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Wang B, Gao J, Xu J, Fu X, Han H, Li Z, Wang L, Zhang F, Tian Y, Peng R, Yao Q. Optimization and reconstruction of two new complete degradation pathways for 3-chlorocatechol and 4-chlorocatechol in Escherichia coli. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126428. [PMID: 34171665 DOI: 10.1016/j.jhazmat.2021.126428] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/11/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Chlorinated aromatic compounds are a serious environmental concern because of their widespread occurrence throughout the environment. Although several microorganisms have evolved to gain the ability to degrade chlorinated aromatic compounds and use them as carbon sources, they still cannot meet the diverse needs of pollution remediation. In this study, the degradation pathways for 3-chlorocatechol (3CC) and 4-chlorocatechol (4CC) were successfully reconstructed by the optimization, synthesis, and assembly of functional genes from different strains. The addition of a 13C-labeled substrate and functional analysis of different metabolic modules confirmed that the genetically engineered strains can metabolize chlorocatechol similar to naturally degrading strains. The strain containing either of these artificial pathways can degrade catechol, 3CC, and 4CC completely, although differences in the degradation efficiency may be noted. Proteomic analysis and scanning electron microscopy observation showed that 3CC and 4CC have toxic effects on Escherichia coli, but the engineered bacteria can significantly eliminate these inhibitory effects. As core metabolic pathways for the degradation of chloroaromatics, the two chlorocatechol degradation pathways constructed in this study can be used to construct pollution remediation-engineered bacteria, and the related technologies may be applied to construct complete degradation pathways for complex organic hazardous materials.
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Affiliation(s)
- Bo Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jianjie Gao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jing Xu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Xiaoyan Fu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Hongjuan Han
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Zhenjun Li
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Lijuan Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Fujian Zhang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Yongsheng Tian
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
| | - Rihe Peng
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
| | - Quanhong Yao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
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Pérez-Pantoja D, Kim J, Silva-Rocha R, de Lorenzo V. The differential response of thePbenpromoter ofPseudomonas putida mt-2 to BenR and XylS prevents metabolic conflicts inm-xylene biodegradation. Environ Microbiol 2014; 17:64-75. [DOI: 10.1111/1462-2920.12443] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 02/13/2014] [Accepted: 02/21/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Danilo Pérez-Pantoja
- Systems and Synthetic Biology Program; Centro Nacional de Biotecnologia; Madrid Spain
| | - Juhyun Kim
- Systems and Synthetic Biology Program; Centro Nacional de Biotecnologia; Madrid Spain
| | - Rafael Silva-Rocha
- Systems and Synthetic Biology Program; Centro Nacional de Biotecnologia; Madrid Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program; Centro Nacional de Biotecnologia; Madrid Spain
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Nielsen TK, Xu Z, Gözdereliler E, Aamand J, Hansen LH, Sørensen SR. Novel insight into the genetic context of the cadAB genes from a 4-chloro-2-methylphenoxyacetic acid-degrading Sphingomonas. PLoS One 2013; 8:e83346. [PMID: 24391756 PMCID: PMC3877037 DOI: 10.1371/journal.pone.0083346] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 11/01/2013] [Indexed: 11/19/2022] Open
Abstract
The 2-methyl-4-chlorophenoxyacetic (MCPA) acid-degrader Sphingomonas sp. ERG5 has recently been isolated from MCPA-degrading bacterial communities. Using Illumina-sequencing, the 5.7 Mb genome of this isolate was sequenced in this study, revealing the 138 kbp plasmid pCADAB1 harboring the 32.5 kbp composite transposon Tn6228 which contains genes encoding proteins for the removal of 2,4-dichlorophenoxyacetic acid (2,4-D) and MCPA, as well as the regulation of this pathway. Transposon Tn6228 was confirmed by PCR to be situated on the plasmid and also exist in a circular intermediate state - typical of IS3 elements. The canonical tfdAα-gene of group III 2,4-D degraders, encoding the first step in degradation of 2,4-D and related compounds, was not present in the chromosomal contigs. However, the alternative cadAB genes, also providing the initial degradation step, were found in Tn6228, along with the 2,4-D-degradation-associated genes tfdBCDEFKR and cadR. Putative reductase and ferredoxin genes cadCD of Rieske non-heme iron oxygenases were also present in close proximity to cadAB, suggesting that these might have an unknown role in the initial degradation reaction. Parts of the composite transposon contain sequence displaying high similarity to previously analyzed 2,4-D degradation genes, suggesting rapid dissemination and high conservation of the chlorinated-phenoxyacetic acid (PAA)-degradation genotype among the sphingomonads.
