1
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Wang J, Wan L, Guo X, Wang X, Zhao ZK. Competitive inhibition of a non-natural cofactor dependent formaldehyde dehydrogenase by imidazole. Biotechnol Lett 2023; 45:679-687. [PMID: 37071383 DOI: 10.1007/s10529-023-03372-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/18/2023] [Accepted: 03/31/2023] [Indexed: 04/19/2023]
Abstract
OBJECTIVES To better understand the unique inhibitory behavior of a non-natural cofactor preferred formaldehyde dehydrogenase (FalDH) mutant 9B2. RESULTS We described our serendipitous observation that 9B2 was reversibly inhibited by residual imidazole introduced during protein preparation, while the wild-type enzyme was not sensitive to imidazole. Kinetic analysis showed that imidazole was a competitive inhibitor of formaldehyde with a Ki of 16 μM and an uncompetitive inhibitor of Nicotinamide Cytosine Dinucleotide for 9B2, indicating that formaldehyde and imidazole were combined in the same position. Molecular docking results of 9B2 showed that imidazole could favorably bind very close to the nicotinamide moiety of the cofactor, where formaldehyde was expected to reside for catalysis, which was in line with a competitive inhibition. CONCLUSION The mutant 9B2 can be competitively inhibited by imidazole, suggesting that cautions should be taken to evaluate activities as protein mutants might attain unexpected sensitivity to a component in buffers for purification or activity assays.
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Affiliation(s)
- Junting Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Wan
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojia Guo
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xueying Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Zongbao K Zhao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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2
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Wang L, Yan L, Ye L, Chen J, Li Y, Zhang Q, Jing C. Identification and Characterization of a Au(III) Reductase from Erwinia sp. IMH. JACS AU 2022; 2:1435-1442. [PMID: 35783184 PMCID: PMC9241155 DOI: 10.1021/jacsau.2c00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms contribute to the formation of secondary gold (Au) deposits through enzymatic reduction of Au(III) to Au(0). However, the enzyme that catalyzes the reduction of Au(III) remains enigmatic. Here, we identified and characterized a previously unknown Au reductase (GolR) in the cytoplasm of Erwinia sp. IMH. The expression of golR was strongly up-regulated in response to increasing Au(III) concentrations and exposure time. Mutant with in-frame deletion of golR was incapable of reducing Au(III), and the capability was rescued by reintroducing wild-type golR into the mutant strain. The Au(III) reduction was determined to occur in the cytoplasmic space by comparing the TEM images of the wild-type, mutant, and complemented strains. In vitro assays of the purified GolR protein confirmed its ability to reduce Au(III) to Au nanoparticles. Molecular dynamic simulations demonstrated that the hydrophobic cavity of GolR may selectively bind AuCl2(OH)2 -, the predominant auric chloride species at neutral pH. Density functional theory calculations revealed that AuCl2(OH)2 - may be coordinated at the Fe-containing active site of GolR and is probably reduced via three consecutive proton-coupled electron transfer processes. The new class of reductase, GolR, opens the chapter for the mechanistic understanding of Au(III) bioreduction.
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Affiliation(s)
- Liying Wang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, China
| | - Li Yan
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, China
| | - Li Ye
- School
of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Jinfeng Chen
- Environment
Research Institute, Shandong University, Qingdao 266237, China
| | - Yanwei Li
- Environment
Research Institute, Shandong University, Qingdao 266237, China
| | - Qingzhu Zhang
- Environment
Research Institute, Shandong University, Qingdao 266237, China
| | - Chuanyong Jing
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, China
- School
of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
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3
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Wang J, Guo X, Wan L, Liu Y, Xue H, Zhao ZK. Engineering formaldehyde dehydrogenase from Pseudomonas putida to favor nicotinamide cytosine dinucleotide. Chembiochem 2022; 23:e202100697. [PMID: 35146861 DOI: 10.1002/cbic.202100697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/09/2022] [Indexed: 11/05/2022]
Abstract
The enzyme formaldehyde dehydrogenase (FalDH) from Pseudomonas putida is of particular interest for biotechnological applications as it catalyses the oxidation of formaldehyde independent of glutathione. However, the consumption of a stoichiometric amount of nicotinamide adenine dinucleotide (NAD) can be challenging at the metabolic level as this may affect many other NAD-linked processes. A potential solution is to engineer FalDH to utilize non-natural cofactors. Here we devised FalDH variants to favor nicotinamide cytosine dinucleotide (NCD) by structure-guided modification of the binding pocket for the adenine moiety of NAD. Several mutants were obtained and the best one FalDH 9B2 had over 150-fold higher preference for NCD than NAD. Molecular docking analysis indicated that the cofactor binding pocket shrinked to better fit NCD, a smaller-sized cofactor. FalDH 9B2 together with other NCD-linked enzymes offer opportunities to assemble orthogonal pathways for biological conversion of C1 molecules.
