# Patent

## Title
DNA FRAGMENT CARRYING TOLUENE MONOOXYGENASE, GENE, RECOMBINANT PLASMID, TRANSFORMED MICROORGANISM, METHOD FOR DEGRADING CHLORINATED ALIPHATIC HYDROCARBON COMPOUNDS AND AROMATIC COMPOUNDS, AND METHOD FOR ENVIRONMENTAL REMEDIATION

## Abstract

A recombinant DNA is constructed by using a toluene monooxygenase gene isolated from Ralstonia eutropha strain TB64 and employed to provide the transformant which can express toluene monooxygenase useful for cleaning of aqueous media such as drain and waste water containing halogenated aliphatic hydrocarbon compounds or aromatic compounds, for remediation of soil polluted with such compounds, and cleaning of air (gas phase) polluted with volatile organic chlorine compounds.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a division of parent application Ser. No. 09/453,956 filed on Dec. 3, 1999 now U.S. Pat. No. 6,472,191.


BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention relates to a novel DNA fragment carrying a toluene monooxygenase gene, a novel recombinant DNA containing the DNA fragment, a transformant containing the recombinant DNA, and a method for degrading chlorinated aliphatic hydrocarbon compounds such as trichloroethylene (TCE) and dichloroethylene (DCE) and aromatic compounds such as toluene, benzene, phenol, and cresol. The present invention also relates to a method for environmental remediation useful for cleaning of aqueous media such as wastewater and effluent containing at least either a chlorinated aliphatic hydrocarbon compound or an aromatic compound and air (gas phase) and soil polluted with chlorinated aliphatic hydrocarbon compounds.
2. Related Background Art
Recently, it has become a serious problem the environmental pollution with volatile organic chlorinated compounds which are harmful to the organisms and hardly degradable. Especially, the soil in the industrial areas in Japan as well as abroad is considered to be contaminated with chlorinated aliphatic hydrocarbon compounds such as tetrachloroethylene (PCE), trichloroethylene (TCE), and dichloroethylene (DCE) and aromatic compounds such as toluene, benzene, phenol, and cresol. In fact, there have been a number of reports on actual detection of such pollutants through environmental surveys. It is supposed that these compounds remaining in soil dissolve in ground water via rainwater, and thereby spread over the surrounding areas. There is a strong suspicion that these compounds are carcinogens, and further, these are quite stable in the environment; therefore contamination of groundwater, which is used as a source of drinking water, has become a serious social problem. Therefore, cleaning of soil and aqueous media such as contaminated groundwater by removal and degradation of these compounds and accompanying cleaning of the surrounding gas phase is quite important in view of the environment protection, and technologies for remedying the environment (for example, adsorption treatment using activated carbon, degradation treatment using light and heat) have been developed. Current technologies, however, are not always practical in terms of cost and operability. Recently, microbial degradation of chlorinated aliphatic hydrocarbon compounds such as TCE that is stable in environment has been reported. The microbial degradation method has advantages such as: (1) degradation of chlorinated aliphatic hydrocarbon compounds into harmless substances by using appropriately selected microorganism; (2) no requirement for any special chemicals in principle; and (3) reduction of the labor and costs of maintenance.
