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Wang S, Yun Y, Tian X, Su Z, Liao Z, Li G, Ma T. HMDB: A curated database of genes involved in hydrocarbon monooxygenation reaction with homologous genes as background. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132397. [PMID: 37639797 DOI: 10.1016/j.jhazmat.2023.132397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 08/10/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
The investigation of hydrocarbon degradation potential of environmental microorganisms is an important research topic, whether for the global carbon cycle or oil pollution remediation. Under aerobic conditions, the microorganisms employ a range of monooxygenases to use hydrocarbons substrates as a source of carbon and energy. With the explosion of sequencing data, mining genes in genomes or metagenomes has become computationally expensive and time-consuming. We proposed the HMDB, which is a professional gene database of hydrocarbon monooxygenases. HMDB contains 38 genes, which encode 11 monooxygenases responsible for the hydroxylation of 8 hydrocarbons. To reduce false positives, the strategy of using homologous genes as background noise was applied for HMDB. We added 10,095 gene sequences of homologous enzymes which took non-hydrocarbons as substrates to HMDB. The classic BLAST method and best-hit strategy were recommended for HMDB usage, but not limited. The performance of HMDB was validated using 264,402 prokaryote genomes from RefSeq and 51 metagenomes from SRA. The results showed that HMDB database had high sensitivity and low false positive rate. We release the HMDB database here, hoping to speed up the process for investigation of hydrocarbon monooxygenases in massive metagenomic data. HMDB is freely available at http://www.orgene.net/HMDB/.
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Affiliation(s)
- Shaojing Wang
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yuan Yun
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xuefeng Tian
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhaoying Su
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zitong Liao
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Guoqiang Li
- College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Ting Ma
- College of Life Sciences, Nankai University, Tianjin 300071, China.
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Bretschneider L, Heuschkel I, Ahmed A, Bühler K, Karande R, Bühler B. Characterization of different biocatalyst formats for BVMO-catalyzed cyclohexanone oxidation. Biotechnol Bioeng 2021; 118:2719-2733. [PMID: 33844297 DOI: 10.1002/bit.27791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/03/2021] [Accepted: 04/04/2021] [Indexed: 01/05/2023]
Abstract
Cyclohexanone monooxygenase (CHMO), a member of the Baeyer-Villiger monooxygenase family, is a versatile biocatalyst that efficiently catalyzes the conversion of cyclic ketones to lactones. In this study, an Acidovorax-derived CHMO gene was expressed in Pseudomonas taiwanensis VLB120. Upon purification, the enzyme was characterized in vitro and shown to feature a broad substrate spectrum and up to 100% conversion in 6 h. Furthermore, we determined and compared the cyclohexanone conversion kinetics for different CHMO-biocatalyst formats, that is, isolated enzyme, suspended whole cells, and biofilms, the latter two based on recombinant CHMO-containing P. taiwanensis VLB120. Biofilms showed less favorable values for KS (9.3-fold higher) and kcat (4.8-fold lower) compared with corresponding KM and kcat values of isolated CHMO, but a favorable KI for cyclohexanone (5.3-fold higher). The unfavorable KS and kcat values are related to mass transfer- and possibly heterogeneity issues and deserve further investigation and engineering, to exploit the high potential of biofilms regarding process stability. Suspended cells showed only 1.8-fold higher KS , but 1.3- and 4.2-fold higher kcat and KI values than isolated CHMO. This together with the efficient NADPH regeneration via glucose metabolism makes this format highly promising from a kinetics perspective.
