1
|
Ishizuka T, Kojima T. Oxidative and Reductive Manipulation of C1 Resources by Bio-Inspired Molecular Catalysts to Produce Value-Added Chemicals. Acc Chem Res 2024; 57:2437-2447. [PMID: 39116211 DOI: 10.1021/acs.accounts.4c00390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
ConspectusTo tackle the energy and environmental concerns the world faces, much attention is given to catalytic reactions converting methane (CH4) and carbon dioxide (CO2) as abundant C1 resources into value-added chemicals with high efficiency and selectivity. In the oxidative conversion of CH4 to methanol, it is necessary to solve the requirement of strong oxidants due to the large bond-dissociation energy (BDE) of the C-H bonds in methane and achieve suppression of overoxidation due to the smaller BDE of the C-H bond in methanol as the product. On the other hand, to efficiently perform CO2 reduction, proton-coupled electron transfer (PCET) processes are required since the reduction potential of CO2 becomes positive by using proton-coupled processes; however, under the acidic conditions required for PCET, hydrogen evolution by the reduction of protons becomes competitive with CO2 reduction. Thus, it is indispensable to develop efficient catalysts for selective CO2 reduction. Recently, we have developed efficient catalytic reactions toward the alleviation of the concerns mentioned above. Concerning CH4 oxidation, inspired by metalloenzymes that oxidize hydrophobic organic substrates, a hydrophobic second coordination sphere (SCS) was introduced to an FeII complex bearing a pentadentate N-heterocyclic carbene ligand, and the FeII complex was used as a catalyst for CH4 oxidation in aqueous media. Consequently, CH4 was efficiently and selectively oxidized to methanol with 83% selectivity and a turnover number of 500. In contrast, when methanol was used as a substrate for catalytic oxidation by the FeII complex, oxidation products were obtained in a negligible yield, which was comparable to that of the control experiment without the catalyst. Therefore, the hydrophobic SCS of the FeII complex can capture only hydrophobic substrates such as CH4 and release hydrophilic products such as methanol to the aqueous medium for suppressing overoxidation ("catch-and-release" mechanism). On the other hand, for photocatalytic CO2 reduction, we have developed NiII complexes with N2S2-chelating ligands as catalysts, which have been inspired by carbon monoxide dehydrogenase, and have also introduced a binding site of Lewis-acidic metal ions to the SCS of the Ni complex. When Mg2+ was applied as a moderate Lewis acid, a Mg2+-bound Ni catalyst allowed us to achieve remarkable enhancement of the photocatalytic CO2 reduction to afford CO as the product with over 99% selectivity and a quantum yield of 11.4%. Divalent metal ions besides Mg2+ also showed similar positive impacts on photocatalytic CO2 reduction, whereas monovalent metal ions exhibited almost no effects and trivalent metal ions exclusively promoted hydrogen evolution. In this Account, we highlight our recent progress in the catalytic manipulations of CH4 and CO2 as C1 resources.
Collapse
Affiliation(s)
- Tomoya Ishizuka
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Takahiko Kojima
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| |
Collapse
|
2
|
De Tovar J, Leblay R, Wang Y, Wojcik L, Thibon-Pourret A, Réglier M, Simaan AJ, Le Poul N, Belle C. Copper-oxygen adducts: new trends in characterization and properties towards C-H activation. Chem Sci 2024; 15:10308-10349. [PMID: 38994420 PMCID: PMC11234856 DOI: 10.1039/d4sc01762e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/11/2024] [Indexed: 07/13/2024] Open
Abstract
This review summarizes the latest discoveries in the field of C-H activation by copper monoxygenases and more particularly by their bioinspired systems. This work first describes the recent background on copper-containing enzymes along with additional interpretations about the nature of the active copper-oxygen intermediates. It then focuses on relevant examples of bioinorganic synthetic copper-oxygen intermediates according to their nuclearity (mono to polynuclear). This includes a detailed description of the spectroscopic features of these adducts as well as their reactivity towards the oxidation of recalcitrant Csp3 -H bonds. The last part is devoted to the significant expansion of heterogeneous catalytic systems based on copper-oxygen cores (i.e. within zeolite frameworks).
Collapse
Affiliation(s)
- Jonathan De Tovar
- Université Grenoble-Alpes, CNRS, Département de Chimie Moléculaire Grenoble France
| | - Rébecca Leblay
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Institut des Sciences Moléculaires de Marseille Marseille France
| | - Yongxing Wang
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Institut des Sciences Moléculaires de Marseille Marseille France
| | - Laurianne Wojcik
- Université de Brest, Laboratoire de Chimie, Electrochimie Moléculaires et Chimie Analytique Brest France
| | | | - Marius Réglier
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Institut des Sciences Moléculaires de Marseille Marseille France
| | - A Jalila Simaan
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Institut des Sciences Moléculaires de Marseille Marseille France
| | - Nicolas Le Poul
- Université de Brest, Laboratoire de Chimie, Electrochimie Moléculaires et Chimie Analytique Brest France
| | - Catherine Belle
- Université Grenoble-Alpes, CNRS, Département de Chimie Moléculaire Grenoble France
| |
Collapse
|
3
|
He Z, Shen J, Zhu Y, Gao J, Zhang D, Pan X. Active anaerobic methane oxidation in the groundwater table fluctuation zone of rice paddies. WATER RESEARCH 2024; 258:121802. [PMID: 38796914 DOI: 10.1016/j.watres.2024.121802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/30/2024] [Accepted: 05/18/2024] [Indexed: 05/29/2024]
Abstract
Rice paddies are globally important sources of methane emissions and also active regions for methane consumption. However, the impact of fluctuating groundwater levels on methane cycling has received limited attention. In this study, we delved into the activity and microbial mechanisms underlying anaerobic oxidation of methane (AOM) in paddy fields. A comprehensive approach was employed, including 13C stable isotope assays, inhibition experiments, real-time quantitative reverse transcription PCR, metagenomic sequencing, and binning technology. Geochemical profiles revealed the abundant coexistence of both methane and electron acceptors in the groundwater table fluctuation (GTF) zone, at a depth of 40-60 cm. Notably, the GTF zone exhibited the highest rate of AOM, potentially linked to the reduction of iron oxides and nitrate. Within this zone, Candidatus Methanoperedens (belonging to the ANME-2d group) dominated the Archaea population, accounting for a remarkable 85.4 %. Furthermore, our results from inhibition experiments, RT-qPCR, and metagenome-assembled genome (MAG) analysis highlighted the active role of Ca. Methanoperedens GTF50 in the GTF zone. This microorganism could independently mediate AOM process through the intriguing "reverse methanogenesis" pathway. Considering the similarity in geochemical conditions across different paddy fields, it is likely that Ca. Methanoperedens-mediated AOM is prevalent in the GTF zones.
Collapse
Affiliation(s)
- Zhanfei He
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jiaquan Shen
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yinghong Zhu
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jingxun Gao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
| |
Collapse
|
4
|
Guo Z, Ma XS, Ni SQ. Journey of the swift nitrogen transformation: Unveiling comammox from discovery to deep understanding. CHEMOSPHERE 2024; 358:142093. [PMID: 38679176 DOI: 10.1016/j.chemosphere.2024.142093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/02/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024]
Abstract
COMplete AMMonia OXidizer (comammox) refers to microorganisms that have the function of oxidizing NH4+ to NO3- alone. The discovery of comammox overturned the two-step theory of nitrification in the past century and triggered many important scientific questions about the nitrogen cycle in nature. This comprehensive review delves into the origin and discovery of comammox, providing a detailed account of its detection primers, clades metabolic variations, and environmental factors. An in-depth analysis of the ecological niche differentiation among ammonia oxidizers was also discussed. The intricate role of comammox in anammox systems and the relationship between comammox and nitrogen compound emissions are also discussed. Finally, the relationship between comammox and anammox is displayed, and the future research direction of comammox is prospected. This review reveals the metabolic characteristics and distribution patterns of comammox in ecosystems, providing new perspectives for understanding nitrogen cycling and microbial ecology. Additionally, it offers insights into the potential application value and prospects of comammox.
