51
|
Ernst L, Steinfeld B, Barayeu U, Klintzsch T, Kurth M, Grimm D, Dick TP, Rebelein JG, Bischofs IB, Keppler F. Methane formation driven by reactive oxygen species across all living organisms. Nature 2022; 603:482-487. [PMID: 35264795 DOI: 10.1038/s41586-022-04511-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 02/03/2022] [Indexed: 11/09/2022]
Abstract
Methane (CH4), the most abundant hydrocarbon in the atmosphere, originates largely from biogenic sources1 linked to an increasing number of organisms occurring in oxic and anoxic environments. Traditionally, biogenic CH4 has been regarded as the final product of anoxic decomposition of organic matter by methanogenic archaea. However, plants2,3, fungi4, algae5 and cyanobacteria6 can produce CH4 in the presence of oxygen. Although methanogens are known to produce CH4 enzymatically during anaerobic energy metabolism7, the requirements and pathways for CH4 production by non-methanogenic cells are poorly understood. Here, we demonstrate that CH4 formation by Bacillus subtilis and Escherichia coli is triggered by free iron and reactive oxygen species (ROS), which are generated by metabolic activity and enhanced by oxidative stress. ROS-induced methyl radicals, which are derived from organic compounds containing sulfur- or nitrogen-bonded methyl groups, are key intermediates that ultimately lead to CH4 production. We further show CH4 production by many other model organisms from the Bacteria, Archaea and Eukarya domains, including in several human cell lines. All these organisms respond to inducers of oxidative stress by enhanced CH4 formation. Our results imply that all living cells probably possess a common mechanism of CH4 formation that is based on interactions among ROS, iron and methyl donors, opening new perspectives for understanding biochemical CH4 formation and cycling.
Collapse
Affiliation(s)
- Leonard Ernst
- BioQuant Center, Heidelberg University, Heidelberg, Germany. .,Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany. .,Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany.
| | - Benedikt Steinfeld
- BioQuant Center, Heidelberg University, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany.,Zentrum für Molekulare Biologie Heidelberg (ZMBH), Heidelberg University, Heidelberg, Germany
| | - Uladzimir Barayeu
- Division of Redox Regulation, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Thomas Klintzsch
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany.,Department for Plant Nutrition, Gießen University, Gießen, Germany
| | - Markus Kurth
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Dirk Grimm
- BioQuant Center, Heidelberg University, Heidelberg, Germany.,Department of Infectious Diseases/Virology, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Tobias P Dick
- Division of Redox Regulation, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | | | - Ilka B Bischofs
- BioQuant Center, Heidelberg University, Heidelberg, Germany. .,Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany. .,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
| | - Frank Keppler
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany. .,Heidelberg Center for the Environment (HCE), Heidelberg University, Heidelberg, Germany.
| |
Collapse
|
52
|
Proenca AM, Oliveira MM, Neves PFR, Giongo A, de Oliveira RR, Ott CT, Marconatto L, de Barros Neto HMC, Ketzer JMM, Medina-Silva R. Genomic, biochemical, and phylogenetic evaluation of bacteria isolated from deep-sea sediment harboring methane hydrates. Arch Microbiol 2022; 204:205. [PMID: 35266047 DOI: 10.1007/s00203-022-02814-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/04/2022] [Accepted: 02/18/2022] [Indexed: 11/25/2022]
Abstract
Over half of the organic carbon on Earth's surface is trapped in marine sediment as methane hydrates. Ocean warming causes hydrate dissociation and methane leakage to the water column, rendering the characterization of microbes from hydrate depositions a pressing matter. Through genomic, phylogenetic, and biochemical assays, we characterize the first microorganisms isolated from the Rio Grande Cone (Brazil), reservoir responsible for massive methane releases to the water column. From sediment harboring rich benthic communities, we obtained 43 strains of Brevibacillus sp., Paenibacillus sp. and groups of Bacillus sp. Methane-enriched samples yielded strains of the Pseudomonas fluorescens complex, exhibiting fluorescent siderophore production and broad multi-carbon catabolism. Genomic characterization of a novel Pseudomonas sp. strain indicated 32 genes not identified in the closest related type-species, including proteins involved with mercury resistance. Our results provide phylogenetic and genomic insights on the first bacterial isolates retrieved from a poorly explored region of the South Atlantic Ocean.
Collapse
Affiliation(s)
- Audrey Menegaz Proenca
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.,Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.,Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Maiara Monteiro Oliveira
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.,Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Paula Fernanda Ribas Neves
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.,Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Adriana Giongo
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Rafael Rodrigues de Oliveira
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Carolina Telles Ott
- Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Letícia Marconatto
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | | | | | - Renata Medina-Silva
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil. .,Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.
| |
Collapse
|
53
|
Wang Z, Fang W, Peng W, Wu P, Wang B. Recent Computational Insights into the Oxygen Activation by Copper-Dependent Metalloenzymes. Top Catal 2022. [DOI: 10.1007/s11244-021-01444-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
54
|
Das B, Al-Hunaiti A, Carey A, Lidin S, Demeshko S, Repo T, Nordlander E. A di‑iron(III) μ-oxido complex as catalyst precursor in the oxidation of alkanes and alkenes. J Inorg Biochem 2022; 231:111769. [DOI: 10.1016/j.jinorgbio.2022.111769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 11/30/2022]
|
55
|
Rhoda HM, Heyer AJ, Snyder BER, Plessers D, Bols ML, Schoonheydt RA, Sels BF, Solomon EI. Second-Sphere Lattice Effects in Copper and Iron Zeolite Catalysis. Chem Rev 2022; 122:12207-12243. [PMID: 35077641 DOI: 10.1021/acs.chemrev.1c00915] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Transition-metal-exchanged zeolites perform remarkable chemical reactions from low-temperature methane to methanol oxidation to selective reduction of NOx pollutants. As with metalloenzymes, metallozeolites have impressive reactivities that are controlled in part by interactions outside the immediate coordination sphere. These second-sphere effects include activating a metal site through enforcing an "entatic" state, controlling binding and access to the metal site with pockets and channels, and directing radical rebound vs cage escape. This review explores these effects with emphasis placed on but not limited to the selective oxidation of methane to methanol with a focus on copper and iron active sites, although other transition-metal-ion zeolite reactions are also explored. While the actual active-site geometric and electronic structures are different in the copper and iron metallozeolites compared to the metalloenzymes, their second-sphere interactions with the lattice or the protein environments are found to have strong parallels that contribute to their high activity and selectivity.
Collapse
Affiliation(s)
- Hannah M Rhoda
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Alexander J Heyer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Benjamin E R Snyder
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Dieter Plessers
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Max L Bols
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Robert A Schoonheydt
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Bert F Sels
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States.,Photon Science, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| |
Collapse
|
56
|
Genome Sequence of a Thermoacidophilic Methanotroph Belonging to the Verrucomicrobiota Phylum from Geothermal Hot Springs in Yellowstone National Park: A Metagenomic Assembly and Reconstruction. Microorganisms 2022; 10:microorganisms10010142. [PMID: 35056591 PMCID: PMC8779874 DOI: 10.3390/microorganisms10010142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 02/04/2023] Open
Abstract
Verrucomicrobiotal methanotrophs are thermoacidophilic methane oxidizers that have been isolated from volcanic and geothermal regions of the world. We used a metagenomic approach that entailed obtaining the whole genome sequence of a verrucomicrobiotal methanotroph from a microbial consortium enriched from samples obtained from Nymph Lake (89.9 °C, pH 2.73) in Yellowstone National Park in the USA. To identify and reconstruct the verrucomicrobiotal genome from Illumina NovaSeq 6000 sequencing data, we constructed a bioinformatic pipeline with various combinations of de novo assembly, alignment, and binning algorithms. Based on the marker gene (pmoA), we identified and assembled the Candidatus Methylacidiphilum sp. YNP IV genome (2.47 Mbp, 2392 ORF, and 41.26% GC content). In a comparison of average nucleotide identity between Ca. Methylacidiphilum sp. YNP IV and Ca. Methylacidiphilum fumariolicum SolV, its closest 16S rRNA gene sequence relative, is lower than 95%, suggesting that Ca. Methylacidiphilum sp. YNP IV can be regarded as a different species. The Ca. Methylacidiphilum sp. YNP IV genome assembly showed most of the key genes for methane metabolism, the CBB pathway for CO2 fixation, nitrogen fixation and assimilation, hydrogenases, and rare earth elements transporter, as well as defense mechanisms. The assembly and reconstruction of a thermoacidophilic methanotroph belonging to the Verrucomicrobiota phylum from a geothermal environment adds further evidence and knowledge concerning the diversity of biological methane oxidation and on the adaptation of this geochemically relevant reaction in extreme environments.
Collapse
|
57
|
Hall JN, Li M, Bollini P. Light alkane oxidation over well-defined active sites in metal–organic framework materials. Catal Sci Technol 2022. [DOI: 10.1039/d1cy01876k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We review structure–catalytic property relationships for MOF materials used in the direct oxidation of light alkanes, focusing specifically on the elucidation of active site structures and probes for reaction mechanisms.