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Affiliation(s)
- Lisa Bretschneider
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ingeborg Heuschkel
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Afaq Ahmed
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Katja Bühler
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Rohan Karande
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
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Tan L, Nishimura H, Wang YF, Sun ZY, Tang YQ, Kida K, Morimura S. Effect of organic loading rate on thermophilic methane fermentation of stillage eluted from ethanol fermentation of waste paper and kitchen waste. J Biosci Bioeng 2019; 127:582-588. [DOI: 10.1016/j.jbiosc.2018.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/02/2018] [Accepted: 10/09/2018] [Indexed: 10/27/2022]
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Fungal biotransformation of short-chain n-alkylcycloalkanes. Appl Microbiol Biotechnol 2019; 103:4137-4151. [PMID: 30941461 DOI: 10.1007/s00253-019-09749-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/25/2019] [Accepted: 03/03/2019] [Indexed: 10/27/2022]
Abstract
The cycloalkanes, comprising up to 45% of the hydrocarbon fraction, occur in crude oil or refined oil products (e.g., gasoline) mainly as alkylated cyclohexane derivatives and have been increasingly found in environmental samples of soil and water. Furthermore, short-chain alkylated cycloalkanes are components of the so-called volatile organic compounds (VOCs). This study highlights the biotransformation of methyl- and ethylcyclohexane by the alkane-assimilating yeast Candida maltosa and the phenol- and benzoate-utilizing yeast Trichosporon mucoides under laboratory conditions. In the course of this biotransformation, we detected 25 different metabolites, which were analyzed by HPLC and GC-MS. The biotransformation process of methylcyclohexane in both yeasts involve (A) ring hydroxylation at different positions (C2, C3, and C4) and subsequent oxidation to ketones as well as (B) oxidation of the alkyl side chain to hydroxylated and acid products. The yeast T. mucoides additionally performs ring hydroxylation at the C1-position and (C) oxidative decarboxylation and (D) aromatization of cyclohexanecarboxylic acid. Both yeasts also oxidized the saturated ring system and the side chain of ethylcyclohexane. However, the cyclohexylacetic acid, which was formed, seemed not to be substrate for aromatization. This is the first report of several new transformation reactions of alkylated cycloalkanes for eukaryotic microorganisms.
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Deng Y, Deng C, Yang J, Li B, Wang E, Yuan H. Novel Butane-Oxidizing Bacteria and Diversity of bmoX Genes in Puguang Gas Field. Front Microbiol 2018; 9:1576. [PMID: 30065710 PMCID: PMC6056644 DOI: 10.3389/fmicb.2018.01576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/25/2018] [Indexed: 11/13/2022] Open
Abstract
To investigate the diversity of butane-oxidizing bacteria in soils contaminated by long-term light hydrocarbon microseepage and the influence of butane on the soil microbial community, a quantitative study and identification of butane-oxidizing bacteria (BOB) in soils at the Puguang gas field were performed by DNA-based stable isotope probing (DNA-SIP). For the first time, two phylotypes corresponding to the genera Giesbergeria and Ramlibacter were identified as being directly involved in butane oxidation, in addition to the well-known light hydrocarbon degrader Pseudomonas. Furthermore, bmoX genes were strongly labeled by 13C-butane, and their abundances in gas field soils increased by 43.14-, 17.39-, 21.74-, and 30.14-fold when incubated with butane for 6, 9, 12, and 14 days, respectively, indicating that these bmoX-harboring bacteria could use butane as the sole carbon and energy source and they play an important role in butane degradation. We also found that the addition of butane rapidly shaped the bacterial community and reduced the diversity of bmoX genes in the gas field soils. These findings improve our understanding of BOB in the gas field environment and reveal the potential for their applications in petroleum exploration and bioremediation.
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Affiliation(s)
- Yue Deng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chunping Deng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Baozhen Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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Yan DZ, Li X, Li CZ, Mao LQ, Chi XQ, Zhou NY, Liu DY. Genome-wide identification and characterization of genes encoding cyclohexylamine degradation in a novel cyclohexylamine-degrading bacterial strain of Pseudomonas plecoglossicida NyZ12. J Biotechnol 2017; 251:166-173. [DOI: 10.1016/j.jbiotec.2017.04.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 04/22/2017] [Accepted: 04/28/2017] [Indexed: 10/19/2022]
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Salamanca D, Karande R, Schmid A, Dobslaw D. Novel cyclohexane monooxygenase from Acidovorax sp. CHX100. Appl Microbiol Biotechnol 2015; 99:6889-97. [DOI: 10.1007/s00253-015-6599-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/31/2015] [Accepted: 04/03/2015] [Indexed: 11/28/2022]