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Affiliation(s)
- Junting Wang
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Xiaojia Guo
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Li Wan
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Yuxue Liu
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Haizhao Xue
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Zongbao Kent Zhao
- Dalian Institute of Chemical Physics, Division of Biotechnology, 457 Zhongshan Road, 116023, Dalian, CHINA
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4
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Singh P, Srivastava R. Utilization of bio-inspired catalyst for CO2 reduction into green fuels: Recent advancement and future perspectives. J CO2 UTIL 2021. [DOI: 10.1016/j.jcou.2021.101748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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5
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Suzuki Y, Otsuka Y, Araki T, Kamimura N, Masai E, Nakamura M, Katayama Y. Lignin valorization through efficient microbial production of β-ketoadipate from industrial black liquor. BIORESOURCE TECHNOLOGY 2021; 337:125489. [PMID: 34320768 DOI: 10.1016/j.biortech.2021.125489] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Vanillin and vanillate are the major lignin-derived aromatic compounds produced through the alkaline oxidation of softwood lignin. Because the production of higher-value added chemicals from these compounds is essential for lignin valorization, the microbial production of β-ketoadipate, a promising raw material for the synthesis of novel nylons, from lignin was considered. Pseudomonas putida KT2440 was engineered to convert vanillin and vanillate to β-ketoadipate. By examining the culture conditions with an initial culture volume of 1 L, the engineered strain completely converted 25 g of vanillin and 25 g of vanillate and produced approximately 23 g of β-ketoadipate from each of them with a yield of 93% or higher. Furthermore, this strain showed the ability to efficiently produce β-ketoadipate from softwood lignin extracts in black liquor, a byproduct of pulp production. These results suggest that the production of β-ketoadipate from industrial black liquor is highly feasible for substantial lignin valorization.
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Affiliation(s)
- Yuzo Suzuki
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687 Japan.
| | - Yuichiro Otsuka
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687 Japan
| | - Takuma Araki
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687 Japan
| | - Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Masaya Nakamura
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687 Japan
| | - Yoshihiro Katayama
- Bio-based Solution Division, Kantechs Co. Ltd., Bunkyo, Tokyo 112-0004, Japan
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6
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Henson WR, Meyers AW, Jayakody LN, DeCapite A, Black BA, Michener WE, Johnson CW, Beckham GT. Biological upgrading of pyrolysis-derived wastewater: Engineering Pseudomonas putida for alkylphenol, furfural, and acetone catabolism and (methyl)muconic acid production. Metab Eng 2021; 68:14-25. [PMID: 34438073 DOI: 10.1016/j.ymben.2021.08.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 10/20/2022]
Abstract
While biomass-derived carbohydrates have been predominant substrates for biological production of renewable fuels, chemicals, and materials, organic waste streams are growing in prominence as potential alternative feedstocks to improve the sustainability of manufacturing processes. Catalytic fast pyrolysis (CFP) is a promising approach to generate biofuels from lignocellulosic biomass, but it generates a complex, carbon-rich, and toxic wastewater stream that is challenging to process catalytically but could be biologically upgraded to valuable co-products. In this work, we implemented modular, heterologous catabolic pathways in the Pseudomonas putida KT2440-derived EM42 strain along with the overexpression of native toxicity tolerance machinery to enable utilization of 89% (w/w) of carbon in CFP wastewater. The dmp monooxygenase and meta-cleavage pathway from Pseudomonas putida CF600 were constitutively expressed to enable utilization of phenol, cresols, 2- and 3-ethyl phenol, and methyl catechols, and the native chaperones clpB, groES, and groEL were overexpressed to improve toxicity tolerance to diverse aromatic substrates. Next, heterologous furfural and acetone utilization pathways were incorporated, and a native alcohol dehydrogenase was overexpressed to improve methanol utilization, generating reducing equivalents. All pathways (encoded by genes totaling ~30 kilobases of DNA) were combined into a single strain that can catabolize a mock CFP wastewater stream as a sole carbon source. Further engineering enabled conversion of all aromatic compounds in the mock wastewater stream to (methyl)muconates with a ~90% (mol/mol) yield. Biological upgrading of CFP wastewater as outlined in this work provides a roadmap for future applications in valorizing other heterogeneous waste streams.
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Affiliation(s)
- William R Henson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Alex W Meyers
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Lahiru N Jayakody
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Annette DeCapite
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Brenna A Black
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - William E Michener
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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7
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Imoto S, Yonemitsu H, Totsui N, Kishimoto N. Purification and characterization of formaldehyde dismutases of Methylobacterium sp. FD1. Biosci Biotechnol Biochem 2020; 84:1444-1450. [PMID: 32281473 DOI: 10.1080/09168451.2020.1751582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In the present study, we purified and characterized three formaldehyde dismutases (Fdms) (EC 1.2.98.1) (Fdm1, Fdm2, and Fdm3) of Methylobacterium sp. FD1. These Fdms (with His-tag) were produced in the recombinant E. coli and purified by immobilized metal affinity chromatography from the E. coli extracts. In each of the three Fdms, the enzyme-bound coenzyme was nicotinamide adenine dinucleotide (NAD(H)) and the enzyme-bound metal was zinc. The quaternary structures of these Fdms were estimated as homotetrameric. The optimal pHs and temperatures of Fdm1, Fdm2, and Fdm3 were approximately 6.5, 6.0, and 6.0, and 35°C, 25°C, and 30°C, respectively. The Km values of Fdm1, Fdm2, and Fdm3 were 621, 865, and 414 mM, respectively. These results were similar to the properties of already-known Fdms. However, each of the Fdms of FD1 had methanol:p-nitroso-N,N-dimethylaniline oxidoreductase activity that is not found in already-known Fdms.
