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Zhu Y, Elcin E, Jiang M, Li B, Wang H, Zhang X, Wang Z. Use of whole-cell bioreporters to assess bioavailability of contaminants in aquatic systems. Front Chem 2022; 10:1018124. [PMID: 36247665 PMCID: PMC9561917 DOI: 10.3389/fchem.2022.1018124] [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: 08/12/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
Water contamination has become increasingly a critical global environmental issue that threatens human and ecosystems’ health. Monitoring and risk assessment of toxic pollutants in water bodies is essential to identifying water pollution treatment needs. Compared with the traditional monitoring approaches, environmental biosensing via whole-cell bioreporters (WCBs) has exhibited excellent capabilities for detecting bioavailability of multiple pollutants by providing a fast, simple, versatile and economical way for environmental risk assessment. The performance of WCBs is determined by its elements of construction, such as host strain, regulatory and reporter genes, as well as experimental conditions. Previously, numerous studies have focused on the design and construction of WCB rather than improving the detection process and commercialization of this technology. For investigators working in the environmental field, WCB can be used to detect pollutants is more important than how they are constructed. This work provides a review of the development of WCBs and a brief introduction to genetic construction strategies and aims to summarize key studies on the application of WCB technology in detection of water contaminants, including organic pollutants and heavy metals. In addition, the current status of commercialization of WCBs is highlighted.
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Affiliation(s)
- Yi Zhu
- School of Environmental and Civil Engineering, Institute of Environmental Processes and Pollution Control, Jiangnan University, Wuxi, China
| | - Evrim Elcin
- Department of Agricultural Biotechnology, Division of Enzyme and Microbial Biotechnology, Faculty of Agriculture, Aydın Adnan Menderes University, Aydın, Turkey
| | - Mengyuan Jiang
- School of Environmental and Civil Engineering, Institute of Environmental Processes and Pollution Control, Jiangnan University, Wuxi, China
| | - Boling Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Hailong Wang
- Biochar Engineering Technology Research Center of Guangdong Province, School of Environmental and Chemical Engineering, Foshan University, Foshan, China
| | - Xiaokai Zhang
- School of Environmental and Civil Engineering, Institute of Environmental Processes and Pollution Control, Jiangnan University, Wuxi, China
- *Correspondence: Xiaokai Zhang,
| | - Zhenyu Wang
- School of Environmental and Civil Engineering, Institute of Environmental Processes and Pollution Control, Jiangnan University, Wuxi, China
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Antonucci I, Gallo G, Limauro D, Contursi P, Ribeiro AL, Blesa A, Berenguer J, Bartolucci S, Fiorentino G. Characterization of a promiscuous cadmium and arsenic resistance mechanism in Thermus thermophilus HB27 and potential application of a novel bioreporter system. Microb Cell Fact 2018; 17:78. [PMID: 29776370 PMCID: PMC5960188 DOI: 10.1186/s12934-018-0918-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/03/2018] [Indexed: 11/21/2022] Open
Abstract
Background The characterization of the molecular determinants of metal resistance has potential biotechnological application in biosensing and bioremediation. In this context, the bacterium Thermus thermophilus HB27 is a metal tolerant thermophile containing a set of genes involved in arsenic resistance which, differently from other microbes, are not organized into a single operon. They encode the proteins: arsenate reductase, TtArsC, arsenic efflux membrane transporter, TtArsX, and transcriptional repressor, TtSmtB. Results In this work we show that the arsenic efflux protein TtArsX and the arsenic responsive transcriptional repressor TtSmtB are required to provide resistance to cadmium. We analyzed the sensitivity to Cd(II) of mutants lacking TtArsX, finding that they are more sensitive to this metal than the wild type strain. In addition, using promoter probe reporter plasmids, we show that the transcription of TtarsX is also stimulated by the presence of Cd(II) in a TtSmtB-dependent way. Actually, a regulatory circuit composed of TtSmtB and a reporter gene expressed from the TtarsX promoter responds to variation in Cd(II), As(III) and As(V) concentrations. Conclusions Our results demonstrate that the system composed by TtSmtB and TtArsX is responsible for both the arsenic and cadmium resistance in T. thermophilus. The data also support the use of T. thermophilus as a suitable chassis for the design and development of As-Cd biosensors. Electronic supplementary material The online version of this article (10.1186/s12934-018-0918-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Immacolata Antonucci
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy
| | - Giovanni Gallo
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy
| | - Danila Limauro
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy
| | - Patrizia Contursi
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy
| | - Ana Luisa Ribeiro
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Alba Blesa
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Simonetta Bartolucci
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy
| | - Gabriella Fiorentino
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy.
