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Huang X, Liu X, Xue Y, Pan B, Xiao L, Wang S, Lever MA, Hinrichs KU, Inagaki F, Liu C. Methane Production by Facultative Anaerobic Wood-Rot Fungi via a New Halomethane-Dependent Pathway. Microbiol Spectr 2022; 10:e0170022. [PMID: 36102652 PMCID: PMC9604129 DOI: 10.1128/spectrum.01700-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/26/2022] [Indexed: 12/31/2022] Open
Abstract
The greenhouse gas methane (CH4) is of pivotal importance for Earth's climate system and as a human energy source. A significant fraction of this CH4 is produced by anaerobic Archaea. Here, we describe the first CH4 production by facultative anaerobic wood-rot fungi during growth on hydroxylated/carboxylated aromatic compounds, including lignin and lignite. The amount of CH4 produced by fungi is positively correlated with the amount of CH3Cl produced during the rapid growth period of the fungus. Biochemical, genetic, and stable isotopic tracer analyses reveal the existence of a novel halomethane-dependent fungal CH4 production pathway during the degradation of phenol and benzoic acid monomers and polymers and utilization of cyclic sugars. Even though this halomethane-dependent pathway may only play a side role in anaerobic fungal activity, it could represent a globally significant, previously overlooked source of biogenic CH4 in natural ecosystems. IMPORTANCE Here, we demonstrate that wood-rot fungi produce methane anaerobically without the involvement of methanogenic archaea via a new, halomethane-dependent pathway. These findings of an anaerobic fungal methane formation pathway open another avenue in methane research and will further assist with current efforts in the identification of the processes involved and their ecological implications.
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Affiliation(s)
- Xin Huang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Yarong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Bingcai Pan
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Lei Xiao
- School of Chemical Engineering and Technology, China University of Mining & Technology, Xuzhou, Jiangsu, China
| | - Shuijuan Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Mark A. Lever
- Department of Environmental Systems Science, ETH Zürich, Institute of Biogeochemistry and Pollutant Dynamics, Zürich, Switzerland
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Fumio Inagaki
- Mantle Drilling Promotion Office, Institute for Marine-Earth Exploration and Engineering (MarE3), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Japan
- Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Changhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
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2
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Kröber E, Wende S, Kanukollu S, Buchen-Tschiskale C, Besaury L, Keppler F, Vuilleumier S, Kolb S, Bringel F. 13 C-chloromethane incubations provide evidence for novel bacterial chloromethane degraders in a living tree fern. Environ Microbiol 2021; 23:4450-4465. [PMID: 34121306 DOI: 10.1111/1462-2920.15638] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/20/2022]
Abstract
Chloromethane (CH3 Cl) is the most abundant halogenated volatile organic compound in the atmosphere and contributes to stratospheric ozone depletion. CH3 Cl has mainly natural sources such as emissions from vegetation. In particular, ferns have been recognized as strong emitters. Mitigation of CH3 Cl to the atmosphere by methylotrophic bacteria, a global sink for this compound, is likely underestimated and remains poorly characterized. We identified and characterized CH3 Cl-degrading bacteria associated with intact and living tree fern plants of the species Cyathea australis by stable isotope probing (SIP) with 13 C-labelled CH3 Cl combined with metagenomics. Metagenome-assembled genomes (MAGs) related to Methylobacterium and Friedmanniella were identified as being involved in the degradation of CH3 Cl in the phyllosphere, i.e., the aerial parts of the tree fern, while a MAG related to Sorangium was linked to CH3 Cl degradation in the fern rhizosphere. The only known metabolic pathway for CH3 Cl degradation, via a methyltransferase system including the gene cmuA, was not detected in metagenomes or MAGs identified by SIP. Hence, a yet uncharacterized methylotrophic cmuA-independent pathway may drive CH3 Cl degradation in the investigated tree ferns.
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Affiliation(s)
- Eileen Kröber
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Sonja Wende
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Saranya Kanukollu
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Caroline Buchen-Tschiskale
- Isotope Biogeochemistry and Gas Fluxes, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Ludovic Besaury
- Génétique Moléculaire, Génomique, Microbiologie (GMGM), Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France
| | - Frank Keppler
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany
| | - Stéphane Vuilleumier
- Génétique Moléculaire, Génomique, Microbiologie (GMGM), Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France
| | - Steffen Kolb
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Françoise Bringel
- Génétique Moléculaire, Génomique, Microbiologie (GMGM), Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France
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3
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Kim S, Lee SH, Seo H, Kim KJ. Biochemical properties and crystal structure of formate-tetrahydrofolate ligase from Methylobacterium extorquens CM4. Biochem Biophys Res Commun 2020; 528:426-431. [PMID: 32505353 DOI: 10.1016/j.bbrc.2020.05.198] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 11/28/2022]
Abstract
Methylobacterium extorquens is a methylotroph model organism that has the ability to assimilate formate using the tetrahydrofolate (THF) pathway. The formate-tetrahydrofolate ligase from M. extorquens (MeFtfL) is an enzyme involved in the THF pathway that catalyzes the conversion of formate, THF, and ATP into formyltetrahydrofolate and ADP. To investigate the biochemical properties of MeFtfL, we evaluated the metal usage and enzyme kinetics of the enzyme. MeFtfL uses the Mg ion for catalytic activity, but also has activity for Mn and Ca ions. The enzyme kinetics analysis revealed that Km value of farmate was much higher than THF and ATP, which shows that the ligation activity of MeFtfL is highly dependent on formation concentration. We also determined the crystal structure of MeFtfL at 2.8 Å resolution. MeFtfL functions as a tetramer, and each monomer consists of three domains. The structural superposition of MeFtfL with FtfL from Moorella thermoacetica allowed us to predict the substrate binding site of the enzyme.
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Affiliation(s)
- Seongmin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seul Hoo Lee
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hogyun Seo
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea; Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Abstract
:In this review, we examined the possibility that some halogenated organic derivatives were used in the primitive ocean at the beginning of life on Earth. Firstly, we described the existence of extraterrestrial halogenated molecules, then we studied their nonbiological syntheses on the present Earth, especially in volcanic environments. In order to demonstrate the diversity of today’s halogenated biomolecules, representative examples are given and the biosynthesis of some of them is summarized. Finally, we proposed two aspects of the chemistry of halogenated compounds that may have been useful en route to biomolecules, firstly the use of methyl chloride as the first methylation reagent, secondly the synthesis and use of α-chloro-carbonyl derivatives.
