1
|
Hussain I, Aleti G, Naidu R, Puschenreiter M, Mahmood Q, Rahman MM, Wang F, Shaheen S, Syed JH, Reichenauer TG. Microbe and plant assisted-remediation of organic xenobiotics and its enhancement by genetically modified organisms and recombinant technology: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 628-629:1582-1599. [PMID: 30045575 DOI: 10.1016/j.scitotenv.2018.02.037] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/31/2018] [Accepted: 02/03/2018] [Indexed: 05/18/2023]
Abstract
Environmental problems such as the deterioration of groundwater quality, soil degradation and various threats to human, animal and ecosystem health are closely related to the presence of high concentrations of organic xenobiotics in the environment. Employing appropriate technologies to remediate contaminated soils is crucial due to the site-specificity of most remediation methods. The limitations of conventional remediation technologies include poor environmental compatibility, high cost of implementation and poor public acceptability. This raises the call to employ biological methods for remediation. Bioremediation and microbe-assisted bioremediation (phytoremediation) offer many ecological and cost-associated benefits. The overall efficiency and performance of bio- and phytoremediation approaches can be enhanced by genetically modified microbes and plants. Moreover, phytoremediation can also be stimulated by suitable plant-microbe partnerships, i.e. plant-endophytic or plant-rhizospheric associations. Synergistic interactions between recombinant bacteria and genetically modified plants can further enhance the restoration of environments impacted by organic pollutants. Nevertheless, releasing genetically modified microbes and plants into the environment does pose potential risks. These can be minimized by adopting environmental biotechnological techniques and guidelines provided by environmental protection agencies and other regulatory frameworks. The current contribution provides a comprehensive overview on enhanced bioremediation and phytoremediation approaches using transgenic plants and microbes. It also sheds light on the mitigation of associated environmental risks.
Collapse
Affiliation(s)
- Imran Hussain
- AIT Austrian Institute of Technology, Centre for Energy, Environmental Resources and Technologies, Tulln, Austria; Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Austria
| | - Gajender Aleti
- AIT Austrian Institute of Technology, Centre for Energy, Environmental Resources and Technologies, Tulln, Austria
| | - Ravi Naidu
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, New South Wales, Australia
| | - Markus Puschenreiter
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Qaisar Mahmood
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Mohammad Mahmudur Rahman
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, New South Wales, Australia
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shahida Shaheen
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Jabir Hussain Syed
- Department of Meteorology, COMSATS Institute of Information Technology, Park Road Tarlai Kalan 45550, Islamabad, Pakistan; Department of Civil and Environmental Engineering, Hong Kong Polytechnic University, Hong Kong.
| | - Thomas G Reichenauer
- AIT Austrian Institute of Technology, Centre for Energy, Environmental Resources and Technologies, Tulln, Austria.
| |
Collapse
|
2
|
Tools and Techniques for Genetic Engineering of Bio-Prospective Microorganisms. Microb Biotechnol 2017. [DOI: 10.1007/978-981-10-6847-8_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
3
|
Iwakiri R, Yoshihira K, Futagami T, Goto M, Furukawa K. Total Degradation of Pentachloroethane by an EngineeredAlcaligenesStrain Expressing a Modified Camphor Monooxygenase and a Hybrid Dioxygenase. Biosci Biotechnol Biochem 2014; 68:1353-6. [PMID: 15215602 DOI: 10.1271/bbb.68.1353] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We engineered biphenyl-degrading Alcaligenes sp. strain KF711 for total degradation of pentachloroethane (PCA), which expresses a modified camphor monooxygenase and a hybrid dioxygenase consisting of TodC1 (a large subunit of toluene dioxygenase of Pseudomonas putida F1) and BphA2-BphA3-pbhA4 (a small subunit, ferredoxin and ferredoxin reductase of biphenyl dioxygenase, respectively, in strain KF707). Modified camphor monooxygenase genes (camCAB) were supplied as a plasmid and the todC1 gene was integrated within the chromosomal bph gene cluster by a single crossover recombination. The resultant strain KF711S-3cam dechlorinated PCA to trichloroethene by the action of the modified camphor monooxygenase under anaerobic conditions. The same strain subsequently degraded trichloroethene formed oxidatively by the action of the Tol-Bph hybrid dioxygenase under aerobic conditions. Thus sequential anaerobic and aerobic treatments of the KF711S-3cam resting cells resulted in efficient and total degradation of PCA.
