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Malhotra H, Dhamale T, Kaur S, Kasarlawar ST, Phale PS. Metabolic engineering of Pseudomonas bharatica CSV86 T to degrade Carbaryl (1-naphthyl- N-methylcarbamate) via the salicylate-catechol route. Microbiol Spectr 2024; 12:e0028424. [PMID: 38869268 PMCID: PMC11302072 DOI: 10.1128/spectrum.00284-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/22/2024] [Indexed: 06/14/2024] Open
Abstract
Pseudomonas bharatica CSV86T displays the unique property of preferential utilization of aromatic compounds over simple carbon sources like glucose and glycerol and their co-metabolism with organic acids. Well-characterized growth conditions, aromatic compound metabolic pathways and their regulation, genome sequence, and advantageous eco-physiological traits (indole acetic acid production, alginate production, fusaric acid resistance, organic sulfur utilization, and siderophore production) make it an ideal host for metabolic engineering. Strain CSV86T was engineered for Carbaryl (1-naphthyl-N-methylcarbamate) degradation via salicylate-catechol route by expression of a Carbaryl hydrolase (CH) and a 1-naphthol 2-hydroxylase (1NH). Additionally, the engineered strain exhibited faster growth on Carbaryl upon expression of the McbT protein (encoded by the mcbT gene, a part of Carbaryl degradation upper operon of Pseudomonas sp. C5pp). Bioinformatic analyses predict McbT to be an outer membrane protein, and Carbaryl-dependent expression suggests its probable role in Carbaryl uptake. Enzyme activity and protein analyses suggested periplasmic localization of CH (carrying transmembrane domain plus signal peptide sequence at the N-terminus) and 1NH, enabling compartmentalization of the pathway. Enzyme activity, whole-cell oxygen uptake, spent media analyses, and qPCR results suggest that the engineered strain preferentially utilizes Carbaryl over glucose. The plasmid-encoded degradation property was stable for 75-90 generations even in the absence of selection pressure (kanamycin or Carbaryl). These results indicate the utility of P. bharatica CSV86T as a potential host for engineering various aromatic compound degradation pathways.IMPORTANCEThe current study describes engineering of Carbaryl metabolic pathway in Pseudomonas bharatica CSV86T. Carbaryl, a naphthalene-derived carbamate pesticide, is known to act as an endocrine disruptor, mutagen, cytotoxin, and carcinogen. Removal of xenobiotics from the environment using bioremediation faces challenges, such as slow degradation rates, instability of the degradation phenotype, and presence of simple carbon sources in the environment. The engineered CSV86-MEC2 overcomes these disadvantages as Carbaryl was degraded preferentially over glucose. Furthermore, the plasmid-borne degradation phenotype is stable, and presence of glucose and organic acids does not repress Carbaryl metabolism in the strain. The study suggests the role of outer membrane protein McbT in Carbaryl transport. This work highlights the suitability of P. bharatica CSV86T as an ideal host for engineering aromatic pollutant degradation pathways.
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Affiliation(s)
- Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Tushar Dhamale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Sukhjeet Kaur
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Sravanti T. Kasarlawar
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Prashant S. Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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Malhotra H, Saha BK, Phale PS. Development of efficient modules for recombinant protein expression and periplasmic localiszation in Pseudomonas bharatica CSV86 T. Protein Expr Purif 2023; 210:106310. [PMID: 37211150 DOI: 10.1016/j.pep.2023.106310] [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: 03/23/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/23/2023]
Abstract
Escherichia coli has been widely employed as a host for heterologous protein expression. However, due to certain limitations, alternative hosts like Pseudomonas, Lactococcus and Bacillus are being explored. Pseudomonas bharatica CSV86T, a novel soil isolate, preferentially degrades wide range of aromatics over simple carbon sources like glucose and glycerol. Strain also possesses advantageous eco-physiological traits, making it an ideal host for engineering xenobiotic degradation pathways, which necessitates the development of heterologous expression systems. Based on the efficient growth, short lag-phase and rapid metabolism of naphthalene, Pnah and Psal promoters (regulated by NahR) were selected for expression. Pnah was found to be strong and leaky as compared to Psal, using 1-naphthol 2-hydroxylase (1NH, ∼66 kDa) as reporter gene in strain CSV86T. The Carbaryl hydrolase (CH, ∼72kDa) from Pseudomonas sp. C5pp was expressed under Pnah in strain CSV86T and could successfully be translocated to the periplasm due to the presence of the Tmd + Sp sequence. The recombinant CH was purified from the periplasmic fraction and the kinetic characteristics were found to be similar to the native protein from strain C5pp. These results potentiate the suitability of P. bharatica CSV86T as a desirable host, while Pnah and the Tmd + Sp can be employed for overexpression and periplasmic localisation, respectively. Such tools find application in heterologous protein expression and metabolic engineering applications.
