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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.
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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.
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2
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Yang SNN, Haritos V, Kertesz MA, Coleman NV. A novel soluble di-iron monooxygenase from the soil bacterium Solimonas soli. Environ Microbiol 2024; 26:e16567. [PMID: 38233213 DOI: 10.1111/1462-2920.16567] [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] [Received: 09/02/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024]
Abstract
Soluble di-iron monooxygenase (SDIMO) enzymes enable insertion of oxygen into diverse substrates and play significant roles in biogeochemistry, bioremediation and biocatalysis. An unusual SDIMO was detected in an earlier study in the genome of the soil organism Solimonas soli, but was not characterized. Here, we show that the S. soli SDIMO is part of a new clade, which we define as 'Group 7'; these share a conserved gene organization with alkene monooxygenases but have only low amino acid identity. The S. soli genes (named zmoABCD) could be functionally expressed in Pseudomonas putida KT2440 but not in Escherichia coli TOP10. The recombinants made epoxides from C2 C8 alkenes, preferring small linear alkenes (e.g. propene), but also epoxidating branched, carboxylated and chlorinated substrates. Enzymatic epoxidation of acrylic acid was observed for the first time. ZmoABCD oxidised the organochlorine pollutants vinyl chloride (VC) and cis-1,2-dichloroethene (cDCE), with the release of inorganic chloride from VC but not cDCE. The original host bacterium S. soli could not grow on any alkenes tested but grew well on phenol and n-octane. Further work is needed to link ZmoABCD and the other Group 7 SDIMOs to specific physiological and ecological roles.
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Affiliation(s)
- Sui Nin Nicholas Yang
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Victoria Haritos
- Department of Chemical and Biological Engineering, Monash University, Melbourne, Victoria, Australia
| | - Michael A Kertesz
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Nicholas V Coleman
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
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3
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Chi Z, Liu X, Li H, Liang S, Luo YH, Zhou C, Rittmann BE. Co-metabolic biodegradation of chlorinated ethene in an oxygen- and ethane-based membrane biofilm reactor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167323. [PMID: 37742949 DOI: 10.1016/j.scitotenv.2023.167323] [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: 05/29/2023] [Revised: 09/15/2023] [Accepted: 09/22/2023] [Indexed: 09/26/2023]
Abstract
Groundwater contamination by chlorinated ethenes is an urgent concern worldwide. One approach for detoxifying chlorinated ethenes is aerobic co-metabilims using ethane (C2H6) as the primary substrate. This study evaluated long-term continuous biodegradation of three chlorinated alkenes in a membrane biofilm reactor (MBfR) that delivered C2H6 and O2 via gas-transfer membranes. During 133 days of continuous operation, removals of dichloroethane (DCE), trichloroethene (TCE), and tetrachloroethene (PCE) were as high as 94 % and with effluent concentrations below 5 μM. In situ batch tests showed that the co-metabolic kinetics were faster with more chlorination. C2H6-oxidizing Comamonadaceae and "others," such as Methylococcaceae, oxidized C2H6 via monooxyenation reactions. The abundant non-ethane monooxygenases, particularly propane monooxygenase, appears to have been responsible for C2H6 aerobic metabolism and co-metabolism of chlorinated ethenes. This work proves that the C2H6 + O2 MBfR is a platform for ex-situ bioremediation of chlorinated ethenes, and the generalized action of the monooxygenases may make it applicable for other chlorinated organic contaminants.
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Affiliation(s)
- Zifang Chi
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, PR China
| | - Xinyang Liu
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, PR China
| | - Huai Li
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, PR China.
| | - Shen Liang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, PR China
| | - Yi-Hao Luo
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ 85287-5701, USA; Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, School of Environment, Northeast Normal University, Changchun 130117, PR China.
