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K S, Manian R. Bioremediation of polycyclic aromatic hydrocarbons contaminated soils: recent progress, perspectives and challenges. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1441. [PMID: 37946088 DOI: 10.1007/s10661-023-12042-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
The life of all creatures is supported directly or indirectly by soil, which is a significant environmental matrix. The soil has been polluted partly due to increased human activities and population growth, releasing several foreign substances and persistent contaminants. When toxic substances like polycyclic aromatic hydrocarbons (PAHs) are disposed of, the characteristics of the soil are changed, microbial biodiversity is impacted, and items are destroyed. Because of the mutagenicity, carcinogenicity, and toxicity of petroleum hydrocarbons, the restoration and cleanup of PAH-polluted areas represent a severe technological and environmental challenge for long-term growth and development. Although there are several ways to clean up PAH-contaminated soils, much attention is paid to intriguing bacteria, fungus, and their enzymes. Various factors influence PAH breakdown, including pH, temperature, airflow, moisture level, nutrient availability, and degrading microbial populations. This review discusses how PAHs affect soil characteristics and shows that secondary metabolite and carbon dioxide decomposition are produced due to microbial breakdown processes. Furthermore, the advantages of bioremediation strategies were assessed for correct evaluation and considered dependable on each legislative and scientific research level, as analyzed in this review.
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Affiliation(s)
- Sumathi K
- Department of Biotechnology, School of Biosciences and Technology, VIT University: Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Rameshpathy Manian
- Department of Biotechnology, School of Biosciences and Technology, VIT University: Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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2
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Yesankar PJ, Patil A, Kapley A, Qureshi A. Catalytic resilience of multicomponent aromatic ring-hydroxylating dioxygenases in Pseudomonas for degradation of polycyclic aromatic hydrocarbons. World J Microbiol Biotechnol 2023; 39:166. [PMID: 37076735 DOI: 10.1007/s11274-023-03617-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/11/2023] [Indexed: 04/21/2023]
Abstract
Hydrophobic organic compounds, either natural or introduced through anthropogenic activities, pose a serious threat to all spheres of life, including humankind. These hydrophobic compounds are recalcitrant and difficult to degrade by the microbial system; however, microbes have also evolved their metabolic and degradative potential. Pseudomonas species have been reported to have a multipotential role in the biodegradation of aromatic hydrocarbons through aromatic ring-hydroxylating dioxygenases (ARHDs). The structural complexity of different hydrophobic substrates and their chemically inert nature demands the explicit role of evolutionary conserved multicomponent enzyme ARHDs. These enzymes catalyze ring activation and subsequent oxidation by adding two molecular oxygen atoms onto the vicinal carbon of the aromatic nucleus. This critical metabolic step in the aerobic mode of degradation of polycyclic aromatic hydrocarbons (PAHs) catalyzed by ARHDs can also be explored through protein molecular docking studies. Protein data analysis enables an understanding of molecular processes and monitoring complex biodegradation reactions. This review summarizes the molecular characterization of five ARHDs from Pseudomonas species already reported for PAH degradation. Homology modeling for the amino acid sequences encoding the catalytic α-subunit of ARHDs and their docking analyses with PAHs suggested that the enzyme active sites show flexibility around the catalytic pocket for binding of low molecular weight (LMW) and high molecular weight (HMW) PAH substrates (naphthalene, phenanthrene, pyrene, benzo[α]pyrene). The alpha subunit harbours variable catalytic pockets and broader channels, allowing relaxed enzyme specificity toward PAHs. ARHD's ability to accommodate different LMW and HMW PAHs demonstrates its 'plasticity', meeting the catabolic demand of the PAH degraders.
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Affiliation(s)
- Prerna J Yesankar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India
| | - Ayurshi Patil
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India
| | - Atya Kapley
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India
| | - Asifa Qureshi
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India.
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Sui X, Wang X, Yu L, Ji H. Genomics for the characterization of the mechanisms of microbial strains in degrading petroleum pollutants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:21608-21618. [PMID: 36271069 DOI: 10.1007/s11356-022-23685-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Four petroleum-tolerant bacteria, namely, Pseudomonas hibiscicola, Enterobacter hormaechei, Rhizobium pusense and Pseudomonas japonica were isolated. These strains showed excellent performance in the remediation of petroleum contamination with degradation percentages of 26.13%, 26.47%, 32.27%, and 18.74% for petroleum hydrocarbons, 29.63%, 70.11%, 88.38%, and 67.03% for n-docosane, and 61.00%, 96.36%, 98.00%, and 67.01% for fluorene. Accordingly, the strain of Rhizobium pusense was used to further study its underlying degradation mechanism. N-docosane could be metabolised through the pathway of subterminal oxidation by Rhizobium pusense, while the main pathway for fluorene metabolism is the meta-cleavage. R. pusense contains 10 genes that are involved in the synthetic of biosurfactants and 71 genes that are involved in the metabolism of petroleum hydrocarbons and organic pollutants, such as hydrocarbons, toluene, xylene, ethylbenzene and naphthalene. This study was the first to determine that concerning the metabolism ability and metabolic genes of R. pusense for petroleum pollutant degradation, which is important for understanding the bioremediation mechanism of petroleum pollution.
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Affiliation(s)
- Xin Sui
- Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollution, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Xueyuan Road No. 30, Haidian District, Beijing, 100083, China
| | - Xuemei Wang
- Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollution, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Xueyuan Road No. 30, Haidian District, Beijing, 100083, China
| | - Ling Yu
- Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollution, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Xueyuan Road No. 30, Haidian District, Beijing, 100083, China
| | - Hongbing Ji
- Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollution, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Xueyuan Road No. 30, Haidian District, Beijing, 100083, China.
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4
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Molecular Basis and Evolutionary Origin of 1-Nitronaphthalene Catabolism in Sphingobium sp. Strain JS3065. Appl Environ Microbiol 2023; 89:e0172822. [PMID: 36622195 PMCID: PMC9888181 DOI: 10.1128/aem.01728-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Nitrated polycyclic aromatic hydrocarbons (nitro-PAHs) enter the environment from natural sources and anthropogenic activities. To date, microorganisms able to mineralize nitro-PAHs have not been reported. Here, Sphingobium sp. strain JS3065 was isolated by selective enrichment for its ability to grow on 1-nitronaphthalene as the sole carbon, nitrogen, and energy source. Analysis of the complete genome of strain JS3065 indicated that the gene cluster encoding 1-nitronaphthalene catabolism (nin) is located on a plasmid. Based on the genetic and biochemical evidence, the nin genes share an origin with the nag-like genes encoding naphthalene degradation in Ralstonia sp. strain U2. The initial step in degradation of 1-nitronaphthalene is catalyzed by a three-component dioxygenase, NinAaAbAcAd, resulting in formation of 1,2-dihydroxynaphthalene which is also an early intermediate in the naphthalene degradation pathway. Introduction of the ninAaAbAcAd genes into strain U2 enabled its growth on 1-nitronaphthalene. Phylogenic analysis of NinAc suggested that an ancestral 1-nitronaphthalene dioxygenase was an early step in the evolution of nitroarene dioxygenases. Based on bioinformatic analysis and enzyme assays, the subsequent assimilation of 1,2-dihydroxynaphthalene seems to follow the well-established pathway for naphthalene degradation by Ralstonia sp. strain U2. This is the first report of catabolic pathway for 1-nitronaphthalene and is another example of how expanding the substrate range of Rieske type dioxygenase enables bacteria to grow on recalcitrant nitroaromatic compounds. IMPORTANCE Nitrated polycyclic aromatic hydrocarbons (nitro-PAHs) have been widely detected in the environment and they are more toxic than their corresponding parent PAHs. Although biodegradation of many PAHs has been extensively described at genetic and biochemical levels, little is known about the microbial degradation of nitro-PAHs. This work reports the isolation of a Sphingobium strain growing on 1-nitronaphthalene and the genetic basis for the catabolic pathway. The pathway evolved from an ancestral naphthalene catabolic pathway by a remarkably small modification in the specificity of the initial dioxygenase. Data presented here not only shed light on the biochemical processes involved in the microbial degradation of globally important nitrated polycyclic aromatic hydrocarbons, but also provide an evolutionary paradigm for how bacteria evolve a novel catabolic pathway with minimal alteration of preexisting pathways for natural organic compounds.
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Medić AB, Karadžić IM. Pseudomonas in environmental bioremediation of hydrocarbons and phenolic compounds- key catabolic degradation enzymes and new analytical platforms for comprehensive investigation. World J Microbiol Biotechnol 2022; 38:165. [PMID: 35861883 DOI: 10.1007/s11274-022-03349-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/26/2022] [Indexed: 10/17/2022]
Abstract
Pollution of the environment with petroleum hydrocarbons and phenolic compounds is one of the biggest problems in the age of industrialization and high technology. Species of the genus Pseudomonas, present in almost all hydrocarbon-contaminated areas, play a particular role in biodegradation of these xenobiotics, as the genus has the potential to decompose various hydrocarbons and phenolic compounds, using them as its only source of carbon. Plasticity of carbon metabolism is one of the adaptive strategies used by Pseudomonas to survive exposure to toxic organic compounds, so a good knowledge of its mechanisms of degradation enables the development of new strategies for the treatment of pollutants in the environment. The capacity of microorganisms to metabolize aromatic compounds has contributed to the evolutionally conserved oxygenases. Regardless of the differences in structure and complexity between mono- and polycyclic aromatic hydrocarbons, all these compounds are thermodynamically stable and chemically inert, so for their decomposition, ring activation by oxygenases is crucial. Genus Pseudomonas uses several upper and lower metabolic pathways to transform and degrade hydrocarbons, phenolic compounds, and petroleum hydrocarbons. Data obtained from newly developed omics analytical platforms have enormous potential not only to facilitate our understanding of processes at the molecular level but also enable us to instigate and monitor complex biodegradations by Pseudomonas. Biotechnological application of aromatic metabolic pathways in Pseudomonas to bioremediation of environments polluted with crude oil, biovalorization of lignin for production of bioplastics, biofuel, and bio-based chemicals, as well as Pseudomonas-assisted phytoremediation are also considered.