Collapse
Affiliation(s)
- Zheng Guo
- School of Environmental Science and Engineering, Shandong University, Shandong, 266237, China
| | - Xue Song Ma
- School of Environmental Science and Engineering, Shandong University, Shandong, 266237, China
| | - Shou-Qing Ni
- School of Environmental Science and Engineering, Shandong University, Shandong, 266237, China.
| |
Collapse
|
5
|
He L, Lidstrom ME. Utilisation of low methane concentrations by methanotrophs. Adv Microb Physiol 2024; 85:57-96. [PMID: 39059823 DOI: 10.1016/bs.ampbs.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
The growing urgency regarding climate change points to methane as a key greenhouse gas for slowing global warming to allow other mitigation measures to take effect. One approach to both decreasing methane emissions and removing methane from air is aerobic methanotrophic bacteria, those bacteria that grow on methane as sole carbon and energy source and require O2. A subset of these methanotrophs is able to grow on methane levels of 1000 parts per million (ppm) and below, and these present an opportunity for developing both environmental- and bioreactor-based methane treatment systems. However, relatively little is known about the traits of such methanotrophs that allow them to grow on low methane concentrations. This review assesses current information regarding how methanotrophs grow on low methane concentrations in the context of developing treatment strategies that could be applied for both decreasing methane emissions and removing methane from air.
Collapse
Affiliation(s)
- Lian He
- Department of Chemical Engineering, University of Washington, Seattle, WA United States
| | - Mary E Lidstrom
- Department of Chemical Engineering, University of Washington, Seattle, WA United States; Department of Microbiology, University of Washington, Seattle, WA United States.
| |
Collapse
|
6
|
Yu Y, Shi Y, Kwon YW, Choi Y, Kim Y, Na JG, Huh J, Lee J. A rationally designed miniature of soluble methane monooxygenase enables rapid and high-yield methanol production in Escherichia coli. Nat Commun 2024; 15:4399. [PMID: 38782897 PMCID: PMC11116448 DOI: 10.1038/s41467-024-48671-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Soluble methane monooxygenase (sMMO) oxidizes a wide range of carbon feedstocks (C1 to C8) directly using intracellular NADH and is a useful means in developing green routes for industrial manufacturing of chemicals. However, the high-throughput biosynthesis of active recombinant sMMO and the ensuing catalytic oxidation have so far been unsuccessful due to the structural and functional complexity of sMMO, comprised of three functionally complementary components, which remains a major challenge for its industrial applications. Here we develop a catalytically active miniature of sMMO (mini-sMMO), with a turnover frequency of 0.32 s-1, through an optimal reassembly of minimal and modified components of sMMO on catalytically inert and stable apoferritin scaffold. We characterise the molecular characteristics in detail through in silico and experimental analyses and verifications. Notably, in-situ methanol production in a high-cell-density culture of mini-sMMO-expressing recombinant Escherichia coli resulted in higher yield and productivity (~ 3.0 g/L and 0.11 g/L/h, respectively) compared to traditional methanotrophic production.
Collapse
Affiliation(s)
- Yeonhwa Yu
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Seongbuk-Gu, Seoul, 02841, Republic of Korea
| | - Yongfan Shi
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Young Wan Kwon
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Anam-Dong 5-1, Seongbuk-Gu, Seoul, 02841, Republic of Korea
| | - Yoobin Choi
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Seongbuk-Gu, Seoul, 02841, Republic of Korea
| | - Yusik Kim
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Seongbuk-Gu, Seoul, 02841, Republic of Korea
| | - Jeong-Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - June Huh
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Seongbuk-Gu, Seoul, 02841, Republic of Korea.
| | - Jeewon Lee
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Seongbuk-Gu, Seoul, 02841, Republic of Korea.
| |
Collapse
|
7
|
Sun L, Wang Y, Gu X, Zhao M, Yuan L. One-Pot Cu/SAPO-34 for Continuous Methane Selective Oxidation to Methanol. Molecules 2024; 29:2273. [PMID: 38792136 PMCID: PMC11124382 DOI: 10.3390/molecules29102273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Cu/SAPO-34 synthesized via a one-pot method with relatively low silicon content and copper loading at around 2 wt.% facilitated continuous oxidation of methane to methanol with a methanol space time yield of 504 μmolCH3OH/gcat/h. Remarkably, the methanol yield exceeded 1800 mmolCH3OH/molCu/h at 623 K. Typically, the presence of trace oxygen in the system was the key to maintaining the high selectivity to methanol. Characterization results from a series of techniques, including XRD, SEM, TEM, H2-TPR, NH3-TPD, UV-vis, and FTIR, indicated that Cu2+ existed in the position where it moves from hexagonal rings to elliptical cages as the active center.
Collapse
Affiliation(s)
- Lanlan Sun
- Department of Application Chemistry, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China; (X.G.); (M.Z.); (L.Y.)
| | - Yu Wang
- School of Materials Science and Engineering and National Institute for Advanced Materials, Nankai University, Tianjin 300350, China;
| | - Xuesong Gu
- Department of Application Chemistry, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China; (X.G.); (M.Z.); (L.Y.)
| | - Meng Zhao
- Department of Application Chemistry, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China; (X.G.); (M.Z.); (L.Y.)
| | - Lijuan Yuan
- Department of Application Chemistry, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China; (X.G.); (M.Z.); (L.Y.)
| |
Collapse
|
8
|
Decembrino D, Cannella D. The thin line between monooxygenases and peroxygenases. P450s, UPOs, MMOs, and LPMOs: A brick to bridge fields of expertise. Biotechnol Adv 2024; 72:108321. [PMID: 38336187 DOI: 10.1016/j.biotechadv.2024.108321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Many scientific fields, although driven by similar purposes and dealing with similar technologies, often appear so isolated and far from each other that even the vocabularies to describe the very same phenomenon might differ. Concerning the vast field of biocatalysis, a special role is played by those redox enzymes that employ oxygen-based chemistry to unlock transformations otherwise possible only with metal-based catalysts. As such, greener chemical synthesis methods and environmentally-driven biotechnological approaches were enabled over the last decades by the use of several enzymes and ultimately resulted in the first industrial applications. Among what can be called today the environmental biorefinery sector, biomass transformation, greenhouse gas reduction, bio-gas/fuels production, bioremediation, as well as bulk or fine chemicals and even pharmaceuticals manufacturing are all examples of fields in which successful prototypes have been demonstrated employing redox enzymes. In this review we decided to focus on the most prominent enzymes (MMOs, LPMO, P450 and UPO) capable of overcoming the ∼100 kcal mol-1 barrier of inactivated CH bonds for the oxyfunctionalization of organic compounds. Harnessing the enormous potential that lies within these enzymes is of extreme value to develop sustainable industrial schemes and it is still deeply coveted by many within the aforementioned fields of application. Hence, the ambitious scope of this account is to bridge the current cutting-edge knowledge gathered upon each enzyme. By creating a broad comparison, scientists belonging to the different fields may find inspiration and might overcome obstacles already solved by the others. This work is organised in three major parts: a first section will be serving as an introduction to each one of the enzymes regarding their structural and activity diversity, whereas a second one will be encompassing the mechanistic aspects of their catalysis. In this regard, the machineries that lead to analogous catalytic outcomes are depicted, highlighting the major differences and similarities. Finally, a third section will be focusing on the elements that allow the oxyfunctionalization chemistry to occur by delivering redox equivalents to the enzyme by the action of diverse redox partners. Redox partners are often overlooked in comparison to the catalytic counterparts, yet they represent fundamental elements to better understand and further develop practical applications based on mono- and peroxygenases.
Collapse
Affiliation(s)
- Davide Decembrino
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
| | - David Cannella
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
| |
Collapse
|
9
|
Guo X, Ong WM, Zhao HP, Lai CY. Enzyme-induced reactive oxygen species trigger oxidative degradation of sulfamethoxazole within a methanotrophic biofilm. WATER RESEARCH 2024; 253:121330. [PMID: 38387268 DOI: 10.1016/j.watres.2024.121330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/24/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024]
Abstract
Although microorganisms carrying copper-containing membrane-bound monooxygenase (CuMMOs), such as particulate methane monooxygenase (pMMO) and ammonia monooxygenase (AMO), have been extensively documented for their capability to degrade organic micropollutants (OMPs), the underlying reactive mechanism remains elusive. In this study, we for the first time demonstrate biogenic reactive oxygen species (ROS) play important roles in the degradation of sulfamethoxazole (SMX), a representative OMP, within a methane-fed biofilm. Highly-efficient and consistent SMX biodegradation was achieved in a CH4-based membrane biofilm reactor (MBfR), manifesting a remarkable SMX removal rate of 1210.6 ± 39.0 μg·L-1·d-1. Enzyme inhibition and ROS clearance experiments confirmed the significant contribution of ROS, which were generated through the catalytic reaction of pMMO and AMO enzymes, in facilitating SMX degradation. Through a combination of density functional theory (DFT) calculations, electron paramagnetic resonance (EPR) analysis, and transformation product detection, we elucidated that the ROS primarily targeted the aniline group in the SMX molecule, inducing the formation of aromatic radicals and its progressive mineralization. In contrast, the isoxazole-ring was not susceptible to electrophilic ROS attacks, leading to accumulation of 3-amino-5-methylisoxazole (3A5MI). Furthermore, microbiological analysis suggested Methylosarcina (a methanotroph) and Candidatus Nitrosotenuis (an ammonia-oxidizing archaea) collaborated as the SMX degraders, who carried highly conserved and expressed CuMMOs (pMMO and AMO) for ROS generation, thereby triggering the oxidative degradation of SMX. This study deciphers SMX biodegradation through a fresh perspective of free radical chemistry, and concurrently providing a theoretical framework for the advancement of environmental biotechnologies aimed at OMP removal.