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Affiliation(s)
- Seiji Imoto
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College , Wakayama, Japan
| | - Hiroshi Yonemitsu
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College , Wakayama, Japan
| | - Noriki Totsui
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College , Wakayama, Japan
| | - Noboru Kishimoto
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College , Wakayama, Japan
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8
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Ellis GA, Klein WP, Lasarte-Aragonés G, Thakur M, Walper SA, Medintz IL. Artificial Multienzyme Scaffolds: Pursuing in Vitro Substrate Channeling with an Overview of Current Progress. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02413] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gregory A. Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - William P. Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20001, United States
| | - Guillermo Lasarte-Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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9
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Yonemitsu H, Kikuchi Y. Biodegradation of high concentrations of formaldehyde using Escherichia coli expressing the formaldehyde dismutase gene of Methylobacterium sp. FD1. Biosci Biotechnol Biochem 2018; 82:49-56. [DOI: 10.1080/09168451.2017.1397497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Abstract
In the present study, formaldehyde dismutase from Methylobacterium sp. FD1 was partially purified and analyzed by nanoLC–MS/MS; it was then cloned from the genomic DNA of FD1 by PCR. The open reading frame of the formaldehyde dismutase gene of FD1 was estimated to be 1203 bp in length. The molecular weight and pI of formaldehyde dismutase (401 aa), as deduced from the FD1 gene, were calculated at 42,877.32 and 6.56, respectively. NAD(H)-binding residues and zinc-binding residues were found in the amino acid sequence of the deduced formaldehyde dismutase of FD1 by BLAST search. The resting Escherichia coli cells that were transformed with the FD1 formaldehyde dismutase gene degraded high concentrations of formaldehyde and produced formic acid and methanol that were molar equivalents of one-half of the degraded formaldehyde. The lyophilized cells of the recombinant E. coli also degraded high concentrations of formaldehyde.
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Affiliation(s)
- Hiroshi Yonemitsu
- Department of Applied Chemistry and Biochemistry, Wakayama College, National Institute of Technology, Wakayama, Japan
| | - Yuta Kikuchi
- Department of Applied Chemistry and Biochemistry, Wakayama College, National Institute of Technology, Wakayama, Japan
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10
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Transcriptomic Analysis of 3-Hydroxypropanoic Acid Stress in Escherichia coli. Appl Biochem Biotechnol 2015; 178:527-43. [PMID: 26472673 DOI: 10.1007/s12010-015-1892-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/08/2015] [Indexed: 10/22/2022]
Abstract
The stress response of Escherichia coli to 3-hydroxypropanoic acid (3-HP) was elucidated through global transcriptomic analysis. Around 375 genes showed difference of more than 2-fold in 3-HP-treated samples. Further analysis revealed that the toxicity effect of 3-HP was due to the cation and anion components of this acid and some effects-specific to 3-HP. Genes related to the oxidative stress, DNA protection, and repair were upregulated in treated cells due to the lowered cytoplasmic pH caused by accumulated cations. 3-HP-treated E. coli used the arginine acid tolerance mechanism to increase the cytoplasmic pH. Additionally, the anion effects were manifested as imbalance in the osmotic pressure. Analysis of top ten highly upregulated genes suggests the formation of 3-hydroxypropionaldehyde under 3-HP stress. The transcriptomic analysis shed light on the global genetic reprogramming due to 3-HP stress and suggests strategies for increasing the tolerance of E. coli toward 3-HP.
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11
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Enhancement of Thermal Stabilization of Formaldehyde Dehydrogenase fromPseudomonas putidaby Directed Evolution. Biosci Biotechnol Biochem 2014; 74:1462-5. [DOI: 10.1271/bbb.100026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Draft Genome Sequence of the Formaldehyde-Resistant Fungus Byssochlamys spectabilis No. 5 (Anamorph Paecilomyces variotii No. 5) (NBRC109023). GENOME ANNOUNCEMENTS 2014; 2:2/1/e01162-13. [PMID: 24407650 PMCID: PMC3886963 DOI: 10.1128/genomea.01162-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Byssochlamys spectabilis no. 5 (anamorph Paecilomyces variotii no. 5) (NBRC109023) was isolated from a soil sample in 2001 in Kumamoto Prefecture, Japan. This fungus is highly resistant to formaldehyde. Here, we report a draft genome sequence of P. variotii no. 5; this draft was produced with the intent of investigating the mechanism of formaldehyde resistance. This is the first report of the genome sequence of any Paecilomyces species.
