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Hassan HA, D Enza M, Armengaud J, Pieper DH. Biochemical and genetic characterization comparison of four extradiol dioxygenases in Rhizorhabdus wittichii RW1. Appl Microbiol Biotechnol 2022; 106:5539-5550. [PMID: 35906995 DOI: 10.1007/s00253-022-12099-3] [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: 04/18/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022]
Abstract
Rhizorhabdus (previously Sphingomonas) wittichii RW1 uses a diverse array of aromatic organic compounds as energy and carbon sources, including some extremely recalcitrant compounds such as dibenzo-p-dioxin and dibenzofuran. Extradiol dioxygenases play a key role in the metabolism of dibenzofuran (DBF), dibenzo-p-dioxin (DBD), PCBs, and various other aromatic compounds. In this study, a detailed kinetic analysis of four extradiol dioxygenases identified in R. wittichii RW1 (DbfB, Edo2, Edo3, and Edo4) showed all of them to be typical 2,3dihydroxybiphenyl (DHB) dioxygenases with DHB as preferred substrate (kcat/Km values of 0.13-188 (µM -1 s-1)) and only slightly lower activity against trihydroxybiphenyl (THB) whereas monocyclic substrates were, to different extents, poor substrates due to high km values. All extradiol dioxygenases analyzed were subject to mechanism-based inactivation by 2,2`,3-trihydroxybiphenylether (THBE) the intermediate of DBD degradation. However, Edo4 was superior as reflected by the relatively high partition ratio and the comparably low efficiency of inactivation. Significant differences were observed with respect to their inactivation by 3-chlorocatechol. The absence of any significant mechanism-based inactivation makes Edo3 a perfect candidate for being recruited for chlorobiphenyl degradation where inactivation of extradiol dioxygenases by this intermediate creates significant metabolic problems. KEY POINTS: • Characterization of additional extradiol dioxygenases encoded by RW1 • Identification of differences in 2,2`,3-trihydroxybiphenylether transformation • Identification of differences in inhibition by 3-chlorocatechol.
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Affiliation(s)
- Hamdy A Hassan
- Department of Environmental Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City 32897, Egypt.
- Biology Department, Science and Humanities College, Shaqra University, Al-Quwayiyah, 11726, Riyadh, Saudi Arabia.
| | - Marina D Enza
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jean Armengaud
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Université Paris-Saclay, CEA, INRAE, Département Médicaments Et Technologies Pour La Santé, Bagnols-sur-Cèze, France
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
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Complete Genome Sequence of Thalassococcus sp. Strain S3, a Marine Roseobacter Clade Member Capable of Degrading Carbazole. Microbiol Resour Announc 2019; 8:8/28/e00231-19. [PMID: 31296670 PMCID: PMC6624753 DOI: 10.1128/mra.00231-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We determined the complete genome sequence of Thalassococcus sp. strain S3, a marine carbazole degrader isolated from Tokyo Bay in Japan that carries genes for aerobic anoxygenic phototrophy. Strain S3 has a 4.7-Mb chromosome that harbors the carbazole-degradative gene cluster and three (96-, 63-, and 46-kb) plasmids. We determined the complete genome sequence of Thalassococcus sp. strain S3, a marine carbazole degrader isolated from Tokyo Bay in Japan that carries genes for aerobic anoxygenic phototrophy. Strain S3 has a 4.7-Mb chromosome that harbors the carbazole-degradative gene cluster and three (96-, 63-, and 46-kb) plasmids.
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Murugan K, Vasudevan N. Intracellular toxicity exerted by PCBs and role of VBNC bacterial strains in biodegradation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 157:40-60. [PMID: 29605643 DOI: 10.1016/j.ecoenv.2018.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/22/2018] [Accepted: 03/06/2018] [Indexed: 06/08/2023]
Abstract
Polychlorinated biphenyls (PCBs) are xenobiotic compounds that persists in the environment for long-term, though its productivity is banned. Abatement of the pollutants have become laborious due to it's recalcitrant nature in the environment leading to toxic effects in humans and other living beings. Biphenyl degrading bacteria co-metabolically degrade low chlorinated PCBs using the active metabolic pathway. bph operon possess different genetic arrangements in gram positive and gram negative bacteria. The binding ability of the genes and the active sites were determined by PCB docking studies. The active site of bphA gene with conserved amino acid residues determines the substrate specificity and biodegradability. Accumulation of toxic intermediates alters cellular behaviour, biomass production and downturn the metabolic activity. Several bacteria in the environment attain unculturable state which is viable and metabolically active but not cultivable (VBNC). Resuscitation-promoting factor (Rpf) and Rpf homologous protein retrieve the culturability of the so far uncultured bacteria. Recovery of this adaptive mechanism against various physical and chemical stressors make a headway in understanding the functionality of both environmental and medically important unculturable bacteria. Thus, this paper review about the general aspects of PCBs, cellular toxicity exerted by PCBs, role of unculturable bacterial strains in biodegradation, genes involved and degradation pathways. It is suggested to extrapolate the research findings on extracellular organic matters produced in culture supernatant of VBNC thus transforming VBNC to culturable state.
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Affiliation(s)
- Karuvelan Murugan
- Centre for Environmental Studies, Anna University, CEG Campus, Chennai, Tamil Nadu, India.
| | - Namasivayam Vasudevan
- Centre for Environmental Studies, Anna University, CEG Campus, Chennai, Tamil Nadu, India.
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Chen YL, Yu CP, Lee TH, Goh KS, Chu KH, Wang PH, Ismail W, Shih CJ, Chiang YR. Biochemical Mechanisms and Catabolic Enzymes Involved in Bacterial Estrogen Degradation Pathways. Cell Chem Biol 2017; 24:712-724.e7. [PMID: 28552583 DOI: 10.1016/j.chembiol.2017.05.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/16/2017] [Accepted: 05/03/2017] [Indexed: 11/29/2022]
Abstract
Estrogens have been classified as group 1 carcinogens by the World Health Organization and represent a significant concern given that they are found in surface waters worldwide, and long-term exposure to estrogen-contaminated water can disrupt sexual development in animals. To date, the estrogen catabolic enzymes and genes remain unknown. Using a tiered functional genomics approach, we identified three estrogen catabolic gene clusters in Sphingomonas sp. strain KC8. We identified several estrone-derived compounds, including 4-hydroxyestrone, a meta-cleavage product, and pyridinestrone acid. The yeast-based estrogen assay suggested that pyridinestrone acid exhibits negligible estrogenic activity. We characterized 17β-estradiol dehydrogenase and 4-hydroxyestrone 4,5-dioxygenase, responsible for the 17-dehydrogenation and meta-cleavage of the estrogen A ring, respectively. The characteristic pyridinestrone acid was detected in estrone-spiked samples collected from two wastewater treatment plants and two suburban rivers in Taiwan. The results significantly expand our understanding of microbial degradation of aromatic steroids at molecular level.
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Affiliation(s)
- Yi-Lung Chen
- Biodiversity Research Center, Academia Sinica, 128 Academia Road Section 2, Nankang, Taipei 115, Taiwan; Department of Life Science, National Taiwan Normal University, Taipei 106, Taiwan; Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei 115, Taiwan
| | - Chang-Ping Yu
- Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Tzong-Huei Lee
- Institute of Fisheries Science, National Taiwan University, Taipei 106, Taiwan
| | - King-Siang Goh
- Biodiversity Research Center, Academia Sinica, 128 Academia Road Section 2, Nankang, Taipei 115, Taiwan
| | - Kung-Hui Chu
- Zachry Department of Civil Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| | - Po-Hsiang Wang
- Biodiversity Research Center, Academia Sinica, 128 Academia Road Section 2, Nankang, Taipei 115, Taiwan
| | - Wael Ismail
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama 26671, Kingdom of Bahrain
| | - Chao-Jen Shih
- Biodiversity Research Center, Academia Sinica, 128 Academia Road Section 2, Nankang, Taipei 115, Taiwan
| | - Yin-Ru Chiang
- Biodiversity Research Center, Academia Sinica, 128 Academia Road Section 2, Nankang, Taipei 115, Taiwan; Department of Life Science, National Taiwan Normal University, Taipei 106, Taiwan; Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei 115, Taiwan.
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5
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Ahn E, Choi KY, Kang BS, Zylstra GJ, Kim D, Kim E. Salicylate degradation by a cold-adapted Pseudomonas sp. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1273-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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6
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Duarte M, Nielsen A, Camarinha-Silva A, Vilchez-Vargas R, Bruls T, Wos-Oxley ML, Jauregui R, Pieper DH. Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation. Environ Microbiol 2017; 19:2992-3011. [PMID: 28401633 DOI: 10.1111/1462-2920.13756] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 03/29/2017] [Accepted: 04/06/2017] [Indexed: 11/27/2022]
Abstract
A culture-independent function-based screening approach was used to assess the microbial aerobic catabolome for polycyclic aromatic hydrocarbons degradation of a soil subjected to 12 years of in situ bioremediation. A total of 422 750 fosmid clones were screened for key aromatic ring-cleavage activities using 2,3-dihydroxybiphenyl as substrate. Most of the genes encoding ring-cleavage enzymes on the 768 retrieved positive fosmids could not be identified using primer-based approaches and, thus, 205 fosmid inserts were sequenced. Nearly two hundred extradiol dioxygenase encoding genes of three different superfamilies could be identified. Additional key genes of aromatic metabolic pathways were identified, including a high abundance of Rieske non-heme iron oxygenases that provided detailed information on enzymes activating aromatic compounds and enzymes involved in activation of the side chain of methylsubstituted aromatics. The gained insights indicated a complex microbial network acting at the site under study, which comprises organisms similar to recently identified Immundisolibacter cernigliae TR3.2 and Rugosibacter aromaticivorans Ca6 and underlined the great potential of an approach that combines an activity-screening, a cost-effective high-throughput sequencing of fosmid clones and a phylogenomic-routed and manually curated database to carefully identify key proteins dedicated to aerobic degradation of aromatic compounds.
