1
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Chawley P, Rana A, Jagadevan S. Envisioning role of ammonia oxidizing bacteria in bioenergy production and its challenges: a review. Crit Rev Biotechnol 2021; 42:931-952. [PMID: 34641754 DOI: 10.1080/07388551.2021.1976099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Ammonia oxidizing bacteria (AOB) play a key role in the biological oxidation of ammonia to nitrite and mark their significance in the biogeochemical nitrogen cycle. There has been significant development in harnessing the ammonia oxidizing potential of AOB in the past few decades. However, very little is known about the potential applications of AOB in the bioenergy sector. As alternate sources of energy represent a thrust area for environmental sustainability, the role of AOB in bioenergy production becomes a significant area of exploration. This review highlights the role of AOB in bioenergy production and emphasizes the understanding of the genetic make-up and key cellular biochemical reactions occurring in AOB, thereby leading to the exploration of its various functional aspects. Recent outcomes in novel ammonia/nitrite oxidation steps occurring in a model AOB - Nitrosomonas europaea propel us to explore several areas of environmental implementation. Here we present the significant role of AOB in microbial fuel cells (MFC) where Nitrosomonas sp. play both anodic and cathodic functions in the generation of bioelectricity. This review also presents the potential role of AOB in curbing fuel demand by producing alternative liquid fuel such as methanol and biodiesel. Herein, the multiple roles of AOB in bioenergy production namely: bioelectricity generation, bio-methanol, and biodiesel production have been presented.
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Affiliation(s)
- Parmita Chawley
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
| | - Anu Rana
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
| | - Sheeja Jagadevan
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
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2
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Niu XZ, Field JA, Paniego R, Pepel RD, Chorover J, Abrell L, Sierra-Alvarez R. Bioconcentration potential and microbial toxicity of onium cations in photoacid generators. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:8915-8921. [PMID: 33400114 DOI: 10.1007/s11356-020-12250-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/26/2020] [Indexed: 06/12/2023]
Abstract
Despite the widespread utilization of onium salts as photoacid generators (PAGs) in semiconductor photolithography, their environmental, health, and safety (EHS) properties remain poorly understood. The present work reports the bioconcentration potential of five representative onium species (four sulfonium and one iodonium compound) by determining the octanol-water partition coefficient (POW) and lipid membrane affinity coefficient (KMA); microbial toxicity was evaluated using the bioluminescent bacterium Aliivibrio fischeri (Microtox bioassay). Four of the oniums exhibited varying degrees of hydrophobic (lipophilic) partitioning (log POW: 0.08-4.12; KMA: 1.70-5.62). A strong positive linear correlation was observed between log POW and KMA (KMA = log POW + 1.76, R2 = 0.99). The bioconcentration factors (log BCF) estimated from POW and KMA for the four oniums ranged from 0.13 to 3.67 L kg-1. Bis-(4-tert-butyl phenyl)-iodonium and triphenylsulfonium had 50% inhibitory concentrations (IC50) of 4.8 and 84.6 μM, whereas the IC50 values of the other three oniums were not determined because these values were higher than their aqueous solubility. Given the increased regulatory scrutiny regarding the use and potential health impacts from onium PAGs, this study fulfills critical knowledge gaps concerning the EHS properties of PAG oniums, enabling more comprehensive evaluation of their environmental impacts and potential risk management strategies.
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Affiliation(s)
- Xi-Zhi Niu
- Department of Chemical & Environmental Engineering, The University of Arizona, 1133 James E. Rogers Way, P.O. Box 210011, Tucson, AZ, 85721, USA
- Department of Environmental Science & Arizona Laboratory for Emerging Contaminants, The University of Arizona, Tucson, AZ, 85721, USA
| | - Jim A Field
- Department of Chemical & Environmental Engineering, The University of Arizona, 1133 James E. Rogers Way, P.O. Box 210011, Tucson, AZ, 85721, USA
| | - Rodrigo Paniego
- Department of Chemical & Environmental Engineering, The University of Arizona, 1133 James E. Rogers Way, P.O. Box 210011, Tucson, AZ, 85721, USA
| | - Richard D Pepel
- Department of Chemical & Environmental Engineering, The University of Arizona, 1133 James E. Rogers Way, P.O. Box 210011, Tucson, AZ, 85721, USA
| | - Jon Chorover
- Department of Environmental Science & Arizona Laboratory for Emerging Contaminants, The University of Arizona, Tucson, AZ, 85721, USA
| | - Leif Abrell
- Department of Environmental Science & Arizona Laboratory for Emerging Contaminants, The University of Arizona, Tucson, AZ, 85721, USA
| | - Reyes Sierra-Alvarez
- Department of Chemical & Environmental Engineering, The University of Arizona, 1133 James E. Rogers Way, P.O. Box 210011, Tucson, AZ, 85721, USA.
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3
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Musiani F, Broll V, Evangelisti E, Ciurli S. The model structure of the copper-dependent ammonia monooxygenase. J Biol Inorg Chem 2020; 25:995-1007. [PMID: 32926231 PMCID: PMC7584546 DOI: 10.1007/s00775-020-01820-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/02/2020] [Indexed: 12/24/2022]
Abstract
Abstract Ammonia monooxygenase is a copper-dependent membrane-bound enzyme that catalyzes the first step of nitrification in ammonia-oxidizing bacteria to convert ammonia to hydroxylamine, through the reductive insertion of a dioxygen-derived O atom in an N–H bond. This reaction is analogous to that carried out by particulate methane monooxygenase, which catalyzes the conversion of methane to methanol. The enzymatic activity of ammonia monooxygenase must be modulated to reduce the release of nitrogen-based soil nutrients for crop production into the atmosphere or underground waters, a phenomenon known to significantly decrease the efficiency of primary production as well as increase air and water pollution. The structure of ammonia monooxygenase is not available, rendering the rational design of enzyme inhibitors impossible. This study describes a successful attempt to build a structural model of ammonia monooxygenase, and its accessory proteins AmoD and AmoE, from Nitrosomonas europaea, taking advantage of the high sequence similarity with particulate methane monooxygenase and the homologous PmoD protein, for which crystal structures are instead available. The results obtained not only provide the structural details of the proteins ternary and quaternary structures, but also suggest a location for the copper-containing active site for both ammonia and methane monooxygenases, as well as support a proposed structure of a CuA-analogue dinuclear copper site in AmoD and PmoD. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s00775-020-01820-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy.
| | - Valquiria Broll
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Elisa Evangelisti
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy.