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Auffret MD, Yergeau E, Labbé D, Fayolle-Guichard F, Greer CW. Importance of Rhodococcus strains in a bacterial consortium degrading a mixture of hydrocarbons, gasoline, and diesel oil additives revealed by metatranscriptomic analysis. Appl Microbiol Biotechnol 2014; 99:2419-30. [PMID: 25343979 DOI: 10.1007/s00253-014-6159-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/12/2014] [Indexed: 11/29/2022]
Abstract
A bacterial consortium (Mix3) composed of microorganisms originating from different environments (soils and wastewater) was obtained after enrichment in the presence of a mixture of 16 hydrocarbons, gasoline, and diesel oil additives. After addition of the mixture, the development of the microbial composition of Mix3 was monitored at three different times (35, 113, and 222 days) using fingerprinting method and dominant bacterial species were identified. In parallel, 14 bacteria were isolated after 113 days and identified. Degradation capacities for Mix3 and the isolated bacterial strains were characterized and compared. At day 113, we induced the expression of catabolic genes in Mix3 by adding the substrate mixture to resting cells and the metatranscriptome was analyzed. After addition of the substrate mixture, the relative abundance of Actinobacteria increased at day 222 while a shift between Rhodococcus and Mycobacterium was observed after 113 days. Mix3 was able to degrade 13 compounds completely, with partial degradation of isooctane and 2-ethylhexyl nitrate, but tert-butyl alcohol was not degraded. Rhodococcus wratislaviensis strain IFP 2016 isolated from Mix3 showed almost the same degradation capacities as Mix3: these results were not observed with the other isolated strains. Transcriptomic results revealed that Actinobacteria and in particular, Rhodococcus species, were major contributors in terms of total and catabolic gene transcripts while other species were involved in cyclohexane degradation. Not all the microorganisms identified at day 113 were active except R. wratislaviensis IFP 2016 that appeared to be a major player in the degradation activity observed in Mix3.
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Affiliation(s)
- Marc D Auffret
- Institut Français du Pétrole (IFP), 1-4 Avenue de Bois-Préau, 92852, Rueil-Malmaison, France,
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SmoXYB1C1Z of Mycobacterium sp. strain NBB4: a soluble methane monooxygenase (sMMO)-like enzyme, active on C2 to C4 alkanes and alkenes. Appl Environ Microbiol 2014; 80:5801-6. [PMID: 25015887 DOI: 10.1128/aem.01338-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Monooxygenase (MO) enzymes initiate the aerobic oxidation of alkanes and alkenes in bacteria. A cluster of MO genes (smoXYB1C1Z) of thus-far-unknown function was found previously in the genomes of two Mycobacterium strains (NBB3 and NBB4) which grow on hydrocarbons. The predicted Smo enzymes have only moderate amino acid identity (30 to 60%) to their closest homologs, the soluble methane and butane MOs (sMMO and sBMO), and the smo gene cluster has a different organization from those of sMMO and sBMO. The smoXYB1C1Z genes of NBB4 were cloned into pMycoFos to make pSmo, which was transformed into Mycobacterium smegmatis mc(2)-155. Cells of mc(2)-155(pSmo) metabolized C2 to C4 alkanes, alkenes, and chlorinated hydrocarbons. The activities of mc(2)-155(pSmo) cells were 0.94, 0.57, 0.12, and 0.04 nmol/min/mg of protein with ethene, ethane, propane, and butane as substrates, respectively. The mc(2)-155(pSmo) cells made epoxides from ethene, propene, and 1-butene, confirming that Smo was an oxygenase. Epoxides were not produced from larger alkenes (1-octene and styrene). Vinyl chloride and 1,2-dichloroethane were biodegraded by cells expressing Smo, with production of inorganic chloride. This study shows that Smo is a functional oxygenase which is active against small hydrocarbons. M. smegmatis mc(2)-155(pSmo) provides a new model for studying sMMO-like monooxygenases.
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Zeyhle P, Bauer JS, Kalinowski J, Shin-ya K, Gross H, Heide L. Genome-based discovery of a novel membrane-bound 1,6-dihydroxyphenazine prenyltransferase from a marine actinomycete. PLoS One 2014; 9:e99122. [PMID: 24892559 PMCID: PMC4044012 DOI: 10.1371/journal.pone.0099122] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 05/11/2014] [Indexed: 12/02/2022] Open
Abstract
Recently, novel prenylated derivatives of 1,6-dihydroxyphenazine have been isolated from the marine sponge-associated Streptomyces sp. SpC080624SC-11. Genome sequencing of this strain now revealed a gene cluster containing all genes necessary for the synthesis of the phenazine and the isoprenoid moieties. Unexpectedly, however, the cluster did not contain a gene with similarity to previously investigated phenazine prenyltransferases, but instead a gene with modest similarity to the membrane-bound prenyltransferases of ubiquinone and menaquinone biosynthesis. Expression of this gene in E. coli and isolation of the membrane fraction proved that the encoded enzyme, Mpz10, catalyzes two successive prenylations of 1,6-dihydroxyphenazine. Mpz10 is the first example of a membrane-bound enzyme catalyzing the prenylation of a phenazine substrate, and one of few examples of membrane-bound enzymes involved in the prenylation of aromatic secondary metabolites in microorganisms.
