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Pan P, Gu Y, Li T, Zhou NY, Xu Y. Deciphering the triclosan degradation mechanism in Sphingomonas sp. strain YL-JM2C: Implications for wastewater treatment and marine resources. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135511. [PMID: 39173390 DOI: 10.1016/j.jhazmat.2024.135511] [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: 05/10/2024] [Revised: 07/16/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024]
Abstract
Triclosan (TCS), an antimicrobial agent extensively incorporated into pharmaceuticals and personal care products, poses significant environmental risks because of its persistence and ecotoxicity. So far, a few microorganisms were suggested to degrade TCS, but the microbial degradation mechanism remains elusive. Here, a two-component angular dioxygenase (TcsAaAb) responsible for the initial TCS degradation was characterized in Sphingomonas sp. strain YL-JM2C. Whole-cell biotransformation and crude enzyme assays demonstrated that TcsAaAb catalyzed the conversion of TCS to 4-chlorocatechol and 3,5-dichlorocatechol rather than the commonly suggested product 2,4-dichlorophenol. Then two intermediates were catabolized by tcsCDEF cluster via an ortho-cleavage pathway. Critical residues (N262, F279, and F391) for substrate binding were identified via molecular docking and mutagenesis. Further, TcsAaAb showed activity toward methyl triclosan and nitrofen, suggesting its versatile potential for bioremediation. In addition, TCS-degrading genes were also present in diverse bacterial genomes in wastewater, ocean and soil, and a relatively high gene abundance was observed in marine metagenomes, revealing the transformation fate of TCS in environments and the microbial potential in pollutant removal. These findings extend the understanding of the microbe-mediated TCS degradation and contribute to the mining of TCS-degrading strains and enzymes, as well as their application in the bioremediation of contaminated environments.
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Affiliation(s)
- Piaopiao Pan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Yichao Gu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Tao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Ying Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China.
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2
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Prešern U, Goličnik M. Enzyme Databases in the Era of Omics and Artificial Intelligence. Int J Mol Sci 2023; 24:16918. [PMID: 38069254 PMCID: PMC10707154 DOI: 10.3390/ijms242316918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
Enzyme research is important for the development of various scientific fields such as medicine and biotechnology. Enzyme databases facilitate this research by providing a wide range of information relevant to research planning and data analysis. Over the years, various databases that cover different aspects of enzyme biology (e.g., kinetic parameters, enzyme occurrence, and reaction mechanisms) have been developed. Most of the databases are curated manually, which improves reliability of the information; however, such curation cannot keep pace with the exponential growth in published data. Lack of data standardization is another obstacle for data extraction and analysis. Improving machine readability of databases is especially important in the light of recent advances in deep learning algorithms that require big training datasets. This review provides information regarding the current state of enzyme databases, especially in relation to the ever-increasing amount of generated research data and recent advancements in artificial intelligence algorithms. Furthermore, it describes several enzyme databases, providing the reader with necessary information for their use.
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Affiliation(s)
| | - Marko Goličnik
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia;
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Li S, Shen W, Lian S, Wu Y, Qu Y, Deng Y. DARHD: A sequence database for aromatic ring-hydroxylating dioxygenase analysis and primer evaluation. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129230. [PMID: 35739750 DOI: 10.1016/j.jhazmat.2022.129230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Biodegradation of aromatic compounds is ubiquitous in the environment and important for controlling organic pollutants. Aromatic ring-hydroxylating dioxygenases (ARHDs) are responsible for the first and rate-limiting step of aerobic biodegradation of aromatic compounds. The ARHD α subunit is a good biomarker for studying functional microorganisms in the environment, however their diversity and corresponding primer coverage are unclear, both of which require a comprehensive sequence database for the ARHD α subunit. Here amino acid sequences of the ARHD α subunit were collected, and a total of 103 sequences were selected as seed sequences that were distributed in 72 bacterial genera with 34 gene names. Based on both homolog search and keyword confirmation against the GenBank, a sequence database of ARHD (DARHD) has been established and 6367 highly credible sequences were retrieved. DARHD contained 407 bacterial genera capable of degrading 38 aromatic substrates, and intricate relationships among the gene name, aromatic substrate and microbial taxa were observed. Thereafter, a total of 136 pairs of primers were collected and assessed. Results showed coverages of most published primers were low. Our research provides new insights for understanding the diversity of ARHD α subunit, and gives guidance on the design and application of primers in the future.