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4
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Appetecchia F, Consalvi S, Scarpecci C, Biava M, Poce G. SAR Analysis of Small Molecules Interfering with Energy-Metabolism in Mycobacterium tuberculosis. Pharmaceuticals (Basel) 2020; 13:E227. [PMID: 32878317 PMCID: PMC7557483 DOI: 10.3390/ph13090227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis remains the world's top infectious killer: it caused a total of 1.5 million deaths and 10 million people fell ill with TB in 2018. Thanks to TB diagnosis and treatment, mortality has been falling in recent years, with an estimated 58 million saved lives between 2000 and 2018. However, the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mtb strains is a major concern that might reverse this progress. Therefore, the development of new drugs acting upon novel mechanisms of action is a high priority in the global health agenda. With the approval of bedaquiline, which targets mycobacterial energy production, and delamanid, which targets cell wall synthesis and energy production, the energy-metabolism in Mtb has received much attention in the last decade as a potential target to investigate and develop new antimycobacterial drugs. In this review, we describe potent anti-mycobacterial agents targeting the energy-metabolism at different steps with a special focus on structure-activity relationship (SAR) studies of the most advanced compound classes.
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Affiliation(s)
| | | | | | | | - Giovanna Poce
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, piazzale A. Moro 5, 00185 Rome, Italy; (F.A.); (S.C.); (C.S.); (M.B.)
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5
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Sharma N, Lee Y, Nam W, Fukuzumi S. Photoinduced Generation of Superoxidants for the Oxidation of Substrates with High C−H Bond Dissociation Energies. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Namita Sharma
- Department of Chemistry and Nano ScienceEwha Womans University Seoul 03760 Korea
| | - Yong‐Min Lee
- Department of Chemistry and Nano ScienceEwha Womans University Seoul 03760 Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano ScienceEwha Womans University Seoul 03760 Korea
| | - Shunichi Fukuzumi
- Department of Chemistry and Nano ScienceEwha Womans University Seoul 03760 Korea
- Graduate School of Science and EngineeringMeijo University, Nagoya Aichi 468-8502 Japan
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6
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Miyaji A, Nitta M, Baba T. Influence of copper ions removal from membrane-bound form of particulate methane monooxygenase from Methylosinus trichosporium OB3b on its activity for methane hydroxylation. J Biotechnol 2019; 306S:100001. [PMID: 34112370 DOI: 10.1016/j.btecx.2018.100001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 12/11/2018] [Accepted: 12/14/2018] [Indexed: 11/26/2022]
Abstract
The influence of metal removal with a chelating reagent, ethylenediaminetetraacetic acid (EDTA), and metal reconstitution on the activity of particulate methane monooxygenase (pMMO) from Methylosinus trichosporium OB3b toward methane oxidation to methanol was investigated. For this study, a membrane fraction containing pMMO and bacterial cell membrane components was prepared. pMMO activity was assessed with two different reductants, nicotinamide adenine dinucleotide (NADH) and 2,3,5,6-tetramethyl hydroquinone (duroquinol). The partial removal of metal ions with EDTA resulted in the selective inhibition of NADH-driven activity. The NADH-driven activity was restored by exogenous copper ions, but not by other divalent metal cations. Furthermore, both NADH- and duroquinol-driven activities were lost completely by increasing the amount of metal removed. Duroquinol-driven activity of the metal-deficient membrane fraction increased with increasing the amount of copper ions added, while NADH-driven activity increased when more than 5 mol of copper ions per mol of pMMO monomer was added. These results suggest that NADH-driven pMMO activity requires not only the catalytic copper center of pMMO but also copper ions outside the catalytic site.
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Affiliation(s)
- Akimitsu Miyaji
- Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, G1-14, Nagatsuta-cho, Midori-ku, Yokohama 226-8502, Japan.
| | - Muneyuki Nitta
- Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, G1-14, Nagatsuta-cho, Midori-ku, Yokohama 226-8502, Japan
| | - Toshihide Baba
- Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, G1-14, Nagatsuta-cho, Midori-ku, Yokohama 226-8502, Japan
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7
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Lieven C, Petersen LAH, Jørgensen SB, Gernaey KV, Herrgard MJ, Sonnenschein N. A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase. Front Microbiol 2018; 9:2947. [PMID: 30564208 PMCID: PMC6288188 DOI: 10.3389/fmicb.2018.02947] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/16/2018] [Indexed: 12/21/2022] Open
Abstract
Background: Genome-scale metabolic models allow researchers to calculate yields, to predict consumption and production rates, and to study the effect of genetic modifications in silico, without running resource-intensive experiments. While these models have become an invaluable tool for optimizing industrial production hosts like Escherichia coli and S. cerevisiae, few such models exist for one-carbon (C1) metabolizers. Results: Here, we present a genome-scale metabolic model for Methylococcus capsulatus (Bath), a well-studied obligate methanotroph, which has been used as a production strain of single cell protein (SCP). The model was manually curated, and spans a total of 879 metabolites connected via 913 reactions. The inclusion of 730 genes and comprehensive annotations, make this model not only a useful tool for modeling metabolic physiology, but also a centralized knowledge base for M. capsulatus (Bath). With it, we determined that oxidation of methane by the particulate methane monooxygenase could be driven both through direct coupling or uphill electron transfer, both operating at reduced efficiency, as either scenario matches well with experimental data and observations from literature. Conclusion: The metabolic model will serve the ongoing fundamental research of C1 metabolism, and pave the way for rational strain design strategies toward improved SCP production processes in M. capsulatus.
