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Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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2
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Hwang Y, Na JG, Lee SJ. Transcriptional regulation of soluble methane monooxygenase via enhancer-binding protein derived from Methylosinus sporium 5. Appl Environ Microbiol 2023; 89:e0210422. [PMID: 37668365 PMCID: PMC10537576 DOI: 10.1128/aem.02104-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/07/2023] [Indexed: 09/06/2023] Open
Abstract
Methane is a major greenhouse gas, and methanotrophs regulate the methane level in the carbon cycle. Soluble methane monooxygenase (sMMO) is expressed in various methanotroph genera, including Alphaproteobacteria and Gammaproteobacteria, and catalyzes the hydroxylation of methane to methanol. It has been proposed that MmoR regulates the expression of sMMO as an enhancer-binding protein under copper-limited conditions; however, details on this transcriptional regulation remain limited. Herein, we elucidate the transcriptional pathway of sMMO depending on copper ion concentration, which affects the interaction of MmoR and sigma factor. MmoR and sigma-54 (σ54) from Methylosinus sporium 5 were successfully overexpressed in Escherichia coli and purified to investigate sMMO transcription in methanotrophs. The results indicated that σ54 binds to a promoter positioned -24 (GG) and -12 (TGC) upstream between mmoG and mmoX1. The binding affinity and selectivity are lower (Kd = 184.6 ± 6.2 nM) than those of MmoR. MmoR interacts with the upstream activator sequence (UAS) with a strong binding affinity (Kd = 12.5 ± 0.5 nM). Mutational studies demonstrated that MmoR has high selectivity to its binding partner (ACA-xx-TGT). Titration assays have demonstrated that MmoR does not coordinate with copper ions directly; however, its binding affinity to UAS decreases in a low-copper-containing medium. MmoR strongly interacts with adenosine triphosphate (Kd = 62.8 ± 0.5 nM) to generate RNA polymerase complex. This study demonstrated that the binding events of both MmoR and σ54 that regulate transcription in M. sporium 5 depend on the copper ion concentration. IMPORTANCE This study provides biochemical evidence of transcriptional regulation of soluble methane monooxygenase (sMMO) in methanotrophs that control methane levels in ecological systems. Previous studies have proposed transcriptional regulation of MMOs, including sMMO and pMMO, while we provide further evidence to elucidate its mechanism using a purified enhancer-binding protein (MmoR) and transcription factor (σ54). The characterization studies of σ54 and MmoR identified the promoter binding sites and enhancer-binding sequences essential for sMMO expression. Our findings also demonstrate that MmoR functions as a trigger for sMMO expression due to the high specificity and selectivity for enhancer-binding sequences. The UV-visible spectrum of purified MmoR suggested an iron coordination like other GAF domain, and that ATP is essential for the initiation of enhancer elements. Binding assays indicated that these interactions are blocked by the copper ion. These results provide novel insights into gene regulation of methanotrophs.
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Affiliation(s)
- Yunha Hwang
- Department of Chemistry, Jeonbuk National University , Jeonju, South Korea
| | - Jeong-Geol Na
- Department of Chemical Engineering, Sogang University , Seoul, South Korea
| | - Seung Jae Lee
- Department of Chemistry, Jeonbuk National University , Jeonju, South Korea
- Institute of Molecular Biology and Genetics, Jeonbuk National University , Jeonju, South Korea
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3
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Enhancement of Methane Catalysis Rates in Methylosinus trichosporium OB3b. Biomolecules 2022; 12:biom12040560. [PMID: 35454149 PMCID: PMC9024549 DOI: 10.3390/biom12040560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 02/05/2023] Open
Abstract
Particulate methane monooxygenase (pMMO), a membrane-bound enzyme having three subunits (α, β, and γ) and copper-containing centers, is found in most of the methanotrophs that selectively catalyze the oxidation of methane into methanol. Active sites in the pMMO of Methylosinus trichosporium OB3b were determined by docking the modeled structure with ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene. The docking energy between the modeled pMMO structure and ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene was −5.2, −5.7, −4.2, and −3.8 kcal/mol, respectively, suggesting the existence of more than one active site within the monomeric subunits due to the presence of multiple binding sites within the pMMO monomer. The evaluation of tunnels and cavities of the active sites and the docking results showed that each active site is specific to the radius of the substrate. To increase the catalysis rates of methane in the pMMO of M. trichosporium OB3b, selected amino acid residues interacting at the binding site of ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene were mutated. Based on screening the strain energy, docking energy, and physiochemical properties, five mutants were downselected, B:Leu31Ser, B:Phe96Gly, B:Phe92Thr, B:Trp106Ala, and B:Tyr110Phe, which showed the docking energy of −6.3, −6.7, −6.3, −6.5, and −6.5 kcal/mol, respectively, as compared to the wild type (−5.2 kcal/mol) with ethylbenzene. These results suggest that these five mutants would likely increase methane oxidation rates compared to wild-type pMMO.
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Abstract
Methanotrophic bacteria represent a potential route to methane utilization and mitigation of methane emissions. In the first step of their metabolic pathway, aerobic methanotrophs use methane monooxygenases (MMOs) to activate methane, oxidizing it to methanol. There are two types of MMOs: a particulate, membrane-bound enzyme (pMMO) and a soluble, cytoplasmic enzyme (sMMO). The two MMOs are completely unrelated, with different architectures, metal cofactors, and mechanisms. The more prevalent of the two, pMMO, is copper-dependent, but the identity of its copper active site remains unclear. By contrast, sMMO uses a diiron active site, the catalytic cycle of which is well understood. Here we review the current state of knowledge for both MMOs, with an emphasis on recent developments and emerging hypotheses. In addition, we discuss obstacles to developing expression systems, which are needed to address outstanding questions and to facilitate future protein engineering efforts.
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Affiliation(s)
- Christopher W Koo
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA.