The examples of microorganisms capable of degrading TCE are as follows:
Welchia alkenophila sero 5 (U.S. Pat. No. 4,877,736, ATCC 53570, Welchia alkenophila sero 33 (U.S. Pat. No. 4,877,736, ATCC 53571), Methylocystis sp. Strain M (Agric. Biol. Chem., 53, 2903 (1989), Biosci. Biotech. Bichem., 56, 486 (1992), ibid. 56, 736 (1992)), Methylosinus trichosporium OB3b (Am. Chem. Soc. Natl. meet. Div. Environ. Microbiol., 29, 365 (1989), Appl. Environ. Microbiol., 55, 3155 (1989), Appl. Biochem. Biotechnol. 28, 877 (1991), Japanese Patent Application Laid-Open No. 2-92274 specification, Japanese Patent Laid-Open Application No. 3-292970), Methylomonas sp. MM2 (Appl. Environ. Microbiol., 57, 236 (1991), Alcaligenes denitrificans ssp. Xylosoxidans JE75 (Arch. Microbiol., 154, 410 (1990), Alcaligenes eutrophus JMP134 (Appl. Environ. Microbiol., 56, 1179 (1990), Alcaligenes eutrophus FERM-13761 (Japanese Patent Laid-Open Application No. 7-123976), Pseudomonas aeruginosa J1104 (Japanese Patent Application Laid-Open No. 7-236895), Mycobacterium vaccae J0B5 (J. Gen. Microbiol., 82, 163 (1974), Appl. Environ. Microbiol., 55, 2960 (1989), ATCC 29678), Pseudomonas putida BH (Gesuidou Kyoukai-shi (Japan Sewage Works Association Journal), 24, 27 (1987)), Pseudomonas sp. strain G4 (Appl. Environ. Microbiol., 52, 383 (1968), ibid. 53, 949 (1987), ibid. 54, 951 (1988), ibid. 56, 279 (1990), ibid. 57, 193 (1991), U.S. Pat. No. 4,925,802, ATCC 53617, this strain was first classified as Pseudomonas cepacia and then changed to Pseudomonas sp.), Pseudomonas mendocia KR-1 (Bio/Technol.; 7, 282 (1989)), Pseudomonas putida F1 (Appl. Environ Microbiol., 54, 1703 (1988), ibid. 54, 2578 (1988)), fluorescens PFL12 (Appl. Environ. Microbiol., 54, 2578 (1988)), Pseudomonas putida KWI-9 (Japanese Patent Application Laid-Open No. 6-70753), Burkholderia cepacia KK01 (Japanese Patent Application Laid-Open No. 6-22769), Nitrosomonas europaea (Appl. Environ. Microbio., 56, 1169 (1990), Lactobacillus vaginalis sp. nov (Int. J. Syst. Bacteriol., 39, 368 (1989), ATCC 49540), Nocardia corallina B-276 (Japanese Patent Application Laid-Open No. 8-70881, FERM BP-5124, ATCC 31338), and so on.
The problem in actually using these degrading microorganisms in environmental remediation treatment, however, resides in optimizing and maintaining expression of their degradation activity for chlorinated aliphatic hydrocarbon compounds such as TCE. In an environmental remediation treatment which utilizes phenol, toluene, methane, or the like as an inducer, continuous supply of the inducer is indispensable, since depletion of such inducers directly results in stoppage of degradation of chlorinated aliphatic hydrocarbon compounds. Presence of such inducers, on the other hand, may inhibit the efficient degradation of the target substance such as TCE, since the affinity of the chlorinated aliphatic hydrocarbon compounds such as TCE as a substrate is considerably low in comparison with these inducers. In addition, precise control of the inducer concentration on the treatment spot is difficult.
Thus, use of an inducer is a large problem in practical application of environmental remediation treatment utilizing microorganisms.
In order to solve the problem, Nelson et al. developed a method using tryptophan as an inducer for degradation of volatile organic chlorinated compounds (Japanese Patent Application Laid-Open No. 4-502277). Tryptophan, however, is a very expensive substance, and although tryptophane has no toxicity or risk as a substance, it is not preferable to introduce excessive carbon and nitrogen sources into environment since it may induce eutrophication. In addition, the problem that tryptophan serves as a competitive inhibitor in degradation of TCE still remains.
Shields et al. obtained a mutant strain of Pseudomonas cepacia G4 (changed to Pseudomonas sp. upon deposition to ATCC) by the transposon technique, which mutant strain does not require an inducer (in this case, phenol or toluene) and can degrade TCE (Appl. Environ. Microbiol., 58, 3977 (1992), International Publication No. WO/19738). Also, a mutant not requiring methane as the inducer has been isolated from Methylosinus trichosporium OB3b, a methanotroph capable of degrading TCE (U.S. Pat. No. 5,316,940).
Japanese Patent Application Laid-Open No. 8-294387 also discloses strain JM1 (FERM BP-5352) capable of degrading volatile organic chlorinated compounds and aromatic compounds without requiring an inducer, isolated by nitrosoguanidine mutagenization of strain J1 (FERM BP-5102). While, it has been studied to introduce resting cells expressing TCE-degrading activity into the remediation site after the preculture of the cells in the presence of an inducer (Environ. Sci. Technol., 30, 1982 (1996)).