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Affiliation(s)
- Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, 400076, India
| | - Braja Kishor Saha
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, 400076, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, 400076, India.
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Zhou Y, Xia C, Zhang J, Shen Z, Li Z, Zhang M, Sun L, Liu D, Hong Q. Co-inducible Catabolism of 2-Naphthol Initiated by Hydroxylase CehC1C2 in Rhizobium sp. X9 Removed Its Ecotoxicity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:626-634. [PMID: 36583641 DOI: 10.1021/acs.jafc.2c06619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
2-Naphthol, which originates from various industrial activities, is widely disseminated through the discharge of industrial wastewater and is, thus, harmful to the water ecosystem, agricultural production, and human health. In this study, the carbaryl degrading strain Rhizobium sp. X9 was proven to be able to degrade 2-naphthol and reduce its toxicity to rice (Oryza sativa) and Chlorella ellipsoidea. Two-component hydroxylase CehC1C2 is responsible for the initial step of degradation and generates 1,2-dihydroxynaphthalene, which is further degraded by the ceh cluster. The transcription of gene cluster cehC1C2 could be induced when both 2-naphthol and glucose were added. A bioinformatic analysis revealed that two transcriptional regulators, the inhibitor CehR2 and the activator CehR3, could be involved in this process. Our study elucidated the molecular mechanism of microbial degradation of 2-naphthol and provided an effective strategy for the in situ remediation of 2-naphthol contamination in the environment.
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Affiliation(s)
- Yidong Zhou
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, People's Republic of China
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Chunli Xia
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, People's Republic of China
| | - Jiazhuo Zhang
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, People's Republic of China
| | - Zhenyang Shen
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, People's Republic of China
| | - Zhaojing Li
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, People's Republic of China
| | - Mingliang Zhang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Lijun Sun
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, People's Republic of China
| | - Dong Liu
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, People's Republic of China
| | - Qing Hong
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
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Malhotra H, Kaur S, Phale PS. Conserved Metabolic and Evolutionary Themes in Microbial Degradation of Carbamate Pesticides. Front Microbiol 2021; 12:648868. [PMID: 34305823 PMCID: PMC8292978 DOI: 10.3389/fmicb.2021.648868] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
Carbamate pesticides are widely used as insecticides, nematicides, acaricides, herbicides and fungicides in the agriculture, food and public health sector. However, only a minor fraction of the applied quantity reaches the target organisms. The majority of it persists in the environment, impacting the non-target biota, leading to ecological disturbance. The toxicity of these compounds to biota is mediated through cholinergic and non-cholinergic routes, thereby making their clean-up cardinal. Microbes, specifically bacteria, have adapted to the presence of these compounds by evolving degradation pathways and thus play a major role in their removal from the biosphere. Over the past few decades, various genetic, metabolic and biochemical analyses exploring carbamate degradation in bacteria have revealed certain conserved themes in metabolic pathways like the enzymatic hydrolysis of the carbamate ester or amide linkage, funnelling of aryl carbamates into respective dihydroxy aromatic intermediates, C1 metabolism and nitrogen assimilation. Further, genomic and functional analyses have provided insights on mechanisms like horizontal gene transfer and enzyme promiscuity, which drive the evolution of degradation phenotype. Compartmentalisation of metabolic pathway enzymes serves as an additional strategy that further aids in optimising the degradation efficiency. This review highlights and discusses the conclusions drawn from various analyses over the past few decades; and provides a comprehensive view of the environmental fate, toxicity, metabolic routes, related genes and enzymes as well as evolutionary mechanisms associated with the degradation of widely employed carbamate pesticides. Additionally, various strategies like application of consortia for efficient degradation, metabolic engineering and adaptive laboratory evolution, which aid in improvising remediation efficiency and overcoming the challenges associated with in situ bioremediation are discussed.