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5
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Metabolic engineering of type II methanotroph, Methylosinus trichosporium OB3b, for production of 3-hydroxypropionic acid from methane via a malonyl-CoA reductase-dependent pathway. Metab Eng 2020; 59:142-150. [PMID: 32061966 DOI: 10.1016/j.ymben.2020.02.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/07/2020] [Accepted: 02/09/2020] [Indexed: 12/21/2022]
Abstract
We engineered a type II methanotroph, Methylosinus trichosporium OB3b, for 3-hydroxypropionic acid (3HP) production by reconstructing malonyl-CoA pathway through heterologous expression of Chloroflexus aurantiacus malonyl-CoA reductase (MCR), a bifunctional enzyme. Two strategies were designed and implemented to increase the malonyl-CoA pool and thus, increase in 3HP production. First, we engineered the supply of malonyl-CoA precursors by overexpressing endogenous acetyl-CoA carboxylase (ACC), substantially enhancing the production of 3HP. Overexpression of biotin protein ligase (BPL) and malic enzyme (NADP+-ME) led to a ∼22.7% and ∼34.5% increase, respectively, in 3HP titer in ACC-overexpressing cells. Also, the acetyl-CoA carboxylation bypass route was reconstructed to improve 3HP productivity. Co-expression of methylmalonyl-CoA carboxyltransferase (MMC) of Propionibacterium freudenreichii and phosphoenolpyruvate carboxylase (PEPC), which provides the MMC precursor, further improved the 3HP titer. The highest 3HP production of 49 mg/L in the OB3b-MCRMP strain overexpressing MCR, MMC and PEPC resulted in a 2.4-fold improvement of titer compared with that in the only MCR-overexpressing strain. Finally, we could obtain 60.59 mg/L of 3HP in 42 h using the OB3b-MCRMP strain through bioreactor operation, with a 6.36-fold increase of volumetric productivity compared than that in the flask cultures. This work demonstrates metabolic engineering of type II methanotrophs, opening the door for using type II methanotrophs as cell factories for biochemical production along with mitigation of greenhouse gases.
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Ro SY, Rosenzweig AC. Recent Advances in the Genetic Manipulation of Methylosinus trichosporium OB3b. Methods Enzymol 2018; 605:335-349. [PMID: 29909832 DOI: 10.1016/bs.mie.2018.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Methanotrophic bacteria utilize methane as their sole carbon and energy source. Studies of the model Type II methanotroph Methylosinus trichosporium OB3b have provided insight into multiple aspects of methanotrophy, including methane assimilation, copper accumulation, and metal-dependent gene expression. Development of genetic tools for chromosomal editing was crucial for advancing these studies. Recent interest in methanotroph metabolic engineering has led to new protocols for genetic manipulation of methanotrophs that are effective and simple to use. We have incorporated these newer molecular tools into existing protocols for Ms. trichosporium OB3b. The modifications include additional shuttle and replicative plasmids as well as improved gene delivery and genotyping. The methods described here render gene editing in Ms. trichosporium OB3b efficient and accessible.
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Affiliation(s)
- Soo Y Ro
- Northwestern University, Evanston, IL, United States
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7
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Choi H, Ryu HW, Cho KS. Biocomplex textile as an alternative daily cover for the simultaneous mitigation of methane and malodorous compounds. WASTE MANAGEMENT (NEW YORK, N.Y.) 2018; 72:339-348. [PMID: 29129467 DOI: 10.1016/j.wasman.2017.11.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/04/2017] [Accepted: 11/06/2017] [Indexed: 06/07/2023]
Abstract
Space-saving biocomplex textiles, which can be used as covers or rolled up as needed, have been demonstrated as alternative daily covers for the simultaneous mitigation of greenhouse gases (GHGs) and odors in landfills. The biocomplex textiles were made by inserting inorganic biocarriers (perlite (P), tobermolite (T) and their mixture (P/T)) between nonwoven fabrics. Methane (CH4) and dimethyl sulfide (DMS) were used as model compounds for GHGs and odors, and a CH4 and DMS co-degrading microbial consortium was used as an inoculum source. CH4 and DMS could be biologically degraded by methanotrophs and sulfur-oxidizing bacteria in the biocomplex textiles. Both biocomplex textiles made with either P or T were able to maintain the removability for CH4 and DMS after storage for 70 days, although their removal efficiencies for CH4 and DMS were 70-71% and 62-65% of those before storage, respectively. CH4 and DMS were simultaneously removed in lab-scale landfill simulation reactors employed with the biocomplex textiles. After 17 days of starvation, only 2-3 days were needed to recover their removability. Among the 3 kinds of biocarriers evaluated, the biocomplex textile generated using the P/T showed the highest removability and was the most stable. The maximum elimination capacities of the biocomplex textile generated with the P/T were 11.5 g-CH4·m-2-fabric·d-1 and 0.5 g-DMS·m-2-fabric·d-1, respectively. These results suggest that the biocomplex textiles are promising alternative daily covers to mitigate the emission of greenhouse gas and odor in operational landfills.
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Affiliation(s)
- Hyungjoo Choi
- Department of Environmental Science and Engineering, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Hee Wook Ryu
- Department of Chemical Engineering, Soongsil University, 369, Sangdo-ro, Dongjak-gu, Seoul 06978, Republic of Korea
| | - Kyung-Suk Cho
- Department of Environmental Science and Engineering, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea.
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DiSpirito AA, Semrau JD, Murrell JC, Gallagher WH, Dennison C, Vuilleumier S. Methanobactin and the Link between Copper and Bacterial Methane Oxidation. Microbiol Mol Biol Rev 2016; 80:387-409. [PMID: 26984926 PMCID: PMC4867365 DOI: 10.1128/mmbr.00058-15] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Methanobactins (mbs) are low-molecular-mass (<1,200 Da) copper-binding peptides, or chalkophores, produced by many methane-oxidizing bacteria (methanotrophs). These molecules exhibit similarities to certain iron-binding siderophores but are expressed and secreted in response to copper limitation. Structurally, mbs are characterized by a pair of heterocyclic rings with associated thioamide groups that form the copper coordination site. One of the rings is always an oxazolone and the second ring an oxazolone, an imidazolone, or a pyrazinedione moiety. The mb molecule originates from a peptide precursor that undergoes a series of posttranslational modifications, including (i) ring formation, (ii) cleavage of a leader peptide sequence, and (iii) in some cases, addition of a sulfate group. Functionally, mbs represent the extracellular component of a copper acquisition system. Consistent with this role in copper acquisition, mbs have a high affinity for copper ions. Following binding, mbs rapidly reduce Cu(2+) to Cu(1+). In addition to binding copper, mbs will bind most transition metals and near-transition metals and protect the host methanotroph as well as other bacteria from toxic metals. Several other physiological functions have been assigned to mbs, based primarily on their redox and metal-binding properties. In this review, we examine the current state of knowledge of this novel type of metal-binding peptide. We also explore its potential applications, how mbs may alter the bioavailability of multiple metals, and the many roles mbs may play in the physiology of methanotrophs.
