1
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Pan-genome Analysis Reveals Comparative Genomic Features of Central Metabolic Pathways in Methylorubrum extorquens. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0154-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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2
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Benninghaus L, Walter T, Mindt M, Risse JM, Wendisch VF. Metabolic Engineering of Pseudomonas putida for Fermentative Production of l-Theanine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:9849-9858. [PMID: 34465093 DOI: 10.1021/acs.jafc.1c03240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
N-alkylated amino acids are intermediates of natural biological pathways and can be found incorporated in peptides or have physiological roles in their free form. The N-ethylated amino acid l-theanine shows taste-enhancing properties and health benefits. It naturally occurs in green tea as major free amino acid. Isolation of l-theanine from Camilla sinensis shows low efficiency, and chemical synthesis results in a racemic mixture. Therefore, biochemical approaches for the production of l-theanine gain increasing interest. Here, we describe metabolic engineering of Pseudomonas putida KT2440 for the fermentative production of l-theanine from monoethylamine and carbon sources glucose, glycerol, or xylose using heterologous enzymes from Methylorubrum extorquens for l-theanine production and heterologous enzymes from Caulobacter crescentus for growth with xylose. l-Theanine (15.4 mM) accumulated in shake flasks with minimal medium containing monoethylamine and glucose, 15.2 mM with glycerol and 7 mM with xylose. Fed-batch bioreactor cultures yielded l-theanine titers of 10 g L-1 with glucose plus xylose, 17.2 g L-1 with glycerol, 4 g L-1 with xylose, and 21 g L-1 with xylose plus glycerol, respectively. To the best of our knowledge, this is the first l-theanine process using P. putida and the first compatible with the use of various alternative carbon sources.
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Affiliation(s)
- Leonie Benninghaus
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld 33615, Germany
| | - Tatjana Walter
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld 33615, Germany
| | - Melanie Mindt
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld 33615, Germany
| | - Joe Max Risse
- Fermentation Technology, Technical Faculty and CeBiTec, Bielefeld University, Bielefeld 33615, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld 33615, Germany
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3
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Molecular Docking and Site-Directed Mutagenesis of Dichloromethane Dehalogenase to Improve Enzyme Activity for Dichloromethane Degradation. Appl Biochem Biotechnol 2019; 190:487-505. [DOI: 10.1007/s12010-019-03106-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/18/2019] [Indexed: 10/26/2022]
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4
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Mindt M, Walter T, Risse JM, Wendisch VF. Fermentative Production of N-Methylglutamate From Glycerol by Recombinant Pseudomonas putida. Front Bioeng Biotechnol 2018; 6:159. [PMID: 30474025 PMCID: PMC6237917 DOI: 10.3389/fbioe.2018.00159] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/16/2018] [Indexed: 12/02/2022] Open
Abstract
N-methylated amino acids are present in diverse biological molecules in bacteria, archaea and eukaryotes. There is an increasing interest in this molecular class of alkylated amino acids by the pharmaceutical and chemical industries. N-alkylated amino acids have desired functions such as higher proteolytic stability, enhanced membrane permeability and longer peptide half-lives, which are important for the peptide-based drugs, the so-called peptidomimetics. Chemical synthesis of N-methylated amino acids often is limited by incomplete stereoselectivity, over-alkylation or the use of hazardous chemicals. Here, we describe metabolic engineering of Pseudomonas putida KT2440 for the fermentative production of N-methylglutamate from simple carbon sources and monomethylamine. P. putida KT2440, which is generally recognized as safe and grows with glucose and the alternative feedstock glycerol as sole carbon and energy source, was engineered for the production of N-methylglutamate using heterologous enzymes from Methylobacterium extorquens. About 3.9 g L−1N-methylglutamate accumulated within 48 h in shake flask cultures with minimal medium containing monomethylamine and glycerol. A fed-batch cultivation process yielded a N-methylglutamate titer of 17.9 g L−1.
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Affiliation(s)
- Melanie Mindt
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Tatjana Walter
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Joe Max Risse
- Fermentation Technology, Technical Faculty and CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
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5
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Park C, Lee YS, Park SY, Park W. Methylobacterium currus sp. nov., isolated from a car air conditioning system. Int J Syst Evol Microbiol 2018; 68:3621-3626. [DOI: 10.1099/ijsem.0.003045] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Chulwoo Park
- 1Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Yun Suk Lee
- 1Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - So-yoon Park
- 2Thermal Management Research Lab, Hyundai Motor Group, Seoul, Republic of Korea
| | - Woojun Park
- 1Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
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6
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N-terminome and proteogenomic analysis of the Methylobacterium extorquens DM4 reference strain for dichloromethane utilization. J Proteomics 2018; 179:131-139. [DOI: 10.1016/j.jprot.2018.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/28/2018] [Accepted: 03/16/2018] [Indexed: 12/29/2022]
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7
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Wright J, Kirchner V, Bernard W, Ulrich N, McLimans C, Campa MF, Hazen T, Macbeth T, Marabello D, McDermott J, Mackelprang R, Roth K, Lamendella R. Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation. Front Microbiol 2017; 8:2300. [PMID: 29213257 PMCID: PMC5702783 DOI: 10.3389/fmicb.2017.02300] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 11/07/2017] [Indexed: 01/05/2023] Open
Abstract
The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L. Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. Across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges, indicating niche-specific responses of these autochthonous populations. Altogether, our findings suggest that monitored natural attenuation is an appropriate remediation strategy for DCM contamination, and that high-throughput sequencing technologies are a robust method for assessing the potential role of biodegrading bacterial assemblages in the apparent reduction of DCM concentrations in environmental scenarios.