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Affiliation(s)
- Christian Lieven
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Leander A H Petersen
- Unibio A/S, Kongens Lyngby, Denmark.,Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sten Bay Jørgensen
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Krist V Gernaey
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Markus J Herrgard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nikolaus Sonnenschein
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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8
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Ito H, Kondo R, Yoshimori K, Kamachi T. Methane Hydroxylation with Water as an Electron Donor under Light Irradiation in the Presence of Reconstituted Membranes Containing both Photosystem II and a Methane Monooxygenase. Chembiochem 2018; 19:2152-2155. [DOI: 10.1002/cbic.201800324] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Hidehiro Ito
- Department of Life Science and Technology; Tokyo Institute of Technology; 2-12-1-M6-7 Ookayama Meguro-ku Tokyo 152-8550 Japan
| | - Ryuichi Kondo
- Department of Life Science and Technology; Tokyo Institute of Technology; 2-12-1-M6-7 Ookayama Meguro-ku Tokyo 152-8550 Japan
| | - Kosei Yoshimori
- Department of Life Science and Technology; Tokyo Institute of Technology; 2-12-1-M6-7 Ookayama Meguro-ku Tokyo 152-8550 Japan
| | - Toshiaki Kamachi
- Department of Life Science and Technology; Tokyo Institute of Technology; 2-12-1-M6-7 Ookayama Meguro-ku Tokyo 152-8550 Japan
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9
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Vilajeliu-Pons A, Koch C, Balaguer MD, Colprim J, Harnisch F, Puig S. Microbial electricity driven anoxic ammonium removal. WATER RESEARCH 2018; 130:168-175. [PMID: 29220717 DOI: 10.1016/j.watres.2017.11.059] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/07/2017] [Accepted: 11/27/2017] [Indexed: 05/03/2023]
Abstract
Removal of nitrogen, mainly in form of ammonium (NH4+), in wastewater treatment plants (WWTPs) is a highly energy demanding process, mainly due to aeration. It causes costs of about half a million Euros per year in an average European WWTP. Alternative, more economical technologies for the removal of nitrogen compounds from wastewater are required. This study proves the complete anoxic conversion of ammonium (NH4+) to dinitrogen gas (N2) in continuously operated bioelectrochemical systems at the litre-scale. The removal rate is comparable to conventional WWTPs with 35 ± 10 g N m-3 d-1 with low accumulation of NO2-, NO3-, N2O. In contrast to classical aerobic nitrification, the energy consumption is considerable lower (1.16 ± 0.21 kWh kg-1 N, being more than 35 times less than for the conventional wastewater treatment). Biotic and abiotic control experiments confirmed that the anoxic nitrification was an electrochemical biological process mainly performed by Nitrosomonas with hydroxylamine as the main substrate (mid-point potential, Eox = +0.67 ± 0.08 V vs. SHE). This article proves the technical feasibility and reduction of costs for ammonium removal from wastewater, investigates the underlying mechanisms and discusses future engineering needs.
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Affiliation(s)
| | - Christin Koch
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany.
| | - Maria D Balaguer
- LEQUiA, Institute of the Environment, University of Girona, Girona, Spain
| | - Jesús Colprim
- LEQUiA, Institute of the Environment, University of Girona, Girona, Spain
| | - Falk Harnisch
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Sebastià Puig
- LEQUiA, Institute of the Environment, University of Girona, Girona, Spain
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10
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Nguyen N, Wilson DW, Nagalingam G, Triccas JA, Schneider EK, Li J, Velkov T, Baell J. Broad activity of diphenyleneiodonium analogues against Mycobacterium tuberculosis, malaria parasites and bacterial pathogens. Eur J Med Chem 2017; 148:507-518. [PMID: 29269132 DOI: 10.1016/j.ejmech.2017.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/07/2017] [Accepted: 10/04/2017] [Indexed: 01/06/2023]
Abstract
In this study, a structure-activity relationship (SAR) compound series based on the NDH-2 inhibitor diphenyleneiodonium (DPI) was synthesised. Compounds were evaluated primarily for in vitro efficacy against Gram-positive and Gram-negative bacteria, commonly responsible for nosocomial and community acquired infections. In addition, we also assessed the activity of these compounds against Mycobacterium tuberculosis (Tuberculosis) and Plasmodium spp. (Malaria). This led to the discovery of highly potent compounds active against bacterial pathogens and malaria parasites in the low nanomolar range, several of which were significantly less toxic to mammalian cells.
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Affiliation(s)
- Nghi Nguyen
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences Monash University, VIC, 3052, Australia
| | - Danny W Wilson
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria 3004, Australia
| | - Gayathri Nagalingam
- Microbial Pathogenesis and Immunity Group, Discipline of Infectious Diseases and Immunology, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - James A Triccas
- Microbial Pathogenesis and Immunity Group, Discipline of Infectious Diseases and Immunology, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Elena K Schneider
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences Monash University, VIC, 3052, Australia
| | - Jian Li
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, VIC, 3800, Australia
| | - Tony Velkov
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences Monash University, VIC, 3052, Australia.
| | - Jonathan Baell
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences Monash University, VIC, 3052, Australia; School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China.
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11
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Lawton TJ, Rosenzweig AC. Methane-Oxidizing Enzymes: An Upstream Problem in Biological Gas-to-Liquids Conversion. J Am Chem Soc 2016; 138:9327-40. [PMID: 27366961 PMCID: PMC5242187 DOI: 10.1021/jacs.6b04568] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biological conversion of natural gas to liquids (Bio-GTL) represents an immense economic opportunity. In nature, aerobic methanotrophic bacteria and anaerobic archaea are able to selectively oxidize methane using methane monooxygenase (MMO) and methyl coenzyme M reductase (MCR) enzymes. Although significant progress has been made toward genetically manipulating these organisms for biotechnological applications, the enzymes themselves are slow, complex, and not recombinantly tractable in traditional industrial hosts. With turnover numbers of 0.16-13 s(-1), these enzymes pose a considerable upstream problem in the biological production of fuels or chemicals from methane. Methane oxidation enzymes will need to be engineered to be faster to enable high volumetric productivities; however, efforts to do so and to engineer simpler enzymes have been minimally successful. Moreover, known methane-oxidizing enzymes have different expression levels, carbon and energy efficiencies, require auxiliary systems for biosynthesis and function, and vary considerably in terms of complexity and reductant requirements. The pros and cons of using each methane-oxidizing enzyme for Bio-GTL are considered in detail. The future for these enzymes is bright, but a renewed focus on studying them will be critical to the successful development of biological processes that utilize methane as a feedstock.