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Affiliation(s)
- Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - J Colin Murrell
- Earth and Life Systems Alliance, School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Warren H Gallagher
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, USA
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Stéphane Vuilleumier
- Department of Microbiology, Genomics and the Environment, UMR 7156 UNISTRA-CNRS, Université de Strasbourg, Strasbourg, France
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9
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Competition between metals for binding to methanobactin enables expression of soluble methane monooxygenase in the presence of copper. Appl Environ Microbiol 2014; 81:1024-31. [PMID: 25416758 DOI: 10.1128/aem.03151-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It is well known that copper is a key factor regulating expression of the two forms of methane monooxygenase found in proteobacterial methanotrophs. Of these forms, the cytoplasmic, or soluble, methane monooxygenase (sMMO) is expressed only at low copper concentrations. The membrane-bound, or particulate, methane monooxygenase (pMMO) is constitutively expressed with respect to copper, and such expression increases with increasing copper. Recent findings have shown that copper uptake is mediated by a modified polypeptide, or chalkophore, termed methanobactin. Although methanobactin has high specificity for copper, it can bind other metals, e.g., gold. Here we show that in Methylosinus trichosporium OB3b, sMMO is expressed and active in the presence of copper if gold is also simultaneously present. Such expression appears to be due to gold binding to methanobactin produced by M. trichosporium OB3b, thereby limiting copper uptake. Such expression and activity, however, was significantly reduced if methanobactin preloaded with copper was also added. Further, quantitative reverse transcriptase PCR (RT-qPCR) of transcripts of genes encoding polypeptides of both forms of MMO and SDS-PAGE results indicate that both sMMO and pMMO can be expressed when copper and gold are present, as gold effectively competes with copper for binding to methanobactin. Such findings suggest that under certain geochemical conditions, both forms of MMO may be expressed and active in situ. Finally, these findings also suggest strategies whereby field sites can be manipulated to enhance sMMO expression, i.e., through the addition of a metal that can compete with copper for binding to methanobactin.
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Mai BK, Kim Y. Substrate-dependent H/D kinetic isotope effects and the role of the di(μ-oxo)diiron(IV) core in soluble methane monooxygenase: a theoretical study. Chemistry 2014; 20:6532-41. [PMID: 24715359 DOI: 10.1002/chem.201303466] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/28/2014] [Indexed: 11/07/2022]
Abstract
Soluble methane monooxygenase (sMMO) is an enzyme that converts alkanes to alcohols using a di(μ-oxo)diiron(IV) intermediate Q at the active site. Very large kinetic isotope effects (KIEs) indicative of significant tunneling are observed for the hydrogen transfer (H-transfer) of CH4 and CH3 CN; however, a relatively small KIE is observed for CH3NO2. The detailed mechanism of the enzymatic H-transfer responsible for the diverse range of KIEs is not yet fully understood. In this study, variational transition-state theory including the multidimensional tunneling approximation is used to calculate rate constants to predict KIEs based on the quantum-mechanically generated intrinsic reaction coordinates of the H-transfer by the di(μ-oxo)diiron(IV) complex. The results of our study reveal that the role of the di(μ-oxo)diiron(IV) core and the H-transfer mechanism are dependent on the substrate. For CH4 , substrate binding induces an electron transfer from the oxygen to one Fe(IV) center, which in turn makes the μ-O ligand more electrophilic and assists the H-transfer by abstracting an electron from the C-H σ orbital. For CH3CN, the reduction of Fe(IV) to Fe(III) occurs gradually with substrate binding and H-transfer. The charge density and electrophilicity of the μ-O ligand hardly change upon substrate binding; however, for CH3NO2, there seems to be no electron movement from μ-O to Fe(IV) during the H-transfer. Thus, the μ-O ligand appears to abstract a proton without an electron from the C-H σ orbital. The calculated KIEs for CH4, CH3CN, and CH3NO2 are 24.4, 49.0, and 8.27, respectively, at 293 K, in remarkably good agreement with the experimental values. This study reveals that diverse KIE values originate mainly from tunneling to the same di(μ-oxo)diiron(IV) core for all substrates, and demonstrate that the reaction dynamics are essential for reproducing experimental results and understanding the role of the diiron core for methane oxidation in sMMO.
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Affiliation(s)
- Binh Khanh Mai
- Department of Applied Chemistry, Kyung Hee University, 1 Seochun-Dong, Giheung-Gu, Yongin-Si, Gyeonggi-Do, 446-701 (Korea), Fax: (+82) 31-203-5773
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11
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Jhala YK, Vyas RV, Shelat HN, Patel HK, Patel HK, Patel KT. Isolation and characterization of methane utilizing bacteria from wetland paddy ecosystem. World J Microbiol Biotechnol 2014; 30:1845-60. [PMID: 24469547 DOI: 10.1007/s11274-014-1606-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 01/17/2014] [Indexed: 11/30/2022]
Abstract
Methylotrophic bacteria which are known to utilize C1 compounds including methane. Research during past few decades increased the interest in finding out novel genera of methane degrading bacteria to efficiently utilize methane to decrease global warming effect. Moreover, evaluation of certain known plant growth promoting strains for their methane degrading potential may open up a new direction for multiple utility of such cultures. In this study, efficient methylotrophic cultures were isolated from wetland paddy fields of Gujarat. From the overall morphological, biochemical and molecular characterization studies, the isolates were identified and designated as Bacillus aerius AAU M 8; Rhizobium sp. AAU M 10; B. subtilis AAU M 14; Paenibacillus illinoisensis AAU M 17 and B. megaterium AAU M 29. Gene specific PCR analysis of the isolates, P. illinoisensis, B. aerius, Rhizobium sp. and B. subtilis showed presence of pmoA gene encoding α subunit particulate methane monooxygenase cluster. B. megaterium, P. illinoisensis, Rhizobium sp. and Methylobacterium extrorquens showed presence of mmoX gene encoding α subunit of the hydroxylase component of the soluble methane monooxygenase cluster. P. illinoisensis and Rhizobium sp. showed presence mxaF gene encoding α subunit region of methanol dehydrogenase gene cluster showing that both isolates are efficient utilizers of methane. To the best of our knowledge, this is the first time report showing presence of methane degradation enzymes and genes within the known PGPB group of organisms from wet land paddy agro-ecosystem, which is considered as one of the leading methane producer.