Collapse
Affiliation(s)
- Jacklyn N. Hall
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Mengying Li
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Praveen Bollini
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| |
Collapse
|
58
|
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Yoshiharu Iwabuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Sendai 980-8578, Japan
| |
Collapse
|
59
|
Hassan Z, Bräse S. Metal-to-Metal Distance Modulation by Ligand Design: A Case Study of Structure-Property Correlation in Planar Chiral Cyclophanyl Metal Complexes. Chemistry 2021; 27:15020-15026. [PMID: 34449116 PMCID: PMC8597128 DOI: 10.1002/chem.202102336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 11/25/2022]
Abstract
Multinuclear metal complexes have seen tremendous progress in synthetic advances, their versatile structural features, and emerging applications. Here, we conceptualize Metal-to-Metal distance modulation in cyclophanyl metal complexes by bridging ligand design employing the co-facially stacked cyclophanyl-derived pseudo-geminal, -ortho, -meta, and -para constitutional isomers grafted with N-, O-, and P- containing chelates that allow the installation of diverse (hetero)metallic moieties in a distance-defined and spatially-oriented relation to one another. Metal-to-Metal distance modulation and innate transannular "through-space" π-π electronic interactions via the co-facially stacked benzene rings in cyclophanyl-derived complexes as well as their specific stereochemical structural features (element of planar chirality) are crucial factors that contribute to the tuning of structure-property relationships, which stand at the very center from the perspective of cooperative effects in catalysis as well as emerging material applications.
Collapse
Affiliation(s)
- Zahid Hassan
- Institute of Organic Chemistry (IOC)Karlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC)Karlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
- Institute of Biological and Chemical SystemsFunctional Molecular Systems (IBCS-FMS)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| |
Collapse
|
60
|
Gęsicka A, Oleskowicz-Popiel P, Łężyk M. Recent trends in methane to bioproduct conversion by methanotrophs. Biotechnol Adv 2021; 53:107861. [PMID: 34710553 DOI: 10.1016/j.biotechadv.2021.107861] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/11/2021] [Accepted: 10/20/2021] [Indexed: 12/26/2022]
Abstract
Methane is an abundant and low-cost gas with high global warming potential and its use as a feedstock can help mitigate climate change. Variety of valuable products can be produced from methane by methanotrophs in gas fermentation processes. By using methane as a sole carbon source, methanotrophic bacteria can produce bioplastics, biofuels, feed additives, ectoine and variety of other high-value chemical compounds. A lot of studies have been conducted through the years for natural methanotrophs and engineered strains as well as methanotrophic consortia. These have focused on increasing yields of native products as well as proof of concept for the synthesis of new range of chemicals by metabolic engineering. This review shows trends in the research on key methanotrophic bioproducts since 2015. Despite certain limitations of the known production strategies that makes commercialization of methane-based products challenging, there is currently much attention placed on the promising further development.
Collapse
Affiliation(s)
- Aleksandra Gęsicka
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland
| | - Piotr Oleskowicz-Popiel
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland.
| | - Mateusz Łężyk
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland.
| |
Collapse
|
61
|
Spedalotto G, Lovisari M, McDonald AR. Reactivity Properties of Mixed- and High-Valent Bis(μ-Hydroxide)-Dinickel Complexes. ACS OMEGA 2021; 6:28162-28170. [PMID: 34723014 PMCID: PMC8554787 DOI: 10.1021/acsomega.1c04225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Despite their potential role in enzymatic systems, there is a dearth of hydroxide-bridged high-valent oxidants. We recently reported the synthesis and characterization of NiIINiIII(μ-OH)2 (2) and Ni2 III(μ-OH)2 (3) species supported by a dicarboxamidate ligand (N,N'-bis(2,6-dimethyl-phenyl)-2,2-dimethylmalonamide). Herein, we explore the oxidative reactivity of these species using a series of para-substituted 2,6-di-tert-butyl-phenols (4-X-2,6-DTBP, X = -OCH3, -CH2CH3, -CH3, -C(CH3)3, -H, -Br, -CN, and -NO2) as a mechanistic probe. Interestingly, upon reaction of 3 with the substrates, the formation of a new transient species, 2', was observed. 2' is postulated to be a protic congener of 2. All three species were demonstrated to react with the substituted phenols through a hydrogen atom transfer reaction mechanism, which was elucidated further by analysis of the postreaction mixtures. Critically, 3 was demonstrated to react at far superior rates to 2 and 2', and oxidized substrates more efficiently than any bis-μ-oxo-Ni2 III reported to date. The kinetic superiority of 3 with respect to 2 and 2' was attributed to a stronger bond in the product of oxidation by 3 when compared to those calculated for 2 and 2'.
Collapse
|
62
|
Neodymium as Metal Cofactor for Biological Methanol Oxidation: Structure and Kinetics of an XoxF1-Type Methanol Dehydrogenase. mBio 2021; 12:e0170821. [PMID: 34544276 PMCID: PMC8546591 DOI: 10.1128/mbio.01708-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The methane-oxidizing bacterium Methylacidimicrobium thermophilum AP8 thrives in acidic geothermal ecosystems that are characterized by high degassing of methane (CH4), H2, H2S, and by relatively high lanthanide concentrations. Lanthanides (atomic numbers 57 to 71) are essential in a variety of high-tech devices, including mobile phones. Remarkably, the same elements are actively taken up by methanotrophs/methylotrophs in a range of environments, since their XoxF-type methanol dehydrogenases require lanthanides as a metal cofactor. Lanthanide-dependent enzymes seem to prefer the lighter lanthanides (lanthanum, cerium, praseodymium, and neodymium), as slower methanotrophic/methylotrophic growth is observed in medium supplemented with only heavier lanthanides. Here, we purified XoxF1 from the thermoacidophilic methanotroph Methylacidimicrobium thermophilum AP8, which was grown in medium supplemented with neodymium as the sole lanthanide. The neodymium occupancy of the enzyme is 94.5% ± 2.0%, and through X-ray crystallography, we reveal that the structure of the active site shows interesting differences from the active sites of other methanol dehydrogenases, such as an additional aspartate residue in close proximity to the lanthanide. Nd-XoxF1 oxidizes methanol at a maximum rate of metabolism (Vmax) of 0.15 ± 0.01 μmol · min-1 · mg protein-1 and an affinity constant (Km) of 1.4 ± 0.6 μM. The structural analysis of this neodymium-containing XoxF1-type methanol dehydrogenase will expand our knowledge in the exciting new field of lanthanide biochemistry. IMPORTANCE Lanthanides comprise a group of 15 elements with atomic numbers 57 to 71 that are essential in a variety of high-tech devices, such as mobile phones, but were considered biologically inert for a long time. The biological relevance of lanthanides became evident when the acidophilic methanotroph Methylacidiphilum fumariolicum SolV, isolated from a volcanic mud pot, could only grow when lanthanides were supplied to the growth medium. We expanded knowledge in the exciting and rapidly developing field of lanthanide biochemistry by the purification and characterization of a neodymium-containing methanol dehydrogenase from a thermoacidophilic methanotroph.
Collapse
|
63
|
DeLucia AA, Kelly KA, Herrera KA, Gray DL, Olshansky L. Intramolecular Hydrogen-Bond Interactions Tune Reactivity in Biomimetic Bis(μ-hydroxo)dicobalt Complexes. Inorg Chem 2021; 60:15599-15609. [PMID: 34606250 DOI: 10.1021/acs.inorgchem.1c02210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Active site hydrogen-bond (H-bond) networks represent a key component by which metalloenzymes control the formation and deployment of high-valent transition metal-oxo intermediates. We report a series of dinuclear cobalt complexes that serve as structural models for the nonheme diiron enzyme family and feature a Co2(μ-OH)2 diamond core stabilized by intramolecular H-bond interactions. We define the conditions required for the kinetically controlled synthesis of these complexes: [Co2(μ-OH)2(μ-OAc)(κ1-OAc)2(pyR)4][PF6] (1R), where OAc = acetate and pyR = pyridine with para-substituent R, and we describe a homologous series of 1R in which the para-R substituent on pyridine is modulated. The solid state X-ray diffraction (XRD) structures of 1R are similar across the series, but in solution, their 1H NMR spectra reveal a linear free energy relationship (LFER) where, as R becomes increasingly electron-withdrawing, the intramolecular H-bond interaction between bridging μ-OH and κ1-acetate ligands results in increasingly "oxo-like" μ-OH bridges. Deprotonation of the bridging μ-OH results in the quantitative conversion to corresponding cubane complexes: [Co4(μ-O)4(μ3-OAc)4(pyR)4] (2R), which represent the thermodynamic sink of self-assembly. These reactions are unusually slow for rate-limiting deprotonation events, but rapid-mixing experiments reveal a 6000-fold rate acceleration on going from R = OMe to R = CN. These results suggest that we can tune reactivity by modulating the μ-OH pKa in the presence of intramolecular H-bond interactions to maintain stability as the octahedral d6 centers become increasingly acidic. Nature may similarly employ dynamic carboxylate-mediated H-bond interactions to control the reactivity of acidic transition metal-oxo intermediates.