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Affiliation(s)
- Ana B Medić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia.
| | - Ivanka M Karadžić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia
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Pati SG, Bopp CE, Kohler HPE, Hofstetter TB. Substrate-Specific Coupling of O 2 Activation to Hydroxylations of Aromatic Compounds by Rieske Non-heme Iron Dioxygenases. ACS Catal 2022; 12:6444-6456. [PMID: 35692249 PMCID: PMC9171724 DOI: 10.1021/acscatal.2c00383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/09/2022] [Indexed: 02/07/2023]
Abstract
![]()
Rieske dioxygenases
catalyze the initial steps in the hydroxylation
of aromatic compounds and are critical for the metabolism of xenobiotic
substances. Because substrates do not bind to the mononuclear non-heme
FeII center, elementary steps leading to O2 activation
and substrate hydroxylation are difficult to delineate, thus making
it challenging to rationalize divergent observations on enzyme mechanisms,
reactivity, and substrate specificity. Here, we show for nitrobenzene
dioxygenase, a Rieske dioxygenase capable of transforming nitroarenes
to nitrite and substituted catechols, that unproductive O2 activation with the release of the unreacted substrate and reactive
oxygen species represents an important path in the catalytic cycle.
Through correlation of O2 uncoupling for a series of substituted
nitroaromatic compounds with 18O and 13C kinetic
isotope effects of dissolved O2 and aromatic substrates,
respectively, we show that O2 uncoupling occurs after the
rate-limiting formation of FeIII-(hydro)peroxo species
from which substrates are hydroxylated. Substituent effects on the
extent of O2 uncoupling suggest that the positioning of
the substrate in the active site rather than the susceptibility of
the substrate for attack by electrophilic oxygen species is responsible
for unproductive O2 uncoupling. The proposed catalytic
cycle provides a mechanistic basis for assessing the very different
efficiencies of substrate hydroxylation vs unproductive O2 activation and generation of reactive oxygen species in reactions
catalyzed by Rieske dioxygenases.
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Affiliation(s)
- Sarah G. Pati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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Chen Z, Hu H, Xu P, Tang H. Soil bioremediation by Pseudomonas brassicacearum MPDS and its enzyme involved in degrading PAHs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152522. [PMID: 34953839 DOI: 10.1016/j.scitotenv.2021.152522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) commonly coexist in contaminated sites, posing a significant threat to ecosystem. Strains that degrade a wide range of substrates play important roles in bioremediation of contaminated environment. In this study, we reveal that Pseudomonas brassicacearum MPDS was able to remove 31.1% naphthalene of 500 mg/kg from soil within 2 d, while its relative abundance decreased significantly on Day 20, indicating its applicable potential in soil remediation. In addition to naphthalene, dibenzofuran, dibenzothiophene, and fluorene as reported previously, strain MPDS is able to degrade carbazole, phenanthrene, pyrene, and 2-bromonaphthalene. Moreover, NahA from strain MPDS has multi-substrate catalytic capacities on naphthalene, dibenzofuran, dibenzothiophene, phenanthrene, and 2-bromonaphthalene into dihydrodiols, while converts fluorene and carbazole into monohydroxy compounds according to GC-MS analysis. This study provides further insights into the exploration of soil remediation by strain MPDS and the mining of enzymes involved in the degradation of PAHs.
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Affiliation(s)
- Zhengshi Chen
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
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Csizi KS, Eckert L, Brunken C, Hofstetter TB, Reiher M. The Apparently Unreactive Substrate Facilitates the Electron Transfer for Dioxygen Activation in Rieske Dioxygenases. Chemistry 2022; 28:e202103937. [PMID: 35072969 PMCID: PMC9306888 DOI: 10.1002/chem.202103937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 12/29/2022]
Abstract
Rieske dioxygenases belong to the non‐heme iron family of oxygenases and catalyze important cis‐dihydroxylation as well as O‐/N‐dealkylation and oxidative cyclization reactions for a wide range of substrates. The lack of substrate coordination at the non‐heme ferrous iron center, however, makes it particularly challenging to delineate the role of the substrate for productive O2
activation. Here, we studied the role of the substrate in the key elementary reaction leading to O2
activation from a theoretical perspective by systematically considering (i) the 6‐coordinate to 5‐coordinate conversion of the non‐heme FeII upon abstraction of a water ligand, (ii) binding of O2
, and (iii) transfer of an electron from the Rieske cluster. We systematically evaluated the spin‐state‐dependent reaction energies and structural effects at the active site for all combinations of the three elementary processes in the presence and absence of substrate using naphthalene dioxygenase as a prototypical Rieske dioxygenase. We find that reaction energies for the generation of a coordination vacancy at the non‐heme FeII
center through thermoneutral H2O reorientation and exothermic O2
binding prior to Rieske cluster oxidation are largely insensitive to the presence of naphthalene and do not lead to formation of any of the known reactive Fe‐oxygen species. By contrast, the role of the substrate becomes evident after Rieske cluster oxidation and exclusively for the 6‐coordinate non‐heme FeII
sites in that the additional electron is found at the substrate instead of at the iron and oxygen atoms. Our results imply an allosteric control of the substrate on Rieske dioxygenase reactivity to happen prior to changes at the non‐heme FeII
in agreement with a strategy that avoids unproductive O2
activation.
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Affiliation(s)
- Katja-Sophia Csizi
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Lina Eckert
- ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Christoph Brunken
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Thomas B Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Markus Reiher
- ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
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Monooxygenase- and Dioxygenase-Catalyzed Oxidative Dearomatization of Thiophenes by Sulfoxidation, cis-Dihydroxylation and Epoxidation. Int J Mol Sci 2022; 23:ijms23020909. [PMID: 35055091 PMCID: PMC8777831 DOI: 10.3390/ijms23020909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 11/17/2022] Open
Abstract
Enzymatic oxidations of thiophenes, including thiophene-containing drugs, are important for biodesulfurization of crude oil and drug metabolism of mono- and poly-cyclic thiophenes. Thiophene oxidative dearomatization pathways involve reactive metabolites, whose detection is important in the pharmaceutical industry, and are catalyzed by monooxygenase (sulfoxidation, epoxidation) and dioxygenase (sulfoxidation, dihydroxylation) enzymes. Sulfoxide and epoxide metabolites of thiophene substrates are often unstable, and, while cis-dihydrodiol metabolites are more stable, significant challenges are presented by both types of metabolite. Prediction of the structure, relative and absolute configuration, and enantiopurity of chiral metabolites obtained from thiophene enzymatic oxidation depends on the substrate, type of oxygenase selected, and molecular docking results. The racemization and dimerization of sulfoxides, cis/trans epimerization of dihydrodiol metabolites, and aromatization of epoxides are all factors associated with the mono- and di-oxygenase-catalyzed metabolism of thiophenes and thiophene-containing drugs and their applications in chemoenzymatic synthesis and medicine.
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Medić A, Lješević M, Inui H, Beškoski V, Kojić I, Stojanović K, Karadžić I. Efficient biodegradation of petroleum n-alkanes and polycyclic aromatic hydrocarbons by polyextremophilic Pseudomonas aeruginosa san ai with multidegradative capacity. RSC Adv 2020; 10:14060-14070. [PMID: 35498501 PMCID: PMC9051604 DOI: 10.1039/c9ra10371f] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/30/2020] [Indexed: 11/21/2022] Open
Abstract
Pseudomonas aeruginosa san ai degraded individual selected petroleum compounds: n-hexadecane, n-nonadecane, fluorene, phenanthrene, and pyrene with high efficiency, at initial concentrations of 20 mg L−1 and in seven days.
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Affiliation(s)
- Ana Medić
- Department of Chemistry
- Faculty of Medicine
- University of Belgrade
- 11000 Belgrade
- Serbia
| | - Marija Lješević
- Department of Chemistry
- Institute of Chemistry, Technology and Metallurgy
- University of Belgrade
- 11000 Belgrade
- Serbia
| | | | | | - Ivan Kojić
- Innovation Center of the Faculty of Chemistry
- University of Belgrade
- 11000 Belgrade
- Serbia
| | | | - Ivanka Karadžić
- Department of Chemistry
- Faculty of Medicine
- University of Belgrade
- 11000 Belgrade
- Serbia
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Boyd DR, Sharma ND, McGivern CJ, Stevenson PJ, Hoering P, Allen CCR. Chemoenzymatic Synthesis of (-)-Ribisins A and B from Dibenzo[ b,d]furan. J Org Chem 2019; 84:15165-15172. [PMID: 31692354 DOI: 10.1021/acs.joc.9b02171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
cis-Dihydrodiols, derived from monocyclic aromatic compounds, are valuable chiral pool intermediates for the synthesis of cyclic natural products. A drawback of this approach, to the synthesis of polycyclic secondary metabolites, is that additional rings must be annulated. To date, relatively few chiral natural products have been synthesized from polycyclic arene cis-dihydrodiols. Fungal metabolites, (-)-ribisins A and B, have now been obtained by functional group manipulation of a tricyclic arene metabolite, obtained from toluene dioxygenase-catalyzed regioselective and stereoselective cis-dihydroxylations of dibenzo[b,d]furan. The synthetic sequences were marginally shorter than the alternative routes, using monocyclic arene cis-dihydrodiols, and required no carbon-carbon bond-forming reactions.
