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Benninghaus L, Zagami L, Tassini G, Meyer F, Wendisch VF. γ-Glutamylation of Isopropylamine by Fermentation. Chembiochem 2024; 25:e202300608. [PMID: 37987374 DOI: 10.1002/cbic.202300608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 11/22/2023]
Abstract
Glutamylation yields N-functionalized amino acids in several natural pathways. γ-Glutamylated amino acids may exhibit improved properties for their industrial application, e. g., as taste enhancers or in peptide drugs. γ-Glutamyl-isopropylamide (GIPA) can be synthesized from isopropylamine (IPA) and l-glutamate. In Pseudomonas sp. strain KIE171, GIPA is an intermediate in the biosynthesis of l-alaninol (2-amino-1-propanol), a precursor of the fluorochinolone antibiotic levofloxacin and of the chloroacetanilide herbicide metolachlor. In this study, fermentative production of GIPA with metabolically engineered Pseudomonas putida KT2440 using γ-glutamylmethylamide synthetase (GMAS) from Methylorubrum extorquens was established. Upon addition of IPA during growth with glycerol as carbon source in shake flasks, the recombinant strain produced up to 21.8 mM GIPA. In fed-batch bioreactor cultivations, GIPA accumulated to a titer of 11 g L-1 with a product yield of 0.11 g g-1 glycerol and a volumetric productivity of 0.24 g L-1 h-1 . To the best of our knowledge, this is the first fermentative production of GIPA.
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Affiliation(s)
- Leonie Benninghaus
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Laura Zagami
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Giulio Tassini
- School of Science Mathematics Physical and Natural Sciences, University of Florence, Piazza San Marco 4, 50121, Firenze, Italy
| | - Florian Meyer
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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2
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Liu Y, Okano K, Iwaki H. Identification and characterization of a pab gene cluster responsible for the 4-aminobenzoate degradation pathway, including its involvement in the formation of a γ-glutamylated intermediate in Paraburkholderia terrae strain KU-15. J Biosci Bioeng 2024; 137:38-46. [PMID: 37977976 DOI: 10.1016/j.jbiosc.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/01/2023] [Accepted: 11/04/2023] [Indexed: 11/19/2023]
Abstract
Paraburkholderia terrae strain KU-15 grows on 2- and 4-nitrobenzoate and 2- and 4-aminobenzoate (ABA) as the sole nitrogen and carbon sources. The genes responsible for the potential degradation of 2- and 4-nitrobenzoate and 2-ABA have been predicted from its genome sequence. In this study, we identified the pab operon in P. terrae strain KU-15. This operon is responsible for the 4-ABA degradation pathway, which involves the formation of a γ-glutamylated intermediate. Reverse transcription-polymerase chain reaction revealed that the pab operon was induced by 4-ABA. Herein, studying the deletion of pabA and pabB1 in strain KU-15 and the examining of Escherichia coli expressing the pab operon revealed the involvement of the operon in 4-ABA degradation. The first step of the degradation pathway is the formation of a γ-glutamylated intermediate, whereby 4-ABA is converted to γ-glutamyl-4-carboxyanilide (γ-GCA). Subsequently, γ-GCA is oxidized to protocatechuate. Overexpression of various genes in E. coli and purification of recombinant proteins permitted the functional characterization of relevant pathway proteins: PabA is a γ-GCA synthetase, PabB1-B3 functions in a multicomponent dioxygenase system responsible for γ-GCA dioxygenation, and PabC is a γ-GCA hydrolase that reverses the formation of γ-GCA by PabA.
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Affiliation(s)
- Yaxuan Liu
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Kenji Okano
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Hiroaki Iwaki
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan.