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13
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Expression, purification, and characterization of formaldehyde dehydrogenase from Pseudomonas aeruginosa. Protein Expr Purif 2013; 92:208-13. [PMID: 24125754 DOI: 10.1016/j.pep.2013.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 09/26/2013] [Accepted: 09/30/2013] [Indexed: 11/21/2022]
Abstract
As a member of zinc-containing medium-chain alcohol dehydrogenase family, formaldehyde dehydrogenase (FDH) can oxidize toxic formaldehyde to less active formate with NAD(+) as a cofactor and exists in both prokaryotes and eukaryotes. Most FDHs are well known to be glutathione-dependent in the catalysis of formaldehyde oxidation, but the enzyme from Pseudomonas putida is an exception, which is independent of glutathione. To identify novel glutathione-independent FDHs from other bacterial strains and facilitate the corresponding structural and enzymatic studies, high-level soluble expression and efficient purification of these enzymes need to be achieved. Here, we present molecular cloning, expression, and purification of the FDH from Pseudomonas aeruginosa, which is a Gram-negative pathogenic bacterium causing opportunistic human infection. The FDH of P. aeruginosa shows high sequence identity (87.97%) with that of P. putida. Our results indicated that coexpression with molecular chaperones GroES, GroEL, and Tig has significantly attenuated inclusion body formation and improved the solubility of the recombinant FDH in Escherichiacoli cells. A purification protocol including three chromatographic steps was also established to isolate the recombinant FDH to homogeneity with a yield of ∼3.2 mg from 1L of cell culture. The recombinant P. aeruginosa FDH was properly folded and biologically functional, as demonstrated by the mass spectrometric, crystallographic, and enzymatic characterizations of the purified proteins.
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14
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Liao Y, Chen S, Wang D, Zhang W, Wang S, Ding J, Wang Y, Cai L, Ran X, Wang X, Zhu H. Structure of formaldehyde dehydrogenase from Pseudomonas aeruginosa: the binary complex with the cofactor NAD+. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:967-72. [PMID: 23989142 PMCID: PMC3758142 DOI: 10.1107/s174430911302160x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/02/2013] [Indexed: 11/11/2022]
Abstract
Formaldehyde dehydrogenase (FDH) is a member of the zinc-containing medium-chain alcohol dehydrogenase family which oxidizes toxic formaldehyde to formate using NAD(+) as an electron carrier. Three-dimensional structures have been reported for FDHs from several different species. Most FDHs are dependent on glutathione for catalysis, but the enzyme from Pseudomonas putida is an exception. In this structural communication, the recombinant production, crystallization and X-ray structure determination at 2.7 Å resolution of FDH from P. aeruginosa are described. Both the tetrameric assembly and the NAD(+)-binding mode of P. aeruginosa FDH are similar to those of P. putida FDH, which is in good agreement with the high sequence identity (87.97%) between these two proteins. Preliminary enzymatic kinetics studies of P. aeruginosa FDH also revealed a conserved glutathione-independent `ping-pong' mechanism of formaldehyde oxidization.
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Affiliation(s)
- Yuanping Liao
- R&D Department, Novoprotein Scientific Inc. (Shanghai), R202, Building 2, 720 Cailun Road, Shanghai 201203, People’s Republic of China
| | - Shuai Chen
- R&D Department, Novoprotein Scientific Inc. (Shanghai), R202, Building 2, 720 Cailun Road, Shanghai 201203, People’s Republic of China
| | - Dingli Wang
- R&D Department, Novoprotein Scientific Inc. (Shanghai), R202, Building 2, 720 Cailun Road, Shanghai 201203, People’s Republic of China
| | - Wangluo Zhang
- R&D Department, Novoprotein Scientific Inc. (Shanghai), R202, Building 2, 720 Cailun Road, Shanghai 201203, People’s Republic of China
| | - Shuang Wang
- R&D Department, Novoprotein Scientific Inc. (Shanghai), R202, Building 2, 720 Cailun Road, Shanghai 201203, People’s Republic of China
| | - Jianfeng Ding
- R&D Department, Novoprotein Scientific Inc. (Shanghai), R202, Building 2, 720 Cailun Road, Shanghai 201203, People’s Republic of China
| | - Yingming Wang
- R&D Department, Novoprotein Scientific Inc. (Shanghai), R202, Building 2, 720 Cailun Road, Shanghai 201203, People’s Republic of China
| | - Lijun Cai
- R&D Department, Novoprotein Scientific Inc. (Shanghai), R202, Building 2, 720 Cailun Road, Shanghai 201203, People’s Republic of China
| | - Xiaoyuan Ran
- R&D Department, Novoprotein Scientific Inc. (Shanghai), R202, Building 2, 720 Cailun Road, Shanghai 201203, People’s Republic of China
| | - Xinquan Wang
- Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Huaxing Zhu
- R&D Department, Novoprotein Scientific Inc. (Shanghai), R202, Building 2, 720 Cailun Road, Shanghai 201203, People’s Republic of China
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15
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Liu F, Banta S, Chen W. Functional assembly of a multi-enzyme methanol oxidation cascade on a surface-displayed trifunctional scaffold for enhanced NADH production. Chem Commun (Camb) 2013; 49:3766-8. [PMID: 23535691 DOI: 10.1039/c3cc40454d] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a simple and low-cost strategy that allows the sequential and site-specific assembly of a dehydrogenase-based multi-enzyme cascade for methanol oxidation on the yeast surface using the high-affinity interactions between three orthogonal cohesin-dockerin pairs. The multi-enzyme cascade showed 5 times higher NADH production rate than the non-complexed enzyme mixture, a result of efficient substrate channeling.