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Affiliation(s)
- Tue Kjærgaard Nielsen
- Department of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
- Section for Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Zhuofei Xu
- Section for Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Erkin Gözdereliler
- Department of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Jens Aamand
- Department of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | | | - Sebastian R. Sørensen
- Department of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
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Biodegradation of 4-chlorobenzoic acid by Pseudomonas aeruginosa PA01 NC. Biodegradation 2010; 22:509-16. [DOI: 10.1007/s10532-010-9423-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 09/23/2010] [Indexed: 11/25/2022]
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Saavedra JM, Acevedo F, González M, Seeger M. Mineralization of PCBs by the genetically modified strain Cupriavidus necator JMS34 and its application for bioremediation of PCBs in soil. Appl Microbiol Biotechnol 2010; 87:1543-54. [DOI: 10.1007/s00253-010-2575-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 03/18/2010] [Accepted: 03/18/2010] [Indexed: 11/29/2022]
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Modified 3-oxoadipate pathway for the biodegradation of methylaromatics in Pseudomonas reinekei MT1. J Bacteriol 2010; 192:1543-52. [PMID: 20061479 DOI: 10.1128/jb.01208-09] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Catechols are central intermediates in the metabolism of aromatic compounds. Degradation of 4-methylcatechol via intradiol cleavage usually leads to the formation of 4-methylmuconolactone (4-ML) as a dead-end metabolite. Only a few microorganisms are known to mineralize 4-ML. The mml gene cluster of Pseudomonas reinekei MT1, which encodes enzymes involved in the metabolism of 4-ML, is shown here to encode 10 genes found in a 9.4-kb chromosomal region. Reverse transcription assays revealed that these genes form a single operon, where their expression is controlled by two promoters. Promoter fusion assays identified 4-methyl-3-oxoadipate as an inducer. Mineralization of 4-ML is initiated by the 4-methylmuconolactone methylisomerase encoded by mmlI. This reaction produces 3-ML and is followed by a rearrangement of the double bond catalyzed by the methylmuconolactone isomerase encoded by mmlJ. Deletion of mmlL, encoding a protein of the metallo-beta-lactamase superfamily, resulted in a loss of the capability of the strain MT1 to open the lactone ring, suggesting its function as a 4-methyl-3-oxoadipate enol-lactone hydrolase. Further metabolism can be assumed to occur by analogy with reactions known from the 3-oxoadipate pathway. mmlF and mmlG probably encode a 4-methyl-3-oxoadipyl-coenzyme A (CoA) transferase, and the mmlC gene product functions as a thiolase, transforming 4-methyl-3-oxoadipyl-CoA into methylsuccinyl-CoA and acetyl-CoA, as indicated by the accumulation of 4-methyl-3-oxoadipate in the respective deletion mutant. Accumulation of methylsuccinate by an mmlK deletion mutant indicates that the encoded acetyl-CoA hydrolase/transferase is crucial for channeling methylsuccinate into the central metabolism.
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Pérez-Pantoja D, Donoso RA, Sánchez MA, González B. Genuine genetic redundancy in maleylacetate-reductase-encoding genes involved in degradation of haloaromatic compounds by Cupriavidus necator JMP134. Microbiology (Reading) 2009; 155:3641-3651. [DOI: 10.1099/mic.0.032086-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Maleylacetate reductases (MAR) are required for biodegradation of several substituted aromatic compounds. To date, the functionality of two MAR-encoding genes (tfdF
I and tfdF
II) has been reported in Cupriavidus necator JMP134(pJP4), a known degrader of aromatic compounds. These two genes are located in tfd gene clusters involved in the turnover of 2,4-dichlorophenoxyacetate (2,4-D) and 3-chlorobenzoate (3-CB). The C. necator JMP134 genome comprises at least three other genes that putatively encode MAR (tcpD, hqoD and hxqD), but confirmation of their functionality and their role in the catabolism of haloaromatic compounds has not been assessed. RT-PCR expression analyses of C. necator JMP134 cells exposed to 2,4-D, 3-CB, 2,4,6-trichlorophenol (2,4,6-TCP) or 4-fluorobenzoate (4-FB) showed that tfdF
I and tfdF
II are induced by haloaromatics channelled to halocatechols as intermediates. In contrast, 2,4,6-TCP only induces tcpD, and any haloaromatic compounds tested did not induce hxqD and hqoD. However, the tcpD, hxqD and hqoD gene products showed MAR activity in cell extracts and provided the MAR function for 2,4-D catabolism when heterologously expressed in MAR-lacking strains. Growth tests for mutants of the five MAR-encoding genes in strain JMP134 showed that none of these genes is essential for degradation of the tested compounds. However, the role of tfdF
I/tfdF
II and tcpD genes in the expression of MAR activity during catabolism of 2,4-D and 2,4,6-TCP, respectively, was confirmed by enzyme activity tests in mutants. These results reveal a striking example of genetic redundancy in the degradation of aromatic compounds.