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Affiliation(s)
- Y K Jhala
- Department of Microbiology, Anand Agricultural University, Anand, Gujarat, India,
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12
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Khanh Mai B, Kim Y. Theoretical studies for large tunneling and the hydrogen-transfer mechanism in the C-H activation of CH3CN by a di(μ-oxo)diiron(IV) complex: a model for intermediate Q in soluble methane monooxygenase. Chemistry 2013; 19:3568-72. [PMID: 23400929 DOI: 10.1002/chem.201204488] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Binh Khanh Mai
- Department of Applied Chemistry, Kyung Hee University, 1 Seochun-Dong, Giheung-Gu, Yongin-Si, Gyeonggi-Do, 446-701, Korea
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13
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Gopakumar G, Belanzoni P, Baerends EJ. Hydroxylation catalysis by mononuclear and dinuclear iron oxo catalysts: a methane monooxygenase model system versus the Fenton reagent Fe(IV)O(H2O)5(2+). Inorg Chem 2011; 51:63-75. [PMID: 22221279 DOI: 10.1021/ic200754w] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxylation of aliphatic C-H bonds is a chemically and biologically important reaction, which is catalyzed by the oxidoiron group FeO(2+) in both mononuclear (heme and nonheme) and dinuclear complexes. We investigate the similarities and dissimilarities of the action of the FeO(2+) group in these two configurations, using the Fenton-type reagent [FeO(2+) in a water solution, FeO(H(2)O)(5)(2+)] and a model system for the methane monooxygenase (MMO) enzyme as representatives. The high-valent iron oxo intermediate MMOH(Q) (compound Q) is regarded as the active species in methane oxidation. We show that the electronic structure of compound Q can be understood as a dimer of two Fe(IV)O(2+) units. This implies that the insights from the past years in the oxidative action of this ubiquitous moiety in oxidation catalysis can be applied immediately to MMOH(Q). Electronically the dinuclear system is not fundamentally different from the mononuclear system. However, there is an important difference of MMOH(Q) from FeO(H(2)O)(5)(2+): the largest contribution to the transition state (TS) barrier in the case of MMOH(Q) is not the activation strain (which is in this case the energy for the C-H bond lengthening to the TS value), but it is the steric hindrance of the incoming CH(4) with the ligands representing glutamate residues. The importance of the steric factor in the dinuclear system suggests that it may be exploited, through variation in the ligand framework, to build a synthetic oxidation catalyst with the desired selectivity for the methane substrate.
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Affiliation(s)
- G Gopakumar
- Theoretische Chemie, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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14
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Yang N, Lü F, He P, Shao L. Response of methanotrophs and methane oxidation on ammonium application in landfill soils. Appl Microbiol Biotechnol 2011; 92:1073-82. [DOI: 10.1007/s00253-011-3389-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 05/15/2011] [Accepted: 05/15/2011] [Indexed: 10/18/2022]
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15
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Phylogenetic and multivariate analyses to determine the effects of different tillage and residue management practices on soil bacterial communities. Appl Environ Microbiol 2010; 76:3685-91. [PMID: 20382808 DOI: 10.1128/aem.02726-09] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial communities are important not only in the cycling of organic compounds but also in maintaining ecosystems. Specific bacterial groups can be affected as a result of changes in environmental conditions caused by human activities, such as agricultural practices. The aim of this study was to analyze the effects of different forms of tillage and residue management on soil bacterial communities by using phylogenetic and multivariate analyses. Treatments involving zero tillage (ZT) and conventional tillage (CT) with their respective combinations of residue management, i.e., removed residue (-R) and kept residue (+R), and maize/wheat rotation, were selected from a long-term field trial started in 1991. Analysis of bacterial diversity showed that soils under zero tillage and crop residue retention (ZT/+R) had the highest levels of diversity and richness. Multivariate analysis showed that beneficial bacterial groups such as fluorescent Pseudomonas spp. and Burkholderiales were favored by residue retention (ZT/+R and CT/+R) and negatively affected by residue removal (ZT/-R). Zero-tillage treatments (ZT/+R and ZT/-R) had a positive effect on the Rhizobiales group, with its main representatives related to Methylosinus spp. known as methane-oxidizing bacteria. It can be concluded that practices that include reduced tillage and crop residue retention can be adopted as safer agricultural practices to preserve and improve the diversity of soil bacterial communities.
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Ali H, Murrell JC. Development and validation of promoter-probe vectors for the study of methane monooxygenase gene expression in Methylococcus capsulatus Bath. Microbiology (Reading) 2009; 155:761-771. [DOI: 10.1099/mic.0.021816-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A series of integrative and versatile broad-host-range promoter-probe vectors carrying reporter genes encoding green fluorescent protein (GFP), catechol 2,3-dioxygenase (XylE) or β-galactosidase (LacZ) were constructed for use in methanotrophs. These vectors facilitated the measurement of in vivo promoter activity in methanotrophs under defined growth conditions. They were tested by constructing transcriptional fusions between the soluble methane monooxygenase (sMMO) σ
54 promoter or particulate methane monooxygenase (pMMO) σ
70 promoter from Methylococcus capsulatus and the reporter genes. Reporter gene activity was measured under high- and low-copper growth conditions and the data obtained closely reflected transcriptional regulation of the sMMO or pMMO operon, thus demonstrating the suitability of these vectors for assessing promoter activity in methanotrophs. When β-galactosidase expression was coupled with the fluorogenic substrate 4-methylumbelliferyl β-d-glucuronide it yielded a sensitive and powerful screening system for detecting cells expressing this reporter gene. These data were substantiated with independent experiments using RT-PCR and RNA dot-blot analysis.
