl halides. Moreover, it was found that the emission of methyl iodide from plants was affected by the iodide concentration in the cultures. The recombinant RsHTMT demonstrated enzymatic properties similar to those of Brassica oleracea HTMT, especially in terms of its high specificity for iodide, bisulfide, and thiocyanate ions. A survey of biogenic emissions of methyl halides strongly suggests that the HTM/HTMT reaction is the key to understanding the biogenesis of methyl halides and methylated sulfur compounds in nature.
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Affiliation(s)
- Nobuya Itoh
- Department of Biotechnology, Faculty of Engineering (Biotechnology Research Center), Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Hiroshi Toda
- Department of Biotechnology, Faculty of Engineering (Biotechnology Research Center), Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Michiko Matsuda
- Department of Biotechnology, Faculty of Engineering (Biotechnology Research Center), Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Takashi Negishi
- Department of Biotechnology, Faculty of Engineering (Biotechnology Research Center), Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Tomokazu Taniguchi
- Department of Biotechnology, Faculty of Engineering (Biotechnology Research Center), Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Noboru Ohsawa
- Department of Biotechnology, Faculty of Engineering (Biotechnology Research Center), Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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17
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Bayer TS, Widmaier DM, Temme K, Mirsky EA, Santi DV, Voigt CA. Synthesis of methyl halides from biomass using engineered microbes. J Am Chem Soc 2009; 131:6508-15. [PMID: 19378995 DOI: 10.1021/ja809461u] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methyl halides are used as agricultural fumigants and are precursor molecules that can be catalytically converted to chemicals and fuels. Plants and microorganisms naturally produce methyl halides, but these organisms produce very low yields or are not amenable to industrial production. A single methyl halide transferase (MHT) enzyme transfers the methyl group from the ubiquitous metabolite S-adenoyl methionine (SAM) to a halide ion. Using a synthetic metagenomic approach, we chemically synthesized all 89 putative MHT genes from plants, fungi, bacteria, and unidentified organisms present in the NCBI sequence database. The set was screened in Escherichia coli to identify the rates of CH(3)Cl, CH(3)Br, and CH(3)I production, with 56% of the library active on chloride, 85% on bromide, and 69% on iodide. Expression of the highest activity MHT and subsequent engineering in Saccharomyces cerevisiae results in productivity of 190 mg/L-h from glucose and sucrose. Using a symbiotic co-culture of the engineered yeast and the cellulolytic bacterium Actinotalea fermentans, we are able to achieve methyl halide production from unprocessed switchgrass (Panicum virgatum), corn stover, sugar cane bagasse, and poplar (Populus sp.). These results demonstrate the potential of producing methyl halides from non-food agricultural resources.
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Affiliation(s)
- Travis S Bayer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, MC 2540, Room 408C, 1700 4th Street, San Francisco, California 94158-2330, USA
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18
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Nagatoshi Y, Nakamura T. Arabidopsis HARMLESS TO OZONE LAYER protein methylates a glucosinolate breakdown product and functions in resistance to Pseudomonas syringae pv. maculicola. J Biol Chem 2009; 284:19301-9. [PMID: 19419967 DOI: 10.1074/jbc.m109.001032] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Almost all of the chlorine-containing gas emitted from natural sources is methyl chloride (CH(3)Cl), which contributes to the destruction of the stratospheric ozone layer. Tropical and subtropical plants emit substantial amounts of CH(3)Cl. A gene involved in CH(3)Cl emission from Arabidopsis was previously identified and designated HARMLESS TO OZONE LAYER (hereafter AtHOL1) based on the mutant phenotype. Our previous studies demonstrated that AtHOL1 and its homologs, AtHOL2 and AtHOL3, have S-adenosyl-l-methionine-dependent methyltransferase activities. However, the physiological functions of AtHOLs have yet to be elucidated. In the present study, our comparative kinetic analyses with possible physiological substrates indicated that all of the AtHOLs have low activities toward chloride. AtHOL1 was highly reactive to thiocyanate (NCS(-)), a pseudohalide, synthesizing methylthiocyanate (CH(3)SCN) with a very high k(cat)/K(m) value. We demonstrated in vivo that substantial amounts of NCS(-) were synthesized upon tissue damage in Arabidopsis and that NCS(-) was largely derived from myrosinase-mediated hydrolysis of glucosinolates. Analyses with the T-DNA insertion Arabidopsis mutants (hol1, hol2, and hol3) revealed that only hol1 showed increased sensitivity to NCS(-) in medium and a concomitant lack of CH(3)SCN synthesis upon tissue damage. Bacterial growth assays indicated that the conversion of NCS(-) into CH(3)SCN dramatically increased antibacterial activities against Arabidopsis pathogens that normally invade the wound site. Furthermore, hol1 seedlings showed an increased susceptibility toward an Arabidopsis pathogen, Pseudomonas syringae pv. maculicola. Here we propose that AtHOL1 is involved in glucosinolate metabolism and defense against phytopathogens. Moreover, CH(3)Cl synthesized by AtHOL1 could be considered a byproduct of NCS(-) metabolism.
