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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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Zhu Y, Koo CW, Cassidy CK, Spink MC, Ni T, Zanetti-Domingues LC, Bateman B, Martin-Fernandez ML, Shen J, Sheng Y, Song Y, Yang Z, Rosenzweig AC, Zhang P. Structure and activity of particulate methane monooxygenase arrays in methanotrophs. Nat Commun 2022; 13:5221. [PMID: 36064719 PMCID: PMC9445010 DOI: 10.1038/s41467-022-32752-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/16/2022] [Indexed: 01/29/2023] Open
Abstract
Methane-oxidizing bacteria play a central role in greenhouse gas mitigation and have potential applications in biomanufacturing. Their primary metabolic enzyme, particulate methane monooxygenase (pMMO), is housed in copper-induced intracytoplasmic membranes (ICMs), of which the function and biogenesis are not known. We show by serial cryo-focused ion beam (cryoFIB) milling/scanning electron microscope (SEM) volume imaging and lamellae-based cellular cryo-electron tomography (cryoET) that these ICMs are derived from the inner cell membrane. The pMMO trimer, resolved by cryoET and subtomogram averaging to 4.8 Å in the ICM, forms higher-order hexagonal arrays in intact cells. Array formation correlates with increased enzymatic activity, highlighting the importance of studying the enzyme in its native environment. These findings also demonstrate the power of cryoET to structurally characterize native membrane enzymes in the cellular context.
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Affiliation(s)
- Yanan Zhu
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christopher W Koo
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
| | - C Keith Cassidy
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Matthew C Spink
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Tao Ni
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Laura C Zanetti-Domingues
- Central Laser Facility, Science and Technology Facility Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire, UK
| | - Benji Bateman
- Central Laser Facility, Science and Technology Facility Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire, UK
| | - Marisa L Martin-Fernandez
- Central Laser Facility, Science and Technology Facility Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire, UK
| | - Juan Shen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuewen Sheng
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Yun Song
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Zhengyi Yang
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA.
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
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3
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An Overview on Methanotrophs and the Role of Methylosinus trichosporium OB3b for Biotechnological Applications. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0046-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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4
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Naizabekov S, Lee EY. Genome-Scale Metabolic Model Reconstruction and in Silico Investigations of Methane Metabolism in Methylosinus trichosporium OB3b. Microorganisms 2020; 8:microorganisms8030437. [PMID: 32244934 PMCID: PMC7144005 DOI: 10.3390/microorganisms8030437] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/16/2020] [Accepted: 03/19/2020] [Indexed: 01/09/2023] Open
Abstract
Methylosinus trichosporium OB3b is an obligate aerobic methane-utilizing alpha-proteobacterium. Since its isolation, M. trichosporium OB3b has been established as a model organism to study methane metabolism in type II methanotrophs. M. trichosporium OB3b utilizes soluble and particulate methane monooxygenase (sMMO and pMMO respectively) for methane oxidation. While the source of electrons is known for sMMO, there is less consensus regarding electron donor to pMMO. To investigate this and other questions regarding methane metabolism, the genome-scale metabolic model for M. trichosporium OB3b (model ID: iMsOB3b) was reconstructed. The model accurately predicted oxygen: methane molar uptake ratios and specific growth rates on nitrate-supplemented medium with methane as carbon and energy source. The redox-arm mechanism which links methane oxidation with complex I of electron transport chain has been found to be the most optimal mode of electron transfer. The model was also qualitatively validated on ammonium-supplemented medium indicating its potential to accurately predict methane metabolism in different environmental conditions. Finally, in silico investigations regarding flux distribution in central carbon metabolism of M. trichosporium OB3b were performed. Overall, iMsOB3b can be used as an organism-specific knowledgebase and a platform for hypothesis-driven theoretical investigations of methane metabolism.
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Semrau JD, DiSpirito AA. Methanobactin: A Novel Copper-Binding Compound Produced by Methanotrophs. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/978-3-030-23261-0_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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6
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A Mutagenic Screen Identifies a TonB-Dependent Receptor Required for the Lanthanide Metal Switch in the Type I Methanotroph "Methylotuvimicrobium buryatense" 5GB1C. J Bacteriol 2019; 201:JB.00120-19. [PMID: 31085692 DOI: 10.1128/jb.00120-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/07/2019] [Indexed: 12/23/2022] Open
Abstract
Several of the metabolic enzymes in methanotrophic bacteria rely on metals for both their expression and their catalysis. The MxaFI methanol dehydrogenase enzyme complex uses calcium as a cofactor to oxidize methanol, while the alternative methanol dehydrogenase XoxF uses lanthanide metals such as lanthanum and cerium for the same function. Lanthanide metals, abundant in the earth's crust, strongly repress the transcription of mxaF yet activate the transcription of xoxF This regulatory program, called the "lanthanide switch," is central to methylotrophic metabolism, but only some of its components are known. To uncover additional components of the lanthanide switch, we developed a chemical mutagenesis system in the type I gammaproteobacterial methanotroph "Methylotuvimicrobium buryatense" 5GB1C and designed a selection system for mutants unable to repress the mxaF promoter in the presence of lanthanum. Whole-genome resequencing for multiple lanthanide switch mutants identified several unique point mutations in a single gene encoding a TonB-dependent receptor, which we have named LanA. The LanA TonB-dependent receptor is absolutely required for the lanthanide switch and controls the expression of a small set of genes. While mutation of the lanA gene does not affect the amount of cell-associated lanthanum, it is essential for growth in the absence of the MxaF methanol dehydrogenase, suggesting that LanA is involved in lanthanum uptake to supply the XoxF methanol dehydrogenase with its critical metal ion cofactor. The discovery of this novel component of the lanthanide regulatory system highlights the complexity of this circuit and suggests that further components are likely involved.IMPORTANCE Lanthanide metals, or rare earth elements, are abundant in nature and used heavily in technological devices. Biological interactions with lanthanides are just beginning to be unraveled. Until very recently, microbial mechanisms of lanthanide metal interaction and uptake were unknown. The TonB-dependent receptor LanA is the first lanthanum receptor identified in a methanotroph. Sequence homology searches with known metal transporters and regulators could not be used to identify LanA or other lanthanide metal switch components, and this method for mutagenesis and selection was required to identify the receptor. This work advances the knowledge of microbe-metal interactions in environmental niches that impact atmospheric methane levels and are thus relevant to climate change.
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7
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Fisher OS, Kenney GE, Ross MO, Ro SY, Lemma BE, Batelu S, Thomas PM, Sosnowski VC, DeHart CJ, Kelleher NL, Stemmler TL, Hoffman BM, Rosenzweig AC. Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria. Nat Commun 2018; 9:4276. [PMID: 30323281 PMCID: PMC6189053 DOI: 10.1038/s41467-018-06681-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/20/2018] [Indexed: 12/24/2022] Open
Abstract
Methane-oxidizing microbes catalyze the oxidation of the greenhouse gas methane using the copper-dependent enzyme particulate methane monooxygenase (pMMO). Isolated pMMO exhibits lower activity than whole cells, however, suggesting that additional components may be required. A pMMO homolog, ammonia monooxygenase (AMO), converts ammonia to hydroxylamine in ammonia-oxidizing bacteria (AOB) which produce another potent greenhouse gas, nitrous oxide. Here we show that PmoD, a protein encoded within many pmo operons that is homologous to the AmoD proteins encoded within AOB amo operons, forms a copper center that exhibits the features of a well-defined CuA site using a previously unobserved ligand set derived from a cupredoxin homodimer. PmoD is critical for copper-dependent growth on methane, and genetic analyses strongly support a role directly related to pMMO and AMO. These findings identify a copper-binding protein that may represent a missing link in the function of enzymes critical to the global carbon and nitrogen cycles. Methane- and ammonia-oxidizing bacteria use the integral membrane, copper-dependent enzymes particulate methane monooxygenase (pMMO) and ammonia monooxygenase (AMO) to oxidize methane and ammonia. Here the authors structurally characterize the copper-binding protein PmoD, which contains an unusual CuA site and their genetic analyses strongly support a pMMO and AMO related function of PmoD.
