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Yang H, Liu S, Chen S, Lu P, Huang J, Sun L, Liu H. Novel 4-chlorophenoxyacetate dioxygenase-mediated phenoxyalkanoic acid herbicides initial catabolism in Cupriavidus sp. DL-D2. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135427. [PMID: 39116741 DOI: 10.1016/j.jhazmat.2024.135427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
Abstract
Microbial metabolism is an important driving force for the elimination of 4-chlorophenoxyacetic acid residues in the environment. The α-Ketoglutarate-dependent dioxygenase (TfdA) or 2,4-D oxygenase (CadAB) catalyzes the cleavage of the aryl ether bond of 4-chlorophenoxyacetic acid to 4-chlorophenol, which is one of the important pathways for the initial metabolism of 4-chlorophenoxyacetic acid by microorganisms. However, strain Cupriavidus sp. DL-D2 could utilize 4-chlorophenoxyacetic acid but not 4-chlorophenol for growth. This scarcely studied degradation pathway may involve novel enzymes that has not yet been characterized. Here, a gene cluster (designated cpd) responsible for the catabolism of 4-chlorophenoxyacetic acid in strain DL-D2 was cloned and identified, and the dioxygenase CpdA/CpdB responsible for the initial degradation of 4-chlorophenoxyacetic acid was successfully expressed, which could catalyze the conversion of 4-chlorphenoxyacetic acid to 4-chlorocatechol. Then, an aromatic cleavage enzyme CpdC further converts 4-chlorocatechol into 3-chloromuconate. The results of substrate degradation experiments showed that CpdA/CpdB could also degrade 3-chlorophenoxyacetic acid and phenoxyacetic acid, and homologous cpd gene clusters were widely discovered in microbial genomes. Our findings revealed a novel degradation mechanism of 4-chlorophenoxyacetic acid at the molecular level.
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Affiliation(s)
- Hao Yang
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, Anhui Normal University, Wuhu 241000, Anhui, PR China; Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, PR China
| | - Shiyan Liu
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, Anhui Normal University, Wuhu 241000, Anhui, PR China; Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, PR China
| | - Sitong Chen
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, Anhui Normal University, Wuhu 241000, Anhui, PR China; Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, PR China
| | - Peng Lu
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, Anhui Normal University, Wuhu 241000, Anhui, PR China; Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, PR China
| | - Junwei Huang
- College of Resources and Environment, Anhui Agricultural University, Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, Hefei 230036, PR China
| | - Lina Sun
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China.
| | - Hongming Liu
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, Anhui Normal University, Wuhu 241000, Anhui, PR China; Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, PR China.
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Metabolic Pathway of Phenol Degradation of a Cold-Adapted Antarctic Bacteria, Arthrobacter sp. Catalysts 2022. [DOI: 10.3390/catal12111422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Phenol is an important pollutant widely discharged as a component of hydrocarbon fuels, but its degradation in cold regions is challenging due to the harsh environmental conditions. To date, there is little information available concerning the capability for phenol biodegradation by indigenous Antarctic bacteria. In this study, enzyme activities and genes encoding phenol degradative enzymes identified using whole genome sequencing (WGS) were investigated to determine the pathway(s) of phenol degradation of Arthrobacter sp. strains AQ5-05 and AQ5-06, originally isolated from Antarctica. Complete phenol degradative genes involved only in the ortho-cleavage were detected in both strains. This was validated using assays of the enzymes catechol 1,2-dioxygenase and catechol 2,3-dioxygenase, which indicated the activity of only catechol 1,2-dioxygenase in both strains, in agreement with the results from the WGS. Both strains were psychrotolerant with the optimum temperature for phenol degradation, being between 10 and 15 °C. This study suggests the potential use of cold-adapted bacteria in the bioremediation of phenol pollution in cold environments.
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Characterization and Expression Analysis of Extradiol and Intradiol Dioxygenase of Phenol-Degrading Haloalkaliphilic Bacterial Isolates. Curr Microbiol 2022; 79:294. [PMID: 35989347 PMCID: PMC9393131 DOI: 10.1007/s00284-022-02981-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/17/2022] [Indexed: 11/15/2022]
Abstract
Haloalkophilic bacteria have a potential advantage as a bioremediation organism of high oil-polluted and industrial wastewater. In the current study, Haloalkaliphilic isolates were obtained from Hamralake, Wadi EL-Natrun, Egypt. The phenotype script, biochemical characters, and sequence analysis of bacterial-16S rRNA were used to identify the bacterial isolates; Halomonas HA1 and Marinobacter HA2. These strains required high concentrations of NaCl to ensure bacterial growth, especially Halomonas HA1 strain. Notably, both isolates can degrade phenol at optimal pH values, between 8 and 9, with the ability to grow in pH levels up to 11, like what was seen in the Halomonas HA1 strain. Moreover, both isolates represent two different mechanistic pathways for phenol degradation. Halomonas HA1 exploits the 1,2 phenol meta-cleavage pathway, while Marinobacter HA2 uses the 2,3 ortho-cleavage pathway as indicated by universal primers for 1,2 and 2,3 CTD genes. Interestingly, Marinobacter HA2 isolate eliminated the added phenol within an incubation period of 72 h, while the Halomonas HA1 isolate invested 96 h in degrading 84% of the same amount of phenol. Phylogenetic analysis of these 1,2 CTD (catechol dioxygenase) sequences clearly showed an evolutionary relationship between 1,2 dioxygenases of both Halomonadaceae and Pseudomonadaceae. In comparison, 2,3 CTD of Marinobacter HA2 shared the main domains of the closely related species. Furthermore, semi-quantitative RT-PCR analysis proved the constitutive expression pattern of both dioxygenase genes. These findings provide new isolates of Halomonas sp. and Marinobacter sp. that can degrade phenol at high salt and pH conditions via two independent mechanisms.