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Biodegradation of phenol and its derivatives by engineered bacteria: current knowledge and perspectives. World J Microbiol Biotechnol 2017; 33:174. [DOI: 10.1007/s11274-017-2339-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/01/2017] [Indexed: 11/26/2022]
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Novel Three-Component Phenazine-1-Carboxylic Acid 1,2-Dioxygenase in Sphingomonas wittichii DP58. Appl Environ Microbiol 2017; 83:AEM.00133-17. [PMID: 28188209 DOI: 10.1128/aem.00133-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/06/2017] [Indexed: 11/20/2022] Open
Abstract
Phenazine-1-carboxylic acid, the main component of shenqinmycin, is widely used in southern China for the prevention of rice sheath blight. However, the fate of phenazine-1-carboxylic acid in soil remains uncertain. Sphingomonas wittichii DP58 can use phenazine-1-carboxylic acid as its sole carbon and nitrogen sources for growth. In this study, dioxygenase-encoding genes, pcaA1A2, were found using transcriptome analysis to be highly upregulated upon phenazine-1-carboxylic acid biodegradation. PcaA1 shares 68% amino acid sequence identity with the large oxygenase subunit of anthranilate 1,2-dioxygenase from Rhodococcus maanshanensis DSM 44675. The dioxygenase was coexpressed in Escherichia coli with its adjacent reductase-encoding gene, pcaA3, and ferredoxin-encoding gene, pcaA4, and showed phenazine-1-carboxylic acid consumption. The dioxygenase-, ferredoxin-, and reductase-encoding genes were expressed in Pseudomonas putida KT2440 or E. coli BL21, and the three recombinant proteins were purified. A phenazine-1-carboxylic acid conversion capability occurred in vitro only when all three components were present. However, P. putida KT2440 transformed with pcaA1A2 obtained phenazine-1-carboxylic acid degradation ability, suggesting that phenazine-1-carboxylic acid 1,2-dioxygenase has low specificities for its ferredoxin and reductase. This was verified by replacing PcaA3 with RedA2 in the in vitro enzyme assay. High-performance liquid chromatography-mass spectrometry (HPLC-MS) and nuclear magnetic resonance (NMR) analysis showed that phenazine-1-carboxylic acid was converted to 1,2-dihydroxyphenazine through decarboxylation and hydroxylation, indicating that PcaA1A2A3A4 constitutes the initial phenazine-1-carboxylic acid 1,2-dioxygenase. This study fills a gap in our understanding of the biodegradation of phenazine-1-carboxylic acid and illustrates a new dioxygenase for decarboxylation.IMPORTANCE Phenazine-1-carboxylic acid is widely used in southern China as a key fungicide to prevent rice sheath blight. However, the degradation characteristics of phenazine-1-carboxylic acid and the environmental consequences of the long-term application are not clear. S. wittichii DP58 can use phenazine-1-carboxylic acid as its sole carbon and nitrogen sources. In this study, a three-component dioxygenase, PcaA1A2A3A4, was determined to be the initial dioxygenase for phenazine-1-carboxylic acid degradation in S. wittichii DP58. Phenazine-1-carboxylic acid was converted to 1,2-dihydroxyphenazine through decarboxylation and hydroxylation. This finding may help us discover the pathway for phenazine-1-carboxylic acid degradation.