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Affiliation(s)
| | | | - Prashant S. Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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Hu K, Wang X, Zhu J, Liu A, Ao X, He L, Chen S, Zhou K, Yang Y, Zou L, Liu S. Characterization of carbaryl-degrading strain Bacillus licheniformis B-1 and its hydrolase identification. Biodegradation 2020; 31:139-152. [PMID: 32306137 DOI: 10.1007/s10532-020-09899-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/08/2020] [Indexed: 10/24/2022]
Abstract
Pesticides introduced inadvertently or deliberately into environment by anthropogenic activity have caused growing global public concern, therefore the search of approaches for elimination of such xenobiotics should be encouraged. A cypermethrin-degrading bacterial strain Bacillus licheniformis B-1 was found to efficiently degrade carbaryl in LB medium at concentrations of 50-300 mg L-1 within 48 h, during which temperature and pH played important roles as reflected by increase in pollutant depletion. A stimulatory effect of Fe3+ and Mn2+ on microbial growth was observed, whereas Cu2+ caused inhibition of degradation. Results showed that 1-naphthol was a major transformation product of carbaryl which was further metabolised. An approximately 29 kDa carbaryl-degrading enzyme was purified from B-1 with 15.93-fold purification and an overall yield of 6.02% was achieved using ammonium sulphate precipitation, DEAE-Sepharose CL-6B anion-exchange chromatography and Sephadex G-100 gel filtration. The enzyme was identified through nano reversed-phase liquid chromatography coupled with hybrid triple quadrupole time-of-flight mass spectrometry as a phosphodiesterase (PDE). This is the first report on the characterization of carbaryl-degrading by Bacillus spp. and the role of a PDE in carbaryl-detoxifying. Also, strain B-1 showed versatile in carbosulfan, isoprocarb and chlorpyrifos degradation, demonstrating as ideal candidate for environment bioremediation.
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Affiliation(s)
- Kaidi Hu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, People's Republic of China.,Departament d'Enginyeria Química, Biològica i Ambiental, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Xingjie Wang
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, People's Republic of China
| | - Jiawen Zhu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, People's Republic of China
| | - Aiping Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, People's Republic of China
| | - Xiaolin Ao
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, People's Republic of China.,Institute of Food Processing and Safety, Sichuan Agricultural University, Ya'an, Sichuan, 625014, People's Republic of China
| | - Li He
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, People's Republic of China
| | - Shujuan Chen
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, People's Republic of China
| | - Kang Zhou
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, People's Republic of China
| | - Yong Yang
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, People's Republic of China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Wenjiang, Sichuan, 611130, People's Republic of China
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, People's Republic of China. .,Institute of Food Processing and Safety, Sichuan Agricultural University, Ya'an, Sichuan, 625014, People's Republic of China.
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Fareed A, Riaz S, Nawaz I, Iqbal M, Ahmed R, Hussain J, Hussain A, Rashid A, Naqvi TA. Immobilized cells of a novel bacterium increased the degradation of N-methylated carbamates under low temperature conditions. Heliyon 2019; 5:e02740. [PMID: 31768430 PMCID: PMC6872827 DOI: 10.1016/j.heliyon.2019.e02740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/05/2019] [Accepted: 10/23/2019] [Indexed: 11/16/2022] Open
Abstract
Carbamates are synthetic pesticides, extensively used throughout the world due to their broad specificity against various insect pests. However, their enormous and inadequate use have made them a potential threat to the environment. At low temperature, degradation of carbamates becomes difficult mainly because of low biological activity. In the present study, we isolated a bacterial strain from a low temperature climate where the N-methylated carbamates are used for crop protection. The bacterium, was identified as Pseudomonas plecoglossicida strain (TA3) by 16S rRNA analysis. Degradation experiments with both free and immobilized cells in minimal salt medium indicated that the strain TA3 utilized carbaryl, carbofuran and aldicarb as both carbon and nitrogen source. TA3 can grow well at 4 °C and demonstrated the ability to degrade three carbamates (50 μgml-1) at low temperature. The immobilized cells were found more efficient than their free cells counter parts. Immobilized cells has ability to degrade 100% of carbamates at 30 °C while 80% at 4 °C but incase of their free cells counter parts the efficiency to degrade carbamates was less which was 60% at 4 °C and 80% at 30 °C. TA3 free cellsextract also depicted high activity against all the three carbamates even at 4 °C indicating a possible enzymatic mechanism of degradation.
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Affiliation(s)
- Anum Fareed
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Pakistan
| | - Sania Riaz
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Pakistan
| | - Ismat Nawaz
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Pakistan
| | - Mazhar Iqbal
- Department of Environmental Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Raza Ahmed
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Pakistan
| | - Jamshaid Hussain
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Pakistan
| | - Azhar Hussain
- Department of Agriculture and Food Technology, Karakoram International University, Gilgit-Baltistan, Pakistan
| | - Azhar Rashid
- Pakistan Atomic Energy Commission, Nuclear Institute for Food and Agriculture, Peshawar, Pakistan
| | - Tatheer Alam Naqvi
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Pakistan
- Corresponding author.