Collapse
Affiliation(s)
- Ryo Iwakiri
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | | | | | | | | |
Collapse
|
4
|
Guan X, Liu F, Xie Y, Zhu L, Han B. Microbiota associated with the migration and transformation of chlorinated aliphatic hydrocarbons in groundwater. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2013; 35:535-549. [PMID: 23420483 DOI: 10.1007/s10653-013-9513-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 02/10/2013] [Indexed: 06/01/2023]
Abstract
Pollution of groundwater with chlorinated aliphatic hydrocarbons (CAHs) is a serious environmental problem which is threatening human health. Microorganisms are the major participants in degrading these contaminants. Here, groundwater contaminated for a decade with CAHs was investigated. Numerical simulation and field measurements were used to track and forecast the migration and transformation of the pollutants. The diversity, abundance, and possible activity of groundwater microbial communities at CAH-polluted sites were characterized by molecular approaches. The number of microorganisms was between 5.65E+05 and 1.49E+08 16S rRNA gene clone numbers per liter according to quantitative real-time PCR analysis. In 16S rRNA gene clone libraries constructed from samples along the groundwater flow, eight phyla were detected, and Proteobacteria were dominant (72.8 %). The microbial communities varied with the composition and concentration of pollutants. Meanwhile, toluene monooxygenases and methane monooxygenases capable of degradation of PCE and TCE were detected, demonstrating the major mechanism for PCE and TCE degradation and possibility for in situ remediation by addition of oxygen in this study.
Collapse
MESH Headings
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteria/metabolism
- China
- Environmental Monitoring
- Gas Chromatography-Mass Spectrometry
- Groundwater/chemistry
- Groundwater/microbiology
- Hydrocarbons, Chlorinated/analysis
- Hydrocarbons, Chlorinated/metabolism
- Molecular Sequence Data
- Phylogeny
- Polymerase Chain Reaction
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Sequence Analysis, RNA
- Water Pollutants, Chemical/analysis
- Water Pollutants, Chemical/metabolism
Collapse
Affiliation(s)
- Xiangyu Guan
- Beijing Key Laboratory of Water Resources and Environmental Engineering, School of Water Resources and Environment, China University of Geosciences, No.29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China
| | | | | | | | | |
Collapse
|
5
|
Das N, Chandran P. Microbial degradation of petroleum hydrocarbon contaminants: an overview. BIOTECHNOLOGY RESEARCH INTERNATIONAL 2010; 2011:941810. [PMID: 21350672 PMCID: PMC3042690 DOI: 10.4061/2011/941810] [Citation(s) in RCA: 449] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 06/28/2010] [Accepted: 07/07/2010] [Indexed: 11/20/2022]
Abstract
One of the major environmental problems today is hydrocarbon contamination resulting from the activities related to the petrochemical industry. Accidental releases of petroleum products are of particular concern in the environment. Hydrocarbon components have been known to belong to the family of carcinogens and neurotoxic organic pollutants. Currently accepted disposal methods of incineration or burial insecure landfills can become prohibitively expensive when amounts of contaminants are large. Mechanical and chemical methods generally used to remove hydrocarbons from contaminated sites have limited effectiveness and can be expensive. Bioremediation is the promising technology for the treatment of these contaminated sites since it is cost-effective and will lead to complete mineralization. Bioremediation functions basically on biodegradation, which may refer to complete mineralization of organic contaminants into carbon dioxide, water, inorganic compounds, and cell protein or transformation of complex organic contaminants to other simpler organic compounds by biological agents like microorganisms. Many indigenous microorganisms in water and soil are capable of degrading hydrocarbon contaminants. This paper presents an updated overview of petroleum hydrocarbon degradation by microorganisms under different ecosystems.
Collapse
Affiliation(s)
- Nilanjana Das
- Environmental Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu 632014, India
| | - Preethy Chandran
- Environmental Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu 632014, India
| |
Collapse
|
6
|
Suenaga H, Nonaka K, Fujihara H, Goto M, Furukawa K. Hybrid pseudomonads engineered by two-step homologous recombination acquire novel degradation abilities toward aromatics and polychlorinated biphenyls. Appl Microbiol Biotechnol 2010; 88:915-23. [PMID: 20809076 DOI: 10.1007/s00253-010-2840-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 08/11/2010] [Accepted: 08/12/2010] [Indexed: 10/19/2022]
Abstract
Pseudomonas pseudoalcaligenes KF707 possesses a chromosomally encoded bph gene cluster responsible for the catabolism of biphenyl and polychlorinated biphenyls. Previously, we constructed chimeric versions of the bphA1 gene, which encodes a large subunit of biphenyl dioxygenase, by using DNA shuffling between bphA1 genes from P. pseudoalcaligenes KF707 and Burkholderia xenovorans LB400. In this study, we demonstrate replacement of the bphA1 gene with chimeric bphA1 sequence within the chromosomal bph gene cluster by two-step homologous recombination. Notably, some of the hybrid strains acquired enhanced and/or expanded degradation capabilities for specific aromatic compounds, including single aromatic hydrocarbons and polychlorinated biphenyls.