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Affiliation(s)
- Hanif Ali
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - J. Colin Murrell
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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17
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Molecular sequencing and analysis of soluble methane monooxygenase gene clusters from methanotroph Methylomonas sp. GYJ3. World J Microbiol Biotechnol 2006. [DOI: 10.1007/s11274-006-9227-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Blazyk JL, Gassner GT, Lippard SJ. Intermolecular electron-transfer reactions in soluble methane monooxygenase: a role for hysteresis in protein function. J Am Chem Soc 2005; 127:17364-76. [PMID: 16332086 PMCID: PMC2117352 DOI: 10.1021/ja0554054] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electron transfer from reduced nicotinamide adenine dinucleotide (NADH) to the hydroxylase component (MMOH) of soluble methane monooxygenase (sMMO) primes its non-heme diiron centers for reaction with dioxygen to generate high-valent iron intermediates that convert methane to methanol. This intermolecular electron-transfer step is facilitated by a reductase (MMOR), which contains [2Fe-2S] and flavin adenine dinucleotide (FAD) prosthetic groups. To investigate interprotein electron transfer, chemically reduced MMOR was mixed rapidly with oxidized MMOH in a stopped-flow apparatus, and optical changes associated with reductase oxidation were recorded. The reaction proceeds via four discrete kinetic phases corresponding to the transfer of four electrons into the two dinuclear iron sites of MMOH. Pre-equilibrating the hydroxylase with sMMO auxiliary proteins MMOB or MMOD severely diminishes electron-transfer throughput from MMOR, primarily by shifting the bulk of electron transfer to the slowest pathway. The biphasic reactions for electron transfer to MMOH from several MMOR ferredoxin analogues are also inhibited by MMOB and MMOD. These results, in conjunction with the previous finding that MMOB enhances electron-transfer rates from MMOR to MMOH when preformed MMOR-MMOH-MMOB complexes are allowed to react with NADH [Gassner, G. T.; Lippard, S. J. Biochemistry 1999, 38, 12768-12785], suggest that isomerization of the initial ternary complex is required for maximal electron-transfer rates. To account for the slow electron transfer observed for the ternary precomplex in this work, a model is proposed in which conformational changes imparted to the hydroxylase by MMOR are retained throughout the catalytic cycle. Several electron-transfer schemes are discussed with emphasis on those that invoke multiple interconverting MMOH populations.
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Affiliation(s)
- Jessica L Blazyk
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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19
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Ward N, Larsen Ø, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methé B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, Eisen JA. Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol 2004; 2:e303. [PMID: 15383840 PMCID: PMC517821 DOI: 10.1371/journal.pbio.0020303] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2004] [Accepted: 07/14/2004] [Indexed: 11/23/2022] Open
Abstract
Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. Despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. We report the first complete genome sequence to our knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath), obtained by the shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a methanotrophic lifestyle, including redundant pathways predicted to be involved in methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases. We used phylogenomic analysis, gene order information, and comparative analysis with the partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests the ability of M. capsulatus to scavenge copper (including a previously unreported nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project is evidence suggesting the existence of previously unsuspected metabolic flexibility in M. capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph ecology. The availability of the complete genome of M. capsulatus (Bath) deepens our understanding of methanotroph biology and its relationship to global carbon cycles. We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential.
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Affiliation(s)
- Naomi Ward
- The Institute for Genomic Research, Rockville, Maryland, USA.
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20
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Elsaied HE, Hayashi T, Naganuma T. Molecular analysis of deep-sea hydrothermal vent aerobic methanotrophs by targeting genes of 16S rRNA and particulate methane monooxygenase. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2004; 6:503-509. [PMID: 15791492 DOI: 10.1007/s10126-004-3042-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2003] [Accepted: 03/07/2004] [Indexed: 05/24/2023]
Abstract
Molecular diversity of deep-sea hydrothermal vent aerobic methanotrophs was studied using both 16S ribosomalDNA and pmoA encoding the subunit A of particulate methane monooxygenase (pMOA). Hydrothermal vent plume and chimney samples were collected from back-arc vent at Mid-Okinawa Trough (MOT), Japan, and the Trans-Atlantic Geotraverse (TAG) site along Mid-Atlantic Ridge, respectively. The target genes were amplified by polymerase chain reaction from the bulk DNA using specific primers and cloned. Fifty clones from each clone library were directly sequenced. The 16S rDNA sequences were grouped into 3 operational taxonomic units (OTUs), 2 from MOT and 1 from TAG. Two OTUs (1 MOT and 1 TAG) were located within the branch of type I methanotrophic ?-Proteobacteria. Another MOT OTU formed a unique phylogenetic lineage related to type I methanotrophs. Direct sequencing of 50 clones each from the MOT and TAG samples yielded 17 and 4 operational pmoA units (OPUs), respectively. The phylogenetic tree based on the pMOA amino acid sequences deduced from OPUs formed diverse phylogenetic lineages within the branch of type I methanotrophs, except for the OPU MOT-pmoA-8 related to type X methanotrophs. The deduced pMOA topologies were similar to those of all known pMOA, which may suggest that the pmoA gene is conserved through evolution. Neither the 16S rDNA nor pmoA molecular analysis could detect type II methanotrophs, which suggests the absence of type II methanotrophs in the collected vent samples.
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Affiliation(s)
- Hosam Easa Elsaied
- School of Biosphere Sciences, Hiroshima University, Higashi-hiroshima 739-8528, Japan
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21
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Blazyk JL, Lippard SJ. Domain engineering of the reductase component of soluble methane monooxygenase from Methylococcus capsulatus (Bath). J Biol Chem 2003; 279:5630-40. [PMID: 14613937 DOI: 10.1074/jbc.m308940200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Soluble methane monooxygenase (sMMO) from Methylococcus capsulatus (Bath) is a three-component enzyme system that catalyzes the conversion of methane to methanol. A reductase (MMOR), which contains [2Fe-2S] and FAD cofactors, facilitates electron transfer from NADH to the hydroxylase diiron active sites where dioxygen activation and substrate hydroxylation take place. By separately expressing the ferredoxin (MMORFd, MMOR residues 1-98) and FAD/NADH (MMOR-FAD, MMOR residues 99-348) domains of the reductase, nearly all biochemical properties of full-length MMOR are retained, except for interdomain electron transfer rates. To investigate the extent to which rapid electron transfer between domains might be restored and further to explore the modularity of MMOR, MMOR-Fd and MMOR-FAD were connected in a non-native fashion. Four different linker sequences were employed to create MMOR reversed-domain (MMOR-RD) constructs, MMOR(99-342)-linker-MMOR(2-98), with a domain connectivity observed in other homologous oxidoreductases. The optical, redox, and electron transfer properties of the four MMOR-RD proteins were characterized and compared with those of wild-type MMOR. The linker sequence plays a key role in controlling solvent accessibility to the FAD cofactor, as evidenced by perturbed flavin optical spectra, decreased FADox/FADsq redox potentials, and increased steady-state oxidase activities in three of the constructs. Stopped-flow optical spectroscopy revealed slow interdomain electron transfer (k < 0.04 s(-1) at 4 degrees C, compared with 90 s(-1) for wild-type MMOR) for all three MMOR-RD proteins with 7-residue linkers. A long (14-residue), flexible linker afforded much faster electron transfer between the FAD and [2Fe-2S] cofactors (k = 0.9 s(-1) at 4 degrees C).