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Saroja NR, Mohan AHS, Srividya D, Supreetha K. Chaperone-assisted expression and purification of putrescine monooxygenase from Shewanella putrefaciens-95. Protein Expr Purif 2019; 157:9-16. [PMID: 30654014 DOI: 10.1016/j.pep.2019.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/09/2019] [Accepted: 01/09/2019] [Indexed: 01/22/2023]
Abstract
A putrescine monooxygenase from Shewanella putrefaciens 95 (SpPMO) is the initial enzyme catalyzing the hydroxylation of putrescine to N-hydroxyl putrescine, the precursor for the synthesis of a siderophore putrebactin was identified. This PMO clustered together with known characterized NMOs from Shewanella baltica, Bordetella pertussis, Erwinia amylovora, Streptomyces sp. Gordonia rubripertincta, Pseudomonas aeruginosa and outgrouped from Escherichia coli, Nocardia farcinica, and Rhodococcus erythropolis. The deduced SpPMO protein showed 53% and 36% sequence identity with other characterized bacterial NMOs from Erwinia amylovora and Gordonia rubripertincta respectively. In this investigation, we have cloned the complete 1518bp coding sequence of pubA from Shewanella putrefaciens 95 encoding the corresponding protein SpPMO. It comprises 505 amino acid residues in length and has approximately a molecular weight of 54 kDa. Chaperone-assisted heterologous expression of SpPMO in pET151Topo expression vector under the control of bacteriophage T7 promoter permitted a stringent IPTG dependent expression. It has been successfully cloned, overexpressed and purified as a soluble His6 -tagged enzyme using E. coli as a cloning and expression host. The expression of recombinant SpPMO was confirmed by Western blotting using anti-His6 antibody. The purified protein showed FAD and NADPH dependent N-hydroxylation activity. This study has paved a way to understand the hydroxylation step of putrebactin synthesis which can be further investigated by studying its kinetic mechanism and physiological role.
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Affiliation(s)
- Narsing Rao Saroja
- Pesticide Residue and Food Quality Analysis Laboratory, University of Agricultural Sciences, Raichur, 584104, Karnataka, India.
| | - Anil H Shyam Mohan
- Department of Biotechnology, Dayananda Sagar College of Engineering, Kumaraswamy Layout, Shavige Malleswara Hills, Bengaluru, 78, Karnataka, India
| | - D Srividya
- Pesticide Residue and Food Quality Analysis Laboratory, University of Agricultural Sciences, Raichur, 584104, Karnataka, India
| | - K Supreetha
- Department of Biotechnology, Dayananda Sagar College of Engineering, Kumaraswamy Layout, Shavige Malleswara Hills, Bengaluru, 78, Karnataka, India
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Agu CV, Ujor V, Ezeji TC. Metabolic engineering of Clostridium beijerinckii to improve glycerol metabolism and furfural tolerance. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:50. [PMID: 30899330 PMCID: PMC6408787 DOI: 10.1186/s13068-019-1388-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 02/25/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Inefficient utilization of glycerol by Clostridium beijerinckii (Cb) is a major impediment to adopting glycerol metabolism as a strategy for increasing NAD(P)H regeneration, which would in turn, alleviate the toxicity of lignocellulose-derived microbial inhibitory compounds (LDMICs, e.g., furfural), and improve the fermentation of lignocellulosic biomass hydrolysates (LBH) to butanol. To address this problem, we employed a metabolic engineering strategy to enhance glycerol utilization by Cb. RESULTS By overexpressing two glycerol dehydrogenase (Gldh) genes (dhaD1 and gldA1) from the glycerol hyper-utilizing Clostridium pasteurianum (Cp) as a fused protein in Cb, we achieved approximately 43% increase in glycerol consumption, when compared to the plasmid control. Further, Cb_dhaD1 + gldA1 achieved a 59% increase in growth, while butanol and acetone-butanol-ethanol (ABE) concentrations and productivities increased 14.0%, 17.3%, and 55.6%, respectively, relative to the control. Co-expression of dhaD1 + gldA1 and gldA1 + dihydroxyacetone kinase (dhaK) resulted in significant payoffs in cell growth and ABE production compared to expression of one Gldh. In the presence of 4-6 g/L furfural, increased glycerol consumption by the dhaD1 + gldA1 strain increased cell growth (> 50%), the rate of furfural detoxification (up to 68%), and ABE production (up to 40%), relative to the plasmid control. Likewise, over-expression of [(dhaD1 + gldA1) dhaK] improved butanol and ABE production by 70% and 50%, respectively, in the presence of 5 and 6 g/L furfural relative to the plasmid control. CONCLUSIONS Overexpression of Cp gldhs and dhaK in Cb significantly enhanced glycerol utilization, ABE production, and furfural tolerance by Cb. Future research will address the inability of recombinant Cb to metabolize glycerol as a sole substrate.