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Affiliation(s)
- Fang Liu
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
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16
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Nian H, Meng Q, Zhang W, Chen L. Overexpression of the formaldehyde dehydrogenase gene from Brevibacillus brevis to enhance formaldehyde tolerance and detoxification of tobacco. Appl Biochem Biotechnol 2013; 169:170-80. [PMID: 23160947 DOI: 10.1007/s12010-012-9957-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 11/06/2012] [Indexed: 10/27/2022]
Abstract
The faldh gene coding for a putative Brevibacillus brevis formaldehyde dehydrogenase (FALDH) was isolated and then transformed into tobacco. A total of three lines of transgenic plants were generated, with each showing 2- to 3-fold higher specific formaldehyde dehydrogenase activities than wild-type tobacco, a result that demonstrates the functional activity of the enzyme in formaldehyde (HCHO) oxidation. Overexpression of faldh in tobacco confers a high tolerance to exogenous HCHO and an increased ability to take up HCHO. A (13)C-nuclear magnetic resonance technique revealed that the transgenic plants were able to oxidize more aqueous HCHO to formate than the wild-type (WT) plants. When treated with gaseous HCHO, the transgenic tobacco exhibited an enhanced ability to transform more HCHO into formate, citrate acid, and malate but less glycine than the WT plants. These results indicate that the increased capacity of the transgenic tobacco to take up, tolerate, and metabolize higher concentrations of HCHO was due to the overexpression of B. brevis FALDH, revealing the essential function of this enzyme in HCHO detoxification. Our results provide a potential genetic engineering strategy for improving the phytoremediation of HCHO pollution.
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Affiliation(s)
- Hongjuan Nian
- Biotechnology Research Center, Kunming University of Science and Technology, Kunming 650500, China.
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Lateral transfer of genes for hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) degradation. Appl Environ Microbiol 2009; 75:3258-62. [PMID: 19270122 DOI: 10.1128/aem.02396-08] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent studies demonstrated that degradation of the military explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by species of Rhodococcus, Gordonia, and Williamsia is mediated by a novel cytochrome P450 with a fused flavodoxin reductase domain (XplA) in conjunction with a flavodoxin reductase (XplB). Pulse field gel analysis was used to localize xplA to extrachromosomal elements in a Rhodococcus sp. and distantly related Microbacterium sp. strain MA1. Comparison of Rhodococcus rhodochrous 11Y and Microbacterium plasmid sequences in the vicinity of xplB and xplA showed near identity (6,710 of 6,721 bp). Sequencing of the associated 52.2-kb region of the Microbacterium plasmid pMA1 revealed flanking insertion sequence elements and additional genes implicated in RDX uptake and degradation.
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18
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Persson B, Hedlund J, Jörnvall H. Medium- and short-chain dehydrogenase/reductase gene and protein families : the MDR superfamily. Cell Mol Life Sci 2009; 65:3879-94. [PMID: 19011751 PMCID: PMC2792335 DOI: 10.1007/s00018-008-8587-z] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The MDR superfamily with ~350-residue subunits contains the classical liver alcohol dehydrogenase (ADH), quinone reductase, leukotriene B4 dehydrogenase and many more forms. ADH is a dimeric zinc metalloprotein and occurs as five different classes in humans, resulting from gene duplications during vertebrate evolution, the first one traced to ~500 MYA (million years ago) from an ancestral formaldehyde dehydrogenase line. Like many duplications at that time, it correlates with enzymogenesis of new activities, contributing to conditions for emergence of vertebrate land life from osseous fish. The speed of changes correlates with function, as do differential evolutionary patterns in separate segments. Subsequent recognitions now define at least 40 human MDR members in the Uniprot database (corresponding to 25 genes when excluding close homologues), and in all species at least 10888 entries. Overall, variability is large, but like for many dehydrogenases, subdivided into constant and variable forms, corresponding to household and emerging enzyme activities, respectively. This review covers basic facts and describes eight large MDR families and nine smaller families. Combined, they have specific substrates in metabolic pathways, some with wide substrate specificity, and several with little known functions.
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Affiliation(s)
- B Persson
- IFM Bioinformatics, Linköping University, Sweden.
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19
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Roy TW, Bhagwat AS. Kinetic studies of Escherichia coli AlkB using a new fluorescence-based assay for DNA demethylation. Nucleic Acids Res 2007; 35:e147. [PMID: 18003660 PMCID: PMC2175350 DOI: 10.1093/nar/gkm1031] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The Escherichia coli AlkB protein catalyzes the direct reversal of alkylation damage to DNA; primarily 1-methyladenine (1mA) and 3-methylcytosine (3mC) lesions created by endogenous or environmental alkylating agents. AlkB is a member of the non-heme iron (II) α-ketoglutarate-dependent dioxygenase superfamily, which removes the alkyl group through oxidation eliminating a methyl group as formaldehyde. We have developed a fluorescence-based assay for the dealkylation activity of this family of enzymes. It uses formaldehyde dehydrogenase to convert formaldehyde to formic acid and monitors the creation of an NADH analog using fluorescence. This assay is a great improvement over the existing assays for DNA demethylation in that it is continuous, rapid and does not require radioactively labeled material. It may also be used to study other demethylation reactions including demethylation of histones. We used it to determine the kinetic constants for AlkB and found them to be somewhat different than previously reported values. The results show that AlkB demethylates 1mA and 3mC with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart.