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Prévéral S, Brutesco C, Descamps ECT, Escoffier C, Pignol D, Ginet N, Garcia D. A bioluminescent arsenite biosensor designed for inline water analyzer. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:25-32. [PMID: 26769474 DOI: 10.1007/s11356-015-6000-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 12/22/2015] [Indexed: 06/05/2023]
Abstract
Whole-cell biosensors based on the reporter gene system can offer rapid detection of trace levels of organic or metallic compounds in water. They are well characterized in laboratory conditions, but their transfer into technological devices for the surveillance of water networks remains at a conceptual level. The development of a semi-autonomous inline water analyzer stumbles across the conservation of the bacterial biosensors over a period of time compatible with the autonomy requested by the end-user while maintaining a satisfactory sensitivity, specificity, and time response. We focused here on assessing the effect of lyophilization on two biosensors based on the reporter gene system and hosted in Escherichia coli. The reporter gene used here is the entire bacterial luciferase lux operon (luxCDABE) for an autonomous bioluminescence emission without the need to add any substrate. In the cell-survival biosensor that is used to determine the overall fitness of the bacteria when mixed with the water sample, lux expression is driven by a constitutive E. coli promoter PrpoD. In the arsenite biosensor, the arsenite-inducible promoter P ars involved in arsenite resistance in E. coli controls lux expression. Evaluation of the shelf life of these lyophilized biosensors kept at 4 °C over a year evidenced that about 40 % of the lyophilized cells can be revived in such storage conditions. The performances of the lyophilized biosensor after 7 months in storage are maintained, with a detection limit of 0.2 μM arsenite for a response in about an hour with good reproducibility. These results pave the way to the use in tandem of both biosensors (one for general toxicity and one for arsenite contamination) as consumables of an autonomous analyzer in the field.
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Affiliation(s)
- Sandra Prévéral
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, F-13108, France
- CNRS, UMR 7265 Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France
- Aix-Marseille Université, BVME UMR7265, Marseille, F-13284, France
| | - Catherine Brutesco
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, F-13108, France
- CNRS, UMR 7265 Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France
- Aix-Marseille Université, BVME UMR7265, Marseille, F-13284, France
| | - Elodie C T Descamps
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, F-13108, France
- CNRS, UMR 7265 Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France
- Aix-Marseille Université, BVME UMR7265, Marseille, F-13284, France
| | - Camille Escoffier
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, F-13108, France
- CNRS, UMR 7265 Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France
- Aix-Marseille Université, BVME UMR7265, Marseille, F-13284, France
| | - David Pignol
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, F-13108, France
- CNRS, UMR 7265 Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France
- Aix-Marseille Université, BVME UMR7265, Marseille, F-13284, France
| | - Nicolas Ginet
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, F-13108, France.
- CNRS, UMR 7265 Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France.
- Aix-Marseille Université, BVME UMR7265, Marseille, F-13284, France.