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Affiliation(s)
- Márcia Duarte
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany
| | - Agnes Nielsen
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany
| | - Amélia Camarinha-Silva
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany
| | - Ramiro Vilchez-Vargas
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany.,Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University, Magdeburg, Germany
| | - Thomas Bruls
- Institut de Génomique, Genoscope, UMR8030 (CNRS, CEA, Université d'Evry), Evry, France
| | - Melissa L Wos-Oxley
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany.,AgResearch Grasslands, Tennent drive, Palmerston North, New Zealand
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany
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Crombie AT, Khawand ME, Rhodius VA, Fengler KA, Miller MC, Whited GM, McGenity TJ, Murrell JC. Regulation of plasmid-encoded isoprene metabolism in Rhodococcus, a representative of an important link in the global isoprene cycle. Environ Microbiol 2015; 17:3314-29. [PMID: 25727256 PMCID: PMC4676930 DOI: 10.1111/1462-2920.12793] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 01/26/2015] [Indexed: 01/25/2023]
Abstract
Emissions of biogenic volatile organic compounds (VOCs) form an important part of the global carbon cycle, comprising a significant proportion of net ecosystem productivity. They impact atmospheric chemistry and contribute directly and indirectly to greenhouse gases. Isoprene, emitted largely from plants, comprises one third of total VOCs, yet in contrast to methane, which is released in similar quantities, we know little of its biodegradation. Here, we report the genome of an isoprene degrading isolate, Rhodococcus sp. AD45, and, using mutagenesis shows that a plasmid-encoded soluble di-iron centre isoprene monooxygenase (IsoMO) is essential for isoprene metabolism. Using RNA sequencing (RNAseq) to analyse cells exposed to isoprene or epoxyisoprene in a substrate-switch time-course experiment, we show that transcripts from 22 contiguous genes, including those encoding IsoMO, were highly upregulated, becoming among the most abundant in the cell and comprising over 25% of the entire transcriptome. Analysis of gene transcription in the wild type and an IsoMO-disrupted mutant strain showed that epoxyisoprene, or a subsequent product of isoprene metabolism, rather than isoprene itself, was the inducing molecule. We provide a foundation of molecular data for future research on the environmental biological consumption of this important, climate-active compound.
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Affiliation(s)
| | | | - Virgil A Rhodius
- DuPont Industrial Biosciences925 Page Mill Road, Palo Alto, CA, 94304, USA
| | | | - Michael C Miller
- DuPont Industrial Biosciences925 Page Mill Road, Palo Alto, CA, 94304, USA
| | - Gregg M Whited
- DuPont Industrial Biosciences925 Page Mill Road, Palo Alto, CA, 94304, USA
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He Y, Li X, Shen X, Jiang Q, Chen J, Shi J, Tang X, Xu J. Plant-assisted rhizoremediation of decabromodiphenyl ether for e-waste recycling area soil of Taizhou, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:9976-9988. [PMID: 25666473 DOI: 10.1007/s11356-015-4179-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/28/2015] [Indexed: 06/04/2023]
Abstract
To develop an effective phytoremediation approach to purify soils polluted by decabromodiphenyl ether (BDE-209) in e-waste recycling area, pot experiments were conducted through greenhouse growth of seven plant species in BDE-209-polluted soils. The hygrocolous rice (Oryza sativa L.) cultivars (XiuS and HuangHZ) and the xerophyte ryegrass (Lolium perenne L.) were found to be as the most effective functional plants for facilitating BDE-209 dissipation, with the removal of 52.9, 41.9, and 38.7% in field-contaminated soils (collected directly from field, with an average pollution concentration of 394.6 μg BDE-209 kg(-1) soil), as well as 21.7, 27.6, and 28.1% in freshly spiked soils (an average pollution concentration of 4413.57 μg BDE-209 kg(-1) soil, with additional BDE-209 added to field-contaminated soils), respectively. Changes in soil phospholipid fatty acid (PLFA) profiles revealed that different selective enrichments of functional microbial groups (e.g., arbuscular mycorrhizal fungi and gram-positive bacteria) were induced due to plant growth under contrasting water management (flooded-drained sequentially, flooded only, and drained only, respectively). The abundance of available electron donors and acceptors and the activities of soil oxido-reductases were also correspondingly modified, with the activity of catalase, and the content of NO3(-) and Fe(3+) increased generally toward most of the xerophyte treatments, while the activity of dehydrogenase and the content of dissolved organic carbon (DOC) and NH4(+) increased toward the hygrophyte treatments. This differentiated dissipation of BDE-209 in soils as function of plant species, pollution doses and time, and water-dependent redox condition. This study illustrates a possibility of phytoremediation for BDE-209-polluted soils by successive cultivation of rice followed by ryegrass coupling with suitable water management, possibly through dissipation pathway of microbial reductive debromination and subsequent aerobic oxidative cleavage of benzene ring.
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Affiliation(s)
- Yan He
- College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Zhejiang University, Hangzhou, 310058, China,
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9
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Duarte M, Jauregui R, Vilchez-Vargas R, Junca H, Pieper DH. AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau118. [PMID: 25468931 PMCID: PMC4250580 DOI: 10.1093/database/bau118] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Understanding prokaryotic transformation of recalcitrant pollutants and the in-situ metabolic nets require the integration of massive amounts of biological data. Decades of biochemical studies together with novel next-generation sequencing data have exponentially increased information on aerobic aromatic degradation pathways. However, the majority of protein sequences in public databases have not been experimentally characterized and homology-based methods are still the most routinely used approach to assign protein function, allowing the propagation of misannotations. AromaDeg is a web-based resource targeting aerobic degradation of aromatics that comprises recently updated (September 2013) and manually curated databases constructed based on a phylogenomic approach. Grounded in phylogenetic analyses of protein sequences of key catabolic protein families and of proteins of documented function, AromaDeg allows query and data mining of novel genomic, metagenomic or metatranscriptomic data sets. Essentially, each query sequence that match a given protein family of AromaDeg is associated to a specific cluster of a given phylogenetic tree and further function annotation and/or substrate specificity may be inferred from the neighboring cluster members with experimentally validated function. This allows a detailed characterization of individual protein superfamilies as well as high-throughput functional classifications. Thus, AromaDeg addresses the deficiencies of homology-based protein function prediction, combining phylogenetic tree construction and integration of experimental data to obtain more accurate annotations of new biological data related to aerobic aromatic biodegradation pathways. We pursue in future the expansion of AromaDeg to other enzyme families involved in aromatic degradation and its regular update. Database URL:http://aromadeg.siona.helmholtz-hzi.de
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Affiliation(s)
- Márcia Duarte
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Ramiro Vilchez-Vargas
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Howard Junca
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
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10
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de Carvalho CCCR, Costa SS, Fernandes P, Couto I, Viveiros M. Membrane transport systems and the biodegradation potential and pathogenicity of genus Rhodococcus. Front Physiol 2014; 5:133. [PMID: 24772091 PMCID: PMC3983516 DOI: 10.3389/fphys.2014.00133] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/18/2014] [Indexed: 11/13/2022] Open
Abstract
The Rhodococcus genus contains species with remarkable ability to tolerate toxic compounds and to degrade a myriad of substrates. These substrates have to cross a distinctive cell envelope dominated by mycolic acids anchored in a scaffold of arabinogalactan covalently attached to the cell wall peptidoglycan, and a cellular membrane with phospholipids, whose composition in fatty acids can be rapidly altered in response to environmental conditions. The hydrophobic nature of the cell envelope facilitates the entrance of hydrophobic molecules but some substrates require active transport systems. Additionally, toxic compounds may also be extruded by energy spending efflux systems. In this review, physiological evidences of the use of transport systems by Rhodococcus strains and genomic studies that corroborate their existence are presented and discussed. The recently released complete genomes of several Rhodococcus strains will be the basis for an in silico correlation analysis between the efflux pumps present in the genome and their role on active transport of substrates. These transport systems will be placed on an integrative perspective of the impact of this important genus on biotechnology and health, ranging from bioremediation to antibiotic and biocide resistance.
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Affiliation(s)
- Carla C C R de Carvalho
- Department of Bioengineering, Centre for Biological and Chemical Engineering, Institute of Biotechnology and Bioengineering, Instituto Superior Técnico, Universidade de Lisboa Lisboa, Portugal
| | - Sofia S Costa
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa Lisboa, Portugal ; Centro de Recursos Microbiológicos, Universidade Nova de Lisboa Caparica, Portugal
| | - Pedro Fernandes
- Department of Bioengineering, Centre for Biological and Chemical Engineering, Institute of Biotechnology and Bioengineering, Instituto Superior Técnico, Universidade de Lisboa Lisboa, Portugal
| | - Isabel Couto
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa Lisboa, Portugal ; Centro de Recursos Microbiológicos, Universidade Nova de Lisboa Caparica, Portugal
| | - Miguel Viveiros
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa Lisboa, Portugal ; Centro de Malária e Outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa Lisboa, Portugal
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11
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Defining a kinetic mechanism for l-DOPA 2,3 dioxygenase, a single-domain type I extradiol dioxygenase from Streptomyces lincolnensis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:607-14. [DOI: 10.1016/j.bbapap.2013.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 11/11/2013] [Accepted: 12/09/2013] [Indexed: 11/22/2022]
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12
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Cao L, Gao Y, Wu G, Li M, Xu J, He J, Li S, Hong Q. Cloning of three 2,3-dihydroxybiphenyl-1,2-dioxygenase genes from Achromobacter sp. BP3 and the analysis of their roles in the biodegradation of biphenyl. JOURNAL OF HAZARDOUS MATERIALS 2013; 261:246-252. [PMID: 23948567 DOI: 10.1016/j.jhazmat.2013.07.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/10/2013] [Accepted: 07/11/2013] [Indexed: 06/02/2023]
Abstract
Three 2,3-dihydroxybiphenyl 1,2-dioxygenase genes (designated as bphC1, bphC2 and bphC3) were cloned from a biphenyl-degrading strain Achromobacter sp. BP3. The amino acid sequence of BphC1 and BphC3 had high similarity (>99%) with the reported BphCs, while BphC2 showed relatively low identity (29.51-50.17%) with the reported BphCs, which indicated that bphC2 might be a novel gene. The bphC1, bphC2 and bphC3 genes were expressed in Escherichia coli BL21 and the products were homogenously purified. BphC1, BphC2 and BphC3 displayed maximum activity at 30°C, 30°C and 40°C, respectively. Their optimal catalysis pH was 8.0, 9.0 and 9.0, respectively. BphC1 and BphC2 had higher substrate affinity and catalytic efficiency on 2,3-dihydroxybiphenyl, while BphC3 exhibited these features on aromatic monocyclic substrates. The bphC1 gene was only induced by biphenyl and bphC3 was induced by both biphenyl and toluene, while bphC2 was constitutively expressed in strain BP3. These results suggested that BphC1 and BphC3 played a role in the upstream and downstream metabolic pathways of biphenyl, respectively. However, BphC2 might play a supplementary role and contribute more to the upstream than to the downstream pathway.