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Affiliation(s)
- Thomas J Lawton
- Departments of Molecular Biosciences and of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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12
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Abstract
Methane monooxygenases (MMOs) are enzymes that catalyze the oxidation of methane to methanol in methanotrophic bacteria. As potential targets for new gas-to-liquid methane bioconversion processes, MMOs have attracted intense attention in recent years. There are two distinct types of MMO, a soluble, cytoplasmic MMO (sMMO) and a membrane-bound, particulate MMO (pMMO). Both oxidize methane at metal centers within a complex, multisubunit scaffold, but the structures, active sites, and chemical mechanisms are completely different. This Current Topic review article focuses on the overall architectures, active site structures, substrate reactivities, protein-protein interactions, and chemical mechanisms of both MMOs, with an emphasis on fundamental aspects. In addition, recent advances, including new details of interactions between the sMMO components, characterization of sMMO intermediates, and progress toward understanding the pMMO metal centers are highlighted. The work summarized here provides a guide for those interested in exploiting MMOs for biotechnological applications.
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Affiliation(s)
- Sarah Sirajuddin
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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13
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Kalyuzhnaya MG, Puri AW, Lidstrom ME. Metabolic engineering in methanotrophic bacteria. Metab Eng 2015; 29:142-152. [PMID: 25825038 DOI: 10.1016/j.ymben.2015.03.010] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 02/26/2015] [Accepted: 03/17/2015] [Indexed: 12/19/2022]
Abstract
Methane, as natural gas or biogas, is the least expensive source of carbon for (bio)chemical synthesis. Scalable biological upgrading of this simple alkane to chemicals and fuels can bring new sustainable solutions to a number of industries with large environmental footprints, such as natural gas/petroleum production, landfills, wastewater treatment, and livestock. Microbial biocatalysis with methane as a feedstock has been pursued off and on for almost a half century, with little enduring success. Today, biological engineering and systems biology provide new opportunities for metabolic system modulation and give new optimism to the concept of a methane-based bio-industry. Here we present an overview of the most recent advances pertaining to metabolic engineering of microbial methane utilization. Some ideas concerning metabolic improvements for production of acetyl-CoA and pyruvate, two main precursors for bioconversion, are presented. We also discuss main gaps in the current knowledge of aerobic methane utilization, which must be solved in order to release the full potential of methane-based biosystems.
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Affiliation(s)
- Marina G Kalyuzhnaya
- Biology Department, San Diego State University, San Diego, CA 92182-4614, United States; Department of Microbiology, University of Washington, Seattle, WA 98195, United States
| | - Aaron W Puri
- Department of Chemical Engineering, Seattle, WA 98195, United States
| | - Mary E Lidstrom
- Department of Chemical Engineering, Seattle, WA 98195, United States; Department of Microbiology, University of Washington, Seattle, WA 98195, United States.
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14
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Culpepper MA, Rosenzweig AC. Structure and protein-protein interactions of methanol dehydrogenase from Methylococcus capsulatus (Bath). Biochemistry 2014; 53:6211-9. [PMID: 25185034 PMCID: PMC4188263 DOI: 10.1021/bi500850j] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
In
the initial steps of their metabolic pathway, methanotrophic
bacteria oxidize methane to methanol with methane monooxygenases (MMOs)
and methanol to formaldehyde with methanol dehydrogenases (MDHs).
Several lines of evidence suggest that the membrane-bound or particulate
MMO (pMMO) and MDH interact to form a metabolic supercomplex. To further
investigate the possible existence of such a supercomplex, native
MDH from Methylococcus capsulatus (Bath) has been
purified and characterized by size exclusion chromatography with multi-angle
light scattering and X-ray crystallography. M. capsulatus (Bath) MDH is primarily a dimer in solution, although an oligomeric
species with a molecular mass of ∼450–560 kDa forms
at higher protein concentrations. The 2.57 Å resolution crystal
structure reveals an overall fold and α2β2 dimeric architecture similar to those of other MDH structures.
In addition, biolayer interferometry studies demonstrate specific
protein–protein interactions between MDH and M. capsulatus (Bath) pMMO as well as between MDH and the truncated recombinant
periplasmic domains of M. capsulatus (Bath) pMMO
(spmoB). These interactions exhibit KD values of 833 ± 409 nM and 9.0 ± 7.7 μM, respectively.
The biochemical data combined with analysis of the crystal lattice
interactions observed in the MDH structure suggest a model in which
MDH and pMMO associate not as a discrete, stoichiometric complex but
as a larger assembly scaffolded by the intracytoplasmic membranes.
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Affiliation(s)
- Megen A Culpepper
- Departments of Molecular Biosciences and Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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Sirajuddin S, Barupala D, Helling S, Marcus K, Stemmler TL, Rosenzweig AC. Effects of zinc on particulate methane monooxygenase activity and structure. J Biol Chem 2014; 289:21782-94. [PMID: 24942740 PMCID: PMC4118136 DOI: 10.1074/jbc.m114.581363] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/11/2014] [Indexed: 11/06/2022] Open
Abstract
Particulate methane monooxygenase (pMMO) is a membrane-bound metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Zinc is a known inhibitor of pMMO, but the details of zinc binding and the mechanism of inhibition are not understood. Metal binding and activity assays on membrane-bound pMMO from Methylococcus capsulatus (Bath) reveal that zinc inhibits pMMO at two sites that are distinct from the copper active site. The 2.6 Å resolution crystal structure of Methylocystis species strain Rockwell pMMO reveals two previously undetected bound lipids, and metal soaking experiments identify likely locations for the two zinc inhibition sites. The first is the crystallographic zinc site in the pmoC subunit, and zinc binding here leads to the ordering of 10 previously unobserved residues. A second zinc site is present on the cytoplasmic side of the pmoC subunit. Parallels between these results and zinc inhibition studies of several respiratory complexes suggest that zinc might inhibit proton transfer in pMMO.