Collapse
Affiliation(s)
- Xu Guo
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058
| | - Weng Mun Ong
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058
| | - Chun-Yu Lai
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058.
| |
Collapse
|
10
|
Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
Collapse
Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
11
|
Kang NK, Chau THT, Lee EY. Engineered methane biocatalysis: strategies to assimilate methane for chemical production. Curr Opin Biotechnol 2024; 85:103031. [PMID: 38101295 DOI: 10.1016/j.copbio.2023.103031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
Methane (CH4), one of the greenhouse gases, is considered a promising feedstock for the biological production of fuels and chemicals. Although recent studies have demonstrated the capability of methanotrophs to convert CH4 into various bioproducts by metabolic engineering, the productivity has not reached commercial levels. As such, there is a growing interest in synthetic methanotrophic systems as an alternative. This review summarizes the strategies for enhancing native CH4 assimilation and discusses the challenges for the construction of synthetic methanotrophy into nonmethanotrophic industrial strains. Additionally, we suggest a mixed heterotrophic approach that integrates CH4 assimilation with glucose and xylose metabolism to improve productivity. The synthetic methanotrophic system presented in this review could pave the way for sustainable and efficient biomanufacturing using CH4.
Collapse
Affiliation(s)
- Nam Kyu Kang
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 17104 Yongin-si, Gyeonggi-do, South Korea
| | - Tin Hoang Trung Chau
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 17104 Yongin-si, Gyeonggi-do, South Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 17104 Yongin-si, Gyeonggi-do, South Korea.
| |
Collapse
|
12
|
Peng P, Yang J, DiSpirito AA, Semrau JD. MmoD regulates soluble methane monooxygenase and methanobactin production in Methylosinus trichosporium OB3b. Appl Environ Microbiol 2023; 89:e0160123. [PMID: 38014956 PMCID: PMC10734442 DOI: 10.1128/aem.01601-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/10/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Aerobic methanotrophs play a critical role in the global carbon cycle, particularly in controlling net emissions of methane to the atmosphere. As methane is a much more potent greenhouse gas than carbon dioxide, there is increasing interest in utilizing these microbes to mitigate future climate change by increasing their ability to consume methane. Any such efforts, however, require a detailed understanding of how to manipulate methanotrophic activity. Herein, we show that methanotrophic activity is strongly controlled by MmoD, i.e., MmoD regulates methanotrophy through the post-transcriptional regulation of the soluble methane monooxygenase and controls the ability of methanotrophs to collect copper. Such data are likely to prove quite useful in future strategies to enhance the use of methanotrophs to not only reduce methane emissions but also remove methane from the atmosphere.
Collapse
Affiliation(s)
- Peng Peng
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Junwon Yang
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Alan A. DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Jeremy D. Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
13
|
Tucci FJ, Jodts RJ, Hoffman BM, Rosenzweig AC. Product analog binding identifies the copper active site of particulate methane monooxygenase. Nat Catal 2023; 6:1194-1204. [PMID: 38187819 PMCID: PMC10766429 DOI: 10.1038/s41929-023-01051-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/22/2023] [Indexed: 01/09/2024]
Abstract
Nature's primary methane-oxidizing enzyme, the membrane-bound particulate methane monooxygenase (pMMO), catalyzes the oxidation of methane to methanol. pMMO activity requires copper, and decades of structural and spectroscopic studies have sought to identify the active site among three candidates: the CuB, CuC, and CuD sites. Challenges associated with the isolation of active pMMO have hindered progress toward locating its catalytic center. However, reconstituting pMMO into native lipid nanodiscs stabilizes its structure and recovers its activity. Here, these active samples were incubated with 2,2,2,-trifluoroethanol (TFE), a product analog that serves as a readily visualized active-site probe. Interactions of TFE with the CuD site were observed by both pulsed ENDOR spectroscopy and cryoEM, implicating CuD and the surrounding hydrophobic pocket as the likely site of methane oxidation. Use of these orthogonal techniques on parallel samples is a powerful approach that can circumvent difficulties in interpreting metalloenzyme cryoEM maps.
Collapse
Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
- These authors contributed equally
| | - Richard J Jodts
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
- These authors contributed equally
| | - Brian M Hoffman
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
| |
Collapse
|
14
|
Bai X, Huang D, Chen Y, Shao M, Wang N, Wang Q, Xu Q. Enhanced methane oxidation efficiency by digestate biochar in landfill cover soil: Microbial shifts and carbon metabolites insights. CHEMOSPHERE 2023; 343:140279. [PMID: 37758092 DOI: 10.1016/j.chemosphere.2023.140279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/07/2023] [Accepted: 09/24/2023] [Indexed: 09/30/2023]
Abstract
The ability of biochar to enhance the oxidation of methane (CH4) in landfill cover soil by promoting the growth and activity of methane-oxidizing bacteria (MOB) has attracted significant attention. However, the optimal characteristics of digestate-derived biochar (DBC) for promoting the MOB community and CH4 removal performance remain unclear. This study examined how the CH4 oxidation capacity and respiratory metabolism of MOB life process are affected by the application of DBC compared with the most commonly used woody-derived biochar (WBC). The addition of both WBC and DBC enhanced CH4 oxidation, with DBC exhibiting a nearly twofold increase in cumulative CH4 oxidation mass (7.14 mg CH4 g-1) compared to WBC. The high ion-exchange capacity of DBC was found to be more favorable for the growth of Type I MOB, which have more efficient metabolic pathways for CH4 oxidation. Type I MOB which are abundant in DBC may prefer monovalent positive ions, while the charge-rich nature of DBC may also have hindered extracellular protein aggregation. The superiority of DBC in terms of CH4 oxidation thus highlights the underlying mechanisms of biochar-MOB interactions, offering potential biochar options for landfill cover soil.
Collapse
Affiliation(s)
- Xinyue Bai
- Shenzhen Engineering Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Xili, Nanshan District, Shenzhen, 518055, PR China.
| | - Dandan Huang
- School of Ecology, Sun Yat-sen University, Shenzhen, 518107, PR China
| | - Yuke Chen
- Shenzhen Engineering Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Xili, Nanshan District, Shenzhen, 518055, PR China
| | - Mingshuai Shao
- Shenzhen Engineering Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Xili, Nanshan District, Shenzhen, 518055, PR China
| | - Ning Wang
- Shenzhen Engineering Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Xili, Nanshan District, Shenzhen, 518055, PR China
| | - Qian Wang
- Shenzhen Engineering Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Xili, Nanshan District, Shenzhen, 518055, PR China
| | - Qiyong Xu
- Shenzhen Engineering Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Xili, Nanshan District, Shenzhen, 518055, PR China.
| |
Collapse
|
15
|
Peng W, Wang Z, Zhang Q, Yan S, Wang B. Unraveling the Valence State and Reactivity of Copper Centers in Membrane-Bound Particulate Methane Monooxygenase. J Am Chem Soc 2023; 145:25304-25317. [PMID: 37955571 DOI: 10.1021/jacs.3c08834] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Particulate methane monooxygenase (pMMO) plays a critical role in catalyzing the conversion of methane to methanol, constituting the initial step in the C1 metabolic pathway within methanotrophic bacteria. However, the membrane-bound pMMO's structure and catalytic mechanism, notably the copper's valence state and genuine active site for methane oxidation, have remained elusive. Based on the recently characterized structure of membrane-bound pMMO, extensive computational studies were conducted to address these long-standing issues. A comprehensive analysis comparing the quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulated structures with cryo-EM data indicates that both the CuC and CuD sites tend to stay in the Cu(I) valence state within the membrane environment. Additionally, the concurrent presence of Cu(I) at both CuC and CuD sites leads to the significant reduction of the ligand-binding cavity situated between them, making it less likely to accommodate a reductant molecule such as durohydroquinone (DQH2). Subsequent QM/MM calculations reveal that the CuD(I) site is more reactive than the CuC(I) site in oxygen activation, en route to H2O2 formation and the generation of Cu(II)-O•- species. Finally, our simulations demonstrate that the natural reductant ubiquinol (CoQH2) assumes a productive binding conformation at the CuD(I) site but not at the CuC(I) site. This provides evidence that the true active site of membrane-bound pMMOs may be CuD rather than CuC. These findings clarify pMMO's catalytic mechanism and emphasize the membrane environment's pivotal role in modulating the coordination structure and the activity of copper centers within pMMO.