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Affiliation(s)
- Li Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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Hydroquinone: environmental pollution, toxicity, and microbial answers. BIOMED RESEARCH INTERNATIONAL 2013; 2013:542168. [PMID: 23936816 PMCID: PMC3727088 DOI: 10.1155/2013/542168] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 06/20/2013] [Indexed: 12/12/2022]
Abstract
Hydroquinone is a major benzene metabolite, which is a well-known haematotoxic and carcinogenic agent associated with malignancy in occupational environments. Human exposure to hydroquinone can occur by dietary, occupational, and environmental sources. In the environment, hydroquinone showed increased toxicity for aquatic organisms, being less harmful for bacteria and fungi. Recent pieces of evidence showed that hydroquinone is able to enhance carcinogenic risk by generating DNA damage and also to compromise the general immune responses which may contribute to the impaired triggering of the host immune reaction. Hydroquinone bioremediation from natural and contaminated sources can be achieved by the use of a diverse group of microorganisms, ranging from bacteria to fungi, which harbor very complex enzymatic systems able to metabolize hydroquinone either under aerobic or anaerobic conditions. Due to the recent research development on hydroquinone, this review underscores not only the mechanisms of hydroquinone biotransformation and the role of microorganisms and their enzymes in this process, but also its toxicity.
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14
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New constitutive vectors: useful genetic engineering tools for biocatalysis. Appl Environ Microbiol 2013; 79:2836-40. [PMID: 23416993 DOI: 10.1128/aem.03746-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Constitutive vectors are useful tools for genetic engineering. Two constitutive vectors with high levels of expression and broad host ranges were developed and used in a range of Pseudomonas hosts. The vectors showed superior characteristics compared to the inducible vectors as well as the potential to be used as improved genetic tools for biocatalysis.
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15
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Expression in Escherichia coli of biphenyl 2,3-dioxygenase genes from a Gram-positive polychlorinated biphenyl degrader, Rhodococcus jostii RHA1. Biosci Biotechnol Biochem 2011; 75:26-33. [PMID: 21228494 DOI: 10.1271/bbb.100452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Rhodococcus jostii RHA1 is a polychlorinated biphenyl degrader. Multi-component biphenyl 2,3-dioxygenase (BphA) genes of RHA1 encode large and small subunits of oxygenase component and ferredoxin and reductase components. They did not express enzyme activity in Escherichia coli. To obtain BphA activity in E. coli, hybrid BphA gene derivatives were constructed by replacing ferredoxin and/or reductase component genes of RHA1 with those of Pseudomonas pseudoalcaligenes KF707. The results obtained indicate a lack of catalytic activity of the RHA1 ferredoxin component gene, bphAc in E. coli. To determine the cause of inability of RHA1 bphAc to express in E. coli, the bphAc gene was introduced into Rosetta (DE3) pLacI, which has extra tRNA genes for rare codons in E. coli. The resulting strain abundantly produced the bphAc product, and showed activity. These results suggest that codon usage bias is involved in inability of RHA1 bphAc to express its catalytic activity in E. coli.
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16
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Development of a strain for efficient degradation of polychlorinated biphenyls by patchwork assembly of degradation pathways. J Biosci Bioeng 2011; 111:437-42. [DOI: 10.1016/j.jbiosc.2010.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 11/15/2010] [Accepted: 12/01/2010] [Indexed: 11/21/2022]
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17
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Xiong F, Shuai JJ, Peng RH, Tian YS, Zhao W, Yao QH, Xiong AS. Expression, purification and functional characterization of a recombinant 2,3-dihydroxybiphenyl-1,2-dioxygenase from Rhodococcus rhodochrous. Mol Biol Rep 2010; 38:4303-8. [PMID: 21113668 DOI: 10.1007/s11033-010-0554-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 11/17/2010] [Indexed: 11/28/2022]
Abstract
A 2,3-dihydroxybiphenyl (2,3-DHBP) dioxygenase gene from a Rhodococcus sp. strain, named RrbphCI and involved in the degradation of polychlorinated biphenyls (PCBs), was synthesized. RrbphCI was expressed in Escherichia coli and its encoded enzyme was purified. SDS-PAGE analysis indicated that the size of the protein encoded by RrbphCI was about 32 kDa. The activity of the 2,3-DHBP dioxygenase was 82.8 U/mg when the substrate was 2,3-DHBP, with optimum pH 8.0 at 30°C, and optimum temperature was 40°C at pH 8.0. The RrbphCI gene was transformed into Pseudomonas putida strain EG11, to determine the ability of the enzyme to degrade 2,3-DHBP. The wild type EG11 degraded 61.86% of supplied 2,3-DHBP and the transformed EG11 (hosting the RrbphCI gene) utilized 52.68% after 2 min of treatment at 30°C. The overexpressed and purified enzyme was able to degrade 2,3-DHBP. The 2,3-DHBP dioxygenase is a key enzyme in the PCB degradation pathway. RrbphCI and its encoded 2,3-DHBP dioxygenase may have transgenic applications in bioremediation of PCBs.
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Affiliation(s)
- Fei Xiong
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnological Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, 201106 Shanghai, China
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18
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Vilchez-Vargas R, Junca H, Pieper DH. Metabolic networks, microbial ecology and ‘omics’ technologies: towards understanding in situ biodegradation processes. Environ Microbiol 2010; 12:3089-104. [DOI: 10.1111/j.1462-2920.2010.02340.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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19
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Seto M, Masai E, Ida M, Hatta T, Kimbara K, Fukuda M, Yano K. Multiple Polychlorinated Biphenyl Transformation Systems in the Gram-Positive Bacterium Rhodococcus sp. Strain RHA1. Appl Environ Microbiol 2010; 61:4510-3. [PMID: 16535201 PMCID: PMC1388666 DOI: 10.1128/aem.61.12.4510-4513.1995] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cloned bphA gene of the polychlorinated biphenyl (PCB) degrader Rhodococcus sp. strain RHA1 was expressed in Rhodococcus erythropolis IAM1399 cells, resulting in the transformation of di-, tri-, and tetrachlorobiphenyls. Disruption of the bphA1 gene in RHA1 resulted in a lack of growth on biphenyl and a loss of PCB transformation activity. However, the bphA1 insertion mutant of RHA1, designated RDA1, retained the ability to transform PCB congeners when grown on ethylbenzene as its carbon source. It also transformed 4-chlorobiphenyl to 4-chlorobenzoate, although it was suspected to be deficient in bphB and bphC gene activities as well as bphA. This suggested that an alternative PCB degradation system distinct from the one encoded by the cloned bph genes was present.
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20
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Liu X, Germaine KJ, Ryan D, Dowling DN. Whole-cell fluorescent biosensors for bioavailability and biodegradation of polychlorinated biphenyls. SENSORS 2010; 10:1377-98. [PMID: 22205873 PMCID: PMC3244019 DOI: 10.3390/s100201377] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Revised: 01/14/2010] [Accepted: 01/29/2010] [Indexed: 11/30/2022]
Abstract
Whole-cell microbial biosensors are one of the newest molecular tools used in environmental monitoring. Such biosensors are constructed through fusing a reporter gene such as lux, gfp or lacZ, to a responsive promoter. There have been many reports of the applications of biosensors, particularly their use in assaying pollutant toxicity and bioavailability. This paper reviews the basic concepts behind the construction of whole-cell microbial biosensors for pollutant monitoring, and describes the applications of two such biosensors for detecting the bioavailability and biodegradation of Polychlorinated Biphenyls (PCBs).
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Affiliation(s)
- Xuemei Liu
- Department of Science and Health, Institute of Technology Carlow, Kilkenny Road, Carlow, Ireland.