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Affiliation(s)
- Sarah Sirajuddin
- From the Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Dulmini Barupala
- the Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201, and
| | - Stefan Helling
- the Medical Proteome Center, Department of Functional Proteomics, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Katrin Marcus
- the Medical Proteome Center, Department of Functional Proteomics, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Timothy L Stemmler
- the Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201, and
| | - Amy C Rosenzweig
- From the Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208,
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16
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Keltjens JT, Pol A, Reimann J, Op den Camp HJM. PQQ-dependent methanol dehydrogenases: rare-earth elements make a difference. Appl Microbiol Biotechnol 2014; 98:6163-83. [PMID: 24816778 DOI: 10.1007/s00253-014-5766-8] [Citation(s) in RCA: 239] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 01/06/2023]
Abstract
Methanol dehydrogenase (MDH) catalyzes the first step in methanol use by methylotrophic bacteria and the second step in methane conversion by methanotrophs. Gram-negative bacteria possess an MDH with pyrroloquinoline quinone (PQQ) as its catalytic center. This MDH belongs to the broad class of eight-bladed β propeller quinoproteins, which comprise a range of other alcohol and aldehyde dehydrogenases. A well-investigated MDH is the heterotetrameric MxaFI-MDH, which is composed of two large catalytic subunits (MxaF) and two small subunits (MxaI). MxaFI-MDHs bind calcium as a cofactor that assists PQQ in catalysis. Genomic analyses indicated the existence of another MDH distantly related to the MxaFI-MDHs. Recently, several of these so-called XoxF-MDHs have been isolated. XoxF-MDHs described thus far are homodimeric proteins lacking the small subunit and possess a rare-earth element (REE) instead of calcium. The presence of such REE may confer XoxF-MDHs a superior catalytic efficiency. Moreover, XoxF-MDHs are able to oxidize methanol to formate, rather than to formaldehyde as MxaFI-MDHs do. While structures of MxaFI- and XoxF-MDH are conserved, also regarding the binding of PQQ, the accommodation of a REE requires the presence of a specific aspartate residue near the catalytic site. XoxF-MDHs containing such REE-binding motif are abundantly present in genomes of methylotrophic and methanotrophic microorganisms and also in organisms that hitherto are not known for such lifestyle. Moreover, sequence analyses suggest that XoxF-MDHs represent only a small part of putative REE-containing quinoproteins, together covering an unexploited potential of metabolic functions.
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Affiliation(s)
- Jan T Keltjens
- Department of Microbiology, Institute of Wetland and Water Research, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
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17
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Deris ZZ, Akter J, Sivanesan S, Roberts KD, Thompson PE, Nation RL, Li J, Velkov T. A secondary mode of action of polymyxins against Gram-negative bacteria involves the inhibition of NADH-quinone oxidoreductase activity. J Antibiot (Tokyo) 2014; 67:147-51. [PMID: 24169795 PMCID: PMC3943757 DOI: 10.1038/ja.2013.111] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/22/2013] [Accepted: 09/30/2013] [Indexed: 11/29/2022]
Abstract
Polymyxin B and colistin were examined for their ability to inhibit the type II NADH-quinone oxidoreductases (NDH-2) of three species of Gram-negative bacteria. Polymyxin B and colistin inhibited the NDH-2 activity in preparations from all of the isolates in a concentration-dependent manner. The mechanism of NDH-2 inhibition by polymyxin B was investigated in detail with Escherichia coli inner membrane preparations and conformed to a mixed inhibition model with respect to ubiquinone-1 and a non-competitive inhibition model with respect to NADH. These suggest that the inhibition of vital respiratory enzymes in the bacterial inner membrane represents one of the secondary modes of action for polymyxins.
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Affiliation(s)
- Zakuan Z. Deris
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Jesmin Akter
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Sivashangarie Sivanesan
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Kade D. Roberts
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences
| | | | - Roger L. Nation
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Jian Li
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Tony Velkov
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
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18
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Sun W, Gamez VM, Otero-Gonzalez L, Cho Y, Ober CK, Sierra-Alvarez R. Biodegradability, cytotoxicity, and physicochemical treatability of two novel perfluorooctane sulfonate-free photoacid generators. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2013; 64:187-197. [PMID: 23104522 DOI: 10.1007/s00244-012-9822-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 10/01/2012] [Indexed: 06/01/2023]
Abstract
There is a need for effective, environmentally compatible photoacid generators (PAGs) for application in photolithography for microelectronic device fabrication. Perfluoroalkyl sulfonates (PFAS) used in conventional PAG formulations, such as perfluorooctane sulfonate (PFOS), are under increasing scrutiny due to their widespread environmental distribution and toxicity. Recently, two new PFAS-free, PAG anions with semifluorinated sulfonate anions containing biomolecules (γ-butyrolactone or D-glucose groups) were successfully applied as PAGs. In this study, the biodegradation potential, cytotoxicity, and physicochemical treatability of the new PAG anions was evaluated. PFOS and perfluorobutane sulfonate (PFBS) were used as reference materials in all of the assays. The new PAGs were susceptible to partial degradation by microorganisms in aerobic activated sludge, and these were also readily removed by chemical oxidative treatment with Fenton's reagent [H(2)O(2)/Fe(II)]. In contrast, the compounds were resistant to microbial and chemical attack under reductive conditions as indicated by the low removal efficiencies observed with anaerobic biodegradation assays and chemical assays with zero-valent iron, respectively. The enhanced biodegradation potential and treatability make of the new PAGs attractive materials to resolve current issues related to the lithographic performance and environmental concerns.
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Affiliation(s)
- Wenjie Sun
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, AZ 85721, USA.
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19
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Abstract
Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria, organisms that live on methane gas as their sole carbon source. Understanding pMMO function has important implications for bioremediation applications and for the development of new, environmentally friendly catalysts for the direct conversion of methane to methanol. Crystal structures of pMMOs from three different methanotrophs reveal a trimeric architecture, consisting of three copies each of the pmoB, pmoA, and pmoC subunits. There are three distinct metal centers in each protomer of the trimer, mononuclear and dinuclear copper sites in the periplasmic regions of pmoB and a mononuclear site within the membrane that can be occupied by copper or zinc. Various models for the pMMO active site have been proposed within these structural constraints, including dicopper, tricopper, and diiron centers. Biochemical and spectroscopic data on pMMO and recombinant soluble fragments, denoted spmoB proteins, indicate that the active site involves copper and is located at the site of the dicopper center in the pmoB subunit. Initial spectroscopic evidence for O(2) binding at this site has been obtained. Despite these findings, questions remain about the active site identity and nuclearity and will be the focus of future studies.