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Chen K, Xu X, Yang M, Liu T, Liu B, Zhu J, Wang B, Jiang J. Genetic redundancy of 4-hydroxybenzoate 3-hydroxylase genes ensures the catabolic safety of Pigmentiphaga sp. H8 in 3-bromo-4-hydroxybenzoate-contaminated habitats. Environ Microbiol 2022; 24:5123-5138. [PMID: 35876302 DOI: 10.1111/1462-2920.16141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/17/2022] [Accepted: 07/17/2022] [Indexed: 11/28/2022]
Abstract
Genetic redundancy is prevalent in organisms and plays important roles in the evolution of biodiversity and adaptation to environmental perturbation. However, selective advantages of genetic redundancy in overcoming metabolic disturbance due to structural analogues have received little attention. Here, functional divergence of the three 4-hydroxybenzoate 3-hydroxylase (PHBH) genes (phbh1~3) was found in Pigmentiphaga sp. strain H8. The genes phbh1/phbh2 were responsible for 3-bromo-4-hydroxybenzoate (3-Br-4-HB, an anthropogenic pollutant) catabolism, whereas phbh3 was primarily responsible for 4-hydroxybenzoate (4-HB, a natural intermediate of lignin) catabolism. 3-Br-4-HB inhibited 4-HB catabolism by competitively binding PHBH3, and was toxic to strain H8 cells especially at high concentrations. The existence of phbh1/phbh2 not only enabled strain H8 to utilize 3-Br-4-HB, but also ensured the catabolic safety of 4-HB. Molecular docking and site-directed mutagenesis analyses revealed that Val199 and Phe384 of PHBH1/PHBH2 were required for the hydroxylation activity towards 3-Br-4-HB. Phylogenetic analysis indicated that phbh1 and phbh2 originated from a common ancestor and evolved specifically in strain H8 to adapt to 3-Br-4-HB-contaminated habitats, whereas phbh3 evolved independently. This study deepens our understanding of selective advantages of genetic redundancy in prokaryote's metabolic robustness and reveals the factors driving the divergent evolution of redundant genes in adaptation to environmental perturbation. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kai Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Muji Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Tairong Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Bin Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Jianchun Zhu
- Laboratory Centre of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
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Meier A, Worch S, Hartmann A, Marzec M, Mock HP, Bode R, Kunze G, Matthes F. Characterization of Catechol-1,2-Dioxygenase (Acdo1p) From Blastobotrys raffinosifermentans and Investigation of Its Role in the Catabolism of Aromatic Compounds. Front Microbiol 2022; 13:872298. [PMID: 35722288 PMCID: PMC9204233 DOI: 10.3389/fmicb.2022.872298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022] Open
Abstract
Gallic acid, protocatechuic acid, catechol, and pyrogallol are only a few examples of industrially relevant aromatics. Today much attention is paid to the development of new microbial factories for the environmentally friendly biosynthesis of industrially relevant chemicals with renewable resources or organic pollutants as the starting material. The non–conventional yeast, Blastobotrys raffinosifermentans, possesses attractive properties for industrial bio-production processes such as thermo- and osmotolerance. An additional advantage is its broad substrate spectrum, with tannins at the forefront. The present study is dedicated to the characterization of catechol-1,2-dioxygenase (Acdo1p) and the analysis of its function in B. raffinosifermentans tannic acid catabolism. Acdo1p is a dimeric protein with higher affinity for catechol (KM = 0.004 ± 0.001 mM, kcat = 15.6 ± 0.4 s–1) than to pyrogallol (KM = 0.1 ± 0.02 mM, kcat = 10.6 ± 0.4 s–1). It is an intradiol dioxygenase and its reaction product with catechol as the substrate is cis,cis-muconic acid. B. raffinosifermentans G1212/YIC102-AYNI1-ACDO1-6H, which expresses the ACDO1 gene under the control of the strong nitrate-inducible AYNI1 promoter, achieved a maximum catechol-1,2-dioxygenase activity of 280.6 U/L and 26.9 U/g of dry cell weight in yeast grown in minimal medium with nitrate as the nitrogen source and 1.5% glucose as the carbon source. In the same medium with glucose as the carbon source, catechol-1,2-dioxygenase activity was not detected for the control strain G1212/YIC102 with ACDO1 expression under the regulation of its respective endogenous promoter. Gene expression analysis showed that ACDO1 is induced by gallic acid and protocatechuic acid. In contrast to the wild-type strain, the B. raffinosifermentans strain with a deletion of the ACDO1 gene was unable to grow on medium supplemented with gallic acid or protocatechuic acid as the sole carbon source. In summary, we propose that due to its substrate specificity, its thermal stability, and its ability to undergo long-term storage without significant loss of activity, B. raffinosifermentans catechol-1,2-dioxygenase (Acdo1p) is a promising enzyme candidate for industrial applications.
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Affiliation(s)
- Anna Meier
- Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Sebastian Worch
- Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Anja Hartmann
- Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Marek Marzec
- Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Hans-Peter Mock
- Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Rüdiger Bode
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Gotthard Kunze
- Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- *Correspondence: Gotthard Kunze,
| | - Falko Matthes
- Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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Shi S, Yang L, Yang C, Li S, Zhao H, Ren L, Wang X, Lu F, Li Y, Zhao H. Function and Molecular Ecology Significance of Two Catechol-Degrading Gene Clusters in Pseudomonas putida ND6. J Microbiol Biotechnol 2021; 31:259-271. [PMID: 33323670 PMCID: PMC9705993 DOI: 10.4014/jmb.2009.09026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022]
Abstract
Many bacteria metabolize aromatic compounds via catechol as a catabolic intermediate, and possess multiple genes or clusters encoding catechol-cleavage enzymes. The presence of multiple isozyme-encoding genes is a widespread phenomenon that seems to give the carrying strains a selective advantage in the natural environment over those with only a single copy. In the naphthalene-degrading strain Pseudomonas putida ND6, catechol can be converted into intermediates of the tricarboxylic acid cycle via either the ortho- or meta-cleavage pathways. In this study, we demonstrated that the catechol ortho-cleavage pathway genes (catBICIAI and catBIICIIAII) on the chromosome play an important role. The catI and catII operons are co-transcribed, whereas catAI and catAII are under independent transcriptional regulation. We examined the binding of regulatory proteins to promoters. In the presence of cis-cis-muconate, a well-studied inducer of the cat gene cluster, CatRI and CatRII occupy an additional downstream site, designated as the activation binding site. Notably, CatRI binds to both the catI and catII promoters with high affinity, while CatRII binds weakly. This is likely caused by a T to G mutation in the G/T-N11-A motif. Specifically, we found that CatRI and CatRII regulate catBICIAI and catBIICIIAII in a cooperative manner, which provides new insights into naphthalene degradation.