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Affiliation(s)
- Derek R Boyd
- School of Chemistry and Chemical Engineering , Queen's University , Belfast BT9 5AG , U.K
| | - Narain D Sharma
- School of Chemistry and Chemical Engineering , Queen's University , Belfast BT9 5AG , U.K
| | - Christopher J McGivern
- School of Chemistry and Chemical Engineering , Queen's University , Belfast BT9 5AG , U.K
| | - Paul J Stevenson
- School of Chemistry and Chemical Engineering , Queen's University , Belfast BT9 5AG , U.K
| | - Patrick Hoering
- School of Biological Sciences , Queen's University , Belfast BT9 5DL , U.K
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12
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Ali F, Hu H, Wang W, Zhou Z, Shah SB, Xu P, Tang H. Characterization of a Dibenzofuran-degrading strain of Pseudomonas aeruginosa, FA-HZ1. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 250:262-273. [PMID: 30999203 DOI: 10.1016/j.envpol.2019.04.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/11/2019] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
Dibenzofuran (DBF) derivatives have caused serious environmental problems, especially those produced by paper pulp bleaching and incineration processes. Prominent for its resilient mutagenicity and toxicity, DBF poses a major challenge to human health. In the present study, a new strain of Pseudomonas aeruginosa, FA-HZ1, with high DBF-degrading activity was isolated and identified. The determined optimum conditions for cell growth of strain FA-HZ1 were a temperature of 30 °C, pH 5.0, rotation rate of 200 rpm and 0.1 mM DBF as a carbon source. The biochemical and physiological features as well as usage of different carbon sources by FA-HZ1 were studied. The new strain was positive for arginine double hydrolase, gelatinase and citric acid, while it was negative for urease and lysine decarboxylase. It could utilize citric acid as its sole carbon source, but was negative for indole and H2S production. Intermediates of DBF 1,2-dihydroxy-1,2-dihydrodibenzofuran, 1,2-dihydroxydibenzofuran, 2-hydroxy-4-(3'-oxo-3'H-benzofuran-2'-yliden)but-2-enoic acid, 2,3-dihydroxybenzofuran, 2-oxo-2-(2'-hydrophenyl)lactic acid, and 2-hydroxy-2-(2'-hydroxyphenyl)acetic acid were detected and identified through liquid chromatography-mass analyses. FA-HZ1 metabolizes DBF by both the angular and lateral dioxygenation pathways. The genomic study identified 158 genes that were involved in the catabolism of aromatic compounds. To identify the key genes responsible for DBF degradation, a proteomic study was performed. A total of 1459 proteins were identified in strain FA-HZ1, of which 100 were up-regulated and 104 were down-regulated. A novel enzyme "HZ6359 dioxygenase", was amplified and expressed in pET-28a in E. coli BL21(DE3). The recombinant plasmid was successfully constructed, and was used for further experiments to verify its function. In addition, the strain FA-HZ1 can also degrade halogenated analogues such as 2, 8-dibromo dibenzofuran and 4-(4-bromophenyl) dibenzofuran. Undoubtedly, the isolation and characterization of new strain and the designed pathways is significant, as it could lead to the development of cost-effective and alternative remediation strategies. The degradation pathway of DBF by P. aeruginosa FA-HZ1 is a promising tool of biotechnological and environmental significance.
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Affiliation(s)
- Fawad Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Zikang Zhou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Syed Bilal Shah
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
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Boyd DR, Sharma ND, Brannigan IN, McGivern CJ, Nockemann P, Stevenson PJ, McRoberts C, Hoering P, Allen CCR. Cis‐Dihydroxylation of Tricyclic Arenes and Heteroarenes Catalyzed by Toluene Dioxygenase: A Molecular Docking Study and Experimental Validation. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Derek R. Boyd
- School of Chemistry and Chemical EngineeringQueen's University of Belfast Belfast BT9 5AG UK
| | - Narain D. Sharma
- School of Chemistry and Chemical EngineeringQueen's University of Belfast Belfast BT9 5AG UK
| | - Ian N. Brannigan
- School of Chemistry and Chemical EngineeringQueen's University of Belfast Belfast BT9 5AG UK
| | - Christopher J. McGivern
- School of Chemistry and Chemical EngineeringQueen's University of Belfast Belfast BT9 5AG UK
| | - Peter Nockemann
- School of Chemistry and Chemical EngineeringQueen's University of Belfast Belfast BT9 5AG UK
| | - Paul J. Stevenson
- School of Chemistry and Chemical EngineeringQueen's University of Belfast Belfast BT9 5AG UK
| | - Colin McRoberts
- Agri-food and Biosciences Institute for Northern Ireland Belfast BT9 5PX UK
| | - Patrick Hoering
- School of Biological SciencesQueen's University of Belfast Belfast BT9 7BL, UK
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14
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Verma N, Kantiwal U, Nitika, Yadav YK, Teli S, Goyal D, Pandey J. Catalytic Promiscuity of Aromatic Ring-Hydroxylating Dioxygenases and Their Role in the Plasticity of Xenobiotic Compound Degradation. MICROORGANISMS FOR SUSTAINABILITY 2019. [DOI: 10.1007/978-981-13-7462-3_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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15
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Liu X, Wang W, Hu H, Lu X, Zhang L, Xu P, Tang H. 2-Hydroxy-4-(3′-oxo-3′H-benzofuran-2′-yliden)but-2-enoic acid biosynthesis from dibenzofuran using lateral dioxygenation in a Pseudomonas putida strain B6-2 (DSM 28064). BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0209-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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16
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Boyd DR, Sharma ND, Goodrich PA, Malone JF, McConville G, Harrison JS, Stevenson PJ, Allen CCR. Enantiopurity and absolute configuration determination of arene cis-dihydrodiol metabolites and derivatives using chiral boronic acids. Chirality 2017; 30:5-18. [PMID: 29024058 DOI: 10.1002/chir.22764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 02/03/2023]
Abstract
The relative merits of the methods employed to determine enantiomeric excess (ee) values and absolute configurations of chiral arene and alkene cis-1,2-diol metabolites, including boronate formation, using racemic or enantiopure (+) and (-)-2-(1-methoxyethyl)phenylboronic acid (MEPBA), are discussed. Further applications of: 1) MEPBA derived boronates of chiral mono- and poly-cyclic arene cis-dihydrodiol, cyclohex-2-en-1-one cis-diol, heteroarene cis/trans-2,3-diol, and catechol metabolites in estimating their ee values, and 2) new chiral phenylboronic acids, 2-[1-methoxy-2,2-dimethylpropyl]phenyl boronic acid (MDPBA) and 2-[1-methoxy-1-phenylmethyl]phenyl boronic acid (MPPBA) and their advantages over MEPBA, as reagents for stereochemical analysis of arene and alkene cis-diol metabolites, are presented.
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Affiliation(s)
- Derek R Boyd
- School of Chemistry and Chemical Engineering, Queen's University, Belfast, UK
| | - Narain D Sharma
- School of Chemistry and Chemical Engineering, Queen's University, Belfast, UK
| | - Peter A Goodrich
- School of Chemistry and Chemical Engineering, Queen's University, Belfast, UK
| | - John F Malone
- School of Chemistry and Chemical Engineering, Queen's University, Belfast, UK
| | - Gareth McConville
- School of Chemistry and Chemical Engineering, Queen's University, Belfast, UK
| | - John S Harrison
- School of Chemistry and Chemical Engineering, Queen's University, Belfast, UK
| | - Paul J Stevenson
- School of Chemistry and Chemical Engineering, Queen's University, Belfast, UK
| | - Christopher C R Allen
- School of Biological Sciences and Institute for Global and Food Security, Queen's University, Belfast, UK
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17
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Ferraro DJ, Okerlund A, Brown E, Ramaswamy S. One enzyme, many reactions: structural basis for the various reactions catalyzed by naphthalene 1,2-dioxygenase. IUCRJ 2017; 4:648-656. [PMID: 28989720 PMCID: PMC5619856 DOI: 10.1107/s2052252517008223] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/02/2017] [Indexed: 06/07/2023]
Abstract
Rieske nonheme iron oxygenases (ROs) are a well studied class of enzymes. Naphthalene 1,2-dioxygenase (NDO) is used as a model to study ROs. Previous work has shown how side-on binding of oxygen to the mononuclear iron provides this enzyme with the ability to catalyze stereospecific and regiospecific cis-dihydroxylation reactions. It has been well documented that ROs catalyze a variety of other reactions, including mono-oxygenation, desaturation, O- and N-dealkylation, sulfoxidation etc. NDO itself catalyzes a variety of these reactions. Structures of NDO in complex with a number of different substrates show that the orientation of the substrate in the active site controls not only the regiospecificity and stereospecificity, but also the type of reaction catalyzed. It is proposed that the mononuclear iron-activated dioxygen attacks the atoms of the substrate that are most proximal to it. The promiscuity of delivering two products (apparently by two different reactions) from the same substrate can be explained by the possible binding of the substrate in slightly different orientations aided by the observed flexibility of residues in the binding pocket.