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21
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Pathway and evolutionary implications of diphenylamine biodegradation by Burkholderia sp. strain JS667. Appl Environ Microbiol 2009; 75:2694-704. [PMID: 19251893 DOI: 10.1128/aem.02198-08] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diphenylamine (DPA) is a common contaminant at munitions-contaminated sites as well as at aniline manufacturing sites. Little is known about the biodegradation of the compound, and bacteria able to use DPA as the growth substrate have not been reported. Burkholderia sp. strain JS667 and Ralstonia sp. strain JS668 were isolated by selective enrichment from DPA-contaminated sediment. The isolates grew aerobically with DPA as the sole carbon, nitrogen, and energy source. During induction of DPA degradation, stoichiometric amounts of aniline accumulated and then disappeared, which suggested that aniline is on the DPA degradation pathway. Genes encoding the enzymes that catalyze the initial steps in DPA degradation were cloned from the genomic DNA of strain JS667. The Escherichia coli clone catalyzed stoichiometric transformation of DPA to aniline and catechol. Transposon mutagenesis, the sequence similarity of putative open reading frames to those of well-characterized dioxygenases, and (18)O(2) experiments support the conclusion that the initial reaction in DPA degradation is catalyzed by a multicomponent ring-hydroxylating dioxygenase. DPA is converted to aniline and catechol via dioxygenation at the 1,2 position of the aromatic ring and spontaneous rearomatization. Aniline and catechol are further biodegraded by the well-established aniline degradation pathway. Genes that encode the complete aniline degradation pathway were found 12 kb downstream of the genes that encode the initial dioxygenase. Expression of the relevant dioxygenases was confirmed by reverse transcription-PCR analysis. Both the sequence similarity and the gene organization suggest that the DPA degradation pathway evolved recently by the recruitment of two gene clusters that encode the DPA dioxygenase and aniline degradation pathway.
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22
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Biochemical characterization of l-DOPA 2,3-dioxygenase, a single-domain type I extradiol dioxygenase from lincomycin biosynthesis. Arch Biochem Biophys 2008; 479:131-8. [DOI: 10.1016/j.abb.2008.08.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 08/27/2008] [Accepted: 08/27/2008] [Indexed: 11/23/2022]
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23
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Pérez-Pantoja D, De la Iglesia R, Pieper DH, González B. Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacteriumCupriavidus necatorJMP134. FEMS Microbiol Rev 2008; 32:736-94. [DOI: 10.1111/j.1574-6976.2008.00122.x] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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24
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Purification, characterization, and substrate specificity of two 2,3-dihydroxybiphenyl 1,2-dioxygenase from Rhodococcus sp. R04, showing their distinct stability at various temperature. Biochimie 2008; 90:1530-8. [PMID: 18585431 DOI: 10.1016/j.biochi.2008.05.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Accepted: 05/29/2008] [Indexed: 11/20/2022]
Abstract
The genes of two 2,3-dihydroxybiphenyl 1,2-dioxygenases (BphC1 and BphC2) were obtained from the gene library of Rhodococcus sp. R04. The enzymes have been purified to apparent electrophoretic homogeneity from the cell extracts of the recombinant harboring bphC1 and bphC2. Both BphC1 and BphC2 were hexamers, consisting of six subunits of 35 and 33 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, respectively. The enzymes had similar optimal pH (pH 9.0), but different temperatures for their maximum activity (30 degrees C for BphC1, 80 degrees C for BphC2). In addition, they exhibited distinct stability at various temperatures. The enzymes could cleave a wide range of catechols, with 2,3-dihydroxybiphenyl being the optimum substrate for BphC1 and BphC2. BphC1 was inhibited by 2,3-dihydroxybiphenyl, catechol and 3-chlorocatechol, whereas BphC2 showed strong substrate inhibition for all the given substrates. BphC2 exhibited a half-life of 15 min at 80 degrees C and 50 min at 70 degrees C, making it the most thermostable extradiol dioxygenase studied in mesophilic bacteria. After disruption of bphC1 and bphC2 genes, R04DeltaC1 (bphC1 mutant) delayed the time of their completely eliminating biphenyl another 15 h compared with its parent strain R04, but R04DeltaC2 (bphC2 mutant) lost the ability to grow on biphenyl, suggesting that BphC1 plays an assistant role in the degrading of biphenyl by strain R04, while BphC2 is essential for the growth of strain R04 on biphenyl.
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25
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Furukawa K, Fujihara H. Microbial degradation of polychlorinated biphenyls: Biochemical and molecular features. J Biosci Bioeng 2008; 105:433-49. [PMID: 18558332 DOI: 10.1263/jbb.105.433] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 02/04/2008] [Indexed: 11/17/2022]
Affiliation(s)
- Kensuke Furukawa
- Depatment of Food and Bioscience, Faculty of Food and Nutrition, Beppu University, Beppu, Ohita 874-8501, Japan.
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26
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Solyanikova IP, Travkin VM, Rybkina DO, Plotnikova EG, Golovleva LA. Variability of enzyme system of Nocardioform bacteria as a basis of their metabolic activity. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2008; 43:241-252. [PMID: 18368545 DOI: 10.1080/03601230701771180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The present review describes some aspects of organization of biodegradative pathways of Nocardioform microorganisms, first of all, with respect to their ability to degrade aromatic compounds, mostly methylbenzoate, chlorosubstituted phenols, and chlorinated biphenyls and the intermediates of their transformation: 4-chlorobenzoate and para-hydroxybenzoate. Various enzyme systems induced during degradation processes are defined. The ability of microorganisms to induce a few key enzymes under the influence of xenobiotics is described. This ability may increase the biodegradative potential of strains allowing them to survive in the changing environment or demonstrate to some extent the unspecific response of microorganisms to the effect of toxicants. Nocardioform microorganisms responsible for degradation of such persistent compounds as polychlorinated biphenyls, polyaromatic hydrocarbons, chlorinated benzoates and phenols and other xenobiotics are characterized. The possibility of using Nocardioform microorganisms in some aspects of biotechnology due to their ability to produce some compounds important for industry is also estimated.
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Affiliation(s)
- Inna P Solyanikova
- Skryabin' Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
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27
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Suenaga H, Ohnuki T, Miyazaki K. Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds. Environ Microbiol 2007; 9:2289-97. [PMID: 17686025 DOI: 10.1111/j.1462-2920.2007.01342.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A metagenomic approach was taken to retrieve catabolic operons for aromatic compounds from activated sludge used to treat coke plant wastewater. Metagenomic DNA extracted from the sludge was cloned into fosmids and the resulting Escherichia coli library was screened for extradiol dioxygenases (EDOs) using catechol as a substrate, yielding 91 EDO-positive clones. Based on their substrate specificity for various catecholic compounds, 38 clones were subjected to sequence analysis. Each insert contained at least one EDO gene, and a total of 43 EDO genes were identified. More than half of these belonged to new EDO subfamilies: I.1.C (2 clones), I.2.G (20 clones), I.3.M (2 clones) and I.3.N (1 clone). The fact that novel I.2.G family genes were over-represented in these clones suggested that these genes play a specific role in environmental aromatic degradation. The I.2.G clones were further classified into six groups based on single-nucleotide polymorphisms (SNPs). Based on the combination of the SNPs, the evolutionary lineage of the genes was reconstructed; further, taking the activities of the clones into account, potential adaptive mutations were identified. The metagenomic approach was thus used to retrieve novel EDO genes as well as to gain insights into the gene evolution of EDOs.
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Affiliation(s)
- Hikaru Suenaga
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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28
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Morono Y, Kitagawa W, Kimura N, Noda N, Nakamura K, Kamagata Y. “Mark the Gene”: a Method for Nondestructive Introduction of Marker Sequences Inside the Gene Frame of Transgenes. Appl Environ Microbiol 2007; 73:4915-21. [PMID: 17526781 PMCID: PMC1951010 DOI: 10.1128/aem.00068-07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
A specific marking and detection technique is a fundamental requirement for the safer use of genetically modified (GM) organisms. Here we propose a simple and effective method for directly marking functional transgenes in GM organisms. For that purpose, we introduced nucleotide substitutions (NS), based on the degeneracy of codons as markers (NS markers), into the
bphC
(2,3-dihydroxybiphenyl dioxygenase) and
tomA3
(toluene-
ortho
-monooxygenase) gene frames using a PCR-based method. No change was observed in the enzyme activity of translated proteins, and alignments with homologous genes showed the uniqueness of the NS markers. Furthermore, we constructed
tomA3
variations harboring NS markers in different positions. Although the translational products were identical, the constructed variation genes could be distinguished through their marker patterns by multiplex PCR, showing that NS markers could serve as product-specific tags for identifying individual GM organisms. This direct method of marking the functional transgene provides a simple, low-risk, and robust marking method without causing the gene functions to deteriorate.
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Affiliation(s)
- Yuki Morono
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
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29
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Choi KY, Kim D, Chae JC, Zylstra GJ, Kim E. Requirement of duplicated operons for maximal metabolism of phthalate by Rhodococcus sp. strain DK17. Biochem Biophys Res Commun 2007; 357:766-71. [PMID: 17449009 DOI: 10.1016/j.bbrc.2007.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 04/02/2007] [Indexed: 11/15/2022]
Abstract
The operons encoding the transformation of phthalate to protocatechuate are duplicated and present on two different megaplasmids [pDK2 (330 kb) and pDK3 (750 kb)] in Rhodococcus sp. strain DK17. RT-PCR experiments using gene-specific primers showed that both the pDK2- and the pDK3-encoded dihydroxyphthalate decarboxylase genes are simultaneously expressed during growth on phthalate. The doubling time of the pDK2-cured mutant strain DK176 in minimal liquid medium with 5mM phthalate is 52.5% of that of the wild-type strain DK17. The data indicate that both copies of the phthalate operon are equally functional in DK17, and gene dosage is the main reason for slower growth of DK176 on phthalate.