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Affiliation(s)
- Yukari Nagatoshi
- Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa 240-8501, Japan
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19
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20
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Eustáquio AS, Pojer F, Noel JP, Moore BS. Discovery and characterization of a marine bacterial SAM-dependent chlorinase. Nat Chem Biol 2007; 4:69-74. [PMID: 18059261 PMCID: PMC2762381 DOI: 10.1038/nchembio.2007.56] [Citation(s) in RCA: 160] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Accepted: 10/25/2007] [Indexed: 11/09/2022]
Abstract
Halogen atom incorporation into a scaffold of bioactive compounds often amplifies biological activity, as is the case for the anticancer agent salinosporamide A (1), a chlorinated natural product from the marine bacterium Salinispora tropica. Significant effort in understanding enzymatic chlorination shows that oxidative routes predominate to form reactive electrophilic or radical chlorine species. Here we report the genetic, biochemical and structural characterization of the chlorinase SalL, which halogenates S-adenosyl-L-methionine (2) with chloride to generate 5'-chloro-5'-deoxyadenosine (3) and L-methionine (4) in a rarely observed nucleophilic substitution strategy analogous to that of Streptomyces cattleya fluorinase. Further metabolic tailoring produces a halogenated polyketide synthase substrate specific for salinosporamide A biosynthesis. SalL also accepts bromide and iodide as substrates, but not fluoride. High-resolution crystal structures of SalL and active site mutants complexed with substrates and products support the S(N)2 nucleophilic substitution mechanism and further illuminate halide specificity in this newly discovered halogenase family.
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Affiliation(s)
- Alessandra S Eustáquio
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
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21
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Vaillancourt FH, Yeh E, Vosburg DA, Garneau-Tsodikova S, Walsh CT. Nature's inventory of halogenation catalysts: oxidative strategies predominate. Chem Rev 2007; 106:3364-78. [PMID: 16895332 DOI: 10.1021/cr050313i] [Citation(s) in RCA: 402] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Frédéric H Vaillancourt
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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22
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Schäfer H, Miller LG, Oremland RS, Murrell JC. Bacterial Cycling of Methyl Halides. ADVANCES IN APPLIED MICROBIOLOGY 2007; 61:307-46. [PMID: 17448794 DOI: 10.1016/s0065-2164(06)61009-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Hendrik Schäfer
- Department of Biological Sciences, University of Warwick, Coventry, United Kingdom
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23
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Deng H, Cobb SL, McEwan AR, McGlinchey RP, Naismith JH, O'Hagan D, Robinson DA, Spencer JB. The Fluorinase fromStreptomyces cattleya Is Also a Chlorinase. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200503582] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Deng H, Cobb SL, McEwan AR, McGlinchey RP, Naismith JH, O’Hagan D, Robinson DA, Spencer JB. The fluorinase from Streptomyces cattleya is also a chlorinase. Angew Chem Int Ed Engl 2006; 45:759-62. [PMID: 16370017 PMCID: PMC3314195 DOI: 10.1002/anie.200503582] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | | | | | | | - David O’Hagan
- Dr. H. Deng, Dr. S. L. Cobb, A. R. McEwan, R. P. McGlinchey, Prof. Dr. J. H. Naismith, Prof. Dr. D. O’Hagan, Dr. D. A. Robinson, School of Chemistry and Centre for Biomolecular Science, University of St Andrews, St Andrews, KY16 9ST (UK), Fax: (+ 44)1334-463-808, ; Dr. J. B. Spencer, Chemistry Laboratories, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW (UK)
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25
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Rhew RC, Østergaard L, Saltzman ES, Yanofsky MF. Genetic control of methyl halide production in Arabidopsis. Curr Biol 2004; 13:1809-13. [PMID: 14561407 DOI: 10.1016/j.cub.2003.09.055] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Methyl chloride (CH(3)Cl) and methyl bromide (CH(3)Br) are the primary carriers of natural chlorine and bromine, respectively, to the stratosphere, where they catalyze the destruction of ozone, whereas methyl iodide (CH(3)I) influences aerosol formation and ozone loss in the boundary layer. CH(3)Br is also an agricultural pesticide whose use is regulated by international agreement. Despite the economic and environmental importance of these methyl halides, their natural sources and biological production mechanisms are poorly understood. Besides CH(3)Br fumigation, important sources include oceans, biomass burning, tropical plants, salt marshes, and certain crops and fungi. Here, we demonstrate that the model plant Arabidopsis thaliana produces and emits methyl halides and that the enzyme primarily responsible for the production is encoded by the HARMLESS TO OZONE LAYER (HOL) gene. The encoded protein belongs to a group of methyltransferases capable of catalyzing the S-adenosyl-L-methionine (SAM)-dependent methylation of chloride (Cl(-)), bromide (Br(-)), and iodide (I(-)) to produce methyl halides. In mutant plants with the HOL gene disrupted, methyl halide production is largely eliminated. A phylogenetic analysis with the HOL gene suggests that the ability to produce methyl halides is widespread among vascular plants. This approach provides a genetic basis for understanding and predicting patterns of methyl halide production by plants.