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3
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Yin Y, Zhang Q, Peng H. Retrospect and prospect of aerobic biodegradation of aniline: Overcome existing bottlenecks and follow future trends. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 330:117133. [PMID: 36584469 DOI: 10.1016/j.jenvman.2022.117133] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Aniline is a highly bio-toxic industrial product, even at low concentrations, whose related wastewater has been flowing out worldwide on a large scale along with human production. As a green technology, aerobic biological treatment has been widely applied in industrial wastewater and exhibited various characteristics in the field of aniline wastewater. Meanwhile, this technology has shown its potential of synchronous nitrogen removal, but it still consumes energy badly. In the face of resource scarcity, this review comprehensively discusses the existing research in aerobic biodegradation of aniline wastewater to find out the developmental dawn of aerobic biological treatment. Primarily, it put forward the evolution history details of aniline biodegradation from pure culture to mixed culture and then to simultaneous nitrogen removal. On this basis, it presented the existing challenges to further expand the application of aerobic biotechnology, including the confusions of aniline metabolic mechanism, the development of co-degradation of multiple pollutants and the lack of practical experience of bioreactor operation for aniline and nitrogen removal. Additionally, the prospects of the technological shift to meet the needs of an energy-conserving society was described according to existing experiences and feasibility. Including but not limiting to the development of multifunctional bacteria, the reduction of greenhouse gases and the combination of green technologies.
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Affiliation(s)
- Yixin Yin
- School of Resources & Environmental Engineering, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - Qian Zhang
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, China.
| | - Haojin Peng
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
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4
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Cheng M, Chen D, Parales RE, Jiang J. Oxygenases as Powerful Weapons in the Microbial Degradation of Pesticides. Annu Rev Microbiol 2022; 76:325-348. [PMID: 35650666 DOI: 10.1146/annurev-micro-041320-091758] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Oxygenases, which catalyze the reductive activation of O2 and incorporation of oxygen atoms into substrates, are widely distributed in aerobes. They function by switching the redox states of essential cofactors that include flavin, heme iron, Rieske non-heme iron, and Fe(II)/α-ketoglutarate. This review summarizes the catalytic features of flavin-dependent monooxygenases, heme iron-dependent cytochrome P450 monooxygenases, Rieske non-heme iron-dependent oxygenases, Fe(II)/α-ketoglutarate-dependent dioxygenases, and ring-cleavage dioxygenases, which are commonly involved in pesticide degradation. Heteroatom release (hydroxylation-coupled hetero group release), aromatic/heterocyclic ring hydroxylation to form ring-cleavage substrates, and ring cleavage are the main chemical fates of pesticides catalyzed by these oxygenases. The diversity of oxygenases, specificities for electron transport components, and potential applications of oxygenases are also discussed. This article summarizes our current understanding of the catalytic mechanisms of oxygenases and a framework for distinguishing the roles of oxygenases in pesticide degradation. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Minggen Cheng
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China;
| | - Dian Chen
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, California, USA
| | - Jiandong Jiang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China;
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5
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Yamamoto T, Liu Y, Sumiyoshi T, Hasegawa Y, Iwaki H. A novel piperidine degradation mechanism in a newly isolated piperidine degrader Pseudomonas sp. strain KU43P. J GEN APPL MICROBIOL 2020; 66:265-272. [PMID: 32641635 DOI: 10.2323/jgam.2019.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The degradation pathways in microorganisms for piperidine, a secondary amine with various applications, are not yet fully understood, especially in non-Mycobacterium species. In this study, we have identified a piperidine-degrading isolate (KU43P) from a soil sample collected in a cultivation field in Osaka, Japan, and characterized its mechanisms of piperidine degradation, thereby furthering current understanding of the process. The genome of isolate KU43P consists of a 5,869,691-bp circular chromosome with 62.67% GC content and with 5,294 predicted protein-coding genes, 77 tRNA genes, and 22 rRNA genes. 16S rRNA gene sequence analysis and average nucleotide identity analysis suggest that the isolate is a novel species of the Pseudomonas putida group in the genus Pseudomonas. The genomic region encoding the piperidine degradation pathway, designated as the pip gene cluster, was identified using transposon mutagenesis and reverse transcription polymerase chain reaction. Deletion analyses of pipA, which encodes a glutamine synthetase (GS)-like protein, and pipBa, which encodes a cytochrome P450 monooxygenase, indicate that pipA and pipBa are involved in piperidine metabolism and suggest that pipA is involved in the first step of the piperidine metabolic pathway. Escherichia coli whole cells overexpressing PipA converted piperidine and glutamate to γ-glutamylpiperidide, and crude cell extract enzyme assays of PipA showed that this reaction requires ATP and Mg2+. These results clearly show that pipA encodes γ-glutamylpiperidide synthetase and that piperidine is first glutamylated and then hydroxylated in the piperidine degradation pathway of Pseudomonas sp. strain KU43P. This study has filled a void in the general knowledge of the microbial degradation of amine compounds.