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Affiliation(s)
- Ki Young Choi
- Department of Biology, Yonsei University, Seoul 120-749, Republic of Korea
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30
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Urai M, Yoshizaki H, Anzai H, Ogihara J, Iwabuchi N, Harayama S, Sunairi M, Nakajima M. Structural analysis of an acidic, fatty acid ester-bonded extracellular polysaccharide produced by a pristane-assimilating marine bacterium, Rhodococcus erythropolis PR4. Carbohydr Res 2007; 342:933-42. [PMID: 17316581 DOI: 10.1016/j.carres.2007.02.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Revised: 01/31/2007] [Accepted: 01/31/2007] [Indexed: 11/29/2022]
Abstract
Rhodococcus erythropolis PR4 is a marine bacterium that can degrade various alkanes including pristane, a C(19) branched alkane. This strain produces a large quantity of extracellular polysaccharides, which are assumed to play an important role in the hydrocarbon tolerance of this bacterium. The strain produced two acidic extracellular polysaccharides, FR1 and FR2, and the latter showed emulsifying activity toward clove oil, whereas the former did not. FR2 was composed of D-galactose, D-glucose, D-mannose, D-glucuronic acid, and pyruvic acid at a molar ratio of 1:1:1:1:1, and contained 2.9% (w/w) stearic acid and 4.3% (w/w) palmitic acid attached via ester bonds. Therefore, we designated FR2 as a PR4 fatty acid-containing extracellular polysaccharide or FACEPS. The chemical structure of the PR4 FACEPS polysaccharide chain was determined by 1D (1)H and (13)C NMR spectroscopies as well as by 2D DQF-COSY, TOCSY, HMQC, HMBC, and NOESY experiments. The sugar chain of PR4 FACEPS was shown to consist of tetrasaccharide repeating units having the following structure: [structure: see text].
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Affiliation(s)
- Makoto Urai
- Laboratory of Molecular Microbiology, Department of Applied Biological Science, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-8510, Japan
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31
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Sekine M, Tanikawa S, Omata S, Saito M, Fujisawa T, Tsukatani N, Tajima T, Sekigawa T, Kosugi H, Matsuo Y, Nishiko R, Imamura K, Ito M, Narita H, Tago S, Fujita N, Harayama S. Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4. Environ Microbiol 2006; 8:334-46. [PMID: 16423019 DOI: 10.1111/j.1462-2920.2005.00899.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Rhodococcus erythropolis strain PR4 has been isolated as an alkane-degrading bacterium. The strain harbours one linear plasmid, pREL1 (271 577 bp) and two circular plasmids, pREC1 (104 014 bp) and pREC2 (3637 bp), all with some sequence similarities to other Rhodococcus plasmids. For pREL1, pREC1 and pREC2, 298, 102 and 3 open reading frames, respectively, were predicted. Linear plasmid pREL1 has several regions homologous to plasmid pBD2 found in R. erythropolis BD2. Sequence analysis of pREL1 and pBD2 identified common metal-resistance genes on both, but pREL1 also encodes alkane-degradation genes not found on pBD2, with enzyme constituents some of which are quite different from those of other organisms. The alkane hydroxylase consisted of a cytochrome P450 monooxygenase, a 2Fe-2S ferredoxin, and a ferredoxin reductase. The ferredoxin reductase amino acid sequence resembles the AlkT (rubredoxin reductase) sequence. A zinc-containing alcohol dehydrogenase further oxydizes alkanols, alkane oxidation products catalysed by alkane hydroxylase. Of the circular plasmids, the pREC1 sequence is partially similar to the sequence of pREAT701, the virulence plasmid found in Rhodococcus equi. pREC1 has no pREAT701 virulence genes and encodes genes for beta-oxidation of fatty acids. Thus, joint actions of enzymes encoded by pREL1 and pREC1 may enable efficient mineralization of alkanes.
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Affiliation(s)
- Mitsuo Sekine
- NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), Shibuya-ku, Tokyo, Japan
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Choi KY, Kim D, Sul WJ, Chae JC, Zylstra GJ, Kim YM, Kim E. Molecular and biochemical analysis of phthalate and terephthalate degradation byRhodococcussp. strain DK17. FEMS Microbiol Lett 2006; 252:207-13. [PMID: 16181748 DOI: 10.1016/j.femsle.2005.08.045] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2005] [Revised: 08/29/2005] [Accepted: 08/30/2005] [Indexed: 10/25/2022] Open
Abstract
Alkylbenzene-degrading Rhodococcus sp. strain DK17 is able to utilize phthalate and terephthalate as growth substrates. The genes encoding the transformation of phthalate and terephthalate to protocatechuate are organized as two separate operons, located 6.7kb away from each other. Interestingly, both the phthalate and terephthalate operons are induced in response to terephthalate while expression of the terephthalate genes is undetectable in phthalate-grown cells. In addition to two known plasmids (380-kb pDK1 and 330-kb pDK2), a third megaplasmid (750-kb pDK3) was newly identified in DK17. The phthalate and terephthalate operons are duplicated and are present on both pDK2 and pDK3. RT-PCR experiments, coupled with sequence analysis, suggest that phthalate and terephthalate degradation in DK17 proceeds through oxygenation at carbons 3 and 4 and at carbons 1 and 2 to form 3,4-dihydro-3,4-dihydroxyphthalate and 1,2-dihydro-1,2-dihydroxyterephthalate, respectively. The 3,4-dihydroxyphthalate pathway was further corroborated through colorometric tests. Apparently, the two dihydrodiol metabolites are subsequently dehydrogenated and decarboxylated to form protocatechuate, which is further degraded by a protocatechuate 3,4-dioxygenase as confirmed by a ring-cleavage enzyme assay.
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Affiliation(s)
- Ki Young Choi
- Department of Biology, Yonsei University, Seoul, Republic of Korea
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33
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Mukerjee-Dhar G, Shimura M, Miyazawa D, Kimbara K, Hatta T. bph genes of the thermophilic PCB degrader, Bacillus sp. JF8: characterization of the divergent ring-hydroxylating dioxygenase and hydrolase genes upstream of the Mn-dependent BphC. Microbiology (Reading) 2005; 151:4139-4151. [PMID: 16339959 DOI: 10.1099/mic.0.28437-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacillussp. JF8 is a thermophilic polychlorinated biphenyl (PCB) degrader, which utilizes biphenyl and naphthalene. A thermostable, Mn-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase, BphC_JF8, has been characterized previously. Upstream ofbphCare five ORFs exhibiting low homology with, and a different gene order from, previously characterizedbphgenes. From the 5′ to 3′ direction the genes are: a putative regulatory gene (bphR), a hydrolase (bphD), the large and small subunits of a ring-hydroxylating dioxygenase(bphA1A2), and acis-diol dehydrogenase (bphB). Hybridization studies indicate that the genes are located on a plasmid. Ring-hydroxylating activity of recombinant BphA1A2_JF8 towards biphenyl, PCB, naphthalene and benzene was observed inEscherichia colicells, with complementation of non-specific ferredoxin and ferredoxin reductase by host cell proteins. PCB degradation by recombinant BphA1A2_JF8 showed that the congener specificity of the recombinant enzyme was similar toBacillussp. JF8. BphD_JF8, with an optimum temperature of 85 °C, exhibited a narrow substrate preference for 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid. The Arrhenius plot of BphD_JF8 was biphasic, with two characteristic energies of activation and a break point at 47 °C.
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Affiliation(s)
- Gouri Mukerjee-Dhar
- Environmental Biotechnology Laboratory, Railway Technical Research Institute, Kokubunji, Tokyo 185-8540, Japan
| | - Minoru Shimura
- Environmental Biotechnology Laboratory, Railway Technical Research Institute, Kokubunji, Tokyo 185-8540, Japan
| | - Daisuke Miyazawa
- Department of Built Environment, Tokyo Institute of Technology, Yokohama 226-8502, Japan
| | - Kazuhide Kimbara
- Department of Built Environment, Tokyo Institute of Technology, Yokohama 226-8502, Japan
- Environmental Biotechnology Laboratory, Railway Technical Research Institute, Kokubunji, Tokyo 185-8540, Japan
| | - Takashi Hatta
- Research Institute of Technology, Okayama University of Science, Okayama 703-8232, Japan
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Sakai M, Masai E, Asami H, Sugiyama K, Kimbara K, Fukuda M. Diversity of 2,3-dihydroxybiphenyl dioxygenase genes in a strong PCB degrader, Rhodococcus sp. strain RHA1. J Biosci Bioeng 2005; 93:421-7. [PMID: 16233225 DOI: 10.1016/s1389-1723(02)80078-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2001] [Accepted: 02/08/2002] [Indexed: 11/17/2022]
Abstract
Two 2,3-dihydroxybiphenyl (23DHBP) dioxygenase genes, bphC1 and etbC involved in the degradation of polychlorinated biphenyl(s) (PCBs) have been isolated and characterized from a strong PCB degrader, Rhodococcus sp. RHA1. In this study, four new 23DHBP dioxygenase genes, designated as bphC2, bphC3, bphC4, and bphC5 were isolated from RHA1, and their nucleotide sequences were determined. Based on amino acid sequence similarities, all of the newly isolated bphC genes could be categorized into type I along with BphC1 and EtbC [Eltis, L.D. and Bolin, J.T., J. Bacteriol., 178, 5930-5937 (1996)]. Six bphC genes, including bphC1, etbC, and four new genes, were expressed in Escherichia coli to determine their substrate specificity. The activities of BphC2, BphC3, BphC4, and BphC5 were found to be specific to 23DHBP, while BphC1 and EtbC exhibited activities towards compounds other than 23DHBP, including catechol (CAT) and 3-methylcatechol (3MC). RNA slot blot hybridization analysis indicated that only bphC5 was transcribed among the newly isolated bphC in RHA1 cells grown on biphenyl and ethylbenzene. The nucleotide sequence of the flanking region of each bphC revealed a homolog of the 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (HOPD) hydrolase gene, bphD, just upstream of bphC5. The bphC5 and putative bphD genes may constitute an operon and play a role in the degradation of biphenyl and PCBs together with bphC1 and etbC. In contrast, the bphC2, bphC3, and bphC4 genes may not be involved in biphenyl and PCB degradation.