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Affiliation(s)
- Oriana S Fisher
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Grace E Kenney
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Matthew O Ross
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Soo Y Ro
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Betelehem E Lemma
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Sharon Batelu
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, 48201, MI, USA
| | - Paul M Thomas
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Victoria C Sosnowski
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Caroline J DeHart
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Neil L Kelleher
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, 48201, MI, USA
| | - Brian M Hoffman
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA.
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8
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Abstract
Copper-binding metallophores, or chalkophores, play a role in microbial copper homeostasis that is analogous to that of siderophores in iron homeostasis. The best-studied chalkophores are members of the methanobactin (Mbn) family-ribosomally produced, posttranslationally modified natural products first identified as copper chelators responsible for copper uptake in methane-oxidizing bacteria. To date, Mbns have been characterized exclusively in those species, but there is genomic evidence for their production in a much wider range of bacteria. This review addresses the current state of knowledge regarding the function, biosynthesis, transport, and regulation of Mbns. While the roles of several proteins in these processes are supported by substantial genetic and biochemical evidence, key aspects of Mbn manufacture, handling, and regulation remain unclear. In addition, other natural products that have been proposed to mediate copper uptake as well as metallophores that have biologically relevant roles involving copper binding, but not copper uptake, are discussed.
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Affiliation(s)
- Grace E Kenney
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA; ,
| | - Amy C Rosenzweig
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA; ,
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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9
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Kenney GE, Rosenzweig AC. Methanobactins: Maintaining copper homeostasis in methanotrophs and beyond. J Biol Chem 2018; 293:4606-4615. [PMID: 29348173 PMCID: PMC5880147 DOI: 10.1074/jbc.tm117.000185] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Methanobactins (Mbns) are ribosomally produced, post-translationally modified natural products that bind copper with high affinity and specificity. Originally identified in methanotrophic bacteria, which have a high need for copper, operons encoding these compounds have also been found in many non-methanotrophic bacteria. The proteins responsible for Mbn biosynthesis include several novel enzymes. Mbn transport involves export through a multidrug efflux pump and re-internalization via a TonB-dependent transporter. Release of copper from Mbn and the molecular basis for copper regulation of Mbn production remain to be elucidated. Future work is likely to result in the identification of new enzymatic chemistry, opportunities for bioengineering and drug targeting of copper metabolism, and an expanded understanding of microbial metal homeostasis.
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Affiliation(s)
- Grace E Kenney
- Departments of Molecular Biosciences, Evanston, Illinois 60208
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences, Evanston, Illinois 60208; Chemistry, Northwestern University, Evanston, Illinois 60208.
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10
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Abstract
Aerobic methanotrophs have long been known to play a critical role in the global carbon cycle, being capable of converting methane to biomass and carbon dioxide. Interestingly, these microbes exhibit great sensitivity to copper and rare-earth elements, with the expression of key genes involved in the central pathway of methane oxidation controlled by the availability of these metals. That is, these microbes have a "copper switch" that controls the expression of alternative methane monooxygenases and a "rare-earth element switch" that controls the expression of alternative methanol dehydrogenases. Further, it has been recently shown that some methanotrophs can detoxify inorganic mercury and demethylate methylmercury; this finding is remarkable, as the canonical organomercurial lyase does not exist in these methanotrophs, indicating that a novel mechanism is involved in methylmercury demethylation. Here, we review recent findings on methanotrophic interactions with metals, with a particular focus on these metal switches and the mechanisms used by methanotrophs to bind and sequester metals.
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11
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Abstract
Methanobactins (Mbns) are ribosomally produced, post-translationally modified peptide (RiPP) natural products that bind copper with high affinity using nitrogen-containing heterocycles and thioamide groups. In some methanotrophic bacteria, Mbns are secreted under conditions of copper starvation and then re-internalized as a copper source for the enzyme particulate methane monooxygenase (pMMO). Genome mining studies have led to the identification and classification of operons encoding the Mbn precursor peptide (MbnA) as well as a number of putative transport, regulatory, and biosynthetic proteins. These Mbn operons are present in non-methanotrophic bacteria as well, suggesting a broader role in and perhaps beyond copper acquisition. Genetic and biochemical studies indicate that specific operon-encoded proteins are involved in Mbn transport and provide insight into copper-responsive gene regulation in methanotrophs. Mbn biosynthesis is not yet understood, but combined analysis of Mbn structures, MbnA sequences, and operon content represents a powerful approach to elucidating the roles of specific biosynthetic enzymes. Future work will likely lead to the discovery of unique pathways for natural product biosynthesis and new mechanisms of microbial metal homeostasis.
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Affiliation(s)
- Laura M K Dassama
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | - Grace E Kenney
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | - Amy C Rosenzweig
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA. and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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12
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Gu W, Farhan Ul Haque M, Semrau JD. Characterization of the role of copCD in copper uptake and the ‘copper-switch’ in Methylosinus trichosporium OB3b. FEMS Microbiol Lett 2017; 364:3796321. [DOI: 10.1093/femsle/fnx094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/03/2017] [Indexed: 11/13/2022] Open
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13
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Kenney GE, Sadek M, Rosenzweig AC. Copper-responsive gene expression in the methanotroph Methylosinus trichosporium OB3b. Metallomics 2016; 8:931-40. [PMID: 27087171 PMCID: PMC6195801 DOI: 10.1039/c5mt00289c] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Methanotrophic bacteria convert methane to methanol using methane monooxygenase (MMO) enzymes. In many strains, either an iron-containing soluble (sMMO) or a copper-containing particulate (pMMO) enzyme can be produced depending on copper availability; the mechanism of this copper switch has not been elucidated. A key player in methanotroph copper homeostasis is methanobactin (Mbn), a ribosomally produced, post-translationally modified natural product with a high affinity for copper. The Mbn precursor peptide is encoded within an operon that contains a range of putative transporters, regulators, and biosynthetic proteins, but the involvement of these genes in Mbn-related processes remains unclear. Extensive time-dependent qRT-PCR studies of Methylosinus trichosporium OB3b and the constitutive sMMO-producing mutant M. trichosporium OB3b PP358 show that the Mbn operon is indeed copper-regulated, providing experimental support for its bioinformatics-based identification. Moreover, the Mbn operon is co-regulated with the sMMO operon and reciprocally regulated with the pMMO operon. Within the Mbn and sMMO operons, a subset of regulatory genes exhibits a distinct and shared pattern of expression, consistent with their proposed functions as internal regulators. In addition, genome sequencing of the M. trichosporium OB3b PP358 mutant provides new evidence for the involvement of genes adjacent to the pMMO operon in methanotroph copper homeostasis.
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Affiliation(s)
- Grace E. Kenney
- Department of Molecular Biosciences, Northwestern University, Evanston,IL 60208, USA.
| | - Monica Sadek
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences, Northwestern University, Evanston,IL 60208, USA.
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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14
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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: 84] [Impact Index Per Article: 10.5] [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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15
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Kim K, Seo K, Lee J, Kim MG, Ha KS, Kim C. Investigation and prediction of the salting-out effect of methane in various aqueous electrolyte solutions. J IND ENG CHEM 2016. [DOI: 10.1016/j.jiec.2015.10.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Biological conversion of methane to liquid fuels: status and opportunities. Biotechnol Adv 2014; 32:1460-75. [PMID: 25281583 DOI: 10.1016/j.biotechadv.2014.09.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 09/01/2014] [Accepted: 09/24/2014] [Indexed: 12/21/2022]
Abstract
Methane is the main component of natural gas and biogas. As an abundant energy source, methane is crucial not only to meet current energy needs but also to achieve a sustainable energy future. Conversion of methane to liquid fuels provides energy-dense products and therefore reduces costs for storage, transportation, and distribution. Compared to thermochemical processes, biological conversion has advantages such as high conversion efficiency and using environmentally friendly processes. This paper is a comprehensive review of studies on three promising groups of microorganisms (methanotrophs, ammonia-oxidizing bacteria, and acetogens) that hold potential in converting methane to liquid fuels; their habitats, biochemical conversion mechanisms, performance in liquid fuels production, and genetic modification to enhance the conversion are also discussed. To date, methane-to-methanol conversion efficiencies (moles of methanol produced per mole methane consumed) of up to 80% have been reported. A number of issues that impede scale-up of this technology, such as mass transfer limitations of methane, inhibitory effects of H2S in biogas, usage of expensive chemicals as electron donors, and lack of native strains capable of converting methane to liquid fuels other than methanol, are discussed. Future perspectives and strategies in addressing these challenges are also discussed.