Collapse
Affiliation(s)
- Hikaru Suenaga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan.
| | | | | | | | | |
Collapse
|
7
|
Biodegradation of aromatic compounds: current status and opportunities for biomolecular approaches. Appl Microbiol Biotechnol 2010; 85:207-28. [PMID: 19730850 DOI: 10.1007/s00253-009-2192-4] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 08/05/2009] [Accepted: 08/05/2009] [Indexed: 02/03/2023]
Abstract
Biodegradation can achieve complete and cost-effective elimination of aromatic pollutants through harnessing diverse microbial metabolic processes. Aromatics biodegradation plays an important role in environmental cleanup and has been extensively studied since the inception of biodegradation. These studies, however, are diverse and scattered; there is an imperative need to consolidate, summarize, and review the current status of aromatics biodegradation. The first part of this review briefly discusses the catabolic mechanisms and describes the current status of aromatics biodegradation. Emphasis is placed on monocyclic, polycyclic, and chlorinated aromatic hydrocarbons because they are the most prevalent aromatic contaminants in the environment. Among monocyclic aromatic hydrocarbons, benzene, toluene, ethylbenzene, and xylene; phenylacetic acid; and structurally related aromatic compounds are highlighted. In addition, biofilms and their applications in biodegradation of aromatic compounds are briefly discussed. In recent years, various biomolecular approaches have been applied to design and understand microorganisms for enhanced biodegradation. In the second part of this review, biomolecular approaches, their applications in aromatics biodegradation, and associated biosafety issues are discussed. Particular attention is given to the applications of metabolic engineering, protein engineering, and "omics" technologies in aromatics biodegradation.
Collapse
|
8
|
Peng RH, Xiong AS, Xue Y, Fu XY, Gao F, Zhao W, Tian YS, Yao QH. A profile of ring-hydroxylating oxygenases that degrade aromatic pollutants. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2010; 206:65-94. [PMID: 20652669 DOI: 10.1007/978-1-4419-6260-7_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Numerous aromatic compounds are pollutants to which exposure exists or is possible, and are of concern because they are mutagenic, carcinogenic, or display other toxic characteristics. Depending on the types of dioxygenation reactions of which microorganisms are capable, they utilize ring-hydroxylating oxygenases (RHOs) to initiate the degradation and detoxification of such aromatic compound pollutants. Gene families encoding for RHOs appear to be most common in bacteria. Oxygenases are important in degrading both natural and synthetic aromatic compounds and are particularly important for their role in degrading toxic pollutants; for this reason, it is useful for environmental scientists and others to understand more of their characteristics and capabilities. It is the purpose of this review to address RHOs and to describe much of their known character, starting with a review as to how RHOs are classified. A comprehensive phylogenetic analysis has revealed that all RHOs are, in some measure, related, presumably by divergent evolution from a common ancestor, and this is reflected in how they are classified. After we describe RHO classification schemes, we address the relationship between RHO structure and function. Structural differences affect substrate specificity and product formation. In the alpha subunit of the known terminal oxygenase of RHOs, there is a catalytic domain with a mononuclear iron center that serves as a substrate-binding site and a Rieske domain that retains a [2Fe-2S] cluster that acts as an entity of electron transfer for the mononuclear iron center. Oxygen activation and substrate dihydroxylation occurring at the catalytic domain are dependent on the binding of substrate at the active site and the redox state of the Rieske center. The electron transfer from NADH to the catalytic pocket of RHO and catalyzing mechanism of RHOs is depicted in our review and is based on the results of recent studies. Electron transfer involving the RHO system typically involves four steps: NADH-ferredoxin reductase receives two electrons from NADH; ferredoxin binds with NADH-ferredoxin reductase and accepts electron from it; the reduced ferredoxin dissociates from NADH-ferredoxin reductase and shuttles the electron to the Rieske domain of the terminal oxygenase; the Rieske cluster donates electrons to O2 through the mononuclear iron. On the basis of crystal structure studies, it has been proposed that the broad specificity of the RHOs results from the large size and specific topology of its hydrophobic substrate-binding pocket. Several amino acids that determine the substrate specificity and enantioselectivity of RHOs have been identified through sequence comparison and site-directed mutagenesis at the active site. Exploiting the crystal structure data and the available active site information, engineered RHO enzymes have been and can be designed to improve their capacity to degrade environmental pollutants. Such attempts to enhance degradation capabilities of RHOs have been made. Dioxygenases have been modified to improve the degradation capacities toward PCBs, PAHs, dioxins, and some other aromatic hydrocarbons. We hope that the results of this review and future research on enhancing RHOs will promote their expanded usage and effectiveness for successfully degrading environmental aromatic pollutants.