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Affiliation(s)
- Justin Wright
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States.,Wright Labs, LLC, Huntingdon, PA, United States
| | - Veronica Kirchner
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - William Bernard
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Nikea Ulrich
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Christopher McLimans
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Maria F Campa
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.,Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States
| | - Terry Hazen
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.,Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States.,Department of Microbiology, University of Tennessee, Knoxville, TN, United States.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States.,Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, United States
| | | | | | | | - Rachel Mackelprang
- Department of Biology, California State University Northridge, Northridge, PA, United States
| | - Kimberly Roth
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Regina Lamendella
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States.,Wright Labs, LLC, Huntingdon, PA, United States
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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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9
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Michener JK, Camargo Neves AA, Vuilleumier S, Bringel F, Marx CJ. Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post-transfer refinement. eLife 2014; 3:e04279. [PMID: 25418043 PMCID: PMC4271186 DOI: 10.7554/elife.04279] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 11/22/2014] [Indexed: 01/09/2023] Open
Abstract
When microbes acquire new abilities through horizontal gene transfer, the genes and pathways must function under conditions with which they did not coevolve. If newly-acquired genes burden the host, their utility will depend on further evolutionary refinement of the recombinant strain. We used laboratory evolution to recapitulate this process of transfer and refinement, demonstrating that effective use of an introduced dichloromethane degradation pathway required one of several mutations to the bacterial host that are predicted to increase chloride efflux. We then used this knowledge to identify parallel, beneficial mutations that independently evolved in two natural dichloromethane-degrading strains. Finally, we constructed a synthetic mobile genetic element carrying both the degradation pathway and a chloride exporter, which preempted the adaptive process and directly enabled effective dichloromethane degradation across diverse Methylobacterium environmental isolates. Our results demonstrate the importance of post-transfer refinement in horizontal gene transfer, with potential applications in bioremediation and synthetic biology.
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Affiliation(s)
- Joshua K Michener
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - Aline A Camargo Neves
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Stéphane Vuilleumier
- CNRS Molecular Genetics, Genomics, Microbiology, Université de Strasbourg, Strasbourg, France
| | - Françoise Bringel
- CNRS Molecular Genetics, Genomics, Microbiology, Université de Strasbourg, Strasbourg, France
| | - Christopher J Marx
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, United States
- Department of Biological Sciences, University of Idaho, Moscow, United States
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, United States
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10
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Phylogeny poorly predicts the utility of a challenging horizontally transferred gene in Methylobacterium strains. J Bacteriol 2014; 196:2101-7. [PMID: 24682326 DOI: 10.1128/jb.00034-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Horizontal gene transfer plays a crucial role in microbial evolution. While much is known about the mechanisms that determine whether physical DNA can be transferred into a new host, the factors determining the utility of the transferred genes are less clear. We have explored this issue using dichloromethane consumption in Methylobacterium strains. Methylobacterium extorquens DM4 expresses a dichloromethane dehalogenase (DcmA) that has been acquired through horizontal gene transfer and allows the strain to grow on dichloromethane as the sole carbon and energy source. We transferred the dcmA gene into six Methylobacterium strains that include both close and distant evolutionary relatives. The transconjugants varied in their ability to grow on dichloromethane, but their fitness on dichloromethane did not correlate with the phylogeny of the parental strains or with any single tested physiological factor. This work highlights an important limiting factor in horizontal gene transfer, namely, the capacity of the recipient strain to accommodate the stress and metabolic disruption resulting from the acquisition of a new enzyme or pathway. Understanding these limitations may help to rationalize historical examples of horizontal transfer and aid deliberate genetic transfers in biotechnology for metabolic engineering.
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11
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Carroll SM, Xue KS, Marx CJ. Laboratory divergence of Methylobacterium extorquens AM1 through unintended domestication and past selection for antibiotic resistance. BMC Microbiol 2014; 14:2. [PMID: 24384040 PMCID: PMC3926354 DOI: 10.1186/1471-2180-14-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 12/16/2013] [Indexed: 01/25/2023] Open
Abstract
Background A common assumption of microorganisms is that laboratory stocks will remain genetically and phenotypically constant over time, and across laboratories. It is becoming increasingly clear, however, that mutations can ruin strain integrity and drive the divergence or “domestication” of stocks. Since its discovery in 1960, a stock of Methylobacterium extorquens AM1 (“AM1”) has remained in the lab, propagated across numerous growth and storage conditions, researchers, and facilities. To explore the extent to which this lineage has diverged, we compared our own “Modern” stock of AM1 to a sample archived at a culture stock center shortly after the strain’s discovery. Stored as a lyophilized sample, we hypothesized that this Archival strain would better reflect the first-ever isolate of AM1 and reveal ways in which our Modern stock has changed through laboratory domestication or other means. Results Using whole-genome re-sequencing, we identified some 29 mutations – including single nucleotide polymorphisms, small indels, the insertion of mobile elements, and the loss of roughly 36 kb of DNA - that arose in the laboratory-maintained Modern lineage. Contrary to our expectations, Modern was both slower and less fit than Archival across a variety of growth substrates, and showed no improvement during long-term growth and storage. Modern did, however, outperform Archival during growth on nutrient broth, and in resistance to rifamycin, which was selected for by researchers in the 1980s. Recapitulating selection for rifamycin resistance in replicate Archival populations showed that mutations to RNA polymerase B (rpoB) substantially decrease growth in the absence of antibiotic, offering an explanation for slower growth in Modern stocks. Given the large number of genomic changes arising from domestication (28), it is somewhat surprising that the single other mutation attributed to purposeful laboratory selection accounts for much of the phenotypic divergence between strains. Conclusions These results highlight the surprising degree to which AM1 has diverged through a combination of unintended laboratory domestication and purposeful selection for rifamycin resistance. Instances of strain divergence are important, not only to ensure consistency of experimental results, but also to explore how microbes in the lab diverge from one another and from their wild counterparts.