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Affiliation(s)
- Jessica L Blazyk
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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22
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Baik MH, Newcomb M, Friesner RA, Lippard SJ. Mechanistic studies on the hydroxylation of methane by methane monooxygenase. Chem Rev 2003; 103:2385-419. [PMID: 12797835 DOI: 10.1021/cr950244f] [Citation(s) in RCA: 355] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Mu-Hyun Baik
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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23
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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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24
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Merkx M, Kopp DA, Sazinsky MH, Blazyk JL, Müller J, Lippard SJ. Dioxygen Activation and Methane Hydroxylation by Soluble Methane Monooxygenase: A Tale of Two Irons and Three Proteins. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3773(20010803)40:15%3c2782::aid-anie2782%3e3.0.co;2-p] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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25
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Merkx M, Kopp DA, Sazinsky MH, Blazyk JL, Müller J, Lippard SJ. Aktivierung von Disauerstoff und Hydroxylierung von Methan durch lösliche Methan-Monooxygenase: eine Geschichte von zwei Eisenatomen und drei Proteinen. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010803)113:15<2860::aid-ange2860>3.0.co;2-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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26
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Merkx M, Kopp DA, Sazinsky MH, Blazyk JL, Müller J, Lippard SJ. Dioxygen Activation and Methane Hydroxylation by Soluble Methane Monooxygenase: A Tale of Two Irons and Three Proteins. Angew Chem Int Ed Engl 2001; 40:2782-2807. [PMID: 29711993 DOI: 10.1002/1521-3773(20010803)40:15<2782::aid-anie2782>3.0.co;2-p] [Citation(s) in RCA: 461] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2001] [Revised: 05/03/2001] [Indexed: 11/11/2022]
Affiliation(s)
- Maarten Merkx
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue 18-590 Cambridge, MA 02139 (USA) Fax: (+1) 617-258-8150
| | - Daniel A Kopp
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue 18-590 Cambridge, MA 02139 (USA) Fax: (+1) 617-258-8150
| | - Matthew H Sazinsky
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue 18-590 Cambridge, MA 02139 (USA) Fax: (+1) 617-258-8150
| | - Jessica L Blazyk
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue 18-590 Cambridge, MA 02139 (USA) Fax: (+1) 617-258-8150
| | - Jens Müller
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue 18-590 Cambridge, MA 02139 (USA) Fax: (+1) 617-258-8150
| | - Stephen J Lippard
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue 18-590 Cambridge, MA 02139 (USA) Fax: (+1) 617-258-8150
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27
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Eguchi M, Kitagawa M, Suzuki Y, Nakamuara M, Kawai T, Okamura K, Sasaki S, Miyake Y. A field evaluation of in situ biodegradation of trichloroethylene through methane injection. WATER RESEARCH 2001; 35:2145-2152. [PMID: 11358293 DOI: 10.1016/s0043-1354(00)00494-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A field study of biodegradation of trichloroethylene (TCE) through methane injection was conducted at the yard of a home in Japan. Methane was selected as the safest substrate for injection into groundwater. Methane, oxygen, nitrate, and phosphate were introduced into groundwater contaminated with 220 microg/L of TCE. After a week of biostimulation, methane concentrations gradually decreased below the detection limit. Methane oxidizing bacterial numbers increased from 10 to 10(4) cells/mL with methane consumptions. During methane injection. 10-20% of TCE removal was observed. The biotransformation yield was 3-13 mgTCE/gCH4 in this field test. After methane injections were stopped, TCE removal was not observed. These results indicated that bioremediation using methane was useful as a safe technology for a TCE-contaminated area near homes.
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Affiliation(s)
- M Eguchi
- Central Research Laboratories, Organo Corporation, Toda, Japan.
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28
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Kovács KL, Bagyinka C, Bodrossy L, Csáki R, Fodor B, Gyõrfi K, Hanczár T, Kálmán M, Õsz J, Perei K, Polyák B, Rákhely G, Takács M, Tóth A, Tusz J. Recent advances in biohydrogen research. Pflugers Arch 2000. [DOI: 10.1007/bf03376530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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29
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Iwamoto T, Tani K, Nakamura K, Suzuki Y, Kitagawa M, Eguchi M, Nasu M. Monitoring impact of in situ biostimulation treatment on groundwater bacterial community by DGGE. FEMS Microbiol Ecol 2000; 32:129-141. [PMID: 10817866 DOI: 10.1111/j.1574-6941.2000.tb00707.x] [Citation(s) in RCA: 169] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Changes in bacterial diversity during the field experiment on biostimulation were monitored by denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rDNA fragments. The results revealed that the bacterial community was disturbed after the start of treatment, continued to change for 45 days or 60 days and then formed a relatively stable community different from the original community structure. DGGE analysis of soluble methane monooxygenase (sMMO) hydroxylase gene fragments, mmoX, was performed to monitor the shifts in the numerically dominant sMMO-containing methanotrophs during the field experiment. Sequence analysis on the mmoX gene fragments from the DGGE bands implied that the biostimulation treatment caused a shift of potential dominant sMMO-containing methanotrophs from type I methanotrophs to type II methanotrophs.
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Affiliation(s)
- T Iwamoto
- Environmental Science and Microbiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka, Japan
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30
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Frenzel P. Plant-Associated Methane Oxidation in Rice Fields and Wetlands. ADVANCES IN MICROBIAL ECOLOGY 2000. [DOI: 10.1007/978-1-4615-4187-5_3] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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31
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Bourne DG, Holmes AJ, Iversen N, Murrell JC. Fluorescent oligonucleotide rDNA probes for specific detection of methane oxidising bacteria. FEMS Microbiol Ecol 2000; 31:29-38. [PMID: 10620716 DOI: 10.1111/j.1574-6941.2000.tb00668.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Oligonucleotide probes targeting the 16S rRNA of distinct phylogenetic groups of methanotrophs were designed for the in situ detection of these organisms. A probe, MG-64, detected specifically type I methanotrophs, while probes MA-221 and MA-621, detected type II methanotrophs in whole cell hybridisations. A probe Mc1029 was also designed which targeted only organisms from the Methylococcus genus after whole cell hybridisations. All probes were labelled with the fluorochrome Cy3 and optimum conditions for hybridisation were determined. Non-specific target sites of the type I (MG-64) and type II (MA-621) probes to non-methanotrophic organisms are highlighted. The probes are however used in studying enrichment cultures and environments where selective pressure favours the growth of methanotrophs over other organisms. The application of these probes was demonstrated in the detection of type I methanotrophs with the MG-64 probe in an enrichment culture from an estuarine sample demonstrating methane oxidation. The detection of type I methanotrophs was confirmed by a 16S rDNA molecular analysis of the estuarine enrichment culture which demonstrated that the most abundant bacterial clone type in the 16S rDNA library was most closely related to Methylobacter sp. strain BB5.1, a type I methanotroph also isolated from an estuarine environment.