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Affiliation(s)
- Shuzhen Li
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Wenli Shen
- Institute for Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Shengyang Lian
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yueni Wu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute for Marine Science and Technology, Shandong University, Qingdao 266237, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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4
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Bygd MD, Aukema KG, Richman JE, Wackett LP. Unexpected Mechanism of Biodegradation and Defluorination of 2,2-Difluoro-1,3-Benzodioxole by Pseudomonas putida F1. mBio 2021; 12:e0300121. [PMID: 34781746 PMCID: PMC8593668 DOI: 10.1128/mbio.03001-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Perfluorinated carbon atoms in a diether linkage are common in commercial anesthetics, drugs, fungicides, and insecticides. An important chemical group comprising perfluorodiethers is the 2,2-fluoro-1,3-benzodioxole (DFBD) moiety. The fluorine atoms stabilize the molecule by mitigating against metabolism by humans and microbes, as used in drugs and pesticides, respectively. Pseudomonas putida F1 catalyzed defluorination of DFBD at an initial rate of 2,100 nmol/h per mg cellular protein. This is orders of magnitude higher than previously reported microbial defluorination rates with multiply fluorinated carbon atoms. Defluorination rates declined after several hours, and the medium darkened. Significant defluorination activity was observed with cells grown on toluene but not l-arginine. Defluorination required only toluene dioxygenase. Pseudomonas and recombinant Escherichia coli cells expressing toluene dioxygenase oxidized DFBD to DFBD-4,5-dihydrodiol. The dihydrodiol could be oxidized to 4,5-dihydroxy-DFBD via the dihydrodiol dehydrogenase from P. putida F1. The dihydrodiol dehydrated with acid to yield a mixture of 4-hydroxy-DFBD and 5-hydroxy-DFBD. All those metabolites retained the difluoromethylene group; no fluoride or dark color was observed. The major route of DFBD-4,5-dihydrodiol decomposition produced fluoride and 1,2,3-trihydroxybenzene, or pyrogallol, and that was shown to be the source of the dark colors in the medium. A mechanism for DFBD-4,5-dihydrodiol transformation to two fluoride ions and pyrogallol is proposed. The Pseudomonas genome database and other databases revealed hundreds of bacteria with enzymes sharing high amino acid sequence identity to toluene dioxygenase from P. putida F1, suggesting the mechanism revealed here may apply to the defluorination of DFBD-containing compounds in the environment. IMPORTANCE There are more than 9,000 polyfluorinated compounds developed for commercial use, some negatively impacting human health, and they are generally considered to be resistant to biodegradation. Only a limited number of studies have identified microbes with enzymes sufficiently reactive to defluorinate difluoromethylene carbon groups. The present study examined one important group of commercial fluorinated chemicals and showed its rapid defluorination by a bacterium and its key enzyme, a Rieske dioxygenase. Rieske dioxygenases are common in environmental bacteria, and those closely resembling toluene dioxygenase from Pseudomonas putida F1 are candidates for biodegradative defluorination of the common 2,2-fluoro-1,3-benzodioxole (DFBD) moiety.