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Affiliation(s)
- Sparta Youssef-Saliba
- Department of Molecular Chemistry, University Grenoble Alpes, CNRS, DCM, Campus, F-38058 Grenoble, France
| | - Yannick Vallée
- Department of Molecular Chemistry, University Grenoble Alpes, CNRS, DCM, Campus, F-38058 Grenoble, France
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5
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Keppler F, Barnes JD, Horst A, Bahlmann E, Luo J, Nadalig T, Greule M, Hartmann SC, Vuilleumier S. Chlorine Isotope Fractionation of the Major Chloromethane Degradation Processes in the Environment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:1634-1645. [PMID: 31880153 DOI: 10.1021/acs.est.9b06139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chloromethane (CH3Cl) is an important source of chlorine in the stratosphere, but detailed knowledge of the magnitude of its sources and sinks is missing. Here, we measured the stable chlorine isotope fractionation (εCl) associated with the major abiotic and biotic CH3Cl sinks in the environment, namely, CH3Cl degradation by hydroxyl (·OH) and chlorine (·Cl) radicals in the troposphere and by reference bacteria Methylorubrum extorquens CM4 and Leisingera methylohalidivorans MB2 from terrestrial and marine environments, respectively. No chlorine isotope fractionation was detected for reaction of CH3Cl with ·OH and ·Cl radicals, whereas a large chlorine isotope fractionation (εCl) of -10.9 ± 0.7‰ (n = 3) and -9.4 ± 0.9 (n = 3) was found for CH3Cl degradation by M. extorquens CM4 and L. methylohalidivorans MB2, respectively. The large difference in chlorine isotope fractionation observed between tropospheric and bacterial degradation of CH3Cl provides an effective isotopic tool to characterize and distinguish between major abiotic and biotic processes contributing to the CH3Cl sink in the environment. Our findings demonstrate the potential of emerging triple-element isotopic approaches including chlorine to carbon and hydrogen analysis for the assessment of global cycling of organochlorines.
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Affiliation(s)
- Frank Keppler
- Institute of Earth Sciences , Heidelberg University , Im Neuenheimer Feld 236 , 69120 Heidelberg , Germany
| | - Jaime D Barnes
- Department of Geological Sciences , University of Texas , Austin , Texas 78712 , United States
| | - Axel Horst
- Department of Isotope Biogeochemistry , Helmholtz Centre for Environmental Research - UFZ , Permoserstr.15 , 04318 Leipzig , Germany
| | - Enno Bahlmann
- Leibniz Institute for Baltic Sea Research Warnemünde , Seestrasse 15 , 18119 Rostock , Germany
| | - Jing Luo
- UMR 7156 CNRS Génétique Moléculaire, Génomique, Microbiologie , Université de Strasbourg , 4 allée Konrad Roentgen , 67000 Strasbourg , France
| | - Thierry Nadalig
- UMR 7156 CNRS Génétique Moléculaire, Génomique, Microbiologie , Université de Strasbourg , 4 allée Konrad Roentgen , 67000 Strasbourg , France
| | - Markus Greule
- Institute of Earth Sciences , Heidelberg University , Im Neuenheimer Feld 236 , 69120 Heidelberg , Germany
| | - S Christoph Hartmann
- Institute of Earth Sciences , Heidelberg University , Im Neuenheimer Feld 236 , 69120 Heidelberg , Germany
- Max Planck Institute for Chemistry , Hahn-Meitner-Weg 1 , 55128 Mainz , Germany
| | - Stéphane Vuilleumier
- UMR 7156 CNRS Génétique Moléculaire, Génomique, Microbiologie , Université de Strasbourg , 4 allée Konrad Roentgen , 67000 Strasbourg , France
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6
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Holland SI, Edwards RJ, Ertan H, Wong YK, Russell TL, Deshpande NP, Manefield MJ, Lee M. Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture. PeerJ 2019; 7:e7775. [PMID: 31592187 PMCID: PMC6778437 DOI: 10.7717/peerj.7775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/27/2019] [Indexed: 01/07/2023] Open
Abstract
Bacteria capable of dechlorinating the toxic environmental contaminant dichloromethane (DCM, CH2Cl2) are of great interest for potential bioremediation applications. A novel, strictly anaerobic, DCM-fermenting bacterium, "DCMF", was enriched from organochlorine-contaminated groundwater near Botany Bay, Australia. The enrichment culture was maintained in minimal, mineral salt medium amended with dichloromethane as the sole energy source. PacBio whole genome SMRTTM sequencing of DCMF allowed de novo, gap-free assembly despite the presence of cohabiting organisms in the culture. Illumina sequencing reads were utilised to correct minor indels. The single, circularised 6.44 Mb chromosome was annotated with the IMG pipeline and contains 5,773 predicted protein-coding genes. Based on 16S rRNA gene and predicted proteome phylogeny, the organism appears to be a novel member of the Peptococcaceae family. The DCMF genome is large in comparison to known DCM-fermenting bacteria. It includes an abundance of methyltransferases, which may provide clues to the basis of its DCM metabolism, as well as potential to metabolise additional methylated substrates such as quaternary amines. Full annotation has been provided in a custom genome browser and search tool, in addition to multiple sequence alignments and phylogenetic trees for every predicted protein, http://www.slimsuite.unsw.edu.au/research/dcmf/.
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Affiliation(s)
- Sophie I. Holland
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Haluk Ertan
- Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
- School of Chemical Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Yie Kuan Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Tonia L. Russell
- Ramaciotti Centre for Genomics, University of New South Wales, Sydney, New South Wales, Australia
| | - Nandan P. Deshpande
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael J. Manefield
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales, Australia
- School of Chemical Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew Lee
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales, Australia
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7
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Ghashghavi M, Belova SE, Bodelier PLE, Dedysh SN, Kox MAR, Speth DR, Frenzel P, Jetten MSM, Lücker S, Lüke C. Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments. mSphere 2019; 4:e00631-18. [PMID: 31167950 PMCID: PMC6553558 DOI: 10.1128/msphere.00631-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 05/09/2019] [Indexed: 01/08/2023] Open
Abstract
Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the Proteobacteria, Verrucomicrobia, and NC10 phyla. Within the Proteobacteria phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs (Methylococcus and Methylocaldum) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named "Methylotetracoccus oryzae" C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C16:1ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two pmoCAB operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems.IMPORTANCE Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions.
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Affiliation(s)
- Mohammad Ghashghavi
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Svetlana E Belova
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradski Institute of Microbiology, Moscow, Russia
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Svetlana N Dedysh
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradski Institute of Microbiology, Moscow, Russia
| | - Martine A R Kox
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Daan R Speth
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Peter Frenzel
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | - Sebastian Lücker
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Claudia Lüke
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
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8
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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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9
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Howat AM, Vollmers J, Taubert M, Grob C, Dixon JL, Todd JD, Chen Y, Kaster AK, Murrell JC. Comparative Genomics and Mutational Analysis Reveals a Novel XoxF-Utilizing Methylotroph in the Roseobacter Group Isolated From the Marine Environment. Front Microbiol 2018; 9:766. [PMID: 29755426 PMCID: PMC5934484 DOI: 10.3389/fmicb.2018.00766] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/04/2018] [Indexed: 11/13/2022] Open
Abstract
The Roseobacter group comprises a significant group of marine bacteria which are involved in global carbon and sulfur cycles. Some members are methylotrophs, using one-carbon compounds as a carbon and energy source. It has recently been shown that methylotrophs generally require a rare earth element when using the methanol dehydrogenase enzyme XoxF for growth on methanol. Addition of lanthanum to methanol enrichments of coastal seawater facilitated the isolation of a novel methylotroph in the Roseobacter group: Marinibacterium anthonyi strain La 6. Mutation of xoxF5 revealed the essential nature of this gene during growth on methanol and ethanol. Physiological characterization demonstrated the metabolic versatility of this strain. Genome sequencing revealed that strain La 6 has the largest genome of all Roseobacter group members sequenced to date, at 7.18 Mbp. Multilocus sequence analysis (MLSA) showed that whilst it displays the highest core gene sequence similarity with subgroup 1 of the Roseobacter group, it shares very little of its pangenome, suggesting unique genetic adaptations. This research revealed that the addition of lanthanides to isolation procedures was key to cultivating novel XoxF-utilizing methylotrophs from the marine environment, whilst genome sequencing and MLSA provided insights into their potential genetic adaptations and relationship to the wider community.