Collapse
Affiliation(s)
- Alyssa A DeLucia
- Department of Chemistry, University of Illinois, Urbana-Champaign, 600 S. Mathews Ave. Urbana, Illinois 61801, United States
| | - Kimberly A Kelly
- Department of Chemistry, University of Illinois, Urbana-Champaign, 600 S. Mathews Ave. Urbana, Illinois 61801, United States
| | - Kevin A Herrera
- Department of Chemistry, University of Illinois, Urbana-Champaign, 600 S. Mathews Ave. Urbana, Illinois 61801, United States
| | - Danielle L Gray
- Department of Chemistry, University of Illinois, Urbana-Champaign, 600 S. Mathews Ave. Urbana, Illinois 61801, United States
| | - Lisa Olshansky
- Department of Chemistry, University of Illinois, Urbana-Champaign, 600 S. Mathews Ave. Urbana, Illinois 61801, United States
| |
Collapse
|
64
|
Fang G, Lin J, Wang X. Low-temperature conversion of methane to oxygenates by supported metal catalysts: From nanoparticles to single atoms. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2021.04.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
65
|
Murphy SMC, Bautista MA, Cramm MA, Hubert CRJ. Diesel and Crude Oil Biodegradation by Cold-Adapted Microbial Communities in the Labrador Sea. Appl Environ Microbiol 2021; 87:e0080021. [PMID: 34378990 PMCID: PMC8478444 DOI: 10.1128/aem.00800-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/24/2021] [Indexed: 11/20/2022] Open
Abstract
Oil spills in the subarctic marine environment off the coast of Labrador, Canada, are increasingly likely due to potential oil production and increases in ship traffic in the region. To understand the microbiome response and how nutrient biostimulation promotes biodegradation of oil spills in this cold marine setting, marine sediment microcosms amended with diesel or crude oil were incubated at in situ temperature (4°C) for several weeks. Sequencing of 16S rRNA genes following these spill simulations revealed decreased microbial diversity and enrichment of putative hydrocarbonoclastic bacteria that differed depending on the petroleum product. Metagenomic sequencing revealed that the genus Paraperlucidibaca harbors previously unrecognized capabilities for alkane biodegradation, which were also observed in Cycloclasticus. Genomic and amplicon sequencing together suggest that Oleispira and Thalassolituus degraded alkanes from diesel, while Zhongshania and the novel PGZG01 lineage contributed to crude oil alkane biodegradation. Greater losses in PAHs from crude oil than from diesel were consistent with Marinobacter, Pseudomonas_D, and Amphritea genomes exhibiting aromatic hydrocarbon biodegradation potential. Biostimulation with nitrogen and phosphorus (4.67 mM NH4Cl and 1.47 mM KH2PO4) was effective at enhancing n-alkane and PAH degradation following low-concentration (0.1% [vol/vol]) diesel and crude oil amendments, while at higher concentrations (1% [vol/vol]) only n-alkanes in diesel were consumed, suggesting toxicity induced by compounds in unrefined crude oil. Biostimulation allowed for a more rapid shift in the microbial community in response to petroleum amendments, more than doubling the rates of CO2 increase during the first few weeks of incubation. IMPORTANCE Increases in transportation of diesel and crude oil in the Labrador Sea will pose a significant threat to remote benthic and shoreline environments, where coastal communities and wildlife are particularly vulnerable to oil spill contaminants. Whereas marine microbiology has not been incorporated into environmental assessments in the Labrador Sea, there is a growing demand for microbial biodiversity evaluations given the pronounced impact of climate change in this region. Benthic microbial communities are important to consider given that a fraction of spilled oil typically sinks such that its biodegradation occurs at the seafloor, where novel taxa with previously unrecognized potential to degrade hydrocarbons were discovered in this work. Understanding how cold-adapted microbiomes catalyze hydrocarbon degradation at low in situ temperature is crucial in the Labrador Sea, which remains relatively cold throughout the year.
Collapse
Affiliation(s)
- Sean M. C. Murphy
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - María A. Bautista
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Margaret A. Cramm
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
66
|
Jodts RJ, Ross MO, Koo CW, Doan PE, Rosenzweig AC, Hoffman BM. Coordination of the Copper Centers in Particulate Methane Monooxygenase: Comparison between Methanotrophs and Characterization of the Cu C Site by EPR and ENDOR Spectroscopies. J Am Chem Soc 2021; 143:15358-15368. [PMID: 34498465 DOI: 10.1021/jacs.1c07018] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In nature, methane is oxidized to methanol by two enzymes, the iron-dependent soluble methane monooxygenase (sMMO) and the copper-dependent particulate MMO (pMMO). While sMMO's diiron metal active site is spectroscopically and structurally well-characterized, pMMO's copper sites are not. Recent EPR and ENDOR studies have established the presence of two monocopper sites, but the coordination environment of only one has been determined, that within the PmoB subunit and denoted CuB. Moreover, this recent work only focused on a type I methanotrophic pMMO, while previous observations of the type II enzyme were interpreted in terms of the presence of a dicopper site. First, this report shows that the type II Methylocystis species strain Rockwell pMMO, like the type I pMMOs, contains two monocopper sites and that its CuB site has a coordination environment identical to that of type I enzymes. As such, for the full range of pMMOs this report completes the refutation of prior and ongoing suggestions of multicopper sites. Second, and of primary importance, EPR/ENDOR measurements (a) for the first time establish the coordination environment of the spectroscopically observed site, provisionally denoted CuC, in both types of pMMO, thereby (b) establishing the assignment of this site observed by EPR to the crystallographically observed metal-binding site in the PmoC subunit. Finally, these results further indicate that CuC is the likely site of biological methane oxidation by pMMO, a conclusion that will serve as a foundation for proposals regarding the mechanism of this reaction.
Collapse
Affiliation(s)
- Richard J Jodts
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Matthew O Ross
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Christopher W Koo
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Peter E Doan
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Brian M Hoffman
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
67
|
Zheng A, Zhou Q, Ding B, Li D, Zhang T, Hou Z. Reduced Amino Acid Schiff Base‐Iron(III) Complexes Catalyzing Oxidation of Cyclohexane with Hydrogen Peroxide. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Anna Zheng
- Key Laboratory for Advanced Materials, Research Institute of Industrial Catalysis School of Chemistry and Molecular Engineering East China University of Science and Technology Shanghai 200237 China
| | - Qingqing Zhou
- Key Laboratory for Advanced Materials, Research Institute of Industrial Catalysis School of Chemistry and Molecular Engineering East China University of Science and Technology Shanghai 200237 China
| | - Bingjie Ding
- Key Laboratory for Advanced Materials, Research Institute of Industrial Catalysis School of Chemistry and Molecular Engineering East China University of Science and Technology Shanghai 200237 China
| | - Difan Li
- Key Laboratory for Advanced Materials, Research Institute of Industrial Catalysis School of Chemistry and Molecular Engineering East China University of Science and Technology Shanghai 200237 China
| | - Tong Zhang
- Key Laboratory for Advanced Materials, Research Institute of Industrial Catalysis School of Chemistry and Molecular Engineering East China University of Science and Technology Shanghai 200237 China
| | - Zhenshan Hou
- Key Laboratory for Advanced Materials, Research Institute of Industrial Catalysis School of Chemistry and Molecular Engineering East China University of Science and Technology Shanghai 200237 China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes East China Normal University School of Chemistry and Molecular Engineering Shanghai 200062 China
| |
Collapse
|
68
|
Itoh S, Shinke T, Itoh M, Wada T, Morimoto Y, Yanagisawa S, Sugimoto H, Kubo M. Revisiting Alkane Hydroxylation with m-CPBA (mChloroperbenzoic Acid) Catalyzed by Nickel(II) Complexes. Chemistry 2021; 27:14730-14737. [PMID: 34402568 DOI: 10.1002/chem.202102532] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Indexed: 11/09/2022]
Abstract
Mechanistic studies are performed on the alkane hydroxylation with m -CPBA ( m -chloroperbenzoic acid) catalyzed by nickel(II) complexes, Ni II (L). In the oxidation of cycloalkanes, Ni II (TPA) acts as an efficient catalyst with a high yield and a high alcohol selectivity. In the oxidation of adamantane, the tertiary carbon is predominantly oxidized. The reaction rate shows first-order dependence on [substrate] and [Ni II (L)] but is independent on [ m CPBA]; v obs = k 2 [substrate][ Ni II (L)]. The reaction exhibited a relatively large kinetic deuterium isotope effect ( KIE ) of 6.7, demonstrating that the hydrogen atom abstraction is involved in the rate-limiting step of the catalytic cycle. Furthermore, Ni II (L) supported by related tetradentate ligands exhibit apparently different catalytic activity, suggesting contribution of the Ni II (L) in the catalytic cycle. Based on the kinetic analysis and the significant effects of O 2 and CCl 4 on the product distribution pattern, possible contributions of (L)Ni II -O• and the acyloxyl radical as the reactive oxidants are discussed.
Collapse
Affiliation(s)
- Shinobu Itoh
- Osaka University, Graduate School of Engineering, 2-1 Yamadaoka, 565-0871, Suita, JAPAN
| | - Tomoya Shinke
- Osaka University School of Engineering Graduate School of Engineering: Osaka Daigaku Kogakubu Daigakuin Kogaku Kenkyuka, Applied Chemistry, JAPAN
| | - Mayu Itoh
- Osaka University School of Engineering Graduate School of Engineering: Osaka Daigaku Kogakubu Daigakuin Kogaku Kenkyuka, Applied Chemistry, JAPAN
| | - Takuma Wada
- Osaka University School of Engineering Graduate School of Engineering: Osaka Daigaku Kogakubu Daigakuin Kogaku Kenkyuka, Applied Chemistry, JAPAN
| | - Yuma Morimoto
- Osaka University School of Engineering Graduate School of Engineering: Osaka Daigaku Kogakubu Daigakuin Kogaku Kenkyuka, Applied Chemistry, JAPAN
| | | | - Hideki Sugimoto
- Osaka University School of Engineering Graduate School of Engineering: Osaka Daigaku Kogakubu Daigakuin Kogaku Kenkyuka, Applied Chemistry, JAPAN
| | - Minoru Kubo
- Graduate School of Science, Life Science, JAPAN
| |
Collapse
|
69
|
Salem R, ElDyasti A, Audette GF. Biomedical Applications of Biomolecules Isolated from Methanotrophic Bacteria in Wastewater Treatment Systems. Biomolecules 2021; 11:1217. [PMID: 34439884 PMCID: PMC8392503 DOI: 10.3390/biom11081217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022] Open
Abstract
Wastewater treatment plants and other remediation facilities serve important roles, both in public health, but also as dynamic research platforms for acquiring useful resources and biomolecules for various applications. An example of this is methanotrophic bacteria within anaerobic digestion processes in wastewater treatment plants. These bacteria are an important microbial source of many products including ectoine, polyhydroxyalkanoates, and methanobactins, which are invaluable to the fields of biotechnology and biomedicine. Here we provide an overview of the methanotrophs' unique metabolism and the biochemical pathways involved in biomolecule formation. We also discuss the potential biomedical applications of these biomolecules through creation of beneficial biocompatible products including vaccines, prosthetics, electronic devices, drug carriers, and heart stents. We highlight the links between molecular biology, public health, and environmental science in the advancement of biomedical research and industrial applications using methanotrophic bacteria in wastewater treatment systems.