| | - Daniel Garcia
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, F-13108, France
- CNRS, UMR 7265 Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France
- Aix-Marseille Université, BVME UMR7265, Marseille, F-13284, France
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Brutesco C, Prévéral S, Escoffier C, Descamps ECT, Prudent E, Cayron J, Dumas L, Ricquebourg M, Adryanczyk-Perrier G, de Groot A, Garcia D, Rodrigue A, Pignol D, Ginet N. Bacterial host and reporter gene optimization for genetically encoded whole cell biosensors. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:52-65. [PMID: 27234828 DOI: 10.1007/s11356-016-6952-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/20/2016] [Indexed: 06/05/2023]
Abstract
Whole-cell biosensors based on reporter genes allow detection of toxic metals in water with high selectivity and sensitivity under laboratory conditions; nevertheless, their transfer to a commercial inline water analyzer requires specific adaptation and optimization to field conditions as well as economical considerations. We focused here on both the influence of the bacterial host and the choice of the reporter gene by following the responses of global toxicity biosensors based on constitutive bacterial promoters as well as arsenite biosensors based on the arsenite-inducible Pars promoter. We observed important variations of the bioluminescence emission levels in five different Escherichia coli strains harboring two different lux-based biosensors, suggesting that the best host strain has to be empirically selected for each new biosensor under construction. We also investigated the bioluminescence reporter gene system transferred into Deinococcus deserti, an environmental, desiccation- and radiation-tolerant bacterium that would reduce the manufacturing costs of bacterial biosensors for commercial water analyzers and open the field of biodetection in radioactive environments. We thus successfully obtained a cell survival biosensor and a metal biosensor able to detect a concentration as low as 100 nM of arsenite in D. deserti. We demonstrated that the arsenite biosensor resisted desiccation and remained functional after 7 days stored in air-dried D. deserti cells. We also report here the use of a new near-infrared (NIR) fluorescent reporter candidate, a bacteriophytochrome from the magnetotactic bacterium Magnetospirillum magneticum AMB-1, which showed a NIR fluorescent signal that remained optimal despite increasing sample turbidity, while in similar conditions, a drastic loss of the lux-based biosensors signal was observed.
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Affiliation(s)
- Catherine Brutesco
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Sandra Prévéral
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Camille Escoffier
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Elodie C T Descamps
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Elsa Prudent
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, Villeurbanne, 69622, France
| | - Julien Cayron
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, Villeurbanne, 69622, France
| | - Louis Dumas
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Manon Ricquebourg
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Géraldine Adryanczyk-Perrier
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Arjan de Groot
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Daniel Garcia
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Agnès Rodrigue
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, Villeurbanne, 69622, France
| | - David Pignol
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Nicolas Ginet
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France.
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France.
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France.
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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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Jung J, Park W. Acinetobacter species as model microorganisms in environmental microbiology: current state and perspectives. Appl Microbiol Biotechnol 2015; 99:2533-48. [PMID: 25693672 DOI: 10.1007/s00253-015-6439-y] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 01/11/2023]
Abstract
Acinetobacter occupies an important position in nature because of its ubiquitous presence in diverse environments such as soils, fresh water, oceans, sediments, and contaminated sites. Versatile metabolic characteristics allow species of this genus to catabolize a wide range of natural compounds, implying active participation in the nutrient cycle in the ecosystem. On the other hand, multi-drug-resistant Acinetobacter baumannii causing nosocomial infections with high mortality has been raising serious concerns in medicine. Due to the ecological and clinical importance of the genus, Acinetobacter was proposed as a model microorganism for environmental microbiological studies, pathogenicity tests, and industrial production of chemicals. For these reasons, Acinetobacter has attracted significant attention in scientific and biotechnological fields, but only limited research areas such as natural transformation and aromatic compound degradation have been intensively investigated, while important physiological characteristics including quorum sensing, motility, and stress response have been neglected. The aim of this review is to summarize the recent achievements in Acinetobacter research with a special focus on strain DR1 and to compare the similarities and differences between species or other genera. Research areas that require more attention in future research are also suggested.
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Affiliation(s)
- Jaejoon Jung
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 136-713, Republic of Korea
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Molecular manipulations for enhancing luminescent bioreporters performance in the detection of toxic chemicals. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 145:137-49. [PMID: 25216954 DOI: 10.1007/978-3-662-43619-6_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Microbial whole-cell bioreporters are genetically modified microorganisms that produce a quantifiable output in response to the presence of toxic chemicals or other stress factors. These bioreporters harbor a genetic fusion between a sensing element (usually a gene regulatory element responsive to the target) and a reporter element, the product of which may be quantitatively monitored either by its presence or by its activity. In this chapter we review genetic manipulations undertaken in order to improve bioluminescent bioreporter performance by increasing luminescent output, lowering the limit of detection, and shortening the response time. We describe molecular manipulations applied to all aspects of whole-cell bioreporters: the host strain, the expression system, the sensing element, and the reporter element. The molecular construction of whole-cell luminescent bioreporters, harboring fusions of gene promoter elements to reporter genes, has been around for over three decades; in most cases, these two genetic elements are combined "as is." This chapter outlines diverse molecular manipulations for enhancing the performance of such sensors.