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Affiliation(s)
- Alexandra M. Howat
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - John Vollmers
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Carolina Grob
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - J. C. Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
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10
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Jaeger N, Besaury L, Kröber E, Delort AM, Greule M, Lenhart K, Nadalig T, Vuilleumier S, Amato P, Kolb S, Bringel F, Keppler F. Chloromethane Degradation in Soils: A Combined Microbial and Two-Dimensional Stable Isotope Approach. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:254-262. [PMID: 29634809 DOI: 10.2134/jeq2017.09.0358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Chloromethane (CHCl, methyl chloride) is the most abundant volatile halocarbon in the atmosphere and involved in stratospheric ozone depletion. The global CHCl budget, and especially the CHCl sink from microbial degradation in soil, still involves large uncertainties. These may potentially be resolved by a combination of stable isotope analysis and bacterial diversity studies. We determined the stable isotope fractionation of CHCl hydrogen and carbon and investigated bacterial diversity during CHCl degradation in three soils with different properties (forest, grassland, and agricultural soils) and at different temperatures and headspace mixing ratios of CHCl. The extent of chloromethane degradation decreased in the order forest > grassland > agricultural soil. Rates ranged from 0.7 to 2.5 μg g dry wt. d for forest soil, from 0.1 to 0.9 μg g dry wt. d for grassland soil, and from 0.1 to 0.4 μg g dry wt. d for agricultural soil and increased with increasing temperature and CHCl supplementation. The measured mean stable hydrogen enrichment factor of CHCl of -50 ± 13‰ was unaffected by temperature, mixing ratio, or soil type. In contrast, the stable carbon enrichment factor depended on CHCl degradation rates and ranged from -38 to -11‰. Bacterial community composition correlated with soil properties was independent from CHCl degradation or isotope enrichment. Nevertheless, increased abundance after CHCl incubation was observed in 21 bacterial operational taxonomical units (OTUs at the 97% 16S RNA sequence identity level). This suggests that some of these bacterial taxa, although not previously associated with CHCl degradation, may play a role in the microbial CHCl sink in soil.
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Correlated production and consumption of chloromethane in the Arabidopsis thaliana phyllosphere. Sci Rep 2017; 7:17589. [PMID: 29242530 PMCID: PMC5730606 DOI: 10.1038/s41598-017-17421-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/24/2017] [Indexed: 11/24/2022] Open
Abstract
Chloromethane (CH3Cl) is a toxic gas mainly produced naturally, in particular by plants, and its emissions contribute to ozone destruction in the stratosphere. Conversely, CH3Cl can be degraded and used as the sole carbon and energy source by specialised methylotrophic bacteria, isolated from a variety of environments including the phyllosphere, i.e. the aerial parts of vegetation. The potential role of phyllospheric CH3Cl-degrading bacteria as a filter for plant emissions of CH3Cl was investigated using variants of Arabidopsis thaliana with low, wild-type and high expression of HOL1 methyltransferase previously shown to be responsible for most of CH3Cl emissions by A. thaliana. Presence and expression of the bacterial chloromethane dehalogenase cmuA gene in the A. thaliana phyllosphere correlated with HOL1 genotype, as shown by qPCR and RT-qPCR. Production of CH3Cl by A. thaliana paralleled HOL1 expression, as assessed by a fluorescence-based bioreporter. The relation between plant production of CH3Cl and relative abundance of CH3Cl-degrading bacteria in the phyllosphere suggests that CH3Cl-degrading bacteria co-determine the extent of plant emissions of CH3Cl to the atmosphere.
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Chaignaud P, Maucourt B, Weiman M, Alberti A, Kolb S, Cruveiller S, Vuilleumier S, Bringel F. Genomic and Transcriptomic Analysis of Growth-Supporting Dehalogenation of Chlorinated Methanes in Methylobacterium. Front Microbiol 2017; 8:1600. [PMID: 28919881 PMCID: PMC5585157 DOI: 10.3389/fmicb.2017.01600] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 08/07/2017] [Indexed: 11/13/2022] Open
Abstract
Bacterial adaptation to growth with toxic halogenated chemicals was explored in the context of methylotrophic metabolism of Methylobacterium extorquens, by comparing strains CM4 and DM4, which show robust growth with chloromethane and dichloromethane, respectively. Dehalogenation of chlorinated methanes initiates growth-supporting degradation, with intracellular release of protons and chloride ions in both cases. The core, variable and strain-specific genomes of strains CM4 and DM4 were defined by comparison with genomes of non-dechlorinating strains. In terms of gene content, adaptation toward dehalogenation appears limited, strains CM4 and DM4 sharing between 75 and 85% of their genome with other strains of M. extorquens. Transcript abundance in cultures of strain CM4 grown with chloromethane and of strain DM4 grown with dichloromethane was compared to growth with methanol as a reference C1 growth substrate. Previously identified strain-specific dehalogenase-encoding genes were the most transcribed with chlorinated methanes, alongside other genes encoded by genomic islands (GEIs) and plasmids involved in growth with chlorinated compounds as carbon and energy source. None of the 163 genes shared by strains CM4 and DM4 but not by other strains of M. extorquens showed higher transcript abundance in cells grown with chlorinated methanes. Among the several thousand genes of the M. extorquens core genome, 12 genes were only differentially abundant in either strain CM4 or strain DM4. Of these, 2 genes of known function were detected, for the membrane-bound proton translocating pyrophosphatase HppA and the housekeeping molecular chaperone protein DegP. This indicates that the adaptive response common to chloromethane and dichloromethane is limited at the transcriptional level, and involves aspects of the general stress response as well as of a dehalogenation-specific response to intracellular hydrochloric acid production. Core genes only differentially abundant in either strain CM4 or strain DM4 total 13 and 58 CDS, respectively. Taken together, the obtained results suggest different transcriptional responses of chloromethane- and dichloromethane-degrading M. extorquens strains to dehalogenative metabolism, and substrate- and pathway-specific modes of growth optimization with chlorinated methanes.
