Article
Microbiology
Kangli Guo, Anna Hakobyan, Timo Glatter, Nicole Paczia, Werner Liesack
Summary: High NH4+ load inhibits bacterial methane oxidation by competing with CH4 for the active site of pMMO. Methylocystis sp. strain SC2 shows cellular acclimatization response to high NH4+ levels involving stress-responsive proteins, synthesis of compatible solutes, and induction of glutathione metabolism pathway. Increased NH4+ load leads to increased pMMO-based oxidation of NH3 to toxic hydroxylamine, resulting in accumulation of NO2- and N2O.
Article
Chemistry, Physical
Wei Peng, Xiaoyang Qu, Sason Shaik, Binju Wang
Summary: This study deciphers the catalytic cycle of pMMO in the presence of the physiological reductant duroquinol (DQH(2)), revealing that O-2 activation is initiated by the Cu-C(ii)-DQH(-) species. The research also uncovers the important roles of the phenol co-substrate for O-2 activation.
Review
Biotechnology & Applied Microbiology
Noemi Poma, Andrea Bonini, Federico Vivaldi, Denise Biagini, Mariagrazia Di Luca, Daria Bottai, Fabio Di Francesco, Arianna Tavanti
Summary: Climate change due to increased greenhouse gas emissions has had a significant impact on the sustainability of life on Earth. Methane, a greenhouse gas, is increasing in concentration and its measurement is important for the environment and safety. The use of methane-oxidizing bacteria in biosensing systems shows promise for methane quantification and monitoring.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Engineering, Environmental
Leticia Oliveira Bispo Cardoso, Bruno Karolski, Louise Hase Gracioso, Bruna Bacaro Borrego, Claudio Augusto Oller do Nascimento, Elen Aquino Perpetuo
Summary: This study proposes an alternative method to solve the environmental problems caused by the unrestrained production of oil-based plastics and the increase in greenhouse gas emissions. The bioconversion of methane into a biodegradable polymer called polyhydroxybutyrate (PHB) is suggested as a substitute for plastics and to sequester greenhouse gases. Through the investigation of microbial consortia in mangrove areas, it was found that they can produce PHB under high methane concentrations. The study determined suitable conditions for PHB production by adjusting copper and methane concentrations as well as cultivation time. The results demonstrate the potential of this microbial consortium in methane bioconversion and microbial interactions in mangrove ecosystems.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
Article
Materials Science, Biomaterials
Haifeng Wu, Shichao Xu, Peidong Du, Yuanxi Liu, Hui Li, Haijun Yang, Ting Wang, Zhen-Gang Wang
Summary: In this study, a nucleotide-Cu2+ complex capable of catalyzing ortho-hydroxylation reactions resembling those of minimalistic monooxygenases was synthesized and investigated. Experimental and theoretical findings revealed that the catalyst formed a ternary complex intermediate with H2O2 and tyramine substrates through weak interactions, leading to the ortho-hydroxylation of tyramine. Moreover, the Cu2+ bound to nucleotides or oligonucleotides exhibited thermophilic catalytic properties.
JOURNAL OF MATERIALS CHEMISTRY B
(2023)
Article
Engineering, Environmental
Yulu Wang, Chun-Yu Lai, Mengxiong Wu, Xuanyu Lu, Shihu Hu, Zhiguo Yuan, Jianhua Guo
Summary: This study showed that increasing copper concentration significantly enhanced the perchlorate reduction rate in a methane-based membrane biofilm reactor, as well as promoted methane oxidation and perchlorate reduction rates through adjusting the abundance of functional genes. A higher copper concentration also increased microbial community diversity and facilitated the synergistic association between methanotrophs and perchlorate reducers.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Multidisciplinary Sciences
Wafa Ali Eltayb, Mohnad Abdalla, Amr Ahmed EL-Arabey, Ahmed Boufissiou, Mohammad Azam, Saud I. Al-Resayes, Mahboob Alam
Summary: Researchers used bioinformatics tools and molecular docking studies to analyze the structure of pMMO and its interactions with quinone, duroquinone, and P450 enzymes. They discovered that pMMO can produce methanol without Cu in the presence of quinone and duroquinone, and that pmoB1 interacts with P450. This study highlights the importance of studying the membrane of pMMO for understanding its functions.
JOURNAL OF KING SAUD UNIVERSITY SCIENCE
(2023)
Article
Ecology
Marie E. Kroeger, Laura K. Meredith, Kyle M. Meyer, Kevin D. Webster, Plinio Barbosa de Camargo, Leandro Fonseca de Souza, Siu Mui Tsai, Joost van Haren, Scott Saleska, Brendan J. M. Bohannan, Jorge L. Mazza Rodrigues, Erika Berenguer, Jos Barlow, Klaus Nusslein
Summary: The study revealed a significant increase in the abundance and activity of active methanogens in pasture soils, potentially driving increased soil methane emissions. Additionally, secondary rainforests showed decreased methanogenic activity similar to primary rainforests, with the potential to recover as methane sinks.