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Affiliation(s)
- Chidozie Victor Agu
- Department of Animal Sciences and Ohio State Agricultural Research and Development Center (OARDC), The Ohio State University, 305 Gerlaugh Hall, 1680 Madison Avenue, Wooster, OH 44691 USA
- INanoBio Inc., 320 Logue Ave., Suite 212, Mountain View, CA 94043 USA
| | - Victor Ujor
- Bioenergy and Biological Waste Management Program, Agricultural Technical Institute, The Ohio State University, 1328 Dover Road, Wooster, OH 44691 USA
| | - Thaddeus Chukwuemeka Ezeji
- Department of Animal Sciences and Ohio State Agricultural Research and Development Center (OARDC), The Ohio State University, 305 Gerlaugh Hall, 1680 Madison Avenue, Wooster, OH 44691 USA
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Trivedi VD, Bharadwaj A, Varunjikar MS, Singha AK, Upadhyay P, Gautam K, Phale PS. Insights into metabolism and sodium chloride adaptability of carbaryl degrading halotolerant Pseudomonas sp. strain C7. Arch Microbiol 2017; 199:907-916. [PMID: 28374062 DOI: 10.1007/s00203-017-1363-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 03/11/2017] [Accepted: 03/15/2017] [Indexed: 11/25/2022]
Abstract
Pseudomonas sp. strain C7 isolated from sediment of Thane creek near Mumbai, India, showed the ability to grow on glucose and carbaryl in the presence of 7.5 and 3.5% of NaCl, respectively. It also showed good growth in the absence of NaCl indicating the strain to be halotolerant. Increasing salt concentration impacted the growth on carbaryl; however, the specific activity of various enzymes involved in the metabolism remained unaffected. Among various enzymes, 1-naphthol 2-hydroxylase was found to be sensitive to chloride as compared to carbaryl hydrolase and gentisate 1,2-dioxygenase. The intracellular concentration of Cl- ions remained constant (6-8 mM) for cells grown on carbaryl either in the presence or absence of NaCl. Thus the ability to adapt to the increasing concentration of NaCl is probably by employing chloride efflux pump and/or increase in the concentration of osmolytes as mechanism for halotolerance. The halotolerant nature of the strain will be beneficial to remediate carbaryl from saline agriculture fields, ecosystems and wastewaters.
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Affiliation(s)
- Vikas D Trivedi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Anahita Bharadwaj
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Madhushri S Varunjikar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Arminder K Singha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Priya Upadhyay
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Kamini Gautam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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Trivedi VD, Jangir PK, Sharma R, Phale PS. Insights into functional and evolutionary analysis of carbaryl metabolic pathway from Pseudomonas sp. strain C5pp. Sci Rep 2016; 6:38430. [PMID: 27924916 PMCID: PMC5141477 DOI: 10.1038/srep38430] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/09/2016] [Indexed: 11/25/2022] Open
Abstract
Carbaryl (1-naphthyl N-methylcarbamate) is a most widely used carbamate pesticide in the agriculture field. Soil isolate, Pseudomonas sp. strain C5pp mineralizes carbaryl via 1-naphthol, salicylate and gentisate, however the genetic organization and evolutionary events of acquisition and assembly of pathway have not yet been studied. The draft genome analysis of strain C5pp reveals that the carbaryl catabolic genes are organized into three putative operons, ‘upper’, ‘middle’ and ‘lower’. The sequence and functional analysis led to identification of new genes encoding: i) hitherto unidentified 1-naphthol 2-hydroxylase, sharing a common ancestry with 2,4-dichlorophenol monooxygenase; ii) carbaryl hydrolase, a member of a new family of esterase; and iii) 1,2-dihydroxy naphthalene dioxygenase, uncharacterized type-II extradiol dioxygenase. The ‘upper’ pathway genes were present as a part of a integron while the ‘middle’ and ‘lower’ pathway genes were present as two distinct class-I composite transposons. These findings suggest the role of horizontal gene transfer event(s) in the acquisition and evolution of the carbaryl degradation pathway in strain C5pp. The study presents an example of assembly of degradation pathway for carbaryl.