Collapse
Affiliation(s)
- Rana Salem
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada;
| | - Ahmed ElDyasti
- Department of Civil Engineering, York University, Toronto, ON M3J 1P3, Canada;
| | - Gerald F. Audette
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada;
- The Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| |
Collapse
|
70
|
Del Campo P, Martínez C, Corma A. Activation and conversion of alkanes in the confined space of zeolite-type materials. Chem Soc Rev 2021; 50:8511-8595. [PMID: 34128513 DOI: 10.1039/d0cs01459a] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Microporous zeolite-type materials, with crystalline porous structures formed by well-defined channels and cages of molecular dimensions, have been widely employed as heterogeneous catalysts since the early 1960s, due to their wide variety of framework topologies, compositional flexibility and hydrothermal stability. The possible selection of the microporous structure and of the elements located in framework and extraframework positions enables the design of highly selective catalysts with well-defined active sites of acidic, basic or redox character, opening the path to their application in a wide range of catalytic processes. This versatility and high catalytic efficiency is the key factor enabling their use in the activation and conversion of different alkanes, ranging from methane to long chain n-paraffins. Alkanes are highly stable molecules, but their abundance and low cost have been two main driving forces for the development of processes directed to their upgrading over the last 50 years. However, the availability of advanced characterization tools combined with molecular modelling has enabled a more fundamental approach to the activation and conversion of alkanes, with most of the recent research being focused on the functionalization of methane and light alkanes, where their selective transformation at reasonable conversions remains, even nowadays, an important challenge. In this review, we will cover the use of microporous zeolite-type materials as components of mono- and bifunctional catalysts in the catalytic activation and conversion of C1+ alkanes under non-oxidative or oxidative conditions. In each case, the alkane activation will be approached from a fundamental perspective, with the aim of understanding, at the molecular level, the role of the active sites involved in the activation and transformation of the different molecules and the contribution of shape-selective or confinement effects imposed by the microporous structure.
Collapse
Affiliation(s)
- Pablo Del Campo
- Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022 Valencia, Spain.
| | | | | |
Collapse
|
71
|
Cu-promoted intramolecular hydroxylation of CH bonds using directing groups with varying denticity. J Inorg Biochem 2021; 223:111557. [PMID: 34352714 DOI: 10.1016/j.jinorgbio.2021.111557] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/11/2021] [Accepted: 07/16/2021] [Indexed: 12/31/2022]
Abstract
In this research article, we describe the Cu-promoted intramolecular hydroxylation of sp2 and sp3 CH bonds using directing groups with varying denticity (bi-, tri- and tetradentate) and natural oxidants (O2 and H2O2). We found that bidentate directing groups, in combination with Cu and H2O2, led to high hydroxylation yields. On the other hand, tetradentate directing groups did not form the hydroxylation products. Our mechanistic investigations suggest that bidentate directing groups allow for generating reactive mononuclear copper(II) hydroperoxide intermediates while tetradentate systems form dinuclear Cu2O2 species that do not oxidize CH bonds. Our findings might shed light on the reaction mechanism(s) by which Cu-dependent metalloenzymes such as particulate methane monooxygenase or lytic polysaccharide monooxygenase oxidize strong CH bonds.
Collapse
|
72
|
Snyder BER, Bols ML, Rhoda HM, Plessers D, Schoonheydt RA, Sels BF, Solomon EI. Cage effects control the mechanism of methane hydroxylation in zeolites. Science 2021; 373:327-331. [PMID: 34437151 PMCID: PMC10353845 DOI: 10.1126/science.abd5803] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 03/22/2021] [Accepted: 05/10/2021] [Indexed: 11/03/2022]
Abstract
Catalytic conversion of methane to methanol remains an economically tantalizing but fundamentally challenging goal. Current technologies based on zeolites deactivate too rapidly for practical application. We found that similar active sites hosted in different zeolite lattices can exhibit markedly different reactivity with methane, depending on the size of the zeolite pore apertures. Whereas zeolite with large pore apertures deactivates completely after a single turnover, 40% of active sites in zeolite with small pore apertures are regenerated, enabling a catalytic cycle. Detailed spectroscopic characterization of reaction intermediates and density functional theory calculations show that hindered diffusion through small pore apertures disfavors premature release of CH3 radicals from the active site after C-H activation, thereby promoting radical recombination to form methanol rather than deactivated Fe-OCH3 centers elsewhere in the lattice.
Collapse
Affiliation(s)
| | - Max L Bols
- Department of Microbial and Molecular Systems, Centre for Sustainable Catalysis and Engineering, KU Leuven-University of Leuven, B-3001 Leuven, Belgium
| | - Hannah M Rhoda
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Dieter Plessers
- Department of Microbial and Molecular Systems, Centre for Sustainable Catalysis and Engineering, KU Leuven-University of Leuven, B-3001 Leuven, Belgium
| | - Robert A Schoonheydt
- Department of Microbial and Molecular Systems, Centre for Sustainable Catalysis and Engineering, KU Leuven-University of Leuven, B-3001 Leuven, Belgium.
| | - Bert F Sels
- Department of Microbial and Molecular Systems, Centre for Sustainable Catalysis and Engineering, KU Leuven-University of Leuven, B-3001 Leuven, Belgium.
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| |
Collapse
|
73
|
Caldas Nogueira ML, Pastore AJ, Davidson VL. Diversity of structures and functions of oxo-bridged non-heme diiron proteins. Arch Biochem Biophys 2021; 705:108917. [PMID: 33991497 PMCID: PMC8165033 DOI: 10.1016/j.abb.2021.108917] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023]
Abstract
Oxo-bridged diiron proteins are a distinct class of non-heme iron proteins. Their active sites are composed of two irons that are coordinated by amino acid side chains, and a bridging oxygen that interacts with each iron. These proteins are members of the ferritin superfamily and share the structural feature of a four α-helix bundle that provides the residues that coordinate the irons. The different proteins also display a wide range of structures and functions. A prototype of this family is hemerythrin, which functions as an oxygen transporter. Several other hemerythrin-like proteins have been described with a diversity of functions including oxygen and iron sensing, and catalytic activities. Rubrerythrins react with hydrogen peroxide and rubrerythrin-like proteins possess a rubredoxin domain, in addition to the oxo-bridged diiron center. Other redox enzymes with oxo-bridged irons include flavodiiron proteins that act as O2 or NO reductases, ribonucleotide reductase and methane monooxygenase. Ferritins have an oxo-bridged diiron in the ferroxidase center of the protein, which plays a role in the iron storage function of these proteins. There are also bacterial ferritins that exhibit catalytic activities. The structures and functions of this broad class of oxo-bridged diiron proteins are described and compared in this review.
Collapse
Affiliation(s)
- Maria Luiza Caldas Nogueira
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States
| | - Anthony J Pastore
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States.
| |
Collapse
|
74
|
Affiliation(s)
- Judith Münch
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Pascal Püllmann
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West seventh Avenue, Tianjin 300308, China
| | - Martin J. Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
- Institute of Chemistry, MartinLuther-University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120, Halle, Saale, Germany
| |
Collapse
|
75
|
Jones JC, Banerjee R, Shi K, Semonis MM, Aihara H, Pomerantz WCK, Lipscomb JD. Soluble Methane Monooxygenase Component Interactions Monitored by 19F NMR. Biochemistry 2021; 60:1995-2010. [PMID: 34100595 PMCID: PMC8345336 DOI: 10.1021/acs.biochem.1c00293] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme capable of catalyzing the fissure of the C-H bond of methane and the insertion of one atom of oxygen from O2 to yield methanol. Efficient multiple-turnover catalysis occurs only in the presence of all three sMMO protein components: hydroxylase (MMOH), reductase (MMOR), and regulatory protein (MMOB). The complex series of sMMO protein component interactions that regulate the formation and decay of sMMO reaction cycle intermediates is not fully understood. Here, the two tryptophan residues in MMOB and the single tryptophan residue in MMOR are converted to 5-fluorotryptophan (5FW) by expression in defined media containing 5-fluoroindole. In addition, the mechanistically significant N-terminal region of MMOB is 19F-labeled by reaction of the K15C variant with 3-bromo-1,1,1-trifluoroacetone (BTFA). The 5FW and BTFA modifications cause minimal structural perturbation, allowing detailed studies of the interactions with sMMOH using 19F NMR. Resonances from the 275 kDa complexes of sMMOH with 5FW-MMOB and BTFA-K15C-5FW-MMOB are readily detected at 5 μM labeled protein concentration. This approach shows directly that MMOR and MMOB competitively bind to sMMOH with similar KD values, independent of the oxidation state of the sMMOH diiron cluster. These findings suggest a new model for regulation in which the dynamic equilibration of MMOR and MMOB with sMMOH allows a transient formation of key reactive complexes that irreversibly pull the reaction cycle forward. The slow kinetics of exchange of the sMMOH:MMOB complex is proposed to prevent MMOR-mediated reductive quenching of the high-valent reaction cycle intermediate Q before it can react with methane.