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Affiliation(s)
- Madison D. Bygd
- Microbial Engineering, University of Minnesota, St. Paul, Minnesota, USA
| | - Kelly G. Aukema
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, USA
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Jack E. Richman
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, USA
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Lawrence P. Wackett
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, USA
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
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A Novel Gene Cluster Is Involved in the Degradation of Lignin-Derived Monoaromatics in Thermus oshimai JL-2. Appl Environ Microbiol 2021; 87:AEM.01589-20. [PMID: 33741620 DOI: 10.1128/aem.01589-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 03/09/2021] [Indexed: 11/20/2022] Open
Abstract
A novel gene cluster involved in the degradation of lignin-derived monoaromatics such as p-hydroxybenzoate, vanillate, and ferulate has been identified in the thermophilic nitrate reducer Thermus oshimai JL-2. Based on conserved domain analyses and metabolic pathway mapping, the cluster was classified into upper- and peripheral-pathway operons. The upper-pathway genes, responsible for the degradation of p-hydroxybenzoate and vanillate, are located on a 0.27-Mb plasmid, whereas the peripheral-pathway genes, responsible for the transformation of ferulate, are spread throughout the plasmid and the chromosome. In addition, a lower-pathway operon was also identified in the plasmid that corresponds to the meta-cleavage pathway of catechol. Spectrophotometric and gene induction data suggest that the upper and lower operons are induced by p-hydroxybenzoate, which the strain can degrade completely within 4 days of incubation, whereas the peripheral genes are expressed constitutively. The upper degradation pathway follows a less common route, proceeding via the decarboxylation of protocatechuate to form catechol, and involves a novel thermostable γ-carboxymuconolactone decarboxylase homolog, identified as protocatechuate decarboxylase based on gene deletion experiments. This gene cluster is conserved in only a few members of the Thermales and shows traces of vertical expansion of catabolic pathways in these organisms toward lignoaromatics.IMPORTANCE High-temperature steam treatment of lignocellulosic biomass during the extraction of cellulose and hemicellulose fractions leads to the release of a wide array of lignin-derived aromatics into the natural ecosystem, some of which can have detrimental effects on the environment. Not only will identifying organisms capable of using such aromatics aid in environmental cleanup, but thermostable enzymes, if characterized, can also be used for efficient lignin valorization. However, no thermophilic lignin degraders have been reported thus far. The present study reports T. oshimai JL-2 as a thermophilic bacterium with the potential to use lignin-derived aromatics. The identification of a novel thermostable protocatechuate decarboxylase gene in the strain further adds to its significance, as such an enzyme can be efficiently used in the biosynthesis of cis,cis-muconate, an important intermediate in the commercial production of plastics.
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Macchi M, Festa S, Nieto E, Irazoqui JM, Vega-Vela NE, Junca H, Valacco MP, Amadio AF, Morelli IS, Coppotelli BM. Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 29:e00588. [PMID: 33489789 PMCID: PMC7809168 DOI: 10.1016/j.btre.2021.e00588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/22/2020] [Accepted: 12/31/2020] [Indexed: 01/15/2023]
Abstract
Two synthetic bacterial consortia (SC) composed of bacterial strains Sphingobium sp. (AM), Klebsiella aerogenes (B), Pseudomonas sp. (Bc-h and T), Burkholderia sp. (Bk) and Inquilinus limosus (Inq) isolated from a natural phenanthrene (PHN)-degrading consortium (CON) were developed and evaluated as an alternative approach to PHN biodegradation in bioremediation processes. A metabolic network showing the potential role of strains was reconstructed by in silico study of the six genomes and classification of dioxygenase enzymes using RHObase and AromaDeg databases. Network analysis suggested that AM and Bk were responsible for PHN initial attack, while Inq, B, T and Bc-h would degrade PHN metabolites. The predicted roles were further confirmed by physiological, RT-qPCR and metaproteomic assays. SC-1 with AM as the sole PHN degrader was the most efficient. The ecological roles inferred in this study can be applied to optimize the design of bacterial consortia and tackle the biodegradation of complex environmental pollutants.
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Affiliation(s)
- Marianela Macchi
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata, Argentina
| | - Sabrina Festa
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata, Argentina
| | - Esteban Nieto
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata, Argentina
| | - José M. Irazoqui
- E.E.A. Rafaela, Instituto Nacional de Tecnología Agropecuaria (INTA), CCT Santa Fe, CONICET, Rafaela, Argentina
| | - Nelson E. Vega-Vela
- Pontificia Universidad Javeriana, Bogotá, Colombia
- Universidad de Bogotá Jorge Tadeo Lozano, Bogotá, Colombia
| | - Howard Junca
- Microbiomas Foundation, Div. Ecogenomics & Holobionts, RG Microbial Ecology: Metabolism, Genomics & Evolution, Chía, Colombia
| | | | - Ariel F. Amadio
- E.E.A. Rafaela, Instituto Nacional de Tecnología Agropecuaria (INTA), CCT Santa Fe, CONICET, Rafaela, Argentina
| | - Irma S. Morelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata, Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Argentina
| | - Bibiana M. Coppotelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata, Argentina
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Jaiswal S, Shukla P. Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology. Front Microbiol 2020; 11:808. [PMID: 32508759 PMCID: PMC7249858 DOI: 10.3389/fmicb.2020.00808] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.