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Affiliation(s)
- Sanyuan Shi
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Liu Yang
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Chen Yang
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Shanshan Li
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an 710048, P.R. China
| | - Hong Zhao
- Tianjin Entry-Exit Inspection and Quarantine Bureau, Tianjin 00457, P.R. China
| | - Lu Ren
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Xiaokang Wang
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Fuping Lu
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Ying Li
- China Animal Disease Control Center, Beijing 100000, P.R. China,Y. Li Phone: +86-10-59198969 Fax: +86-10-59198969 E-mail:
| | - Huabing Zhao
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China,Corresponding authors H. Zhao Phone: +86-22-60601958 Fax: +86-22-60602298 E-mail:
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Vaidya SS, Patel AB, Jain K, Amin S, Madamwar D. Characterizing the bacterial consortium ASDF capable of catabolic degradation of fluoranthene and other mono- and poly-aromatic hydrocarbons. 3 Biotech 2020; 10:491. [PMID: 33134009 DOI: 10.1007/s13205-020-02478-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/12/2020] [Indexed: 10/23/2022] Open
Abstract
In this study, a bacterial consortium ASDF was developed, capable of degrading fluoranthene (a non-alternant poly-aromatic hydrocarbon). It comprised of three bacterial strains: Pseudomonas sp. ASDF1, Burkholderia sp. ASDF2 and Mycobacterium sp. ASDF3 capable of degrading 100 mg/L of fluoranthene under experimentally defined and optimum conditions (37 °C, pH 7.0, 150 rpm) within 7 days. Consortium had metabolized fluoranthene as sole source of carbon and energy with maximum degradation rate of 0.52 mg/L/h and growth rate of 0.054/h. Fluoranthene degradation is an aerobic process, therefore with increasing the gyratory shaking from 50 to 150 rpm, degradation was concurrently enhanced by 7.1-fold. The synthetic surfactants SDS and CTAB had antagonistic effect on fluoranthene degradation (decreased up to 2.8-fold). The proficiency of consortium was assessed for its inherent ability to degrade seven other hydrocarbons both individually as well as in mixture. The degradation profile was studied using HPLC and the detection of two degraded intermediates (salicylic acid and derivatives of phthalic acid) suggested that fluoranthene degradation might have occurred via ortho- and meta-cleavage pathways. The competency of consortium was further validated through simulated microcosm studies, which showed 96% degradation of fluoranthene in soil ecosystem under the ambient conditions. Hence, the study suggested that the consortium ASDF has an inherent potential for its wide applicability in bioremediation of hydrocarbon-contaminated sites.
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Affiliation(s)
- Sagar S Vaidya
- Post Graduate Department of Biosciences, UGC Centre of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol, Anand, Gujarat 388 315 India
| | - Avani Bharatkumar Patel
- Post Graduate Department of Biosciences, UGC Centre of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol, Anand, Gujarat 388 315 India
| | - Kunal Jain
- Post Graduate Department of Biosciences, UGC Centre of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol, Anand, Gujarat 388 315 India
| | - Seema Amin
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Charusat Campus, Changa, Anand, Gujarat 388 421 India
| | - Datta Madamwar
- Post Graduate Department of Biosciences, UGC Centre of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol, Anand, Gujarat 388 315 India.,P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Charusat Campus, Changa, Anand, Gujarat 388 421 India
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Li N, Peng Q, Yao L, He Q, Qiu J, Cao H, He J, Niu Q, Lu Y, Hui F. Roles of the Gentisate 1,2-Dioxygenases DsmD and GtdA in the Catabolism of the Herbicide Dicamba in Rhizorhabdus dicambivorans Ndbn-20. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9287-9298. [PMID: 32786824 DOI: 10.1021/acs.jafc.0c01523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
3-Chlorogentisate is a key intermediate in the catabolism of the herbicide dicamba in R. dicambivorans Ndbn-20. In this study, we identified two gentisate 1,2-dioxygenases (GDOs), DsmD and GtdA, from Ndbn-20. The amino acid sequence similarity between DsmD and GtdA is 51%. Both of them are dimers and showed activities to gentisate and 3-chlorogentisate but not 3,6-dichlorogentisate (3,6-DCGA) or 6-chlorogentisate in vitro. The kcat/Km of DsmD for 3-chlorogentisate was 28.7 times higher than that of GtdA, whereas the kcat/Km of DsmD for gentisate was only one-fourth of that of GtdA. Transcription of dsmD was dramatically induced by 3-chlorogentisate but not gentisate, whereas gtdA was not induced. Disruption of dsmD resulted in a significant decline in the degradation rates of 3-chlorogentisate and dicamba but had no effect on the degradation of gentisate, whereas the result of disruption of gtdA was converse; the disruption of both dsmD and gtdA led to the inability to degrade 3-chlorogentisate and gentisate. This study revealed that 3-chlorogentisate but not gentisate or 3,6-DCGA is the ring-cleavage substrate in the dicamba degradation pathway in R. dicambivorans Ndbn-20; DsmD is specifically responsible for cleavage of 3-chlorogentisate, whereas GtdA is a general GDO involved in the catabolism of various natural aromatic compounds.
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Affiliation(s)
- Na Li
- School of Life Science and Technology, Nanyang Normal University, Nanyang, Henan 473061, China
| | - Qian Peng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Li Yao
- School of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224002, China
| | - Qin He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Qiuhong Niu
- School of Life Science and Technology, Nanyang Normal University, Nanyang, Henan 473061, China
| | - Yunfeng Lu
- School of Life Science and Technology, Nanyang Normal University, Nanyang, Henan 473061, China
- State Key Laboratory of Motor Vehicle Biofuel Technology, Nanyang, Henan 473000, China
| | - Fengli Hui
- School of Life Science and Technology, Nanyang Normal University, Nanyang, Henan 473061, China
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Cloning and characterisation of four catA genes located on the chromosome and large plasmid of Pseudomonas putida ND6. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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10
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Indole Biodegradation in Acinetobacter sp. Strain O153: Genetic and Biochemical Characterization. Appl Environ Microbiol 2017; 83:AEM.01453-17. [PMID: 28778892 DOI: 10.1128/aem.01453-17] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/26/2017] [Indexed: 01/30/2023] Open
Abstract
Indole is a molecule of considerable biochemical significance, acting as both an interspecies signal molecule and a building block of biological elements. Bacterial indole degradation has been demonstrated for a number of cases; however, very little is known about genes and proteins involved in this process. This study reports the cloning and initial functional characterization of genes (iif and ant cluster) responsible for indole biodegradation in Acinetobacter sp. strain O153. The catabolic cascade was reconstituted in vitro with recombinant proteins, and each protein was assigned an enzymatic function. Degradation starts with oxidation, mediated by the IifC and IifD flavin-dependent two-component oxygenase system. Formation of indigo is prevented by IifB, and the final product, anthranilic acid, is formed by IifA, an enzyme which is both structurally and functionally comparable to cofactor-independent oxygenases. Moreover, the iif cluster was identified in the genomes of a wide range of bacteria, suggesting the potential of widespread Iif-mediated indole degradation. This work provides novel insights into the genetic background of microbial indole biodegradation.IMPORTANCE The key finding of this research is identification of the genes responsible for microbial biodegradation of indole, a toxic N-heterocyclic compound. A large amount of indole is present in urban wastewater and sewage sludge, creating a demand for an efficient and eco-friendly means to eliminate this pollutant. A common strategy of oxidizing indole to indigo has the major drawback of producing insoluble material. Genes and proteins of Acinetobacter sp. strain O153 (DSM 103907) reported here pave the way for effective and indigo-free indole removal. In addition, this work suggests possible novel means of indole-mediated bacterial interactions and provides the basis for future research on indole metabolism.