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Affiliation(s)
- Vikas D Trivedi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pramod Kumar Jangir
- Microbial Biotechnology and Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Rakesh Sharma
- Microbial Biotechnology and Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Draft Genome Sequence of Carbaryl-Degrading Soil Isolate Pseudomonas sp. Strain C5pp. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00526-16. [PMID: 27284139 PMCID: PMC4901230 DOI: 10.1128/genomea.00526-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the draft genome sequence of carbaryl-degrading Pseudomonas sp. strain C5pp. Genes encoding salicylate and gentisate metabolism, large amounts of oxygenase, nitrogen metabolism, and heavy metal tolerance were identified. The sequence will provide further insight into the biochemical and evolutionary aspects of carbaryl degradation.
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Trivedi VD, Majhi P, Phale PS. Kinetic and spectroscopic characterization of 1-naphthol 2-hydroxylase from Pseudomonas sp. strain C5. Appl Biochem Biotechnol 2014; 172:3964-77. [PMID: 24599669 DOI: 10.1007/s12010-014-0815-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 02/17/2014] [Indexed: 11/27/2022]
Abstract
1-Naphthol 2-hydroxylase (1-NH) catalyzes the conversion of 1-naphthol to 1,2-dihydroxynaphthalene. 1-NH from carbaryl degrading Pseudomonas strain C5 was purified and characterized for its kinetic and spectroscopic properties. The enzyme was found to be NAD(P)H-dependent external flavin monooxygenase. Though the kinetic parameters of 1-NH from strain C5 appear to be similar to 1-NH enzyme from strains C4 and C6, however, they differ in their N-terminal sequences, mole content of flavin adenine dinucleotide (FAD), reconstitution of apoenzyme, and K i. 1-NH showed narrow substrate specificity with comparable hydroxylation efficiency on 1-naphthol and 5-amino 1-naphthol (~30 %) followed by 4-chloro 1-naphthol (~9 %). Salicylate was found to be the nonsubstrate effector. The flavin fluorescence of 1-NH was found to increase in the presence of 1-naphthol (K d = 11.3 μM) and salicylate (K d = 1027 μM). The circular dichroism (CD) spectra showed significant perturbations in the presence of NAD(P)H, whereas no changes were observed in the presence of 1-naphthol. Naphthalene, 1-chloronaphthalene, 2-napthol, and 2-naphthoic acid were found to be the mixed inhibitors. Chemical modification studies showed the probable involvement of His, Cys, and Tyr in the binding of 1-naphthol, whereas Trp was found to be involved in the binding of NAD(P)H.
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Affiliation(s)
- Vikas D Trivedi
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, 400 076, India
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Singh R, Trivedi VD, Phale PS. Metabolic regulation and chromosomal localization of carbaryl degradation pathway in Pseudomonas sp. strains C4, C5 and C6. Arch Microbiol 2013; 195:521-35. [PMID: 23728496 DOI: 10.1007/s00203-013-0903-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 05/06/2013] [Accepted: 05/15/2013] [Indexed: 11/24/2022]
Abstract
Pseudomonas sp. strains C4, C5 and C6 degrade carbaryl (1-naphthyl N-methylcarbamate) via 1-naphthol, 1,2-dihydroxynaphthalene, salicylate and gentisate. Carbon source-dependent metabolic studies suggest that enzymes responsible for carbaryl degradation are probably organized into 'upper' (carbaryl to salicylate), 'middle' (salicylate to gentisate) and 'lower' (gentisate to TCA cycle) pathway. Carbaryl and 1-naphthol were found to induce all carbaryl pathway enzymes, while salicylate and gentisate induce middle and lower pathway enzymes. The strains were found to harbor plasmid(s), and carbaryl degradation property was found to be stable. Genes encoding enzymes of the degradative pathway such as 1-naphthol 2-hydroxylase, salicylaldehyde dehydrogenase, salicylate 5-hydroxylase and gentisate 1,2-dioxygenase were amplified from chromosomal DNA of these strains. The gene-specific PCR products were sequenced from strain C6, and phylogenetic tree was constructed. Southern hybridization and PCR analysis using gel eluted DNA as template supported the presence of pathway genes onto the chromosome and not on the plasmid(s).