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Affiliation(s)
- Todd W Roy
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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20
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Yoshimoto T. [Biochemistry and structural biology of microbial enzymes and their medical applications]. YAKUGAKU ZASSHI 2007; 127:1035-45. [PMID: 17603262 DOI: 10.1248/yakushi.127.1035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microbial enzymes were studied from two medicinal viewpoints. First, we examined proline-specific peptidases from pathogenic microorganisms. We found several proline-specific peptidases in pathogenic bacteria. Among them, prolyl tripeptidyl aminopeptidase from Porphylomonas gingivals and prolyl aminopeptidase from Serratia marcescens were crystallized. The complex structures of those enzymes and inhibitors were clarified in X-ray crystallography. Aminopeptidase N, which has wide specificity for amino acids, was distributed in the pathogens. The crystal structure of the aminopeptidase N elucidated the reasons for its wide substrate specificity but inertness to the X-Pro bond. It was also revealed that proline-specific peptidases and aminopeptidase N cooperatively degrade collagen for the uptake of amino acids as nutrition when these bacteria infect cells. Second, we applied enzymes from microorganisms to diagnostic analyses. We found a series of creatinine-metabolizing enzymes in Pseudomonas putida. Creatininase, creatinase, and sarcosine oxidase were coupled and have been developed for a diagnostic analysis kit that examines renal function. The structures of the native and the Mn2+-activated creatininases were determined in X-ray crystallography. Based on the structure, the activated enzyme was used for an improved assay kit. The structure of D-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi was also clarified in crystallography. The enzyme is useful for diagnostic analysis of diabetes mellitus while monitoring ketone bodies.
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Affiliation(s)
- Tadashi Yoshimoto
- Department of Molecular Medicinal Sciences, Division of Biotechnology, Nagasaki University, Japan.
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21
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Gonzalez CF, Proudfoot M, Brown G, Korniyenko Y, Mori H, Savchenko AV, Yakunin AF. Molecular basis of formaldehyde detoxification. Characterization of two S-formylglutathione hydrolases from Escherichia coli, FrmB and YeiG. J Biol Chem 2006; 281:14514-22. [PMID: 16567800 DOI: 10.1074/jbc.m600996200] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli genes frmB (yaiM) and yeiG encode two uncharacterized proteins that share 54% sequence identity and contain a serine esterase motif. We demonstrated that purified FrmB and YeiG have high carboxylesterase activity against the model substrates, p-nitrophenyl esters of fatty acids (C2-C6) and alpha-naphthyl acetate. However, both proteins had the highest hydrolytic activity toward S-formylglutathione, an intermediate of the glutathione-dependent pathway of formaldehyde detoxification. With this substrate, both proteins had similar affinity (Km = 0.41-0.43 mM), but FrmB was almost 5 times more active. Alanine replacement mutagenesis of YeiG demonstrated that Ser145, Asp233, and His256 are absolutely required for activity, indicating that these residues represent a serine hydrolase catalytic triad in this protein and in other S-formylglutathione hydrolases. This was confirmed by inspecting the crystal structure of the Saccharomyces cerevisiae S-formylglutathione hydrolase YJG8 (Protein Data Bank code 1pv1), which has 45% sequence identity to YeiG. The structure revealed a canonical alpha/beta-hydrolase fold and a classical serine hydrolase catalytic triad (Ser161, His276, Asp241). In E. coli cells, the expression of frmB was stimulated 45-75 times by the addition of formaldehyde to the growth medium, whereas YeiG was found to be a constitutive enzyme. The simultaneous deletion of both frmB and yeiG genes was required to increase the sensitivity of the growth of E. coli cells to formaldehyde, suggesting that both FrmB and YeiG contribute to the detoxification of formaldehyde. Thus, FrmB and YeiG are S-formylglutathione hydrolases with a Ser-His-Asp catalytic triad involved in the detoxification of formaldehyde in E. coli.
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Affiliation(s)
- Claudio F Gonzalez
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
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22
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Tanaka N, Kusakabe Y, Ito K, Yoshimoto T, Nakamura KT. Crystal structure of glutathione-independent formaldehyde dehydrogenase. Chem Biol Interact 2003; 143-144:211-8. [PMID: 12604206 DOI: 10.1016/s0009-2797(02)00168-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Formaldehyde dehydrogenase from Pseudomonas putida (PFDH) is a member of the zinc-containing medium-chain alcohol dehydrogenase (ADH) family. The pyridine nucleotide NAD(H) in PFDH, which is distinct from the coenzyme (as co-substrate) in typical ADHs, is tightly but not covalently bound to the protein and acts as a cofactor. Such enzymes with tightly bound NAD(P)(H) acting as a cofactor are called nicotinoproteins. The structural basis of the tightly bound cofactor of PFDH is unknown. The crystal structure of PFDH has been solved by the multiwavelength anomalous diffraction method using intrinsic zinc ions and has been refined at a 1.65 A resolution. The 170-kDa-homotetrameric PFDH molecule shows 222-point group symmetry. Although the secondary structure arrangement and the binding mode of catalytic and structural zinc ions in PFDH are similar to those of typical ADHs, a number of loop structures that differ between PFDH and ADHs in their lengths and conformations are observed.