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Affiliation(s)
- Daniel J. Ferraro
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Adam Okerlund
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Eric Brown
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - S. Ramaswamy
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- TAS, Institute for Stem Cell Biology and Regenerative Medicine, GKVK POST, Bangalore 560 065, India
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18
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Sakkos JK, Mutlu BR, Wackett LP, Aksan A. Adsorption and Biodegradation of Aromatic Chemicals by Bacteria Encapsulated in a Hydrophobic Silica Gel. ACS APPLIED MATERIALS & INTERFACES 2017; 9:26848-26858. [PMID: 28719174 DOI: 10.1021/acsami.7b06791] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
An adsorbent silica biogel material was developed via silica gel encapsulation of Pseudomonas sp. NCIB 9816-4, a bacterium that degrades a broad spectrum of aromatic pollutants. The adsorbent matrix was synthesized using silica precursors methyltrimethoxysilane and tetramethoxysilane to maximize the adsorption capacity of the matrix while maintaining a highly networked and porous microstructure. The encapsulated bacteria enhanced the removal rate and capacity of the matrix for an aromatic chemical mixture. Repeated use of the material over four cycles was conducted to demonstrate that the removal capacity could be maintained with combined adsorption and biodegradation. The silica biogel can thus be used extensively without the need for disposal, as a result of continuous biodegradation by the encapsulated bacteria. However, an inverse trend was observed with the ratio of biodegradation to adsorption as a function of log Kow, suggesting increasing mass-transport limitation for the most hydrophobic chemicals used (log Kow > 4).
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Affiliation(s)
| | | | - Lawrence P Wackett
- The BioTechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - Alptekin Aksan
- The BioTechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
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19
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Crampon M, Cébron A, Portet-Koltalo F, Uroz S, Le Derf F, Bodilis J. Low effect of phenanthrene bioaccessibility on its biodegradation in diffusely contaminated soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 225:663-673. [PMID: 28390702 DOI: 10.1016/j.envpol.2017.03.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 06/07/2023]
Abstract
This study focused on the role of bioaccessibility in the phenanthrene (PHE) biodegradation in diffusely contaminated soil, by combining chemical and microbiological approaches. First, we determined PHE dissipation rates and PHE sorption/desorption isotherms for two soils (PPY and Pv) presenting similar chronic PAH contamination, but different physico-chemical properties. Our results revealed that the PHE dissipation rate was significantly higher in the Pv soil compared to the PPY soil, while PHE sorption/desorption isotherms were similar. Interestingly, increases of PHE desorption and potentially of PHE bioaccessibility were observed for both soils when adding rhamnolipids (biosurfactants produced by Pseudomonas aeruginosa). Second, using 13C-PHE incubated in the same soils, we analyzed the PHE degrading bacterial communities. The combination of stable isotope probing (DNA-SIP) and 16S rRNA gene pyrosequencing revealed that Betaproteobacteria were the main PHE degraders in the Pv soil, while a higher bacterial diversity (Alpha-, Beta-, Gammaproteobacteria and Actinobacteria) was involved in PHE degradation in the PPY soil. The amendment of biosurfactants commonly used in biostimulation methods (i.e. rhamnolipids) to the two soils clearly modified the PHE sorption/desorption isotherms, but had no significant impact on PHE degradation rates and PHE-degraders identity. These results demonstrated that increasing the bioaccessibility of PHE has a low impact on its degradation and on the functional populations involved in this degradation.
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Affiliation(s)
- M Crampon
- COBRA UMR CNRS 6014, Université de Rouen-Normandie, 55 rue saint Germain, 27000 Evreux, France; Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Université de Rouen, 76821 Mont Saint Aignan, France
| | - A Cébron
- CNRS, LIEC UMR 7360, Faculté des Sciences et Technologies, BP70239, 54506 Vandoeuvre-lès-Nancy Cedex, France; Université de Lorraine, LIEC UMR 7360, Faculté des Sciences et Technologies, BP70239, 54506 Vandoeuvre-lès-Nancy Cedex, France
| | - F Portet-Koltalo
- COBRA UMR CNRS 6014, Université de Rouen-Normandie, 55 rue saint Germain, 27000 Evreux, France
| | - S Uroz
- UMR 1138 INRA, Centre de Nancy, Biogéochimie des Ecosystèmes forestiers, Route d'Amance, 54280 Champenoux, France
| | - F Le Derf
- COBRA UMR CNRS 6014, Université de Rouen-Normandie, 55 rue saint Germain, 27000 Evreux, France
| | - J Bodilis
- Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Université de Rouen, 76821 Mont Saint Aignan, France; Université de Lyon, France, CNRS, INRA, Ecole Nationale Vétérinaire de Lyon, Université Lyon 1, UMR 5557 Ecologie Microbienne, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France.
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20
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Shi S, Qu Y, Tan L, Ma F. Biosynthesis of 1,2-dihydroxydibenzofuran by magnetically immobilized cells of Escherichia coli expressing phenol hydroxylase in liquid-liquid biphasic systems. BIORESOURCE TECHNOLOGY 2015; 197:72-78. [PMID: 26318924 DOI: 10.1016/j.biortech.2015.08.052] [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: 06/25/2015] [Revised: 08/08/2015] [Accepted: 08/11/2015] [Indexed: 06/04/2023]
Abstract
Escherichia coli cells expressing phenol hydroxylase (designated as PHIND) were used to biosynthesize 1,2-dihydroxydibenzofuran (1,2-dihydroxyDBF) from dibenzofuran (DBF). The pathway of DBF biotransformation by strain PHIND was proposed, in which DBF was initially monohydroxylated at C-1 and C-4 positions to produce 1- and 4-hydroxyDBF, then underwent successive hydroxylation to yield 1,2- and 3,4-dihydroxyDBF, of which 1,2-dihydroxyDBF was identified for the first time. Magnetically immobilized cells of strain PHIND in biphasic systems with dodecane as the solvent presented highest biosynthesis activity for 1,2-dihydroxyDBF, which was a 6.5-fold improvement compared to biosynthesis in aqueous system. The recycling experiments demonstrated that magnetically immobilized cells exhibited higher biosynthesis activity for 1,2-dihydroxyDBF than that by nonmagnetically immobilized cells during five cycles in biphasic systems. These works support the development of an efficient biosynthesis process using magnetically immobilized cells in biphasic systems and provide a promising technique for improving the productivity in 1,2-dihydroxyDBF biosynthesis.
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Affiliation(s)
- Shengnan Shi
- School of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Liang Tan
- School of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
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21
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Wald J, Hroudova M, Jansa J, Vrchotova B, Macek T, Uhlik O. Pseudomonads Rule Degradation of Polyaromatic Hydrocarbons in Aerated Sediment. Front Microbiol 2015; 6:1268. [PMID: 26635740 PMCID: PMC4652016 DOI: 10.3389/fmicb.2015.01268] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 10/30/2015] [Indexed: 11/24/2022] Open
Abstract
Given that the degradation of aromatic pollutants in anaerobic environments such as sediment is generally very slow, aeration could be an efficient bioremediation option. Using stable isotope probing (SIP) coupled with pyrosequencing analysis of 16S rRNA genes, we identified naphthalene-utilizing populations in aerated polyaromatic hydrocarbon (PAH)-polluted sediment. The results showed that naphthalene was metabolized at both 10 and 20°C following oxygen delivery, with increased degradation at 20°C as compared to 10°C—a temperature more similar to that found in situ. Naphthalene-derived 13C was primarily assimilated by pseudomonads. Additionally, Stenotrophomonas, Acidovorax, Comamonas, and other minor taxa were determined to incorporate 13C throughout the measured time course. The majority of SIP-detected bacteria were also isolated in pure cultures, which facilitated more reliable identification of naphthalene-utilizing populations as well as proper differentiation between primary consumers and cross-feeders. The pseudomonads acquiring the majority of carbon were identified as Pseudomonas veronii and Pseudomonas gessardii. Stenotrophomonads and Acidovorax defluvii, however, were identified as cross-feeders unable to directly utilize naphthalene as a growth substrate. PAH degradation assays with the isolated bacteria revealed that all pseudomonads as well as Comamonas testosteroni degraded acenaphthene, fluorene, and phenanthrene in addition to naphthalene. Furthermore, P. veronii and C. testosteroni were capable of transforming anthracene, fluoranthene, and pyrene. Screening of isolates for naphthalene dioxygenase genes using a set of in-house designed primers for Gram-negative bacteria revealed the presence of such genes in pseudomonads and C. testosteroni. Overall, our results indicated an apparent dominance of pseudomonads in the sequestration of carbon from naphthalene and potential degradation of other PAHs upon aeration of the sediment at both 20 and 10°C.