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Affiliation(s)
- Masayuki Sakai
- Department of Bioengineering, Nagaoka University of Technology, Kamitomioka, Nagaoka, Niigata 940-2188, Japan
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Hatta T, Nakano O, Imai N, Takizawa N, Kiyohara H. Cloning and sequence analysis of hydroxyquinol 1,2-dioxygenase gene in 2,4,6-trichlorophenol-degrading Ralstonia pickettii DTP0602 and characterization of its product. J Biosci Bioeng 2005; 87:267-72. [PMID: 16232466 DOI: 10.1016/s1389-1723(99)80030-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/1998] [Accepted: 11/20/1998] [Indexed: 11/16/2022]
Abstract
A gene encoding hydroxyquinol 1,2-dioxygenase was cloned from 2,4,6-trichlorophenol-degrading Ralstonia (Pseudomonas) pickettii strain DTP0602. Cell-free extracts of Escherichia coli containing a cloned 1.4-kb StuI-XhoI DNA fragment of R. pickettii DTP0602 hydroxyquinol 1,2-dioxygenase converted hydroxyquinol into maleylacetate and also degraded 6-chlorohydroxyquinol. The 1.4-kb DNA fragment contained one open reading frame (designated hadC) composed of 948 nucleotides. The molecular mass of 34,591 deduced from the gene product (HadC) was in agreement with the size (35 kDa) of the purified HadC protein determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The amino acid sequence of HadC exhibited high homology to that of the hydroxyquinol 1,2-dioxygenase of 2,4,5-trichlorophenoxyacetic acid-degrading Burkholderia cepacia AC1100 (Daubaras, D. L. et al., Appl. Environ. Microbiol., 61, 1279-1289, 1995). The active enzyme had a molecular mass of 68 kDa, suggesting that it is functional as a homodimer. The enzyme also catalyzed the oxidation of pyrogallol and 3-methylcatechol, possible intermediates in the degradation of 2,4,6-trichlorophenol, in addition to 6-chlorohydroxyquinol and hydroxyquinol. The dioxygenase catalyzed both ortho- and meta-cleavage of 3-methylcatechol.
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Affiliation(s)
- T Hatta
- Research Institute of Technology, Okayama University of Science, 401-1 Seki, Okayama 703-8232, Japan
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36
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Shen XH, Jiang CY, Huang Y, Liu ZP, Liu SJ. Functional identification of novel genes involved in the glutathione-independent gentisate pathway in Corynebacterium glutamicum. Appl Environ Microbiol 2005; 71:3442-52. [PMID: 16000747 PMCID: PMC1169049 DOI: 10.1128/aem.71.7.3442-3452.2005] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Corynebacterium glutamicum used gentisate and 3-hydroxybenzoate as its sole carbon and energy source for growth. By genome-wide data mining, a gene cluster designated ncg12918-ncg12923 was proposed to encode putative proteins involved in gentisate/3-hydroxybenzoate pathway. Genes encoding gentisate 1,2-dioxygenase (ncg12920) and fumarylpyruvate hydrolase (ncg12919) were identified by cloning and expression of each gene in Escherichia coli. The gene of ncg12918 encoding a hypothetical protein (Ncg12918) was proved to be essential for gentisate-3-hydroxybenzoate assimilation. Mutant strain RES167Deltancg12918 lost the ability to grow on gentisate or 3-hydroxybenzoate, but this ability could be restored in C. glutamicum upon the complementation with pXMJ19-ncg12918. Cloning and expression of this ncg12918 gene in E. coli showed that Ncg12918 is a glutathione-independent maleylpyruvate isomerase. Upstream of ncg12920, the genes ncg12921-ncg12923 were located, which were essential for gentisate and/or 3-hydroxybenzoate catabolism. The Ncg12921 was able to up-regulate gentisate 1,2-dioxygenase, maleylpyruvate isomerase, and fumarylpyruvate hydrolase activities. The genes ncg12922 and ncg12923 were deduced to encode a gentisate transporter protein and a 3-hydroxybenzoate hydroxylase, respectively, and were essential for gentisate or 3-hydroxybenzoate assimilation. Based on the results obtained in this study, a GSH-independent gentisate pathway was proposed, and genes involved in this pathway were identified.
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Affiliation(s)
- Xi-Hui Shen
- State Key Laboratory of Microbial Resources at the Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, People's Republic of China
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Fortin PD, Lo ATF, Haro MA, Kaschabek SR, Reineke W, Eltis LD. Evolutionarily divergent extradiol dioxygenases possess higher specificities for polychlorinated biphenyl metabolites. J Bacteriol 2005; 187:415-21. [PMID: 15629912 PMCID: PMC543568 DOI: 10.1128/jb.187.2.415-421.2005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The reactivities of four evolutionarily divergent extradiol dioxygenases towards mono-, di-, and trichlorinated (triCl) 2,3-dihydroxybiphenyls (DHBs) were investigated: 2,3-dihydroxybiphenyl dioxygenase (EC 1.13.11.39) from Burkholderia sp. strain LB400 (DHBDLB400), DHBDP6-I and DHBDP6-III from Rhodococcus globerulus P6, and 2,2',3-trihydroxybiphenyl dioxygenase from Sphingomonas sp. strain RW1 (THBDRW1). The specificity of each isozyme for particular DHBs differed by up to 3 orders of magnitude. Interestingly, the Kmapp values of each isozyme for the tested polychlorinated DHBs were invariably lower than those of monochlorinated DHBs. Moreover, each enzyme cleaved at least one of the tested chlorinated (Cl) DHBs better than it cleaved DHB (e.g., apparent specificity constants for 3',5'-dichlorinated [diCl] DHB were 2 to 13.4 times higher than for DHB). These results are consistent with structural data and modeling studies which indicate that the substrate-binding pocket of the DHBDs is hydrophobic and can accommodate the Cl DHBs, particularly in the distal portion of the pocket. Although the activity of DHBDP6-III was generally lower than that of the other three enzymes, six of eight tested Cl DHBs were better substrates for DHBDP6-III than was DHB. Indeed, DHBDP6-III had the highest apparent specificity for 4,3',5'-triCl DHB and cleaved this compound better than two of the other enzymes. Of the four enzymes, THBDRW1 had the highest specificity for 2'-Cl DHB and was at least five times more resistant to inactivation by 2'-Cl DHB, consistent with the similarity between the latter and 2,2',3-trihydroxybiphenyl. Nonetheless, THBDRW1 had the lowest specificity for 2',6'-diCl DHB and, like the other enzymes, was unable to cleave this critical PCB metabolite (kcatapp < 0.001 s(-1)).
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Affiliation(s)
- Pascal D Fortin
- Department of Microbiology and Immunology, University of British Columbia, #300-6174 University Blvd., Vancouver, BC V6T 1Z3, Canada
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38
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Kim D, Chae JC, Jang JY, Zylstra GJ, Kim YM, Kang BS, Kim E. Functional characterization and molecular modeling of methylcatechol 2,3-dioxygenase from o-xylene-degrading Rhodococcus sp. strain DK17. Biochem Biophys Res Commun 2005; 326:880-6. [PMID: 15607751 DOI: 10.1016/j.bbrc.2004.11.123] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2004] [Indexed: 11/19/2022]
Abstract
Rhodococcus sp. strain DK17 is known to metabolize o-xylene and toluene through the intermediates 3,4-dimethylcatechol and 3- and 4-methylcatechol, respectively, which are further cleaved by a common catechol 2,3-dioxygenase. A putative gene encoding this enzyme (akbC) was amplified by PCR, cloned, and expressed in Escherichia coli. Assessment of the enzyme activity expressed in E. coli combined with sequence analysis of a mutant gene demonstrated that the akbC gene encodes the bona fide catechol 2,3-dioxygenase (AkbC) for metabolism of o-xylene and alkylbenzenes such as toluene and ethylbenzene. Analysis of the deduced amino acid sequence indicates that AkbC consists of a new catechol 2,3-dioxygenase class specific for methyl-substituted catechols. A computer-aided molecular modeling studies suggest that amino acid residues (particularly Phe177) in the beta10-beta11 loop play an essential role in characterizing the substrate specificity of AkbC.
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Affiliation(s)
- Dockyu Kim
- Department of Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
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39
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Pieper DH. Aerobic degradation of polychlorinated biphenyls. Appl Microbiol Biotechnol 2004; 67:170-91. [PMID: 15614564 DOI: 10.1007/s00253-004-1810-4] [Citation(s) in RCA: 226] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Revised: 10/10/2004] [Accepted: 10/19/2004] [Indexed: 10/26/2022]
Abstract
The microbial degradation of polychlorinated biphenyls (PCBs) has been extensively studied in recent years. The genetic organization of biphenyl catabolic genes has been elucidated in various groups of microorganisms, their structures have been analyzed with respect to their evolutionary relationships, and new information on mobile elements has become available. Key enzymes, specifically biphenyl 2,3-dioxygenases, have been intensively characterized, structure/sequence relationships have been determined and enzymes optimized for PCB transformation. However, due to the complex metabolic network responsible for PCB degradation, optimizing degradation by single bacterial species is necessarily limited. As PCBs are usually not mineralized by biphenyl-degrading organisms, and cometabolism can result in the formation of toxic metabolites, the degradation of chlorobenzoates has received special attention. A broad set of bacterial strategies to degrade chlorobenzoates has recently been elucidated, including new pathways for the degradation of chlorocatechols as central intermediates of various chloroaromatic catabolic pathways. To optimize PCB degradation in the environment beyond these metabolic limitations, enhancing degradation in the rhizosphere has been suggested, in addition to the application of surfactants to overcome bioavailability barriers. However, further research is necessary to understand the complex interactions between soil/sediment, pollutant, surfactant and microorganisms in different environments.
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Affiliation(s)
- Dietmar H Pieper
- Department of Environmental Microbiology, German Research Center for Biotechnology, Mascheroder Weg 1, 38124, Braunschweig, Germany.