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Enzymatic Bioremediation: Current Status, Challenges of Obtaining Process, and Applications. MICROORGANISMS FOR SUSTAINABILITY 2019. [DOI: 10.1007/978-981-13-7462-3_4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Dangi AK, Sharma B, Hill RT, Shukla P. Bioremediation through microbes: systems biology and metabolic engineering approach. Crit Rev Biotechnol 2018; 39:79-98. [DOI: 10.1080/07388551.2018.1500997] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Arun Kumar Dangi
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Babita Sharma
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Russell T. Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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Sharma B, Dangi AK, Shukla P. Contemporary enzyme based technologies for bioremediation: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 210:10-22. [PMID: 29329004 DOI: 10.1016/j.jenvman.2017.12.075] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/10/2017] [Accepted: 12/29/2017] [Indexed: 05/26/2023]
Abstract
The persistent disposal of xenobiotic compounds like insecticides, pesticides, fertilizers, plastics and other hydrocarbon containing substances is the major source of environmental pollution which needs to be eliminated. Many contemporary remediation methods such as physical, chemical and biological are currently being used, but they are not sufficient to clean the environment. The enzyme based bioremediation is an easy, quick, eco-friendly and socially acceptable approach used for the bioremediation of these recalcitrant xenobiotic compounds from the natural environment. Several microbial enzymes with bioremediation capability have been isolated and characterized from different natural sources, but less production of such enzymes is a limiting their further exploitation. The genetic engineering approach has the potential to get large amount of recombinant enzymes. Along with this, enzyme immobilization techniques can boost the half-life, stability and activity of enzymes at a significant level. Recently, nanozymes may offer the potential bioremediation ability towards a broad range of pollutants. In the present review, we have described a brief overview of the microbial enzymes, different enzymes techniques (genetic engineering and immobilization of enzymes) and nanozymes involved in bioremediation of toxic, carcinogenic and hazardous environmental pollutants.
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Affiliation(s)
- Babita Sharma
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Arun Kumar Dangi
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak-124001, Haryana, India.
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Wanapaisan P, Laothamteep N, Vejarano F, Chakraborty J, Shintani M, Muangchinda C, Morita T, Suzuki-Minakuchi C, Inoue K, Nojiri H, Pinyakong O. Synergistic degradation of pyrene by five culturable bacteria in a mangrove sediment-derived bacterial consortium. JOURNAL OF HAZARDOUS MATERIALS 2018; 342:561-570. [PMID: 28886568 DOI: 10.1016/j.jhazmat.2017.08.062] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 08/17/2017] [Accepted: 08/23/2017] [Indexed: 05/22/2023]
Abstract
A pyrene-degrading microbial consortium was obtained after enrichment with mangrove sediment collected from Thailand. Five cultivable bacteria (Mycobacterium spp. PO1 and PO2, Novosphingobium pentaromativorans PY1, Ochrobactrum sp. PW1, and Bacillus sp. FW1) were successfully isolated from the consortium. Draft genomes of them showed that two different morphotypes of Mycobacterium (PO1 and PO2), possessed a complete gene set for pyrene degradation. PY1 contained genes for phthalate assimilation via protocatechuate, a central intermediate, by meta-cleavage pathway, and PW1 possessed genes for protocatechuate degradation via ortho-cleavage pathway. The occurrence of biosurfactant-producing genes in FW1 suggests the involvement in enhancing the pyrene bioavailability. Biotransformation experiments revealed that Mycobacterium completely degraded 100mgL-1 pyrene within six days, whereas no significant degradation was observed with the others. Notably, PY1 and PW1 exhibited higher activity for protocatechuate degradation than the others. The artificially reconstructed consortia containing Mycobacterium with the other three strains (PY1, PW1 and FW1) showed three-fold higher degradation rate for pyrene than the individual Mycobacterium. The enhanced pyrene biodegradation achieved in the consortium was due to the cooperative interaction of bacterial mixture. Our findings showing that synergistic degradation of pyrene in the consortium will facilitate the application of the defined bacterial consortium in bioremediation.