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17
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Solomon EI, Heppner DE, Johnston EM, Ginsbach JW, Cirera J, Qayyum M, Kieber-Emmons MT, Kjaergaard CH, Hadt RG, Tian L. Copper active sites in biology. Chem Rev 2014; 114:3659-853. [PMID: 24588098 PMCID: PMC4040215 DOI: 10.1021/cr400327t] [Citation(s) in RCA: 1138] [Impact Index Per Article: 113.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - David E. Heppner
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | - Jake W. Ginsbach
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Jordi Cirera
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Munzarin Qayyum
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | | | - Ryan G. Hadt
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Li Tian
- Department of Chemistry, Stanford University, Stanford, CA, 94305
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18
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Semrau JD, Jagadevan S, DiSpirito AA, Khalifa A, Scanlan J, Bergman BH, Freemeier BC, Baral BS, Bandow NL, Vorobev A, Haft DH, Vuilleumier S, Murrell JC. Methanobactin and MmoD work in concert to act as the 'copper-switch' in methanotrophs. Environ Microbiol 2013; 15:3077-86. [PMID: 23682956 DOI: 10.1111/1462-2920.12150] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/21/2013] [Indexed: 10/26/2022]
Abstract
Biological oxidation of methane to methanol by aerobic bacteria is catalysed by two different enzymes, the cytoplasmic or soluble methane monooxygenase (sMMO) and the membrane-bound or particulate methane monooxygenase (pMMO). Expression of MMOs is controlled by a 'copper-switch', i.e. sMMO is only expressed at very low copper : biomass ratios, while pMMO expression increases as this ratio increases. Methanotrophs synthesize a chalkophore, methanobactin, for the binding and import of copper. Previous work suggested that methanobactin was formed from a polypeptide precursor. Here we report that deletion of the gene suspected to encode for this precursor, mbnA, in Methylosinus trichosporium OB3b, abolishes methanobactin production. Further, gene expression assays indicate that methanobactin, together with another polypeptide of previously unknown function, MmoD, play key roles in regulating expression of MMOs. Based on these data, we propose a general model explaining how expression of the MMO operons is regulated by copper, methanobactin and MmoD. The basis of the 'copper-switch' is MmoD, and methanobactin amplifies the magnitude of the switch. Bioinformatic analysis of bacterial genomes indicates that the production of methanobactin-like compounds is not confined to methanotrophs, suggesting that its use as a metal-binding agent and/or role in gene regulation may be widespread in nature.
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Affiliation(s)
- Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
| | - Sheeja Jagadevan
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, 48109-2125, USA
| | - Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Ashraf Khalifa
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.,Botany Department, Faculty of Science, Beni-Suef University, Beni-Suef, 65211, Egypt
| | - Julie Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Brandt H Bergman
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Brittani C Freemeier
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Bipin S Baral
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Nathan L Bandow
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Alexey Vorobev
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, 48109-2125, USA
| | - Daniel H Haft
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA
| | - Stéphane Vuilleumier
- Equipe Adaptations et Interactions Microbiennes dans l'Environnement, Département Micro-organismes, Génomes, Environnement, UMR 7156 Université de Strasbourg - CNRS, Université de Strasbourg, 67083, Strasbourg Cédex, France
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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Matsen JB, Yang S, Stein LY, Beck D, Kalyuzhnaya MG. Global Molecular Analyses of Methane Metabolism in Methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: Transcriptomic Study. Front Microbiol 2013; 4:40. [PMID: 23565111 PMCID: PMC3615186 DOI: 10.3389/fmicb.2013.00040] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 02/17/2013] [Indexed: 11/20/2022] Open
Abstract
Methane utilizing bacteria (methanotrophs) are important in both environmental and biotechnological applications, due to their ability to convert methane to multicarbon compounds. However, systems-level studies of methane metabolism have not been carried out in methanotrophs. In this work we have integrated genomic and transcriptomic information to provide an overview of central metabolic pathways for methane utilization in Methylosinus trichosporium OB3b, a model alphaproteobacterial methanotroph. Particulate methane monooxygenase, PQQ-dependent methanol dehydrogenase, the H4MPT-pathway, and NAD-dependent formate dehydrogenase are involved in methane oxidation to CO2. All genes essential for operation of the serine cycle, the ethylmalonyl-CoA (EMC) pathway, and the citric acid (TCA) cycle were expressed. PEP-pyruvate-oxaloacetate interconversions may have a function in regulation and balancing carbon between the serine cycle and the EMC pathway. A set of transaminases may contribute to carbon partitioning between the pathways. Metabolic pathways for acquisition and/or assimilation of nitrogen and iron are discussed.
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Affiliation(s)
- Janet B Matsen
- Department of Chemical Engineering, University of Washington Seattle, WA, USA
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Kenney GE, Rosenzweig AC. Chemistry and biology of the copper chelator methanobactin. ACS Chem Biol 2012; 7:260-8. [PMID: 22126187 DOI: 10.1021/cb2003913] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Methanotrophic bacteria, organisms that oxidize methane, produce a small copper chelating molecule called methanobactin (Mb). Mb binds Cu(I) with high affinity and is hypothesized to mediate copper acquisition from the environment. Recent advances in Mb characterization include revision of the chemical structure of Mb from Methylosinus trichosporium OB3b and further investigation of its biophysical properties. In addition, Mb production by several other methanotroph strains has been investigated, and preliminary characterization suggests diversity in chemical composition. Initial clues into Mb biosynthesis have been obtained by identification of a putative precursor gene in the M. trichosporium OB3b genome. Finally, direct uptake of intact Mb into the cytoplasm of M. trichosporium OB3b cells has been demonstrated, and studies of the transport mechanism have been initiated. Taken together, these advances represent significant progress and set the stage for exciting new research directions.
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Affiliation(s)
- Grace E. Kenney
- 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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Spectral and thermodynamic properties of methanobactin from γ-proteobacterial methane oxidizing bacteria: a case for copper competition on a molecular level. J Inorg Biochem 2010; 104:1240-7. [PMID: 20817303 DOI: 10.1016/j.jinorgbio.2010.08.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 06/01/2010] [Accepted: 08/05/2010] [Indexed: 11/22/2022]
Abstract
Methanobactin (mb) is a low molecular mass copper-binding molecule analogous to iron-binding siderophores. The molecule is produced by many methanotrophic or methane oxidizing bacteria (MOB), but has only been characterized to date in one MOB, Methylosinus trichosporium OB3b. To explore the potential molecular diversity in this novel class of metal binding compound, the spectral (UV-visible, fluorescent, and electron paramagnetic resonance) and thermodynamic properties of mb from two γ-proteobacterial MOB, Methylococcus capsulatus Bath and Methylomicrobium album BG8, were determined and compared to the mb from the α-proteobacterial MOB, M. trichosporium OB3b. The mb from both γ-proteobacterial MOB differed from the mb from M. trichosporium OB3b in molecular mass and spectral properties. Compared to mb from M. trichosporium OB3b, the extracellular concentrations were low, as were copper-binding constants of mb from both γ-proteobacterial MOB. In addition, the mb from M. trichosporium OB3b removed Cu(I) from the mb of both γ-proteobacterial MOB. Taken together the results suggest mb may be a factor in regulating methanotrophic community structure in copper-limited environments.
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Jiang H, Chen Y, Jiang P, Zhang C, Smith TJ, Murrell JC, Xing XH. Methanotrophs: Multifunctional bacteria with promising applications in environmental bioengineering. Biochem Eng J 2010. [DOI: 10.1016/j.bej.2010.01.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Wendlandt KD, Stottmeister U, Helm J, Soltmann B, Jechorek M, Beck M. The potential of methane-oxidizing bacteria for applications in environmental biotechnology. Eng Life Sci 2010. [DOI: 10.1002/elsc.200900093] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Abstract
Methanotrophs, cells that consume methane (CH(4)) as their sole source of carbon and energy, play key roles in the global carbon cycle, including controlling anthropogenic and natural emissions of CH(4), the second-most important greenhouse gas after carbon dioxide. These cells have also been widely used for bioremediation of chlorinated solvents, and help sustain diverse microbial communities as well as higher organisms through the conversion of CH(4) to complex organic compounds (e.g. in deep ocean and subterranean environments with substantial CH(4) fluxes). It has been well-known for over 30 years that copper (Cu) plays a key role in the physiology and activity of methanotrophs, but it is only recently that we have begun to understand how these cells collect Cu, the role Cu plays in CH(4) oxidation by the particulate CH(4) monooxygenase, the effect of Cu on the proteome, and how Cu affects the ability of methanotrophs to oxidize different substrates. Here we summarize the current state of knowledge of the phylogeny, environmental distribution, and potential applications of methanotrophs for regional and global issues, as well as the role of Cu in regulating gene expression and proteome in these cells, its effects on enzymatic and whole-cell activity, and the novel Cu uptake system used by methanotrophs.