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Affiliation(s)
- Nobutada Tanaka
- School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, 142-8555, Tokyo, Japan.
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23
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Tanaka N, Kusakabe Y, Ito K, Yoshimoto T, Nakamura KT. Crystal structure of formaldehyde dehydrogenase from Pseudomonas putida: the structural origin of the tightly bound cofactor in nicotinoprotein dehydrogenases. J Mol Biol 2002; 324:519-33. [PMID: 12445786 DOI: 10.1016/s0022-2836(02)01066-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Formaldehyde dehydrogenase from Pseudomonas putida (PFDH) is a member of the zinc-containing medium-chain alcohol dehydrogenase family. The pyridine nucleotide NAD(H) in PFDH, which is distinct from the coenzyme (as cosubstrate) in typical alcohol dehydrogenases (ADHs), is tightly but not covalently bound to the protein and acts as a cofactor. PFDH can catalyze aldehyde dismutations without an external addition of NAD(H). The structural basis of the tightly bound cofactor of PFDH is unknown. The crystal structure of PFDH has been solved by the multiwavelength anomalous diffraction method using intrinsic zinc ions and has been refined at a 1.65 A resolution. The 170-kDa homotetrameric PFDH molecule shows 222 point group symmetry. Although the secondary structure arrangement and the binding mode of catalytic and structural zinc ions in PFDH are similar to those of typical ADHs, a number of loop structures that differ between PFDH and ADHs in their lengths and conformations are observed. A comparison of the present structure of PFDH with that of horse liver ADH, a typical example of an ADH, reveals that a long insertion loop of PFDH shields the adenine part of the bound NAD(+) molecule from the solvent, and a tight hydrogen bond network exists between the insertion loop and the adenine part of the cofactor, which is unique to PFDH. This insertion loop is conserved completely among the aldehyde-dismutating formaldehyde dehydrogenases, whereas it is replaced by a short turn among typical ADHs. Thus, the insertion loop specifically found among the aldehyde-dismutating formaldehyde dehydrogenases is responsible for the tight cofactor binding of these enzymes and explains why PFDH can effectively catalyze alternate oxidation and reduction of aldehydes without the release of cofactor molecule from the enzyme.
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Affiliation(s)
- Nobutada Tanaka
- School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, 142-8555, Tokyo, Japan.
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24
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Ito K. [Structural and functional analysis of enzymes and their application to clinical analysis--study on Pseudomonas putida formaldehyde dehydrogenase]. YAKUGAKU ZASSHI 2002; 122:805-11. [PMID: 12400161 DOI: 10.1248/yakushi.122.805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Formaldehyde dehydrogenase (PFDH) was isolated from the creatinine-decomposing bacterium Pseudomonas putida, and its gene has been cloned. PFDH is unique because it was the only enzyme that catalyzed the dehydrogenation of formaldehyde without glutathione. PFDH belongs to a zinc-containing alcohol dehydrogenase family. Quantitative analysis of the reaction products using NMR revealed that the enzyme is not simply a dehydrogenase but is an aldehyde dismutase catalyzing a simultaneous conversion of both aldehyde to carboxylate and aldehyde to alcohol. The enzyme contains a tightly bound cofactor of NAD+/NADH per subunit and is classified as a nicotinoprotein. The enzyme reaction can proceed without external addition of the nucleotide cofactor. The formaldehyde was crystallized using the hanging-drop vapor diffusion method with ammonium sulfate as a precipitant. The crystal structure was determined using the multiwavelength anomalous diffraction method with intrinsic zinc ions. The overall structure of PFDH is similar to that of a classic horse liver alcohol dehydrogenase. However, a comparison of these structures indicated that the insertion loop specifically found in PFDH may be responsible for the tight binding of the cofactor, thereby making PFDH a dismutase.
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Affiliation(s)
- Kiyoshi Ito
- Department of Molecular Medicinal Sciences, Division of Biotechnology, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
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25
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Structural characterization of the zinc site in Escherichia coliL-threonine dehydrogenase using extended X-ray absorption fine structure spectroscopy. Inorganica Chim Acta 1998. [DOI: 10.1016/s0020-1693(97)06107-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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26
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Murdanoto AP, Sakai Y, Konishi T, Yasuda F, Tani Y, Kato N. Purification and properties of methyl formate synthase, a mitochondrial alcohol dehydrogenase, participating in formaldehyde oxidation in methylotrophic yeasts. Appl Environ Microbiol 1997; 63:1715-20. [PMID: 9143107 PMCID: PMC168467 DOI: 10.1128/aem.63.5.1715-1720.1997] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Methyl formate synthase, which catalyzes methyl formate formation during the growth of methylotrophic yeasts, was purified to homogeneity from methanol-grown Candida boidinii and Pichia methanolica cells. Both purified enzymes were tetrameric, with identical subunits with molecular masses of 42 to 45 kDa, containing two atoms of zinc per subunit. The enzymes catalyze NAD(+)-linked dehydrogenation of the hydroxyl group of the hemiacetal adduct [CH2(OH)OCH3] of methanol and formaldehyde, leading to the formation of a stoichiometric amount of methyl formate. Although neither methanol nor formaldehyde alone acted as a substrate for the enzymes, they showed simple NAD(+)-linked alcohol dehydrogenase activity toward aliphatic long-chain alcohols such as octanol, showing that they belong to the class III alcohol dehydrogenase family. The methyl formate synthase activity of C. boidinii was found in the mitochondrial fraction in subcellular fractionation experiments, suggesting that methyl formate synthase is a homolog of Saccharomyces cerevisiae Adh3p. These results indicate that formaldehyde could be oxidized in a glutathione-independent manner by methyl formate synthase in methylotrophic yeasts. The significance of methyl formate synthase in both formaldehyde resistance and energy metabolism is also discussed.