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Pathak A, Chauhan A, Blom J, Indest KJ, Jung CM, Stothard P, Bera G, Green SJ, Ogram A. Comparative Genomics and Metabolic Analysis Reveals Peculiar Characteristics of Rhodococcus opacus Strain M213 Particularly for Naphthalene Degradation. PLoS One 2016; 11:e0161032. [PMID: 27532207 PMCID: PMC4988695 DOI: 10.1371/journal.pone.0161032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 07/27/2016] [Indexed: 12/12/2022] Open
Abstract
The genome of Rhodococcus opacus strain M213, isolated from a fuel-oil contaminated soil, was sequenced and annotated which revealed a genome size of 9,194,165 bp encoding 8680 putative genes and a G+C content of 66.72%. Among the protein coding genes, 71.77% were annotated as clusters of orthologous groups of proteins (COGs); 55% of the COGs were present as paralog clusters. Pulsed field gel electrophoresis (PFGE) analysis of M213 revealed the presence of three different sized replicons- a circular chromosome and two megaplasmids (pNUO1 and pNUO2) estimated to be of 750Kb 350Kb in size, respectively. Conversely, using an alternative approach of optical mapping, the plasmid replicons appeared as a circular ~1.2 Mb megaplasmid and a linear, ~0.7 Mb megaplasmid. Genome-wide comparative analysis of M213 with a cohort of sequenced Rhodococcus species revealed low syntenic affiliation with other R. opacus species including strains B4 and PD630. Conversely, a closer affiliation of M213, at the functional (COG) level, was observed with the catabolically versatile R. jostii strain RHA1 and other Rhodococcii such as R. wratislaviensis strain IFP 2016, R. imtechensis strain RKJ300, Rhodococcus sp. strain JVH1, and Rhodococcus sp. strain DK17, respectively. An in-depth, genome-wide comparison between these functional relatives revealed 971 unique genes in M213 representing 11% of its total genome; many associating with catabolic functions. Of major interest was the identification of as many as 154 genomic islands (GEIs), many with duplicated catabolic genes, in particular for PAHs; a trait that was confirmed by PCR-based identification of naphthalene dioxygenase (NDO) as a representative gene, across PFGE-resolved replicons of strain M213. Interestingly, several plasmid/GEI-encoded genes, that likely participate in degrading naphthalene (NAP) via a peculiar pathway, were also identified in strain M213 using a combination of bioinformatics, metabolic analysis and gene expression measurements of selected catabolic genes by RT-PCR. Taken together, this study provides a comprehensive understanding of the genome plasticity and ecological competitiveness of strain M213 likely facilitated by horizontal gene transfer (HGT), bacteriophage attacks and genomic reshuffling- aspects that continue to be understudied and thus poorly understood, in particular for the soil-borne Rhodococcii.
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Affiliation(s)
- Ashish Pathak
- School of the Environment, Florida A&M University, Tallahassee, Florida, United States of America
| | - Ashvini Chauhan
- School of the Environment, Florida A&M University, Tallahassee, Florida, United States of America
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Karl J. Indest
- Environmental Processes Branch, United States Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America
| | - Carina M. Jung
- Environmental Processes Branch, United States Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Gopal Bera
- Geochemical and Environmental Research Group, Texas A&M University, College Station, Texas, United States of America
| | - Stefan J. Green
- DNA Services Facility, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Andrew Ogram
- Soil and Water Science Department, University of Florida, Gainesville, Florida, United States of America
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Lin J, Milase RN. Purification and Characterization of Catechol 1,2-Dioxygenase from Acinetobacter sp. Y64 Strain and Escherichia coli Transformants. Protein J 2015; 34:421-33. [DOI: 10.1007/s10930-015-9637-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Nešvera J, Rucká L, Pátek M. Catabolism of Phenol and Its Derivatives in Bacteria: Genes, Their Regulation, and Use in the Biodegradation of Toxic Pollutants. ADVANCES IN APPLIED MICROBIOLOGY 2015; 93:107-60. [PMID: 26505690 DOI: 10.1016/bs.aambs.2015.06.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Phenol and its derivatives (alkylphenols, halogenated phenols, nitrophenols) are natural or man-made aromatic compounds that are ubiquitous in nature and in human-polluted environments. Many of these substances are toxic and/or suspected of mutagenic, carcinogenic, and teratogenic effects. Bioremediation of the polluted soil and water using various bacteria has proved to be a promising option for the removal of these compounds. In this review, we describe a number of peripheral pathways of aerobic and anaerobic catabolism of various natural and xenobiotic phenolic compounds, which funnel these substances into a smaller number of central catabolic pathways. Finally, the metabolites are used as carbon and energy sources in the citric acid cycle. We provide here the characteristics of the enzymes that convert the phenolic compounds and their catabolites, show their genes, and describe regulatory features. The genes, which encode these enzymes, are organized on chromosomes and plasmids of the natural bacterial degraders in various patterns. The accumulated data on similarities and the differences of the genes, their varied organization, and particularly, an astonishingly broad range of intricate regulatory mechanism may be read as an exciting adventurous book on divergent evolutionary processes and horizontal gene transfer events inscribed in the bacterial genomes. In the end, the use of this wealth of bacterial biodegradation potential and the manipulation of its genetic basis for purposes of bioremediation is exemplified. It is envisioned that the integrated high-throughput techniques and genome-level approaches will enable us to manipulate systems rather than separated genes, which will give birth to systems biotechnology.