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Affiliation(s)
| | | | - Christopher J Marx
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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12
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Baker JL, Sudarsan N, Weinberg Z, Roth A, Stockbridge RB, Breaker RR. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 2011; 335:233-235. [PMID: 22194412 DOI: 10.1126/science.1215063] [Citation(s) in RCA: 316] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Most riboswitches are metabolite-binding RNA structures located in bacterial messenger RNAs where they control gene expression. We have discovered a riboswitch class in many bacterial and archaeal species whose members are selectively triggered by fluoride but reject other small anions, including chloride. These fluoride riboswitches activate expression of genes that encode putative fluoride transporters, enzymes that are known to be inhibited by fluoride, and additional proteins of unknown function. Our findings indicate that most organisms are naturally exposed to toxic levels of fluoride and that many species use fluoride-sensing RNAs to control the expression of proteins that alleviate the deleterious effects of this anion.
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Affiliation(s)
- Jenny L Baker
- Department of Chemistry, Yale University, Box 208103, New Haven, CT 06520, USA
| | - Narasimhan Sudarsan
- Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520, USA.,Department of Molecular, Cellular, and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520, USA
| | - Zasha Weinberg
- Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520, USA.,Department of Molecular, Cellular, and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520, USA
| | - Adam Roth
- Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520, USA.,Department of Molecular, Cellular, and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520, USA
| | - Randy B Stockbridge
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02454, USA
| | - Ronald R Breaker
- Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520, USA.,Department of Molecular, Cellular, and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520, USA
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13
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Dichloromethane-degrading bacteria in the genomic age. Res Microbiol 2011; 162:869-76. [DOI: 10.1016/j.resmic.2011.01.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 01/03/2011] [Indexed: 11/15/2022]
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14
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Muller EEL, Hourcade E, Louhichi-Jelail Y, Hammann P, Vuilleumier S, Bringel F. Functional genomics of dichloromethane utilization in Methylobacterium extorquens DM4. Environ Microbiol 2011; 13:2518-35. [PMID: 21854516 DOI: 10.1111/j.1462-2920.2011.02524.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dichloromethane (CH(2)Cl(2) , DCM) is a chlorinated solvent mainly produced by industry, and a common pollutant. Some aerobic methylotrophic bacteria are able to grow with this chlorinated methane as their sole carbon and energy source, using a DCM dehalogenase/glutathione S-transferase encoded by dcmA to transform DCM into two molecules of HCl and one molecule of formaldehyde, a toxic intermediate of methylotrophic metabolism. In Methylobacterium extorquens DM4 of known genome sequence, dcmA lies on a 126 kb dcm genomic island not found so far in other DCM-dechlorinating strains. An experimental search for the molecular determinants involved in specific cellular responses of strain DM4 growing with DCM was performed. Random mutagenesis with a minitransposon containing a promoterless reporter gfp gene yielded 25 dcm mutants with a specific DCM-associated phenotype. Differential proteomic analysis of cultures grown with DCM and with methanol defined 38 differentially abundant proteins. The 5.5 kb dcm islet directly involved in DCM dehalogenation is the only one of seven gene clusters specific to the DCM response to be localized within the dcm genomic island. The DCM response was shown to involve mainly the core genome of Methylobacterium extorquens, providing new insights on DCM-dependent adjustments of C1 metabolism and gene regulation, and suggesting a specific stress response of Methylobacterium during growth with DCM. Fatty acid, hopanoid and peptidoglycan metabolisms were affected, hinting at the membrane-active effects of DCM due to its solvent properties. A chloride-induced efflux transporter termed CliABC was also newly identified. Thus, DCM dechlorination driven by the dcm islet elicits a complex adaptive response encoded by the core genome common to dechlorinating as well as non-dechlorinating Methylobacterium strains.
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Affiliation(s)
- Emilie E L Muller
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
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15
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Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources. PLoS One 2009; 4:e5584. [PMID: 19440302 PMCID: PMC2680597 DOI: 10.1371/journal.pone.0005584] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Accepted: 03/30/2009] [Indexed: 11/22/2022] Open
Abstract
Background Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared. Methodology/Principal Findings The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name “island integration determinant” (iid). Conclusion/Significance These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles.