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Affiliation(s)
- Danilo Pérez-Pantoja
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Millennium Nucleus on Microbial Ecology and Environmental Microbiology and Biotechnology, NM-EMBA, Center for Advanced Studies in Ecology and Biodiversity, CASEB, Santiago, Chile
| | - Raúl A. Donoso
- Facultad de Ingeniería y Ciencia, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Miguel A. Sánchez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Millennium Nucleus on Microbial Ecology and Environmental Microbiology and Biotechnology, NM-EMBA, Center for Advanced Studies in Ecology and Biodiversity, CASEB, Santiago, Chile
| | - Bernardo González
- Facultad de Ingeniería y Ciencia, Universidad Adolfo Ibáñez, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Millennium Nucleus on Microbial Ecology and Environmental Microbiology and Biotechnology, NM-EMBA, Center for Advanced Studies in Ecology and Biodiversity, CASEB, Santiago, Chile
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Trefault N, De la Iglesia R, Molina AM, Manzano M, Ledger T, Pérez-Pantoja D, Sánchez MA, Stuardo M, González B. Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways. Environ Microbiol 2004; 6:655-68. [PMID: 15186344 DOI: 10.1111/j.1462-2920.2004.00596.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ralstonia eutropha JMP134 (pJP4) is a useful model for the study of bacterial degradation of substituted aromatic pollutants. Several key degrading capabilities, encoded by tfd genes, are located in the 88 kb, self-transmissible, IncP-1 beta plasmid pJP4. The complete sequence of the 87,688 nucleotides of pJP4, encoding 83 open reading frames (ORFs), is reported. Most of the coding sequence corresponds to a well-conserved IncP-1 beta backbone and the previously reported tfd genes. In addition, we found hypothetical proteins putatively involved in the transport of aromatic compounds and short-chain fatty acid oxidation. ORFs related to mobile elements, including the Tn501-encoded mercury resistance determinants, an IS1071-based composite transposon and a cryptic class II transposon, are also present in pJP4. These mobile elements are inefficient in transposition and are located in two regions of pJP4 that are rich in remnants of lateral gene transfer events. pJP4 plasmid was able to capture chromosomal genes and form hybrid plasmids with the IncP-1 alpha plasmid RP4. These observations are integrated into a model for the evolution of pJP4, which reveals mechanisms of bacterial adaptation to degrade pollutants.
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MESH Headings
- Adaptation, Physiological
- Base Composition
- Biodegradation, Environmental
- Cupriavidus necator/genetics
- Cupriavidus necator/metabolism
- DNA Transposable Elements
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- Drug Resistance, Bacterial/genetics
- Environmental Pollutants/metabolism
- Gene Order
- Gene Transfer, Horizontal
- Genes, Bacterial
- Hydrocarbons, Aromatic/metabolism
- Mercury Compounds/toxicity
- Molecular Sequence Data
- Open Reading Frames
- Operon
- Plasmids/genetics
- Recombination, Genetic
- Sequence Analysis, DNA
- Transcription, Genetic
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Affiliation(s)
- N Trefault
- Laboratorio de Microbiología, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, and Millennium Institute for Fundamental and Applied Biology, Santiago, Chile
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Pérez-Pantoja D, Ledger T, Pieper DH, González B. Efficient turnover of chlorocatechols is essential for growth of Ralstonia eutropha JMP134(pJP4) in 3-chlorobenzoic acid. J Bacteriol 2003; 185:1534-42. [PMID: 12591870 PMCID: PMC148064 DOI: 10.1128/jb.185.5.1534-1542.2003] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ralstonia eutropha JMP134(pJP4) degrades 3-chlorobenzoate (3-CB) by using two not completely isofunctional, pJP4-encoded chlorocatechol degradation gene clusters, tfdC(I)D(I)E(I)F(I) and tfdD(II)C(II)E(II)F(II). Introduction of several copies of each gene cluster into R. eutropha JMP222, which lacks pJP4 and thus accumulates chlorocatechols from 3-CB, allows the derivatives to grow in this substrate. However, JMP222 derivatives containing one chromosomal copy of each cluster did not grow in 3-CB. The failure to grow in 3-CB was the result of accumulation of chlorocatechols due to the limiting activity of chlorocatechol 1,2-dioxygenase (TfdC), the first enzyme in the chlorocatechol degradation pathway. Micromolar concentrations of 3- and 4-chlorocatechol inhibited the growth of strains JMP134 and JMP222 in benzoate, and cells of strain JMP222 exposed to 3 mM 3-CB exhibited a 2-order-of-magnitude decrease in viability. This toxicity effect was not observed with strain JMP222 harboring multiple copies of the tfdC(I) gene, and the derivative of strain JMP222 containing tfdC(I)D(I)E(I)F(I) plus multiple copies of the tfdC(I) gene could efficiently grow in 3-CB. In addition, tfdC(I) and tfdC(II) gene mutants of strain JMP134 exhibited no growth and impaired growth in 3-CB, respectively. The introduction into strain JMP134 of the xylS-xylXYZL genes, encoding a broad-substrate-range benzoate 1,2-dioxygenase system and thus increasing the transformation of 3-CB into chlorocatechols, resulted in derivatives that exhibited a sharp decrease in the ability to grow in 3-CB. These observations indicate that the dosage of chlorocatechol-transforming genes is critical for growth in 3-CB. This effect depends on a delicate balance between chlorocatechol-producing and chlorocatechol-consuming reactions.
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Affiliation(s)
- D Pérez-Pantoja
- Laboratorio de Microbiología, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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