Collapse
Affiliation(s)
- Jason C. Jones
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Manny M. Semonis
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - William C. K. Pomerantz
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
76
|
Hakobyan A, Liesack W. Unexpected metabolic versatility among type II methanotrophs in the Alphaproteobacteria. Biol Chem 2021; 401:1469-1477. [PMID: 32769217 DOI: 10.1515/hsz-2020-0200] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 08/04/2020] [Indexed: 12/16/2022]
Abstract
Aerobic methane-oxidizing bacteria, or methanotrophs, play a crucial role in the global methane cycle. Their methane oxidation activity in various environmental settings has a great mitigation effect on global climate change. Alphaproteobacterial methanotrophs were among the first to be taxonomically characterized, nowadays unified in the Methylocystaceae and Beijerinckiaceae families. Originally thought to have an obligate growth requirement for methane and related one-carbon compounds as a source of carbon and energy, it was later shown that various alphaproteobacterial methanotrophs are facultative, able to grow on multi-carbon compounds such as acetate. Most recently, we expanded our knowledge of the metabolic versatility of alphaproteobacterial methanotrophs. We showed that Methylocystis sp. strain SC2 has the capacity for mixotrophic growth on H2 and CH4. This mini-review will summarize the change in perception from the long-held paradigm of obligate methanotrophy to today's recognition of alphaproteobacterial methanotrophs as having both facultative and mixotrophic capabilities.
Collapse
Affiliation(s)
- Anna Hakobyan
- Research group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany
| | - Werner Liesack
- Research group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany
| |
Collapse
|
77
|
Isolation, Description and Genome Analysis of a Putative Novel Methylobacter Species (‘Ca. Methylobacter coli’) Isolated from the Faeces of a Blackbuck (Indian Antelope). MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12020035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Enteric fermentation of methane by ruminant animals represents a major source of anthropogenic methane. Significantly less information is available on the existence of methanotrophs in the gut of ruminants. Therefore, detailed strain descriptions of methanotrophs isolated from ruminant faeces or gut are rare. We present a first report on the enrichment and isolation of a methanotroph, strain BlB1, from the faeces of an Indian antelope (blackbuck). The 16S rRNA gene sequence of strain BlB1 showed the highest identity (98.40% identity) to Methylobacter marinus A45T and Methylobacter luteus NCIMB 11914T. Strain BlB1 showed coccoidal cells (1.5–2 µm in diameter), which formed chains or aggregates of 3–4 cells of light yellow-coloured colonies on agarose when incubated with methane in the gas phase. The draft genome of BlB1 (JADMKV01) is 4.87 Mbp in size, with a G + C content of 51.3%. The draft genome showed 27.4% digital DNA-DNA hybridization (DDH) and 83.07% average nucleotide identity (ANIb) values with that of its closest phylogenetic neighbour, Methylobacter marinus A45T. Due to the lower values of DDH and ANIb with the nearest species, and <98.7% 16S rRNA gene sequence identity, we propose that strain BlB1 belongs to a novel species of Methylobacter. However, as the culture has to be maintained live and resisted cryopreservation, deposition in culture collections was not possible and hence we propose a Candidatus species name, ‘Ca. Methylobacter coli’ BlB1. ‘Ca. Methylobacter coli’ BlB1 would be the first described methanotroph from ruminants worldwide, with a sequenced draft genome. This strain could be used as a model for studies concerning methane mitigation from ruminants.
Collapse
|
78
|
Jurgeleit R, Grimm-Lebsanft B, Flöser BM, Teubner M, Buchenau S, Senft L, Hoffmann J, Naumova M, Näther C, Ivanović-Burmazović I, Rübhausen M, Tuczek F. Catalytic Oxygenation of Hydrocarbons by Mono-μ-oxo Dicopper(II) Species Resulting from O-O Cleavage of Tetranuclear Cu I /Cu II Peroxo Complexes. Angew Chem Int Ed Engl 2021; 60:14154-14162. [PMID: 33856088 PMCID: PMC8251984 DOI: 10.1002/anie.202101035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/13/2021] [Indexed: 01/11/2023]
Abstract
One of the challenges of catalysis is the transformation of inert C-H bonds to useful products. Copper-containing monooxygenases play an important role in this regard. Here we show that low-temperature oxygenation of dinuclear copper(I) complexes leads to unusual tetranuclear, mixed-valent μ4 -peroxo [CuI /CuII ]2 complexes. These Cu4 O2 intermediates promote irreversible and thermally activated O-O bond homolysis, generating Cu2 O complexes that catalyze strongly exergonic H-atom abstraction from hydrocarbons, coupled to O-transfer. The Cu2 O species can also be produced with N2 O, demonstrating their capability for small-molecule activation. The binding and cleavage of O2 leading to the primary Cu4 O2 intermediate and the Cu2 O complexes, respectively, is elucidated with a range of solution spectroscopic methods and mass spectrometry. The unique reactivities of these species establish an unprecedented, 100 % atom-economic scenario for the catalytic, copper-mediated monooxygenation of organic substrates, employing both O-atoms of O2 .
Collapse
Affiliation(s)
- Ramona Jurgeleit
- Institute of Inorganic Chemistry, Christian-Albrechts-University of Kiel, Max-Eyth-Strasse 2, 24118, Kiel, Germany
| | - Benjamin Grimm-Lebsanft
- Institut für Nanostruktur- und Festkörperphysik, Center for Free Electron Laser Science (CFEL), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Benedikt Maria Flöser
- Institute of Inorganic Chemistry, Christian-Albrechts-University of Kiel, Max-Eyth-Strasse 2, 24118, Kiel, Germany.,Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mühlheim an der Ruhr, Germany
| | - Melissa Teubner
- Institut für Nanostruktur- und Festkörperphysik, Center for Free Electron Laser Science (CFEL), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Department of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany
| | - Sören Buchenau
- Institut für Nanostruktur- und Festkörperphysik, Center for Free Electron Laser Science (CFEL), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Laura Senft
- Department of Chemistry and Pharmacy, Friedrich-Alexander-University of Erlangen-Nürnberg, Egerlandstrasse 1, 91058, Erlangen, Germany
| | - Jonas Hoffmann
- Institute for Analytical and Organic Chemistry, University of Bremen, Leobener Strasse 7, 28359, Bremen, Germany.,MAPEX, Center for Materials and Processes, University of Bremen, Bibliothekstrasse 1, 28359, Bremen, Germany
| | - Maria Naumova
- DESY, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany
| | - Christian Näther
- Institute of Inorganic Chemistry, Christian-Albrechts-University of Kiel, Max-Eyth-Strasse 2, 24118, Kiel, Germany
| | - Ivana Ivanović-Burmazović
- Department of Chemistry and Pharmacy, Friedrich-Alexander-University of Erlangen-Nürnberg, Egerlandstrasse 1, 91058, Erlangen, Germany.,Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, Haus D, 81377, München, Germany
| | - Michael Rübhausen
- Institut für Nanostruktur- und Festkörperphysik, Center for Free Electron Laser Science (CFEL), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Felix Tuczek
- Institute of Inorganic Chemistry, Christian-Albrechts-University of Kiel, Max-Eyth-Strasse 2, 24118, Kiel, Germany
| |
Collapse
|
79
|
Jurgeleit R, Grimm‐Lebsanft B, Flöser BM, Teubner M, Buchenau S, Senft L, Hoffmann J, Naumova M, Näther C, Ivanović‐Burmazović I, Rübhausen M, Tuczek F. Katalytische Oxygenierung von Kohlenwasserstoffen durch Mono‐μ‐oxo‐Dikupfer(II)‐Spezies erzeugt durch O‐O‐Spaltung von tetranuklearen Cu
I
/Cu
II
‐Peroxo‐Komplexen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Ramona Jurgeleit
- Institute of Inorganic Chemistry Christian-Albrechts-University of Kiel Max-Eyth-Straße 2 24118 Kiel Deutschland
| | - Benjamin Grimm‐Lebsanft
- Institut für Nanostruktur- und Festkörperphysik Center for Free Electron Laser Science (CFEL) Universität Hamburg Luruper Chaussee 149 22761 Hamburg Deutschland
| | - Benedikt Maria Flöser
- Institute of Inorganic Chemistry Christian-Albrechts-University of Kiel Max-Eyth-Straße 2 24118 Kiel Deutschland
- Max Planck Institute for Chemical Energy Conversion Stiftstraße 34–36 45470 Mühlheim an der Ruhr Deutschland
| | - Melissa Teubner
- Institut für Nanostruktur- und Festkörperphysik Center for Free Electron Laser Science (CFEL) Universität Hamburg Luruper Chaussee 149 22761 Hamburg Deutschland
- Department of Inorganic Chemistry RWTH Aachen University Landoltweg 1 52074 Aachen Deutschland
| | - Sören Buchenau
- Institut für Nanostruktur- und Festkörperphysik Center for Free Electron Laser Science (CFEL) Universität Hamburg Luruper Chaussee 149 22761 Hamburg Deutschland
| | - Laura Senft
- Department of Chemistry and Pharmacy Friedrich-Alexander-University of Erlangen-Nürnberg Egerlandstraße 1 91058 Erlangen Deutschland
| | - Jonas Hoffmann
- Institute for Analytical and Organic Chemistry University of Bremen Leobener Straße 7 28359 Bremen Deutschland
- MAPEX, Center for Materials and Processes University of Bremen Bibliothekstrasse 1 28359 Bremen Deutschland
| | - Maria Naumova
- DESY, Deutsches Elektronen-Synchrotron (DESY) Notkestraße 85 22607 Hamburg Deutschland
| | - Christian Näther
- Institute of Inorganic Chemistry Christian-Albrechts-University of Kiel Max-Eyth-Straße 2 24118 Kiel Deutschland
| | - Ivana Ivanović‐Burmazović
- Department of Chemistry and Pharmacy Friedrich-Alexander-University of Erlangen-Nürnberg Egerlandstraße 1 91058 Erlangen Deutschland
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13, Haus D 81377 München Deutschland
| | - Michael Rübhausen
- Institut für Nanostruktur- und Festkörperphysik Center for Free Electron Laser Science (CFEL) Universität Hamburg Luruper Chaussee 149 22761 Hamburg Deutschland
| | - Felix Tuczek
- Institute of Inorganic Chemistry Christian-Albrechts-University of Kiel Max-Eyth-Straße 2 24118 Kiel Deutschland
| |
Collapse
|
80
|
Guerrero-Cruz S, Vaksmaa A, Horn MA, Niemann H, Pijuan M, Ho A. Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications. Front Microbiol 2021; 12:678057. [PMID: 34054786 PMCID: PMC8163242 DOI: 10.3389/fmicb.2021.678057] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.