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Affiliation(s)
- Taisei Yamamoto
- Department of Life Science & Biotechnology, Kansai University
| | - Yaxuan Liu
- Department of Life Science & Biotechnology, Kansai University
| | | | - Yoshie Hasegawa
- Department of Life Science & Biotechnology, Kansai University
| | - Hiroaki Iwaki
- Department of Life Science & Biotechnology, Kansai University
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6
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Xie X, Spiteller D, Huhn T, Schink B, Müller N. Desulfatiglans anilini Initiates Degradation of Aniline With the Production of Phenylphosphoamidate and 4-Aminobenzoate as Intermediates Through Synthases and Carboxylases From Different Gene Clusters. Front Microbiol 2020; 11:2064. [PMID: 33013754 PMCID: PMC7500099 DOI: 10.3389/fmicb.2020.02064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/05/2020] [Indexed: 01/22/2023] Open
Abstract
The anaerobic degradation of aniline was studied in the sulfate-reducing bacterium Desulfatiglans anilini. Our aim was to identify the genes and their proteins that are required for the initial activation of aniline as well as to characterize intermediates of this reaction. Aniline-induced genes were revealed by comparison of the proteomes of D. anilini grown with different substrates (aniline, 4-aminobenzoate, phenol, and benzoate). Most genes encoding proteins that were highly abundant in aniline- or 4-aminobenzoate-grown D. anilini cells but not in phenol- or benzoate-grown cells were located in the putative gene clusters ani (aniline degradation), hcr (4-hydroxybenzoyl-CoA reductase) and phe (phenol degradation). Of these putative gene clusters, only the phe gene cluster has been studied previously. Based on the differential proteome analysis, four candidate genes coding for kinase subunits and carboxylase subunits were suspected to be responsible for the initial conversion of aniline to 4-aminobenzoate. These genes were cloned and overproduced in E. coli. The recombinant proteins were obtained in inclusion bodies but could be refolded successfully. Two subunits of phenylphosphoamidate synthase and two carboxylase subunits converted aniline to 4-aminobenzoate with phenylphosphoamidate as intermediate under consumption of ATP. Only when both carboxylase subunits, one from gene cluster ani and the other from gene cluster phe, were combined, phenylphosphoamidate was converted to 4-aminobenzoate in vitro, with Mn2+, K+, and FMN as co-factors. Thus, aniline is degraded by the anaerobic bacterium D. anilini only by recruiting genes for the enzymatic machinery from different gene clusters. We conclude, that D. anilini carboxylates aniline to 4-aminobenzoate via phenylphosphoamidate as an energy rich intermediate analogous to the degradation of phenol to 4-hydroxybenzoate via phenylphosphate.