| | - Chen Zhou
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ 85287-5701, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ 85287-5701, USA
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Chen Y, Ren H, Kong X, Wu H, Lu Z. A multicomponent propane monooxygenase catalyzes the initial degradation of methyl tert-butyl ether in Mycobacterium vaccae JOB5. Appl Environ Microbiol 2023; 89:e0118723. [PMID: 37823642 PMCID: PMC10617536 DOI: 10.1128/aem.01187-23] [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: 07/10/2023] [Accepted: 08/30/2023] [Indexed: 10/13/2023] Open
Abstract
Methyl tert-butyl ether (MTBE) has been recognized as a groundwater contaminant due to its widespread distribution and potential threat to human health. The limited understanding of the enzymes catalyzing MTBE degradation restricts their application in MTBE bioremediation. In this study, an MTBE-degrading soluble di-iron monooxygenase that clusters phylogenetically with a known propane monooxygenase (PRM) encoded by the prmABCD gene cluster was identified and functionally characterized, revealing their role in MTBE metabolism by Mycobacterium vaccae JOB5. Transcriptome analysis demonstrated that the expression of prmABCD was upregulated when JOB5 was induced by MTBE. Escherichia coli Rosetta heterologously expressing prmABCD from JOB5 could transform MTBE, indicating that the PRM of JOB5 is capable of the initial degradation of MTBE. The loss of the gene encoding the oxygenase α-subunit or β-subunit, the coupling protein, or the reductase disrupted MTBE transformation by the recombinant E. coli Rosetta. In addition, the catalytic capacity of PRM is likely affected by residue G95 in the active site pocket and residues I84, P165, A269, and V270 in the substrate tunnel structure. Mutation of amino acids in the active site and substrate tunnel resulted in inefficiency or inactivation of MTBE degradation, and the activity in 1,4-dioxane (1,4-D) degradation was diminished less than that in MTBE degradation.IMPORTANCEMulticomponent monooxygenases catalyzing the initial hydroxylation of MTBE are important in MTBE biodegradation. Previous studies of MTBE degradation enzymes have focused on P450s, alkane monooxygenase and MTBE monooxygenase, but the vital role of soluble di-iron monooxygenases has rarely been reported. In this study, we deciphered the essential catalytic role of a PRM and revealed the key residues of the PRM in MTBE metabolism. Our findings provide new insight into the MTBE-degrading gene cluster and enzymes in bacteria. This characterization of the PRM associated with MTBE degradation expands our understanding of MTBE-degrading gene diversity and provides a novel candidate enzyme for the bioremediation of MTBE-contaminated sites.
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Affiliation(s)
- Yiyang Chen
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Ren
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiangyu Kong
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
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Identification of active gaseous-alkane degraders at natural gas seeps. THE ISME JOURNAL 2022; 16:1705-1716. [PMID: 35319019 PMCID: PMC9213486 DOI: 10.1038/s41396-022-01211-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/30/2022] [Accepted: 02/04/2022] [Indexed: 11/29/2022]
Abstract
Natural gas seeps release significant amounts of methane and other gases including ethane and propane contributing to global climate change. In this study, bacterial actively consuming short-chain alkanes were identified by cultivation, whole-genome sequencing, and stable-isotope probing (SIP)-metagenomics using 13C-propane and 13C-ethane from two different natural gas seeps, Pipe Creek and Andreiasu Everlasting Fire. Nearly 100 metagenome-assembled genomes (MAGs) (completeness 70–99%) were recovered from both sites. Among these, 16 MAGs had genes encoding the soluble di-iron monooxygenase (SDIMO). The MAGs were affiliated to Actinobacteria (two MAGs), Alphaproteobacteria (ten MAGs), and Gammaproteobacteria (four MAGs). Additionally, three gaseous-alkane degraders were isolated in pure culture, all of which could grow on ethane, propane, and butane and possessed SDIMO-related genes. Two Rhodoblastus strains (PC2 and PC3) were from Pipe Creek and a Mycolicibacterium strain (ANDR5) from Andreiasu. Strains PC2 and PC3 encoded putative butane monooxygenases (MOs) and strain ANDR5 contained a propane MO. Mycolicibacterium strain ANDR5 and MAG19a, highly abundant in incubations with 13C-ethane, share an amino acid identity (AAI) of 99.3%. We show using a combination of enrichment and isolation, and cultivation-independent techniques, that these natural gas seeps contain a diverse community of active bacteria oxidising gaseous-alkanes, which play an important role in biogeochemical cycling of natural gas.
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Jones JC, Banerjee R, Semonis MM, Shi K, Aihara H, Lipscomb JD. X-ray Crystal Structures of Methane Monooxygenase Hydroxylase Complexes with Variants of Its Regulatory Component: Correlations with Altered Reaction Cycle Dynamics. Biochemistry 2022; 61:21-33. [PMID: 34910460 PMCID: PMC8727504 DOI: 10.1021/acs.biochem.1c00673] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Full activity of soluble methane monooxygenase (sMMO) depends upon the formation of a 1:1 complex of the regulatory protein MMOB with each alpha subunit of the (αβγ)2 hydroxylase, sMMOH. Previous studies have shown that mutations in the core region of MMOB and in the N- and C-termini cause dramatic changes in the rate constants for steps in the sMMOH reaction cycle. Here, X-ray crystal structures are reported for the sMMOH complex with two double variants within the core region of MMOB, DBL1 (N107G/S110A), and DBL2 (S109A/T111A), as well as two variants in the MMOB N-terminal region, H33A and H5A. DBL1 causes a 150-fold decrease in the formation rate constant of the reaction cycle intermediate P, whereas DBL2 accelerates the reaction of the dinuclear Fe(IV) intermediate Q with substrates larger than methane by three- to fourfold. H33A also greatly slows P formation, while H5A modestly slows both formation of Q and its reactions with substrates. Complexation with DBL1 or H33A alters the position of sMMOH residue R245, which is part of a conserved hydrogen-bonding network encompassing the active site diiron cluster where P is formed. Accordingly, electron paramagnetic resonance spectra of sMMOH:DBL1 and sMMOH:H33A complexes differ markedly from that of sMMOH:MMOB, showing an altered electronic environment. In the sMMOH:DBL2 complex, the position of M247 in sMMOH is altered such that it enlarges a molecular tunnel associated with substrate entry into the active site. The H5A variant causes only subtle structural changes despite its kinetic effects, emphasizing the precise alignment of sMMOH and MMOB required for efficient catalysis.