Collapse
Affiliation(s)
- Simon Guerrero-Cruz
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Universitat de Girona, Girona, Spain
| | - Annika Vaksmaa
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, ’t Horntje, Netherlands
| | - Marcus A. Horn
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Helge Niemann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, ’t Horntje, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
- Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Maite Pijuan
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Universitat de Girona, Girona, Spain
| | - Adrian Ho
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
- Division of Applied Life Sciences, Gyeongsang National University, Jinju, South Korea
| |
Collapse
|
81
|
Schulz CE, Castillo RG, Pantazis DA, DeBeer S, Neese F. Structure-Spectroscopy Correlations for Intermediate Q of Soluble Methane Monooxygenase: Insights from QM/MM Calculations. J Am Chem Soc 2021; 143:6560-6577. [PMID: 33884874 PMCID: PMC8154522 DOI: 10.1021/jacs.1c01180] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The determination
of the diiron core intermediate structures involved
in the catalytic cycle of soluble methane monooxygenase (sMMO), the
enzyme that selectively catalyzes the conversion of methane to methanol,
has been a subject of intense interest within the bioinorganic scientific
community. Particularly, the specific geometry and electronic structure
of the intermediate that precedes methane binding, known as intermediate
Q (or MMOHQ), has been debated for over 30 years. Some
reported studies support a bis-μ-oxo-bridged Fe(IV)2O2 closed-core conformation Fe(IV)2O2 core, whereas others favor an open-core geometry, with a longer
Fe–Fe distance. The lack of consensus calls for a thorough
re-examination and reinterpretation of the spectroscopic data available
on the MMOHQ intermediate. Herein, we report extensive
simulations based on a hybrid quantum mechanics/molecular mechanics
approach (QM/MM) approach that takes into account the complete enzyme
to explore possible conformations for intermediates MMOHox and MMOHQ of the sMMOH catalytic cycle. High-level quantum
chemical approaches are used to correlate specific structural motifs
with geometric parameters for comparison with crystallographic and
EXAFS data, as well as with spectroscopic data from Mössbauer
spectroscopy, Fe K-edge high-energy resolution X-ray absorption spectroscopy
(HERFD XAS), and resonance Raman 16O–18O difference spectroscopy. The results provide strong support for
an open-core-type configuration in MMOHQ, with the most
likely topology involving mono-oxo-bridged Fe ions and alternate terminal
Fe-oxo and Fe-hydroxo groups that interact via intramolecular hydrogen
bonding. The implications of an open-core intermediate Q on the reaction
mechanism of sMMO are discussed.
Collapse
Affiliation(s)
- Christine E Schulz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Rebeca G Castillo
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
82
|
Brezicki G, Zheng J, Paolucci C, Schlögl R, Davis RJ. Effect of the Co-cation on Cu Speciation in Cu-Exchanged Mordenite and ZSM-5 Catalysts for the Oxidation of Methane to Methanol. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00543] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Gordon Brezicki
- Department of Chemical Engineering, University of Virginia, 102 Engineer’s Way, P.O. Box 400741, Charlottesville, Virginia 22904-4741, United States
| | - Jonathan Zheng
- Department of Chemical Engineering, University of Virginia, 102 Engineer’s Way, P.O. Box 400741, Charlottesville, Virginia 22904-4741, United States
| | - Christopher Paolucci
- Department of Chemical Engineering, University of Virginia, 102 Engineer’s Way, P.O. Box 400741, Charlottesville, Virginia 22904-4741, United States
| | - Robert Schlögl
- Department of Inorganic Chemistry, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Robert J. Davis
- Department of Chemical Engineering, University of Virginia, 102 Engineer’s Way, P.O. Box 400741, Charlottesville, Virginia 22904-4741, United States
| |
Collapse
|
83
|
Peng W, Qu X, Shaik S, Wang B. Deciphering the oxygen activation mechanism at the CuC site of particulate methane monooxygenase. Nat Catal 2021. [DOI: 10.1038/s41929-021-00591-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
84
|
Cutsail GE, Ross MO, Rosenzweig AC, DeBeer S. Towards a unified understanding of the copper sites in particulate methane monooxygenase: an X-ray absorption spectroscopic investigation. Chem Sci 2021; 12:6194-6209. [PMID: 33996018 PMCID: PMC8098663 DOI: 10.1039/d1sc00676b] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The enzymatic conversion of the greenhouse gas, methane, to a liquid fuel, methanol, is performed by methane monooxygenases (MMOs) under mild conditions. The copper stoichiometry of particulate MMO (pMMO) has been long debated, with a dicopper site previously proposed on the basis of a 2.51 Å Cu–Cu feature in extended X-ray absorption fine structure (EXAFS) data. However, recent crystallographic data and advanced electron paramagnetic resonance (EPR) characterization support the presence of only mononuclear copper sites. To reconcile these data, we have collected high-energy resolution fluorescence detected (HERFD) and partial fluorescence yield (PFY) EXAFS spectra of Methylococcus (M.) capsulatus (Bath) pMMO. Both methods reveal only monocopper sites. These data were compared to previously published pMMO PFY-EXAFS data from M. capsulatus (Bath) and Methylomicrobium alcaliphilum 20Z, supporting dicopper and monocopper sites, respectively. The FT-EXAFS feature previously attributed to a dicopper site can be reproduced by the inclusion of a metallic copper background signal. The exact position of this feature is dependent on the nature of the sample and the percentage of background contamination, indicating that visual inspection is not sufficient for identifying background metallic contributions. Additionally, an undamaged X-ray absorption spectrum was obtained, consistent with the copper oxidation-state speciation determined by EPR quantification. X-ray photodamage studies suggest that the previously observed Cu(i) XAS features are in part attributable to photodamage. This study illustrates the complex array of factors involved in EXAFS measurement and modeling of pMMO and more generally, dilute metalloproteins with multiple metal centers. Extended X-ray absorption fine structure spectroscopic analysis of particulate methane monooxygenase reveals only monocopper sites and investigates the possible origins of the previous observed dicopper signals.![]()
Collapse
Affiliation(s)
- George E Cutsail
- Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34-36 D-45470 Mülheim an der Ruhr Germany .,University of Duisburg-Essen Universitätsstrasse 7 D-45151 Essen Germany
| | - Matthew O Ross
- 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
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34-36 D-45470 Mülheim an der Ruhr Germany
| |
Collapse
|
85
|
Khider MLK, Brautaset T, Irla M. Methane monooxygenases: central enzymes in methanotrophy with promising biotechnological applications. World J Microbiol Biotechnol 2021; 37:72. [PMID: 33765207 PMCID: PMC7994243 DOI: 10.1007/s11274-021-03038-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/09/2021] [Indexed: 12/02/2022]
Abstract
Worldwide, the use of methane is limited to generating power, electricity, heating, and for production of chemicals. We believe this valuable gas can be employed more widely. Here we review the possibility of using methane as a feedstock for biotechnological processes based on the application of synthetic methanotrophs. Methane monooxygenase (MMO) enables aerobic methanotrophs to utilize methane as a sole carbon and energy source, in contrast to industrial microorganisms that grow on carbon sources, such as sugar cane, which directly compete with the food market. However, naturally occurring methanotrophs have proven to be difficult to manipulate genetically and their current industrial use is limited to generating animal feed biomass. Shifting the focus from genetic engineering of methanotrophs, towards introducing metabolic pathways for methane utilization in familiar industrial microorganisms, may lead to construction of efficient and economically feasible microbial cell factories. The applications of a technology for MMO production are not limited to methane-based industrial synthesis of fuels and value-added products, but are also of interest in bioremediation where mitigating anthropogenic pollution is an increasingly relevant issue. Published research on successful functional expression of MMO does not exist, but several attempts provide promising future perspectives and a few recent patents indicate that there is an ongoing research in this field. Combining the knowledge on genetics and metabolism of methanotrophy with tools for functional heterologous expression of MMO-encoding genes in non-methanotrophic bacterial species, is a key step for construction of synthetic methanotrophs that holds a great biotechnological potential.