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Affiliation(s)
- Jan Nešvera
- Institute of Microbiology CAS, v. v. i., Prague, Czech Republic
| | - Lenka Rucká
- Institute of Microbiology CAS, v. v. i., Prague, Czech Republic
| | - Miroslav Pátek
- Institute of Microbiology CAS, v. v. i., Prague, Czech Republic
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Biosynthesis of cis,cis-muconic acid and its aromatic precursors, catechol and protocatechuic acid, from renewable feedstocks by Saccharomyces cerevisiae. Appl Environ Microbiol 2012; 78:8421-30. [PMID: 23001678 DOI: 10.1128/aem.01983-12] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adipic acid is a high-value compound used primarily as a precursor for the synthesis of nylon, coatings, and plastics. Today it is produced mainly in chemical processes from petrochemicals like benzene. Because of the strong environmental impact of the production processes and the dependence on fossil resources, biotechnological production processes would provide an interesting alternative. Here we describe the first engineered Saccharomyces cerevisiae strain expressing a heterologous biosynthetic pathway converting the intermediate 3-dehydroshikimate of the aromatic amino acid biosynthesis pathway via protocatechuic acid and catechol into cis,cis-muconic acid, which can be chemically dehydrogenated to adipic acid. The pathway consists of three heterologous microbial enzymes, 3-dehydroshikimate dehydratase, protocatechuic acid decarboxylase composed of three different subunits, and catechol 1,2-dioxygenase. For each heterologous reaction step, we analyzed several potential candidates for their expression and activity in yeast to compose a functional cis,cis-muconic acid synthesis pathway. Carbon flow into the heterologous pathway was optimized by increasing the flux through selected steps of the common aromatic amino acid biosynthesis pathway and by blocking the conversion of 3-dehydroshikimate into shikimate. The recombinant yeast cells finally produced about 1.56 mg/liter cis,cis-muconic acid.
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Pérez-Pantoja D, Donoso R, Agulló L, Córdova M, Seeger M, Pieper DH, González B. Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales. Environ Microbiol 2011; 14:1091-117. [PMID: 22026719 DOI: 10.1111/j.1462-2920.2011.02613.x] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The relevance of the β-proteobacterial Burkholderiales order in the degradation of a vast array of aromatic compounds, including several priority pollutants, has been largely assumed. In this review, the presence and organization of genes encoding oxygenases involved in aromatics biodegradation in 80 Burkholderiales genomes is analysed. This genomic analysis underscores the impressive catabolic potential of this bacterial lineage, comprising nearly all of the central ring-cleavage pathways reported so far in bacteria and most of the peripheral pathways involved in channelling of a broad diversity of aromatic compounds. The more widespread pathways in Burkholderiales include protocatechuate ortho ring-cleavage, catechol ortho ring-cleavage, homogentisate ring-cleavage and phenylacetyl-CoA ring-cleavage pathways found in at least 60% of genomes analysed. In general, a genus-specific pattern of positional ordering of biodegradative genes is observed in the catabolic clusters of these pathways indicating recent events in its evolutionary history. In addition, a significant bias towards secondary chromosomes, now termed chromids, is observed in the distribution of catabolic genes across multipartite genomes, which is consistent with a genus-specific character. Strains isolated from environmental sources such as soil, rhizosphere, sediment or sludge show a higher content of catabolic genes in their genomes compared with strains isolated from human, animal or plant hosts, but no significant difference is found among Alcaligenaceae, Burkholderiaceae and Comamonadaceae families, indicating that habitat is more of a determinant than phylogenetic origin in shaping aromatic catabolic versatility.
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Affiliation(s)
- Danilo Pérez-Pantoja
- Center for Advanced Studies in Ecology and Biodiversity, Millennium Nucleus in Plant Functional Genomics, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Santiago, Chile
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16
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Pathway and evolutionary implications of diphenylamine biodegradation by Burkholderia sp. strain JS667. Appl Environ Microbiol 2009; 75:2694-704. [PMID: 19251893 DOI: 10.1128/aem.02198-08] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diphenylamine (DPA) is a common contaminant at munitions-contaminated sites as well as at aniline manufacturing sites. Little is known about the biodegradation of the compound, and bacteria able to use DPA as the growth substrate have not been reported. Burkholderia sp. strain JS667 and Ralstonia sp. strain JS668 were isolated by selective enrichment from DPA-contaminated sediment. The isolates grew aerobically with DPA as the sole carbon, nitrogen, and energy source. During induction of DPA degradation, stoichiometric amounts of aniline accumulated and then disappeared, which suggested that aniline is on the DPA degradation pathway. Genes encoding the enzymes that catalyze the initial steps in DPA degradation were cloned from the genomic DNA of strain JS667. The Escherichia coli clone catalyzed stoichiometric transformation of DPA to aniline and catechol. Transposon mutagenesis, the sequence similarity of putative open reading frames to those of well-characterized dioxygenases, and (18)O(2) experiments support the conclusion that the initial reaction in DPA degradation is catalyzed by a multicomponent ring-hydroxylating dioxygenase. DPA is converted to aniline and catechol via dioxygenation at the 1,2 position of the aromatic ring and spontaneous rearomatization. Aniline and catechol are further biodegraded by the well-established aniline degradation pathway. Genes that encode the complete aniline degradation pathway were found 12 kb downstream of the genes that encode the initial dioxygenase. Expression of the relevant dioxygenases was confirmed by reverse transcription-PCR analysis. Both the sequence similarity and the gene organization suggest that the DPA degradation pathway evolved recently by the recruitment of two gene clusters that encode the DPA dioxygenase and aniline degradation pathway.
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Pérez-Pantoja D, De la Iglesia R, Pieper DH, González B. Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacteriumCupriavidus necatorJMP134. FEMS Microbiol Rev 2008; 32:736-94. [DOI: 10.1111/j.1574-6976.2008.00122.x] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Field-based stable isotope probing reveals the identities of benzoic acid-metabolizing microorganisms and their in situ growth in agricultural soil. Appl Environ Microbiol 2008; 74:4111-8. [PMID: 18469130 DOI: 10.1128/aem.00464-08] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We used a combination of stable isotope probing (SIP), gas chromatography-mass spectrometry-based respiration, isolation/cultivation, and quantitative PCR procedures to discover the identity and in situ growth of soil microorganisms that metabolize benzoic acid. We added [(13)C]benzoic acid or [(12)C]benzoic acid (100 microg) once, four times, or five times at 2-day intervals to agricultural field plots. After monitoring (13)CO(2) evolution from the benzoic acid-dosed soil, field soils were harvested and used for nucleic acid extraction and for cultivation of benzoate-degrading bacteria. Exposure of soil to benzoate increased the number of culturable benzoate degraders compared to unamended soil, and exposure to benzoate shifted the dominant culturable benzoate degraders from Pseudomonas species to Burkholderia species. Isopycnic separation of heavy [(13)C]DNA from the unlabeled fraction allowed terminal restriction fragment length polymorphism (T-RFLP) analyses to confirm that distinct 16S rRNA genes were localized in the heavy fraction. Phylogenetic analysis of sequenced 16S rRNA genes revealed a predominance (15 of 58 clones) of Burkholderia species in the heavy fraction. Burkholderia sp. strain EBA09 shared 99.5% 16S rRNA sequence similarity with a group of clones representing the dominant RFLP pattern, and the T-RFLP fragment for strain EBA09 and a clone from that cluster matched the fragment enriched in the [(13)C]DNA fraction. Growth of the population represented by EBA09 during the field-dosing experiment was demonstrated by using most-probable-number-PCR and primers targeting EBA09 and the closely related species Burkholderia hospita. Thus, the target population identified by SIP not only actively metabolized benzoic acid but reproduced in the field upon the addition of the substrate.