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Affiliation(s)
- Jeremy D Semrau
- Department of Civil and Environmental Engineering, The University of Michigan, Ann Arbor, MI, USA.
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Use of allylthiourea to produce soluble methane monooxygenase in the presence of copper. Appl Microbiol Biotechnol 2009; 82:333-9. [DOI: 10.1007/s00253-008-1814-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Revised: 11/18/2008] [Accepted: 11/20/2008] [Indexed: 10/21/2022]
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26
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Balasubramanian R, Rosenzweig AC. Copper methanobactin: a molecule whose time has come. Curr Opin Chem Biol 2008; 12:245-9. [PMID: 18313412 DOI: 10.1016/j.cbpa.2008.01.043] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Accepted: 01/21/2008] [Indexed: 11/16/2022]
Abstract
Copper plays a key role in the physiology of methanotrophs. One way that these bacteria meet their high copper requirement is by the biosynthesis and release of high affinity copper binding compounds called methanobactins. Recent advances in methanobactin characterization include the first crystal structure, detailed spectroscopic analyses, and studies of metal ion specificity. Methanobactin may function in copper uptake, regulation of methane monooxygenase expression, protection against copper toxicity, and particulate methane monooxygenase activity. Methanobactin can extract copper from insoluble minerals and could be important for mineral weathering. Many methanobactin properties are reminiscent of iron siderophores, suggesting a similar mechanism of handling. Methanobactin-like compounds have also been identified in yeast mitochondria, suggesting that these molecules are a more universal phenomenon.
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Affiliation(s)
- Ramakrishnan Balasubramanian
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, IL 60208, United States
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27
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Abstract
Methanotrophic bacteria oxidize methane to methanol in the first step of their metabolic pathway. Two forms of methane monooxygenase (MMO) enzymes catalyze this reaction: soluble MMO (sMMO) and membrane-bound or particulate MMO (pMMO). pMMO is expressed when copper is available, and its active site is believed to contain copper. Whereas sMMO is well characterized, most aspects of pMMO biochemistry remain unknown and somewhat controversial. This review emphasizes advances in the past two to three years related to pMMO and to copper uptake and copper-dependent regulation in methanotrophs. The pMMO metal centers have been characterized spectroscopically, and the first pMMO crystal structure has been determined. Significant effort has been devoted to improving in vitro pMMO activity. Proteins involved in sMMO regulation and additional copper-regulated proteins have been identified, and the Methylococcus capsulatus (Bath) genome has been sequenced. Finally, methanobactin (mb), a small copper chelator proposed to facilitate copper uptake, has been characterized.
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Affiliation(s)
- Amanda S Hakemian
- Department of Biochemistry, Northwestern University, Evanston, Illinois 60208, USA.
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28
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Structure, Function and Formation of Bacterial Intracytoplasmic Membranes. MICROBIOLOGY MONOGRAPHS 2006. [DOI: 10.1007/7171_025] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Hesselsoe M, Boysen S, Iversen N, Jørgensen L, Murrell JC, McDonald I, Radajewski S, Thestrup H, Roslev P. Degradation of organic pollutants by methane grown microbial consortia. Biodegradation 2005; 16:435-48. [PMID: 15865157 DOI: 10.1007/s10532-004-4721-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Microbial consortia were enriched from various environmental samples with methane as the sole carbon and energy source. Selected consortia that showed a capacity for co-oxidation of naphthalene were screened for their ability to degrade methyl-tert-butyl-ether (MTBE), phthalic acid esters (PAE), benzene, xylene and toluene (BTX). MTBE was not removed within 24 h by any of the consortia examined. One consortium enriched from activated sludge ("AAE-A2"), degraded PAE, including (butyl-benzyl)phthalate (BBP), and di-(butyl)phthalate (DBP). PAE have not previously been described as substrates for methanotrophic consortia. The apparent Km and Vmax for DBP degradation by AAE-A2 at 20 degrees C was 3.1 +/- 1.2 mg l(-1) and 8.7 +/- 1.1 mg DBP (g protein x h)(-1), respectively. AAE-A2 also showed fast degradation of BTX (230 +/- 30 nmol benzene (mg protein x h)(-1) at 20 degrees C). Additionally, AAE-A2 degraded benzene continuously for 2 weeks. In contrast, a pure culture of the methanotroph Methylosinus trichosporium OB3b ceased benzene degradation after only 2 days. Experiments with methane mono-oxygenase inhibitors or competitive substrates suggested that BTX degradation was carried out by methane-oxidizing bacteria in the consortium, whereas the degradation of PAE was carried out by non-methanotrophic bacteria co-existing with methanotrophs. The composition of the consortium (AAE-A2) based on polar lipid fatty acid (PLFA) profiles showed dominance of type II methanotrophs (83-92% of biomass). Phylogeny based on a 16S-rRNA gene clone library revealed that the dominating methanotrophs belonged to Methylosinus/Methylocystis spp. and that members of at least 4 different non-methanotrophic genera were present (Pseudomonas, Flavobacterium, Janthinobacterium and Rubivivax).
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Affiliation(s)
- Martin Hesselsoe
- Aalborg University, Department of Life Sciences, Section of Environmental Engineering, Aalborg, Denmark.
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30
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Pressman JG, Georgiou G, Speitel GE. Scale-up considerations for a hollow-fiber-membrane bioreactor treating trichloroethylene-contaminated water. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2005; 77:533-42. [PMID: 16274088 DOI: 10.2175/106143005x67458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Scale-up of a hollow-fiber-membrane (HFM) bioreactor treating trichloroethylene- (TCE-) contaminated water via co-metabolism with the methanotroph Methylosinus trichosporium OB3b PP358 was investigated through cost comparisons, bioreactor experiments, and mathematical modeling. Cost comparisons, based on a hypothetical treatment scenario of 568-L/min (150-gpm) flowrate with an influent TCE concentration of 100 microg/L, resulted in a configuration of treatment trains with two HFM modules in series and an overall annual cost of US dollar 0.36/m3 treated. Biological experiments were conducted with short lumen and shell residence times, 0.16 and 0.40 min, respectively, as a result of the cost comparisons. A new variable, specific transformation, was defined for characterizing the cometabolic transformation in continuous-flow systems, and values as large as 38.5 microg TCE/mg total suspended solids were sustainable for TCE treatment. Using mathematical modeling, HFM bioreactor system design was investigated, resulting in a five-step system design strategy to facilitate sizing of the unit processes.
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Affiliation(s)
- Jonathan G Pressman
- U.S. Environmental Protection Agency, National Risk Management Research Laboratory,Cincinnati, OH 45268, USA.
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31
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Lieberman RL, Rosenzweig AC. Biological methane oxidation: regulation, biochemistry, and active site structure of particulate methane monooxygenase. Crit Rev Biochem Mol Biol 2005; 39:147-64. [PMID: 15596549 DOI: 10.1080/10409230490475507] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Particulate methane monooxygenase (pMMO) is a three-subunit integral membrane enzyme that catalyzes the oxidation of methane to methanol. Although pMMO is the predominant methane oxidation catalyst in nature, it has proved difficult to isolate, and most questions regarding its molecular structure, active site composition, chemical mechanism, and genetic regulation remain unanswered. Copper ions are believed to play a key role in both pMMO regulation and catalysis, and there is some evidence that the enzyme contains iron as well. A number of research groups have solubilized and purified or partially purified pMMO. These preparations have been characterized by biochemical and biophysical methods. In addition, aspects of methane monooxygenase gene regulation and copper accumulation in methanotrophs have been studied. This review summarizes for the first time the often controversial pMMO literature, focusing on recent progress and highlighting unresolved issues.