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Affiliation(s)
- Jiri Wald
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Miluse Hroudova
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences Prague, Czech Republic
| | - Jan Jansa
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences Prague, Czech Republic
| | - Blanka Vrchotova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Tomas Macek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Prague, Czech Republic
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Kimes NE, Callaghan AV, Suflita JM, Morris PJ. Microbial transformation of the Deepwater Horizon oil spill-past, present, and future perspectives. Front Microbiol 2014; 5:603. [PMID: 25477866 PMCID: PMC4235408 DOI: 10.3389/fmicb.2014.00603] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/23/2014] [Indexed: 01/24/2023] Open
Abstract
The Deepwater Horizon blowout, which occurred on April 20, 2010, resulted in an unprecedented oil spill. Despite a complex effort to cap the well, oil and gas spewed from the site until July 15, 2010. Although a large proportion of the hydrocarbons was depleted via natural processes and human intervention, a substantial portion of the oil remained unaccounted for and impacted multiple ecosystems throughout the Gulf of Mexico. The depth, duration and magnitude of this spill were unique, raising many questions and concerns regarding the fate of the hydrocarbons released. One major question was whether or not microbial communities would be capable of metabolizing the hydrocarbons, and if so, by what mechanisms and to what extent? In this review, we summarize the microbial response to the oil spill as described by studies performed during the past four years, providing an overview of the different responses associated with the water column, surface waters, deep-sea sediments, and coastal sands/sediments. Collectively, these studies provide evidence that the microbial response to the Deepwater Horizon oil spill was rapid and robust, displaying common attenuation mechanisms optimized for low molecular weight aliphatic and aromatic hydrocarbons. In contrast, the lack of evidence for the attenuation of more recalcitrant hydrocarbon components suggests that future work should focus on both the environmental impact and metabolic fate of recalcitrant compounds, such as oxygenated oil components.
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Affiliation(s)
- Nikole E. Kimes
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel HernándezSan Juan, Spain
| | - Amy V. Callaghan
- Department of Microbiology and Plant Biology, University of OklahomaNorman, OK, USA
| | - Joseph M. Suflita
- Department of Microbiology and Plant Biology, University of OklahomaNorman, OK, USA
| | - Pamela J. Morris
- Belle W. Baruch Institute for Marine and Coastal Sciences, University of South CarolinaGeorgetown, SC, USA
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Okazaki T, Nakagawa M, Kitagawa T, Laali KK. Experimental NMR and DFT Studies of Persistent Carbocations Derived from Hetero-Polycyclic Aromatic Hydrocarbons Containing Oxygen Atom: Dibenzo[b,d]furan, Benzo[b]naphtho[1,2-d]furan, Benzo[b]naphtho[2,3-d]furan, Benzo[b]naphtho[2,1-d]furan, and Dinaphtho[2,1-b:1′,2′-d]furan. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20140182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Takao Okazaki
- Department of Chemistry for Materials, Graduate School of Engineering, Mie University
| | - Madoka Nakagawa
- Department of Chemistry for Materials, Graduate School of Engineering, Mie University
| | - Toshikazu Kitagawa
- Department of Chemistry for Materials, Graduate School of Engineering, Mie University
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Xia W, Du Z, Cui Q, Dong H, Wang F, He P, Tang Y. Biosurfactant produced by novel Pseudomonas sp. WJ6 with biodegradation of n-alkanes and polycyclic aromatic hydrocarbons. JOURNAL OF HAZARDOUS MATERIALS 2014; 276:489-498. [PMID: 24929788 DOI: 10.1016/j.jhazmat.2014.05.062] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/25/2014] [Accepted: 05/22/2014] [Indexed: 06/03/2023]
Abstract
Alkanes and polycyclic aromatic hydrocarbons (PAHs) have threatened the environment due to toxicity and poor bioavailability. Interest in degradation of these hazardous materials by biosurfactant-producing bacteria has been steadily increasing in recent years. In this work, a novel biosurfactant-producing Pseudomonas sp. WJ6 was isolated to degrade a wide range of n-alkanes and polycyclic aromatic hydrocarbons. Production of lipopeptide biosurfactant was observed in all biodegradable studies. These lipopeptides were purified and identified by C18 RP-HPLC system and electrospray ionization-mass spectrometry. Results of structural analysis showed that these lipopeptides generated from different hydrocarbons were classified to be surfactin, fengycin and lichenysin. Heavy-oil sludge washing experiments demonstrated that lipopeptides produced by Pseudomonas sp. WJ6 have 92.46% of heavy-oil washing efficiency. The obtained results indicate that this novel bacterial strain and its lipopeptides have great potentials in the environmental remediation and petroleum recovery.
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Affiliation(s)
- Wenjie Xia
- Power Environmental Energy Research Institute, Covina, CA 91722, USA; Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, PR China; Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, PR China.
| | - Zhifeng Du
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, PR China
| | - Qingfeng Cui
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, PR China
| | - Hao Dong
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, PR China
| | - Fuyi Wang
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, PR China.
| | - Panqing He
- Power Environmental Energy Research Institute, Covina, CA 91722, USA
| | - YongChun Tang
- Power Environmental Energy Research Institute, Covina, CA 91722, USA.
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25
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Use of silica-encapsulated Pseudomonas sp. strain NCIB 9816-4 in biodegradation of novel hydrocarbon ring structures found in hydraulic fracturing waters. Appl Environ Microbiol 2014; 80:4968-76. [PMID: 24907321 DOI: 10.1128/aem.01100-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The most problematic hydrocarbons in hydraulic fracturing (fracking) wastewaters consist of fused, isolated, bridged, and spiro ring systems, and ring systems have been poorly studied with respect to biodegradation, prompting the testing here of six major ring structural subclasses using a well-characterized bacterium and a silica encapsulation system previously shown to enhance biodegradation. The direct biological oxygenation of spiro ring compounds was demonstrated here. These and other hydrocarbon ring compounds have previously been shown to be present in flow-back waters and waters produced from hydraulic fracturing operations. Pseudomonas sp. strain NCIB 9816-4, containing naphthalene dioxygenase, was selected for its broad substrate specificity, and it was demonstrated here to oxidize fundamental ring structures that are common in shale-derived waters but not previously investigated with this or related enzymes. Pseudomonas sp. NCIB 9816-4 was tested here in the presence of a silica encasement, a protocol that has previously been shown to protect bacteria against the extremes of salinity present in fracking wastewaters. These studies demonstrate the degradation of highly hydrophobic compounds by a silica-encapsulated model bacterium, demonstrate what it may not degrade, and contribute to knowledge of the full range of hydrocarbon ring compounds that can be oxidized using Pseudomonas sp. NCIB 9816-4.
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Lin Y, Wang F, Yang LJ, Chun Z, Bao JK, Zhang GL. Anti-inflammatory phenanthrene derivatives from stems of Dendrobium denneanum. PHYTOCHEMISTRY 2013; 95:242-51. [PMID: 24042064 DOI: 10.1016/j.phytochem.2013.08.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 08/03/2013] [Accepted: 08/03/2013] [Indexed: 05/16/2023]
Abstract
Cultivated Dendrobium denneanum has been substituted for other endangered Dendrobium species in recent years, but there have been few studies regarding either its chemical constituents or pharmacological effects. In this study, three phenanthrene glycosides, three 9,10-dihydrophenanthrenes, two 9,10-dihydrophenanthrenes glycosides, and four known phenanthrene derivatives, were isolated from the stems of D. denneanum. Their structures were elucidated on the basis of MS and NMR spectroscopic data. Ten compounds were found to inhibit nitric oxide (NO) production in lipopolysaccharide (LPS)-activated mouse macrophage RAW264.7 cells with IC50 values of 0.7-41.5 μM, and exhibited no cytotoxicity in RAW264.7, HeLa, or HepG2 cells. Additionally, it was found that 2,5-dihydroxy-4-methoxy-phenanthrene 2-O-β-d-glucopyranoside, and 5-methoxy-2,4,7,9S-tetrahydroxy-9,10-dihydrophenanthrene suppressed LPS-induced expression of inducible NO synthase (iNOS) inhibited phosphorylation of p38, JNK as well as mitogen-activated protein kinase (MAPK), and inhibitory kappa B-α (IκBα). This indicated that both compounds exert anti-inflammatory effects by inhibiting MAPKs and nuclear factor κB (NF-κB) pathways.
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Affiliation(s)
- Yuan Lin
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
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Ma J, Xu L, Jia L. Characterization of pyrene degradation by Pseudomonas sp. strain Jpyr-1 isolated from active sewage sludge. BIORESOURCE TECHNOLOGY 2013; 140:15-21. [PMID: 23669098 DOI: 10.1016/j.biortech.2013.03.184] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 05/02/2023]
Abstract
Using pyrene as a sole carbon, a new polycyclic aromatic hydrocarbons (PAHs)-degrading bacterial strain was isolated from the active sewage sludge. This strain was identified as Pseudomonas sp. Jpyr-1 by 16S rRNA gene sequence analysis. The maximum degradation rate of pyrene was 3.07 mg L(-1)h(-1) in 48 h incubation with initial pyrene concentration of 200 mg L(-1). Moreover, in binary system consisting of pyrene and another PAH, the enzyme system of Jpyr-1 showed a preference toward pyrene. Furthermore, competitive inhibition of pyrene degradation by other PAH compounds occurred in the binary system. Jpyr-1 could also rapidly degrade other PAHs, such as benzanthracene, chrysene and benzo[a]pyrene. Moreover, several metabolites were detected during pyrene degradation which indicated that Jpyr-1 degraded pyrene through the o-phthalate pathway. Taken together, these results indicated that Pseudomonas sp. Jpyr-1 was a new PAHs-degrading strain that might be useful in the bioremediation of sites contaminated with PAHs.