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Affiliation(s)
- Megen A. Culpepper
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA
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20
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Vajrala N, Sayavedra-Soto LA, Bottomley PJ, Arp DJ. Role of a Fur homolog in iron metabolism in Nitrosomonas europaea. BMC Microbiol 2011; 11:37. [PMID: 21338516 PMCID: PMC3050691 DOI: 10.1186/1471-2180-11-37] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 02/21/2011] [Indexed: 11/24/2022] Open
Abstract
Background In response to environmental iron concentrations, many bacteria coordinately regulate transcription of genes involved in iron acquisition via the ferric uptake regulation (Fur) system. The genome of Nitrosomonas europaea, an ammonia-oxidizing bacterium, carries three genes (NE0616, NE0730 and NE1722) encoding proteins belonging to Fur family. Results Of the three N. europaea fur homologs, only the Fur homolog encoded by gene NE0616 complemented the Escherichia coli H1780 fur mutant. A N. europaea fur:kanP mutant strain was created by insertion of kanamycin-resistance cassette in the promoter region of NE0616 fur homolog. The total cellular iron contents of the fur:kanP mutant strain increased by 1.5-fold compared to wild type when grown in Fe-replete media. Relative to the wild type, the fur:kanP mutant exhibited increased sensitivity to iron at or above 500 μM concentrations. Unlike the wild type, the fur:kanP mutant was capable of utilizing iron-bound ferrioxamine without any lag phase and showed over expression of several outer membrane TonB-dependent receptor proteins irrespective of Fe availability. Conclusions Our studies have clearly indicated a role in Fe regulation by the Fur protein encoded by N. europaea NE0616 gene. Additional studies are required to fully delineate role of this fur homolog.
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Affiliation(s)
- Neeraja Vajrala
- Department of Botany and Plant Pathology, 2082 Cordley, Oregon State University, Corvallis, OR 97331, USA
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21
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Abstract
The anaerobic acetogenic bacterium Acetobacterium woodii carries out a unique type of Na(+)-motive, anaerobic respiration with caffeate as electron acceptor, termed "caffeate respiration." Central, and so far the only identified membrane-bound reaction in this respiration pathway, is a ferredoxin:NAD(+) oxidoreductase (Fno) activity. Here we show that inverted membrane vesicles of A. woodii couple electron transfer from reduced ferredoxin to NAD(+) with the transport of Na(+) from the outside into the lumen of the vesicles. Na(+) transport was electrogenic, and accumulation was inhibited by sodium ionophores but not protonophores, demonstrating a direct coupling of Fno activity to Na(+) transport. Results from inhibitor studies are consistent with the hypothesis that Fno activity coupled to Na(+) translocation is catalyzed by the Rnf complex, a membrane-bound, iron-sulfur and flavin-containing electron transport complex encoded by many bacterial and some archaeal genomes. Fno is a unique type of primary Na(+) pump and represents an early evolutionary mechanism of energy conservation that expands the redox range known to support life. In addition, it explains the lifestyle of many anaerobic bacteria and gives a mechanistic explanation for the enigma of the energetic driving force for the endergonic reduction of ferredoxin with NADH plus H(+) as reductant in a number of aerobic bacteria.
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22
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Huizinga DH, Denton R, Koehler KG, Tomasello A, Wood L, Sen SE, Crowell DN. Farnesylcysteine lyase is involved in negative regulation of abscisic acid signaling in Arabidopsis. MOLECULAR PLANT 2010; 3:143-55. [PMID: 19969520 PMCID: PMC2807925 DOI: 10.1093/mp/ssp091] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 09/22/2009] [Indexed: 05/21/2023]
Abstract
The Arabidopsis FCLY gene encodes a specific farnesylcysteine (FC) lyase, which is responsible for the oxidative metabolism of FC to farnesal and cysteine. In addition, fcly mutants with quantitative decreases in FC lyase activity exhibit an enhanced response to ABA. However, the enzymological properties of the FCLY-encoded enzyme and its precise role in ABA signaling remain unclear. Here, we show that recombinant Arabidopsis FC lyase expressed in insect cells exhibits high selectivity for FC as a substrate and requires FAD and molecular oxygen for activity. Arabidopsis FC lyase is also shown to undergo post-translational N-glycosylation. FC, which is a competitive inhibitor of isoprenylcysteine methyltransferase (ICMT), accumulates in fcly mutants. Moreover, the enhanced response of fcly mutants to ABA is reversed by ICMT overexpression. These observations support the hypothesis that the ABA hypersensitive phenotype of fcly plants is the result of FC accumulation and inhibition of ICMT.
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Affiliation(s)
- David H. Huizinga
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 West Michigan Street, Indianapolis, IN 46202, USA
| | - Ryan Denton
- Department of Chemistry, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, IN 46202, USA
| | - Kelly G. Koehler
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 West Michigan Street, Indianapolis, IN 46202, USA
| | - Ashley Tomasello
- Department of Chemistry, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628, USA
| | - Lyndsay Wood
- Department of Chemistry, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628, USA
| | - Stephanie E. Sen
- Department of Chemistry, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628, USA
| | - Dring N. Crowell
- Department of Biological Sciences, Idaho State University, 650 Memorial Drive, Pocatello, ID 83209, USA
- To whom correspondence should be addressed. E-mail , fax 208-282-4570, tel. 208-282-3171
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23
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Epoxypropane biosynthesis by whole cell suspension of methanol-growth Methylosinus trichosporium IMV 3011. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0225-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Abstract
Methanotrophic bacteria oxidize methane to methanol in the first step of their metabolic pathway. Two forms of methane monooxygenase (MMO) enzymes catalyze this reaction: soluble MMO (sMMO) and membrane-bound or particulate MMO (pMMO). pMMO is expressed when copper is available, and its active site is believed to contain copper. Whereas sMMO is well characterized, most aspects of pMMO biochemistry remain unknown and somewhat controversial. This review emphasizes advances in the past two to three years related to pMMO and to copper uptake and copper-dependent regulation in methanotrophs. The pMMO metal centers have been characterized spectroscopically, and the first pMMO crystal structure has been determined. Significant effort has been devoted to improving in vitro pMMO activity. Proteins involved in sMMO regulation and additional copper-regulated proteins have been identified, and the Methylococcus capsulatus (Bath) genome has been sequenced. Finally, methanobactin (mb), a small copper chelator proposed to facilitate copper uptake, has been characterized.
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Affiliation(s)
- Amanda S Hakemian
- Department of Biochemistry, Northwestern University, Evanston, Illinois 60208, USA.