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Affiliation(s)
- Pauline Chaignaud
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France.,Department of Ecological Microbiology, University of BayreuthBayreuth, Germany
| | - Bruno Maucourt
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France
| | - Marion Weiman
- UMR 8030 Centre National de la Recherche Scientifique-CEA, DSV/IG/Genoscope, LABGeMEvry, France
| | - Adriana Alberti
- UMR 8030 Centre National de la Recherche Scientifique-CEA, DSV/IG/Genoscope, LABGeMEvry, France
| | - Steffen Kolb
- Department of Ecological Microbiology, University of BayreuthBayreuth, Germany.,Institute of Landscape Biogeochemistry-Leibniz Centre for Agricultural Landscape Research (ZALF)Müncheberg, Germany
| | - Stéphane Cruveiller
- UMR 8030 Centre National de la Recherche Scientifique-CEA, DSV/IG/Genoscope, LABGeMEvry, France
| | - Stéphane Vuilleumier
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France
| | - Françoise Bringel
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France
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Michener JK, Vuilleumier S, Bringel F, Marx CJ. Transfer of a Catabolic Pathway for Chloromethane in Methylobacterium Strains Highlights Different Limitations for Growth with Chloromethane or with Dichloromethane. Front Microbiol 2016; 7:1116. [PMID: 27486448 PMCID: PMC4949252 DOI: 10.3389/fmicb.2016.01116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/04/2016] [Indexed: 11/14/2022] Open
Abstract
Chloromethane (CM) is an ozone-depleting gas, produced predominantly from natural sources, that provides an important carbon source for microbes capable of consuming it. CM catabolism has been difficult to study owing to the challenging genetics of its native microbial hosts. Since the pathways for CM catabolism show evidence of horizontal gene transfer, we reproduced this transfer process in the laboratory to generate new CM-catabolizing strains in tractable hosts. We demonstrate that six putative accessory genes improve CM catabolism, though heterologous expression of only one of the six is strictly necessary for growth on CM. In contrast to growth of Methylobacterium strains with the closely related compound dichloromethane (DCM), we find that chloride export does not limit growth on CM and, in general that the ability of a strain to grow on DCM is uncorrelated with its ability to grow on CM. This heterologous expression system allows us to investigate the components required for effective CM catabolism and the factors that limit effective catabolism after horizontal transfer.
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Affiliation(s)
- Joshua K Michener
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridge, MA, USA; Department of Organismic and Evolutionary Biology, Harvard UniversityCambridge, MA, USA; Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | | | | | - Christopher J Marx
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridge, MA, USA; Department of Biological Sciences, University of IdahoMoscow, ID, USA; Institute for Bioinformatics and Evolutionary Studies, University of IdahoMoscow, ID, USA; Center for Modeling Complex Interactions, University of IdahoMoscow, ID, USA
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14
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Ochsner AM, Sonntag F, Buchhaupt M, Schrader J, Vorholt JA. Methylobacterium extorquens: methylotrophy and biotechnological applications. Appl Microbiol Biotechnol 2014; 99:517-34. [PMID: 25432674 DOI: 10.1007/s00253-014-6240-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/14/2014] [Accepted: 11/16/2014] [Indexed: 01/06/2023]
Abstract
Methylotrophy is the ability to use reduced one-carbon compounds, such as methanol, as a single source of carbon and energy. Methanol is, due to its availability and potential for production from renewable resources, a valuable feedstock for biotechnology. Nature offers a variety of methylotrophic microorganisms that differ in their metabolism and represent resources for engineering of value-added products from methanol. The most extensively studied methylotroph is the Alphaproteobacterium Methylobacterium extorquens. Over the past five decades, the metabolism of M. extorquens has been investigated physiologically, biochemically, and more recently, using complementary omics technologies such as transcriptomics, proteomics, metabolomics, and fluxomics. These approaches, together with a genome-scale metabolic model, facilitate system-wide studies and the development of rational strategies for the successful generation of desired products from methanol. This review summarizes the knowledge of methylotrophy in M. extorquens, as well as the available tools and biotechnological applications.
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Affiliation(s)
- Andrea M Ochsner
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
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15
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Nadalig T, Greule M, Bringel F, Keppler F, Vuilleumier S. Probing the diversity of chloromethane-degrading bacteria by comparative genomics and isotopic fractionation. Front Microbiol 2014; 5:523. [PMID: 25360131 PMCID: PMC4197683 DOI: 10.3389/fmicb.2014.00523] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/19/2014] [Indexed: 11/13/2022] Open
Abstract
Chloromethane (CH3Cl) is produced on earth by a variety of abiotic and biological processes. It is the most important halogenated trace gas in the atmosphere, where it contributes to ozone destruction. Current estimates of the global CH3Cl budget are uncertain and suggest that microorganisms might play a more important role in degrading atmospheric CH3Cl than previously thought. Its degradation by bacteria has been demonstrated in marine, terrestrial, and phyllospheric environments. Improving our knowledge of these degradation processes and their magnitude is thus highly relevant for a better understanding of the global budget of CH3Cl. The cmu pathway, for chloromethane utilisation, is the only microbial pathway for CH3Cl degradation elucidated so far, and was characterized in detail in aerobic methylotrophic Alphaproteobacteria. Here, we reveal the potential of using a two-pronged approach involving a combination of comparative genomics and isotopic fractionation during CH3Cl degradation to newly address the question of the diversity of chloromethane-degrading bacteria in the environment. Analysis of available bacterial genome sequences reveals that several bacteria not yet known to degrade CH3Cl contain part or all of the complement of cmu genes required for CH3Cl degradation. These organisms, unlike bacteria shown to grow with CH3Cl using the cmu pathway, are obligate anaerobes. On the other hand, analysis of the complete genome of the chloromethane-degrading bacterium Leisingera methylohalidivorans MB2 showed that this bacterium does not contain cmu genes. Isotope fractionation experiments with L. methylohalidivorans MB2 suggest that the unknown pathway used by this bacterium for growth with CH3Cl can be differentiated from the cmu pathway. This result opens the prospect that contributions from bacteria with the cmu and Leisingera-type pathways to the atmospheric CH3Cl budget may be teased apart in the future.