Collapse
Affiliation(s)
- Ri-He Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, People's Republic of China
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Affiliation(s)
- Nobutada Kimura
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST)
| |
Collapse
|
10
|
Ishida H, Nakamura K. Trichloroethylene degradation by Ralstonia sp. KN1-10A constitutively expressing phenol hydroxylase: transformation products, NADH limitation, and product toxicity. J Biosci Bioeng 2005; 89:438-45. [PMID: 16232774 DOI: 10.1016/s1389-1723(00)89093-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/1999] [Accepted: 02/08/2000] [Indexed: 10/18/2022]
Abstract
Ralstonia sp. KN1-10A, which was constructed by inserting the tac promoter upstream of the phenol hydroxylase (PH) gene in the chromosomal DNA of the wild-type strain, Ralstonia sp. KN1, is a useful recombinant strain for eliminating trichloroethylene (TCE) from contaminated sites because it exhibits constitutive TCE oxidation activity. During TCE degradation by Ralstonia sp. KN1-10A, noxious chlorinated compounds, such as dichloroacetic acid, trichloroacetic acid, 2,2,2-trichloroethanol, and chloral, were not detected, and more than 95% of chlorine in TCE was released as chloride ions. Among the possible TCE transformation products, only carbon monoxide was detected, and its conversion percentage was 7 mol%. The addition of formate, which Ralstonia sp. KN1-10A could use as an exogenous electron donor, did not enhance the TCE degradation performance, suggesting that NADH depletion did not limit the degradation. The phenol degradation activity of Ralstonia sp. KN1-10A that previously degraded TCE was not markedly lower than that of cells not exposed to TCE, suggesting that Ralstonia sp. KN1-10A was not susceptible to product toxicity associated with TCE degradation. Furthermore, to clarify the mechanisms underlying TCE degradation by PH from Ralstonia sp. KN1, this enzyme was compared with another enzyme, a hybrid aromatic ring dioxygenase exhibiting a high TCE degradation activity in Escherichia coli and Pseudomonas sp. The initial TCE degradation rate of Ralstonia sp. KN1 (pKTP100), which produced PH, was 1 50 lower than that of Ralstonia sp. KN1 (pKTF200), which produced the hybrid aromatic ring dioxygenase. However, because of its lower product toxicity, the strain producing PH could degrade 2.3 times more TCE than that generated by the strain producing the hybrid aromatic ring dioxygenase.
Collapse
Affiliation(s)
- H Ishida
- Kurita Water Industries Ltd., 7-1 Wakamiya, Morinosato, Atsugi-city, Kanagawa 243-0124, Japan
| | | |
Collapse
|
11
|
Gibello A, Garbi C, Allende JL, Martin M. Improving dioxygenase stability by gene chromosome insertion: implementation in immobilized-cell systems. Curr Microbiol 2005; 49:390-5. [PMID: 15696613 DOI: 10.1007/s00284-004-4283-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The immobilization of recombinant cells by using the unstable 3,4-dihydroxyphenylacetate 2,3-dioxygenase was studied as a model. Dioxygenase activity and cell viability were compared in immobilized-cell systems and cells in suspension. Immobilization increased enzyme stability and the efficient degradation of 3,4-dihydroxyphenylacetate. The stability of the cloned enzyme and the viability of the immobilized recombinant cells were well maintained for at least 15 days. We used the strain Escherichia coli CC118-D in which the hpaB gene from Klebsiella pneumoniae, coding for the subunit of 3,4-dihydroxyphenylacetate 2,3-dioxygenase, was inserted into the chromosome. This study has demonstrated that the implementation of E. coli CC118-D in a pilot-scale bioreactor resulted in a 100% stabilization of dioxygenase activity, and could be a useful tool for bioremediation processes.
Collapse
Affiliation(s)
- A Gibello
- Departamento Patologia Animal (Microbiologia), Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
| | | | | | | |
Collapse
|
12
|
Abstract
Chlorinated organic compounds are among the most significant pollutants in the world. Sequential use of anaerobic halorespiring bacteria, which are the key players in biological dehalogenation processes, and aerobic bacteria whose oxygenases are modified by directed evolution could lead to efficient and total degradation of highly chlorinated organic pollutants. Recently three interesting papers on halorespiration and polychlorinated biphenyl biodegradation were published.
Collapse
Affiliation(s)
- Kensuke Furukawa
- Department of Bioscience and Biotechnology, Kyushu University, Fukuoka 812-8581, Japan.
| |
Collapse
|
13
|
Dennis PC, Sleep BE, Fulthorpe RR, Liss SN. Phylogenetic analysis of bacterial populations in an anaerobic microbial consortium capable of degrading saturation concentrations of tetrachloroethylene. Can J Microbiol 2003; 49:15-27. [PMID: 12674344 DOI: 10.1139/w03-008] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An anaerobic microbial consortium able to biodegrade saturation levels of perchloroethylene (PCE) in a column containing a source zone of PCE was examined phylogenetically to determine microbial community structure and spatial variation in relation to the PCE source. The consortium was comprised of at least 34 members with 7 organisms sharing affiliations with known respiratory or cometabolic dechlorinators. Seven other organisms had their closest phylogenetic relative detected in other environments containing chlorinated compounds. Based on denaturing gradient gel electrophoresis, significant Bacteria were Dehalococcoides ethenogenes, Shewanella putrefaciens, and an Acetobacterium species. Spatial variations in community structure of the consortium relative to the PCE source zone were observed. A Pseudomonas species was predominant in a zone 30 cm from the PCE source. A Methanothrix species was predominant at points over 85 cm from the source zone. A Trichlorobacter species was detected where PCE concentrations were highest, up to 85 cm from the PCE source, whereas D. ethenogenes was ubiquitous to over 128 cm from the PCE source.