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Xu T, Close DM, Sayler GS, Ripp S. Genetically modified whole-cell bioreporters for environmental assessment. ECOLOGICAL INDICATORS 2013; 28:125-141. [PMID: 26594130 PMCID: PMC4649933 DOI: 10.1016/j.ecolind.2012.01.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Living whole-cell bioreporters serve as environmental biosentinels that survey their ecosystems for harmful pollutants and chemical toxicants, and in the process act as human and other higher animal proxies to pre-alert for unfavorable, damaging, or toxic conditions. Endowed with bioluminescent, fluorescent, or colorimetric signaling elements, bioreporters can provide a fast, easily measured link to chemical contaminant presence, bioavailability, and toxicity relative to a living system. Though well tested in the confines of the laboratory, real-world applications of bioreporters are limited. In this review, we will consider bioreporter technologies that have evolved from the laboratory towards true environmental applications, and discuss their merits as well as crucial advancements that still require adoption for more widespread utilization. Although the vast majority of environmental monitoring strategies rely upon bioreporters constructed from bacteria, we will also examine environmental biosensing through the use of less conventional eukaryotic-based bioreporters, whose chemical signaling capacity facilitates a more human-relevant link to toxicity and health-related consequences.
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Affiliation(s)
- Tingting Xu
- The University of Tennessee Center for Environmental Biotechnology, 676 Dabney Hall, Knoxville, TN 37996, USA
| | - Dan M. Close
- The Joint Institute for Biological Sciences, Oak Ridge National Laboratory, PO Box 2008, MS6342 Oak Ridge, TN 37831, USA
| | - Gary S. Sayler
- The University of Tennessee Center for Environmental Biotechnology, 676 Dabney Hall, Knoxville, TN 37996, USA
- The Joint Institute for Biological Sciences, Oak Ridge National Laboratory, PO Box 2008, MS6342 Oak Ridge, TN 37831, USA
| | - Steven Ripp
- The University of Tennessee Center for Environmental Biotechnology, 676 Dabney Hall, Knoxville, TN 37996, USA
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Gupta S, Saxena M, Saini N, Mahmooduzzafar, Kumar R, Kumar A. An effective strategy for a whole-cell biosensor based on putative effector interaction site of the regulatory DmpR protein. PLoS One 2012; 7:e43527. [PMID: 22937060 PMCID: PMC3427379 DOI: 10.1371/journal.pone.0043527] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 07/23/2012] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION AND RATIONALE The detection of bioavailable phenol is a very important issue in environmental and human hazard assessment. Despite modest developments recently, there is a stern need for development of novel biosensors with high sensitivity for priority phenol pollutants. DmpR (Dimethyl phenol regulatory protein), an NtrC-like regulatory protein for the phenol degradation of Pseudomonas sp. strain CF600, represents an attractive biosensor regimen. Thus, we sought to design a novel biosensor by modifying the phenol detection capacity of DmpR by using mutagenic PCR. METHODS Binding sites of 'A' domain of DmpR were predicted by LIGSITE, and molecular docking was performed by using GOLD to identify the regions where phenol may interact with DmpR. Total five point mutations, one single at position 42 (Phe-to-Leu), two double at 140 (Asp-to-Glu) and 143 (Gln-to-Leu), and two double at L113M (Leu-to- Met) and D116A (Asp-to- Ala) were created in DmpR by site-directed mutagenesis to construct the reporter plasmids pRLuc42R, pRLuc140p143R, and pRLuc113p116R, respectively. Luciferase assays were performed to measure the activity of luc gene in the presence of phenol and its derivatives, while RT-PCR was used to check the expression of luc gene in the presence of phenol. RESULTS Only pRLuc42R and pRLuc113p116R showed positive responses to phenolic effectors. The lowest detectable concentration of phenol was 0.5 µM (0.047 mg/L), 0.1 µM for 2, 4-dimethylphenol and 2-nitrophenol, 10 µM for 2, 4, 6-trichlorophenol and 2-chlorophenol, 100 µM for 2, 4-dichlorophenol, 0.01 µM for 4-nitrophenol, and 1 µM for o-cresol. These concentrations were measured by modified luciferase assay within 3 hrs compared to 6-7 hrs in previous studies. Importantly, increased expression of luciferase gene of pRLuc42R was observed by RT-PCR. CONCLUSIONS The present study offers an effective strategy to design a quick and sensitive biosensor for phenol by constructing recombinant bacteria having DmpR gene.