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Trotsenko YA, Torgonskaya ML. The aerobic degradation of dichloromethane: Structural-functional aspects (a review). APPL BIOCHEM MICRO+ 2009. [DOI: 10.1134/s0003683809030016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Bailón L, Nikolausz M, Kästner M, Veiga MC, Kennes C. Removal of dichloromethane from waste gases in one- and two-liquid-phase stirred tank bioreactors and biotrickling filters. WATER RESEARCH 2009; 43:11-20. [PMID: 18945466 DOI: 10.1016/j.watres.2008.09.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 09/19/2008] [Accepted: 09/23/2008] [Indexed: 05/27/2023]
Abstract
The removal of dichloromethane (DCM) from polluted air was studied both in biotrickling filters and in continuous stirred tank bioreactors, using either a single-liquid aqueous phase or a combination of an aqueous-organic liquid phase. The presence of the organic phase, i.e. silicone oil, at a volume ratio of 10% of the liquid phase, increased the maximum EC by about 25% in the BTF, reaching 200 gm(3)/h, and by as much as 300% in the CSTB, reaching 350 gm(3)/h. Based on data of chloride release in the aqueous phase and carbon dioxide production in the gas phase, complete dechlorination and mineralization of the pollutant could be confirmed. When applying shock loads, a more stable behaviour was observed in the presence of the organic phase. Generally, the completely mixed reactors were also more stable than the plug-flow biotrickling filters, irrespective of the presence of the organic phase. The use of molecular techniques allowed showing that the originally inoculated DCM-degrading Hyphomicrobium strains remained present, although not dominant, after long-term bioreactor operation. Different new bacterial populations did also appear in the systems, some of which were unable to degrade DCM.
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Affiliation(s)
- Laura Bailón
- Chemical Engineering Laboratory, Faculty of Sciences, University of La Coruña, Rua Alejandro de la Sota 1, 15008 - La Coruña, Spain
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18
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Emanuelsson MAE, Osuna MB, Ferreira Jorge RM, Castro PML. Isolation of a Xanthobacter sp. degrading dichloromethane and characterization of the gene involved in the degradation. Biodegradation 2008; 20:235-44. [DOI: 10.1007/s10532-008-9216-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Accepted: 09/02/2008] [Indexed: 11/27/2022]
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19
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Yu JM, Chen JM, Wang JD. Removal of dichloromethane from waste gases by a biotrickling filter. J Environ Sci (China) 2006; 18:1073-6. [PMID: 17294944 DOI: 10.1016/s1001-0742(06)60041-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Dichloromethane is harmful to human health and hazardous to atmospheric environment. In this study, two strains were isolated which were identified as Pseudomonas sp. and Mycobacterium sp., and utilized dichloromethane (DCM) as sole carbon and energy sources. The optimal culture conditions were temperature of 28 degrees C and pH of 6.5 for obtaining the two mixed bacterial strains. The investigation on the purification of DCM-contaminated gas was carried out in a bench-scale biotrickling filter which was inoculated with the two strains and operated under these optimal conditions. The DCM removal efficiencies varied between 72% and 99% in the biotrickling filter when empty-bed residence time was 9.6 s with the inlet concentrations ranged from 0.7 to 3.12 g/m(3) under the conditions of pH of 6.5 +/-0.5 and temperature of 28 degrees C. It was also found that NaCl accumulation in the broth would inhibit the DCM biodegradation dramatically when the accumulated NaCl concentration was over 35.1 g/L.
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Affiliation(s)
- Jian-ming Yu
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, China
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20
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Nikolausz M, Kappelmeyer U, Nijenhuis I, Ziller K, Kästner M. Molecular characterization of dichloromethane-degrading Hyphomicrobium strains using 16S rDNA and DCM dehalogenase gene sequences. Syst Appl Microbiol 2005; 28:582-7. [PMID: 16156115 DOI: 10.1016/j.syapm.2005.03.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A phylogenetic analysis of 6 strains of dichloromethane (DCM) utilizing bacteria was performed. Based on the almost complete 16S rDNA sequence determination, all strains clustered together and showed high sequence similarity to Hyphomicrobium denitrificans, except for the strain MC8b, which is only moderately related to them and probably represents a distinct species. The 16S rDNA-based phylogenetic tree was compared to the one obtained from the DNA sequence data of the dcmA gene coding DCM dehalogenase, the key enzyme of DCM utilization. The topology of the two trees is in good agreement and may suggest an ancient origin of DCM dehalogenase, but also raises questions about the original role of the enzyme.
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Affiliation(s)
- Marcell Nikolausz
- UFZ Centre for Environmental Research Leipzig-Halle, Bioremediation Department, Permoserstrasse 15, 04318 Leipzig, Germany
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21
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Krausova VI, Robb FT, González JM. Bacterial degradation of dichloromethane in cultures and natural environments. J Microbiol Methods 2003; 54:419-22. [PMID: 12842489 DOI: 10.1016/s0167-7012(03)00062-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Dichloromethane (DCM) is a toxic pollutant showing prolonged persistence in water. DCM biodegradation is usually determined from increases in Cl ions, gas chromatography, or by using radioisotopes. Herein, we present an original and easy spectrophotometric method to estimate DCM concentrations in cultures and environmental samples during DCM biodegradation experiments.
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Affiliation(s)
- Valentina I Krausova
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
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22
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Doronina NV, Trotsenko YA, Tourova TP, Kuznetsov BB, Leisinger T. Methylopila helvetica sp. nov. and Methylobacterium dichloromethanicum sp. nov.--novel aerobic facultatively methylotrophic bacteria utilizing dichloromethane. Syst Appl Microbiol 2000; 23:210-8. [PMID: 10930073 DOI: 10.1016/s0723-2020(00)80007-7] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Eight strains of Gram-negative, aerobic, asporogenous, neutrophilic, mesophilic, facultatively methylotrophic bacteria are taxonomically described. These icl- serine pathway methylobacteria utilize dichloromethane, methanol and methylamine as well as a variety of polycarbon compounds as the carbon and energy source. The major cellular fatty acids of the non-pigmented strains DM1, DM3, and DM5 to DM9 are C18:1, C16:0, C18:0, Ccy19:0 and that of the pink-pigmented strain DM4 is C18:1. The main quinone of all the strains is Q-10. The non-pigmented strains have similar phenotypic properties and a high level of DNA-DNA relatedness (81-98%) as determined by hybridization. All strains belong to the alpha-subgroup of the alpha-Proteobacteria. 16S rDNA sequence analysis led to the classification of these dichloromethane-utilizers in the genus Methylopila as a new species - Methylopila helvetica sp.nov. with the type strain DM9 (=VKM B-2189). The pink-pigmented strain DM4 belongs to the genus Methylobacterium but differs from the known members of this genus by some phenotypic properties, DNA-DNA relatedness (14-57%) and 16S rDNA sequence. Strain DM4 is named Methylobacterium dichloromethanicum sp. nov. (VKM B-2191 = DSMZ 6343).