It has been reported that remediation treatment not requiring the inducer actually makes the remediation treatment easy and efficient compared to the conventional treatment using inducers.
However, the growth control of the degrading microorganisms is very important for both the expression of the degradation activity on demand and the continuation of degradation. When resting cells are used, it is a problem to be solved that TCE cannot be degraded beyond the amount and period of degradation capacity of the introduced resting cells. In addition, in a large scale treatment, there are further problems that degradation activity will decrease since it takes a long time to prepare resting cells; the treating apparatus must be large in scale; treatment process is complicated; and the cost may be unfavorably high. Accordingly, it has been attempted to introduce a plasmid carrying a DNA fragment containing a gene region encoding oxygenase or hydroxylase into a host microorganism to make the host express the TCE degradation activity constitutively or inducibly using a harmless inducer. For example, there are Pseudomonas mendocina KR-1 (Japanese Patent Application Laid-Open No. 2-503866, Pseudomonas putida KWI-9 (Japanese Patent Application Laid-Open No. 6-105691), Pseudomonas putida BH (Summary of 3rd Conference on Pollution of Ground Water/Soil and Its Protective Countermeasure, p.213 (1994)), and a transformant carrying both a toluene degradation enzyme gene derived from Pseudomonas putida F1 and a biphenyl degradation enzyme gene derived from Pseudomonas pseudoalkaligenes (Japanese Patent Application Laid-Open No. 7-143882). However, the reported TCE degradation activity of the transformants are low, and the advantages of the transformants has not been fully exploited for efficient degradation of TCE, such as the ease of degradation control, freedom in designing recombinant, and no requirements for inducers, far from efficient TCE degradation.
SUMMARY OF THE INVENTION
It is an object of the present invention to provide a novel DNA fragment encoding a toluene monooxygenase of a high efficiency in degrading aromatic compounds and/or organic chorine compounds, a novel recombinant DNA containing the DNA fragment, and a transformant containing the recombinant DNA. It is another object of the present invention to provide an efficient biodegradation method for halogenated aliphatic compounds such as trichloroethylene (TCE) and dichloroethylene (DCE) and aromatic compounds such as toluene, benzene, phenol, and cresol using the transformant, specifically an efficient environmental remediation method useful for cleaning aqueous media such as wastewater and effluent containing halogenated aliphatic hydrocarbon compounds and/or aromatic compounds, remedying soil polluted with halogenated aliphatic hydrocarbon compounds or aromatic compounds, and cleaning air (gas phase) polluted with halogenated aliphatic hydrocarbon compounds.
The inventors of the present invention isolated a microorganism Ralstonia eutropha strain TB64 having a toluene monooxygenase that oxidizes toluene to ortho-cresol and 3-methylcatechol and deposited it in the National Institute of Bioscience and Human Technology, Agency of Industrial Science and Technology in accordance with the requirements of the Budapest Treaty, Deposit Date: Sep. 3, 1998, Accession No. FERM BP-6933). The inventors strained to isolate the toluene monooxygenase gene from the above strain TB64 and successful isolation and characterization of the gene completed the present invention.
According to one aspect of the present invention, there is provided a DNA fragment of about 5.3 Kb containing a toluene monooxygenase gene, having 3 BamHI, 1 ClaI, 1 EcoRI, 3 KpnI, 2 NcoI, 2 NspV, 2 ScaI, 2 SmaI, 2 SphI, 1 StuI, 0 DraI, 0 EcoRV, 0 HindIII, 0 HpaI, 0 NdeI, 0 PvuII, 0 ScaI, 0 Sse83871, 0 XbaI, 0 XhoI restriction sites, and having a restriction map of: 




According to another aspect of the present invention, there is provided a DNA fragment having a nucleotide sequence of SEQ ID NO: 1 in the Sequence Listing.
According to another aspect of the present invention, there is provided a DNA fragment having a nucleotide sequence of SEQ ID NO: 1 with deletion, substitution, and/or addition of one or more nucleotides encoding a protein having a toluene monooxygenase activity.