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Affiliation(s)
- Xiaoman Xie
- Department of Biology, Universität Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, Konstanz, Germany
| | - Dieter Spiteller
- Department of Biology, Universität Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, Konstanz, Germany
| | - Thomas Huhn
- Konstanz Research School Chemical Biology, Konstanz, Germany.,Department of Chemistry, Universität Konstanz, Konstanz, Germany
| | - Bernhard Schink
- Department of Biology, Universität Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, Konstanz, Germany
| | - Nicolai Müller
- Department of Biology, Universität Konstanz, Konstanz, Germany
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7
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Ji J, Zhang J, Liu Y, Zhang Y, Liu Y, Yan X. The substrate specificity of aniline dioxygenase is mainly determined by two of its components: glutamine synthetase-like enzyme and oxygenase. Appl Microbiol Biotechnol 2019; 103:6333-6344. [DOI: 10.1007/s00253-019-09871-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 04/14/2019] [Accepted: 04/15/2019] [Indexed: 11/29/2022]
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8
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Iradi-Serrano M, Tola-García L, Cortese MS, Ugalde U. The Early Asexual Development Regulator fluG Codes for a Putative Bifunctional Enzyme. Front Microbiol 2019; 10:778. [PMID: 31057506 PMCID: PMC6478659 DOI: 10.3389/fmicb.2019.00778] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/27/2019] [Indexed: 11/13/2022] Open
Abstract
FluG is a long recognized early regulator of asexual development in Aspergillus nidulans. fluG null mutants show profuse aerial growth and no conidial production. Initial studies reported sequence homology of FluG with a prokaryotic type I glutamine synthetase, but catalytic activity has not been demonstrated. In this study, we conducted an in-depth analysis of the FluG sequence, which revealed a single polypeptide containing a putative N-terminal amidohydrolase region linked to a putative C-terminal γ-glutamyl ligase region. Each region corresponded, separately and completely, to respective single function bacterial enzymes. Separate expression of these regions confirmed that the C-terminal region was essential for asexual development. The N-terminal region alone did not support conidial development, but contributed to increased conidial production under high nutrient availability. Point mutations directed at respective key catalytic residues in each region demonstrated that they were essential for biological function. Moreover, the substitution of the N- and C-terminal regions with homologs from Lactobacillus paracasei and Pseudomonas aeruginosa, respectively, maintained functionality, albeit with altered characteristics. Taken together, the results lead us to conclude that FluG is a bifunctional enzyme that participates in an as yet unidentified metabolic or signaling pathway involving a γ-glutamylated intermediate that contributes to developmental fate.
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Affiliation(s)
| | | | | | - Unai Ugalde
- Microbial Biochemistry Laboratory, Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country, San Sebastian, Spain
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9
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Taweetanawanit P, Ratpukdi T, Siripattanakul-Ratpukdi S. Performance and kinetics of triclocarban removal by entrapped Pseudomonas fluorescens strain MC46. BIORESOURCE TECHNOLOGY 2019; 274:113-119. [PMID: 30502601 DOI: 10.1016/j.biortech.2018.11.085] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/21/2018] [Accepted: 11/23/2018] [Indexed: 05/22/2023]
Abstract
This study investigated removal of triclocarban (TCC) from contaminated wastewater by Pseudomonas fluorescens strain MC46 entrapped in barium alginate. Appropriate entrapped cell preparation conditions (cell-to-entrapment material ratio and cell loading) for removing TCC were examined. The highest TCC removal by the entrapped and free cell systems at the initial TCC concentration of 10 mg/L was 72 and 45%, respectively. TCC was degraded to less toxic compounds. Self-substrate inhibition was found at TCC concentration of 30 mg/L. The kinetics of TCC removal by entrapped and free cells fitted well with Edwards model. Scanning and transmission electron microscopic observations revealed that entrapment matrices reduced TCC-microbe contact, which lessened TCC inhibition. A live/dead cell assay also confirmed reduced microbial cell damage in the entrapped cell system compared to the free cell system. This study reveals the potential of entrapment technology to improve antibiotic removal from the environment.
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Affiliation(s)
- Pongsatorn Taweetanawanit
- Department of Environmental Engineering, Faculty of Engineering and Research Center for Environmental and Hazardous Substance Management, Khon Kaen University, Khon Kaen 40002, Thailand.
| | - Thunyalux Ratpukdi
- Department of Environmental Engineering, Faculty of Engineering and Research Center for Environmental and Hazardous Substance Management, Khon Kaen University, Khon Kaen 40002, Thailand; Center of Excellence on Hazardous Substance Management (HSM), Bangkok 10330, Thailand.
| | - Sumana Siripattanakul-Ratpukdi
- Department of Environmental Engineering, Faculty of Engineering and Research Center for Environmental and Hazardous Substance Management, Khon Kaen University, Khon Kaen 40002, Thailand; Center of Excellence on Hazardous Substance Management (HSM), Bangkok 10330, Thailand.