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19
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Hristova KR, Schmidt R, Chakicherla AY, Legler TC, Wu J, Chain PS, Scow KM, Kane SR. Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol. Appl Environ Microbiol 2007; 73:7347-57. [PMID: 17890343 PMCID: PMC2168209 DOI: 10.1128/aem.01604-07] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High-density whole-genome cDNA microarrays were used to investigate substrate-dependent gene expression of Methylibium petroleiphilum PM1, one of the best-characterized aerobic methyl tert-butyl ether (MTBE)-degrading bacteria. Differential gene expression profiling was conducted with PM1 grown on MTBE and ethanol as sole carbon sources. Based on microarray high scores and protein similarity analysis, an MTBE regulon located on the megaplasmid was identified for further investigation. Putative functions for enzymes encoded in this regulon are described with relevance to the predicted MTBE degradation pathway. A new unique dioxygenase enzyme system that carries out the hydroxylation of tert-butyl alcohol to 2-methyl-2-hydroxy-1-propanol in M. petroleiphilum PM1 was discovered. Hypotheses regarding the acquisition and evolution of MTBE genes as well as the involvement of IS elements in these complex processes were formulated. The pathways for toluene, phenol, and alkane oxidation via toluene monooxygenase, phenol hydroxylase, and propane monooxygenase, respectively, were upregulated in MTBE-grown cells compared to ethanol-grown cells. Four out of nine putative cyclohexanone monooxygenases were also upregulated in MTBE-grown cells. The expression data allowed prediction of several hitherto-unknown enzymes of the upper MTBE degradation pathway in M. petroleiphilum PM1 and aided our understanding of the regulation of metabolic processes that may occur in response to pollutant mixtures and perturbations in the environment.
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Affiliation(s)
- Krassimira R Hristova
- Department of Land Air and Water Resources, Plant and Environmental Sciences Building, University of California, Davis, Davis, CA 95616.
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20
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Kolomytseva MP, Baskunov BP, Golovleva LA. Intradiol pathway of para-cresol conversion by Rhodococcus opacus 1CP. Biotechnol J 2007; 2:886-93. [PMID: 17506026 DOI: 10.1002/biot.200700013] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The growth of Rhodococcus opacus 1CP in medium with different concentrations of p-cresol as the sole source of carbon and energy was studied. It was shown that the optimal concentration of p-cresol was 600 mg/L. The ability of this strain to transform practically all amounts of p-cresol to 4-methylcatechol followed by its utilization through ortho-pathway was shown. New enzymes (4-methylcatechol 1,2-dioxygenase, catechol 1,2-dioxygenase, and methylmuconate cycloisomerase) were purified to homogeneity and characterized. Based on the data obtained on p-cresol degradation, formation of intermediates, and the enzymes participating in this pathway, we suggest an ortho-pathway of p-cresol degradation by R. opacus 1CP through 4-methylcatechol and 3-methyl-cis, cis-muconate.
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Affiliation(s)
- Marina P Kolomytseva
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Pushchino, Russia
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21
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Yoon YH, Yun SH, Park SH, Seol SY, Leem SH, Kim SI. Characterization of a new catechol branch of the β-ketoadipate pathway induced for benzoate degradation in Acinetobacter lwoffii K24. Biochem Biophys Res Commun 2007; 360:513-9. [PMID: 17610839 DOI: 10.1016/j.bbrc.2007.05.132] [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: 05/10/2007] [Accepted: 05/22/2007] [Indexed: 11/29/2022]
Abstract
Acinetobacter lwoffii K24 is a known aniline-degrading bacterium. In previous studies, two catechol branches of the beta-ketoadipate pathway were reported to be induced for aniline degradation, and related enzymes (CatA(1) and CatA(2)) were identified from the aniline-induced proteome of A. lwoffii K24 [S.I. Kim, S.H. Leem, J.S. Choi, Y.H. Chung, S. Kim, Y.M. Park, Y.K. Park, Y.N. Lee, K.S. Ha, Cloning and characterization of two catA genes in Acinetobacter lwoffii K24, J. Bacteriol. 179 (1997) 5226-5231; and E.A. Kim, J.Y. Kim, S.J. Kim, K.R. Park, H.J. Chung, S.H. Leem, S.I. Kim, Proteomic analysis of Acinetobacter lwoffii K24 by 2-D gel electrophoresis and electrospray ionization quadrupole-time of flight mass spectrometry, J. Microbiol. Methods 57 (2004) 337-349]. A. lwoffii K24 has also been found to utilize other aromatic compounds such as p-hydroxybenzoate, salicylate, and benzoate. In this study, we performed a comparative 2-DE/MS analysis of a benzoate-induced proteome and found that a new catechol 1,2-dioxygenase (CatA(3)) and benzoate 1,2-dioxygenase were up-regulated as the primary dioxygenases responsible for benzoate degradation in A. lwoffii K24. However, CatA(1) and CatA(2) were not detected on the same 2D gel as CatA(3). Transcription analysis of three catA genes from A. lwoffii K24 showed that these cat genes were specifically expressed under certain growth conditions using different aromatic compounds as the carbon source. While catA(1) and catA(2) were expressed under the aniline culture condition, catA(3) was expressed under the benzoate culture condition. A new cat gene cluster (catB(3)C(3)A(3)F(3)) was cloned and found to share sequence homology and a similar gene structure with the cat genes of Acinetobacter radioresistens. This result suggests that the third catechol branch (cat(3)) of the beta-ketoadipate pathway was selectively induced for the degradation of benzoate in A. lwoffii K24. It also provides evidence of multiple catechol branches in the beta-ketoadipate pathway and the independent regulation of monocyclic aromatic compound degradation in A. lwoffii K24.