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Affiliation(s)
- Philipp Zeyhle
- Pharmazeutische Biologie, Pharmazeutisches Institut, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Judith S. Bauer
- Pharmazeutische Biologie, Pharmazeutisches Institut, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Kazuo Shin-ya
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Harald Gross
- Pharmazeutische Biologie, Pharmazeutisches Institut, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Lutz Heide
- Pharmazeutische Biologie, Pharmazeutisches Institut, Eberhard Karls Universität Tübingen, Tübingen, Germany
- * E-mail:
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Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME JOURNAL 2014; 8:1464-75. [PMID: 24451203 PMCID: PMC4069396 DOI: 10.1038/ismej.2013.254] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/18/2013] [Accepted: 12/20/2013] [Indexed: 11/28/2022]
Abstract
The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of ∼4.1 million barrels of oil to the Gulf of Mexico; >22% of this oil is unaccounted for, with unknown environmental consequences. Here we investigated the impact of oil deposition on microbial communities in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using 14C-labeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant hydrocarbon degradation pathway encoded genes involved in degrading aliphatic and simple aromatics via butane monooxygenase. The activity of key hydrocarbon degradation pathways by sediment microbes was confirmed by determining the mineralization of 14C-labeled model substrates in the following order: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)'s benchmarks for polycyclic aromatic hydrocarbons (PAHs) compared with those that did not. Importantly, these data demonstrate that the indigenous sediment microbiota contributed an important ecosystem service for remediation of oil in the Gulf. However, PAHs were more recalcitrant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem.
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Dudek HM, Fink MJ, Shivange AV, Dennig A, Mihovilovic MD, Schwaneberg U, Fraaije MW. Extending the substrate scope of a Baeyer–Villiger monooxygenase by multiple-site mutagenesis. Appl Microbiol Biotechnol 2013; 98:4009-20. [DOI: 10.1007/s00253-013-5364-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/25/2013] [Accepted: 10/28/2013] [Indexed: 10/26/2022]
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13
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Toward biotechnological production of adipic acid and precursors from biorenewables. J Biotechnol 2013; 167:75-84. [DOI: 10.1016/j.jbiotec.2012.07.008] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/07/2012] [Accepted: 07/13/2012] [Indexed: 11/23/2022]
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14
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Barr WJ, Yi T, Aga D, Acevedo O, Harper WF. Using electronic theory to identify metabolites present in 17α-ethinylestradiol biotransformation pathways. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:760-768. [PMID: 22129464 DOI: 10.1021/es201774r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This research used electronic theory to model the biotransformation of 17α-ethinylestradiol (EE(2)) under aerobic conditions in mixed culture. The methodology involved determining the Frontier Electron Density (FED) for EE(2) and various metabolites, as well as invoking well-established degradation rules to predict transformation pathways. We show that measured EE(2) metabolites are in good agreement with what is expected based on FED-based modeling. Initiating reactions occur at Ring A, producing metabolites that have been experimentally detected. When OH-EE(2) and 6AH-EE(2) are transformed, Ring A is cleaved before Ring B. The metabolites involved in these pathways have different estrogenic potentials, as implied by our analysis of the log P values and the hydrogen bonding characteristics. The OH-EE(2) and 6AH-EE(2) transformation pathways also show redox-induced electron rearrangement (RIER), where oxidation reactions lead to the reduction of carbon units present along the bond axis. Sulfo-EE(2) appears to be difficult to biotransform. These findings clarify theoretical and practical aspects of EE(2) biotransformation.