Collapse
Affiliation(s)
- Wei Peng
- 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 and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
- Key Laboratory of Aerosol Chemistry and Physics, State Key Laboratory of Loess and Quaternary Geology (SKLLQG), Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, P. R. China
| | - Zikuan Wang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Qiaoyu Zhang
- 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 and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Shengheng Yan
- 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 and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - 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 and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| |
Collapse
|
16
|
Wang L, Li A. Ammonia monooxygenase-mediated transformation of 17α-ethinylestradiol: Underlying molecular mechanism. ENVIRONMENTAL RESEARCH 2023; 237:116930. [PMID: 37604224 DOI: 10.1016/j.envres.2023.116930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/08/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
17α-ethinylestradiol (EE2) has received increasing attention as an emerging and difficult-to-remove emerging contaminant in recent years. Ammonia-oxidizing bacteria (AOB) have been reported to be effective in EE2 removal, and ammonia monooxygenase (AMO) is considered as the primary enzyme for EE2 removal. However, the molecular mechanism underlying the transformation of EE2 by AOB and AMO is still unclear. This study investigated the molecular mechanism of EE2 degradation using a combination of experimental and computational simulation methods. The results revealed that ammonia nitrogen was essential for the co-metabolism of EE2 by AOB, and that NH3 bound with CuC (one active site of AMO) to induce a conformational change in AMO, allowing EE2 to bind with the other active site (CuB), and then EE2 underwent biological transformation. These results provide a theoretical basis and a novel research perspective on the removal of ammonia nitrogen and emerging contaminants (e.g., EE2) in wastewater treatment.
Collapse
Affiliation(s)
- Lili Wang
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China; Laboratory of Environmental Protection in Water Transport Engineering, Tianjin Research Institute of Water Transport Engineering, Tanggu, Tianjin, 300456, China
| | - Anjie Li
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China.
| |
Collapse
|
17
|
Liu Y, Harnden KA, Van Stappen C, Dikanov SA, Lu Y. A designed Copper Histidine-brace enzyme for oxidative depolymerization of polysaccharides as a model of lytic polysaccharide monooxygenase. Proc Natl Acad Sci U S A 2023; 120:e2308286120. [PMID: 37844252 PMCID: PMC10614608 DOI: 10.1073/pnas.2308286120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/03/2023] [Indexed: 10/18/2023] Open
Abstract
The "Histidine-brace" (His-brace) copper-binding site, composed of Cu(His)2 with a backbone amine, is found in metalloproteins with diverse functions. A primary example is lytic polysaccharide monooxygenase (LPMO), a class of enzymes that catalyze the oxidative depolymerization of polysaccharides, providing not only an energy source for native microorganisms but also a route to more effective industrial biomass conversion. Despite its importance, how the Cu His-brace site performs this unique and challenging oxidative depolymerization reaction remains to be understood. To answer this question, we have designed a biosynthetic model of LPMO by incorporating the Cu His-brace motif into azurin, an electron transfer protein. Spectroscopic studies, including ultraviolet-visible (UV-Vis) absorption and electron paramagnetic resonance, confirm copper binding at the designed His-brace site. Moreover, the designed protein is catalytically active towards both cellulose and starch, the native substrates of LPMO, generating degraded oligosaccharides with multiturnovers by C1 oxidation. It also performs oxidative cleavage of the model substrate 4-nitrophenyl-D-glucopyranoside, achieving a turnover number ~9% of that of a native LPMO assayed under identical conditions. This work presents a rationally designed artificial metalloenzyme that acts as a structural and functional mimic of LPMO, which provides a promising system for understanding the role of the Cu His-brace site in LPMO activity and potential application in polysaccharide degradation.
Collapse
Affiliation(s)
- Yiwei Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Chemistry, University of Texas at Austin, Austin, TX78712
| | - Kevin A. Harnden
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, Austin, TX78712
| | - Sergei A. Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Chemistry, University of Texas at Austin, Austin, TX78712
| |
Collapse
|
18
|
Spatola Rossi T, Tolmie AF, Nichol T, Pain C, Harrison P, Smith TJ, Fricker M, Kriechbaumer V. Recombinant expression and subcellular targeting of the particulate methane monooxygenase (pMMO) protein components in plants. Sci Rep 2023; 13:15337. [PMID: 37714899 PMCID: PMC10504283 DOI: 10.1038/s41598-023-42224-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 09/07/2023] [Indexed: 09/17/2023] Open
Abstract
Methane is a potent greenhouse gas, which has contributed to approximately a fifth of global warming since pre-industrial times. The agricultural sector produces significant methane emissions, especially from livestock, waste management and rice cultivation. Rice fields alone generate around 9% of total anthropogenic emissions. Methane is produced in waterlogged paddy fields by methanogenic archaea, and transported to the atmosphere through the aerenchyma tissue of rice plants. Thus, bioengineering rice with catalysts to detoxify methane en route could contribute to an efficient emission mitigation strategy. Particulate methane monooxygenase (pMMO) is the predominant methane catalyst found in nature, and is an enzyme complex expressed by methanotrophic bacteria. Recombinant expression of pMMO has been challenging, potentially due to its membrane localization, multimeric structure, and polycistronic operon. Here we show the first steps towards the engineering of plants for methane detoxification with the three pMMO subunits expressed in the model systems tobacco and Arabidopsis. Membrane topology and protein-protein interactions were consistent with correct folding and assembly of the pMMO subunits on the plant ER. Moreover, a synthetic self-cleaving polypeptide resulted in simultaneous expression of all three subunits, although low expression levels precluded more detailed structural investigation. The work presents plant cells as a novel heterologous system for pMMO allowing for protein expression and modification.
Collapse
Affiliation(s)
- Tatiana Spatola Rossi
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - A Frances Tolmie
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Tim Nichol
- Molecular Microbiology Research Group, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, S1 1WB, UK
| | - Charlotte Pain
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Patrick Harrison
- Department of Biological and Marine Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Thomas J Smith
- Molecular Microbiology Research Group, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, S1 1WB, UK
| | - Mark Fricker
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
- Centre for Bioimaging, Oxford Brookes University, Oxford, UK.
| |
Collapse
|
19
|
Wright CL, Lehtovirta-Morley LE. Nitrification and beyond: metabolic versatility of ammonia oxidising archaea. THE ISME JOURNAL 2023; 17:1358-1368. [PMID: 37452095 PMCID: PMC10432482 DOI: 10.1038/s41396-023-01467-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/09/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.
Collapse
Affiliation(s)
- Chloe L Wright
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | | |
Collapse
|
20
|
Hall K, Joseph C, Ayuso-Fernández I, Tamhankar A, Rieder L, Skaali R, Golten O, Neese F, Røhr ÅK, Jannuzzi SAV, DeBeer S, Eijsink VGH, Sørlie M. A Conserved Second Sphere Residue Tunes Copper Site Reactivity in Lytic Polysaccharide Monooxygenases. J Am Chem Soc 2023; 145:18888-18903. [PMID: 37584157 PMCID: PMC10472438 DOI: 10.1021/jacs.3c05342] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Indexed: 08/17/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are powerful monocopper enzymes that can activate strong C-H bonds through a mechanism that remains largely unknown. Herein, we investigated the role of a conserved glutamine/glutamate in the second coordination sphere. Mutation of the Gln in NcAA9C to Glu, Asp, or Asn showed that the nature and distance of the headgroup to the copper fine-tune LPMO functionality and copper reactivity. The presence of Glu or Asp close to the copper lowered the reduction potential and decreased the ratio between the reduction and reoxidation rates by up to 500-fold. All mutants showed increased enzyme inactivation, likely due to changes in the confinement of radical intermediates, and displayed changes in a protective hole-hopping pathway. Electron paramagnetic resonance (EPR) and X-ray absorption spectroscopic (XAS) studies gave virtually identical results for all NcAA9C variants, showing that the mutations do not directly perturb the Cu(II) ligand field. DFT calculations indicated that the higher experimental reoxidation rate observed for the Glu mutant could be reconciled if this residue is protonated. Further, for the glutamic acid form, we identified a Cu(III)-hydroxide species formed in a single step on the H2O2 splitting path. This is in contrast to the Cu(II)-hydroxide and hydroxyl intermediates, which are predicted for the WT and the unprotonated glutamate variant. These results show that this second sphere residue is a crucial determinant of the catalytic functioning of the copper-binding histidine brace and provide insights that may help in understanding LPMOs and LPMO-inspired synthetic catalysts.