Collapse
Affiliation(s)
- May L K Khider
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Trygve Brautaset
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Marta Irla
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway.
| |
Collapse
|
86
|
Chalupský J, Srnec M. Beyond the Classical Contributions to Exchange Coupling in Binuclear Transition Metal Complexes. J Phys Chem A 2021; 125:2276-2283. [PMID: 33724818 DOI: 10.1021/acs.jpca.0c11237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Complexes with two or more magnetically coupled metal ions have attracted considerable attention as catalysts of many vital processes, single-molecule magnets, or spin-crossover compounds. Elucidation of their electronic structures is essential for understanding their catalytic and magnetic properties. Here, we provide an unprecedented insight into exchange-coupling mechanisms between the magnetic centers in six prototypical bis-μ-oxo bimetallic M2O2 complexes, including two biologically relevant models of non-heme iron enzymes. Employing multiconfigurational/multireference methods and related orbital entanglement analysis, we revealed the essential and counterintuitive role of predominantly unoccupied valence metal d orbitals in their strong antiferromagnetic coupling. We found that the participation of these orbitals is twofold. First, they enhance the superexchange between the singly occupied d orbitals. Second, they become substantially occupied and thus directly magnetically active, which we perceive as a new mechanism of the exchange interaction between the magnetic transition metal centers.
Collapse
Affiliation(s)
- Jakub Chalupský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, Prague 6 16610, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague 8 18223, Czech Republic
| |
Collapse
|
87
|
Abstract
Methanotrophic bacteria represent a potential route to methane utilization and mitigation of methane emissions. In the first step of their metabolic pathway, aerobic methanotrophs use methane monooxygenases (MMOs) to activate methane, oxidizing it to methanol. There are two types of MMOs: a particulate, membrane-bound enzyme (pMMO) and a soluble, cytoplasmic enzyme (sMMO). The two MMOs are completely unrelated, with different architectures, metal cofactors, and mechanisms. The more prevalent of the two, pMMO, is copper-dependent, but the identity of its copper active site remains unclear. By contrast, sMMO uses a diiron active site, the catalytic cycle of which is well understood. Here we review the current state of knowledge for both MMOs, with an emphasis on recent developments and emerging hypotheses. In addition, we discuss obstacles to developing expression systems, which are needed to address outstanding questions and to facilitate future protein engineering efforts.
Collapse
Affiliation(s)
- Christopher W Koo
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA.
| | | |
Collapse
|
88
|
Methane utilizing plant growth-promoting microbial diversity analysis of flooded paddy ecosystem of India. World J Microbiol Biotechnol 2021; 37:56. [PMID: 33619649 DOI: 10.1007/s11274-021-03018-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/01/2021] [Indexed: 01/10/2023]
Abstract
Methane utilizing bacteria (MUB) are known to inhabit the flooded paddy ecosystem where they play an important role in regulating net methane (CH4) emission. We hypothesize that efficient MUB having plant growth-promoting (PGP) attributes can be used for developing novel bio-inoculant for flooded paddy ecosystem which might not only reduce methane emission but also assist in improving the plant growth parameters. Hence, soil and plant samples were collected from the phyllosphere, rhizosphere, and non-rhizosphere of five rice-growing regions of India at the tillering stage and investigated for efficient methane-oxidizing and PGP bacteria. Based on the monooxygenase activity and percent methane utilization on NMS medium with methane as the sole C source, 123 isolates were identified and grouped phylogenetically into 13 bacteria and 2 yeast genera. Among different regions, a significantly higher number of isolates were obtained from lowland flooded paddy ecosystems of Aduthurai (33.33%) followed by Ernakulum (20.33%) and Brahmaputra valley (19.51%) as compared to upland irrigated regions of Gaya (17.07%) and Varanasi (8.94%). Among sub-samples, a significantly higher number of isolates were found inhabiting the phyllosphere (58.54%) followed by non-rhizosphere (25.20%) and rhizosphere (15.45%). Significantly higher utilization of methane and PGP attributes were observed in 30 isolates belonging to genera Hyphomicrobium, Burkholderia, Methylobacterium, Paenibacillus, Pseudomonas, Rahnella, and Meyerozyma. M. oryzae MNL7 showed significantly better growth with 74.33% of CH4 utilization at the rate of 302.9 ± 5.58 and exhibited half-maximal growth rate, Ks of 1.92 ± 0.092 mg CH4 L-1. Besides the ability to utilize CH4, P. polymyxa MaAL70 possessed PGP attributes such as solubilization of P, K, and Zn, fixation of atmospheric N and production of indole acetic acid (IAA). Both these promising isolates can be explored in the future for developing novel biofertilizers for flooded paddies.
Collapse
|
89
|
Calisto F, Sousa FM, Sena FV, Refojo PN, Pereira MM. Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins. Chem Rev 2021; 121:1804-1844. [PMID: 33398986 DOI: 10.1021/acs.chemrev.0c00830] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.
Collapse
Affiliation(s)
- Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| |
Collapse
|
90
|
Schmitz RA, Peeters SH, Versantvoort W, Picone N, Pol A, Jetten MSM, Op den Camp HJM. Verrucomicrobial methanotrophs: ecophysiology of metabolically versatile acidophiles. FEMS Microbiol Rev 2021; 45:6125968. [PMID: 33524112 PMCID: PMC8498564 DOI: 10.1093/femsre/fuab007] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/15/2021] [Indexed: 12/26/2022] Open
Abstract
Methanotrophs are an important group of microorganisms that counteract methane emissions to the atmosphere. Methane-oxidising bacteria of the Alpha- and Gammaproteobacteria have been studied for over a century, while methanotrophs of the phylum Verrucomicrobia are a more recent discovery. Verrucomicrobial methanotrophs are extremophiles that live in very acidic geothermal ecosystems. Currently, more than a dozen strains have been isolated, belonging to the genera Methylacidiphilum and Methylacidimicrobium. Initially, these methanotrophs were thought to be metabolically confined. However, genomic analyses and physiological and biochemical experiments over the past years revealed that verrucomicrobial methanotrophs, as well as proteobacterial methanotrophs, are much more metabolically versatile than previously assumed. Several inorganic gases and other molecules present in acidic geothermal ecosystems can be utilised, such as methane, hydrogen gas, carbon dioxide, ammonium, nitrogen gas and perhaps also hydrogen sulfide. Verrucomicrobial methanotrophs could therefore represent key players in multiple volcanic nutrient cycles and in the mitigation of greenhouse gas emissions from geothermal ecosystems. Here, we summarise the current knowledge on verrucomicrobial methanotrophs with respect to their metabolic versatility and discuss the factors that determine their diversity in their natural environment. In addition, key metabolic, morphological and ecological characteristics of verrucomicrobial and proteobacterial methanotrophs are reviewed.
Collapse
Affiliation(s)
- Rob A Schmitz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Stijn H Peeters
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Nunzia Picone
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Arjan Pol
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| |
Collapse
|
91
|
Feng X, Song Y, Chen JS, Xu Z, Dunn SJ, Lin W. Rational Construction of an Artificial Binuclear Copper Monooxygenase in a Metal–Organic Framework. J Am Chem Soc 2021; 143:1107-1118. [DOI: 10.1021/jacs.0c11920] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xuanyu Feng
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Yang Song
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Justin S. Chen
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Ziwan Xu
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Soren J. Dunn
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Wenbin Lin
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| |
Collapse
|
92
|
A three-component monooxygenase from Rhodococcus wratislaviensis may expand industrial applications of bacterial enzymes. Commun Biol 2021; 4:16. [PMID: 33398074 PMCID: PMC7782822 DOI: 10.1038/s42003-020-01555-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/03/2020] [Indexed: 12/14/2022] Open
Abstract
The high-valent iron-oxo species formed in the non-heme diiron enzymes have high oxidative reactivity and catalyze difficult chemical reactions. Although the hydroxylation of inert methyl groups is an industrially promising reaction, utilizing non-heme diiron enzymes as such a biocatalyst has been difficult. Here we show a three-component monooxygenase system for the selective terminal hydroxylation of α-aminoisobutyric acid (Aib) into α-methyl-D-serine. It consists of the hydroxylase component, AibH1H2, and the electron transfer component. Aib hydroxylation is the initial step of Aib catabolism in Rhodococcus wratislaviensis C31-06, which has been fully elucidated through a proteome analysis. The crystal structure analysis revealed that AibH1H2 forms a heterotetramer of two amidohydrolase superfamily proteins, of which AibHm2 is a non-heme diiron protein and functions as a catalytic subunit. The Aib monooxygenase was demonstrated to be a promising biocatalyst that is suitable for bioprocesses in which the inert C–H bond in methyl groups need to be activated. Makoto Hibi et al. report a novel three-component monooxygenase system in Rhodococcus wratislaviensis. This enzyme catalyzes the activation of an inert C–H bond and may be potentially important as a biocatalyst for industrial applications.