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Affiliation(s)
- Raquel L Lieberman
- Departments of Biochemistry, Molecular Biology, Cell Biology, and Chemistry, Northwestern University, Evanston, IL 60208, USA
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Dunfield PF, Khmelenina VN, Suzina NE, Trotsenko YA, Dedysh SN. Methylocella silvestris sp. nov., a novel methanotroph isolated from an acidic forest cambisol. Int J Syst Evol Microbiol 2003; 53:1231-1239. [PMID: 13130000 DOI: 10.1099/ijs.0.02481-0] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped, methane-oxidizing bacteria were isolated from an acidic forest cambisol near Marburg, Germany, and were designated as strains BL2(T) and A1. These bacteria were morphologically and phenotypically similar to Methylocella palustris K(T). The cells possess a highly specific bipolar appearance. They lack the intracytoplasmic membranes common to all methane-oxidizing bacteria except Methylocella, but contain a vesicular membrane system connected to the cytoplasmic membrane. A soluble methane monooxygenase was present, but no particulate methane monooxygenase could be detected. These bacteria utilize the serine pathway for carbon assimilation. Strains BL2(T) and A1 are moderately acidophilic, mesophilic organisms capable of growth at pH values between 4.5 and 7 (with an optimum at pH 5.5) and at temperatures between 4 and 30 degrees C. Compared with Methylocella palustris K(T), these strains have greater tolerance of cold temperatures, dissolved salts and methanol. On the basis of 16S rRNA gene sequence identity, of species with validly published names, strain BL2(T) is most closely related to Methylocella palustris K(T) (97.3 % identity), Beijerinckia indica subsp. indica ATCC 9039(T) (97.1 %) and Methylocapsa acidiphila B2(T) (96.2 %). The DNA G+C content is 60 mol% and the major phospholipid fatty acid is 18 : 1omega7. Strain BL2(T) showed only 21-22 % DNA-DNA hybridization with Methylocella palustris K(T). The data therefore suggest that strains BL2(T) and A1 represent a novel species of Methylocella; the name Methylocella silvestris sp. nov. is proposed, with strain BL2(T) (=DSM 15510(T)=NCIMB 13906(T)) as the type strain.
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Affiliation(s)
- Peter F Dunfield
- Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - Valentina N Khmelenina
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region 142292, Russia
| | - Natalia E Suzina
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region 142292, Russia
| | - Yuri A Trotsenko
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region 142292, Russia
| | - Svetlana N Dedysh
- Institute of Microbiology, Russian Academy of Sciences, Moscow 117811, Russia
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Csáki R, Bodrossy L, Klem J, Murrell JC, Kovács KL. Genes involved in the copper-dependent regulation of soluble methane monooxygenase of Methylococcus capsulatus (Bath): cloning, sequencing and mutational analysis. MICROBIOLOGY (READING, ENGLAND) 2003; 149:1785-1795. [PMID: 12855730 DOI: 10.1099/mic.0.26061-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The key enzyme in methane metabolism is methane monooxygenase (MMO), which catalyses the oxidation of methane to methanol. Some methanotrophs, including Methylococcus capsulatus (Bath), possess two distinct MMOs. The level of copper in the environment regulates the biosynthesis of the MMO enzymes in these methanotrophs. Under low-copper conditions, soluble MMO (sMMO) is expressed and regulation takes place at the level of transcription. The structural genes of sMMO were previously identified as mmoXYBZ, mmoD and mmoC. Putative transcriptional start sites, containing a sigma(70)- and a sigma(N)-dependent motif, were identified in the 5' region of mmoX. The promoter region of mmoX was mapped using truncated 5' end regions fused to a promoterless green fluorescent protein gene. A 9.5 kb region, adjacent to the sMMO structural gene cluster, was analysed. Downstream (3') from the last gene of the operon, mmoC, four ORFs were found, mmoG, mmoQ, mmoS and mmoR. mmoG shows significant identity to the large subunit of the bacterial chaperonin gene, groEL. In the opposite orientation, two genes, mmoQ and mmoS, showed significant identity to two-component sensor-regulator system genes. Next to mmoS, a gene encoding a putative sigma(N)-dependent transcriptional activator, mmoR was identified. The mmoG and mmoR genes were mutated by marker-exchange mutagenesis and the effects of these mutations on the expression of sMMO was investigated. sMMO transcription was impaired in both mutants. These results indicate that mmoG and mmoR are essential for the expression of sMMO in Mc. capsulatus (Bath).
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Affiliation(s)
- Róbert Csáki
- Institute of Biophysics, Biological Research Center, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Levente Bodrossy
- Institute of Biophysics, Biological Research Center, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - József Klem
- Institute of Biophysics, Biological Research Center, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - J Colin Murrell
- Department of Biological Sciences, University of Warwick, Coventry, UK
| | - Kornél L Kovács
- Institute of Biophysics, Biological Research Center, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
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Canada KA, Iwashita S, Shim H, Wood TK. Directed evolution of toluene ortho-monooxygenase for enhanced 1-naphthol synthesis and chlorinated ethene degradation. J Bacteriol 2002; 184:344-9. [PMID: 11751810 PMCID: PMC139589 DOI: 10.1128/jb.184.2.344-349.2002] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Trichloroethylene (TCE) is the most frequently detected groundwater contaminant, and 1-naphthol is an important chemical manufacturing intermediate. Directed evolution was used to increase the activity of toluene ortho-monooxygenase (TOM) of Burkholderia cepacia G4 for both chlorinated ethenes and naphthalene oxidation. When expressed in Escherichia coli, the variant TOM-Green degraded TCE (2.5 +/- 0.3 versus 1.39 +/- 0.05 nmol/min/mg of protein), 1,1-dichloroethylene, and trans-dichloroethylene more rapidly. Whole cells expressing TOM-Green synthesized 1-naphthol at a rate that was six times faster than that mediated by the wild-type enzyme at a concentration of 0.1 mM (0.19 +/- 0.03 versus 0.029 +/- 0.004 nmol/min/mg of protein), whereas at 5 mM, the mutant enzyme was active (0.07 +/- 0.03 nmol/min/mg of protein) in contrast to the wild-type enzyme, which had no detectable activity. The regiospecificity of TOM-Green was unchanged, with greater than 97% 1-naphthol formed. The beneficial mutation of TOM-Green is the substitution of valine to alanine in position 106 of the alpha-subunit of the hydroxylase, which appears to act as a smaller "gate" to the diiron active center. This hypothesis was supported by the ability of E. coli expressing TOM-Green to oxidize the three-ring compounds, phenanthrene, fluorene, and anthracene faster than the wild-type enzyme. These results show clearly that random, in vitro protein engineering can be used to improve a large multisubunit protein for multiple functions, including environmental restoration and green chemistry.
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Affiliation(s)
- Keith A Canada
- Department of Chemical Engineering, University of Connecticut, Storrs, Connecticut 06269-3222, USA
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Shakoori AR, Muneer B. Copper-resistant bacteria from industrial effluents and their role in remediation of heavy metals in wastewater. Folia Microbiol (Praha) 2002; 47:43-50. [PMID: 11980269 DOI: 10.1007/bf02818564] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Six copper-resistant bacterial strains were isolated from wastewater of tanneries of Kasur and Rohi Nala. Two strains tolerated copper at 380 mg/L, four up to 400 mg/L. Three strains were identified as members of the genus Salmonella; one strain was identified as Streptococcus pyrogenes, one as Vagococcus fluvialis and the last was identified as Escherichia coli. The pH and temperature optimum for two of them were 7.0 and 30 degrees C, respectively; four strains had corresponding optima at 7.5 and 37 degrees C, respectively. All bacterial isola-tes showed resistance against Ag+ (280-350 mg/L), Co2+ (200-420), CrVI (280-400), Cd2+ (250-350), Hg2+ (110-200), Mn2+ (300-380), Pb2+ (300-400), Sn2+ (480-520) and Zn2+ (300-450). Large-sized plasmids (> 20 kb), were detected in all of the strains. After the isolates were cured of plasmids with ethidium bromide, the efficiency of curing was estimated in the range of 60-90%. Reference strain of E. coli was transformed with the plasmids of the bacterial isolates which grew in Luria-Bertani medium containing 100 mg/L Cu2+. The capability to adsorb and afterwards accumulate Cu2+ inside their cells was assayed by atomic absorption spectrophotometer; all bacterial cells had the ability to adsorb 50-80% of the Cu2+ and accumulate 30-45% Cu2+ inside them after 1 d of incubation.