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Affiliation(s)
- N V Doronina
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino
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23
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Gisi D, Willi L, Traber H, Leisinger T, Vuilleumier S. Effects of bacterial host and dichloromethane dehalogenase on the competitiveness of methylotrophic bacteria growing with dichloromethane. Appl Environ Microbiol 1998; 64:1194-202. [PMID: 9546153 PMCID: PMC106129 DOI: 10.1128/aem.64.4.1194-1202.1998] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/1997] [Accepted: 01/14/1998] [Indexed: 02/07/2023] Open
Abstract
Methylobacterium sp. strain DM4 and Methylophilus sp. strain DM11 can grow with dichloromethane (DCM) as the sole source of carbon and energy by virtue of homologous glutathione-dependent DCM dehalogenases with markedly different kinetic properties (the kcat values of the enzymes of these strains are 0.6 and 3.3 S-1, respectively, and the Km values are 9 and 59 microM, respectively). These strains, as well as transconjugant bacteria expressing the DCM dehalogenase gene (dcmA) from DM11 or DM4 on a broad-host-range plasmid in the background of dcmA mutant DM4-2cr, were investigated by growing them under growth-limiting conditions and in the presence of an excess of DCM. The maximal growth rates and maximal levels of dehalogenase for chemostat-adapted bacteria were higher than the maximal growth rates and maximal levels of dehalogenase for batch-grown bacteria. The substrate saturation constant of strain DM4 was much lower than the Km of its associated dehalogenase, suggesting that this strain is adapted to scavenge low concentrations of DCM. Strains and transconjugants expressing the DCM dehalogenase from strain DM11, on the other hand, had higher growth rates than bacteria expressing the homologous dehalogenase from strain DM4. Competition experiments performed with pairs of DCM-degrading strains revealed that a strain expressing the dehalogenase from DM4 had a selective advantage in continuous culture under substrate-limiting conditions, while strains expressing the DM11 dehalogenase were superior in batch culture when there was an excess of substrate. Only DCM-degrading bacteria with a dcmA gene similar to that from strain DM4, however, were obtained in batch enrichment cultures prepared with activated sludge from sewage treatment plants.
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Affiliation(s)
- D Gisi
- Mikrobiologisches Institut, ETH Zürich, ETH-Zentrum, Switzerland
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24
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Schmid-Appert M, Zoller K, Traber H, Vuilleumier S, Leisinger T. Association of newly discovered IS elements with the dichloromethane utilization genes of methylotrophic bacteria. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 8):2557-2567. [PMID: 9274009 DOI: 10.1099/00221287-143-8-2557] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Dichloromethane (DCM) dehalogenases enable facultative methylotrophic bacteria to utilize DCM as sole carbon and energy source. DCM-degrading aerobic methylotrophic bacteria expressing a type A DCM dehalogenase were previously shown to share a conserved 4.2 kb BamHI DNA fragment containing the dehalogenase structural gene, dcmA, and dcmR, the gene encoding a putative regulatory protein. Sequence analysis of a 10 kb DNA fragment including this region led to the identification of three types of insertion sequences identified as IS1354, IS1355 and IS1357, and also two ORFs, orf353 and orf192, of unknown function. Two identical copies of element IS1354 flank the conserved 4.2 kb fragment as a direct repeat. The occurrence of these newly identified IS elements was shown to be limited to DCM-utilizing methylotrophs containing a type A DCM dehalogenase. The organization of the corresponding dcm regions in 12 DCM-utilizing strains was examined by hybridization analysis using IS-specific probes. Six different groups could be defined on the basis of the occurrence, position and copy number of IS sequences. All groups shared a conserved 5.6 kb core region with dcmA, dcmR, orf353 and orf192 as well as IS1357. One group of strains including Pseudomonas sp. DM1 contained two copies of this conserved core region. The high degree of sequence conservation observed within the genomic region responsible for DCM utilization and the occurrence of clusters of insertion sequences in the vicinity of the dcm genes suggest that a transposon is involved in the horizontal transfer of the DCM-utilization character among methylotrophic bacteria.