Collapse
Affiliation(s)
- Kelsi
R. Hall
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Chris Joseph
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Iván Ayuso-Fernández
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Ashish Tamhankar
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Lukas Rieder
- Institute
for Molecular Biotechnology, Graz University
of Technology, 8010, Graz, Austria
| | - Rannei Skaali
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Ole Golten
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Åsmund K. Røhr
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Sergio A. V. Jannuzzi
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Vincent G. H. Eijsink
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Morten Sørlie
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| |
Collapse
|
21
|
Powell M, Rao G, Britt RD, Rittle J. Enzymatic Hydroxylation of Aliphatic C-H Bonds by a Mn/Fe Cofactor. J Am Chem Soc 2023; 145:16526-16537. [PMID: 37471626 PMCID: PMC10401708 DOI: 10.1021/jacs.3c03419] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Indexed: 07/22/2023]
Abstract
The aerobic oxidation of carbon-hydrogen (C-H) bonds in biology is currently known to be accomplished by a limited set of cofactors that typically include heme, nonheme iron, and copper. While manganese cofactors perform difficult oxidation reactions, including water oxidation within Photosystem II, they are generally not known to be used for C-H bond activation, and those that do catalyze this important reaction display limited intrinsic reactivity. Here we report that the 2-aminoisobutyric acid hydroxylase from Rhodococcus wratislaviensis, AibH1H2, requires manganese to functionalize a strong, aliphatic C-H bond (BDE = 100 kcal/mol). Structural and spectroscopic studies of this enzyme reveal a redox-active, heterobimetallic manganese-iron active site at the locus of O2 activation and substrate coordination. This result expands the known reactivity of biological manganese-iron cofactors, which was previously restricted to single-electron transfer or stoichiometric protein oxidation. Furthermore, the AibH1H2 cofactor is supported by a protein fold distinct from typical bimetallic oxygenases, and bioinformatic analyses identify related proteins abundant in microorganisms. This suggests that many uncharacterized monooxygenases may similarly require manganese to perform oxidative biochemical tasks.
Collapse
Affiliation(s)
- Magan
M. Powell
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Guodong Rao
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - R. David Britt
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - Jonathan Rittle
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
| |
Collapse
|
22
|
Okada T, Tomoike F. Distance-based global analysis of consistent cis-bonds in protein backbones. Heliyon 2023; 9:e18598. [PMID: 37576297 PMCID: PMC10413078 DOI: 10.1016/j.heliyon.2023.e18598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/15/2023] Open
Abstract
Biological polypeptides are known to contain cis-linkage in their main chain as a minor but important feature. Such anomalous connection of amino acids has different structural and functional effects on proteins. Experimental evidence of cis-bonds in proteins is mainly obtained using X-ray crystallography and other methods in the field of structural biology. To date, extensive analyses have been carried out on the experimentally found cis-bonds using the Protein Data Bank (PDB) entry-wise or residue-wise; however, their consistency in each protein has not been examined on a global scale. Data accumulation and advances in computational methodology enable the use of new approaches from a proteomic point of view. Here, we sought to carry out protein-wise analysis and describe a simple procedure for the detection and confirmation of cis-bonds from a set of experimental PDB chains for a protein to discriminate this type of bond from isomerizable and/or misassigned bonds. The resulting set of consistent cis bonds (found at identical positions in multiple chains) provides unprecedented insights into the trend of "high cis content" proteins and the upper limit of consistent cis bonds per polypeptide length. Recognizing such limit would not only be important for a practical check of upcoming structures, but also for the design of novel protein folds beyond the evolutionally-acquired repertoire.
Collapse
Affiliation(s)
- Tetsuji Okada
- Department of Life Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
| | | |
Collapse
|
23
|
Lim H, Brueggemeyer MT, Transue WJ, Meier KK, Jones SM, Kroll T, Sokaras D, Kelemen B, Hedman B, Hodgson KO, Solomon EI. Kβ X-ray Emission Spectroscopy of Cu(I)-Lytic Polysaccharide Monooxygenase: Direct Observation of the Frontier Molecular Orbital for H 2O 2 Activation. J Am Chem Soc 2023; 145:16015-16025. [PMID: 37441786 PMCID: PMC10557184 DOI: 10.1021/jacs.3c04048] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) catalyze the degradation of recalcitrant carbohydrate polysaccharide substrates. These enzymes are characterized by a mononuclear Cu(I) active site with a three-coordinate T-shaped "His-brace" configuration including the N-terminal histidine and its amine group as ligands. This study explicitly investigates the electronic structure of the d10 Cu(I) active site in a LPMO using Kβ X-ray emission spectroscopy (XES). The lack of inversion symmetry in the His-brace site enables the 3d/p mixing required for intensity in the Kβ valence-to-core (VtC) XES spectrum of Cu(I)-LPMO. These Kβ XES data are correlated to density functional theory (DFT) calculations to define the bonding, and in particular, the frontier molecular orbital (FMO) of the Cu(I) site. These experimentally validated DFT calculations are used to evaluate the reaction coordinate for homolytic cleavage of the H2O2 O-O bond and understand the contribution of this FMO to the low barrier of this reaction and how the geometric and electronic structure of the Cu(I)-LPMO site is activated for rapid reactivity with H2O2.
Collapse
Affiliation(s)
- Hyeongtaek Lim
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | | | - Wesley J Transue
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Katlyn K Meier
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Stephen M Jones
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Bradley Kelemen
- IFF Health and Biosciences, Palo Alto, California 94304, United States
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| |
Collapse
|
24
|
Thi Quynh Le H, Yeol Lee E. Methanotrophs: Metabolic versatility from utilization of methane to multi-carbon sources and perspectives on current and future applications. BIORESOURCE TECHNOLOGY 2023:129296. [PMID: 37302766 DOI: 10.1016/j.biortech.2023.129296] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/29/2023] [Accepted: 06/07/2023] [Indexed: 06/13/2023]
Abstract
The development of biorefineries for a sustainable bioeconomy has been driven by the concept of utilizing environmentally friendly and cost-effective renewable energy sources. Methanotrophic bacteria with a unique capacity to utilize methane as a carbon and energy source can serve as outstanding biocatalysts to develop C1 bioconversion technology. By establishing the utilization of diverse multi-carbon sources, integrated biorefinery platforms can be created for the concept of the circular bioeconomy. An understanding of physiology and metabolism could help to overcome challenges for biomanufacturing. This review summaries fundamental gaps for methane oxidation and the capability to utilize multi-carbon sources in methanotrophic bacteria. Subsequently, breakthroughs and challenges in harnessing methanotrophs as robust microbial chassis for industrial biotechnology were compiled and overviewed. Finally, capabilities to exploit the inherent advantages of methanotrophs to synthesize various target products in higher titers are proposed.
Collapse
Affiliation(s)
- Hoa Thi Quynh Le
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, Republic of Korea.
| |
Collapse
|
25
|
Hodgskiss LH, Melcher M, Kerou M, Chen W, Ponce-Toledo RI, Savvides SN, Wienkoop S, Hartl M, Schleper C. Unexpected complexity of the ammonia monooxygenase in archaea. THE ISME JOURNAL 2023; 17:588-599. [PMID: 36721060 PMCID: PMC10030591 DOI: 10.1038/s41396-023-01367-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 02/02/2023]
Abstract
Ammonia oxidation, as the first step of nitrification, constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase, is lacking, in particular for the environmentally abundant ammonia-oxidizing archaea (AOA). Here the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Besides the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modeling and in-gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase but also reveals clear differences in extracellular domains of the enzyme. These data open avenues for further structure-function studies of this ecologically important nitrification complex.
Collapse
Affiliation(s)
- Logan H Hodgskiss
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Michael Melcher
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Melina Kerou
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Weiqiang Chen
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter (VBC), Vienna, Austria
| | - Rafael I Ponce-Toledo
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Stefanie Wienkoop
- Molecular Systems Biology Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Markus Hartl
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter (VBC), Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.
| |
Collapse
|
26
|
Powell MM, Rao G, Britt RD, Rittle J. Enzymatic Hydroxylation of Aliphatic C-H Bonds by a Mn/Fe Cofactor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.10.532131. [PMID: 36945426 PMCID: PMC10029006 DOI: 10.1101/2023.03.10.532131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Manganese cofactors activate strong chemical bonds in many essential enzymes. Yet very few manganese-dependent enzymes are known to functionalize ubiquitous carbon-hydrogen (C-H) bonds, and those that catalyze this important reaction display limited intrinsic reactivity. Herein, we report that the 2-aminoisobutyric acid hydroxylase from Rhodococcus wratislaviensis requires manganese to functionalize a C-H bond possessing a bond dissociation enthalpy (BDE) exceeding 100 kcal/mol. Structural and spectroscopic studies of this enzyme reveal a redox-active, heterobimetallic manganese-iron active site that utilizes a manganese ion at the locus for O 2 activation and substrate coordination. Accordingly, this enzyme represents the first documented Mn-dependent monooxygenase in biology. Related proteins are widespread in microorganisms suggesting that many uncharacterized monooxygenases may utilize manganese-containing cofactors to accomplish diverse biological tasks.