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Affiliation(s)
- Thierry Nadalig
- Université de Strasbourg, Equipe Adaptations et Interactions Microbiennes dans l'Environnement, Unitès Mixtes de Recherche 7156 Centre National de la Recherche Scientifique, Génétique Moléculaire, Génomique, Microbiologie Strasbourg, France
| | - Markus Greule
- Institute of Earth Sciences, Ruprecht Karls University Heidelberg Heidelberg, Germany
| | - Françoise Bringel
- Université de Strasbourg, Equipe Adaptations et Interactions Microbiennes dans l'Environnement, Unitès Mixtes de Recherche 7156 Centre National de la Recherche Scientifique, Génétique Moléculaire, Génomique, Microbiologie Strasbourg, France
| | - Frank Keppler
- Institute of Earth Sciences, Ruprecht Karls University Heidelberg Heidelberg, Germany
| | - Stéphane Vuilleumier
- Université de Strasbourg, Equipe Adaptations et Interactions Microbiennes dans l'Environnement, Unitès Mixtes de Recherche 7156 Centre National de la Recherche Scientifique, Génétique Moléculaire, Génomique, Microbiologie Strasbourg, France
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Nadalig T, Greule M, Bringel F, Vuilleumier S, Keppler F. Hydrogen and carbon isotope fractionation during degradation of chloromethane by methylotrophic bacteria. Microbiologyopen 2013; 2:893-900. [PMID: 24019296 PMCID: PMC3892336 DOI: 10.1002/mbo3.124] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 07/10/2013] [Accepted: 07/21/2013] [Indexed: 01/12/2023] Open
Abstract
Chloromethane (CH3 Cl) is a widely studied volatile halocarbon involved in the destruction of ozone in the stratosphere. Nevertheless, its global budget still remains debated. Stable isotope analysis is a powerful tool to constrain fluxes of chloromethane between various environmental compartments which involve a multiplicity of sources and sinks, and both biotic and abiotic processes. In this study, we measured hydrogen and carbon isotope fractionation of the remaining untransformed chloromethane following its degradation by methylotrophic bacterial strains Methylobacterium extorquens CM4 and Hyphomicrobium sp. MC1, which belong to different genera but both use the cmu pathway, the only pathway for bacterial degradation of chloromethane characterized so far. Hydrogen isotope fractionation for degradation of chloromethane was determined for the first time, and yielded enrichment factors (ε) of -29‰ and -27‰ for strains CM4 and MC1, respectively. In agreement with previous studies, enrichment in (13) C of untransformed CH3 Cl was also observed, and similar isotope enrichment factors (ε) of -41‰ and -38‰ were obtained for degradation of chloromethane by strains CM4 and MC1, respectively. These combined hydrogen and carbon isotopic data for bacterial degradation of chloromethane will contribute to refine models of the global atmospheric budget of chloromethane.
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Affiliation(s)
- Thierry Nadalig
- Equipe Adaptations et Interactions Microbiennes dans l'Environnement, UMR 7156 Université de Strasbourg - CNRS, 28 rue Goethe, Strasbourg, 67083, France
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Fluorescence-based bacterial bioreporter for specific detection of methyl halide emissions in the environment. Appl Environ Microbiol 2013; 79:6561-7. [PMID: 23956392 DOI: 10.1128/aem.01738-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Methyl halides are volatile one-carbon compounds responsible for substantial depletion of stratospheric ozone. Among them, chloromethane (CH3Cl) is the most abundant halogenated hydrocarbon in the atmosphere. Global budgets of methyl halides in the environment are still poorly understood due to uncertainties in their natural sources, mainly from vegetation, and their sinks, which include chloromethane-degrading bacteria. A bacterial bioreporter for the detection of methyl halides was developed on the basis of detailed knowledge of the physiology and genetics of Methylobacterium extorquens CM4, an aerobic alphaproteobacterium which utilizes chloromethane as the sole source of carbon and energy. A plasmid construct with the promoter region of the chloromethane dehalogenase gene cmuA fused to a promotorless yellow fluorescent protein gene cassette resulted in specific methyl halide-dependent fluorescence when introduced into M. extorquens CM4. The bacterial whole-cell bioreporter allowed detection of methyl halides at femtomolar levels and quantification at concentrations above 10 pM (approximately 240 ppt). As shown for the model chloromethane-producing plant Arabidopsis thaliana in particular, the bioreporter may provide an attractive alternative to analytical chemical methods to screen for natural sources of methyl halide emissions.
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18
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Roselli S, Nadalig T, Vuilleumier S, Bringel F. The 380 kb pCMU01 plasmid encodes chloromethane utilization genes and redundant genes for vitamin B12- and tetrahydrofolate-dependent chloromethane metabolism in Methylobacterium extorquens CM4: a proteomic and bioinformatics study. PLoS One 2013; 8:e56598. [PMID: 23593113 PMCID: PMC3621897 DOI: 10.1371/journal.pone.0056598] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/11/2013] [Indexed: 12/24/2022] Open
Abstract
Chloromethane (CH3Cl) is the most abundant volatile halocarbon in the atmosphere and contributes to the destruction of stratospheric ozone. The only known pathway for bacterial chloromethane utilization (cmu) was characterized in Methylobacterium extorquens CM4, a methylotrophic bacterium able to utilize compounds without carbon-carbon bonds such as methanol and chloromethane as the sole carbon source for growth. Previous work demonstrated that tetrahydrofolate and vitamin B12 are essential cofactors of cmuA- and cmuB-encoded methyltransferases of chloromethane dehalogenase, and that the pathway for chloromethane utilization is distinct from that for methanol. This work reports genomic and proteomic data demonstrating that cognate cmu genes are located on the 380 kb pCMU01 plasmid, which drives the previously defined pathway for tetrahydrofolate-mediated chloromethane dehalogenation. Comparison of complete genome sequences of strain CM4 and that of four other M. extorquens strains unable to grow with chloromethane showed that plasmid pCMU01 harbors unique genes without homologs in the compared genomes (bluB2, btuB, cobA, cbiD), as well as 13 duplicated genes with homologs of chromosome-borne genes involved in vitamin B12-associated biosynthesis and transport, or in tetrahydrofolate-dependent metabolism (folC2). In addition, the presence of both chromosomal and plasmid-borne genes for corrinoid salvaging pathways may ensure corrinoid coenzyme supply in challenging environments. Proteomes of M. extorquens CM4 grown with one-carbon substrates chloromethane and methanol were compared. Of the 49 proteins with differential abundance identified, only five (CmuA, CmuB, PurU, CobH2 and a PaaE-like uncharacterized putative oxidoreductase) are encoded by the pCMU01 plasmid. The mainly chromosome-encoded response to chloromethane involves gene clusters associated with oxidative stress, production of reducing equivalents (PntAA, Nuo complex), conversion of tetrahydrofolate-bound one-carbon units, and central metabolism. The mosaic organization of plasmid pCMU01 and the clustering of genes coding for dehalogenase enzymes and for biosynthesis of associated cofactors suggests a history of gene acquisition related to chloromethane utilization.
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Affiliation(s)
- Sandro Roselli
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
| | - Thierry Nadalig
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
| | - Stéphane Vuilleumier
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
| | - Françoise Bringel
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
- * E-mail:
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Complete genome sequence of the chloromethane-degrading Hyphomicrobium sp. strain MC1. J Bacteriol 2011; 193:5035-6. [PMID: 21868803 DOI: 10.1128/jb.05627-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hyphomicrobium sp. strain MC1 is an aerobic methylotroph originally isolated from industrial sewage. This prosthecate bacterium was the first strain reported to grow with chloromethane as the sole carbon and energy source. Its genome, consisting of a single 4.76-Mb chromosome, is the first for a chloromethane-degrading bacterium to be formally reported.