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Affiliation(s)
- Saurabh Gupta
- Institute of Genomics and Integrative Biology, Mall Road, Delhi, India
- Jamia Hamdard University, Hamdard Nagar, New Delhi, India
| | - Mritunjay Saxena
- Institute of Genomics and Integrative Biology, Mall Road, Delhi, India
| | - Neeru Saini
- Institute of Genomics and Integrative Biology, Mall Road, Delhi, India
| | - Mahmooduzzafar
- Jamia Hamdard University, Hamdard Nagar, New Delhi, India
| | - Rita Kumar
- Institute of Genomics and Integrative Biology, Mall Road, Delhi, India
| | - Anil Kumar
- National Institute of Immunology, New Delhi, India
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Yu H, Peng Z, Zhan Y, Wang J, Yan Y, Chen M, Lu W, Ping S, Zhang W, Zhao Z, Li S, Takeo M, Lin M. Novel regulator MphX represses activation of phenol hydroxylase genes caused by a XylR/DmpR-type regulator MphR in Acinetobacter calcoaceticus. PLoS One 2011; 6:e17350. [PMID: 21455294 PMCID: PMC3063778 DOI: 10.1371/journal.pone.0017350] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 01/31/2011] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter calcoaceticus PHEA-2 utilizes phenol as its sole carbon and energy source and has a multi-component phenol hydroxylase-encoding gene operon (mphKLMNOP) for phenol degradation. Two additional genes, mphR and mphX, were found upstream and downstream of mphKLMNOP, respectively. The mphR gene encodes a XylR/DmpR-type regulator-like protein and is transcribed in the opposite direction to mphKLMNOP. The mphX gene is transcribed in the same direction as mphKLMNOP and encodes a protein with 293 amino acid residues showing weak identity with some unknown proteins encoded in the meta-cleavage pathway gene clusters for aromatic compound degradation. Disruption of mphR by homologous recombination resulted in the loss of phenol degradation while disruption of mphX caused significantly faster phenol degradation than in the wild type strain. Transcriptional assays for mphK, mphR, and mphX revealed that mphR activated mphKLMNOP transcription in the presence of phenol, but mphX partially repressed this activation. Gel mobility-shift assay demonstrated a direct interaction of MphR with the mphK promoter region. These results indicate the involvement of a novel repressor protein MphX in transcriptional regulation of phenol hydroxylase genes caused by a XylR/DmpR-type regulator MphR.
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Affiliation(s)
- Haiying Yu
- College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Zixin Peng
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan
| | - Yuhua Zhan
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Jin Wang
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Yongliang Yan
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
- National Centre for Plant Gene Research, Beijing, China
| | - Ming Chen
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Wei Lu
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Shuzhen Ping
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Wei Zhang
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
- National Centre for Plant Gene Research, Beijing, China
| | - Zhonglin Zhao
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Shuying Li
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Masahiro Takeo
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan
- * E-mail: (MT); (ML)
| | - Min Lin
- College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
- * E-mail: (MT); (ML)
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