Collapse
MESH Headings
- Anaerobiosis
- Bacteria, Anaerobic/classification
- Bacteria, Anaerobic/genetics
- Bacteria, Anaerobic/growth & development
- Bacteria, Anaerobic/metabolism
- Biodegradation, Environmental
- DNA, Ribosomal/analysis
- Ecosystem
- Electrophoresis, Polyacrylamide Gel
- Environmental Pollutants/metabolism
- Phylogeny
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/genetics
- Refuse Disposal
- Sequence Analysis, DNA
- Tetrachloroethylene/metabolism
Collapse
Affiliation(s)
- Philip C Dennis
- Department of Civil Engineering, University of Toronto, 35 St. George St., Toronto, ON M5S 1A4, Canada
| | | | | | | |
Collapse
|
14
|
Maeda T, Takahashi Y, Suenaga H, Suyama A, Goto M, Furukawa K. Functional analyses of Bph-Tod hybrid dioxygenase, which exhibits high degradation activity toward trichloroethylene. J Biol Chem 2001; 276:29833-8. [PMID: 11390387 DOI: 10.1074/jbc.m102025200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Biphenyl dioxygenase (BphDox) in Pseudomonas pseudoalcaligenes KF707 is a multicomponent enzyme consisting of an iron-sulfur protein (ISP) that is composed of alpha (BphA1) and beta (BphA2) subunits, a ferredoxin (FD(BphA3)), and a ferredoxin reductase (FDR(BphA4)). A recombinant Escherichia coli strain expressing hybrid Dox that had replaced BphA1 with TodC1 (alpha subunit of toluene dioxygenase (TolDox) of Pseudomonas putida) exhibited high activity toward trichloroethylene (TCE) (Furukawa, K., Hirose, J., Hayashida, S., and Nakamura, K. (1994) J. Bacteriol. 176, 2121-2123). In this study, ISP, FD, and FDR were purified and characterized. Reconstitution of the dioxygenase components consisting of purified ISP(TodC1BphA2), FD(BphA3), and FDR(BphA4) exhibited oxygenation activities toward biphenyl, toluene, and TCE. Native polyacrylamide gel electrophoresis followed by the Ferguson plot analyses demonstrated that ISP(TodC1BphA2) and ISP(BphA1A2) were present as heterohexamers, whereas ISP(TodC1C2) was present as a heterotetramer. The molecular activity (k(0)) of the hybrid Dox for TCE was 4.1 min(-1), which is comparable to that of TolDox. The K(m) value of the hybrid Dox for TCE was 130 microm, which was lower than 250 microm for TolDox. These results suggest that the alpha subunit of ISP is crucial for the determination of substrate specificity and that the change in the alpha subunit conformation of ISP from alpha(2)beta(2) to alpha(3)beta(3) results in the acquisition of higher affinity to TCE, which may lead to high TCE degradation activity.
Collapse
Affiliation(s)
- T Maeda
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | | | | | | | | | | |
Collapse
|
15
|
Yeates C, Holmes AJ, Gillings MR. Novel forms of ring-hydroxylating dioxygenases are widespread in pristine and contaminated soils. Environ Microbiol 2000; 2:644-53. [PMID: 11214797 DOI: 10.1046/j.1462-2920.2000.00147.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Ring-hydroxylating dioxygenases (RHDs) are of central importance to bacterial recycling of aromatic hydrocarbons, including anthropogenic pollutants. The database of presently characterized RHDs is biased towards those from organisms readily isolated on anthropogenic substrates. To investigate the extent to which RHDs from extant organisms reflect the natural diversity of these enzymes, we developed a polymerase chain reaction (PCR) method for retrieval of RHD gene fragments from environmental samples. Gene libraries from two contaminated and two pristine soil samples were constructed. None of the inferred peptides from clones examined were identical to previously described RHDs; however, all showed significant sequence homology and contained key catalytic residues. On the basis of sequence identity, the environmental clones clustered into six distinct groups, only one of which included known RHDs. One of the new sequence groupings was particularly widespread, being recovered from all soil samples tested. Comparison of inferred peptide sequences of the environmental clones and known RHDs showed the former to have greater sequence variation at sites thought to influence accessibility of the active site than that seen between currently known RHDs. We conclude that presently characterized RHDs do not adequately represent the diversity of function found in in situ forms.