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Halsey KH, Carter AE, Giovannoni SJ. Synergistic metabolism of a broad range of C1 compounds in the marine methylotrophic bacterium HTCC2181. Environ Microbiol 2011; 14:630-40. [PMID: 21981742 DOI: 10.1111/j.1462-2920.2011.02605.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The 1.3 Mbp genome of HTCC2181, a member of the abundant OM43 clade of coastal bacterioplankton, suggested it is an obligate methylotroph. Preliminary experiments demonstrated that methanol and formaldehyde, but not other common C1 compounds such as methylamine, could support growth. Methanol concentrations in seawater are reportedly < 100 nM, suggesting either that the flux of methanol through plankton pools is very rapid, or that methanol may not be the primary growth substrate for HTCC2181. Therefore, we investigated the apparent extreme substrate range restriction of HTCC2181 in greater detail. Growth rate and maximum cell density of HTCC2181 increased with methanol concentration, yielding a K(s) value of 19 µM. In contrast, no growth was observed in the presence of the methylated (C1) compounds, methyl chloride, trimethylamine-oxide (TMAO) or dimethylsulfoniopropionate (DMSP) when they were the sole substrates. However, growth rate, maximum cell density and cellular ATP content were significantly enhanced when any of these methylated compounds were provided in the presence of a limiting concentration of methanol. These observations fit a model in which the metabolic intermediate formaldehyde is required for net carbon assimilation, allowing C1 substrates that do not produce a formaldehyde intermediate to be oxidized for energy, but not assimilated into biomass. Rates of methanol and TMAO oxidation and assimilation were measured with (14)C-radiolabelled compounds in cultures of HTCC2181 and seawater microbial communities collected off the Oregon coast. The results indicated that in nature as well as in culture, C1 substrates are partitioned between those that are mainly oxidized to produce energy and those that are assimilated. These findings indicate that the combined fluxes of C1 compounds in coastal systems are sufficient to support significant populations of obligate methyltrophs by a metabolic strategy that involves the synergistic metabolism of multiple C1 compounds.
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Affiliation(s)
- Kimberly H Halsey
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA.
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21
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Bose A, Kulkarni G, Metcalf WW. Regulation of putative methyl-sulphide methyltransferases in Methanosarcina acetivorans C2A. Mol Microbiol 2009; 74:227-238. [PMID: 19732345 DOI: 10.1111/j.1365-2958.2009.06864.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The regulation of the Methanosarcina acetivorans mtsD, mtsF and mtsH genes, which encode putative corrinoid/methyltransferase isozymes involved in methylsulphide metabolism, was examined by a variety of methods, suggesting that their expression is regulated at both the transcriptional and post-transcriptional levels. Transcripts of all three genes, measured by quantitative reverse transcription PCR, were shown to be most abundant during growth on methanol with dimethylsulphide (DMS). Transcript levels were also high in media with CO or methylamines, but much lower with methanol. In contrast, translational fusions to mtsD showed high expression levels on CO or methanol with DMS, while the mtsF translational fusion showed highest reporter gene activity on methylamines with much lower expression on CO or methanol with DMS. The activity of mtsD and mtsF fusions was very low when the strains were grown in methanol or acetate. Expression of the mtsH fusion was not detected on any substrate, despite the presence of an mRNA transcript. The transcription start sites of all three genes were determined by 5'-RACE revealing large leader sequences for each transcript. Characterization of deletion mutants lacking putative regulatory genes suggests that MA0862 (msrF), MA4383 (msrC) and MA4560 (msrG) act as transcriptional activators of mtsD, mtsF and mtsH respectively.
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Affiliation(s)
- Arpita Bose
- Department of Microbiology, University of Illinois at Urbana-Champaign, B103 CLSL, 601 S. Goodwin, Urbana, IL 61801, USA
| | - Gargi Kulkarni
- Department of Microbiology, University of Illinois at Urbana-Champaign, B103 CLSL, 601 S. Goodwin, Urbana, IL 61801, USA
| | - William W Metcalf
- Department of Microbiology, University of Illinois at Urbana-Champaign, B103 CLSL, 601 S. Goodwin, Urbana, IL 61801, USA
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Oelgeschläger E, Rother M. In vivo role of three fused corrinoid/methyl transfer proteins in Methanosarcina acetivorans. Mol Microbiol 2009; 72:1260-72. [PMID: 19432805 DOI: 10.1111/j.1365-2958.2009.06723.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methanosarcina acetivorans is able to use carbon monoxide (CO) as the sole source of energy for growth. Its carboxidotrophic growth is peculiar as it involves formation of acetate, formate and methylated thiols, besides methane. Under this condition three proteins homologous to both corrinoid proteins and methyltransferases (MA0859, MA4384 and MA4558) are highly abundant. To address their role in M. acetivorans, a set of single and double mutants, and the triple mutant, was constructed by deletion/disruption of the encoding genes. Phenotypic analysis of the mutants rules out an important role of the methyltransferase homologues in the CO(2) reduction pathway of methanogenesis. Instead, the single and double mutants were affected to various degrees in their capacity to generate dimethylsulphide (DMS) from CO and to form methane from DMS. The triple mutant was unable to produce or metabolize DMS, and could not grow with DMS as the sole energy source, which demonstrates that MA0859, MA4384 and MA4558 are involved in, and required for, methylsulphide metabolism of M. acetivorans. Based on these findings we propose to designate MA0859, MA4384 and MA4558 as methyltransferases specific for methylsulphides, MtsD, MtsF and MtsH respectively.
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Affiliation(s)
- Ellen Oelgeschläger
- Molekulare Mikrobiologie und Bioenergetik, Institut für Molekulare Biowissenschaften, Goethe-Universität, Frankfurt am Main, Germany
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Abstract
This chapter reviews the literature on cobalamin- and corrinoid-containing enzymes. These enzymes fall into two broad classes, those using methylcobalamin or related methylcorrinoids as prosthetic groups and catalyzing methyl transfer reactions, and those using adenosylcobalamin as the prosthetic group and catalyzing the generation of substrate radicals that in turn undergo rearrangements and/or eliminations.
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Affiliation(s)
- Rowena G Matthews
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor MI 48109-2216, USA
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Ragsdale SW. Catalysis of methyl group transfers involving tetrahydrofolate and B(12). VITAMINS AND HORMONES 2008; 79:293-324. [PMID: 18804699 PMCID: PMC3037834 DOI: 10.1016/s0083-6729(08)00410-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review focuses on the reaction mechanism of enzymes that use B(12) and tetrahydrofolate (THF) to catalyze methyl group transfers. It also covers the related reactions that use B(12) and tetrahydromethanopterin (THMPT), which is a THF analog used by archaea. In the past decade, our understanding of the mechanisms of these enzymes has increased greatly because the crystal structures for three classes of B(12)-dependent methyltransferases have become available and because biophysical and kinetic studies have elucidated the intermediates involved in catalysis. These steps include binding of the cofactors and substrates, activation of the methyl donors and acceptors, the methyl transfer reaction itself, and product dissociation. Activation of the methyl donor in one class of methyltransferases is achieved by an unexpected proton transfer mechanism. The cobalt (Co) ion within the B(12) macrocycle must be in the Co(I) oxidation state to serve as a nucleophile in the methyl transfer reaction. Recent studies have uncovered important principles that control how this highly reducing active state of B(12) is generated and maintained.