Article
Biochemistry & Molecular Biology
Sunney Chan, Wei-Hau Chang, Shih-Hsin Huang, Hsin-Hung Lin, Steve S-F Yu
Summary: This focused review describes the 2.5 angstrom cyro-EM structure of particulate methane monooxygenase (pMMO), revealing the locations of copper cofactors and active sites, providing insights into the catalytic machinery capable of methane oxidation with high selectivity and efficiency.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2021)
Article
Biochemical Research Methods
Christopher W. Koo, Jasmine M. Hershewe, Michael C. Jewett, Amy C. Rosenzweig
Summary: The study developed a cell-free protein synthesis system based on Escherichia coli lysate, which can be used to express particulate methane monooxygenase (pMMO) in vitro in the presence of nanodiscs. The findings demonstrate that the pMMO complex can form without the need for exogenous translocon machinery or chaperones.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Chemistry, Physical
Zhenzhuo Lan, Jacob Toney, Shaama Mallikarjun Sharada
Summary: This study computationally investigates the mechanism and active site identification of methane hydroxylation by monocopper complexes. The results suggest that the oxyl species is the likely active site, and spin crossing may provide a lower energy pathway for hydroxylation.
CATALYSIS SCIENCE & TECHNOLOGY
(2023)
Article
Biochemical Research Methods
Bashir L. Rumah, Benedict H. Claxton Stevens, Jake E. Yeboah, Christopher E. Stead, Emily L. Harding, Nigel P. Minton, Ying Zhang
Summary: In this study, a CRISPR/Cas9 genome editing system was constructed and successfully utilized to delete and insert genes in two types of methanotrophic bacteria, Methylococcus capsulatus Bath and Methylocystis parvus OBBP. The combination of homology-directed repair achieved high frequencies of gene deletions and insertions. Various parameters were also investigated to optimize the CRISPR/Cas9 system in Methylocystis parvus OBBP. This work demonstrated the first efficient CRISPR/Cas9 system generating scarless clean gene deletions and insertions in methanotroph genomes.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Ecology
Christina S. Kang-Yun, Xujun Liang, Philip Dershwitz, Wenyu Gu, Aloys Schepers, Andrew Flatley, Josef Lichtmannegger, Hans Zischka, Lijie Zhang, Xia Lu, Baohua Gu, Joshua C. Ledesma, Daly J. Pelger, Alan A. DiSpirito, Jeremy D. Semrau
Summary: Aerobic methanotrophy is strongly regulated by copper, with different methanotrophs utilizing various mechanisms for copper uptake, including secreting methanobactin or utilizing proteins like MopE. Certain methanotrophs are able to steal methanobactin from others, enhancing their ability to degrade methylmercury. Understanding these strategies may help manipulate methanotrophic communities to reduce methane emissions and enhance mercury detoxification.
Article
Chemistry, Inorganic & Nuclear
Han Sol Jeong, Sugyeong Hong, Hee Seon Yoo, Jin Kim, Yujeong Kim, Chungwoon Yoon, Seung Jae Lee, Sun Hee Kim
Summary: Methane monooxygenase plays a crucial role in the global carbon cycle by converting methane to methanol, reducing greenhouse effects. This study investigated the electronic structures of two cofactors in MMOR and unveiled their catalytic mechanisms in methane hydroxylation through EPR spectroscopy analysis.
INORGANIC CHEMISTRY FRONTIERS
(2021)
Article
Chemistry, Applied
Zhanfeng Wang, Wenhan Fang, Wei Peng, Peng Wu, Binju Wang
Summary: Activation of dioxygen allows metalloenzymes to mediate various oxidative transformations crucial for biosynthesis and metabolism processes. Recent computational insights into oxygen activation by copper-dependent enzymes are essential for understanding their structure-function relationships and engineering these metalloenzymes for novel functions.
TOPICS IN CATALYSIS
(2022)
Article
Biochemistry & Molecular Biology
Yun Ji Park, Gerri M. Roberts, Rana Montaser, Grace E. Kenney, Paul M. Thomas, Neil L. Kelleher, Amy C. Rosenzweig
Summary: Methanobactins are ribosomally produced peptidic natural products that bind copper with high affinity, originating from methanotrophic bacteria to acquire copper needed for enzymatic methane oxidation. They have unique structures and provide support for the proposed role of unknown biosynthetic enzymes.