Collapse
|
27
|
Wu Y, Zhao C, Su Y, Shaik S, Lai W. Mechanistic Insight into Peptidyl-Cysteine Oxidation by the Copper-Dependent Formylglycine-Generating Enzyme. Angew Chem Int Ed Engl 2023; 62:e202212053. [PMID: 36545867 DOI: 10.1002/anie.202212053] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
The copper-dependent formylglycine-generating enzyme (FGE) catalyzes the oxygen-dependent oxidation of specific peptidyl-cysteine residues to formylglycine. Our QM/MM calculations provide a very likely mechanism for this transformation. The reaction starts with dioxygen binding to the tris-thiolate CuI center to form a triplet CuII -superoxide complex. The rate-determining hydrogen atom abstraction involves a triplet-singlet crossing to form a CuII -OOH species that couples with the substrate radical, leading to a CuI -alkylperoxo intermediate. This is accompanied by proton transfer from the hydroperoxide to the S atom of the substrate via a nearby water molecule. The subsequent O-O bond cleavage is coupled with the C-S bond breaking that generates the formylglycine and a CuII -oxyl complex. Moreover, our results suggest that the aldehyde oxygen of the final product originates from O2 , which will be useful for future experimental work.
Collapse
Affiliation(s)
- Yao Wu
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, Department of Chemistry, Renmin University of China, Beijing, 100872, China
| | - Cong Zhao
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, Department of Chemistry, Renmin University of China, Beijing, 100872, China
| | - Yanzhuang Su
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, Department of Chemistry, Renmin University of China, Beijing, 100872, China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Wenzhen Lai
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, Department of Chemistry, Renmin University of China, Beijing, 100872, China
| |
Collapse
|
28
|
Walton PH, Davies GJ, Diaz DE, Franco‐Cairo JP. The histidine brace: nature's copper alternative to haem? FEBS Lett 2023; 597:485-494. [PMID: 36660911 PMCID: PMC10952591 DOI: 10.1002/1873-3468.14579] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/21/2023]
Abstract
The copper histidine brace is a structural unit in metalloproteins (Proc Natl Acad Sci USA 2011, 108, 15079). It consists of a copper ion chelated by the NH2 and π-N atom of an N-terminal histidine, and the τ-N atom of a further histidine, in an overall T-shaped coordination geometry (Nat Catal 2018, 1, 571). Like haem-containing proteins, histidine-brace-containing proteins have peroxygenase and/or oxygenase activity, where the substrates are notable for resistance to oxidation, for example, lytic polysaccharide monooxygenases (LPMOs). Moreover, the histidine brace is an invariant unit around which different protein structures exert different activities. Given the similarities in the diversity of function of proteins that contain either the copper histidine brace or haem, the question arises as to whether the functions of histidine brace-containing proteins duplicate those containing haem groups.
Collapse
|
29
|
Koo CW, Hershewe JM, Jewett MC, Rosenzweig AC. Cell-Free Protein Synthesis of Particulate Methane Monooxygenase into Nanodiscs. ACS Synth Biol 2022; 11:4009-4017. [PMID: 36417751 PMCID: PMC9910172 DOI: 10.1021/acssynbio.2c00366] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Particulate methane monooxygenase (pMMO) is a multi-subunit membrane metalloenzyme used by methanotrophic bacteria to convert methane to methanol. A major hurdle to studying pMMO is the lack of a recombinant expression system, precluding investigation of individual residues by mutagenesis and hampering a complete understanding of its mechanism. Here, we developed an Escherichia coli lysate-based cell-free protein synthesis (CFPS) system that can be used to express pMMO in vitro in the presence of nanodiscs. We used a SUMO fusion construct to generate the native PmoB subunit and showed that the SUMO protease (Ulp1) cleaves the protein in the reaction mixture. Using an affinity tag to isolate the complete pMMO complex, we demonstrated that the complex forms without the need for exogenous translocon machinery or chaperones, confirmed by negative stain electron microscopy. This work demonstrates the potential for using CFPS to express multi-subunit membrane-bound metalloenzymes directly into lipid bilayers.
Collapse
Affiliation(s)
- Christopher W. Koo
- Department of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jasmine M. Hershewe
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences and of Chemistry and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
30
|
Dummer NF, Willock DJ, He Q, Howard MJ, Lewis RJ, Qi G, Taylor SH, Xu J, Bethell D, Kiely CJ, Hutchings GJ. Methane Oxidation to Methanol. Chem Rev 2022; 123:6359-6411. [PMID: 36459432 PMCID: PMC10176486 DOI: 10.1021/acs.chemrev.2c00439] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The direct transformation of methane to methanol remains a significant challenge for operation at a larger scale. Central to this challenge is the low reactivity of methane at conditions that can facilitate product recovery. This review discusses the issue through examination of several promising routes to methanol and an evaluation of performance targets that are required to develop the process at scale. We explore the methods currently used, the emergence of active heterogeneous catalysts and their design and reaction mechanisms and provide a critical perspective on future operation. Initial experiments are discussed where identification of gas phase radical chemistry limited further development by this approach. Subsequently, a new class of catalytic materials based on natural systems such as iron or copper containing zeolites were explored at milder conditions. The key issues of these technologies are low methane conversion and often significant overoxidation of products. Despite this, interest remains high in this reaction and the wider appeal of an effective route to key products from C-H activation, particularly with the need to transition to net carbon zero with new routes from renewable methane sources is exciting.
Collapse
Affiliation(s)
- Nicholas F. Dummer
- Max Planck−Cardiff Centre on the Fundamentals of Heterogeneous Catalysis FUNCAT, Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, CardiffCF10 3AT, United Kingdom
| | - David J. Willock
- Max Planck−Cardiff Centre on the Fundamentals of Heterogeneous Catalysis FUNCAT, Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, CardiffCF10 3AT, United Kingdom
| | - Qian He
- Department of Materials Science and Engineering, National University of Singapore, Singapore117575, Singapore
| | - Mark J. Howard
- Max Planck−Cardiff Centre on the Fundamentals of Heterogeneous Catalysis FUNCAT, Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, CardiffCF10 3AT, United Kingdom
| | - Richard J. Lewis
- Max Planck−Cardiff Centre on the Fundamentals of Heterogeneous Catalysis FUNCAT, Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, CardiffCF10 3AT, United Kingdom
| | - Guodong Qi
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan430071, P. R. China
- University of Chinese Academy of Sciences, Beijing100049, P. R. China
| | - Stuart H. Taylor
- Max Planck−Cardiff Centre on the Fundamentals of Heterogeneous Catalysis FUNCAT, Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, CardiffCF10 3AT, United Kingdom
| | - Jun Xu
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan430071, P. R. China
- University of Chinese Academy of Sciences, Beijing100049, P. R. China
| | - Don Bethell
- Department of Chemistry, University of Liverpool, Crown Street, LiverpoolL69 7ZD, United Kingdom
| | - Christopher J. Kiely
- Department of Materials Science and Engineering, Lehigh University, 5 East Packer Avenue, Bethlehem, Pennsylvania18015, United States
| | - Graham J. Hutchings
- Max Planck−Cardiff Centre on the Fundamentals of Heterogeneous Catalysis FUNCAT, Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, CardiffCF10 3AT, United Kingdom
| |
Collapse
|
31
|
Recent progress in the engineering of C1-utilizing microbes. Curr Opin Biotechnol 2022; 78:102836. [PMID: 36334444 DOI: 10.1016/j.copbio.2022.102836] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022]
Abstract
The global climate crisis has led to the transition toward the sustainable production of chemicals and fuels with a low carbon footprint. Microbial utilization of one-carbon (C1) substrates, such as carbon dioxide, carbon monoxide, methane, formate, and methanol, may be a promising replacement for the current fossil fuel-based industry. However, natural C1-utilizing microbes are currently unsuitable for industrial applications because of their slow growth and low carbon conversion efficiency, which results in low productivity and yield. Here, we review the recent achievements in engineering C1-utilizing microbes with improved carbon assimilation efficiency and describe the development of synthetic microorganisms by introducing natural C1 assimilation pathways in non-C1-utilizing microbes. Finally, we outline the future directions for realizing the industrial potential of C1-utilizing microbes.