Collapse
|
93
|
Goodman E, Zhou C, Cargnello M. Design of Organic/Inorganic Hybrid Catalysts for Energy and Environmental Applications. ACS CENTRAL SCIENCE 2020; 6:1916-1937. [PMID: 33274270 PMCID: PMC7706093 DOI: 10.1021/acscentsci.0c01046] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Indexed: 05/31/2023]
Abstract
Controlling selectivity between competing reaction pathways is crucial in catalysis. Several approaches have been proposed to achieve this goal in traditional heterogeneous catalysts including tuning nanoparticle size, varying alloy composition, and controlling supporting material. A less explored and promising research area to control reaction selectivity is via the use of hybrid organic/inorganic catalysts. These materials contain inorganic components which serve as sites for chemical reactions and organic components which either provide diffusional control or directly participate in the formation of active site motifs. Despite the appealing potential of these hybrid materials to increase reaction selectivity, there are significant challenges to the rational design of such hybrid nanostructures. Structural and mechanistic characterization of these materials play a key role in understanding and, therefore, designing these organic/inorganic hybrid catalysts. This Outlook highlights the design of hybrid organic/inorganic catalysts with a brief overview of four different classes of materials and discusses the practical catalytic properties and opportunities emerging from such designs in the area of energy and environmental transformations. Key structural and mechanistic characterization studies are identified to provide fundamental insight into the atomic structure and catalytic behavior of hybrid organic/inorganic catalysts. Exemplary works are used to show how specific active site motifs allow for remarkable changes in the reaction selectivity. Finally, to demonstrate the potential of hybrid catalyst materials, we suggest a characterization-based approach toward the design of biomimetic hybrid organic/inorganic materials for a specific application in the energy and environmental research space: the conversion of methane into methanol.
Collapse
|
94
|
Hall JN, Bollini P. Low‐Temperature, Ambient Pressure Oxidation of Methane to Methanol Over Every Tri‐Iron Node in a Metal–Organic Framework Material. Chemistry 2020; 26:16639-16643. [DOI: 10.1002/chem.202003894] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Indexed: 01/15/2023]
Affiliation(s)
- Jacklyn N. Hall
- Chemical & Biomolecular Engineering University of Houston 4722 Calhoun Rd. Houston TX 77004 USA
| | - Praveen Bollini
- Chemical & Biomolecular Engineering University of Houston 4722 Calhoun Rd. Houston TX 77004 USA
| |
Collapse
|
95
|
Wang B, Wang Z, Davies GJ, Walton PH, Rovira C. Activation of O2 and H2O2 by Lytic Polysaccharide Monooxygenases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02914] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Zhanfeng Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Gideon J. Davies
- Department of Chemistry, University of York, Heslington, YO10 5DD, U.K
| | - Paul H. Walton
- Department of Chemistry, University of York, Heslington, YO10 5DD, U.K
| | - Carme Rovira
- Departament de Quı́mica Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martı́ i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluı́s Companys, 23, 08020 Barcelona, Spain
| |
Collapse
|
96
|
Versantvoort W, Pol A, Jetten MSM, van Niftrik L, Reimann J, Kartal B, Op den Camp HJM. Multiheme hydroxylamine oxidoreductases produce NO during ammonia oxidation in methanotrophs. Proc Natl Acad Sci U S A 2020; 117:24459-24463. [PMID: 32913059 PMCID: PMC7533708 DOI: 10.1073/pnas.2011299117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Aerobic and nitrite-dependent methanotrophs make a living from oxidizing methane via methanol to carbon dioxide. In addition, these microorganisms cometabolize ammonia due to its structural similarities to methane. The first step in both of these processes is catalyzed by methane monooxygenase, which converts methane or ammonia into methanol or hydroxylamine, respectively. Methanotrophs use methanol for energy conservation, whereas toxic hydroxylamine is a potent inhibitor that needs to be rapidly removed. It is suggested that many methanotrophs encode a hydroxylamine oxidoreductase (mHAO) in their genome to remove hydroxylamine, although biochemical evidence for this is lacking. HAOs also play a crucial role in the metabolism of aerobic and anaerobic ammonia oxidizers by converting hydroxylamine to nitric oxide (NO). Here, we purified an HAO from the thermophilic verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV and characterized its kinetic properties. This mHAO possesses the characteristic P460 chromophore and is active up to at least 80 °C. It catalyzes the rapid oxidation of hydroxylamine to NO. In methanotrophs, mHAO efficiently removes hydroxylamine, which severely inhibits calcium-dependent, and as we show here, lanthanide-dependent methanol dehydrogenases, which are more prevalent in the environment. Our results indicate that mHAO allows methanotrophs to thrive under high ammonia concentrations in natural and engineered ecosystems, such as those observed in rice paddy fields, landfills, or volcanic mud pots, by preventing the accumulation of inhibitory hydroxylamine. Under oxic conditions, methanotrophs mainly oxidize ammonia to nitrite, whereas in hypoxic and anoxic environments reduction of both ammonia-derived nitrite and NO could lead to nitrous oxide (N2O) production.
Collapse
Affiliation(s)
- Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Arjan Pol
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Laura van Niftrik
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, 6525 AJ Nijmegen, The Netherlands
| |
Collapse
|
97
|
An Unusual Route for p-Aminobenzoate Biosynthesis in Chlamydia trachomatis Involves a Probable Self-Sacrificing Diiron Oxygenase. J Bacteriol 2020; 202:JB.00319-20. [PMID: 32967910 DOI: 10.1128/jb.00319-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/23/2020] [Indexed: 11/20/2022] Open
Abstract
Chlamydia trachomatis lacks the canonical genes required for the biosynthesis of p-aminobenzoate (pABA), a component of essential folate cofactors. Previous studies revealed a single gene from C. trachomatis, the CT610 gene, that rescues Escherichia coli ΔpabA, ΔpabB, and ΔpabC mutants, which are otherwise auxotrophic for pABA. CT610 shares low sequence similarity to nonheme diiron oxygenases, and the previously solved crystal structure revealed a diiron active site. Genetic studies ruled out several potential substrates for CT610-dependent pABA biosynthesis, including chorismate and other shikimate pathway intermediates, leaving the actual precursor(s) unknown. Here, we supplied isotopically labeled potential precursors to E. coli ΔpabA cells expressing CT610 and found that the aromatic portion of tyrosine was highly incorporated into pABA, indicating that tyrosine is a precursor for CT610-dependent pABA biosynthesis. Additionally, in vitro enzymatic experiments revealed that purified CT610 exhibits low pABA synthesis activity under aerobic conditions in the absence of tyrosine or other potential substrates, where only the addition of a reducing agent such as dithiothreitol appears to stimulate pABA production. Furthermore, site-directed mutagenesis studies revealed that two conserved active site tyrosine residues are essential for the pABA synthesis reaction in vitro Thus, the current data are most consistent with CT610 being a unique self-sacrificing enzyme that utilizes its own active site tyrosine residue(s) for pABA biosynthesis in a reaction that requires O2 and a reduced diiron cofactor.IMPORTANCE Chlamydia trachomatis is the most reported sexually transmitted infection in the United States and the leading cause of infectious blindness worldwide. Unlike many other intracellular pathogens that have undergone reductive evolution, C. trachomatis is capable of de novo biosynthesis of the essential cofactor tetrahydrofolate using a noncanonical pathway. Here, we identify the biosynthetic precursor to the p-aminobenzoate (pABA) portion of folate in a process that requires the CT610 enzyme from C. trachomatis We further provide evidence that CT610 is a self-sacrificing or "suicide" enzyme that uses its own amino acid residue(s) as the substrate for pABA synthesis. This work provides the foundation for future investigation of this chlamydial pABA synthase, which could lead to new therapeutic strategies for C. trachomatis infections.
Collapse
|
98
|
Morgan GL, Li B. In Vitro Reconstitution Reveals a Central Role for the N-Oxygenase PvfB in (Dihydro)pyrazine-N-oxide and Valdiazen Biosynthesis. Angew Chem Int Ed Engl 2020; 59:21387-21391. [PMID: 32662921 DOI: 10.1002/anie.202005554] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/18/2020] [Indexed: 12/22/2022]
Abstract
The Pseudomonas virulence factor (pvf) operon is essential for the biosynthesis of two very different natural product scaffolds: the (dihydro)pyrazine-N-oxides and the diazeniumdiolate, valdiazen. PvfB is a member of the non-heme diiron N-oxygenase enzyme family that commonly convert anilines to their nitroaromatic counterparts. In contrast, we show that PvfB catalyzes N-oxygenation of the α-amine of valine, first to the hydroxylamine and then the nitroso, while linked to the carrier protein of PvfC. PvfB modification of PvfC-tethered valine was observed directly by protein NMR spectroscopy, establishing the intermediacy of the hydroxylamine. This work reveals a central role for PvfB in the biosynthesis of (dihydro)pyrazine-N-oxides and valdiazen.
Collapse
Affiliation(s)
- Gina L Morgan
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bo Li
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| |
Collapse
|
99
|
Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI, Daldal F, Koch HG. Cu Homeostasis in Bacteria: The Ins and Outs. MEMBRANES 2020; 10:E242. [PMID: 32962054 PMCID: PMC7558416 DOI: 10.3390/membranes10090242] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022]
Abstract
Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.
Collapse
Affiliation(s)
- Andreea Andrei
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
- Fakultät für Biologie, Albert-Ludwigs Universität Freiburg; Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Yavuz Öztürk
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | | | - Juna Rauch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | - Dorian Marckmann
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | | | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Hans-Georg Koch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| |
Collapse
|
100
|
Morgan GL, Li B. In Vitro Reconstitution Reveals a Central Role for the N‐Oxygenase PvfB in (Dihydro)pyrazine‐
N
‐oxide and Valdiazen Biosynthesis. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Gina L. Morgan
- Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Bo Li
- Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| |
Collapse
|