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Affiliation(s)
- Jing Ma
- School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi District, Dalian, Liaoning 116023, China
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Peng P, Yang H, Jia R, Li L. Biodegradation of dioxin by a newly isolated Rhodococcus sp. with the involvement of self-transmissible plasmids. Appl Microbiol Biotechnol 2012; 97:5585-95. [DOI: 10.1007/s00253-012-4363-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 08/07/2012] [Accepted: 08/09/2012] [Indexed: 10/27/2022]
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Comprehensive GC2/MS for the monitoring of aromatic tar oil constituents during biodegradation in a historically contaminated soil. J Biotechnol 2012; 157:460-6. [DOI: 10.1016/j.jbiotec.2011.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 07/28/2011] [Accepted: 08/08/2011] [Indexed: 11/18/2022]
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31
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Chandra Srivastava V. An evaluation of desulfurization technologies for sulfur removal from liquid fuels. RSC Adv 2012. [DOI: 10.1039/c1ra00309g] [Citation(s) in RCA: 567] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Zhang Z, Hou Z, Yang C, Ma C, Tao F, Xu P. Degradation of n-alkanes and polycyclic aromatic hydrocarbons in petroleum by a newly isolated Pseudomonas aeruginosa DQ8. BIORESOURCE TECHNOLOGY 2011; 102:4111-6. [PMID: 21227683 DOI: 10.1016/j.biortech.2010.12.064] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 12/15/2010] [Accepted: 12/16/2010] [Indexed: 05/02/2023]
Abstract
A bacterial isolate, designated as DQ8, was found capable of degrading diesel, crude oil, n-alkanes and polycyclic aromatic hydrocarbons (PAHs) in petroleum. Strain DQ8 was assigned to the genus Pseudomonas aeruginosa based on biochemical and genetic data. The metabolites identified from n-docosane as substrate suggested that P. aeruginosa DQ8 could oxidize n-alkanes via a terminal oxidation pathway. P. aeruginosa DQ8 could also degrade PAHs of three or four aromatic rings. The metabolites identified from fluorene as substrate suggested that P. aeruginosa DQ8 may degrade fluorene via two pathways. One is monooxygenation at C-9 of fluorene, and the other is initiated by dioxygenation at C-3 and C-4 of fluorene. P. aeruginosa DQ8 should be of great practical significance both in bioremediation of oil-contaminated soils and biotreatment of oil wastewater.
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Affiliation(s)
- Zhengzhi Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
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Structural insight into the expanded PCB-degrading abilities of a biphenyl dioxygenase obtained by directed evolution. J Mol Biol 2010; 405:531-47. [PMID: 21073881 DOI: 10.1016/j.jmb.2010.11.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 11/01/2010] [Accepted: 11/02/2010] [Indexed: 11/23/2022]
Abstract
The biphenyl dioxygenase of Burkholderia xenovorans LB400 is a multicomponent Rieske-type oxygenase that catalyzes the dihydroxylation of biphenyl and many polychlorinated biphenyls (PCBs). The structural bases for the substrate specificity of the enzyme's oxygenase component (BphAE(LB400)) are largely unknown. BphAE(p4), a variant previously obtained through directed evolution, transforms several chlorobiphenyls, including 2,6-dichlorobiphenyl, more efficiently than BphAE(LB400), yet differs from the parent oxygenase at only two positions: T335A/F336M. Here, we compare the structures of BphAE(LB400) and BphAE(p4) and examine the biochemical properties of two BphAE(LB400) variants with single substitutions, T335A or F336M. Our data show that residue 336 contacts the biphenyl and influences the regiospecificity of the reaction, but does not enhance the enzyme's reactivity toward 2,6-dichlorobiphenyl. By contrast, residue 335 does not contact biphenyl but contributes significantly to expansion of the enzyme's substrate range. Crystal structures indicate that Thr335 imposes constraints through hydrogen bonds and nonbonded contacts to the segment from Val320 to Gln322. These contacts are lost when Thr is replaced by Ala, relieving intramolecular constraints and allowing for significant movement of this segment during binding of 2,6-dichlorobiphenyl, which increases the space available to accommodate the doubly ortho-chlorinated congener 2,6-dichlorobiphenyl. This study provides important insight about how Rieske-type oxygenases can expand substrate range through mutations that increase the plasticity and/or mobility of protein segments lining the catalytic cavity.
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Rodríguez-Palenzuela P, Matas IM, Murillo J, López-Solanilla E, Bardaji L, Pérez-Martínez I, Rodríguez-Moskera ME, Penyalver R, López MM, Quesada JM, Biehl BS, Perna NT, Glasner JD, Cabot EL, Neeno-Eckwall E, Ramos C. Annotation and overview of thePseudomonas savastanoipv. savastanoi NCPPB 3335 draft genome reveals the virulence gene complement of a tumour-inducing pathogen of woody hosts. Environ Microbiol 2010; 12:1604-20. [DOI: 10.1111/j.1462-2920.2010.02207.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Location of flavone B-ring controls regioselectivity and stereoselectivity of naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4. Appl Microbiol Biotechnol 2009; 86:1451-62. [PMID: 20091026 DOI: 10.1007/s00253-009-2389-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 11/24/2009] [Accepted: 11/27/2009] [Indexed: 10/20/2022]
Abstract
Naphthalene dioxygenase (NDO) from Pseudomonas sp. strain NCIB 9816-4 incorporated dioxygen at the C7 and C8 positions on the A-rings of flavone and isoflavone with different stereoselectivity, resulting in the formation of (7S,8S)-dihydroxy-2-phenyl-7,8-dihydro-4H-chromen-4-one (flavone-cis-(7S,8S)-dihydrodiol) and (7R,8R)-dihydroxy-3-phenyl-7,8-dihydro-4H-chromen-4-one (isoflavone-cis-(7R,8R)-dihydrodiol), respectively. In addition, NDO was shown to incorporate dioxygen at the C5 and C6 positions on the A-ring and the C2' and C3' positions on the B-ring of isoflavone, resulting in the production of (5S,6R)-dihydroxy-3-phenyl-5,6-dihydro-4H-chromen-4-one (isoflavone-cis-(5S,6R)-dihydrodiol) and 3-[(5S,6R)-5,6-dihydroxycyclohexa-1,3-dienyl]-4H-chromen-4-one (isoflavone-cis-(2'R,3'S)-dihydrodiol), respectively. The metabolites were identified by LC/MS, (1)H, and (13)C NMR analyses and TD-SCF calculations combined with CD spectroscopy. In the case of flavone biotransformation, formation of flavone-(7S,8S)-dihydrodiol is likely to be the result of hydrogen bond interactions between the substrate and the active site of the dioxygenase. On the contrary, regioselective dioxygenation of isoflavone was found not to occur, and this may be due to the fact that the same hydrogen bonds that occur in the case of the flavone reaction cannot be established due to steric hindrance caused by the position of the B-ring. It is therefore proposed that the regioselectivity and stereoselectivity of NDO from strain NCIB 9816-4 are controlled by the position of the phenyl ring on flavone molecules.
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Wackett LP. Questioning our perceptions about evolution of biodegradative enzymes. Curr Opin Microbiol 2009; 12:244-51. [DOI: 10.1016/j.mib.2009.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 05/02/2009] [Accepted: 05/05/2009] [Indexed: 10/20/2022]
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Bacterial degradation of aromatic compounds. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2009; 6:278-309. [PMID: 19440284 PMCID: PMC2672333 DOI: 10.3390/ijerph6010278] [Citation(s) in RCA: 459] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 01/06/2009] [Indexed: 11/21/2022]
Abstract
Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.
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Waldau D, Methling K, Mikolasch A, Schauer F. Characterization of new oxidation products of 9H-carbazole and structure related compounds by biphenyl-utilizing bacteria. Appl Microbiol Biotechnol 2009; 81:1023-31. [DOI: 10.1007/s00253-008-1723-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Revised: 09/12/2008] [Accepted: 09/16/2008] [Indexed: 11/27/2022]
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Gai Z, Yu B, Wang X, Deng Z, Xu P. Microbial transformation of benzothiophenes, with carbazole as the auxiliary substrate, by Sphingomonas sp. strain XLDN2-5. Microbiology (Reading) 2008; 154:3804-3812. [DOI: 10.1099/mic.0.2008/023176-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Zhonghui Gai
- Key Laboratory of Microbial Metabolism, Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Bo Yu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
| | - Xiaoyu Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Zixin Deng
- Key Laboratory of Microbial Metabolism, Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Ping Xu
- Key Laboratory of Microbial Metabolism, Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
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Eddine AN, von Kries JP, Podust MV, Warrier T, Kaufmann SHE, Podust LM. X-ray structure of 4,4'-dihydroxybenzophenone mimicking sterol substrate in the active site of sterol 14alpha-demethylase (CYP51). J Biol Chem 2008; 283:15152-9. [PMID: 18367444 PMCID: PMC2397474 DOI: 10.1074/jbc.m801145200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Revised: 03/13/2008] [Indexed: 11/06/2022] Open
Abstract
A universal step in the biosynthesis of membrane sterols and steroid hormones is the oxidative removal of the 14alpha-methyl group from sterol precursors by sterol 14alpha-demethylase (CYP51). This enzyme is a primary target in treatment of fungal infections in organisms ranging from humans to plants, and development of more potent and selective CYP51 inhibitors is an important biological objective. Our continuing interest in structural aspects of substrate and inhibitor recognition in CYP51 led us to determine (to a resolution of 1.95A) the structure of CYP51 from Mycobacterium tuberculosis (CYP51(Mt)) co-crystallized with 4,4'-dihydroxybenzophenone (DHBP), a small organic molecule previously identified among top type I binding hits in a library screened against CYP51(Mt). The newly determined CYP51(Mt)-DHBP structure is the most complete to date and is an improved template for three-dimensional modeling of CYP51 enzymes from fungal and prokaryotic pathogens. The structure demonstrates the induction of conformational fit of the flexible protein regions and the interactions of conserved Phe-89 essential for both fungal drug resistance and catalytic function, which were obscure in the previously characterized CYP51(Mt)-estriol complex. DHBP represents a benzophenone scaffold binding in the CYP51 active site via a type I mechanism, suggesting (i) a possible new class of CYP51 inhibitors targeting flexible regions, (ii) an alternative catalytic function for bacterial CYP51 enzymes, and (iii) a potential for hydroxybenzophenones, widely distributed in the environment, to interfere with sterol biosynthesis. Finally, we show the inhibition of M. tuberculosis growth by DHBP in a mouse macrophage model.