Collapse
|
32
|
Heyer AJ, Plessers D, Braun A, Rhoda HM, Bols ML, Hedman B, Hodgson KO, Schoonheydt RA, Sels BF, Solomon EI. Methane Activation by a Mononuclear Copper Active Site in the Zeolite Mordenite: Effect of Metal Nuclearity on Reactivity. J Am Chem Soc 2022; 144:19305-19316. [PMID: 36219763 DOI: 10.1021/jacs.2c06269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The direct conversion of methane to methanol would have a wide reaching environmental and industrial impact. Copper-containing zeolites can perform this reaction at low temperatures and pressures at a previously defined O2-activated [Cu2O]2+ site. However, after autoreduction of the copper-containing zeolite mordenite and removal of the [Cu2O]2+ active site, the zeolite is still methane reactive. In this study, we use diffuse reflectance UV-vis spectroscopy, magnetic circular dichroism, resonance Raman spectroscopy, electron paramagnetic resonance, and X-ray absorption spectroscopy to unambiguously define a mononuclear [CuOH]+ as the CH4 reactive active site of the autoreduced zeolite. The rigorous identification of a mononuclear active site allows a reactivity comparison to the previously defined [Cu2O]2+ active site. We perform kinetic experiments to compare the reactivity of the [CuOH]+ and [Cu2O]2+ sites and find that the binuclear site is significantly more reactive. From the analysis of density functional theory calculations, we elucidate that this increased reactivity is a direct result of stabilization of the [Cu2OH]2+ H-atom abstraction product by electron delocalization over the two Cu cations via the bridging ligand. This significant increase in reactivity from electron delocalization over a binuclear active site provides new insights for the design of highly reactive oxidative catalysts.
Collapse
Affiliation(s)
- Alexander J Heyer
- Department of Chemistry, Stanford University, Stanford, California94305, United States
| | - Dieter Plessers
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven-University of Leuven, LeuvenB-3001, Belgium
| | - Augustin Braun
- Department of Chemistry, Stanford University, Stanford, California94305, United States
| | - Hannah M Rhoda
- Department of Chemistry, Stanford University, Stanford, California94305, United States
| | - Max L Bols
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven-University of Leuven, LeuvenB-3001, Belgium
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California94025, United States
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, California94305, United States.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California94025, United States
| | - Robert A Schoonheydt
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven-University of Leuven, LeuvenB-3001, Belgium
| | - Bert F Sels
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven-University of Leuven, LeuvenB-3001, Belgium
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California94305, United States.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California94025, United States
| |
Collapse
|
33
|
Zhu Y, Koo CW, Cassidy CK, Spink MC, Ni T, Zanetti-Domingues LC, Bateman B, Martin-Fernandez ML, Shen J, Sheng Y, Song Y, Yang Z, Rosenzweig AC, Zhang P. Structure and activity of particulate methane monooxygenase arrays in methanotrophs. Nat Commun 2022; 13:5221. [PMID: 36064719 PMCID: PMC9445010 DOI: 10.1038/s41467-022-32752-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/16/2022] [Indexed: 01/29/2023] Open
Abstract
Methane-oxidizing bacteria play a central role in greenhouse gas mitigation and have potential applications in biomanufacturing. Their primary metabolic enzyme, particulate methane monooxygenase (pMMO), is housed in copper-induced intracytoplasmic membranes (ICMs), of which the function and biogenesis are not known. We show by serial cryo-focused ion beam (cryoFIB) milling/scanning electron microscope (SEM) volume imaging and lamellae-based cellular cryo-electron tomography (cryoET) that these ICMs are derived from the inner cell membrane. The pMMO trimer, resolved by cryoET and subtomogram averaging to 4.8 Å in the ICM, forms higher-order hexagonal arrays in intact cells. Array formation correlates with increased enzymatic activity, highlighting the importance of studying the enzyme in its native environment. These findings also demonstrate the power of cryoET to structurally characterize native membrane enzymes in the cellular context.
Collapse
Affiliation(s)
- Yanan Zhu
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christopher W. Koo
- grid.16753.360000 0001 2299 3507Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL USA
| | - C. Keith Cassidy
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, Oxford, UK
| | - Matthew C. Spink
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Tao Ni
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Laura C. Zanetti-Domingues
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facility Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - Benji Bateman
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facility Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - Marisa L. Martin-Fernandez
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facility Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - Juan Shen
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuewen Sheng
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Yun Song
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Zhengyi Yang
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK ,grid.4709.a0000 0004 0495 846XPresent Address: Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Amy C. Rosenzweig
- grid.16753.360000 0001 2299 3507Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL USA
| | - Peijun Zhang
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK ,grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK ,grid.4991.50000 0004 1936 8948Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| |
Collapse
|
34
|
Bete SC, May LK, Woite P, Roemelt M, Otte M. A Copper Cage‐Complex as Mimic of the pMMO Cu
C
Site. Angew Chem Int Ed Engl 2022; 61:e202206120. [PMID: 35731651 PMCID: PMC9544873 DOI: 10.1002/anie.202206120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/05/2022]
Abstract
The active site of particulate methane monooxygenase (pMMO) and its mechanism of action are not known. Recently, the CuC site emerged as a potential active site, but to date it lacks any study on biomimetic resemblance of the coordination environment provided by the enzyme. Here, the synthesis of a cage ligand providing such an environment is reported. Copper is incorporated, and coordination occurs by the two imidazole and one carboxylate group offered by the ligand. Depending on the oxidation state, it can adopt different coordination modes, as evidenced by the solid‐state structures and computational investigation. The copper(I) state readily reacts with dioxygen and thereby undergoes CH activation. Moreover, the catalytic aerobic oxidation of hydroquinones as ubiquinol mimics is shown. Clean one‐electron oxidation occurs under mild conditions and EPR analysis of the copper(II) state in the presence of water reveals striking similarities to the data obtained from pMMO.
Collapse
Affiliation(s)
- Sarah C. Bete
- Institute of Inorganic Chemistry University of Goettingen Tammannstraße 4 37077 Göttingen Germany
| | - Leander K. May
- Institute of Inorganic Chemistry University of Goettingen Tammannstraße 4 37077 Göttingen Germany
| | - Philipp Woite
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Michael Roemelt
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Matthias Otte
- Institute of Inorganic Chemistry University of Goettingen Tammannstraße 4 37077 Göttingen Germany
| |
Collapse
|
35
|
Guo J, Fisher OS. Orchestrating copper binding: structure and variations on the cupredoxin fold. J Biol Inorg Chem 2022; 27:529-540. [PMID: 35994119 DOI: 10.1007/s00775-022-01955-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/07/2022] [Indexed: 11/26/2022]
Abstract
A large number of copper binding proteins coordinate metal ions using a shared three-dimensional fold called the cupredoxin domain. This domain was originally identified in Type 1 "blue copper" centers but has since proven to be a common domain architecture within an increasingly large and diverse group of copper binding domains. The cupredoxin fold has a number of qualities that make it ideal for coordinating Cu ions for purposes including electron transfer, enzyme catalysis, assembly of other copper sites, and copper sequestration. The structural core does not undergo major conformational changes upon metal binding, but variations within the coordination environment of the metal site confer a range of Cu-binding affinities, reduction potentials, and spectroscopic properties. Here, we discuss these proteins from a structural perspective, examining how variations within the overall cupredoxin fold and metal binding sites are linked to distinct spectroscopic properties and biological functions. Expanding far beyond the blue copper proteins, cupredoxin domains are used by a growing number of proteins and enzymes as a means of binding copper ions, with many more likely remaining to be identified.
Collapse
Affiliation(s)
- Jing Guo
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA
| | - Oriana S Fisher
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA.
| |
Collapse
|
36
|
Cutsail GE, Banerjee R, Rice DB, McCubbin Stepanic O, Lipscomb JD, DeBeer S. Determination of the iron(IV) local spin states of the Q intermediate of soluble methane monooxygenase by Kβ X-ray emission spectroscopy. J Biol Inorg Chem 2022; 27:573-582. [PMID: 35988092 PMCID: PMC9470658 DOI: 10.1007/s00775-022-01953-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/07/2022] [Indexed: 11/29/2022]
Abstract
Soluble methane monooxygenase (sMMO) facilitates the conversion of methane to methanol at a non-heme FeIV2 intermediate MMOHQ, which is formed in the active site of the sMMO hydroxylase component (MMOH) during the catalytic cycle. Other biological systems also employ high-valent FeIV sites in catalysis; however, MMOHQ is unique as Nature’s only identified FeIV2 intermediate. Previous 57Fe Mössbauer spectroscopic studies have shown that MMOHQ employs antiferromagnetic coupling of the two FeIV sites to yield a diamagnetic cluster. Unfortunately, this lack of net spin prevents the determination of the local spin state (Sloc) of each of the irons by most spectroscopic techniques. Here, we use Fe Kβ X-ray emission spectroscopy (XES) to characterize the local spin states of the key intermediates of the sMMO catalytic cycle, including MMOHQ trapped by rapid-freeze-quench techniques. A pure XES spectrum of MMOHQ is obtained by subtraction of the contributions from other reaction cycle intermediates with the aid of Mössbauer quantification. Comparisons of the MMOHQ spectrum with those of known Sloc = 1 and Sloc = 2 FeIV sites in chemical and biological models reveal that MMOHQ possesses Sloc = 2 iron sites. This experimental determination of the local spin state will help guide future computational and mechanistic studies of sMMO catalysis.