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40
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Kim D, Chae JC, Zylstra GJ, Kim YS, Kim SK, Nam MH, Kim YM, Kim E. Identification of a novel dioxygenase involved in metabolism of o-xylene, toluene, and ethylbenzene by Rhodococcus sp. strain DK17. Appl Environ Microbiol 2004; 70:7086-92. [PMID: 15574904 PMCID: PMC535206 DOI: 10.1128/aem.70.12.7086-7092.2004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2004] [Accepted: 08/05/2004] [Indexed: 11/20/2022] Open
Abstract
Rhodococcus sp. strain DK17 is able to grow on o-xylene, benzene, toluene, and ethylbenzene. DK17 harbors at least two megaplasmids, and the genes encoding the initial steps in alkylbenzene metabolism are present on the 330-kb pDK2. The genes encoding alkylbenzene degradation were cloned in a cosmid clone and sequenced completely to reveal 35 open reading frames (ORFs). Among the ORFs, we identified two nearly exact copies (one base difference) of genes encoding large and small subunits of an iron sulfur protein terminal oxygenase that are 6 kb apart from each other. Immediately downstream of one copy of the dioxygenase genes (akbA1a and akbA2a) is a gene encoding a dioxygenase ferredoxin component (akbA3), and downstream of the other copy (akbA1b and akbA2b) are genes putatively encoding a meta-cleavage pathway. RT-PCR experiments show that the two copies of the dioxygenase genes are operonic with the downstream putative catabolic genes and that both operons are induced by o-xylene. When expressed in Escherichia coli, AkbA1a-AkbA2a-AkbA3 transformed o-xylene into 2,3- and 3,4-dimethylphenol. These were apparently derived from an unstable o-xylene cis-3,4-dihydrodiol, which readily dehydrates. This indicates a single point of attack of the dioxygenase on the aromatic ring. In contrast, attack of AkbA1a-AkbA2a-AkbA3 on ethylbenzene resulted in the formation of two different cis-dihydrodiols resulting from an oxidation at the 2,3 and the 3,4 positions on the aromatic ring, respectively.
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Affiliation(s)
- Dockyu Kim
- Department of Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul, Korea
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41
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Gürtler V, Mayall BC, Seviour R. Can whole genome analysis refine the taxonomy of the genus Rhodococcus? FEMS Microbiol Rev 2004; 28:377-403. [PMID: 15449609 DOI: 10.1016/j.femsre.2004.01.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The current systematics of the genus Rhodococcus is unclear, partly because many members were originally included before the application of a polyphasic taxonomic approach, central to which is the acquisition of 16S rRNA sequence data. This has resulted in the reclassification and description of many new species. Hence, the literature is replete with new species names that have not been brought together in an organized and easily interpreted form. This taxonomic confusion has been compounded by assigning many xenobiotic degrading isolates with phylogenetic positions but without formal taxonomic descriptions. In order to provide a framework for a taxonomic approach based on multiple genetic loci, a survey was undertaken of the known genome characteristics of members of the genus Rhodococcus including: (i) genetics of cell envelope biosynthesis; (ii) virulence genes; (iii) gene clusters involved in metabolic degradation and industrially relevant pathways; (iv) genetic analysis tools; (v) rapid identification of bacteria including rhodococci with specific gene RFLPs; (vi) genomic organization of rrn operons. Genes encoding virulence factors have been characterized for Rhodococcus equi and Rhodococcus fascians. Based on peptide signature comparisons deduced from gene sequences for cytochrome P-450, mono- and dioxygenases, alkane degradation, nitrile metabolism, proteasomes and desulfurization, phylogenetic relationships can be deduced for Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus ruber and a number of undesignated Rhodococcus spp. that may distinguish the genus Rhodococcus into two further genera. The linear genome topologies that exist in some Rhodococcus species may alter a previously proposed model for the analysis of genomic fingerprinting techniques used in bacterial systematics.
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Affiliation(s)
- Volker Gürtler
- Department of Microbiology, Austin Health, Studley Road, Heidelberg, Vic. 3084, Australia.
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42
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Furukawa K, Suenaga H, Goto M. Biphenyl dioxygenases: functional versatilities and directed evolution. J Bacteriol 2004; 186:5189-96. [PMID: 15292119 PMCID: PMC490896 DOI: 10.1128/jb.186.16.5189-5196.2004] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Kensuke Furukawa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki, Fukuoka 812-8581, Japan.
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43
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Yang X, Sun Y, Qian S. Biodegradation of seven polychlorinated biphenyls by a newly isolated aerobic bacterium (Rhodococcus sp. R04). J Ind Microbiol Biotechnol 2004; 31:415-20. [PMID: 15365854 DOI: 10.1007/s10295-004-0162-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2004] [Accepted: 07/10/2004] [Indexed: 10/26/2022]
Abstract
An aerobic bacterial strain, designated R04, belonging to the genus Rhodococcus has been isolated and characerized by 16S rDNA analysis. The capability of this strain to degrade seven different polychlorinated biphenyls (CBs), 500 ppm 3-CB, 3,4-CB, 4,4'-CB, 2,4,6-CB, 2,4',5-CB, 2,3,4,5-CB and 3,4,3',4'-CB in liquid medium, was evaluated. After 5 days of incubation, the concentration of chloride increased to 0.35 mM in cultures containing 3-CB and R04, whereas in cultures with 3,4-CB, 2,3,4,5-CB or 3,4,3',4'-CB plus R04 the chloride content increased to 0.1 mM. However, non-stoichiometric amounts of chloride were produced in cultures with R04 and 4,4'-CB, 2,4,6-CB and 2,4',5-CB. The spectrum of supernatants from R04 grown on seven PCBs had a UV-visible (UV-VIS) absorption at 200-500 nm, characteristic of biphenyl-derived cleavage products. Gas-chromatographic (GC) analysis showed that R04 was able to transform 100% of 3-CB and 3,4-CB after 1 day of incubation, and 95% of 4,4'-CB, 2,4,6-CB, 2,4',5-CB, 2,3,4,5-CB and 3,4,3',4'-CB after 5 days of incubation. The position of the chlorine substituents on the rings strongly influenced the degradation of polychlorinated biphenyls (PCBs) and their intermediate metabolites by Rhodococcus sp. R04. The degradation of PCBs was further evaluated by monitoring intermediate metabolites of PCBs.
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Affiliation(s)
- Xiuqing Yang
- Department of Enzymology, Institute of Microbiology, Chinese Academy of Sciences, PO Box 2714, 100080, Beijing, China
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Sondossi M, Barriault D, Sylvestre M. Metabolism of 2,2'- and 3,3'-dihydroxybiphenyl by the biphenyl catabolic pathway of Comamonas testosteroni B-356. Appl Environ Microbiol 2004; 70:174-81. [PMID: 14711640 PMCID: PMC321272 DOI: 10.1128/aem.70.1.174-181.2004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The purpose of this investigation was to examine the capacity of the biphenyl catabolic enzymes of Comamonas testosteroni B-356 to metabolize dihydroxybiphenyls symmetrically substituted on both rings. Data show that 3,3'-dihydroxybiphenyl is by far the preferred substrate for strain B-356. However, the dihydrodiol metabolite is very unstable and readily tautomerizes to a dead-end metabolite or is dehydroxylated by elimination of water. The tautomerization route is the most prominent. Thus, a very small fraction of the substrate is converted to other hydroxylated and acidic metabolites. Although 2,2'-dihydroxybiphenyl is a poor substrate for strain B-356 biphenyl dioxygenase, metabolites were produced by the biphenyl catabolic enzymes, leading to production of 2-hydroxybenzoic acid. Data show that the major route of metabolism involves, as a first step, a direct dehydroxylation of one of the ortho-substituted carbons to yield 2,3,2'-trihydroxybiphenyl. However, other metabolites resulting from hydroxylation of carbons 5 and 6 of 2,2'-dihydroxybiphenyl were also produced, leading to dead-end metabolites.
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Affiliation(s)
- M Sondossi
- Department of Microbiology, Weber State University, Ogden, Utah 84408, USA
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45
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Miyazawa D, Mukerjee-Dhar G, Shimura M, Hatta T, Kimbara K. Genes for Mn(II)-dependent NahC and Fe(II)-dependent NahH located in close proximity in the thermophilic naphthalene and PCB degrader, Bacillus sp. JF8: cloning and characterization. Microbiology (Reading) 2004; 150:993-1004. [PMID: 15073308 DOI: 10.1099/mic.0.26858-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A 10 kb DNA fragment was isolated using a DNA probe derived from the N-terminal amino acid sequence of the extradiol dioxygenase purified from naphthalene-grownBacillussp. JF8, a thermophilic naphthalene and polychlorinated biphenyl degrader. The cloned DNA fragment had six open reading frames, designatednahHLOMmocBnahCbased on sequence homology, of which the products NahH_JF8 and NahC_JF8 were extradiol dioxygenases. Although NahC_JF8 and NahH_JF8 exhibit low homology to known extradiol dioxygenases, the active-site residues and metal ion ligands are conserved. The presence of Mn(II) in culture medium was found to be essential for production of active recombinant NahC_JF8, while Fe(II) was necessary for active recombinant NahH_JF8. Inductively coupled plasma mass spectrometry analysis of active NahC_JF8 identified the cofactor to be manganese, indicating a Mn(II)-dependent extradiol dioxygenase. NahC_JF8 exhibitedKmvalues of 32±5 μM for 1,2-dihydroxynaphthalene and 510±90 μM for 2,3-dihydroxybiphenyl at 60 °C. In cell-free extracts, NahH_JF8 exhibited a broad substrate range for 2,3-dihydroxybiphenyl, catechol, and 3- and 4-methylcatechol at 25 °C. Stability studies on the Mn(II)-dependent NahC_JF8 indicated that it was thermostable, retaining 50 % activity after incubation at 80 °C for 20 min, and it exhibited resistance to EDTA and H2O2. Northern hybridization studies clarified that both NahC_JF8 and NahH_JF8 were induced by naphthalene; RT-PCR showed thatnahHLOMmocBnahCis expressed as a single transcript.