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Affiliation(s)
- DG Bourne
- Department of Biological Sciences, University of Warwick, Coventry, UK
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32
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Shigematsu T, Hanada S, Eguchi M, Kamagata Y, Kanagawa T, Kurane R. Soluble methane monooxygenase gene clusters from trichloroethylene-degrading Methylomonas sp. strains and detection of methanotrophs during in situ bioremediation. Appl Environ Microbiol 1999; 65:5198-206. [PMID: 10583965 PMCID: PMC91705 DOI: 10.1128/aem.65.12.5198-5206.1999] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/1999] [Accepted: 09/10/1999] [Indexed: 11/20/2022] Open
Abstract
The soluble MMO (sMMO) gene clusters from group I methanotrophs were characterized. An 8.1-kb KpnI fragment from Methylomonas sp. strain KSWIII and a 7.5-kb SalI fragment from Methylomonas sp. strain KSPIII which contained the sMMO gene clusters were cloned and sequenced. The sequences of these two fragments were almost identical. The sMMO gene clusters in the fragment consisted of six open reading frames which were 52 to 79% similar to the corresponding genes of previously described sMMO gene clusters of the group II and group X methanotrophs. The phylogenetic analysis of the predicted amino acid sequences of sMMO demonstrated that the sMMOs from these strains were closer to that from M. capsulatus Bath in the group X methanotrophs than to those from Methylosinus trichosporium OB3b and Methylocystis sp. strain M in the group II methanotrophs. Based on the sequence data of sMMO genes of our strains and other methanotrophs, we designed a new PCR primer to amplify sMMO gene fragments of all the known methanotrophs harboring the mmoX gene. The primer set was successfully used for detecting methanotrophs in the groundwater of trichloroethylene-contaminated sites during in situ-biostimulation treatments.
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Affiliation(s)
- T Shigematsu
- National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan.
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33
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Abstract
Microbial sulfur-specific transformations have been identified that selectively desulfurize organic sulfur compounds in fossil fuels. Recent discoveries related to biodesulfurization mechanisms may lead to commercial applications of biodesulfurization through engineering recombinant strains for over-expression of biodesulfurization genes, removal of end product repression, and/or by combining relevant industrial and environmental traits with improvements in bioprocess design.
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Affiliation(s)
- B L McFarland
- MicroBioTech Consulting, 1143 Halifax Avenue, Davis, CA 95616-2718, USA.
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34
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McDonald IR, Murrell JC. The particulate methane monooxygenase gene pmoA and its use as a functional gene probe for methanotrophs. FEMS Microbiol Lett 1997; 156:205-10. [PMID: 9513266 DOI: 10.1111/j.1574-6968.1997.tb12728.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The particulate methane monooxygenase gene pmoA, encoding the 27 kDa polypeptide of the membrane-bound particulate methane monooxygenase, was amplified by PCR from DNA isolated from a blanket peat bog and from enrichment cultures established, from the same environment, using methane as sole carbon and energy source. The resulting 525 bp PCR products were cloned and a representative number of clones were sequenced. Phylogenetic analysis of the derived amino acid sequences of the pmoA clones retrieved directly from environmental DNA samples revealed that they form a distinct cluster within representative PmoA sequences from type II methanotrophs and may originate from a novel group of acidophilic methanotrophs. The study also demonstrated the utility of the pmoA gene as a phylogenetic marker for identifying methanotroph-specific DNA sequences in the environment.
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Affiliation(s)
- I R McDonald
- Department of Biological Sciences, University of Warwick, Coventry, UK
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35
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McDonald IR, Murrell JC. The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs. Appl Environ Microbiol 1997; 63:3218-24. [PMID: 9251208 PMCID: PMC168619 DOI: 10.1128/aem.63.8.3218-3224.1997] [Citation(s) in RCA: 199] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The methanol dehydrogenase gene mxaF, encoding the large subunit of the enzyme, was amplified from the DNA of a number of representative methanotrophs, methyletrophs, and environmental samples by PCR using primers designed from regions of conserved amino acid sequence identified by comparison of three known sequences of the large subunit of methanol dehydrogenase. The resulting 550-bp PCR products were cloned and sequenced. Analysis of the predicted amino acid sequences corresponding to these mxaF genes revealed strong sequence conservation. Of the 172 amino acid residues, 47% were conserved among all 22 sequences obtained in this study. Phylogenetic analysis of these MxaF sequences showed that those from type I and type II methanotrophs form two distinct clusters and are separate from MxaF sequences of other gram-negative methylotrophs. MxaF sequences retrieved by PCR from DNA isolated from a blanket bog peat core sample formed a distinct phylogenetic cluster within the MxaF sequences of type II methanotrophs and may originate from a novel group of acidophilic methanotrophs which have yet to be cultured from this environment.
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Affiliation(s)
- I R McDonald
- Department of Biological Sciences, University of Warwick, United Kingdom
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McDonald IR, Uchiyama H, Kambe S, Yagi O, Murrell JC. The soluble methane monooxygenase gene cluster of the trichloroethylene-degrading methanotroph Methylocystis sp. strain M. Appl Environ Microbiol 1997; 63:1898-904. [PMID: 9143121 PMCID: PMC168481 DOI: 10.1128/aem.63.5.1898-1904.1997] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In methanotrophic bacteria, methane is oxidized to methanol by the enzyme methane monooxygenase (MMO). The soluble MMO enzyme complex from Methylocystis sp. strain M also oxidizes a wide range of aliphatic and aromatic compounds, including trichloroethylene. In this study, heterologous DNA probes from the type II methanotroph Methylosinus trichosporium OB3b were used to isolate souble MMO (sMMO) genes from the type II methanotroph Methylocystis sp. strain M. sMMO genes from strain M are clustered on the chromosome and show a high degree of identity with the corresponding genes from Methylosinus trichosporium OB3b. Sequencing and phylogenetic analysis of the 16S rRNA gene from Methylocystis sp. strain M have confirmed that it is most closely related to the type II methanotroph Methylocystis parvus OBBP, which, unlike Methylocystis sp. strain M, does not possess an sMMO. A similar phylogenetic analysis using the pmoA gene, which encodes the 27-kDa polypeptide of the particulate MMO, also places Methylocystis sp. strain M firmly in the genus Methylocystis. This is the first report of isolation and characterization of methane oxidation genes from methanotrophs of the genus Methylocystis.