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Affiliation(s)
- A R Shakoori
- Cell and Molecular Biology Laboratory, Department of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
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Kim HJ, Graham DW. Effect of oxygen level on simultaneous nitrogenase and sMMO expression and activity in Methylosinus trichosporium OB3b and its sMMO(C) mutant, PP319: aerotolerant N2 fixation in PP319. FEMS Microbiol Lett 2001; 201:133-8. [PMID: 11470351 DOI: 10.1111/j.1574-6968.2001.tb10746.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Soluble methane monooxygenase (sMMO) expression and activity were monitored under conditions that either promoted or suppressed the expression of nitrogenase in Methylosinus trichosporium OB3b wild-type (WT) and in its sMMO-constitutive mutant, PP319. Both WT and mutant cultures had reduced sMMO activity and protein levels under elevated O2 conditions (188 microM) compared with low O2 conditions (24 microM). Simultaneous N2 fixation also reduced sMMO activity in both cultures when O2 was low. However, when O2 levels were increased, nitrogenase expression ceased and sMMO activity was reduced by approximately 77% in the WT, whereas sMMO and nitrogenase expression and activity in PP319 were relatively unaffected by the higher O2 levels. Western immunoblot analysis showed that the nitrogenase Fe protein resolved as two components (apparent molecular mass of 30.5 and 32 kDa) in both the WT and PP319 when O2 levels were low. When O2 levels were high, only the 32-kDa form of the Fe protein was present in PP319, whereas neither form was detectable in the WT. Aerotolerant N2 fixation appears to be associated with the 32-kDa Fe protein in M. trichosporium OB3b.
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Affiliation(s)
- H J Kim
- Department of Civil and Environmental Engineering, 4002 Learned Hall, University of Kansas, Lawrence, KS 66045, USA
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Kaluzhnaya M, Khmelenina V, Eshinimaev B, Suzina N, Nikitin D, Solonin A, Lin JL, McDonald I, Murrell C, Trotsenko Y. Taxonomic characterization of new alkaliphilic and alkalitolerant methanotrophs from soda lakes of the Southeastern Transbaikal region and description of Methylomicrobium buryatense sp.nov. Syst Appl Microbiol 2001; 24:166-76. [PMID: 11518319 DOI: 10.1078/0723-2020-00028] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Five strains of obligate methanotrophic bacteria (4G, 5G, 6G, 7G and 5B) isolated from bottom sediments of Southeastern Transbaikal soda lakes (pH 9.5-10.5) are taxonomically described. These bacteria are aerobic, Gram-negative monotrichous rods having tightly packed cup-shaped structures on the outer cell wall surface (S-layers) and Type I intracytoplasmic membranes. All the isolates possess particulate methane monooxygenase (pMMO) and one strain (5G) also contains soluble methane monooxygenase (sMMO). They assimilate methane and methanol via the ribulose monophosphate pathway (RuMP). The isolates are alkalitolerant or facultatively alkaliphilic, able to grow at pH 10.5-11.0 and optimally at pH 8.5-9.5. These organisms are obligately dependent on the presence of sodium ions in the growth medium and tolerate up to 0.9-1.4 M NaCl or 1 M NaHCO3. Although being mesophilic, all the isolates are resistant to heating (80 degrees C, 20 min), freezing and drying. Their cellular fatty acids profiles primarily consist of C(16:1). The major phospholipids are phosphatidylethanolamine and phosphatidylglycerol. The main quinone is Q-8. The DNA G+C content ranges from 49.2-51.5 mol %. Comparative 16S rDNA sequencing showed that the newly isolated methanotrophs are related to membres of the Methylomicrobium genus. However, they differ from the known members of this genus by DNA-DNA relatedness. Based on pheno- and genotypic characteristics, we propose a new species of the genus Methylomicrobium Methylomicrobium buryatense sp. nov.
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Affiliation(s)
- M Kaluzhnaya
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow, Russia
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38
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Liu CY, Speitel GE, Georgiou G. Kinetics of methyl t-butyl ether cometabolism at low concentrations by pure cultures of butane-degrading bacteria. Appl Environ Microbiol 2001; 67:2197-201. [PMID: 11319100 PMCID: PMC92855 DOI: 10.1128/aem.67.5.2197-2201.2001] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Butane-oxidizing Arthrobacter (ATCC 27778) bacteria were shown to degrade low concentrations of methyl t-butyl ether (MTBE; range, 100 to 800 microg/liter) with an apparent half-saturation concentration (K(s)) of 2.14 mg/liter and a maximum substrate utilization rate (k(c)) of 0.43 mg/mg of total suspended solids per day. Arthrobacter bacteria demonstrated MTBE degradation activity when grown on butane but not when grown on glucose, butanol, or tryptose phosphate broth. The presence of butane, tert-butyl alcohol, or acetylene had a negative impact on the MTBE degradation rate. Neither Methylosinus trichosporium OB3b nor Streptomyces griseus was able to cometabolize MTBE.
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Affiliation(s)
- C Y Liu
- Department of Civil Engineering, University of Texas at Austin, Austin, TX 78712-1076, USA
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39
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van Hylckama Vlieg JE, Janssen DB. Formation and detoxification of reactive intermediates in the metabolism of chlorinated ethenes. J Biotechnol 2001; 85:81-102. [PMID: 11165358 DOI: 10.1016/s0168-1656(00)00364-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Short-chain halogenated aliphatics, such as chlorinated ethenes, constitute a large group of priority pollutants. This paper gives an overview on the chemical and physical properties of chlorinated aliphatics that are critical in determining their toxicological characteristics and recalcitrance to biodegradation. The toxic effects and principle metabolic pathways of halogenated ethenes in mammals are briefly discussed. Furthermore, the bacterial degradation of halogenated compounds is reviewed and it is described how product toxicity may explain why most chlorinated ethenes are only degraded cometabolically under aerobic conditions. The cometabolic degradation of chlorinated ethenes by oxygenase-producing microorganisms has been extensively studied. The physiology and bioremediation potential of methanotrophs has been well characterized and an overview of the available data on these organisms is presented. The sensitivity of methanotrophs to product toxicity is a major limitation for the transformation of chlorinated ethenes by these organisms. Most toxic effects arise from the inability to detoxify the reactive chlorinated epoxyethanes occurring as primary metabolites. Therefore, the last part of this review focuses on the metabolic reactions and enzymes that are involved in the detoxification of epoxides in mammals. A key role is played by glutathione S-transferases. Furthermore, an overview is presented on the current knowledge about bacterial enzymes involved in the metabolism of epoxides. Such enzymes might be useful for detoxifying chlorinated ethene epoxides and an example of a glutathione S-transferase with activity for dichloroepoxyethane is highlighted.
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Affiliation(s)
- J E van Hylckama Vlieg
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, NL-9747 AG, Groningen, The Netherlands
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40
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Malashenko Y, Sokolov I, Romanovskaya V. Role of monooxygenase reaction during assimilation of non-growth substrates by methanotrophs. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1381-1177(00)00131-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ryoo D, Shim H, Canada K, Barbieri P, Wood TK. Aerobic degradation of tetrachloroethylene by toluene-o-xylene monooxygenase of Pseudomonas stutzeri OX1. Nat Biotechnol 2000; 18:775-8. [PMID: 10888848 DOI: 10.1038/77344] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Tetrachloroethylene (PCE) is thought to have no natural source, so it is one of the most difficult contaminants to degrade biologically. This common groundwater pollutant was thought completely nonbiodegradable in the presence of oxygen. Here we report that the wastewater bacterium Pseudomonas stutzeri OX1 degrades aerobically 0. 56 micromol of 2.0 micromol PCE in 21 h (Vmax approximately 2.5 nmol min(-1) mg(-1) protein and KM approximately 34 microM). These results were corroborated by the generation of 0.48 micromol of the degradation product, chloride ions. This degradation was confirmed to be a result of expression of toluene-o-xylene monooxygenase (ToMO) by P. stutzeri OX1, since cloning and expressing this enzyme in Escherichia coli led to the aerobic degradation of 0.19 micromol of 2.0 micromol PCE and the generation of stoichiometric amounts of chloride. In addition, PCE induces formation of ToMO, which leads to its own degradation in P. stutzeri OX1. Degradation intermediates reduce the growth rate of this strain by 27%.