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10
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Molecular Characterization of Aniline Biodegradation by Some Bacterial Isolates having Unexpressed Catechol 2,3-Dioxygenase Gene. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.4.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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11
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Takeo M, Yamamoto K, Sonoyama M, Miyanaga K, Kanbara N, Honda K, Kato DI, Negoro S. Characterization of the 3-methyl-4-nitrophenol degradation pathway and genes of Pseudomonas sp. strain TSN1. J Biosci Bioeng 2018; 126:355-362. [PMID: 29699943 DOI: 10.1016/j.jbiosc.2018.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/14/2018] [Accepted: 04/02/2018] [Indexed: 11/18/2022]
Abstract
3-Methyl-4-nitrophenol (3M4NP) is formed in soil as a hydrolysis product of fenitrothion, one of the major organophosphorus pesticides. A Pseudomonas strain was isolated as a 3M4NP degrader from a crop soil and designated TSN1. This strain utilized 3M4NP as a sole carbon and energy source. To elucidate the biodegradation pathway, we performed transposon mutagenesis with pCro2a (mini-Tn5495) and obtained three mutants accumulating a dark pink compound(s) from 3M4NP. Rescue cloning and sequence analysis revealed that in all mutants, the transposon disrupted an identical aromatic compound meta-cleaving dioxygenase gene, and a monooxygenase gene was located just downstream of the dioxygenase gene. These two genes were designated mnpC and mnpB, respectively. The gene products showed high identity with the methylhydroquinone (MHQ) monooxygenase (58%) and the 3-methylcatechol 2,3-dioxygenase (54%) of a different 3M4NP degrader Burkholderia sp. NF100. The transposon mutants converted 3M4NP or MHQ into two identical metabolites, one of which was identified as 2-hydroxy-5-methyl-1,4-benzoquinone (2H5MBQ) by GC/MS analysis. Furthermore, two additional genes (named mnpA1 and mnpA2), almost identical to the p-nitrophenol monooxygenase and the p-benzoquinone reductase genes of Pseudomonas sp. WBC-3, were isolated from the total DNA of strain TSN1. Disruption of mnpA1 resulted in the complete loss of the 3M4NP degradation activity, demonstrating that mnpA1 encodes the initial monooxygenase for 3M4NP degradation. The purified mnpA2 gene product could efficiently reduce methyl p-benzoquinone (MBQ) into MHQ. These results suggest that strain TSN1 degrades 3M4NP via MBQ, MHQ, and 2H5MBQ in combination with mnpA1A2 and mnpCB, existing at different loci on the genome.
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Affiliation(s)
- Masahiro Takeo
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Kenta Yamamoto
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Masashi Sonoyama
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Kana Miyanaga
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Nana Kanbara
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Koichi Honda
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Dai-Ichiro Kato
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
| | - Seiji Negoro
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
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12
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The Two-Component Monooxygenase MeaXY Initiates the Downstream Pathway of Chloroacetanilide Herbicide Catabolism in Sphingomonads. Appl Environ Microbiol 2017; 83:AEM.03241-16. [PMID: 28115384 DOI: 10.1128/aem.03241-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/18/2017] [Indexed: 11/20/2022] Open
Abstract
Due to the extensive use of chloroacetanilide herbicides over the past 60 years, bacteria have evolved catabolic pathways to mineralize these compounds. In the upstream catabolic pathway, chloroacetanilide herbicides are transformed into the two common metabolites 2-methyl-6-ethylaniline (MEA) and 2,6-diethylaniline (DEA) through N-dealkylation and amide hydrolysis. The pathway downstream of MEA is initiated by the hydroxylation of aromatic rings, followed by its conversion to a substrate for ring cleavage after several steps. Most of the key genes in the pathway have been identified. However, the genes involved in the initial hydroxylation step of MEA are still unknown. As a special aniline derivative, MEA cannot be transformed by the aniline dioxygenases that have been characterized. Sphingobium baderi DE-13 can completely degrade MEA and use it as a sole carbon source for growth. In this work, an MEA degradation-deficient mutant of S. baderi DE-13 was isolated. MEA catabolism genes were predicted through comparative genomic analysis. The results of genetic complementation and heterologous expression demonstrated that the products of meaX and meaY are responsible for the initial step of MEA degradation in S. baderi DE-13. MeaXY is a two-component flavoprotein monooxygenase system that catalyzes the hydroxylation of MEA and DEA using NADH and flavin mononucleotide (FMN) as cofactors. Nuclear magnetic resonance (NMR) analysis confirmed that MeaXY hydroxylates MEA and DEA at the para-position. Transcription of meaX was enhanced remarkably upon induction of MEA or DEA in S. baderi DE-13. Additionally, meaX and meaY were highly conserved among other MEA-degrading sphingomonads. This study fills a gap in our knowledge of the