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Affiliation(s)
- Pagakrong Wanapaisan
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Natthariga Laothamteep
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Felipe Vejarano
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Joydeep Chakraborty
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masaki Shintani
- Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Chanokporn Muangchinda
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Tomomi Morita
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; Department of Bioscience and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama, Saitama 337-8570, Japan
| | - Chiho Suzuki-Minakuchi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kengo Inoue
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, Miyazaki 889-2192, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Onruthai Pinyakong
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand; Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand; Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand.
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Chakraborty J, Suzuki-Minakuchi C, Okada K, Nojiri H. Thermophilic bacteria are potential sources of novel Rieske non-heme iron oxygenases. AMB Express 2017; 7:17. [PMID: 28050858 PMCID: PMC5209329 DOI: 10.1186/s13568-016-0318-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/23/2016] [Indexed: 11/10/2022] Open
Abstract
Rieske non-heme iron oxygenases, which have a Rieske-type [2Fe-2S] cluster and a non-heme catalytic iron center, are an important family of oxidoreductases involved mainly in regio- and stereoselective transformation of a wide array of aromatic hydrocarbons. Though present in all domains of life, the most widely studied Rieske non-heme iron oxygenases are found in mesophilic bacteria. The present study explores the potential for isolating novel Rieske non-heme iron oxygenases from thermophilic sources. Browsing the entire bacterial genome database led to the identification of 45 homologs from thermophilic bacteria distributed mainly among Chloroflexi, Deinococcus-Thermus and Firmicutes. Thermostability, measured according to the aliphatic index, showed higher values for certain homologs compared with their mesophilic relatives. Prediction of substrate preferences indicated that a wide array of aromatic hydrocarbons could be transformed by most of the identified oxygenase homologs. Further identification of putative genes encoding components of a functional oxygenase system opens up the possibility of reconstituting functional thermophilic Rieske non-heme iron oxygenase systems with novel properties.
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Festa S, Coppotelli BM, Madueño L, Loviso CL, Macchi M, Neme Tauil RM, Valacco MP, Morelli IS. Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches. PLoS One 2017; 12:e0184505. [PMID: 28886166 PMCID: PMC5591006 DOI: 10.1371/journal.pone.0184505] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 08/27/2017] [Indexed: 11/18/2022] Open
Abstract
The present study describes the behavior of a natural phenanthrene-degrading consortium (CON), a synthetic consortium (constructed with isolated strains from CON) and an isolated strain form CON (Sphingobium sp. AM) in phenanthrene cultures to understand the interactions among the microorganisms present in the natural consortium during phenanthrene degradation as a sole carbon and energy source in liquid cultures. In the contaminant degradation assay, the defined consortium not only achieved a major phenanthrene degradation percentage (> 95%) but also showed a more efficient elimination of the intermediate metabolite. The opposite behavior occurred in the CON culture where the lowest phenanthrene degradation and the highest HNA accumulation were observed, which suggests the presence of positive and also negative interaction in CON. To consider the uncultured bacteria present in CON, a metagenomic library was constructed with total CON DNA. One of the resulting scaffolds (S1P3) was affiliated with the Betaproteobacteria class and resulted in a significant similarity with a genome fragment from Burkholderia sp. HB1 chromosome 1. A complete gene cluster, which is related to one of the lower pathways (meta-cleavage of catechol) involved in PAH degradation (ORF 31-43), mobile genetic elements and associated proteins, was found. These results suggest the presence of at least one other microorganism in CON besides Sphingobium sp. AM, which is capable of degrading PAH through the meta-cleavage pathway. Burkholderiales order was further found, along with Sphingomonadales order, by a metaproteomic approach, which indicated that both orders were metabolically active in CON. Our results show the presence of negative interactions between bacterial populations found in a natural consortium selected by enrichment techniques; moreover, the synthetic syntrophic processing chain with only one microorganism with the capability of degrading phenanthrene was more efficient in contaminant and intermediate metabolite degradation than a generalist strain (Sphingobium sp. AM).