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Affiliation(s)
- D Ryoo
- Department of Chemical Engineering, University of Connecticut, Storrs, CT 06269-3222, USA
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42
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Pressman JG, Georgiou G, Speitel GE. A hollow-fiber membrane bioreactor for the removal of trichloroethylene from the vapor phase. Biotechnol Bioeng 2000; 68:548-56. [PMID: 10797241 DOI: 10.1002/(sici)1097-0290(20000605)68:5<548::aid-bit9>3.0.co;2-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A hollow-fiber membrane bioreactor was used to separate trichloroethylene (TCE) from a gaseous waste stream with subsequent cometabolic biodegradation by a pure culture of Methylosinus trichosporium OB3b PP358. The two-stage bioreactor system was successfully operated for 20 days. PP358 was grown in a continuous-flow chemostat and circulated through the fiber lumen of a hollow-fiber membrane module (HFMM), while TCE contaminated air (141 to 191 microg/L) was pumped through the HFMM shell. Between 54% -84% TCE transfer and 92%-96% TCE cometabolism were obtained in the HFMM reactor loop. Short shell-residence times, 1.6 to 5.0 minutes, demonstrated quick throughput of TCE contaminated air. Best-fit computer modeling of the biological experiments estimated mass transfer coefficients between 2.0 x 10(-3) cm/min and 5.6 x 10(-3) cm/min. The average pseudo-first-order biodegradation rate constant for the biological experiments was 0.46 L/mg TSS/d. These results demonstrate that the hollow-fiber membrane bioreactor represents an attractive technology for the bioremediation of gaseous waste streams.
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Affiliation(s)
- J G Pressman
- Department of Civil Engineering, University of Texas at Austin, 78712, USA
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43
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Aziz CE, Georgiou G, Speitel GE. Cometabolism of chlorinated solvents and binary chlorinated solvent mixtures using M. trichosporium OB3b PP358. Biotechnol Bioeng 1999; 65:100-7. [PMID: 10440676 DOI: 10.1002/(sici)1097-0290(19991005)65:1<100::aid-bit12>3.0.co;2-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The mutant methanotroph, Methylosinus trichosporium OB3b PP358, which constitutively expresses soluble methane monooxygenase (sMMO), was used to study the degradation kinetics of individual chlorinated solvents and binary solvent mixtures. Although sMMO's broad specificity permits a wide range of chlorinated solvents to be degraded, it creates the potential for competitive inhibition of degradation rates in mixtures because multiple chemicals are simultaneously available to the enzyme. To effectively design both ex-situ and in-situ groundwater bioremediation systems using strain PP358, kinetic parameters for chlorinated solvent degradation and accurate kinetic expressions to account for inhibition in mixtures are required. Toward this end, the degradation parameters for six prevalent chlorinated solvents and the verification of enzyme competition model for binary mixtures were the focus of this investigation. M. trichosporium OB3b PP358 degraded trichloroethylene (TCE), chloroform, cis-1,2-dichloroethylene (c-DCE), trans-1,2-dichloroethylene (t-DCE), and 1, 1-dichloroethylene (1,1-DCE) rapidly, with maximum substrate transformation rates of >20.8, 3.1, 9.5 24.8, and >7.5 mg/mg-day, respectively. 1,1,1-trichloroethane (TCA) was not significantly degraded. Half-saturation coefficients ranged from 1 to greater than 10 mg/L. Competition experiments were carried out to observe the effect of a second solvent on degradation rates and to verify the applicability of the Monod model adjusted for competitive inhibition. Binary mixtures of 0.3->0.5 mg/L TCE with up to 5 mg/L c-DCE and up to 7 mg/L 1,1,1-TCA were studied with 20 mM of formate and no growth substrate. No competition was observed at any of these concentrations. Additional competition experiments, using binary mixtures of t-DCE with TCE and t-DCE with c-DCE, were conducted at higher concentrations (i.e., 7-18 mg/L) and enzyme competition was observed. Predictions from a competitive inhibition model compared well with experimental data for these mixtures.
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Affiliation(s)
- C E Aziz
- Department of Civil Engineering, University of Texas at Austin, Austin, Texas 78712, USA
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44
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Sullivan JP, Dickinson D, Chase HA. Methanotrophs, Methylosinus trichosporium OB3b, sMMO, and their application to bioremediation. Crit Rev Microbiol 1999; 24:335-73. [PMID: 9887367 DOI: 10.1080/10408419891294217] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
One of the most problematic groups of the USEPA and EU priority pollutants are the halogenated organic compounds. These substances have a wide range of industrial applications, such as solvents and cleaners. Inadequate disposal techniques and accidental spillages have led to their detection in soil, groundwater, and river sediments. Persistence of these compounds in the environment has resulted from low levels of biodegradation due to chemical structural features that preclude or retard biological attack. Research has indicated the idea that treatment systems based on methanotrophic co-metabolic transformation may be a cost-effective and efficient alternative to physical methods because of the potential for high transformation rates, the possibility of complete compound degradation without the formation of toxic metabolites, applicability to a broad spectrum of compounds, and the use of a widely available and inexpensive growth substrate. A substantial amount of work concerning methanotrophic cometabolic transformations has been carried out using the soluble form of methane monooxygenase (sMMO) from the obligate methanotroph Methylosinus trichosporium OB3b. This NADH-dependent monooxygenase is derepressed when cells are grown under copper stress. sMMO has a wider specificity than the particulate form. sMMO has been shown to degrade trichloroethylene (TCE) at a rate of at least one order of magnitude faster than obtained with other mixed and pure cultures, suggesting it has a wider application to bioremediation. Furthermore, sMMO catalyzes an unusually wide range of oxidation reactions, including the hydroxylation of alkanes, epoxidation of alkenes, ethers, halogenated methanes, cyclic and aromatic compounds including compounds, that are resistant to degradation in the environment. However, the practical application of methantrophs and Methylosinus trichosporium OB3b to the treatment of chlorinated organics has met with mixed success. Although oxidation rates are rapid, compound oxidation with M. trichosporium OB3b is difficult. This fastidious organism grows relatively slowly, which limits the speed with which sMMO expressing biomass can be generated. Furthermore, product toxicity toward the cell, affecting the stability of the enzyme when transforming certain compounds has been observed, for example, by the products of 1,2,3 trichlorobenzene hydroxylation (2,3,4- and 3,4,5-trichlorophenol) and of TCE degradation (chloral hydrate). Because of this toxicity and the inability of sMMO to further oxidize its own hydroxylation products, the ability of methane monoxygenase to carry out the monooxygenation of a wide variety of substituted aromatics and polyaromatics cannot be fully exploited in M. trichosporium OB3b. Many of these problems could be overcome by the use of either a mixed downstream heterotrophic population of organisms that could accommodate the products of hydroxylation or to express sMMO in an organism that could metabolize the products of hydroxylation. The latter of these two approaches would have several advantages. The main benefit would be the removal of the need for methane, which is required to induce sMMO in M. trichosporium OB3b, and supply carbon and energy to the cells that continuously oxidise the target compound, but also acts as a competitive inhibitor of sMMO. Instead, the recombinant could utilize the products of sMMO-mediated hydroxylation as a carbon source.
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Affiliation(s)
- J P Sullivan
- Biology Department, Imperial College of Science, Technology and Medicine, London.