Collapse
Affiliation(s)
- George E Cutsail
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany.
- Institute of Inorganic Chemistry, University of Duisburg-Essen, Universitätsstrasse 5-7, 45117, Essen, Germany.
| | - Rahul Banerjee
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Derek B Rice
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Olivia McCubbin Stepanic
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - John D Lipscomb
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany.
| |
Collapse
|
37
|
Wang B, Zhang X, Fang W, Rovira C, Shaik S. How Do Metalloproteins Tame the Fenton Reaction and Utilize •OH Radicals in Constructive Manners? Acc Chem Res 2022; 55:2280-2290. [PMID: 35926175 DOI: 10.1021/acs.accounts.2c00304] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This Account describes the manner whereby nature controls the Fenton-type reaction of O-O homolysis of hydrogen peroxide and harnesses it to carry out various useful oxidative transformations in metalloenzymes. H2O2 acts as the cosubstrate for the heme-dependent peroxidases, P450BM3, P450SPα, P450BSβ, and the P450 decarboxylase OleT, as well as the nonheme enzymes HppE and the copper-dependent lytic polysaccharide monooxygenases (LPMOs). Whereas heme peroxidases use the Poulos-Kraut heterolytic mechanism for H2O2 activation, some heme enzymes prefer the alternative Fenton-type mechanism, which produces •OH radical intermediates. The fate of the •OH radical is controlled by the protein environment, using tight H-bonding networks around H2O2. The so-generated •OH radical is constrained by the surrounding H-bonding interactions, the orientation of which is targeted to perform H-abstraction from the Fe(III)-OH group and thereby leading to the formation of the active species, called Compound I (Cpd I), Por+•Fe(IV)═O, which performs oxidation of the substrate. Alternatively, for the nonheme HppE enzyme, the O-O homolysis catalyzed by the resting state Fe(II) generates an Fe(III)-OH species that effectively constrains the •OH radical species by a tight H-bonding network. The so-formed H-bonded •OH radical acts directly as the oxidant, since it is oriented to perform H-abstraction from the C-H bond of the substrate (S)-2-HPP. The Fenton-type H2O2 activation is strongly suggested by computations to occur also in copper-dependent LPMOs and pMMO. In LPMOs, the Cu(I)-catalyzed O-O homolysis of the H2O2 cosubstrate generates an •OH radical that abstracts a hydrogen atom from Cu(II)-OH and forms thereby the active species of the enzyme, Cu(II)-O•. Such Fenton-type O-O activation can be shared by both the O2-dependent activations of LPMOs and pMMOs, in which the O2 cosubstrate may be reduced to H2O2 by external reductants. Our studies show that, generally, the H2O2 activation is highly dependent on the protein environment, as well as on the presence/absence of substrates. Since H2O2 is a highly flexible and hydrophilic molecule, the absence of suitable substrates may lead to unproductive binding or even to the release of H2O2 from the active site, as has been suggested in P450cam and LPMOs, whereas the presence of the substrate seems to play a role in steering a Fenton-type H2O2 activation. In the absence of a substrate, the hydrophilic active site of P450BM3 disfavors the binding and activation of H2O2 and protects thereby the enzyme from the damage by the Fenton reaction. Due to the distinct coordination and reaction environment, the Fenton-type H2O2 activation mechanism by enzymes differs from the reaction in synthetic systems. In nonenzymatic reactions, the H-bonding networks are quite dynamic and flexible and the reactivity of H2O2 is not strategically constrained as in the enzymatic environment. As such, our Account describes the controlled Fenton-type mechanism in metalloenzymes, and the role of the protein environment in constraining the •OH radical against oxidative damage, while directing it to perform useful oxidative transformations.
Collapse
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
| | - Xuan Zhang
- 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
| | - Wenhan Fang
- 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
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, 08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| |
Collapse
|
38
|
Bete SC, May LK, Woite P, Roemelt M, Otte M. A Copper Cage‐Complex as Mimic of the pMMO CuC Site. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sarah C. Bete
- University of Göttingen: Georg-August-Universitat Gottingen Institut für Anorganische Chemie GERMANY
| | - Leander K. May
- Georg-August-Universität Göttingen: Georg-August-Universitat Gottingen Institut für Anorganische Chemie GERMANY
| | - Philipp Woite
- Humboldt-Universitat zu Berlin Institut für Chemie GERMANY
| | - Michael Roemelt
- Humboldt-Universitat zu Berlin Institut für Chemie Brook-Taylor-Straße 2 12489 Berlin GERMANY
| | - Matthias Otte
- Georg-August-Universität Göttingen Institut für Anorganische Chemie, Institut für Anorganische Chemie Tammannstraße 4 37077 Göttingen GERMANY
| |
Collapse
|
39
|
Characterization of Protein-Membrane Interactions in Yeast Autophagy. Cells 2022; 11:cells11121876. [PMID: 35741004 PMCID: PMC9221364 DOI: 10.3390/cells11121876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 02/06/2023] Open
Abstract
Cells rely on autophagy to degrade cytosolic material and maintain homeostasis. During autophagy, content to be degraded is encapsulated in double membrane vesicles, termed autophagosomes, which fuse with the yeast vacuole for degradation. This conserved cellular process requires the dynamic rearrangement of membranes. As such, the process of autophagy requires many soluble proteins that bind to membranes to restructure, tether, or facilitate lipid transfer between membranes. Here, we review the methods that have been used to investigate membrane binding by the core autophagy machinery and additional accessory proteins involved in autophagy in yeast. We also review the key experiments demonstrating how each autophagy protein was shown to interact with membranes.
Collapse
|
40
|
Chan SI, Wang VC, Chen PP, Yu SS. Methane oxidation by the copper methane monooxygenase: Before and after the cryogenic electron microscopy structure of particulate methane monooxygenase from
Methylococcus capsulatus
(Bath). J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Sunney I Chan
- Institute of Chemistry, Academia Sinica Taipei City Taiwan
- Department of Chemistry National Taiwan University Taipei City Taiwan
| | - Vincent C.‐C Wang
- Department of Chemistry National Sun Yat‐Sen University Kaohsiung City Taiwan
| | - Peter P.‐Y. Chen
- Department of Chemistry National Chung Hsing University Taichung City Taiwan
| | - Steve S.‐F. Yu
- Institute of Chemistry, Academia Sinica Taipei City Taiwan
| |
Collapse
|
41
|
Karlin KD, Hota PK, Kim B. Concluding remarks: discussion on natural and artificial enzymes including synthetic models. Faraday Discuss 2022; 234:388-404. [PMID: 35507381 PMCID: PMC9148554 DOI: 10.1039/d2fd00073c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper overviews the final remarks lecture delivered (by K. D. K.) at the end of this bioinorganic chemistry Faraday Discussion, held online for a worldwide audience from January 31 - February 3, 2022. This paper provides discussion in six sections: (1) the Introductory lecture, from Ed Solomon, emphasized past and present uses of advanced spectroscopic methods and theoretical approaches to elucidate metalloenzyme active site structure, physical properties and function. (2) The discussion topics are divided into groups having similar research themes, as seen from this author's perspective. Emphasis is given to the non-heme iron group of articles with dioxygen activation research. (3) Small molecule activation (e.g., N2, CO2 and O2 reduction; CH4 or H2O oxidation) is widely covered in this discussion; this authors' view of the important reactions in bioinorganic chemistry is discussed. (4) We discuss current practice and vision for employing materials chemistry to widely apply to electrocatalytic methods to effect small molecule activation (as above) to fulfill societal energy demands. (5) A discussion is given on the topic of synthetic models and the approach utilized therein. (6) New research on the authors' synthetic modeling is presented; preliminary results are given in the area of copper mediated peroxide activation.
Collapse
Affiliation(s)
- Kenneth D Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA.
| | - Pradip K Hota
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA.
| | - Bohee Kim
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA.
| |
Collapse
|