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Affiliation(s)
- Young-Ho Yoon
- Department of Biology, Dong-A University, Busan 604-714, Republic of Korea
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Choi KY, Kim D, Chae JC, Zylstra GJ, Kim E. Requirement of duplicated operons for maximal metabolism of phthalate by Rhodococcus sp. strain DK17. Biochem Biophys Res Commun 2007; 357:766-71. [PMID: 17449009 DOI: 10.1016/j.bbrc.2007.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 04/02/2007] [Indexed: 11/15/2022]
Abstract
The operons encoding the transformation of phthalate to protocatechuate are duplicated and present on two different megaplasmids [pDK2 (330 kb) and pDK3 (750 kb)] in Rhodococcus sp. strain DK17. RT-PCR experiments using gene-specific primers showed that both the pDK2- and the pDK3-encoded dihydroxyphthalate decarboxylase genes are simultaneously expressed during growth on phthalate. The doubling time of the pDK2-cured mutant strain DK176 in minimal liquid medium with 5mM phthalate is 52.5% of that of the wild-type strain DK17. The data indicate that both copies of the phthalate operon are equally functional in DK17, and gene dosage is the main reason for slower growth of DK176 on phthalate.
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Affiliation(s)
- Ki Young Choi
- Department of Biology, Yonsei University, Seoul 120-749, Republic of Korea
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Cámara B, Bielecki P, Kaminski F, dos Santos VM, Plumeier I, Nikodem P, Pieper DH. A gene cluster involved in degradation of substituted salicylates via ortho cleavage in Pseudomonas sp. strain MT1 encodes enzymes specifically adapted for transformation of 4-methylcatechol and 3-methylmuconate. J Bacteriol 2006; 189:1664-74. [PMID: 17172348 PMCID: PMC1855727 DOI: 10.1128/jb.01192-06] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas sp. strain MT1 has recently been reported to degrade 4- and 5-chlorosalicylate by a pathway assumed to consist of a patchwork of reactions comprising enzymes of the 3-oxoadipate pathway. Genes encoding the initial steps in the degradation of salicylate and substituted derivatives were now localized and sequenced. One of the gene clusters characterized (sal) showed a novel gene arrangement, with salA, encoding a salicylate 1-hydroxylase, being clustered with salCD genes, encoding muconate cycloisomerase and catechol 1,2-dioxygenase, respectively, and was expressed during growth on salicylate and chlorosalicylate. A second gene cluster (cat), exhibiting the typical catRBCA arrangement of genes of the catechol branch of the 3-oxoadipate pathway in Pseudomonas strains, was expressed during growth on salicylate. Despite their high sequence similarities with isoenzymes encoded by the cat gene cluster, the catechol 1,2-dioxygenase and muconate cycloisomerase encoded by the sal cluster showed unusual kinetic properties. Enzymes were adapted for turnover of 4-chlorocatechol and 3-chloromuconate; however, 4-methylcatechol and 3-methylmuconate were identified as the preferred substrates. Investigation of the substrate spectrum identified 4- and 5-methylsalicylate as growth substrates, which were effectively converted by enzymes of the sal cluster into 4-methylmuconolactone, followed by isomerization to 3-methylmuconolactone. The function of the sal gene cluster is therefore to channel both chlorosubstituted and methylsubstituted salicylates into a catechol ortho cleavage pathway, followed by dismantling of the formed substituted muconolactones through specific pathways.
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Affiliation(s)
- Beatriz Cámara
- Division of Microbiology, HZI-Helmholtz Zentrum für Infektionsforschung, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
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24
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Liu S, Ogawa N, Senda T, Hasebe A, Miyashita K. Amino acids in positions 48, 52, and 73 differentiate the substrate specificities of the highly homologous chlorocatechol 1,2-dioxygenases CbnA and TcbC. J Bacteriol 2005; 187:5427-36. [PMID: 16030237 PMCID: PMC1196051 DOI: 10.1128/jb.187.15.5427-5436.2005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chlorocatechol 1,2-dioxygenase (CCD) is the first-step enzyme of the chlorocatechol ortho-cleavage pathway, which plays a central role in the degradation of various chloroaromatic compounds. Two CCDs, CbnA from the 3-chlorobenzoate-degrader Ralstonia eutropha NH9 and TcbC from the 1,2,4-trichlorobenzene-degrader Pseudomonas sp. strain P51, are highly homologous, having only 12 different amino acid residues out of identical lengths of 251 amino acids. But CbnA and TcbC are different in substrate specificities against dichlorocatechols, favoring 3,5-dichlorocatechol (3,5-DC) and 3,4-dichlorocatechol (3,4-DC), respectively. A study of chimeric mutants constructed from the two CCDs indicated that the N-terminal parts of the enzymes were responsible for the difference in the substrate specificities. Site-directed mutagenesis studies further identified the amino acid in position 48 (Leu in CbnA and Val in TcbC) as critical in differentiating the substrate specificities of the enzymes, which agreed well with molecular modeling of the two enzymes. Mutagenesis studies also demonstrated that Ile-73 of CbnA and Ala-52 of TcbC were important for their high levels of activity towards 3,5-DC and 3,4-DC, respectively. The importance of Ile-73 for 3,5-DC specificity determination was also shown with other CCDs such as TfdC from Burkholderia sp. NK8 and TfdC from Alcaligenes sp. CSV90 (identical to TfdC from R. eutropha JMP134), which convert 3,5-DC preferentially. Together with amino acid sequence comparisons indicating high conservation of Leu-48 and Ile-73 among CCDs, these results suggested that TcbC of strain P51 had diverged from other CCDs to be adapted to conversion of 3,4-DC.