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Affiliation(s)
- William J Barr
- Department of Civil and Environmental Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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Coleman NV, Yau S, Wilson NL, Nolan LM, Migocki MD, Ly MA, Crossett B, Holmes AJ. Untangling the multiple monooxygenases of Mycobacterium chubuense strain NBB4, a versatile hydrocarbon degrader. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:297-307. [PMID: 23761275 DOI: 10.1111/j.1758-2229.2010.00225.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Mycobacterium strain NBB4 was isolated on ethene as part of a bioprospecting study searching for novel monooxygenase (MO) enzymes of interest to biocatalysis and bioremediation. Previous work indicated that strain NBB4 contained an unprecedented diversity of MO genes, and we hypothesized that each MO type would support growth on a distinct hydrocarbon substrate. Here, we attempted to untangle the relationships between MO types and hydrocarbon substrates. Strain NBB4 was shown to grow on C2 -C4 alkenes and C2 -C16 alkanes. Complete gene clusters encoding six different monooxygenases were recovered from a fosmid library, including homologues of ethene MO (etnABCD), propene MO (pmoABCD), propane MO (smoABCD), butane MO (smoXYB1C1Z), cytochrome P450 (CYP153; fdx-cyp-fdr) and alkB (alkB-rubA1-rubA2). Catabolic enzymes involved in ethene assimilation (EtnA, EtnC, EtnD, EtnE) and alkane assimilation (alcohol and aldehyde dehydrogenases) were identified by proteomics, and we showed for the first time that stress response proteins (catalase/peroxidase, chaperonins) were induced by growth on C2 -C5 alkanes and ethene. Surprisingly, none of the identified MO genes could be specifically associated with oxidation of small alkanes, and thus the nature of the gaseous alkane MO in NBB4 remains mysterious.
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Affiliation(s)
- Nicholas V Coleman
- School of Molecular Bioscience, Building G08, University of Sydney, Sydney, NSW 2006, Australia
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16
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Leisch H, Morley K, Lau PCK. Baeyer−Villiger Monooxygenases: More Than Just Green Chemistry. Chem Rev 2011; 111:4165-222. [DOI: 10.1021/cr1003437] [Citation(s) in RCA: 317] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Hannes Leisch
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
| | - Krista Morley
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
| | - Peter C. K. Lau
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, Quebec H3A 2B4, Canada
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Insertion sequence elements in Cupriavidus metallidurans CH34: Distribution and role in adaptation. Plasmid 2011; 65:193-203. [DOI: 10.1016/j.plasmid.2010.12.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 12/20/2010] [Indexed: 11/20/2022]
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18
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Cooley RB, Bottomley PJ, Arp DJ. Growth of a non-methanotroph on natural gas: ignoring the obvious to focus on the obscure. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:408-413. [PMID: 23765894 DOI: 10.1111/j.1758-2229.2009.00060.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Methanotrophs are well known for their ability to grow on methane in natural gas environments; however, these environments also contain low concentrations of longer-chain-length gaseous alkanes. This mixture of alkanes poses a problem for organisms that might otherwise grow on alkanes ≥ C2 because methane could inhibit oxidation of growth substrates and lead to an accumulation of toxic C1 metabolites. Here, we have characterized the growth of a C2 -C9 alkane-utilizing bacterium, Thauera butanivorans, in conditions containing high concentrations of methane and small amounts (< 3% of total alkane) of C2 -C4 . During such growth, methanol accumulates transiently before being consumed in an O2 -dependent process that leads to the formation of a proton gradient and subsequent ATP generation. In contrast, formaldehyde-dependent O2 consumption is insensitive to uncouplers and does not lead to significant ATP production. This efficient C1 oxidation process that regains much of the energy loss inflicted by oxidizing methane, coupled with an alkane monooxygenase effective at limiting methane oxidation, allows T. butanivorans to grow uninhibited in natural gas environments. Although longer-chain-length gaseous alkane-utilizing organisms have been previously identified to grow in natural gas seepages, the data presented here represent the first detailed characterization of the physiological effects associated with inadvertent methane oxidation by a non-methanotroph, and suggest the presence of a well-evolved series of biochemical processes that allow them to grow in natural gas deposits without the need for developing the unique metabolic machinery characteristic of methanotrophs.