Collapse
Affiliation(s)
- C Yeates
- Key Centre for Biodiversity and Bioresources, School of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | | | | |
Collapse
|
16
|
Abstract
Dioxygenases have recently been engineered to improve their capabilities for environmental pollutant degradation. The techniques used to achieve this include in vitro DNA shuffling and subunit or domain exchanges between dioxygenases of different bacterial origins. Such evolved enzymes acquire novel and enhanced degradation capabilities of xenobiotic compounds, such as polychlorinated biphenyls, trichloroethylene and a variety of aromatic compounds. Hybrid strains in which the evolved genes are integrated into the chromosomal operons exhibit efficient degradation of xenobiotic chlorinated compounds.
Collapse
Affiliation(s)
- K Furukawa
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 812-8581, Japan.
| |
Collapse
|
17
|
Romine MF, Stillwell LC, Wong KK, Thurston SJ, Sisk EC, Sensen C, Gaasterland T, Fredrickson JK, Saffer JD. Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. J Bacteriol 1999; 181:1585-602. [PMID: 10049392 PMCID: PMC93550 DOI: 10.1128/jb.181.5.1585-1602.1999] [Citation(s) in RCA: 238] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete 184,457-bp sequence of the aromatic catabolic plasmid, pNL1, from Sphingomonas aromaticivorans F199 has been determined. A total of 186 open reading frames (ORFs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compounds. Genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. The unusual coclustering of genes associated with different pathways appears to have evolved in response to similarities in biochemical mechanisms required for the degradation of intermediates in different pathways. A putative efflux pump and several hypothetical membrane-associated proteins were identified and predicted to be involved in the transport of aromatic compounds and/or intermediates in catabolism across the cell wall. Several genes associated with integration and recombination, including two group II intron-associated maturases, were identified in the replication region, suggesting that pNL1 is able to undergo integration and excision events with the chromosome and/or other portions of the plasmid. Conjugative transfer of pNL1 to another Sphingomonas sp. was demonstrated, and genes associated with this function were found in two large clusters. Approximately one-third of the ORFs (59 of them) have no obvious homology to known genes.
Collapse
Affiliation(s)
- M F Romine
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Beil S, Mason JR, Timmis KN, Pieper DH. Identification of chlorobenzene dioxygenase sequence elements involved in dechlorination of 1,2,4,5-tetrachlorobenzene. J Bacteriol 1998; 180:5520-8. [PMID: 9791099 PMCID: PMC107608 DOI: 10.1128/jb.180.21.5520-5528.1998] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The TecA chlorobenzene dioxygenase and the TodCBA toluene dioxygenase exhibit substantial sequence similarity yet have different substrate specificities. Escherichia coli cells producing recombinant TecA enzyme dioxygenate and simultaneously eliminate a halogen substituent from 1,2,4,5-tetrachlorobenzene but show no activity toward benzene, whereas those producing TodCBA dioxygenate benzene but not tetrachlorobenzene. A hybrid TecA dioxygenase variant containing the large alpha-subunit of the TodCBA dioxygenase exhibited a TodCBA dioxygenase specificity. Acquisition of dehalogenase activity was achieved by replacement of specific todC1 alpha-subunit subsequences by equivalent sequences of the tecA1 alpha-subunit. Substrate transformation specificities and rates by E. coli resting cells expressing hybrid systems were analyzed by high-performance liquid chromatography. This allowed the identification of both a single amino acid and potentially interacting regions required for dechlorination of tetrachlorobenzene. Hybrids with extended substrate ranges were generated that exhibited activity toward both benzene and tetrachlorobenzene. The regions determining substrate specificity in (chloro)benzene dioxygenases appear to be different from those previously identified in biphenyl dioxygenases.
Collapse
Affiliation(s)
- S Beil
- Division of Microbiology, GBF-National Research Centre for Biotechnology, D-38124 Braunschweig, Germany
| | | | | | | |
Collapse
|
19
|
Kumamaru T, Suenaga H, Mitsuoka M, Watanabe T, Furukawa K. Enhanced degradation of polychlorinated biphenyls by directed evolution of biphenyl dioxygenase. Nat Biotechnol 1998; 16:663-6. [PMID: 9661201 DOI: 10.1038/nbt0798-663] [Citation(s) in RCA: 178] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Biphenyl dioxygenases (BP Dox) from different organisms, which are involved in the initial oxygenation and subsequent degradation of polychlorinated biphenyls (PCB), are similar in structure but have different functions. The large subunit of BP Dox, encoded by the bphA1 gene, is crucial for substrate selectivity. Using the process of DNA shuffling, we randomly recombined the bphA1 genes of Pseudomonas pseudoalcaligenes KF707 and Burkholderia cepacia LB400 and selected for genes that expressed proteins with altered function. Upon expression in Escherichia coli, some of these evolved genes exhibited enhanced degradation capacity, not only for PCB and related biphenyl compounds, but for single aromatic hydrocarbons such as benzene and toluene, which are poor substrates for the original BP Dox.