biochemical pathway that carries out mineralization of chloroacetanilide herbicides in sphingomonads.IMPORTANCE Much attention has been paid to the environmental fate of chloroacetanilide herbicides used for the past 60 years. Microbial degradation is considered an important mechanism in the degradation of these compounds. Bacterial degradation of chloroacetanilide herbicides has been investigated in many recent studies. Pure cultures or consortia able to mineralize these herbicides have been obtained. The catabolic pathway has been proposed, and most key genes involved have been identified. However, the genes responsible for the initiation step (from MEA to hydroxylated MEA or from DEA to hydroxylated DEA) of the downstream pathway have not been reported. The present study demonstrates that a two-component flavin-dependent monooxygenase system, MeaXY, catalyzes the para-hydroxylation of MEA or DEA in sphingomonads. Therefore, this work finds a missing link in the biochemical pathway that carries out the mineralization of chloroacetanilide herbicides in sphingomonads. Additionally, the results expand our understanding of the degradation of a special kind of aniline derivative.
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13
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Complete genome sequence of Novosphingobium resinovorum SA1, a versatile xenobiotic-degrading bacterium capable of utilizing sulfanilic acid. J Biotechnol 2017; 241:76-80. [DOI: 10.1016/j.jbiotec.2016.11.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/04/2016] [Accepted: 11/11/2016] [Indexed: 11/19/2022]
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14
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Yan X, Gu T, Yi Z, Huang J, Liu X, Zhang J, Xu X, Xin Z, Hong Q, He J, Spain JC, Li S, Jiang J. Comparative genomic analysis of isoproturon-mineralizing sphingomonads reveals the isoproturon catabolic mechanism. Environ Microbiol 2016; 18:4888-4906. [DOI: 10.1111/1462-2920.13413] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Xin Yan
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture; College of Life Sciences, Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Tao Gu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture; College of Life Sciences, Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Zhongquan Yi
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture; College of Life Sciences, Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Junwei Huang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture; College of Life Sciences, Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Xiaowei Liu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture; College of Life Sciences, Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Ji Zhang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture; College of Life Sciences, Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Xihui Xu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture; College of Life Sciences, Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Zhihong Xin
- College of Food Science and Technology; Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Qing Hong
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture; College of Life Sciences, Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Jian He
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture; College of Life Sciences, Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Jim C. Spain
- School of Civil and Environmental Engineering; Georgia Institute of Technology; Atlanta GA 30332-0512 USA
| | - Shunpeng Li
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture; College of Life Sciences, Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture; College of Life Sciences, Nanjing Agricultural University; Nanjing 210095 People's Republic of China
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15
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Lee SY, Kim GH, Yun SH, Choi CW, Yi YS, Kim J, Chung YH, Park EC, Kim SI. Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24. PLoS One 2016; 11:e0154233. [PMID: 27124467 PMCID: PMC4849787 DOI: 10.1371/journal.pone.0154233] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/11/2016] [Indexed: 11/19/2022] Open
Abstract
Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, is a soil bacterium capable of utilizing aniline as its sole carbon and nitrogen source. Genomic sequence analysis revealed that this bacterium possesses putative gene clusters for biodegradation of various monocyclic aromatic hydrocarbons (MAHs), including benzene, toluene, and xylene (BTX), as well as aniline. We verified the proposed MAH biodegradation pathways by dioxygenase activity assays, RT-PCR, and LC/MS-based quantitative proteomic analyses. This proteogenomic approach revealed four independent degradation pathways, all converging into the citric acid cycle. Aniline and p-hydroxybenzoate degradation pathways converged into the β-ketoadipate pathway. Benzoate and toluene were degraded through the benzoyl-CoA degradation pathway. The xylene isomers, i.e., o-, m-, and p-xylene, were degraded via the extradiol cleavage pathways. Salicylate was degraded through the gentisate degradation pathway. Our results show that Burkholderia sp. K24 possesses versatile biodegradation pathways, which may be employed for efficient bioremediation of aniline and BTX.