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Affiliation(s)
- Sabrina Festa
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), La Plata, Argentina
| | - Bibiana Marina Coppotelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), La Plata, Argentina
| | - Laura Madueño
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), La Plata, Argentina
| | | | - Marianela Macchi
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), La Plata, Argentina
| | - Ricardo Martin Neme Tauil
- Centro de Estudios Químicos y Biológicos por Espectrometría de Masa- CEQUIBIEM, Facultad de Ciencias Exactas y Naturales, UBA, IQUIBICEN, CONICET
| | - María Pía Valacco
- Centro de Estudios Químicos y Biológicos por Espectrometría de Masa- CEQUIBIEM, Facultad de Ciencias Exactas y Naturales, UBA, IQUIBICEN, CONICET
| | - Irma Susana Morelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), La Plata, Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Argentina
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14
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Molecular Mechanism and Genetic Determinants of Buprofezin Degradation. Appl Environ Microbiol 2017; 83:AEM.00868-17. [PMID: 28710269 DOI: 10.1128/aem.00868-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 07/07/2017] [Indexed: 11/20/2022] Open
Abstract
Buprofezin is a widely used insect growth regulator whose residue has been frequently detected in the environment, posing a threat to aquatic organisms and nontarget insects. Microorganisms play an important role in the degradation of buprofezin in the natural environment. However, the relevant catabolic pathway has not been fully characterized, and the molecular mechanism of catabolism is still completely unknown. Rhodococcus qingshengii YL-1 can utilize buprofezin as a sole source of carbon and energy for growth. In this study, the upstream catabolic pathway in strain YL-1 was identified using tandem mass spectrometry. Buprofezin is composed of a benzene ring and a heterocyclic ring. The degradation is initiated by the dihydroxylation of the benzene ring and continues via dehydrogenation, aromatic ring cleavage, breaking of an amide bond, and the release of the heterocyclic ring 2-tert-butylimino-3-isopropyl-1,3,5-thiadiazinan-4-one (2-BI). A buprofezin degradation-deficient mutant strain YL-0 was isolated. A comparative genomic analysis combined with gene deletion and complementation experiments revealed that the gene cluster bfzBA3A4A1A2C is responsible for the upstream catabolic pathway of buprofezin. The bfzA3A4A1A2 cluster encodes a novel Rieske nonheme iron oxygenase (RHO) system that is responsible for the dihydroxylation of buprofezin at the benzene ring; bfzB is involved in dehydrogenation, and bfzC is in charge of benzene ring cleavage. Furthermore, the products of bfzBA3A4A1A2C can also catalyze dihydroxylation, dehydrogenation, and aromatic ring cleavage of biphenyl, flavanone, flavone, and bifenthrin. In addition, a transcriptional study revealed that bfzBA3A4A1A2C is organized in one transcriptional unit that is constitutively expressed in strain YL-1.IMPORTANCE There is an increasing concern about the residue and environmental fate of buprofezin. Microbial metabolism is an important mechanism responsible for the buprofezin degradation in the natural environment. However, the molecular mechanism and genetic determinants of microbial degradation of buprofezin have not been well identified. This work revealed that gene cluster bfzBA3A4A1A2C is responsible for the upstream catabolic pathway of buprofezin in Rhodococcus qingshengii YL-1. The products of bfzBA3A4A1A2C could also degrade bifenthrin, a widely used pyrethroid insecticide. These findings enhance our understanding of the microbial degradation mechanism of buprofezin and benefit the application of strain YL-1 and bfzBA3A4A1A2C in the bioremediation of buprofezin contamination.