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Affiliation(s)
- Shenghao Liu
- National Institute for Agro-Environmental Sciences, 3-1-3 Kan-nondai, Tsukuba, Ibaraki 305-8604, Japan
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Thiel M, Kaschabek SR, Gröning J, Mau M, Schlömann M. Two unusual chlorocatechol catabolic gene clusters in Sphingomonas sp. TFD44. Arch Microbiol 2004; 183:80-94. [PMID: 15688254 DOI: 10.1007/s00203-004-0748-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Revised: 10/26/2004] [Accepted: 11/03/2004] [Indexed: 11/29/2022]
Abstract
The genes responsible for the degradation of 2,4-dichlorophenoxyacetate (2,4-D) by alpha-Proteobacteria have previously been difficult to detect by using gene probes or polymerase chain reaction (PCR) primers. PCR products of the chlorocatechol 1,2-dioxygenase gene, tfdC, now allowed cloning of two chlorocatechol gene clusters from the Sphingomonas sp. strain TFD44. Sequence characterization showed that the first cluster, tfdD,RFCE, comprises all the genes necessary for the conversion of 3,5-dichlorocatechol to 3-oxoadipate, including a presumed regulatory gene, tfdR, of the LysR-type family. The second gene cluster, tfdC2E2F2, is incomplete and appears to lack a chloromuconate cycloisomerase gene and a regulatory gene. Purification and N-terminal sequencing of selected enzymes suggests that at least representatives of both gene clusters (TfdD of cluster 1 and TfdC2 of cluster 2) are induced during the growth of strain TFD44 with 2,4-D. A mutant constructed to contain an insertion in the chloromuconate cycloisomerase gene tfdD still was able to grow with 2,4-D, but more slowly and with a longer lag phase. This, and the detection of additional activity peaks during protein purification suggest that strain TFD44 harbors at least another chloromuconate cycloisomerase gene. The sequence of the tfdCE region was almost identical to that of a partially characterized chlorocatechol catabolic gene cluster of Sphingomonas herbicidovorans MH, whereas the sequence of the tfdC2E2F2 cluster was different. The similarity of the predicted proteins of the tfdD,RFCE and tfdC2E2F2 clusters to known sequences of other Proteobacteria in the database ranged from 42 to 61% identical positions for the first cluster and from 45.5 to 58% identical positions for the second cluster. Between both clusters, the similarities of their predicted proteins ranged from 44.5 to 64% identical positions. Thus, both clusters (together with those of S. herbicidovorans MH) represent deep-branching lines in the respective dendrograms, and the sequence information will help future primer design for the detection of corresponding genes in the environment.
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Affiliation(s)
- Monika Thiel
- Interdisciplinary Ecological Center, Technische Universität Bergakademie Freiberg, Leipziger Strasse 29, 09599 Freiberg, Germany
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Aguilar C, Friscina A, Devescovi G, Kojic M, Venturi V. Identification of quorum-sensing-regulated genes of Burkholderia cepacia. J Bacteriol 2003; 185:6456-62. [PMID: 14563881 PMCID: PMC219387 DOI: 10.1128/jb.185.21.6456-6462.2003] [Citation(s) in RCA: 40] [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
Quorum sensing is a regulatory mechanism (operating in response to cell density) which in gram-negative bacteria usually involves the production of N-acyl homoserine lactones (HSL). Quorum sensing in Burkholderia cepacia has been associated with the regulation of expression of extracellular proteins and siderophores and also with the regulation of swarming and biofilm formation. In the present study, several quorum-sensing-controlled gene promoters of B. cepacia ATCC 25416 were identified and characterized. A total of 28 putative gene promoters show CepR-C(8)-HSL-dependent expression, suggesting that quorum sensing in B. cepacia is a global regulatory system.
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Affiliation(s)
- Claudio Aguilar
- Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, 34012 Trieste, Italy.
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Chang HK, Mohseni P, Zylstra GJ. Characterization and regulation of the genes for a novel anthranilate 1,2-dioxygenase from Burkholderia cepacia DBO1. J Bacteriol 2003; 185:5871-81. [PMID: 13129960 PMCID: PMC193950 DOI: 10.1128/jb.185.19.5871-5881.2003] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anthranilate (2-aminobenzoate) is an important intermediate in tryptophan metabolism. In order to investigate the degradation of tryptophan through anthranilate by Burkholderia cepacia, several plasposon mutations were constructed of strain DBO1 and one mutant with the plasposon insertion in the anthranilate dioxygenase (AntDO) genes was chosen for further study. The gene sequence obtained from flanking DNA of the plasposon insertion site revealed unexpected information. B. cepacia DBO1 AntDO (designated AntDO-3C) is a three-component Rieske-type [2Fe-2S] dioxygenase composed of a reductase (AndAa), a ferredoxin (AndAb), and a two-subunit oxygenase (AndAcAd). This is in contrast to the two-component (an oxygenase and a reductase) AntDO enzyme from Acinetobacter sp. strain ADP1, P. aeruginosa PAO1, and P. putida P111. AntDO from strains ADP1, PAO1, and P111 are closely related to benzoate dioxygenase, while AntDO-3C is closely related to aromatic hydrocarbon dioxygenases from Novosphingobium aromaticivorans F199 and Sphingomonas yanoikuyae B1 and 2-chlorobenzoate dioxygenase from P. aeruginosa strains 142 and JB2. Escherichia coli cells expressing the functional AntDO-3C genes transform anthranilate and salicylate (but not 2-chlorobenzoate) to catechol. The enzyme includes a novel reductase whose absence results in less efficient transformation of anthranilate by the oxygenase and ferredoxin. AndR, a possible AraC/XylS-type transcriptional regulator, was shown to positively regulate expression of the andAcAdAbAa genes. Anthranilate was the only effector (of 12 aromatic compounds tested) that was able to induce expression of the genes.
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Affiliation(s)
- Hung-Kuang Chang
- Biotechnology Center for Agriculture and the Environment, Cook College, Rutgers University, New Brunswick, New Jersey 08901-8520, USA.
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Ogawa N, Miyashita K, Chakrabarty AM. Microbial genes and enzymes in the degradation of chlorinated compounds. CHEM REC 2003; 3:158-71. [PMID: 12900936 DOI: 10.1002/tcr.10059] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Microorganisms are well known for degrading numerous natural compounds. The synthesis of a multitude of chlorinated compounds by the chemical industry and their release into the natural environment have created major pollution problems. Part of the cause of such pollution is the inability of natural microorganisms to efficiently degrade synthetic chlorinated compounds. Microorganisms are, however, highly adaptable to changes in the environment and have consequently evolved the genes that specify the degradation of chlorinated compounds to varying degrees. Highly selective laboratory techniques have also enabled the isolation of microbial strains capable of utilizing normally recalcitrant highly chlorinated compounds as their sole source of carbon and energy. The evolution and role of microbial genes and enzymes, as well as their mode of regulation and genetic interrelationships, have therefore been the subjects of intense study. This review emphasizes the genetic organization and the regulation of gene expression, as well as evolutionary considerations, regarding the microbial degradation of chlorobenzoates, chlorocatechols, and chlorophenoxyacetic acids.
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Affiliation(s)
- Naoto Ogawa
- National Institute for Agro-Environmental Sciences, 3-1-3 Kan-nondai, Tsukuba, Ibaraki 305-8604, Japan.
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