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Affiliation(s)
- Sang-Yeop Lee
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Gun-Hwa Kim
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Sung Ho Yun
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Chi-Won Choi
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yoon-Sun Yi
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
- Department of Food Science and Technology, Chungnam National University, Daejeon, 305–764, Republic of Korea
| | - Jonghyun Kim
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Young-Ho Chung
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Edmond Changkyun Park
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Seung Il Kim
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
- Bio-Analysis Science, University of Science & Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
- * E-mail:
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16
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Abstract
Amides are widespread in biologically active compounds with a broad range of applications in biotechnology, agriculture and medicine. Therefore, as alternative to chemical synthesis the biocatalytic amide synthesis is a very interesting field of research. As usual, Nature can serve as guide in the quest for novel biocatalysts. Several mechanisms for carboxylate activation involving mainly acyl-adenylate, acyl-phosphate or acyl-enzyme intermediates have been discovered, but also completely different pathways to amides are found. In addition to ribosomes, selected enzymes of almost all main enzyme classes are able to synthesize amides. In this review we give an overview about amide synthesis in Nature, as well as biotechnological applications of these enzymes. Moreover, several examples of biocatalytic amide synthesis are given.
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17
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Walker MC, van der Donk WA. The many roles of glutamate in metabolism. J Ind Microbiol Biotechnol 2015; 43:419-30. [PMID: 26323613 DOI: 10.1007/s10295-015-1665-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 07/25/2015] [Indexed: 12/20/2022]
Abstract
The amino acid glutamate is a major metabolic hub in many organisms and as such is involved in diverse processes in addition to its role in protein synthesis. Nitrogen assimilation, nucleotide, amino acid, and cofactor biosynthesis, as well as secondary natural product formation all utilize glutamate in some manner. Glutamate also plays a role in the catabolism of certain amines. Understanding glutamate's role in these various processes can aid in genome mining for novel metabolic pathways or the engineering of pathways for bioremediation or chemical production of valuable compounds.
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Affiliation(s)
- Mark C Walker
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA.
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18
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Arora PK. Bacterial degradation of monocyclic aromatic amines. Front Microbiol 2015; 6:820. [PMID: 26347719 PMCID: PMC4539516 DOI: 10.3389/fmicb.2015.00820] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/27/2015] [Indexed: 01/13/2023] Open
Abstract
Aromatic amines are an important group of industrial chemicals, which are widely used for manufacturing of dyes, pesticides, drugs, pigments, and other industrial products. These compounds have been considered highly toxic to human beings due to their carcinogenic nature. Three groups of aromatic amines have been recognized: monocyclic, polycyclic, and heterocyclic aromatic amines. Bacterial degradation of several monocyclic aromatic amines has been studied in a variety of bacteria, which utilizes monocyclic aromatic amines as their sole source of carbon and energy. Several degradation pathways have been proposed and the related enzymes and genes have also been characterized. Many reviews have been reviewed toxicity of monocyclic aromatic amines; however, there is lack of review on biodegradation of monocyclic aromatic amines. The aim of this review is to summarize bacterial degradation of monocyclic aromatic amines. This review will increase our current understanding of biochemical and molecular basis of bacterial degradation of monocyclic aromatic amines.