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Affiliation(s)
- M Schmid-Appert
- Mikrobiologisches Institut, Swiss Federal Institute of Technology, ETH-Zentrum, CH-8092 Zürich, Switzerland
| | - K Zoller
- Mikrobiologisches Institut, Swiss Federal Institute of Technology, ETH-Zentrum, CH-8092 Zürich, Switzerland
| | - H Traber
- Mikrobiologisches Institut, Swiss Federal Institute of Technology, ETH-Zentrum, CH-8092 Zürich, Switzerland
| | - S Vuilleumier
- Mikrobiologisches Institut, Swiss Federal Institute of Technology, ETH-Zentrum, CH-8092 Zürich, Switzerland
| | - T Leisinger
- Mikrobiologisches Institut, Swiss Federal Institute of Technology, ETH-Zentrum, CH-8092 Zürich, Switzerland
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25
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Dichloromethane as the sole carbon source forHyphomicrobium sp. strain DM2 under denitrification conditions. Biodegradation 1995. [DOI: 10.1007/bf00700462] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Metabolism and cometabolism of halogenated C-1 and C-2 hydrocarbons. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/s0079-6352(06)80028-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
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27
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Leisinger T, Bader R, Hermann R, Schmid-Appert M, Vuilleumier S. Microbes, enzymes and genes involved in dichloromethane utilization. Biodegradation 1994; 5:237-48. [PMID: 7765835 DOI: 10.1007/bf00696462] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Dichloromethane (DCM) is efficiently utilized as a carbon and energy source by aerobic, Gram-negative, facultative methylotrophic bacteria. It also serves as a sole carbon and energy source for a nitrate-respiring Hyphomicrobium sp. and for a strictly anaerobic co-culture of a DCM-fermenting bacterium and an acetogen. The first step of DCM utilization by methylotrophs is catalyzed by DCM dehalogenase which, in a glutathione-dependent substitution reaction, forms inorganic chloride and S-chloromethyl glutathione. This unstable intermediate decomposes to glutathione, inorganic chloride and formaldehyde, a central metabolite of methylotrophic growth. Genetic studies on DCM utilization are beginning to shed some light on questions pertaining to the evolution of DCM dehalogenases and on the regulation of DCM dehalogenase expression. DCM dehalogenase belongs to the glutathione S-transferase supergene family. Analysis of the amino acid sequences of two bacterial DCM dehalogenases reveals 56% identity, and comparison of these sequences to those of glutathione S-transferases indicates a closer relationship to class Theta eukaryotic glutathione S-transferases than to a number of bacterial glutathione S-transferases whose sequences have recently become available. dcmA, the structural gene of the highly substrate-inducible DCM dehalogenase, is carried in most DCM utilizing methylotrophs on large plasmids. In Methylobacterium sp. DM4 its expression is governed by dcmR, a regulatory gene located upstream of dcmA, dcmR encodes a trans-acting factor which negatively controls DCM dehalogenase formation at the transcriptional level. Our working model thus assumes that the dcmR product is a repressor which, in the absence of DCM, binds to the promoter region of dcmA and thereby inhibits initiation of transcription.
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Affiliation(s)
- T Leisinger
- Mikrobiologisches Institut ETH, ETH-Zentrum, Zürich, Switzerland
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28
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van den Wijngaard AJ, Wind RD, Janssen DB. Kinetics of Bacterial Growth on Chlorinated Aliphatic Compounds. Appl Environ Microbiol 1993; 59:2041-8. [PMID: 16348981 PMCID: PMC182233 DOI: 10.1128/aem.59.7.2041-2048.1993] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
With the pure bacterial cultures
Ancylobacter aquaticus
AD20 and AD25,
Xanthobacter autotrophicus
GJ10, and
Pseudomonas
sp. strain AD1, Monod kinetics was observed during growth in chemostat cultures on 1,2-dichloroethane (AD20, AD25, and GJ10), 2-chloroethanol (AD20 and GJ10), and 1,3-dichloro-2-propanol (AD1). Both the Michaelis-Menten constants (
K
m
) of the first catabolic (dehalogenating) enzyme and the Monod half-saturation constants (
K
s
) followed the order 2-chloroethanol, 1,3-dichloro-2-propanol, epichlorohydrin, and 1,2-dichloroethane. The
K
s
values of strains GJ10, AD20, and AD25 for 1,2-dichloroethane were 260, 222, and 24 μM, respectively. The low
K
s
value of strain AD25 was correlated with a higher haloalkane dehalogenase content of this bacterium. The growth rates of strains AD20 and GJ10 in continuous cultures on 1,2-dichloroethane were higher than the rates predicted from the kinetics of the haloalkane dehalogenase and the concentration of the enzyme in the cells. The results indicate that the efficiency of chlorinated compound removal is indeed influenced by the kinetic properties and cellular content of the first catabolic enzyme. The cell envelope did not seem to act as a barrier for permeation of 1,2-dichloroethane.
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Affiliation(s)
- A J van den Wijngaard
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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29
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Stromeyer SA, Winkelbauer W, Kohler H, Cook AM, Leisinger T. Dichloromethane utilized by an anaerobic mixed culture: acetogenesis and methanogenesis. Biodegradation 1992; 2:129-37. [PMID: 1368154 DOI: 10.1007/bf00114603] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Dichloromethane (8.9 mg/l) was eliminated from industrially polluted, anaerobic groundwater in a fixed-bed reactor (43 m3) which was packed with activated charcoal and operated continuously for over three years. The elimination of dichloromethane over this period was some ten-fold in excess of the sorptive capacity of the charcoal, and the elimination (3.7 mg/h.[kg of charcoal]: residence time, 49 h) was tentatively attributed to dehalogenative microorganisms immobilized on the charcoal. Anaerobic enrichment cultures, with dichloromethane as the sole added source of carbon and energy, were inoculated with material from the reactor. Reproducibly complete substrate disappearance in subcultures was observed when traces of groundwater (1%) or yeast extract (0.01%) were supplied. Fed-batch experiments under an atmosphere of CO2 plus N2 led to the conversion in 11 days of 11 mM dichloromethane to 3 mM acetate and 2 mM methane, with a growth yield of 0.4 g of protein/mol of dichloromethane; insignificant amounts (less than 1 microM) of chloromethane accumulated. Methanogenesis could be inhibited by 50 mM 2-bromoethane sulfonate without any effect on the dehalogenation rate. The maximum dehalogenation rate was 0.13 mmol dichloromethane/h.l (2.6 mkat/kg of protein).