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Affiliation(s)
- Richard B Cooley
- Departments of Biochemistry and Biophysics, Microbiology and Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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Silva TFS, Mishra GS, Guedes da Silva MF, Wanke R, Martins LMDRS, Pombeiro AJL. CuII complexes bearing the 2,2,2-tris(1-pyrazolyl)ethanol or 2,2,2-tris(1-pyrazolyl)ethyl methanesulfonate scorpionates. X-Ray structural characterization and application in the mild catalytic peroxidative oxidation of cyclohexane. Dalton Trans 2009:9207-15. [DOI: 10.1039/b911990f] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lee EH, Cho KS. Characterization of cyclohexane and hexane degradation by Rhodococcus sp. EC1. CHEMOSPHERE 2008; 71:1738-1744. [PMID: 18289631 DOI: 10.1016/j.chemosphere.2007.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2007] [Revised: 12/14/2007] [Accepted: 12/20/2007] [Indexed: 05/25/2023]
Abstract
Cyclohexane is a recalcitrant compound that is more difficult to degrade than even n-alkanes or monoaromatic hydrocarbons. In this study, a cyclohexane-degrading consortium was obtained from oil-contaminated soil by an enrichment culture method. Based on a 16S rDNA polymerase chain reaction-denaturing gradient gel electrophoresis method, this consortium was identified as comprising Alpha-proteobacteria, Actinobacteria, and Gamma-proteobacteria. One of these organisms, Rhodococcus sp. EC1, was isolated and shown to have excellent cyclohexane-degrading ability. The maximum specific cyclohexane degradation rate (Vmax) for EC1 was 246 micromol g-DCW(-1) (dry cell weight)h(-1). The optimum conditions of cyclohexane degradation were 25-35 degrees C and pH 6-8. In addition to its cyclohexane degradation abilities, EC1 was also able to strongly degrade hexane, with a maximum specific hexane degradation rate of 361 micromol g-DCW(-1)h(-1). Experiments using 14C-hexane revealed that EC1 mineralized 40% of hexane into CO2 and converted 53% into biomass. Moreover, EC1 could use other hydrocarbons, including methanol, ethanol, acetone, methyl tert-butyl ether, pyrene, diesel, lubricant oil, benzene, toluene, ethylbenzene, m-xylene, p-xylene and o-xylene. These findings collectively suggest that EC1 may be a useful biological resource for removal of cyclohexane, hexane, and other recalcitrant hydrocarbons.
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Affiliation(s)
- Eun-Hee Lee
- Department of Environmental Science and Engineering, Ewha Womans University, 11-1, Daehyun-dong, Seodaemun-Gu, Seoul 120-750, Republic of Korea
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Aerobic biotransformation of decalin (decahydronaphthalene) by Rhodococcus spp. Biodegradation 2008; 19:785-94. [DOI: 10.1007/s10532-008-9181-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 02/11/2008] [Indexed: 11/27/2022]
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Onaca C, Kieninger M, Engesser KH, Altenbuchner J. Degradation of alkyl methyl ketones by Pseudomonas veronii MEK700. J Bacteriol 2007; 189:3759-67. [PMID: 17351032 PMCID: PMC1913341 DOI: 10.1128/jb.01279-06] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas veronii MEK700 was isolated from a biotrickling filter cleaning 2-butanone-loaded waste air. The strain is able to grow on 2-butanone and 2-hexanol. The genes for degradation of short chain alkyl methyl ketones were identified by transposon mutagenesis using a newly designed transposon, mini-Tn5495, and cloned in Escherichia coli. DNA sequence analysis of a 15-kb fragment revealed three genes involved in methyl ketone degradation. The deduced amino acid sequence of the first gene, mekA, had high similarity to Baeyer-Villiger monooxygenases; the protein of the second gene, mekB, had similarity to homoserine acetyltransferases; the third gene, mekR, encoded a putative transcriptional activator of the AraC/XylS family. The three genes were located between two gene groups: one comprising a putative phosphoenolpyruvate synthase and glycogen synthase, and the other eight genes for the subunits of an ATPase. Inactivation of mekA and mekB by insertion of the mini-transposon abolished growth of P. veronii MEK700 on 2-butanone and 2-hexanol. The involvement of mekR in methyl ketone degradation was observed by heterologous expression of mekA and mekB in Pseudomonas putida. A fragment containing mekA and mekB on a plasmid was not sufficient to allow P. putida KT2440 to grow on 2-butanone. Not until all three genes were assembled in the recombinant P. putida was it able to use 2-butanone as carbon source. The Baeyer-Villiger monooxygenase activity of MekA was clearly demonstrated by incubating a mekB transposon insertion mutant of P. veronii with 2-butanone. Hereby, ethyl acetate was accumulated. To our knowledge, this is the first time that ethyl acetate by gas chromatographic analysis has been definitely demonstrated to be an intermediate of MEK degradation. The mekB-encoded protein was heterologously expressed in E. coli and purified by immobilized metal affinity chromatography. The protein exhibited high esterase activity towards short chain esters like ethyl acetate and 4-nitrophenyl acetate.