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15
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Martirani-Von Abercron SM, Marín P, Solsona-Ferraz M, Castañeda-Cataña MA, Marqués S. Naphthalene biodegradation under oxygen-limiting conditions: community dynamics and the relevance of biofilm-forming capacity. Microb Biotechnol 2017; 10:1781-1796. [PMID: 28840968 PMCID: PMC5658598 DOI: 10.1111/1751-7915.12842] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 11/27/2022] Open
Abstract
Toxic polycyclic aromatic hydrocarbons (PAHs) are frequently released into the environment from anthropogenic sources. PAH remediation strategies focus on biological processes mediated by bacteria. The availability of oxygen in polluted environments is often limited or absent, and only bacteria able to thrive in these conditions can be considered for bioremediation strategies. To identify bacterial strains able to degrade PAHs under oxygen‐limiting conditions, we set up enrichment cultures from samples of an oil‐polluted aquifer, using either anoxic or microaerophilic condition and with PAHs as the sole carbon source. Despite the presence of a significant community of nitrate‐reducing bacteria, the initial community, which was dominated by Betaproteobacteria, was incapable of PAH degradation under strict anoxic conditions, although a clear shift in the structure of the community towards an increase in the Alphaproteobacteria (Sphingomonadaceae), Actinobacteria and an uncultured group of Acidobacteria was observed in the enrichments. In contrast, growth under microaerophilic conditions with naphthalene as the carbon source evidenced the development of a biofilm structure around the naphthalene crystal. The enrichment process selected two co‐dominant groups which finally reached 97% of the bacterial communities: Variovorax spp. (54%, Betaproteobacteria) and Starkeya spp. (43%, Xanthobacteraceae). The two dominant populations were able to grow with naphthalene, although only Starkeya was able to reproduce the biofilm structure around the naphthalene crystal. The pathway for naphthalene degradation was identified, which included as essential steps dioxygenases with high affinity for oxygen, showing 99% identity with Xanthobacter polyaromaticivorans dbd cluster for PAH degradation. Our results suggest that the biofilm formation capacity of Starkeya provided a structure to allocate its cells at an appropriate distance from the toxic carbon source.
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Affiliation(s)
| | - Patricia Marín
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Marta Solsona-Ferraz
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Mayra-Alejandra Castañeda-Cataña
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Silvia Marqués
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
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16
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Jana T, Ghosh A, Das Mandal S, Banerjee R, Saha S. PPIMpred: a web server for high-throughput screening of small molecules targeting protein-protein interaction. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160501. [PMID: 28484602 PMCID: PMC5414239 DOI: 10.1098/rsos.160501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 03/20/2017] [Indexed: 05/31/2023]
Abstract
PPIMpred is a web server that allows high-throughput screening of small molecules for targeting specific protein-protein interactions, namely Mdm2/P53, Bcl2/Bak and c-Myc/Max. Three different kernels of support vector machine (SVM), namely, linear, polynomial and radial basis function (RBF), and two other machine learning techniques including Naive Bayes and Random Forest were used to train the models. A fivefold cross-validation technique was used to measure the performance of these classifiers. The RBF kernel of SVM outperformed and/or was comparable with all other methods with accuracy values of 83%, 79% and 90% for Mdm2/P53, Bcl2/Bak and c-Myc/Max, respectively. About 80% of the predicted SVM scores of training/testing datasets from Mdm2/P53 and Bcl2/Bak have significant IC50 values and docking scores. The proposed models achieved an accuracy of 66-90% with blind sets. The three mentioned (Mdm2/P53, Bcl2/Bak and c-Myc/Max) proposed models were screened in a large dataset of 265 242 small chemicals from National Cancer Institute open database. To further realize the robustness of this approach, hits with high and random SVM scores were used for molecular docking in AutoDock Vina wherein the molecules with high and random predicted SVM scores yielded moderately significant docking scores (p-values < 0.1). In addition to the above-mentioned classification scheme, this web server also allows users to get the structural and chemical similarities with known chemical modulators or drug-like molecules based on Tanimoto coefficient similarity search algorithm. PPIMpred is freely available at http://bicresources.jcbose.ac.in/ssaha4/PPIMpred/.