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Affiliation(s)
- A P Murdanoto
- Department of Agricultural Chemistry, Kyoto University, Japan
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27
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Harms N, Ras J, Reijnders WN, van Spanning RJ, Stouthamer AH. S-formylglutathione hydrolase of Paracoccus denitrificans is homologous to human esterase D: a universal pathway for formaldehyde detoxification? J Bacteriol 1996; 178:6296-9. [PMID: 8892832 PMCID: PMC178503 DOI: 10.1128/jb.178.21.6296-6299.1996] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Downstream of flhA, the Paracoccus denitrificans gene encoding glutathione-dependent formaldehyde dehydrogenase, an open reading frame was identified and called fghA. The gene product of fghA showed appreciable similarity with human esterase D and with the deduced amino acid sequences of open reading frames found in Escherichia coli, Haemophilus influenzae, and Saccharomyces cerevisiae. Mutating fghA strongly reduced S-formylglutathione hydrolase activity. The mutant was unable to grow on methanol and methylamine, indicating that the enzyme is essential for methylotrophic growth. S-Formylglutathione hydrolase appears to be part of a formaldehyde detoxification pathway that is universal in nature.
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Affiliation(s)
- N Harms
- Department of Microbial Physiology, Vrije Universiteit, Amsterdam, The Netherlands.
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28
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Oppenheimer NJ, Henehan GTM, Huete-Pérez JA, Ito K. P. putida Formaldehyde Dehydrogenase. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1996. [DOI: 10.1007/978-1-4615-5871-2_47] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Ras J, Van Ophem PW, Reijnders WN, Van Spanning RJ, Duine JA, Stouthamer AH, Harms N. Isolation, sequencing, and mutagenesis of the gene encoding NAD- and glutathione-dependent formaldehyde dehydrogenase (GD-FALDH) from Paracoccus denitrificans, in which GD-FALDH is essential for methylotrophic growth. J Bacteriol 1995; 177:247-51. [PMID: 7798140 PMCID: PMC176581 DOI: 10.1128/jb.177.1.247-251.1995] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
NAD- and glutathione-dependent formaldehyde dehydrogenase (GD-FALDH) of Paracoccus denitrificans has been purified as a tetramer with a relative molecular mass of 150 kDa. The gene encoding GD-FALDH (flhA) has been isolated, sequenced, and mutated by insertion of a kanamycin resistance gene. The mutant strain is not able to grow on methanol, methylamine, or choline, while heterotrophic growth is not influenced by the mutation. This finding indicates that GD-FALDH of P. denitrificans is essential for the oxidation of formaldehyde produced during methylotrophic growth.
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Affiliation(s)
- J Ras
- Department of Microbiology, Biological Laboratory, Vrije Universiteit, Amsterdam, The Netherlands
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30
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Speer BS, Chistoserdova L, Lidstrom ME. Sequence of the gene for a NAD(P)-dependent formaldehyde dehydrogenase (class III alcohol dehydrogenase) from a marine methanotroph Methylobacter marinus A45. FEMS Microbiol Lett 1994; 121:349-55. [PMID: 7926692 DOI: 10.1111/j.1574-6968.1994.tb07125.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A fragment of Methylobacter marinus A45 DNA has been cloned and sequenced, and an open reading frame has been identified that could code for a 46-kDa polypeptide. Comparison of the deduced amino acid sequence of the polypeptide against the protein data bank has revealed strong similarity with a number of alcohol dehydrogenases, with highest similarity towards class III alcohol dehydrogenases, which recently have been shown to be identical to glutathione-dependent formaldehyde dehydrogenases. We were unable to measure appreciable levels of NAD(P)-dependent formaldehyde dehydrogenases or alcohol dehydrogenase activities using aldehydes or primary or secondary alcohols in cell-free extracts from batch cultures of M. marinus A45. However, formaldehyde dehydrogenases activity was detected on zymograms. Our data suggest that, although NAD(P)-linked formaldehyde dehydrogenase or alcohol dehydrogenase activities are undetectable in cell-free extracts of most methylotrophs employing the ribulose monophosphate pathway for formaldehyde assimilation and dissimilation, the gene encoding formaldehyde dehydrogenase is present in M. marinus A45 and may be present in more of these organisms as well.
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Affiliation(s)
- B S Speer
- W.M. Keck Laboratories 138-78, California Institute of Technology, Pasadena 91125
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