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Affiliation(s)
- Ali Nasser Eddine
- Max-Planck-Institute for Infection Biology, Berlin, 10117, Germany, the Screening Unit, Leibniz-Institute for Molecular Pharmacology (FMP), Berlin, 13125, Germany, and the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158
| | - Jens P. von Kries
- Max-Planck-Institute for Infection Biology, Berlin, 10117, Germany, the Screening Unit, Leibniz-Institute for Molecular Pharmacology (FMP), Berlin, 13125, Germany, and the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158
| | - Mikhail V. Podust
- Max-Planck-Institute for Infection Biology, Berlin, 10117, Germany, the Screening Unit, Leibniz-Institute for Molecular Pharmacology (FMP), Berlin, 13125, Germany, and the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158
| | - Thulasi Warrier
- Max-Planck-Institute for Infection Biology, Berlin, 10117, Germany, the Screening Unit, Leibniz-Institute for Molecular Pharmacology (FMP), Berlin, 13125, Germany, and the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158
| | - Stefan H. E. Kaufmann
- Max-Planck-Institute for Infection Biology, Berlin, 10117, Germany, the Screening Unit, Leibniz-Institute for Molecular Pharmacology (FMP), Berlin, 13125, Germany, and the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158
| | - Larissa M. Podust
- Max-Planck-Institute for Infection Biology, Berlin, 10117, Germany, the Screening Unit, Leibniz-Institute for Molecular Pharmacology (FMP), Berlin, 13125, Germany, and the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158
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Two angular dioxygenases contribute to the metabolic versatility of dibenzofuran-degrading Rhodococcus sp. strain HA01. Appl Environ Microbiol 2008; 74:3812-22. [PMID: 18441103 DOI: 10.1128/aem.00226-08] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhodococcus sp. strain HA01, isolated through its ability to utilize dibenzofuran (DBF) as the sole carbon and energy source, was also capable, albeit with low activity, of transforming dibenzo-p-dioxin (DD). This strain could also transform 3-chlorodibenzofuran (3CDBF), mainly by angular oxygenation at the ether bond-carrying carbon (the angular position) and an adjacent carbon atom, to 4-chlorosalicylate as the end product. Similarly, 2-chlorodibenzofuran (2CDBF) was transformed to 5-chlorosalicylate. However, lateral oxygenation at the 3,4-positions was also observed and yielded the novel product 2-chloro-3,4-dihydro-3,4-dihydroxydibenzofuran. Two gene clusters encoding enzymes for angular oxygenation (dfdA1A2A3A4 and dbfA1A2) were isolated, and expression of both was observed during growth on DBF. Heterologous expression revealed that both oxygenase systems catalyze angular oxygenation of DBF and DD but exhibited complementary substrate specificity with respect to CDBF transformation. While DfdA1A2A3A4 oxygenase, with high similarity to DfdA1A2A3A4 oxygenase from Terrabacter sp. strain YK3, transforms 3CDBF by angular dioxygenation at a rate of 29% +/- 4% that of DBF, 2CDBF was not transformed. In contrast, DbfA1A2 oxygenase, with high similarity to the DbfA1A2 oxygenase from Terrabacter sp. strain DBF63, exhibited complementary activity with angular oxygenase activity against 2CDBF but negligible activity against 3CDBF. Thus, Rhodococcus sp. strain HA01 constitutes the first described example of a bacterial strain where coexpression of two angular dioxygenases was observed. Such complementary activity allows for the efficient transformation of chlorinated DBFs.
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Gai Z, Yu B, Li L, Wang Y, Ma C, Feng J, Deng Z, Xu P. Cometabolic degradation of dibenzofuran and dibenzothiophene by a newly isolated carbazole-degrading Sphingomonas sp. strain. Appl Environ Microbiol 2007; 73:2832-8. [PMID: 17337542 PMCID: PMC1892858 DOI: 10.1128/aem.02704-06] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Accepted: 02/20/2007] [Indexed: 11/20/2022] Open
Abstract
A carbazole-utilizing bacterium was isolated by enrichment from petroleum-contaminated soil. The isolate, designated Sphingomonas sp. strain XLDN2-5, could utilize carbazole (CA) as the sole source of carbon, nitrogen, and energy. Washed cells of strain XLDN2-5 were shown to be capable of degrading dibenzofuran (DBF) and dibenzothiophene (DBT). Examination of metabolites suggested that XLDN2-5 degraded DBF to 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienic acid and subsequently to salicylic acid through the angular dioxygenation pathway. In contrast to DBF, strain XLDN2-5 could transform DBT through the ring cleavage and sulfoxidation pathways. Sphingomonas sp. strain XLDN2-5 could cometabolically degrade DBF and DBT in the growing system using CA as a substrate. After 40 h of incubation, 90% of DBT was transformed, and CA and DBF were completely removed. These results suggested that strain XLDN2-5 might be useful in the bioremediation of environments contaminated by these compounds.
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Affiliation(s)
- Zhonghui Gai
- State Key Laboratory of Microbial Technology, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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Sietmann R, Gesell M, Hammer E, Schauer F. Oxidative ring cleavage of low chlorinated biphenyl derivatives by fungi leads to the formation of chlorinated lactone derivatives. CHEMOSPHERE 2006; 64:672-85. [PMID: 16352329 DOI: 10.1016/j.chemosphere.2005.10.050] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 10/19/2005] [Accepted: 10/27/2005] [Indexed: 05/05/2023]
Abstract
The yeast Trichosporon mucoides and the filamentous fungus Paecilomyces lilacinus as biphenyl oxidizing organisms are able to oxidize chlorinated biphenyl derivatives. Initial oxidation of derivatives chlorinated at C4 position started at the non-halogenated ring and went on up to ring cleavage. The products formed were mono- and dihydroxylated 4-chlorobiphenyls, muconic acid derivatives 2-hydroxy-4-(4-chlorophenyl)-muconic acid and 2-hydroxy-5-(4-chlorophenyl)-muconic acid as well as the corresponding lactones 4-(4-chlorophenyl)-2-pyrone-6-carboxylic acid and 3-(4-chlorophenyl)-2-pyrone-6-carboxylic acid. Altogether T. mucoides formed 12 products and P. lilacinus accumulated five products. Whereas the rate of the first oxidation step at 4-chlorobiphenyl seems to be diminished by the decreased bioavailability of the compound, no considerable differences were observed between the degradation of 4-chloro-4'-hydroxybiphenyl and 4-hydroxybiphenyl. Twofold chlorinated biphenyl derivatives did not serve as substrates for oxidation by either organism with the exception of 2,2'-dichlorobiphenyl, transformed by the yeast Trichosporon mucoides to two monohydroxylated derivatives. The results show, that soil fungi may contribute to the aerobic degradation of low chlorinated biphenyls accumulating from anaerobic dehalogenation of PCB by bacteria.
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Affiliation(s)
- Rabea Sietmann
- Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, D-17487 Greifswald, Germany.
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Jin S, Zhu T, Xu X, Xu Y. Biodegradation of Dibenzofuran by Janibacter terrae Strain XJ-1. Curr Microbiol 2006; 53:30-6. [PMID: 16775784 DOI: 10.1007/s00284-005-0180-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Accepted: 12/02/2005] [Indexed: 10/24/2022]
Abstract
The dibenzofuran (DF)-degrading bacterium, Janibacter terrae strain XJ-1, was isolated from sediment from East Lake in Wuhan, China. This strain grows aerobically on DF as the sole source of carbon and energy; it has a doubling time of 12 hours at 30 degrees C; and it almost completely degraded 100 mg/L(-1) DF in 5 days, producing 2,2',3-trihydroxybiphenyl, salicylic acid, gentisic acid, and other metabolites. The dbdA (DF dioxygenase) gene cluster in the strain is almost identical to that on a large plasmid in Terrabacter sp. YK3. Unlike Janibacter sp. strain YY-1, XJ-1 accumulates gentisic acid rather than catechol as a final product of DF degradation.