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Affiliation(s)
- Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0606, USA
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25
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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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26
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Yu J, Smith G, Gross HB, Hansen RJ, Levenberg J, Walzem RL. Enzymatic O-methylation of flavanols changes lag time, propagation rate, and total oxidation during in vitro model triacylglycerol-rich lipoprotein oxidation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2006; 54:8403-8. [PMID: 17061813 DOI: 10.1021/jf060690b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
3'-O-Methyl derivatives of flavan-3-ols, (+)-catechin (C), (-)-epicatechin (EC), and (-)-catechin gallate (CG) were prepared enzymatically. Hexanal (EC and CG family, 5 mmol/L) and conjugated diene (C and EC family, 0.25-10 mmol/L) formation following CuSO4-mediated triacylglycerol-rich lipoprotein oxidation was measured. All EC and CG compounds significantly reduced hexanal formation (p < 0.02). O-Methylation improved the ability of CG (more polar) while reducing the ability of EC (less polar) to limit hexanal formation. 3'-O-methyl EC was 18% (p < 0.001) and 4'-O-methyl 65% (p < 0.001) less able than EC to suppress hexanal formation. At >1 micromol/L all EC and C compounds significantly increased lag time. Parent compounds were more effective (> 4-fold increase) than metabolites (1.5-fold increase). Parent compounds did not influence propagation rate (DeltaOD/min). At >1 mmol/L O-methylated EC and C reduced propagation by 20-40% (p < 0.01). Notably, at 0.25 mmol/L O-methylated EC and C increased propagation rates 22% (p < 0.01) despite prolonging lag time.
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Affiliation(s)
- Jun Yu
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas 77843, USA
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27
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Warner KL, Larkin MJ, Harper DB, Murrell JC, McDonald IR. Analysis of genes involved in methyl halide degradation in Aminobacter lissarensis CC495. FEMS Microbiol Lett 2006; 251:45-51. [PMID: 16102909 DOI: 10.1016/j.femsle.2005.07.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Revised: 07/17/2005] [Accepted: 07/19/2005] [Indexed: 11/29/2022] Open
Abstract
Aminobacter lissarensis CC495 is an aerobic facultative methylotroph capable of growth on glucose, glycerol, pyruvate and methylamine as well as the methyl halides methyl chloride and methyl bromide. Previously, cells grown on methyl chloride have been shown to express two polypeptides with apparent molecular masses of 67 and 29 kDa. The 67 kDa protein was purified and identified as a halomethane:bisulfide/halide ion methyltransferase. This study describes a single gene cluster in A. lissarensis CC495 containing the methyl halide utilisation genes cmuB, cmuA, cmuC, orf 188, paaE and hutI. The genes correspond to the same order and have a high similarity to a gene cluster found in Aminobacter ciceronei IMB-1 and Hyphomicrobium chloromethanicum strain CM2 indicating that genes encoding methyl halide degradation are highly conserved in these strains.
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Affiliation(s)
- Karen L Warner
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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28
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Borodina E, Cox MJ, McDonald IR, Murrell JC. Use of DNA-stable isotope probing and functional gene probes to investigate the diversity of methyl chloride-utilizing bacteria in soil. Environ Microbiol 2005; 7:1318-28. [PMID: 16104855 DOI: 10.1111/j.1462-5822.2005.00819.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Enrichment and isolation of methyl chloride-utilizing bacteria from various terrestrial environments, including woodland and forest soils, resulted in the identification of seven methyl chloride-utilizing strains belonging to the genus Hyphomicrobium, an Aminobacter strain TW23 and strain WG1, which grouped closely with the genus Mesorhizobium. Methyl chloride enrichment cultures were dominated by Hyphomicrobium species, indicating that these bacteria were most suited to growth under the enrichment and isolation conditions used. However, the application of culture-independent techniques such as DNA-stable isotope probing and the use of a functional gene probe targeting cmuA, which encodes the methyltransferase catalysing the first step in bacterial methyl chloride metabolism, indicated a greater diversity of methyl chloride-utilizing bacteria in the terrestrial environment, compared with the diversity of soil isolates obtained via the enrichment and isolation procedure. It also revealed the presence of as yet uncultured and potentially novel methyl chloride-degrading bacteria in soil.
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Affiliation(s)
- Elena Borodina
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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29
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Affiliation(s)
- Kenneth L Brown
- Department of Chemistry and Biochemistry, Ohio University, Athens, 45701, USA.
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30
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Borodina E, McDonald IR, Murrell JC. Chloromethane-dependent expression of the cmu gene cluster of Hyphomicrobium chloromethanicum. Appl Environ Microbiol 2004; 70:4177-86. [PMID: 15240299 PMCID: PMC444766 DOI: 10.1128/aem.70.7.4177-4186.2004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2004] [Accepted: 03/24/2004] [Indexed: 11/20/2022] Open
Abstract
The methylotrophic bacterium Hyphomicrobium chloromethanicum CM2 can utilize chloromethane (CH(3)Cl) as the sole carbon and energy source. Previously genes cmuB, cmuC, cmuA, and folD were shown to be essential for the growth of Methylobacterium chloromethanicum on CH(3)Cl. These CH(3)Cl-specific genes were subsequently detected in H. chloromethanicum. Transposon and marker exchange mutagenesis studies were carried out to identify the genes essential for CH(3)Cl metabolism in H. chloromethanicum. New developments in genetic manipulation of Hyphomicrobium are presented in this study. An electroporation protocol has been optimized and successfully applied for transformation of mutagenesis plasmids into H. chloromethanicum to generate stable CH(3)Cl-negative mutants. Both transposon and marker exchange mutageneses were highly applicable for genetic analysis of Hyphomicrobium. A reliable and reproducible selection procedure for screening of CH(3)Cl utilization-negative mutants has also been developed. Mutational inactivation of cmuB, cmuC, or hutI resulted in strains that were unable to utilize CH(3)Cl or to express the CH(3)Cl-dependent polypeptide CmuA. Reverse transcription-PCR analysis indicated that cmuB, cmuC, cmuA, fmdB, paaE, hutI, and metF formed a single cmuBCA-metF operon and were coregulated and coexpressed in H. chloromethanicum. This finding led to the conclusion that, in cmuB and cmuC mutants, impaired expression of cmuA was likely to be due to a polar effect of the defective gene (cmuB or cmuC) located upstream (5') of cmuA. The detrimental effect of mutation in hutI on the upstream (5')-located cmuA is not clear but indicated that all the genes located within the cmuBCA-metF operon are coordinately expressed. Expression of the cmuBCA-metF transcript was also shown to be strictly CH(3)Cl inducible and was not repressed by the alternative C(1) substrate methanol. Sequence analysis of a transposon mutant (D20) led to the discovery of the previously undetected hutI and metF genes located 3' of the paaE gene in H. chloromethanicum. MetF, a putative methylene-tetrahydrofolate reductase, had 27% identity to MetF from M. chloromethanicum. Mutational and transcriptional analysis data indicated that, in H. chloromethanicum, CH(3)Cl is metabolized via a corrinoid-specific (cmuA) and tetrahydrofolate-dependent (metF, purU, folD) methyltransfer system.