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Affiliation(s)
- Randhir Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, 400 076 Mumbai, India
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The cucurbitacins E, D and I: Investigation of their cytotoxicity toward human chondrosarcoma SW 1353 cell line and their biotransformation in man liver. Toxicol Lett 2013. [DOI: 10.1016/j.toxlet.2012.11.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Feng TC, Cui CZ, Dong F, Feng YY, Liu YD, Yang XM. Phenanthrene biodegradation by halophilic Martelella sp. AD-3. J Appl Microbiol 2012; 113:779-89. [PMID: 22762374 DOI: 10.1111/j.1365-2672.2012.05386.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 06/10/2012] [Accepted: 06/27/2012] [Indexed: 11/30/2022]
Abstract
AIMS To investigate the phenanthrene-degrading abilities of the halophilic Martelella species AD-3 under different conditions and to propose a possible metabolic pathway. METHODS AND RESULTS Using HPLC and GC-MS analyses, the phenanthrene-degrading properties of the halophilic strain AD-3 and its metabolites were analysed. This isolate efficiently degraded phenanthrene under multiple conditions characterized by different concentrations of phenanthrene (100-400 mg l(-1) ), a broad range of salinities (0·1-15%) and varying pHs (6·0-10·0). Phenanthrene (200 mg l(-1) ) was completely depleted under 3% salinity and a pH of 9·0 within 6 days. The potential toxicity of phenanthrene and its generated metabolites towards the bacterium Vibrio fischeri was significantly reduced 10 days after the bioassay. On the basis of the identified metabolites, enzyme activities and the utilization of probable intermediates, phenanthrene degradation by strain AD-3 was proposed in two distinct routes. In route I, metabolism of phenanthrene was initiated by the dioxygenation at C-3,4 via 1-hydroxy-2-naphthoic acid, 1-naphthol, salicylic acid and gentisic acid. In route II, phenanthrene was metabolized to 9-phenanthrol and 9,10-phenanthrenequinone. Further study indicated that strain AD-3 exhibited a wide spectrum of substrate utilization including other polycyclic aromatic hydrocarbons (PAHs). CONCLUSIONS The results suggest that strain AD-3 possesses a high phenanthrene biodegradability and that the degradation occurs via two routes that remarkably reduce toxicity. SIGNIFICANCE AND IMPACT OF THE STUDY To the best of our knowledge, this work presents the first report of phenanthrene degradation by a halophilic PAH-degrading strain via two routes. In the future, the use of halophilic strain AD-3 provides a potential application for efficient PAH-contaminated hypersaline field remediation.
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Affiliation(s)
- T-C Feng
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
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1-Naphthol 2-hydroxylase from Pseudomonas sp. strain C6: purification, characterization and chemical modification studies. Biodegradation 2010; 22:517-26. [DOI: 10.1007/s10532-010-9424-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 09/29/2010] [Indexed: 10/19/2022]
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Deveryshetty J, Phale PS. Biodegradation of phenanthrene by Alcaligenes sp. strain PPH: partial purification and characterization of 1-hydroxy-2-naphthoic acid hydroxylase. FEMS Microbiol Lett 2010; 311:93-101. [PMID: 20727010 DOI: 10.1111/j.1574-6968.2010.02079.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Alcaligenes sp. strain PPH degrades phenanthrene via 1-hydroxy-2-naphthoic acid (1-H2NA), 1,2-dihydroxynaphthalene (1,2-DHN), salicylic acid and catechol. Enzyme activity versus growth profile and heat stability studies suggested the presence of two distinct hydroxylases, namely 1-hydroxy-2-naphthoic acid hydroxylase and salicylate hydroxylase. 1-Hydroxy-2-naphthoic acid hydroxylase was partially purified (yield 48%, fold 81) and found to be a homodimer with a subunit molecular weight of ∼34 kDa. The enzyme was yellow in color, showed UV-visible absorption maxima at 274, 375 and 445 nm, and fluorescence emission maxima at 527 nm suggested it to be a flavoprotein. The apoenzyme prepared by the acid-ammonium sulfate (2 M) dialysis method was colorless, inactive and lost the characteristic flavin absorption spectra but regained ∼90% activity when reconstituted with FAD. Extraction of the prosthetic group and its analysis by HPLC suggests that the holoenzyme contained FAD. The enzyme was specific for 1-H2NA and failed to show activity with any other hydroxynaphthoic acid analogs or salicylic acid. The K(m) for 1-H2NA in the presence of either NADPH or NADH remained unaltered (72 and 75 μM, respectively), suggesting dual specificity for the coenzyme. The K(m) for FAD was determined to be 4.7 μM. The enzyme catalyzed the conversion of 1-H2NA to 1,2-DHN only under aerobic conditions. These results suggested that 1-hydroxy-2-naphthoic acid hydroxylase is a flavoprotein monooxygenase specific for 1-H2NA and different from salicylate-1-hydroxylase.