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Affiliation(s)
- Robert C Rhew
- Department of Earth System Science, University of California, Irvine, Irvine, CA 92697-3100, USA.
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26
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Attieh J, Djiana R, Koonjul P, Etienne C, Sparace SA, Saini HS. Cloning and functional expression of two plant thiol methyltransferases: a new class of enzymes involved in the biosynthesis of sulfur volatiles. PLANT MOLECULAR BIOLOGY 2002; 50:511-21. [PMID: 12369626 DOI: 10.1023/a:1019865829534] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Glucosinolates are defensive compounds found in several plant families. We recently described five distinct isoforms of a novel plant enzyme, thiol methyltransferase (TMT), which methylate the hydrolysis products of glucosinolates to volatile sulfur compounds that have putative anti-insect and anti-pathogen roles. In the work presented here, two cDNAs encoding these enzymes (cTMT1 and cTMT2) were isolated by screening a cabbage cDNA library with an Arabidopsis EST showing high sequence homology to one TMT isoform. The genomic clone of cTMT1 was subsequently amplified by PCR. Both cDNAs encoded polypeptides of identical lengths (227 amino acids) and similar predicted masses (ca. 25 kDa), but differing in 13 residues. The cDNAs contained the typical methyltransferase signatures, but were otherwise distinct from conventionally known N-, O- or S-methyltransferases. A chloride methyl transferase was the only gene with an assigned function that shared significant similarity with the TMT cDNAs. Southern analysis indicated single copy for each TMT gene. The two cDNAs were expressed in Escherichia coli. The substrate range, kinetic properties and molecular sizes of the purified recombinant proteins were comparable to those of the native enzyme. These data, together with the detection of the sequenced amino acid motif of one native TMT peptide in the cDNAs, confirmed that the latter were authentic TMTs. The expression pattern of the TMTs in various cabbage tissues was consistent with their association with glucosinolates. The cloning of this new class of plant genes furnishes crucial molecular tools to understand the role of this metabolic sector in plant defenses against biotic stress.
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MESH Headings
- Amino Acid Sequence
- Brassica/enzymology
- Brassica/genetics
- Brassica/metabolism
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Escherichia coli/genetics
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Plant
- Genes, Plant/genetics
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Molecular Sequence Data
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sulfur Compounds/metabolism
- Volatilization
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Affiliation(s)
- Jihad Attieh
- Institut de recherche en biologie végétale, Université de Montréal, Quebec, Canada
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27
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Ohsawa N, Tsujita M, Morikawa S, Itoh N. Purification and characterization of a monohalomethane-producing enzyme S-adenosyl-L-methionine: halide ion methyltransferase from a marine microalga, Pavlova pinguis. Biosci Biotechnol Biochem 2001; 65:2397-404. [PMID: 11791711 DOI: 10.1271/bbb.65.2397] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A monohalomethane-producing enzyme, S-adenosyl-L-methionine-dependent halide ion methyltransferase (EC 2.1.1.-) was purified from the marine microalga Pavlova pinguis by two anion exchange, hydroxyapatite and gel filtration chromatographies. The methyltransferase was a monomeric molecule having a molecular weight of 29,000. The enzyme had an isoelectric point at 5.3, and was optimally active at pH 8.0. The Km for iodide and SAM were 12 mM and 12 microM, respectively, which were measured using a partially purified enzyme. Various metal ions had no significant effect on methyl iodide production, suggesting that the enzyme does not require metal ions. The enzyme reaction strictly depended on SAM as a methyl donor, and the enzyme catalyzed methylation of the I-, Br-, and Cl- to corresponding monohalomethanes and of bisulfide to methyl mercaptan.
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Affiliation(s)
- N Ohsawa
- Biotechnology Research Center, Toyama Prefectural University, Japan
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