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25
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Gopalakrishnan S, Subbarao GV, Nakahara K, Yoshihashi T, Ito O, Maeda I, Ono H, Yoshida M. Nitrification Inhibitors from the root tissues of Brachiaria humidicola, a tropical grass. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2007; 55:1385-8. [PMID: 17243702 DOI: 10.1021/jf062593o] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Nitrification inhibitory activity was found in root tissue extracts of Brachiaria humidicola, a tropical pasture grass. Two active inhibitory compounds were isolated by activity-guided fractionation, using recombinant Nitrosomonas europaea containing luxAB genes derived from the bioluminescent marine gram-negative bacterium Vibrio harveyi. The compounds were identified as methyl-p-coumarate and methyl ferulate, respectively. Their nitrification inhibitory properties were confirmed in chemically synthesized preparations of each. The IC50 values of chemically synthesized preparations were 19.5 and 4.4 microM, respectively. The ethyl, propyl, and butyl esters of p-coumaric and ferulic acids inhibited nitrification, whereas the free acid forms did not show inhibitory activity.
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Affiliation(s)
- Subramaniam Gopalakrishnan
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
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26
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Rappert S, Li R, Kokova M, Antholz M, Nagorny S, Francke W, Müller R. Degradation of 2,5-dimethylpyrazine by Rhodococcus erythropolis strain DP-45 isolated from a waste gas treatment plant of a fishmeal processing company. Biodegradation 2006; 18:585-96. [PMID: 17120096 DOI: 10.1007/s10532-006-9091-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Accepted: 10/31/2006] [Indexed: 11/30/2022]
Abstract
A bacterium, strain DP-45, capable of degrading 2,5-dimethylpyrazine (2,5-DMP) was isolated and identified as Rhodococcus erythropolis. The strain also grew on many other pyrazines found in the waste gases of food industries, like 2,3-dimethylpyrazine (2,3-DMP), 2,6-dimethylpyrazine (2,6-DMP), 2-ethyl-5(6)-dimethylpyrazine (EMP), 2-ethylpyrazine (EP), 2-methylpyrazine (MP), and 2,3,5-trimethylpyrazine (TMP). The strain utilized 2,5-DMP as sole source of carbon and nitrogen and grew optimally at 25 degrees C with a doubling time of 7.6 h. The degradation of 2,5-DMP was accompanied by the growth of the strain and by the accumulation of a first intermediate, identified as 2-hydroxy-3,6-dimethylpyrazine (HDMP). The disappearance of HDMP was accompanied by the release of ammonium into the medium. No other metabolite was detected. The degradation of 2,5-DMP and HDMP by strain DP-45 required molecular oxygen. The expression of the first enzyme in the pathway was induced by 2,5-DMP and HDMP whereas the second enzyme was constitutively expressed. The activity of the first enzyme was inhibited by diphenyliodonium (DPI), a flavoprotein inhibitor, methimazole, a competitive inhibitor of flavin-containing monooxygenases, and by cytochrome P450 inhibitors, 1-aminobenzotriazole (ABT) and phenylhydrazine (PHZ). The activity of the second enzyme was inhibited by DPI, ABT, and PHZ. Sodium tungstate, a specific antagonist of molybdate, had no influence on growth and consumption of 2,5-DMP by strain DP-45. These results led us to propose that a flavin-dependent monooxygenase or a cytochrome P450-dependent monooxygenase rather than a molybdenum hydroxylase catalyzed the initial hydroxylation step and that a cytochrome P450 enzyme is responsible for the transformation of HDMP in the second step.
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Affiliation(s)
- Sugima Rappert
- Institute of Technical Biocatalysis, Technical University Hamburg-Harburg, Denickestr. 15, 21071 Hamburg, Germany
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27
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Wei X, Vajrala N, Hauser L, Sayavedra-Soto LA, Arp DJ. Iron nutrition and physiological responses to iron stress in Nitrosomonas europaea. Arch Microbiol 2006; 186:107-18. [PMID: 16802173 DOI: 10.1007/s00203-006-0126-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Revised: 04/11/2006] [Accepted: 05/18/2006] [Indexed: 10/24/2022]
Abstract
Nitrosomonas europaea, as an ammonia-oxidizing bacterium, has a high Fe requirement and has 90 genes dedicated to Fe acquisition. Under Fe-limiting conditions (0.2 microM Fe), N. europaea was able to assimilate up to 70% of the available Fe in the medium even though it is unable to produce siderophores. Addition of exogenous siderophores to Fe-limited medium increased growth (final cell mass). Fe-limited cells had lower heme and cellular Fe contents, reduced membrane layers, and lower NH3- and NH2OH-dependent O2 consumption activities than Fe-replete cells. Fe acquisition-related proteins, such as a number of TonB-dependent Fe-siderophore receptors for ferrichrome and enterobactin and diffusion protein OmpC, were expressed to higher levels under Fe limitation, providing biochemical evidence for adaptation of N. europaea to Fe-limited conditions.
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Affiliation(s)
- Xueming Wei
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-2902, USA
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28
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Therade-Matharan S, Laemmel E, Carpentier S, Obata Y, Levade T, Duranteau J, Vicaut E. Reactive oxygen species production by mitochondria in endothelial cells exposed to reoxygenation after hypoxia and glucose depletion is mediated by ceramide. Am J Physiol Regul Integr Comp Physiol 2005; 289:R1756-62. [PMID: 16278342 DOI: 10.1152/ajpregu.00480.2004] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In endothelium, reoxygenation after hypoxia (H/R) has been shown to induce production of reactive oxygen species (ROS) by complex III of the mitochondrial respiratory chain. The purpose of the present study was to test the involvement of ceramide in this phenomenon. Human umbilical vein endothelial cells underwent 2 h of hypoxia (Po2, ∼20 mmHg) without glucose and 1 h of reoxygenation (Po2, ∼120 mmHg) with glucose. ROS production was measured by the fluorescent marker 2′,7′-dichlorodihydrofluorescein diacetate, and cell death by propidium iodide. We showed that 1) after 1 h of reoxygenation, fluorescence had risen and that ROS production was inhibited by desipramine, an inhibitor of sphingomyelinase, an enzyme responsible for ceramide production (126 ± 7% vs. 48 ± 12%, P < 0.05); 2) administration of ceramide ( N-acetylsphingosine) per se (i.e., in the absence of H/R) induced ROS production (65 ± 3%), which was inhibited by complex III inhibitor: antimycin A (24 ± 3%, P < 0.0001), or stigmatellin (31 ± 2%, P < 0.0001); 3) hypoxia/reoxygenation-induced ROS production was not affected by either ceramide-activated protein kinase inhibitor dimethyl aminopurine or mitochondrial permeability transition inhibitor cyclosporin A but was significantly inhibited by the antiapoptotic protein Bcl-2 (82 ± 8%, P < 0.05); 4) ceramide-induced ROS production was also inhibited by Bcl-2 (41 ± 4%, P < 0.0001). These results demonstrate that in endothelial cells submitted to hypoxia and glucose depletion followed by reoxygenation with glucose, the pathway implicated in mitochondrial complex III ROS production is ceramide dependent and is decreased by the antiapoptotic protein Bcl-2.