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Affiliation(s)
- I R McDonald
- Department of Biological Sciences, University of Warwick, Coventry, United Kingdom
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Conrad R. Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microbiol Rev 1996; 60:609-40. [PMID: 8987358 PMCID: PMC239458 DOI: 10.1128/mr.60.4.609-640.1996] [Citation(s) in RCA: 360] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Production and consumption processes in soils contribute to the global cycles of many trace gases (CH4, CO, OCS, H2, N2O, and NO) that are relevant for atmospheric chemistry and climate. Soil microbial processes contribute substantially to the budgets of atmospheric trace gases. The flux of trace gases between soil and atmosphere is usually the result of simultaneously operating production and consumption processes in soil: The relevant processes are not yet proven with absolute certainty, but the following are likely for trace gas consumption: H2 oxidation by abiontic soil enzymes; CO cooxidation by the ammonium monooxygenase of nitrifying bacteria; CH4 oxidation by unknown methanotrophic bacteria that utilize CH4 for growth; OCS hydrolysis by bacteria containing carbonic anhydrase; N2O reduction to N2 by denitrifying bacteria; NO consumption by either reduction to N2O in denitrifiers or oxidation to nitrate in heterotrophic bacteria. Wetland soils, in contrast to upland soils are generally anoxic and thus support the production of trace gases (H2, CO, CH4, N2O, and NO) by anaerobic bacteria such as fermenters, methanogens, acetogens, sulfate reducers, and denitrifiers. Methane is the dominant gaseous product of anaerobic degradation of organic matter and is released into the atmosphere, whereas the other trace gases are only intermediates, which are mostly cycled within the anoxic habitat. A significant percentage of the produced methane is oxidized by methanotrophic bacteria at anoxic-oxic interfaces such as the soil surface and the root surface of aquatic plants that serve as conduits for O2 transport into and CH4 transport out of the wetland soils. The dominant production processes in upland soils are different from those in wetland soils and include H2 production by biological N2 fixation, CO production by chemical decomposition of soil organic matter, and NO and N2O production by nitrification and denitrification. The processes responsible for CH4 production in upland soils are completely unclear, as are the OCS production processes in general. A problem for future research is the attribution of trace gas metabolic processes not only to functional groups of microorganisms but also to particular taxa. Thus, it is completely unclear how important microbial diversity is for the control of trace gas flux at the ecosystem level. However, different microbial communities may be part of the reason for differences in trace gas metabolism, e.g., effects of nitrogen fertilizers on CH4 uptake by soil; decrease of CH4 production with decreasing temperature; or different rates and modes of NO and N2O production in different soils and under different conditions.
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Affiliation(s)
- R Conrad
- Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, Germany
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McDonald IR, Hall GH, Pickup RW, Colin Murrell J. Methane oxidation potential and preliminary analysis of methanotrophs in blanket bog peat using molecular ecology techniques. FEMS Microbiol Ecol 1996. [DOI: 10.1111/j.1574-6941.1996.tb00347.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Abstract
Methane-utilizing bacteria (methanotrophs) are a diverse group of gram-negative bacteria that are related to other members of the Proteobacteria. These bacteria are classified into three groups based on the pathways used for assimilation of formaldehyde, the major source of cell carbon, and other physiological and morphological features. The type I and type X methanotrophs are found within the gamma subdivision of the Proteobacteria and employ the ribulose monophosphate pathway for formaldehyde assimilation, whereas type II methanotrophs, which employ the serine pathway for formaldehyde assimilation, form a coherent cluster within the beta subdivision of the Proteobacteria. Methanotrophic bacteria are ubiquitous. The growth of type II bacteria appears to be favored in environments that contain relatively high levels of methane, low levels of dissolved oxygen, and limiting concentrations of combined nitrogen and/or copper. Type I methanotrophs appear to be dominant in environments in which methane is limiting and combined nitrogen and copper levels are relatively high. These bacteria serve as biofilters for the oxidation of methane produced in anaerobic environments, and when oxygen is present in soils, atmospheric methane is oxidized. Their activities in nature are greatly influenced by agricultural practices and other human activities. Recent evidence indicates that naturally occurring, uncultured methanotrophs represent new genera. Methanotrophs that are capable of oxidizing methane at atmospheric levels exhibit methane oxidation kinetics different from those of methanotrophs available in pure cultures. A limited number of methanotrophs have the genetic capacity to synthesize a soluble methane monooxygenase which catalyzes the rapid oxidation of environmental pollutants including trichloroethylene.
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Affiliation(s)
- R S Hanson
- Department of Microbiology, University of Minnesota, Minneapolis 55455, USA.
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Nielsen AK, Gerdes K, Degn H, Colin MJ. Regulation of bacterial methane oxidation: transcription of the soluble methane mono-oxygenase operon of Methylococcus capsulatus (Bath) is repressed by copper ions. MICROBIOLOGY (READING, ENGLAND) 1996; 142 ( Pt 5):1289-1296. [PMID: 8704968 DOI: 10.1099/13500872-142-5-1289] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Methane is oxidized to methanol by the enzyme methane mono-oxygenase (MMO) in methanotrophic bacteria. In previous work, this multicomponent enzyme system has been extensively characterized at the biochemical and molecular level. Copper ions have been shown to irreversibly inhibit MMO activity in vivo and in vitro, but the effect of copper ions on transcription of the genes encoding the soluble (cytoplasmic) MMO (sMMO) has not previously been investigated. To examine more closely the regulation of bacterial methane oxidation and to determine the role of copper in this process, we have investigated transcriptional regulation of the sMMO gene cluster in the methanotrophic bacterium Methylococcus capsulatus (Bath). Using Northern blot analysis and primer extension experiments, it was shown that the six ORFs of the sMMO gene cluster are organized as an operon and the transcripts produced upon expression of this operon have been identified. The synthesis of these transcripts was under control of a single copper-regulated promoter, which is as yet not precisely defined.
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Affiliation(s)
- Allan K Nielsen
- Department of Molecular Biology, Odense University, DK-5230 Odense M, Denmark
| | - Kenn Gerdes
- Department of Molecular Biology, Odense University, DK-5230 Odense M, Denmark
| | - Hans Degn
- Department of Biochemistry, Odense University, DK-5230 Odense M, Denmark
| | - Murrell J Colin
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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