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Affiliation(s)
- Christina Onaca
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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Kotani T, Yurimoto H, Kato N, Sakai Y. Novel acetone metabolism in a propane-utilizing bacterium, Gordonia sp. strain TY-5. J Bacteriol 2007; 189:886-93. [PMID: 17071761 PMCID: PMC1797311 DOI: 10.1128/jb.01054-06] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 10/16/2006] [Indexed: 11/20/2022] Open
Abstract
In the propane-utilizing bacterium Gordonia sp. strain TY-5, propane was shown to be oxidized to 2-propanol and then further oxidized to acetone. In this study, the subsequent metabolism of acetone was studied. Acetone-induced proteins were found in extracts of cells induced by acetone, and a gene cluster designated acmAB was cloned on the basis of the N-terminal amino acid sequences of acetone-induced proteins. The acmA and acmB genes encode a Baeyer-Villiger monooxygenase (BVMO) and esterase, respectively. The BVMO encoded by acmA was purified from acetone-induced cells of Gordonia sp. strain TY-5 and characterized. The BVMO exhibited NADPH-dependent oxidation activity for linear ketones (C3 to C10) and cyclic ketones (C4 to C8). Escherichia coli expressing the acmA gene oxidized acetone to methyl acetate, and E. coli expressing the acmB gene hydrolyzed methyl acetate. Northern blot analyses revealed that polycistronic transcription of the acmAB gene cluster was induced by propane, 2-propanol, and acetone. These results indicate that the acmAB gene products play an important role in the metabolism of acetone derived from propane oxidation and clarify the propane metabolism pathway of strain TY-5 (propane --> 2-propanol --> acetone --> methyl acetate --> acetic acid + methanol). This paper provides the first evidence for BVMO-dependent acetone metabolism.
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Affiliation(s)
- Tetsuya Kotani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Kyoto 606-8502, Japan
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Coleman NV, Bui NB, Holmes AJ. Soluble di-iron monooxygenase gene diversity in soils, sediments and ethene enrichments. Environ Microbiol 2006; 8:1228-39. [PMID: 16817931 DOI: 10.1111/j.1462-2920.2006.01015.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Soluble di-iron monooxygenases (SDIMOs) are key enzymes in the bacterial oxidation of hydrocarbons, and have applications in environmental and industrial biotechnology. SDIMOs from pure cultures are unlikely to represent the total diversity of this enzyme family, so we used polymerase chain reaction to survey the diversity of SDIMO alpha subunit genes in environmental samples, ethene enrichments and ethene-degrading bacterial isolates. From 178 cloned amplicons, 98 restriction fragment length polymorphism types were seen, from which 75 representative SDIMO sequences were obtained; 45 from environmental samples, 25 from enrichments and seven from isolates. The sequences were diverse, including genes similar to ethene (etnC), propene (amoC, pmoC), propane (prmA) and butane (bmoX) monooxygenases, in addition to many novel sequences comprising a new SDIMO group (group 6). Environmental samples showed the highest diversity, with strong representation of group 6 SDIMOs and prmA-like genes. Ethene stimulation of samples resulted in increased frequencies of group 4 SDIMOs (etnC-like). Four ethene-utilizing Mycobacterium isolates (NBB1-NBB4) from enrichments all contained etnC; one isolate (NBB4) also contained three additional SDIMO genes (bmoX-like, amoC-like and group 6). The primers, database, clone libraries and strains reported here provide a resource for future bioremediation and biocatalysis studies, with particular relevance for chlorinated alkene and alkane compounds.
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Affiliation(s)
- Nicholas V Coleman
- School of Molecular and Microbial Biosciences, Building G08, University of Sydney, NSW 2006, Australia
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