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Affiliation(s)
- Jason C. Jones
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A.,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A.,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A
| | - Manny M. Semonis
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A.,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A.,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A.,Corresponding Author:
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7
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Lee C, Ha SC, Rao Z, Hwang Y, Kim DS, Kim SY, Yoo H, Yoon C, Na JG, Park JH, Lee SJ. Elucidation of the electron transfer environment in the MMOR FAD-binding domain from Methylosinus sporium 5. Dalton Trans 2021; 50:16493-16498. [PMID: 34734616 DOI: 10.1039/d1dt03273a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
By facilitating electron transfer to the hydroxylase diiron center, MMOR-a reductase-serves as an essential component of the catalytic cycle of soluble methane monooxygenase. Here, the X-ray structure analysis of the FAD-binding domain of MMOR identified crucial residues and its influence on the catalytic cycle.
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Affiliation(s)
- Chaemin Lee
- Department of Chemistry and Institute of Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54796, Republic of Korea.
| | - Sung Chul Ha
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Zhili Rao
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Republic of Korea.
| | - Yunha Hwang
- Department of Chemistry and Institute of Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54796, Republic of Korea.
| | - Da Som Kim
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Republic of Korea.
| | - So Young Kim
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Republic of Korea.
| | - Heeseon Yoo
- Department of Chemistry and Institute of Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54796, Republic of Korea.
| | - Chungwoon Yoon
- Department of Chemistry and Institute of Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54796, Republic of Korea.
| | - Jeong-Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 04107, Republic of Korea.
| | - Jung Hee Park
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Republic of Korea. .,Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - Seung Jae Lee
- Department of Chemistry and Institute of Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54796, Republic of Korea.
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Putkinen A, Siljanen HMP, Laihonen A, Paasisalo I, Porkka K, Tiirola M, Haikarainen I, Tenhovirta S, Pihlatie M. New insight to the role of microbes in the methane exchange in trees: evidence from metagenomic sequencing. THE NEW PHYTOLOGIST 2021; 231:524-536. [PMID: 33780002 DOI: 10.1111/nph.17365] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
Methane (CH4 ) exchange in tree stems and canopies and the processes involved are among the least understood components of the global CH4 cycle. Recent studies have focused on quantifying tree stems as sources of CH4 and understanding abiotic CH4 emissions in plant canopies, with the role of microbial in situ CH4 formation receiving less attention. Moreover, despite initial reports revealing CH4 consumption, studies have not adequately evaluated the potential of microbial CH4 oxidation within trees. In this paper, we discuss the current level of understanding on these processes. Further, we demonstrate the potential of novel metagenomic tools in revealing the involvement of microbes in the CH4 exchange of plants, and particularly in boreal trees. We detected CH4 -producing methanogens and novel monooxygenases, potentially involved in CH4 consumption, in coniferous plants. In addition, our field flux measurements from Norway spruce (Picea abies) canopies demonstrate both net CH4 emissions and uptake, giving further evidence that both production and consumption are relevant to the net CH4 exchange. Our findings, together with the emerging diversity of novel CH4 -producing microbial groups, strongly suggest microbial analyses should be integrated in the studies aiming to reveal the processes and drivers behind plant CH4 exchange.