Collapse
Affiliation(s)
- T Kumamaru
- Department of Agricultural Chemistry, Kyushu University, Fukuoka, Japan
| | | | | | | | | |
Collapse
|
20
|
Berendes F, Sabarth N, Averhoff B, Gottschalk G. Construction and use of an ipb DNA module to generate Pseudomonas strains with constitutive trichloroethene and isopropylbenzene oxidation activity. Appl Environ Microbiol 1998; 64:2454-62. [PMID: 9647815 PMCID: PMC106411 DOI: 10.1128/aem.64.7.2454-2462.1998] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/1998] [Accepted: 04/27/1998] [Indexed: 02/08/2023] Open
Abstract
Pseudomonas sp. strain JR1 exhibits trichloroethene (TCE) oxidation activity with isopropylbenzene (IPB) as the inducer substrate. We previously reported the genes encoding the first three enzymes of the IPB-degradative pathway (ipbA1, ipbA2, ipbA3, ipbA4, ipbB, and ipbC) and identified the initial IPB dioxygenase (IpbA1 A2A3A4) as responsible for TCE cooxidation (U. Pflugmacher, B. Averhoff, and G. Gottschalk, Appl. Environ. Microbiol. 62:3967-3977, 1996). Primer extension analyses revealed multiple transcriptional start points located upstream of the translational initiation codon of ipbA1. The transcription from these start sites was found to be IPB dependent. Thirty-one base pairs upstream of the first transcriptional start point tandemly repeated DNA sequences overlapping the -35 region of a putative sigma 70 promoter were found. These repeats exhibit significant sequence similarity to the operator-promoter region of the xyl meta operon in Pseudomonas putida, which is required for the binding of XylS, a regulatory protein of the XylS (also called AraC) family. These similarities suggest that the transcription of the IPB dioxygenase genes is modulated by a regulatory protein of the XylS/AraC family. The construction of an ipb DNA module devoid of this ipb operator-promoter region and the stable insertion of this DNA module into the genomes of different Pseudomonas strains resulted in pseudomonads with constitutive IPB and TCE oxidation activities. Constitutive TCE oxidation of two such Pseudomonas hybrid strains, JR1A::ipb and CBS-3::ipb, was found to be stable for more than 120 generations in antibiotic-free medium. Evaluation of constitutive TCE degradation rates revealed that continuous cultivation of strain JR1A::ipb resulted in a significant increase in rates of TCE degradation.
Collapse
Affiliation(s)
- F Berendes
- Institut für Mikrobiologie und Genetik, Georg-August-Universität, Göttingen, Germany
| | | | | | | |
Collapse
|
21
|
Moran BN, Hickey WJ. Trichloroethylene biodegradation by mesophilic and psychrophilic ammonia oxidizers and methanotrophs in groundwater microcosms. Appl Environ Microbiol 1997; 63:3866-71. [PMID: 9327550 PMCID: PMC168696 DOI: 10.1128/aem.63.10.3866-3871.1997] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
This study investigated the efficiency of methane and ammonium for stimulating trichloroethylene (TCE) biodegradation in groundwater microcosms (flasks and batch exchange columns) at a psychrophilic temperature (12 degrees C) typical of shallow aquifers in the northern United States or a mesophilic temperature (24 degrees C) representative of most laboratory experiments. After 140 days, TCE biodegradation rates by ammonia oxidizers and methanotrophs in mesophilic flask microcosms were similar (8 to 10 nmol day-1), but [14C]TCE mineralization (biodegradation to 14CO2) by ammonia oxidizers was significantly greater than that by methanotrophs (63 versus 53%). Under psychrophilic conditions, [14C]TCE mineralization in flask systems by ammonia oxidizers and methanotrophs was reduced to 12 and 5%, respectively. In mesophilic batch exchange columns, average TCE biodegradation rates for methanotrophs (900 nmol liter-1 day-1) were not significantly different from those of ammonia oxidizers (775 nmol liter-1 day-1). Psychrophilic TCE biodegradation rates in the columns were similar with both biostimulants and averaged 145 nmol liter-1 day-1. Methanotroph biostimulation was most adversely affected by low temperatures. At 12 degrees C, the biodegradation efficiencies (TCE degradation normalized to microbial activity) of methanotrophs and ammonia oxidizers decreased by factors of 2.6 and 1.6, respectively, relative to their biodegradation efficiencies at 24 degrees C. Collectively, these experiments demonstrated that in situ bioremediation of TCE is feasible at the psychrophilic temperatures common in surficial aquifers in the northern United States and that for such applications biostimulation of ammonia oxidizers could be more effective than has been previously reported.