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Affiliation(s)
- Pankaj K. Arora
- School of Biotechnology, Yeungnam UniversityGyeongsan, South Korea
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19
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Wu Y, Arumugam K, Tay MQX, Seshan H, Mohanty A, Cao B. Comparative genome analysis reveals genetic adaptation to versatile environmental conditions and importance of biofilm lifestyle in Comamonas testosteroni. Appl Microbiol Biotechnol 2015; 99:3519-32. [PMID: 25786738 DOI: 10.1007/s00253-015-6519-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 02/28/2015] [Accepted: 03/02/2015] [Indexed: 01/06/2023]
Abstract
Comamonas testosteroni is an important environmental bacterium capable of degrading a variety of toxic aromatic pollutants and has been demonstrated to be a promising biocatalyst for environmental decontamination. This organism is often found to be among the primary surface colonizers in various natural and engineered ecosystems, suggesting an extraordinary capability of this organism in environmental adaptation and biofilm formation. The goal of this study was to gain genetic insights into the adaption of C. testosteroni to versatile environments and the importance of a biofilm lifestyle. Specifically, a draft genome of C. testosteroni I2 was obtained. The draft genome is 5,778,710 bp in length and comprises 110 contigs. The average G+C content was 61.88 %. A total of 5365 genes with 5263 protein-coding genes were predicted, whereas 4324 (80.60 % of total genes) protein-encoding genes were associated with predicted functions. The catabolic genes responsible for biodegradation of steroid and other aromatic compounds on draft genome were identified. Plasmid pI2 was found to encode a complete pathway for aniline degradation and a partial catabolic pathway for chloroaniline. This organism was found to be equipped with a sophisticated signaling system which helps it find ideal niches and switch between planktonic and biofilm lifestyles. A large number of putative multi-drug-resistant genes coding for abundant outer membrane transporters, chaperones, and heat shock proteins for the protection of cellular function were identified in the genome of strain I2. In addition, the genome of strain I2 was predicted to encode several proteins involved in producing, secreting, and uptaking siderophores under iron-limiting conditions. The genome of strain I2 contains a number of genes responsible for the synthesis and secretion of exopolysaccharides, an extracellular component essential for biofilm formation. Overall, our results reveal the genomic features underlying the adaption of C. testosteroni to versatile environments and highlighting the importance of its biofilm lifestyle.
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Affiliation(s)
- Yichao Wu
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, 639798, Singapore
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20
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Gao J, Ju KS, Yu X, Velásquez JE, Mukherjee S, Lee J, Zhao C, Evans BS, Doroghazi JR, Metcalf WW, van der Donk WA. Use of a phosphonate methyltransferase in the identification of the fosfazinomycin biosynthetic gene cluster. Angew Chem Int Ed Engl 2014; 53:1334-7. [PMID: 24376039 PMCID: PMC3927463 DOI: 10.1002/anie.201308363] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/16/2013] [Indexed: 12/19/2022]
Abstract
Natural product discovery has been boosted by genome mining approaches, but compound purification is often still challenging. We report an enzymatic strategy for "stable isotope labeling of phosphonates in extract" (SILPE) that facilitates their purification. We used the phosphonate methyltransferase DhpI involved in dehydrophos biosynthesis to methylate a variety of phosphonate natural products in crude spent medium with a mixture of labeled and unlabeled S-adenosyl methionine. Mass-guided fractionation then allowed straightforward purification. We illustrate its utility by purifying a phosphonate that led to the identification of the fosfazinomycin biosynthetic gene cluster. This unusual natural product contains a hydrazide linker between a carboxylic acid and a phosphonic acid. Bioinformatic analysis of the gene cluster provides insights into how such a structure might be assembled.
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Affiliation(s)
- Jiangtao Gao
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West, Gregory Drive, Urbana, Illinois 61801, USA
| | - Kou-San Ju
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West, Gregory Drive, Urbana, Illinois 61801, USA
| | - Xiaomin Yu
- Department of Microbiology, 601 South Goodwin Avenue, Urbana, Illinois 61801, USA
| | - Juan E. Velásquez
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600, South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Subha Mukherjee
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600, South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Jaeheon Lee
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West, Gregory Drive, Urbana, Illinois 61801, USA
| | - Changming Zhao
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West, Gregory Drive, Urbana, Illinois 61801, USA
| | - Bradley S. Evans
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West, Gregory Drive, Urbana, Illinois 61801, USA
| | - James R. Doroghazi
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West, Gregory Drive, Urbana, Illinois 61801, USA
| | - William W. Metcalf
- Department of Microbiology, 601 South Goodwin Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600, South Mathews Avenue, Urbana, Illinois 61801, USA
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21
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Gao J, Ju KS, Yu X, Velásquez JE, Mukherjee S, Lee J, Zhao C, Evans BS, Doroghazi JR, Metcalf WW, van der Donk WA. Use of a Phosphonate Methyltransferase in the Identification of the Fosfazinomycin Biosynthetic Gene Cluster. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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