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Affiliation(s)
- Daisuke Miyazawa
- Department of Built Environment, Tokyo Institute of Technology, Yokohama 226-8502, Japan
| | - Gouri Mukerjee-Dhar
- Biotechnology Laboratory, Railway Technical Research Institute, 2-8-38, Hikari-cho, Kokubunji, Tokyo 185-8540, Japan
| | - Minoru Shimura
- Biotechnology Laboratory, Railway Technical Research Institute, 2-8-38, Hikari-cho, Kokubunji, Tokyo 185-8540, Japan
| | - Takashi Hatta
- Research Institute of Technology, Okayama University of Science, Okayama 703-8232, Japan
| | - Kazuhide Kimbara
- Biotechnology Laboratory, Railway Technical Research Institute, 2-8-38, Hikari-cho, Kokubunji, Tokyo 185-8540, Japan
- Department of Built Environment, Tokyo Institute of Technology, Yokohama 226-8502, Japan
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Francova K, Macková M, Macek T, Sylvestre M. Ability of bacterial biphenyl dioxygenases from Burkholderia sp. LB400 and Comamonas testosteroni B-356 to catalyse oxygenation of ortho-hydroxychlorobiphenyls formed from PCBs by plants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2004; 127:41-48. [PMID: 14553993 DOI: 10.1016/s0269-7491(03)00257-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Capacity of enzymes of the biphenyl/chlorobiphenyl pathway, especially biphenyl dioxygenase (BPDO) of two polychlorinated biphenyls (PCB) degrading bacteria, Burkholderia sp. LB400 and Comamonas testosteroni B-356, to metabolize ortho-substituted hydroxybiphenyls was tested.,These compounds found among plant products of PCB metabolism, are carrying chlorine atoms on the hydroxyl-substituted ring. The abilities of His-tagged purified LB400 and B-356 BPDOs to catalyze the oxygenation of 2-hydroxy-3-chlorobiphenyl, 2-hydroxy-5-chlorobiphenyl and 2-hydroxy-3,5-dichlorobiphenyl were compared. Both enzyme preparations catalyzed the hydroxylation of the three chloro-hydroxybiphenyls on the non-substituted ring. Neither LB400 BPDO nor B-356 BPDO oxygenated the substituted ring of the ortho-hydroxylated biphenyl. The fact that metabolites generated by both enzymes were identical for all three hydroxychlorobiphenyls tested; exclude any other mode of attack of these compounds by LB400 BPDOs than the ortho-meta oxygenation.
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Affiliation(s)
- K Francova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, ICT Prague, Technicka 3, 6, 166 28, Prague, Czech Republic
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Iwabuchi N, Sunairi M, Anzai H, Morisaki H, Nakajima M. Relationships among colony morphotypes, cell-surface properties and bacterial adhesion to substrata in Rhodococcus. Colloids Surf B Biointerfaces 2003. [DOI: 10.1016/s0927-7765(03)00036-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Hatta T, Mukerjee-Dhar G, Damborsky J, Kiyohara H, Kimbara K. Characterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8. J Biol Chem 2003; 278:21483-92. [PMID: 12672826 DOI: 10.1074/jbc.m210240200] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl-1,2-dioxygenase (BphC_JF8) catalyzing the meta-cleavage of the hydroxylated biphenyl ring was purified from the thermophilic biphenyl and naphthalene degrader, Bacillus sp. JF8, and the gene was cloned. The native and recombinant BphC enzyme was purified to homogeneity. The enzyme has a molecular mass of 125 +/- 10 kDa and was composed of four identical subunits (35 kDa). BphC_JF8 has a temperature optimum of 85 degrees C and a pH optimum of 7.5. It exhibited a half-life of 30 min at 80 degrees C and 81 min at 75 degrees C, making it the most thermostable extradiol dioxygenase studied. Inductively coupled plasma mass spectrometry analysis confirmed the presence of 4.0-4.8 manganese atoms per enzyme molecule. The EPR spectrum of BphC_JF8 exhibited g = 2.02 and g = 4.06 signals having the 6-fold hyperfine splitting characteristic of Mn(II). The enzyme can oxidize a wide range of substrates, and the substrate preference was in the order 2,3-dihydroxybiphenyl > 3-methylcatechol > catechol > 4-methylcatechol > 4-chlorocatechol. The enzyme is resistant to denaturation by various chelators and inhibitors (EDTA, 1,10-phenanthroline, H2O2, 3-chlorocatechol) and did not exhibit substrate inhibition even at 3 mm 2,3-dihydroxybiphenyl. A decrease in Km accompanied an increase in temperature, and the Km value of 0.095 microm for 2,3-dihydroxybiphenyl (at 60 degrees C) is among the lowest reported. The kinetic properties and thermal stability of the native and recombinant enzyme were identical. The primary structure of BphC_JF8 exhibits less than 25% sequence identity to other 2,3-dihydroxybiphenyl 1,2-dioxygenases. The metal ligands and active site residues of extradiol dioxygenases are conserved, although several amino acid residues found exclusively in enzymes that preferentially cleave bicyclic substrates are missing in BphC_JF8. A three-dimensional homology model of BphC_JF8 provided a basis for understanding the substrate specificity, quaternary structure, and stability of the enzyme.
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Affiliation(s)
- Takashi Hatta
- Research Institute of Technology, Okayama University of Science, 401-1 Seki, Okayama 703-8232, Japan.
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Andújar E, Santero E. Site-directed mutagenesis of an extradiol dioxygenase involved in tetralin biodegradation identifies residues important for activity or substrate specificity. MICROBIOLOGY (READING, ENGLAND) 2003; 149:1559-1567. [PMID: 12777496 DOI: 10.1099/mic.0.26034-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The sequence of the extradiol dioxygenase ThnC, involved in tetralin biodegradation, was aligned with other extradiol dioxygenases involved in biodegradation of polycyclic compounds, and a three-dimensional model of ThnC, based on the structure of the previously crystallized 2,3-dihydroxybiphenyl dioxygenase from Burkholderia fungorum LB400, was built. In order to assess the functional importance of some non-active-site residues whose relevance could not be established by structural information, a number of positions surrounding the substrate-binding site were mutated in ThnC. Ten mutant proteins were purified and their activity towards 1,2-dihydroxytetralin, 1,2-dihydroxynaphthalene and 2,3-dihydroxybiphenyl was characterized. N213H, Q198H, G206M, A282R and A282G mutants increased k(cat)/K(m) at least twofold using 1,2-dihydroxytetralin as the substrate, thus showing that activity of ThnC is not maximized for this substrate. N213H and Q198H mutants increased k(cat)/K(m) using any of the substrates tested, thus showing the relevance for activity of these two histidines, which are highly conserved in dihydroxybiphenyl dioxygenases, but not present in dihydroxynaphthalene dioxygenases. Different substitutions in position 282 had different effects on general activity or substrate specificity, thus showing the functional importance of the most C-terminal beta-sheet of the protein. A251M and G206M mutants showed increased activity specifically for a particular substrate. N213H, G206M, A282R, A282G and Y177I substitutions resulted in enzymes more tolerant to acidic pH, the most striking effect being observed in mutant Y177I, which showed maximal activity at pH 5.5. In addition, Q198D and V175D mutants, which had altered K(m), also showed altered sensitivity to substrate inhibition, thus indicating that inhibition is exerted through the same binding site. This mutational analysis, therefore, identified conserved residues important for activity or substrate specificity, and also shed some light on the mechanism of substrate inhibition exhibited by extradiol dioxygenases.
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Affiliation(s)
- Eloísa Andújar
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Ap. 1095, 41080 Sevilla, Spain
| | - Eduardo Santero
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Ap. 1095, 41080 Sevilla, Spain
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McKay DB, Prucha M, Reineke W, Timmis KN, Pieper DH. Substrate specificity and expression of three 2,3-dihydroxybiphenyl 1,2-dioxygenases from Rhodococcus globerulus strain P6. J Bacteriol 2003; 185:2944-51. [PMID: 12700274 PMCID: PMC154411 DOI: 10.1128/jb.185.9.2944-2951.2003] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhodococcus globerulus strain P6 contains at least three genes, bphC1, bphC2, and bphC3, coding for 2,3-dihydroxybiphenyl 1,2-dioxygenases; the latter two specify enzymes of the family of one-domain extradiol dioxygenases. In order to assess the importance of these different isoenzymes for the broad catabolic activity of this organism towards the degradation of polychlorinated biphenyls (PCBs), the capacities of recombinant enzymes expressed in Escherichia coli to transform different chlorosubstituted dihydroxybiphenyls formed by the action of R. globerulus P6 biphenyl dioxygenase and biphenyl 2,3-dihydrodiol dehydrogenase were determined. Whereas both BphC2 and BphC3 showed similar activities for 2,3-dihydroxybiphenyl and all monochlorinated 2,3-dihydroxybiphenyls, BphC1 exhibited only weak activity for 2'-chloro-2,3-dihydroxybiphenyl. More highly chlorinated 2'-chlorosubstituted 2,3-dihydroxybiphenyls were also transformed at high rates by BphC2 and BphC3 but not BphC1. In R. globerulus P6, BphC2 was constitutively expressed, BphC1 expression was induced during growth on biphenyl, and BphC3 was not expressed at significant levels under the experimental conditions. Although we cannot rule out the expression of BphC3 under certain environmental conditions, it seems that the contrasting substrate specificities of BphC1 and BphC2 contribute significantly to the versatile PCB-degrading phenotype of R. globerulus P6.
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Affiliation(s)
- David B McKay
- Department of Environmental Microbiology, GBF-German Research Center for Biotechnology, D-38124 Braunschweig, Germany
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