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45
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DiSpirito AA, Zahn JA, Graham DW, Kim HJ, Larive CK, Derrick TS, Cox CD, Taylor A. Copper-binding compounds from Methylosinus trichosporium OB3b. J Bacteriol 1998; 180:3606-13. [PMID: 9658004 PMCID: PMC107329 DOI: 10.1128/jb.180.14.3606-3613.1998] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Two copper-binding compounds/cofactors (CBCs) were isolated from the spent media of both the wild type and a constitutive soluble methane monooxygenase (sMMOC) mutant, PP319 (P. A. Phelps et al., Appl. Environ. Microbiol. 58:3701-3708, 1992), of Methylosinus trichosporium OB3b. Both CBCs are small polypeptides with molecular masses of 1,218 and 779 Da for CBC-L1 and CBC-L2, respectively. The amino acid sequence of CBC-L1 is S?MYPGS?M, and that of CBC-L2 is SPMP?S. Copper-free CBCs showed absorption maxima at 204, 275, 333, and 356 with shoulders at 222 and 400 nm. Copper-containing CBCs showed a broad absorption maximum at 245 nm. The low-temperature electron paramagnetic resonance (EPR) spectra of copper-containing CBC-L1 showed the presence of a copper center with an EPR splitting constant between those of type 1 and type 2 copper centers (g = 2.087, g = 2.42 G, A = 128 G). The EPR spectrum of CBC-L2 was more complex and showed two spectrally distinct copper centers. One signal can be attributed to a type 2 Cu2+ center (g = 2.073, g = 2.324 G, A = 144 G) which could be saturated at higher powers, while the second shows a broad, nearly isotropic signal near g = 2.063. In wild-type strains, the concentrations of CBCs in the spent media were highest in cells expressing the pMMO and stressed for copper. In contrast to wild-type strains, high concentrations of CBCs were observed in the extracellular fraction of the sMMOC mutants PP319 and PP359 regardless of the copper concentration in the culture medium.
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Affiliation(s)
- A A DiSpirito
- Department of Microbiology, Immunology, and Preventive Medicine, Iowa State University, Ames, Iowa 50011, USA.
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46
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Téllez CM, Gaus KP, Graham DW, Arnold RG, Guzman RZ. Isolation of copper biochelates from Methylosinus trichosporium OB3b and soluble methane monooxygenase mutants. Appl Environ Microbiol 1998; 64:1115-22. [PMID: 9501450 PMCID: PMC106376 DOI: 10.1128/aem.64.3.1115-1122.1998] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Methylosinus trichosporium OB3b produces an extracellular copper-binding ligand (CBL) with high affinity for copper. Wild-type cells and mutants that express soluble methane monooxygenase (sMMO) in the presence and absence of copper (sMMOc) were used to obtain cell exudates that were separated and analyzed by size exclusion high-performance liquid chromatography. A single chromatographic peak, when present, contained most of the aqueous-phase Cu(II) present in the culture medium. In mutant cultures that were unable to acquire copper, extracellular CBL accumulated to high levels both in the presence and in the absence of copper. Conversely, in wild-type cultures containing 5 microM Cu(II), extracellular CBL was maintained at a low, steady level during exponential growth, after which the external ligand was rapidly consumed. When Cu(II) was omitted from the growth medium, the wild-type organism produced the CBL at a rate that was proportional to cell density. After copper was added to this previously Cu-deprived culture, the CBL and copper concentrations in the medium decreased at approximately the same rate. Apparently, the extracellular CBL was produced throughout the period of cell growth, in the presence and absence of Cu(II), by both the mutant and wild-type cultures and was reinternalized or otherwise utilized by the wild-type cultures when it was bound to copper. CBL produced by the mutant strain facilitated copper uptake by wild-type cells, indicating that the extracellular CBLs produced by the mutant and wild-type organisms are functionally indistinguishable. CBL from the wild-type strain did not promote copper uptake by the mutant. The molecular weight of the CBL was estimated to be 500, and its association constant with copper was 1.4 x 10(16) M-1. CBL exhibited a preference for copper, even in the presence of 20-fold higher concentrations of nickel. External complexation may play a role in normal copper acquisition by M. trichosporium OB3b. The sMMOc phenotype is probably related to the mutant's inability to take up CBL-complexed copper, not to a defective CBL structure.
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Affiliation(s)
- C M Téllez
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson 85721, USA
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47
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Bolesch DG, Nielsen RB, Keasling JD. Complete reductive dechlorination of trichloroethene by a groundwater microbial consortium. Ann N Y Acad Sci 1997; 829:97-102. [PMID: 9472315 DOI: 10.1111/j.1749-6632.1997.tb48568.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Bioremediation promises to be an important technique in the removal of trichloroethene (TCE) and tetrachloroethene (PCE) from contaminated waste sites and contaminated groundwater systems. However, the use of aerobic degradation to degrade these compounds is not always possible. Thus, anaerobic degradation is a promising alternative that may be used to remediate these sites. Recently, literature reports indicate complete anaerobic dechlorination of TCE and PCE by microorganisms enriched from wastewater treatment plants. We report here the complete dechlorination of TCE to ethene in anaerobic microcosms by microorganisms enriched from a TCE contaminated groundwater aquifer using glucose as an electron donor. Initial TCE degradation activity occurred after 10 days of incubation and TCE was no longer detected after 20 days of incubation. During the incubation period, the reductive dechlorination products associated with TCE degradation were detected. Ultimately, all of the TCE was converted to ethene. The glucose culture was further enriched and demonstrated increased rates of TCE conversion to ethene. Our results show that organisms isolated from a contaminated groundwater site are capable of completely degrading TCE to ethene at appreciable rates, and indicate the potential of using in situ anaerobic bioremediation to clean up TCE contaminated sites.
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Affiliation(s)
- D G Bolesch
- Department of Chemical Engineering, University of California, Berkeley 94720-1462, USA
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48
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Brantner CA, Buchholz LA, McSwain CL, Newcomb LL, Remsen CC, Collins MLP. Intracytoplasmic membrane formation in Methylomicrobium album BG8 is stimulated by copper in the growth medium. Can J Microbiol 1997. [DOI: 10.1139/m97-095] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Methylomicrobium album BG8 uses methane as its sole source of carbon and energy. The oxidation of methane to methanol is catalyzed by the enzyme methane monooxygenase. Methane monooxygenase activity, intracytoplasmic membrane abundance, and cell mass increased with increasing copper concentration in the medium. When copper was added to copper-deficient cultures, cell mass and intracytoplasmic membrane structure increased. These findings are consistent with the presence of copper in the particulate methane monooxygenase. Methane monooxygenase activity and intracytoplasmic membrane abundance were correlated, suggesting that the methane monooxygenase may be involved in intracytoplasmic membrane proliferation.Key words: Methylomicrobium album BG8, copper, intracytoplasmic membrane, methane monooxygenase.
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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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50
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Sun AK, Wood TK. Trichloroethylene degradation and mineralization by pseudomonads and Methylosinus trichosporium OB3b. Appl Microbiol Biotechnol 1996; 45:248-56. [PMID: 8920197 DOI: 10.1007/s002530050679] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
To examine the trichloroethylene (C2HCl3)-degrading capability of five microorganisms, the maximum rate, extent, and degree of C2HCl3 mineralization were evaluated for Pseudomonas cepacia G4, Pseudomonas cepacia G4 PR1, Pseudomonas mendocina KR1, Pseudomonas putida F1, and Methylosinus trichosporium OB3b using growth conditions commonly reported in the literature for expression of oxygenases responsible for C2HCl3 degradation. By varying the C2HCl3 concentration from 5 microM to 75 microM, Vmax and Km values for C2HCl3 degradation were calculated as 9 nmol/(min mg protein) and 4 microM for P. cepacia G4, 18 nmol/(min mg protein) and 29 microM for P. cepacia G4 PR1, 20 nmol/(min mg protein) and 10 microM for P. mendocina KR1, and 8 nmol/(min mg protein) and 5 microM for P. putida F1. This is the first report of these Michaelis-Menten parameters for P. mendocina KR1, P. putida F1, and P. cepacia G4 PR1. At 75 microM, the extent of C2HCl3 that was degraded after 6 h of incubation with resting cells was 61%-98%; the highest degradation being achieved by toluene-induced P. mendocina KR1. The extent of C2HCl3 mineralization in 6 h (as indicated by concentration of chloride ion) was also measured and varied from 36% for toluene-induced P. putida F1 to 102% for M. trichosporium OB3b. Since C2HCl3 degradation requires new bio-mass, the specific growth rate (mu max) of each of the C2HCl3-degradation microorganisms was determined and varied from 0.080/h (M. trichosporium OB3b) to 0.864/h (P. cepacia G4 PR1).
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Affiliation(s)
- A K Sun
- Department of Chemical and Biochemical Engineering, University of California, Irvine 92717-2575, USA
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