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Affiliation(s)
- S A Stromeyer
- Microbiology Institute, Swiss Federal Institute of Technology, ETH-Zentrum, Zürich
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30
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La Roche SD, Leisinger T. Identification of dcmR, the regulatory gene governing expression of dichloromethane dehalogenase in Methylobacterium sp. strain DM4. J Bacteriol 1991; 173:6714-21. [PMID: 1938878 PMCID: PMC209020 DOI: 10.1128/jb.173.21.6714-6721.1991] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The genes for dichloromethane utilization by Methylobacterium sp. strain DM4 are encoded on a 2.8-kb sequenced DNA fragment, the dcm region. This fragment contains dcmA, the structural gene of dichloromethane dehalogenase and, upstream of dcmA, a 1.5-kb region responsible for inducibility of dichloromethane dehalogenase by dichloromethane. A fragment of the dcm region covering dcmA and 230 bp of its upstream region was integrated into the chromosome of a Methylobacterium sp. strain DM4 mutant deleted for the dcm region. This yielded a strain expressin dichloromethane dehalogenase constitutively at the induced level. Plasmids carrying various segments of the 1.5-kb regulatory region were tested for their ability to restore regulation. The data obtained led to the identification of dcmR, the structural gene of a putative dcm-specific repressor. Transcription of dcmR was divergent from dcmA. dcmR encoded a 30-kDa protein with a helix-turn-helix motif near the amino terminus. The transcription start sites of dcmA and dcmR were identified by nuclease S1 mapping. The promoter regions of these genes contained nearly identical 12-bp sequences covering positions -14 to -25 relative to the mRNA start sites. Experiments with dcmR'-'lacZ fusions demonstrated that dcmR expression was markedly autoregulated at the level of transcription and less so at the protein level. These findings are compatible with both dcmA and dcmR expression being negatively controlled at the transcriptional level by the DcmR protein.
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Affiliation(s)
- S D La Roche
- Department of Microbiology, Swiss Federal Institute of Technology, ETH-Zentrum, Zürich
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31
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Bitzi U, Egli T, Hamer G. The biodegradation of mixtures of organic solvents by mixed and monocultures of bacteria. Biotechnol Bioeng 1991; 37:1037-42. [DOI: 10.1002/bit.260371108] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Diks RMM, Ottengraf SPP. Verification studies of a simplified model for the removal of dichloromethane from waste gases using a biological trickling filter. ACTA ACUST UNITED AC 1991. [DOI: 10.1007/bf00369249] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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33
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Hartmans S, Tramper J. Dichloromethane removal from waste gases with a trickle-bed bioreactor. ACTA ACUST UNITED AC 1991. [DOI: 10.1007/bf00369060] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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34
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Abstract
As a result of natural production and contamination of the environment by xenobiotic compounds, halogenated substances are widely distributed in the biosphere. Concern arises as a result of the toxic, carcinogenic, and potential teratogenic nature of these substances. The biotransformations of such halogenated substances are reviewed, with particular emphasis on the biocatalytic cleavage of the carbon-halogen bonds. The physiology, biochemistry, and genetics of the biological system involved in the dehalogenation reactions are discussed for three groups of organohalogens: (1) the haloacids, (2) the haloaromatics, and (3) the haloalkanes. Finally, the biotechnological applications of these microbial transformations are discussed. This includes prospects for their future application in biosynthetic processes for the synthesis of halogenated intermediates or novel compounds and also the use of such systems for the detoxification and degradation of environmental pollutants.
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Affiliation(s)
- D J Hardman
- International Institute of Biotechnology, Canterbury, Kent, UK
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35
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La Roche SD, Leisinger T. Sequence analysis and expression of the bacterial dichloromethane dehalogenase structural gene, a member of the glutathione S-transferase supergene family. J Bacteriol 1990; 172:164-71. [PMID: 2104602 PMCID: PMC208414 DOI: 10.1128/jb.172.1.164-171.1990] [Citation(s) in RCA: 141] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The nucleotide sequence of a cloned 2.8-kilobase-pair BamHI-PstI fragment containing dcmA, the dichloromethane dehalogenase structural gene from Methylobacterium sp. strain DM4, was determined. An open reading frame with a coding capacity of 287 amino acids (molecular weight, 37,430) was identified as dcmA by its agreement with the N-terminal amino acid sequence, the total amino acid composition, and the subunit size of the purified enzyme. Alignment of the deduced dichloromethane dehalogenase amino acid sequence with amino acid sequences of the functionally related eucaryotic glutathione S-transferases revealed three regions containing highly conserved amino acid residues and indicated that dcmA is a member of the glutathione S-transferase supergene family. The 5' terminus of in vivo dcmA transcripts was determined by nuclease S1 mapping to be 82 base pairs upstream of the GTG initiation codon of dcmA. Despite a putative promoter sequence with high resemblance to the Escherichia coli -10 and -35 consensus sequences, located at an appropriate distance from the transcription start point, dcmA was only marginally expressed in E. coli. The strong induction of dichloromethane dehalogenase in Methylobacterium sp. by dichloromethane was abolished by deleting the 1.3-kilobase-pair upstream region of dcmA. Plasmid constructs devoid of this region directed expression of dichloromethane dehalogenase at a constitutively induced level.