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Affiliation(s)
- Tanmoy Jana
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Road, Scheme-VII (M), Kolkata, West Bengal, India
| | - Abhirupa Ghosh
- Department of Bioinformatics, Bose Institute, P 1/12, C.I.T. Road, Scheme-VII (M), Kolkata, West Bengal, India
| | - Sukhen Das Mandal
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Road, Scheme-VII (M), Kolkata, West Bengal, India
| | - Raja Banerjee
- Department of Bioinformatics, Bose Institute, P 1/12, C.I.T. Road, Scheme-VII (M), Kolkata, West Bengal, India
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal, India
| | - Sudipto Saha
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Road, Scheme-VII (M), Kolkata, West Bengal, India
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17
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Gong T, Liu R, Che Y, Xu X, Zhao F, Yu H, Song C, Liu Y, Yang C. Engineering Pseudomonas putida KT2440 for simultaneous degradation of carbofuran and chlorpyrifos. Microb Biotechnol 2016; 9:792-800. [PMID: 27418102 PMCID: PMC5072195 DOI: 10.1111/1751-7915.12381] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/21/2016] [Accepted: 06/21/2016] [Indexed: 11/30/2022] Open
Abstract
Currently, chlorpyrifos (CP) and carbofuran are often applied together to control major agricultural pests in many developing countries, in most cases, they are simultaneously detected in agricultural soils. Some cost‐effective techniques are required for the remediation of combined pollution caused by multiple pesticides. In this work, we aim at constructing a detectable recombinant microorganism with the capacity to simultaneously degrade CP and carbofuran. To achieve this purpose, CP/carbofuran hydrolase genes and gfp were integrated into the chromosome of a biosafety strain Pseudomonas putida KT2440 using a chromosomal scarless modification strategy with upp as a counter‐selectable marker. The toxicity of the hydrolysis products was significantly lower compared with the parent compounds. The recombinant strain could utilize CP or carbofuran as the sole source of carbon for growth. The inoculation of the recombinant strain to soils treated with carbofuran and CP resulted in a higher degradation rate than in noninoculated soils. Introduced green fluorescent protein can be employed as a biomarker to track the recombinant strain during bioremediation. Therefore, the recombinant strain has potential to be applied for in situ bioremediation of soil co‐contaminated with carbofuran and CP.
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Affiliation(s)
- Ting Gong
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Ruihua Liu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - You Che
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Xiaoqing Xu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Fengjie Zhao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Huilei Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Cunjiang Song
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
| | - Yanping Liu
- Department of Gynaecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, 300052, China.
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
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18
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Loviso CL, Lozada M, Guibert LM, Musumeci MA, Sarango Cardenas S, Kuin RV, Marcos MS, Dionisi HM. Metagenomics reveals the high polycyclic aromatic hydrocarbon-degradation potential of abundant uncultured bacteria from chronically polluted subantarctic and temperate coastal marine environments. J Appl Microbiol 2015; 119:411-24. [PMID: 25968322 DOI: 10.1111/jam.12843] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/22/2015] [Accepted: 04/30/2015] [Indexed: 01/18/2023]
Abstract
AIMS To investigate the potential to degrade polycyclic aromatic hydrocarbons (PAHs) of yet-to-be-cultured bacterial populations from chronically polluted intertidal sediments. METHODS AND RESULTS A gene variant encoding the alpha subunit of the catalytic component of an aromatic-ring-hydroxylating oxygenase (RHO) was abundant in intertidal sediments from chronically polluted subantarctic and temperate coastal environments, and its abundance increased after PAH amendment. Conversely, this marker gene was not detected in sediments from a nonimpacted site, even after a short-term PAH exposure. A metagenomic fragment carrying this gene variant was identified in a fosmid library of subantarctic sediments. This fragment contained five pairs of alpha and beta subunit genes and a lone alpha subunit gene of oxygenases, classified as belonging to three different RHO functional classes. In silico structural analysis suggested that two of these oxygenases contain large substrate-binding pockets, capable of accepting high molecular weight PAHs. CONCLUSIONS The identified uncultured micro-organism presents the potential to degrade aromatic hydrocarbons with various chemical structures, and could represent an important member of the PAH-degrading community in these polluted coastal environments. SIGNIFICANCE AND IMPACT OF THE STUDY This work provides valuable information for the design of environmental molecular diagnostic tools and for the biotechnological application of RHO enzymes.
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Affiliation(s)
- C L Loviso
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - M Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - L M Guibert
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - M A Musumeci
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - S Sarango Cardenas
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - R V Kuin
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - M S Marcos
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - H M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
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