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Affiliation(s)
- Elena Borodina
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
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31
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Ballschmiter K. Pattern and sources of naturally produced organohalogens in the marine environment: biogenic formation of organohalogens. CHEMOSPHERE 2003; 52:313-24. [PMID: 12738255 DOI: 10.1016/s0045-6535(03)00211-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The pattern of organohalogens found in the marine environment is complex and includes compounds, only assignable to natural (chloromethane) or anthropogenic (hexachlorobenzene, PCBs) sources as well as compounds of a mixed origin (trichloromethane, halogenated methyl phenyl ether).The chemistry of the formation of natural organohalogens is summarized. The focus is put on volatile compounds carrying the halogens Cl, Br, and I, respectively. Though marine natural organohalogens are quite numerous as defined components, they are mostly not produced as major compounds. The most relevant in terms of global annual production is chloromethane (methyl chloride). The global atmospheric mixing ratio requires an annual production of 3.5-5 million tons per year. The chemistry of the group of haloperoxidases is discussed. Incubation experiments reveal that a wide spectrum of unknown compounds is formed in side reactions by haloperoxidases in pathways not yet understood.
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Affiliation(s)
- Karlheinz Ballschmiter
- Department of Analytical and Environmental Chemistry, University of Ulm, Albert-Einstein-Allee 11, D-89081 Ulm, Germany.
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32
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Studer A, McAnulla C, Büchele R, Leisinger T, Vuilleumier S. Chloromethane-induced genes define a third C1 utilization pathway in Methylobacterium chloromethanicum CM4. J Bacteriol 2002; 184:3476-84. [PMID: 12057941 PMCID: PMC135114 DOI: 10.1128/jb.184.13.3476-3484.2002] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2002] [Accepted: 03/27/2002] [Indexed: 11/20/2022] Open
Abstract
Methylobacterium chloromethanicum CM4 is an aerobic alpha-proteobacterium capable of growth with chloromethane as the sole carbon and energy source. Two proteins, CmuA and CmuB, were previously purified and shown to catalyze the dehalogenation of chloromethane and the vitamin B12-mediated transfer of the methyl group of chloromethane to tetrahydrofolate. Three genes located near cmuA and cmuB, designated metF, folD and purU and encoding homologs of methylene tetrahydrofolate (methylene-H4folate) reductase, methylene-H4folate dehydrogenase-methenyl-H4folate cyclohydrolase and formyl-H4folate hydrolase, respectively, suggested the existence of a chloromethane-specific oxidation pathway from methyl-tetrahydrofolate to formate in strain CM4. Hybridization and PCR analysis indicated that these genes were absent in Methylobacterium extorquens AM1, which is unable to grow with chloromethane. Studies with transcriptional xylE fusions demonstrated the chloromethane-dependent expression of these genes. Transcriptional start sites were mapped by primer extension and allowed to define three transcriptional units, each likely comprising several genes, that were specifically expressed during growth of strain CM4 with chloromethane. The DNA sequences of the deduced promoters display a high degree of sequence conservation but differ from the Methylobacterium promoters described thus far. As shown previously for purU, inactivation of the metF gene resulted in a CM4 mutant unable to grow with chloromethane. Methylene-H4folate reductase activity was detected in a cell extract of strain CM4 only in the presence of chloromethane but not in the metF mutant. Taken together, these data provide evidence that M. chloromethanicum CM4 requires a specific set of tetrahydrofolate-dependent enzymes for growth with chloromethane.
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Affiliation(s)
- Alex Studer
- Institut für Mikrobiologie, ETH Zürich, CH-8092 Zürich, Switzerland
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33
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Kayser MF, Ucurum Z, Vuilleumier S. Dichloromethane metabolism and C1 utilization genes in Methylobacterium strains. MICROBIOLOGY (READING, ENGLAND) 2002; 148:1915-1922. [PMID: 12055310 DOI: 10.1099/00221287-148-6-1915] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The ability of methylotrophic alpha-proteobacteria to grow with dichloromethane (DCM) as source of carbon and energy has long been thought to depend solely on a single cytoplasmic enzyme, DCM dehalogenase, which converts DCM to formaldehyde, a central intermediate of methylotrophic growth. The gene dcmA encoding DCM dehalogenase of Methylobacterium dichloromethanicum DM4 was expressed from a plasmid in closely related Methylobacterium strains lacking this enzyme. The ability to grow with DCM could be conferred upon Methylobacterium chloromethanicum CM4, a chloromethane degrader, but not upon Methylobacterium extorquens AM1. In addition, growth of strain AM1 with methanol was impaired in the presence of DCM. The possibility that single-carbon (C1) utilization pathways in dehalogenating Methylobacterium strains differed from those discovered in strain AM1 was addressed. Homologues of tetrahydrofolate-linked and tetrahydromethanopterin-linked C1 utilization genes of strain AM1 were detected in both strain DM4 and strain CM4, and cloning and sequencing of several of these genes from strain DM4 revealed very high sequence identity (96.5-99.7%) to the corresponding genes of strain AM1. The expression of transcriptional xylE fusions of selected genes of the tetrahydrofolate- and tetrahydromethanopterin-linked pathways from strain DM4 was investigated. The data obtained suggest that the expression levels of some C1 utilization genes in M. dichloromethanicum DM4 grown with DCM may differ from those observed during growth with methanol.
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Affiliation(s)
- Martin F Kayser
- Institut für Mikrobiologie, ETH Zürich, Schmelzbergstr. 7, CH-8092 Zürich, Switzerland1
| | - Zöhre Ucurum
- Institut für Mikrobiologie, ETH Zürich, Schmelzbergstr. 7, CH-8092 Zürich, Switzerland1
| | - Stéphane Vuilleumier
- Institut für Mikrobiologie, ETH Zürich, Schmelzbergstr. 7, CH-8092 Zürich, Switzerland1
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McDonald IR, Warner KL, McAnulla C, Woodall CA, Oremland RS, Murrell JC. A review of bacterial methyl halide degradation: biochemistry, genetics and molecular ecology. Environ Microbiol 2002; 4:193-203. [PMID: 12010126 DOI: 10.1046/j.1462-2920.2002.00290.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Methyl halide-degrading bacteria are a diverse group of organisms that are found in both terrestrial and marine environments. They potentially play an important role in mitigating ozone depletion resulting from methyl chloride and methyl bromide emissions. The first step in the pathway(s) of methyl halide degradation involves a methyltransferase and, recently, the presence of this pathway has been studied in a number of bacteria. This paper reviews the biochemistry and genetics of methyl halide utilization in the aerobic bacteria Methylobacterium chloromethanicum CM4T, Hyphomicrobium chloromethanicum CM2T, Aminobacter strain IMB-1 and Aminobacter strain CC495. These bacteria are able to use methyl halides as a sole source of carbon and energy, are all members of the alpha-Proteobacteria and were isolated from a variety of polluted and pristine terrestrial environments. An understanding of the genetics of these bacteria identified a unique gene (cmuA) involved in the degradation of methyl halides, which codes for a protein (CmuA) with unique methyltransferase and corrinoid functions. This unique functional gene, cmuA, is being used to develop molecular ecology techniques to examine the diversity and distribution of methyl halide-utilizing bacteria in the environment and hopefully to understand their role in methyl halide degradation in different environments. These techniques will also enable the detection of potentially novel methyl halide-degrading bacteria.
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Affiliation(s)
- I R McDonald
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
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