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Affiliation(s)
- Jaigeeth Deveryshetty
- Department of Biosciences and Bioengineering, Indian Institute Technology Bombay, Mumbai, Maharashtra, India
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Ruiz-Arias A, Juárez-Ramírez C, de los Cobos-Vasconcelos D, Ruiz-Ordaz N, Salmerón-Alcocer A, Ahuatzi-Chacón D, Galíndez-Mayer J. Aerobic Biodegradation of a Sulfonated Phenylazonaphthol Dye by a Bacterial Community Immobilized in a Multistage Packed-Bed BAC Reactor. Appl Biochem Biotechnol 2010; 162:1689-707. [DOI: 10.1007/s12010-010-8950-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Accepted: 03/15/2010] [Indexed: 11/27/2022]
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Liu X, Dong Y, Li X, Ren Y, Li Y, Wang W, Wang L, Feng L. Characterization of the anthranilate degradation pathway in Geobacillus thermodenitrificans NG80-2. MICROBIOLOGY-SGM 2009; 156:589-595. [PMID: 19942660 DOI: 10.1099/mic.0.031880-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Anthranilate is an important intermediate of tryptophan metabolism. In this study, a hydroxylase system consisting of an FADH(2)-utilizing monooxygenase (GTNG_3160) and an FAD reductase (GTNG_3158), as well as a bifunctional riboflavin kinase/FMN adenylyltransferase (GTNG_3159), encoded in the anthranilate degradation gene cluster in Geobacillus thermodenitrificans NG80-2 were functionally characterized in vitro. GTNG_3159 produces FAD to be reduced by GTNG_3158 and the reduced FAD (FADH(2)) is utilized by GTNG_3160 to convert anthranilate to 3-hydroxyanthranilate (3-HAA), which is further degraded to acetyl-CoA through a meta-cleavage pathway also encoded in the gene cluster. Utilization of this pathway for the degradation of anthranilate and tryptophan by NG80-2 under physiological conditions was confirmed by real-time RT-PCR analysis of representative genes. This is believed to be the first time that the degradation pathway of anthranilate via 3-HAA has been characterized in a bacterium. This pathway is likely to play an important role in the survival of G. thermodenitrificans in the oil reservoir conditions from which strain NG80-2 was isolated.
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Affiliation(s)
- Xueqian Liu
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China.,TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China.,Tianjin Research Center for Functional Genomics and Biochip, Tianjin 300457, PR China
| | - Yangpeng Dong
- Tianjin Research Center for Functional Genomics and Biochip, Tianjin 300457, PR China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China.,TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Xiaomin Li
- Tianjin Research Center for Functional Genomics and Biochip, Tianjin 300457, PR China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China.,TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Yi Ren
- Tianjin Research Center for Functional Genomics and Biochip, Tianjin 300457, PR China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China.,TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Yanxia Li
- Tianjin Research Center for Functional Genomics and Biochip, Tianjin 300457, PR China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China.,TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Wei Wang
- Tianjin Research Center for Functional Genomics and Biochip, Tianjin 300457, PR China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, PR China.,The Engineering and Research Center for Microbial Functional Genomics and Detection Technology, Ministry of Education, PR China.,TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China
| | - Lei Wang
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China.,Tianjin Research Center for Functional Genomics and Biochip, Tianjin 300457, PR China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, PR China.,TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China.,The Engineering and Research Center for Microbial Functional Genomics and Detection Technology, Ministry of Education, PR China
| | - Lu Feng
- The Engineering and Research Center for Microbial Functional Genomics and Detection Technology, Ministry of Education, PR China.,Tianjin Research Center for Functional Genomics and Biochip, Tianjin 300457, PR China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China.,TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, PR China
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Phale PS, Basu A, Majhi PD, Deveryshetty J, Vamsee-Krishna C, Shrivastava R. Metabolic Diversity in Bacterial Degradation of Aromatic Compounds. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2007; 11:252-79. [PMID: 17883338 DOI: 10.1089/omi.2007.0004] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Aromatic compounds pose a major threat to the environment, being mutagenic, carcinogenic, and recalcitrant. Microbes, however, have evolved the ability to utilize these highly reduced and recalcitrant compounds as a potential source of carbon and energy. Aerobic degradation of aromatics is initiated by oxidizing the aromatic ring, making them more susceptible to cleavage by ring-cleaving dioxygenases. A preponderance of aromatic degradation genes on plasmids, transposons, and integrative genetic elements (and their shuffling through horizontal gene transfer) have lead to the evolution of novel aromatic degradative pathways. This enables the microorganisms to utilize a multitude of aromatics via common routes of degradation leading to metabolic diversity. In this review, we emphasize the exquisiteness and relevance of bacterial degradation of aromatics, interlinked degradative pathways, genetic and metabolic regulation, carbon source preference, and biosurfactant production. We have also explored the avenue of metagenomics, which opens doors to a plethora of uncultured and uncharted microbial genetics and metabolism that can be used effectively for bioremediation.
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Affiliation(s)
- Prashant S Phale
- Biotechnology Group, School of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, India.
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