Collapse
Affiliation(s)
- B N Moran
- Environmental Toxicology Center, University of Wisconsin-Madison 53706-1299, USA
| | | |
Collapse
|
22
|
Lloyd-Jones G, Lau PC. Glutathione S-transferase-encoding gene as a potential probe for environmental bacterial isolates capable of degrading polycyclic aromatic hydrocarbons. Appl Environ Microbiol 1997; 63:3286-90. [PMID: 9251217 PMCID: PMC168628 DOI: 10.1128/aem.63.8.3286-3290.1997] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Homologs of the glutathione S-transferase (GST)-encoding gene were identified in a collection of aromatic hydrocarbon-degrading Sphingomonas spp. isolated from New Zealand, Antarctica, and the United States by using PCR primers designed from the GST-encoding gene of Sphingomonas paucimobilis EPA505. Sequence analysis of PCR fragments generated from these isolates and of the GST gene amplified from DNA extracted from polycyclic aromatic hydrocarbon (PAH)-contaminated soil revealed a high degree of conservation, which may make the GST-encoding gene a potentially useful marker for PAH-degrading bacteria.
Collapse
Affiliation(s)
- G Lloyd-Jones
- Manaaki Whenua-Landcare Research Ltd., Hamilton, New Zealand
| | | |
Collapse
|
23
|
Kimura N, Nishi A, Goto M, Furukawa K. Functional analyses of a variety of chimeric dioxygenases constructed from two biphenyl dioxygenases that are similar structurally but different functionally. J Bacteriol 1997; 179:3936-43. [PMID: 9190809 PMCID: PMC179202 DOI: 10.1128/jb.179.12.3936-3943.1997] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The biphenyl dioxygenases (BP Dox) of strains Pseudomonas pseudoalcaligenes KF707 and Pseudomonas cepacia LB400 exhibit a distinct difference in substrate ranges of polychlorinated biphenyls (PCB) despite nearly identical amino acid sequences. The range of congeners oxidized by LB400 BP Dox is much wider than that oxidized by KF707 BP Dox. The PCB degradation abilities of these BP Dox were highly dependent on the recognition of the chlorinated rings and the sites of oxygen activation. The KF707 BP Dox recognized primarily the 4'-chlorinated ring (97%) of 2,5,4'-trichlorobiphenyl and introduced molecular oxygen at the 2',3' position. The LB400 BP Dox recognized primarily the 2,5-dichlorinated ring (95%) of the same compound and introduced O2 at the 3,4 position. It was confirmed that the BphA1 subunit (iron-sulfur protein of terminal dioxygenase encoded by bphA1) plays a crucial role in determining the substrate selectivity. We constructed a variety of chimeric bphA1 genes by exchanging four common restriction fragments between the KF707 bphA1 and the LB400 bphA1. Observation of Escherichia coli cells expressing various chimeric BP Dox revealed that a relatively small number of amino acids in the carboxy-terminal half (among 20 different amino acids in total) are involved in the recognition of the chlorinated ring and the sites of dioxygenation and thereby are responsible for the degradation of PCB. The site-directed mutagenesis of Thr-376 (KF707) to Asn-376 (LB400) in KF707 BP Dox resulted in the expansion of the range of biodegradable PCB congeners.
Collapse
Affiliation(s)
- N Kimura
- Department of Agricultural Chemistry, Kyushu University, Hakozaki, Fukuoka, Japan
| | | | | | | |
Collapse
|
24
|
Abstract
Recent field and laboratory studies have evaluated the potential for aerobic co-metabolism of chlorinated solvents. Different co-metabolic substrates and different methods of application have been tried, including growing indigenous microbes in situ, and injecting into the soil subsurface strains grown in subsurface reactors for their co-metabolic potential. There is much potential for using co-metabolism for treating a broad range of chlorinated aliphatic hydrocarbons. Recirculation wells have potential for adding soluble co-metabolic substrates (i.e. phenol and toluene) into contaminated aquifers, while direct addition of gaseous substrates (i.e. methane and propane) into aquifers also holds promise. Aromatic substrates (phenol and toluene) are best used for treatment of chlorinated ethenes, whereas gaseous co-metabolic substrate (methane and propane) are better suited for the treatment of chlorinated methanes and ethanes. Many factors can enhance co-metabolic transformations, such as nutrients and available energy sources.
Collapse
Affiliation(s)
- L Semprini
- Department of Civil, Construction, and Environmental Engineering, Oregon State University, Corvallis 97331-2302, USA.
| |
Collapse
|
25
|
Abstract
The complete sequencing of several microbial genomes has resulted in the increased availability of genes for metabolic engineering. The number of databases and computational tools to deal with this information has also increased. This development has stimulated, and will continue to stimulate, advances in metabolic engineering. Specific recent advances include improvement of pathways for aromatic metabolites, the development of a more complete understanding of the effect of bacterial hemoglobin on cell performance, the development of NMR-based methods for the monitoring of intracellular metabolites and metabolic flux, and the application of metabolic control analysis and metabolic flux analysis to a variety of systems.
Collapse
|