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Affiliation(s)
- S Therade-Matharan
- Laboratoire d'Etude de la Microcirculation, Faculté de Médecine, Université Paris 7 10, avenue de Verdun, 75010 Paris, France
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29
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Choi DW, Antholine WE, Do YS, Semrau JD, Kisting CJ, Kunz RC, Campbell D, Rao V, Hartsel SC, DiSpirito AA. Effect of methanobactin on the activity and electron paramagnetic resonance spectra of the membrane-associated methane monooxygenase in Methylococcus capsulatus Bath. Microbiology (Reading) 2005; 151:3417-3426. [PMID: 16207923 DOI: 10.1099/mic.0.28169-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Improvements in the purification of methanobactin (mb) from eitherMethylosinus trichosporiumOB3bTorMethylococcus capsulatusBath resulted in preparations that stimulated methane-oxidation activity in both whole-cell and cell-free fractions ofMethylococcus capsulatusBath expressing the membrane-associated methane monooxygenase (pMMO). By using washed membrane factions with pMMO activities in the 290 nmol propylene oxidized min−1(mg protein)−1range, activities approaching 400 nmol propylene oxidized min−1(mg protein)−1were commonly observed following addition of copper-containing mb (Cu–mb), which represented 50–75 % of the total whole-cell activity. The stimulation of methane-oxidation activity by Cu–mb was similar to or greater than that observed with equimolar concentrations of Cu(II), without the inhibitory effects observed with high copper concentrations. Stimulation of pMMO activity was not observed with copper-free mb, nor was it observed when the copper-to-mb ratio was <0·5 Cu atoms per mb. The electron paramagnetic resonance (EPR) spectra of mb differed depending on the copper-to-mb ratio. At copper-to-mb ratios of <0·4 Cu(II) per mb, Cu(II) addition to mb showed an initial coordination by both sulfur and nitrogen, followed by reduction to Cu(I) in <2 min. At Cu(II)-to-mb ratios between 0·4 and 0·9 Cu(II) per mb, the intensity of the Cu(II) signal in EPR spectra was more representative of the Cu(II) added and indicated more nitrogen coordination. The EPR spectral properties of mb and pMMO were also examined in the washed membrane fraction following the addition of Cu(II), mb and Cu–mb in the presence or absence of reductants (NADH or duroquinol) and substrates (CH4and/or O2). The results indicated that Cu–mb increased electron flow to the pMMO, increased the free radical formed following the addition of O2and decreased the residual free radical following the addition of O2plus CH4. The increase in pMMO activity and EPR spectral changes to the pMMO following Cu–mb addition represent the first positive evidence of interactions between the pMMO and Cu–mb.
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Affiliation(s)
- Dong W Choi
- Department of Biochemistry, Biophysics and Molecular Biology, 4164 Molecular Biology Building, Iowa State University, Ames, IA 50011-3211, USA
| | - William E Antholine
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Young S Do
- Department of Biochemistry, Biophysics and Molecular Biology, 4164 Molecular Biology Building, Iowa State University, Ames, IA 50011-3211, USA
| | - Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
| | - Clint J Kisting
- Department of Biochemistry, Biophysics and Molecular Biology, 4164 Molecular Biology Building, Iowa State University, Ames, IA 50011-3211, USA
| | - Ryan C Kunz
- Department of Biochemistry, Biophysics and Molecular Biology, 4164 Molecular Biology Building, Iowa State University, Ames, IA 50011-3211, USA
| | - Damon Campbell
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI 54702, USA
| | - Vinay Rao
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI 54702, USA
| | - Scott C Hartsel
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI 54702, USA
| | - Alan A DiSpirito
- Department of Biochemistry, Biophysics and Molecular Biology, 4164 Molecular Biology Building, Iowa State University, Ames, IA 50011-3211, USA
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Therade-Matharan S, Laemmel E, Duranteau J, Vicaut E. Reoxygenation after hypoxia and glucose depletion causes reactive oxygen species production by mitochondria in HUVEC. Am J Physiol Regul Integr Comp Physiol 2004; 287:R1037-43. [PMID: 15205181 DOI: 10.1152/ajpregu.00048.2004] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In hemorrhagic shock, local hypoxia is present and followed by reoxygenation during the therapeutic process. In endothelium, reactive oxygen species (ROS) have been identified as a cause of inflammatory reactions and tissular lesions in ischemic territory during reoxygenation. This study was designed to identify the enzymatic mechanisms of ROS formation during reoxygenation after hypoxia. Because severe shock, in vivo, can affect both O2and nutriments, we combined hypoxia at a level close to that found in terminal vessels during shock, with glucose depletion, which induces a relevant additional stress. Human umbilical vein endothelial cells (HUVEC) underwent 2 h of hypoxia (Po2∼20 mmHg) without glucose and 1 h of reoxygenation (Po2∼120 mmHg) with glucose. ROS production was measured by the fluorescent marker 2′,7′-dichlorodihydrofluorescein diacetate, and cell death by propidium iodide. After 1 h of reoxygenation, fluorescence had risen by 143 ± 17%. Cell death was equal to 8.6 ± 2.4%. Antimycin A and stigmatellin, which inhibits the type III mitochondrial respiratory chain complex, reduced ROS production to values of 61 ± 10 and 59 ± 7%, respectively, but inhibitors of other chain complexes did not affect it. In addition, the increase in fluorescence was not affected by inhibition of NADPH oxidase, xanthine oxidase, NOS, cyclooxygenase, cytochrome P-450 monooxygenase, or monoamine oxidase. We did not observe any increase in cell death. These results show that, in HUVEC, mitochondria are responsible for ROS production after hypoxia and reoxygenation and suggest that a ROS release site is activated in the cytochrome b of the type III respiratory chain complex.
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Affiliation(s)
- S Therade-Matharan
- Laboratoire d'Etude de la Microcirculation, Université Paris 7, 10, Ave. de Verdun, 75010 Paris, France
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