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Affiliation(s)
- Shiwei Jin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
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Iwai S, Yamazoe A, Takahashi R, Kurisu F, Yagi O. Degradation of Mono-chlorinated Dibenzo-p-Dioxins by Janibacter sp. Strain YA Isolated from River Sediment. Curr Microbiol 2005; 51:353-8. [PMID: 16235020 DOI: 10.1007/s00284-005-0099-6] [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: 04/21/2005] [Accepted: 06/13/2005] [Indexed: 11/26/2022]
Abstract
Strain YA was newly isolated from an enrichment culture of river sediment and was identified as Janibacter sp. It was able to utilize dibenzofuran as the sole source of carbon and energy. Strain YA degraded > 90% of 1-chloro-dibenzo-p-dioxin (1-CDD) and > 80% of 2-chloro-dibenzo-p-dioxin in 18 hours with each initial concentration at 40 mg/L. A novel metabolite, 2-chloro-2',6-dihydroxydiphenylether, was observed in 1-CDD degradation. From the metabolites detected by gas chromatography-mass spectrometry, strain YA was supposed to have at least two types of oxidation pathways in 1-CDD degradation.
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Affiliation(s)
- Shoko Iwai
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hougo, Bunko-Ku, Tokyo, 113-8656, Japan
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Tao Y, Bentley WE, Wood TK. Regiospecific oxidation of naphthalene and fluorene by toluene monooxygenases and engineered toluene 4-monooxygenases of Pseudomonas mendocina KR1. Biotechnol Bioeng 2005; 90:85-94. [PMID: 15723332 DOI: 10.1002/bit.20414] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The regiospecific oxidation of the polycyclic aromatic hydrocarbons naphthalene and fluorene was examined with Escherichia coli strains expressing wildtype toluene 4-monooxygenase (T4MO) from Pseudomonas mendocina KR1, toluene para-monooxygenase (TpMO) from Ralstonia pickettii PKO1, toluene ortho-monooxygenase (TOM) from Burkholderia cepacia G4, and toluene/ortho-xylene monooxygenase (ToMO) from P. stutzeri OX1. T4MO oxidized toluene (12.1+/-0.8 nmol/min/mg protein at 109 microM), naphthalene (7.7+/-1.5 nmol/min/mg protein at 5 mM), and fluorene (0.68+/-0.04 nmol/min/mg protein at 0.2 mM) faster than the other wildtype enzymes (2-22-fold) and produced a mixture of 1-naphthol (52%) and 2-naphthol (48%) from naphthalene, which was successively transformed to a mixture of 2,3-, 2,7-, 1,7-, and 2,6-dihydroxynaphthalenes (7%, 10%, 20%, and 63%, respectively). TOM and ToMO made 1,7-dihydroxynaphthalene from 1-naphthol, and ToMO made a mixture of 2,3-, 2,6-, 2,7-, and 1,7-dihydroxynaphthalene (26%, 22%, 1%, and 44%, respectively) from 2-naphthol. TOM had no activity on 2-naphthol, and T4MO had no activity on 1-naphthol. To take advantage of the high activity of wildtype T4MO but to increase its regiospecificity on naphthalene, seven engineered enzymes containing mutations in T4MO alpha hydroxylase TmoA were examined; the selectivity for 2-naphthol by T4MO I100A, I100S, and I100G was enhanced to 88-95%, and the selectivity for 1-naphthol was enhanced to 87% and 99% by T4MO I100L and G103S/A107G, respectively, while high oxidation rates were maintained except for G103S/A107G. Therefore, the regiospecificity for naphthalene oxidation was altered to practically pure 1-naphthol or 2-naphthol. All four wildtype monooxygenases were able to oxidize fluorene to different monohydroxylated products; T4MO oxidized fluorene successively to 3-hydroxyfluorene and 3,6-dihydroxyfluorene, which was confirmed by gas chromatography-mass spectrometry and 1H nuclear magnetic resonance analysis. TOM and its variant TomA3 V106A oxidize fluorene to a mixture of 1-, 2-, 3-, and 4-hydroxyfluorene. This is the first report of using enzymes to synthesize 1-, 3-, and 4-hydroxyfluorene, and 3,6-dihydroxyfluorene from fluorene as well as 2-naphthol and 2,6-dihydroxynaphthalene from naphthalene.
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Affiliation(s)
- Ying Tao
- Department of Chemical Engineering, University of Connecticut, Storrs, Connecticut 06269-3222, USA
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Mohammadi M, Sylvestre M. Resolving the Profile of Metabolites Generated during Oxidation of Dibenzofuran and Chlorodibenzofurans by the Biphenyl Catabolic Pathway Enzymes. ACTA ACUST UNITED AC 2005; 12:835-46. [PMID: 16039530 DOI: 10.1016/j.chembiol.2005.05.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Revised: 04/15/2005] [Accepted: 05/16/2005] [Indexed: 10/25/2022]
Abstract
Although the metabolism of dibenzofuran by the biphenyl catabolic enzymes had been inferred in previous reports, the metabolic pattern has never been determined unambiguously. In this work, we describe the evolved biphenyl dioxygenase (BPDO) RR41 that exhibits a higher turnover rate of metabolism toward dibenzofuran and chlorodibenzofurans than the parental Burkholderia xenovorans LB400 BPDO. We used RR41 BPDO to identify unambiguously the metabolites produced from the oxygenation of dibenzofuran by LB400 BPDO, and we evaluated their further metabolism by the biphenyl catabolic pathway enzymes of strain LB400. RR41 BPDO was obtained by saturation mutagenesis of targeted amino acid residues. I335F336N338I341L409 of LB400 BphA were replaced by A335M336Q338V341F409 in RR41 BphA. Data confirm the critical role played by these amino acid residues for substrate specificity and regiospecificity.
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Affiliation(s)
- Mahmood Mohammadi
- Institut National de la Recherche Scientifique, INRS-Institut Armand-Frappier, 245 Boulvard Hymus, Pointe-Claire, Québec, H9R 1G6, Canada
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L'Abbée JB, Barriault D, Sylvestre M. Metabolism of dibenzofuran and dibenzo-p-dioxin by the biphenyl dioxygenase of Burkholderia xenovorans LB400 and Comamonas testosteroni B-356. Appl Microbiol Biotechnol 2005; 67:506-14. [PMID: 15700128 DOI: 10.1007/s00253-004-1791-3] [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: 07/22/2004] [Revised: 09/23/2004] [Accepted: 10/04/2004] [Indexed: 10/25/2022]
Abstract
We examined the metabolism of dibenzofuran (DF) and dibenzo-p-dioxin (DD) by the biphenyl dioxygenase (BPDO) of Comamonas testosteroni B-356 and compared it with that of Burkholderia xenovorans LB400. Data showed that both enzymes oxygenated DF at a low rate, but Escherichia coli cells expressing LB400 BPDO degraded DF at higher rate (30 nmol in 18 h) compared with cells expressing B-356 BPDO (2 nmol in 18 h). Furthermore, both BPDOs produced dihydro-dihydroxy-dibenzofuran as a major metabolite, which resulted from the lateral oxygenation of DF. 2,2',3-Trihydroxybiphenyl (resulting from angular oxygenation of DF) was a minor metabolite produced by both enzymes. Deuterated DF was used to demonstrate the production of 2,2',3-dihydroxybiphenyl through angular oxygenation of DF. When tested for their ability to oxygenate DD, both enzymes produced as sole metabolite, 2,2',3-trihydroxybiphenyl ether at about the same rate, indicating similar catalytic properties toward this substrate. Altogether, although LB400 and B-356 BPDOs oxygenate a different range of chlorobiphenyls, their metabolite profiles toward DF and DD are similar. This suggests that co-planarity influences the regiospecificity of BPDO toward DF and DD to a higher extent than the presence of an ortho substituent on the molecule.
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Affiliation(s)
- José-Bruno L'Abbée
- Institut National de la Recherche Scientifique, INRS-Institut Armand-Frappier, Québec, Canada
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Bordenave S, Fourçans A, Blanchard S, Goñi MS, Caumette P, Duran R. Structure and functional analyses of bacterial communities changes in microbial mats following petroleum exposure. ACTA ACUST UNITED AC 2004. [DOI: 10.1080/00785236.2004.10410227] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Gupta N, Roychoudhury PK, Deb JK. Biotechnology of desulfurization of diesel: prospects and challenges. Appl Microbiol Biotechnol 2004; 66:356-66. [PMID: 15538557 DOI: 10.1007/s00253-004-1755-7] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Revised: 07/30/2004] [Accepted: 08/31/2004] [Indexed: 10/26/2022]
Abstract
To meet stringent emission standards stipulated by regulatory agencies, the oil industry is required to make a huge investment to bring down the sulfur content in diesel to the desired level, using conventional hydrodesulfurization (HDS) technology, by which sulfur is catalytically converted to hydrogen sulfide in the presence of hydrogen. These reactions proceed rapidly only at high temperature and pressure and therefore the capital cost as well as the operating cost associated with HDS very high. Biological desulfurization has the potential of being developed as a viable technology downstream of classical HDS. Various attempts have been made to develop biotechnological processes based on microbiological desulfurization employing aerobic and anaerobic bacteria. However, there are several bottlenecks limiting commercialization of the process. This review discusses various aspects of microbial desulfurization and the progress made towards its commercialization.
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Affiliation(s)
- Nidhi Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
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