Article
Multidisciplinary Sciences
Anastasia C. Manesis, Richard J. Jodts, Brian M. Hoffman, Amy C. Rosenzweig
Summary: Some methane-oxidizing bacteria use the natural product methanobactin (Mbn) to acquire copper for their metabolic enzyme, particulate methane monooxygenase. The protein pair MbnH and MbnP are involved in copper homeostasis, but their structure and function remain unclear. The MbnP protein binds a single copper ion with high affinity, dependent on oxidation of a conserved tryptophan to kynurenine through interaction with MbnH.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Roman Davydov, Austin E. Herzog, Richard J. Jodts, Kenneth D. Karlin, Brian M. Hoffman
Summary: In this study, the physical and chemical properties of monocopper Cu(I) superoxo and Cu(II) peroxo and hydroperoxo complexes were investigated. The complexes were prepared using cryoreduction/annealing technique and characterized using EPR and ENDOR spectroscopy.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Maike N. Lundahl, Raymond Sarksian, Hao Yang, Richard J. Jodts, Adrien Pagnier, Donald F. Smith, Martin A. Mosquera, Wilfred A. van der Donk, Brian M. Hoffman, William E. Broderick, Joan B. Broderick
Summary: Using freeze-quench techniques and electron paramagnetic resonance (EPR) spectroscopy, the reaction pathway of an adenosylation reaction catalyzed by the radical SAM enzyme is studied. The results provide snapshots of the process, revealing the formation of organic intermediate Omega and the generation of 5'-deoxyadenosyl radical and adenosylated peptide radical. These findings help to understand the mechanism of the reaction.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Yun Ji Park, Richard J. Jodts, Jeffrey W. Slater, Reyvin M. Reyes, Valerie J. Winton, Rana A. Montaser, Paul M. Thomas, William B. Dowdle, Anahi Ruiz, Neil L. Kelleher, J. Martin Bollinger, Carsten Krebs, Brian M. Hoffman, Amy C. Rosenzweig
Summary: The iron-containing heterodimeric MbnBC enzyme complex plays a central role in the biosynthesis of methanobactins (Mbns) and its active species is a mixed-valent, antiferromagnetically coupled Fe(II)Fe(III) center. MbnC is also involved in recognition of the MbnA leader peptide.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Christopher W. Koo, Frank J. Tucci, Yuan He, Amy C. Rosenzweig
Summary: Bacterial methane oxidation using pMMO can be restored by reconstitution in nanodiscs, and the structures of pMMO in a lipid environment have been determined by cryo-electron microscopy. These findings provide important insights for understanding and engineering the function of pMMO.
Article
Biochemistry & Molecular Biology
Luis F. Schachner, Benjamin Des Soye, Soo Ro, Grace E. Kenney, Ashley N. Ives, Taojunfeng Su, Young Ah Goo, Michael C. Jewett, Amy C. Rosenzweig, Neil L. Kelleher
Summary: The phosphorylation of triosephosphate isomerase (TPI) enhances its activity and facilitates substrate binding to the active site. Hetero-dimerization and subunit asymmetry are key features of TPI, and tetramerization plays a crucial role in enzymatic regulation. This study highlights the importance of studying endogenous proteoforms for understanding the functional role of post-translational modifications (PTMs).
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Madeline B. Ho, Richard J. Jodts, Youngsuk Kim, Alex McSkimming, Daniel L. M. Suess, Brian M. Hoffman
Summary: Members of the radical SAM enzyme superfamily initiate diverse radical transformations through reductive cleavage of SAM, generating different organometallic intermediates. The crystal structure analysis provides insights into the spectroscopic properties of synthetic analogues.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemical Research Methods
Christopher W. Koo, Jasmine M. Hershewe, Michael C. Jewett, Amy C. Rosenzweig
Summary: The study developed a cell-free protein synthesis system based on Escherichia coli lysate, which can be used to express particulate methane monooxygenase (pMMO) in vitro in the presence of nanodiscs. The findings demonstrate that the pMMO complex can form without the need for exogenous translocon machinery or chaperones.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Anastasia C. Manesis, Jeffrey W. Slater, Kenny Cantave, J. Martin Bollinger Jr, Carsten Krebs, Amy C. Rosenzweig
Summary: MbnH is a recently discovered enzyme that converts tryptophan to kynurenine. It forms a bis-Fe(IV) intermediate upon reaction with H2O2 and can also detoxify H2O2 in the absence of substrate. This study expands our understanding of enzymes in the bCcP/MauG superfamily.
Article
Chemistry, Physical
Frank J. Tucci, Richard J. Jodts, Brian M. Hoffman, Amy C. Rosenzweig
Summary: This study used orthogonal techniques to identify the active site of particulate methane monooxygenase (pMMO), which catalyzes the oxidation of methane to methanol. It revealed that the CuD site and its surrounding hydrophobic pocket are likely to be the main site for methane oxidation.
Article
Chemistry, Multidisciplinary
George E. Cutsail, Matthew O. Ross, Amy C. Rosenzweig, Serena DeBeer
Summary: The study investigated the enzymatic conversion of methane to methanol by methane monooxygenases (MMOs) under mild conditions. The results revealed the presence of only monocopper sites in particulate MMO (pMMO), contradicting the previous proposed dicopper site. Additionally, photodamage was found to partially contribute to observed features in X-ray absorption spectrum, highlighting the complexity involved in EXAFS measurement and modeling of dilute metalloproteins with multiple metal centers.
Review
Chemistry, Multidisciplinary
Christopher W. Koo, Amy C. Rosenzweig
Summary: Methanotrophic bacteria are a potential route to utilize and reduce methane emissions. They use MMOs to oxidize methane to methanol, with two types of MMOs having different metal cofactors and mechanisms.
CHEMICAL SOCIETY REVIEWS
(2021)