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Affiliation(s)
- Anuliina Putkinen
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki, 00014, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, 00560, Finland
| | - Henri M P Siljanen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, 70200, Finland
- Department of Ecogenomics and Archaea Biology, University of Vienna, Vienna, A-1090, Austria
| | - Antti Laihonen
- Department of Biological and Environmental Science, University of Jyväskylä, PO Box 35, Jyväskylä, FI-40014, Finland
| | - Inga Paasisalo
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, 70200, Finland
| | - Kaija Porkka
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki, 00014, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, 00560, Finland
- Natural Resources Institute Finland, Savonlinna, FI-57200, Finland
| | - Marja Tiirola
- Department of Biological and Environmental Science, University of Jyväskylä, PO Box 35, Jyväskylä, FI-40014, Finland
| | - Iikka Haikarainen
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki, 00014, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, 00560, Finland
| | - Salla Tenhovirta
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki, 00014, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, 00560, Finland
| | - Mari Pihlatie
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki, 00014, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, 00560, Finland
- Department of Agricultural Sciences, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, 00014, Finland
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Horizontal Gene Transfer of Genes Encoding Copper-Containing Membrane-Bound Monooxygenase (CuMMO) and Soluble Di-iron Monooxygenase (SDIMO) in Ethane- and Propane-Oxidizing Rhodococcus Bacteria. Appl Environ Microbiol 2021; 87:e0022721. [PMID: 33962978 DOI: 10.1128/aem.00227-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The families of copper-containing membrane-bound monooxygenases (CuMMOs) and soluble di-iron monooxygenases (SDIMOs) are involved not only in methane oxidation but also in short-chain alkane oxidation. Here, we describe Rhodococcus sp. strain ZPP, a bacterium able to grow with ethane or propane as the sole carbon and energy source, and report on the horizontal gene transfer (HGT) of actinobacterial hydrocarbon monooxygenases (HMOs) of the CuMMO family and the sMMO (soluble methane monooxygenase)-like SDIMO in the genus Rhodococcus. The key function of HMO in strain ZPP for propane oxidation was verified by allylthiourea inhibition. The HMO genes (designated hmoCAB) and those encoding sMMO-like SDIMO (designated smoXYB1C1Z) are located on a linear megaplasmid (pRZP1) of strain ZPP. Comparative genomic analysis of similar plasmids indicated the mobility of these plasmids within the genus Rhodococcus. The plasmid pRZP1 in strain ZPP could be conjugatively transferred to a recipient Rhodococcus erythropolis strain in a mating experiment and showed similar ethane- and propane-consuming activities. Finally, our findings demonstrate that the horizontal transfer of plasmid-based CuMMO and SDIMO genes confers the ability to use ethane and propane on the recipient. IMPORTANCE CuMMOs and SDIMOs initiate the aerobic oxidation of alkanes in bacteria. Here, the supposition that horizontally transferred plasmid-based CuMMO and SDIMO genes confer on the recipient similar abilities to use ethane and propane was proposed and confirmed in Rhodococcus. This study is a living example of HGT of CuMMOs and SDIMOs and outlines the plasmid-borne properties responsible for gaseous alkane degradation. Our results indicate that plasmids can support the rapid evolution of enzyme-mediated biogeochemical processes.
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Farhan Ul Haque M, Xu HJ, Murrell JC, Crombie A. Facultative methanotrophs - diversity, genetics, molecular ecology and biotechnological potential: a mini-review. MICROBIOLOGY (READING, ENGLAND) 2020; 166:894-908. [PMID: 33085587 PMCID: PMC7660913 DOI: 10.1099/mic.0.000977] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/20/2020] [Indexed: 12/18/2022]
Abstract
Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although Methylocella strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.
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Affiliation(s)
| | - Hui-Juan Xu
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andrew Crombie
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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11
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Jones JC, Banerjee R, Shi K, Aihara H, Lipscomb JD. Structural Studies of the Methylosinus trichosporium OB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal a Transient Substrate Tunnel. Biochemistry 2020; 59:2946-2961. [PMID: 32692178 DOI: 10.1021/acs.biochem.0c00459] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The metalloenzyme soluble methane monooxygenase (sMMO) consists of hydroxylase (sMMOH), regulatory (MMOB), and reductase components. When sMMOH forms a complex with MMOB, the rate constants are greatly increased for the sequential access of O2, protons, and CH4 to an oxygen-bridged diferrous metal cluster located in the buried active site. Here, we report high-resolution X-ray crystal structures of the diferric and diferrous states of both sMMOH and the sMMOH:MMOB complex using the components from Methylosinus trichosporium OB3b. These structures are analyzed for O2 access routes enhanced when the complex forms. Previously reported, lower-resolution structures of the sMMOH:MMOB complex from the sMMO of Methylococcus capsulatus Bath revealed a series of cavities through sMMOH postulated to serve as the O2 conduit. This potential role is evaluated in greater detail using the current structures. Additionally, a search for other potential O2 conduits in the M. trichosporium OB3b sMMOH:MMOB complex revealed a narrow molecular tunnel, termed the W308-tunnel. This tunnel is sized appropriately for O2 and traverses the sMMOH-MMOB interface before accessing the active site. The kinetics of reaction of O2 with the diferrous sMMOH:MMOB complex in solution show that use of the MMOB V41R variant decreases the rate constant for O2 binding >25000-fold without altering the component affinity. The location of Val41 near the entrance to the W308-tunnel is consistent with the tunnel serving as the primary route for the transfer of O2 into the active site. Accordingly, the crystal structures show that formation of the diferrous sMMOH:MMOB complex restricts access through the chain of cavities while opening the W308-tunnel.
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