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Affiliation(s)
- S D La Roche
- Department of Microbiology, Swiss Federal Institute of Technology, ETH-Zentrum, Zürich
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36
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Abstract
The application of specialized microorganisms to treat dichloromethane (DM) containing process effluents was studied. An aerobic fluidized bed reactor with a working volume of 801 filled with sand particles as carriers for the bacteria was used. Oxygen was introduced into the recycle stream by an injector device. DM was monitored semi-continuously. A processor controlled the feed volume according to the DM effluent concentration. Mineralization rates of 12 kg DM/m3bioreactor.d were reached within about three weeks using synthetic wastewater containing 2000 mg/l DM as single carbon compound. DM from process water of a pharmaceutical plant was reduced from about 2000 mg/l in the feed to below 1 mg/l in the effluent at volumetric loading rates of 3 to 4 kg DM/m3bioreactor.d. Degradation of wastewater components like acetone and isopropanol were favoured, thus making the process less attractive for waste streams containing high amounts of DOC other than of DM. DM concentrations of up to 1000 mg/l were tolerated by the immobilized microorganisms and did not influence their DM degradation capacity. The ability to mineralize DM was lost when no DM was fed to the reactor for 10 days.
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Affiliation(s)
- G Stucki
- Ciba-Geigy AG, Schweizerhalle Switzerland
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37
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38
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Scholtz R, Wackett LP, Egli C, Cook AM, Leisinger T. Dichloromethane dehalogenase with improved catalytic activity isolated from a fast-growing dichloromethane-utilizing bacterium. J Bacteriol 1988; 170:5698-704. [PMID: 3142855 PMCID: PMC211671 DOI: 10.1128/jb.170.12.5698-5704.1988] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A methylotrophic bacterium, denoted strain DM11, was isolated from groundwater and shown to utilize dichloromethane or dibromomethane as the sole carbon and energy source. The new isolate grew at the high rate of 0.22 h-1 compared with 11 previously characterized dichloromethane-utilizing bacteria (micromax, 0.08 h-1). The dichloromethane dehalogenase from strain DM11 (group B enzyme) was purified by anion-exchange chromatography. It was shown to be substantially different from the set of dichloromethane dehalogenases from the 11 slow-growing strains (group A enzymes) that had previously been demonstrated to be identical. The Vmax for the group B enzyme was 97 mkat/kg of protein, some 5.6-fold higher than that of the group A enzymes. The group A dehalogenases showed hyperbolic saturation with the cosubstrate glutathione, whereas the group B enzyme showed positive cooperativity in glutathione binding. Only 1 of 15 amino acids occupied common positions at the N termini, and amino acid contents were substantially different in group A and group B dehalogenases. Immunological assays demonstrated weak cross-reactivity between the two enzymes. Despite the observed structural and kinetic differences, there is potentially evolutionary relatedness between group A and group B enzymes, as indicated by (i) hybridization of DM11 DNA with a gene probe of the group A enzyme, (ii) a common requirement for glutathione in catalysis, and (iii) similar subunit molecular weights of about 34,000.
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Affiliation(s)
- R Scholtz
- Department of Microbiology, Eidgenössische Technische Hochschule-Zentrum, Zurich, Switzerland
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39
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Scholtz R, Leisinger T, Suter F, Cook AM. Characterization of 1-chlorohexane halidohydrolase, a dehalogenase of wide substrate range from an Arthrobacter sp. J Bacteriol 1987; 169:5016-21. [PMID: 3667524 PMCID: PMC213902 DOI: 10.1128/jb.169.11.5016-5021.1987] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
1-Chlorohexane halidohydrolase from Arthrobacter sp. strain HA1 was purified to homogeneity by fractional precipitation, ion-exchange chromatography, gel filtration, and high-performance liquid chromatography gel filtration. The enzyme was a monomer with a molecular weight of about 37,000; its amino acid composition and N-terminal sequence were determined. The enzyme had a broad optimum around pH 9.5, a temperature optimum near 50 degrees C, an activation energy of 40 kJ/mol, and a molecular activity of 0.9 kat/mol. The substrate range of the enzyme included at least 50 halogenated compounds. 1-Chloroalkanes (C3 to C10), 1-bromoalkanes (C1 to C9), and 1-iodoalkanes (C1 to C7), but no 1-fluoroalkane, were substrates. Subterminally substituted, branched-chain, and nonsaturated haloalkanes were dehalogenated. Some halogenated aromatic substrates, e.g., bromobenzene and benzyl bromide, were hydrolyzed. Several alpha,omega-dihaloalkanes were subject to double dehalogenation. Thus, 1,2-dibromoethane was hydrolyzed first to 2-bromoethanol and then to 1,2-dihydroxyethane. Crude extracts of strain HA1 were found to contain a debrominase that cleaved bromoalkanes with long alkyl chains.
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Affiliation(s)
- R Scholtz
- Department of Microbiology, Swiss Federal Institute of Technology, Zurich
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Egli C, Scholtz R, Cook AM, Leisinger T. Anaerobic dechlorination of tetrachloromethane and 1,2-dichloroethane to degradable products by pure cultures of Desulfobacterium sp. and Methanobacterium sp. FEMS Microbiol Lett 1987. [DOI: 10.1111/j.1574-6968.1987.tb02154.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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