According to another aspect of the present invention, there is provided a recombinant DNA comprising a vector which can be replicate or maintained in a host and the above mentioned DNA fragment.
According to another aspect of the present invention, there is provided a DNA fragment containing a portion encoding a toluene monooxygenase, the portion comprising a region encoding a polypeptide TomL having an amino acid sequence of SEQ ID NO: 3, a region encoding a polypeptide TomM having an amino acid sequence of SEQ ID NO: 4, a region encoding a polypeptide TomN having an amino acid sequence of SEQ ID NO: 5, a region encoding a polypeptide TomO having an amino acid sequence of SEQ ID NO: 6, and a region encoding a polypeptide TomP having an amino acid sequence of SEQ ID NO: 7 of the Sequence Listing, and the regions are aligned so that expressed TomL-TomP polypeptides can form an active monooxygenase protein.
According to still another aspect of the present invention, there is provided a recombinant DNA comprising a vector, a promoter, and the above mentioned DNA fragment, wherein the vector and the promoter are functionally ligated to the DNA fragment to enable expression of the toluene monooxygenase encoded by the DNA fragment in the host.
According to still another aspect of the present invention, there is provided a DNA fragment comprising a region encoding a polypeptide TomK which has an amino acid sequence of SEQ ID NO: 2 and a property to enhance the toluene monooxygenase activity of a protein comprised of at least TomL-TomP; or a region encoding a variant TomK in which the amino acid sequence of SEQ ID NO: 2 is altered with the proviso that the property to enhance the toluene monooxygenase activity is not impaired.
According to still another aspect of the present invention, there is provided another recombinant DNA comprising a vector, a promoter, a first DNA fragment and a second DNA fragment;
wherein the first DNA encodes a toluene monooxygenase and comprises a region encoding a polypeptide TomL having an amino acid sequence of SEQ ID NO: 3, a region encoding a polypeptide TomM having an amino acid sequence of SEQ ID NO: 4, a region encoding a polypeptide TomN having an amino acid sequence of SEQ ID NO: 5, a region encoding a polypeptide TomO having an amino acid sequence of SEQ ID NO: 6, and a region encoding a polypeptide TomP having an amino acid sequence of SEQ ID NO: 7 of the Sequence Listing,
the second DNA fragment encodes a polypeptide TomK having an amino acid sequence of SEQ ID NO: 2 and a property to enhance the toluene monooxygenase activity of a protein comprised of at least TomL to TomP; or encodes a variant TomK polypeptide in which the amino acid sequence of SEQ ID NO: 2 is altered with the proviso that the property to enhance the toluene monooxygenase activity is not impaired;
the first DNA fragment is functionally linked to the promoter to express the toluene monooxygenase activity, and the second DNA fragment is functionally linked to the promoter to express the property to enhance the activity of the toluene monooxygenase encoded by the first DNA fragment.
According to still another aspect of the present invention, there is provided a recombinant DNA comprising a vector; a first promoter and a first DNA fragment; and a second promoter and a second DNA fragment;
wherein the first DNA encodes a toluene monooxygenase and comprises a region encoding a polypeptide TomL having an amino acid sequence of SEQ ID NO: 3, a region encoding a polypeptide TomM having an amino acid sequence of SEQ ID NO: 4, a region encoding a polypeptide TomN having an amino acid sequence of SEQ ID NO: 5, a region encoding a polypeptide TomO having an amino acid sequence of SEQ ID NO: 6, and a region encoding a polypeptide TomP having an amino acid sequence of SEQ ID NO: 7 of the Sequence Listing,
the second DNA fragment encodes a polypeptide TomK having an amino acid sequence of SEQ ID NO: 2 and a property to enhance the toluene monooxygenase activity of a protein comprised of at least TomL to TomP; or encodes a variant TomK polypeptide in which the amino acid sequence of SEQ ID NO: 2 is altered with the proviso that the property to enhance the toluene monooxygenase activity is not impaired;
the first DNA fragment is functionally linked to the first promoter to express the toluene monooxygenase activity, and the second DNA fragment is functionally linked to the second promoter to express the property to enhance the activity of the toluene monooxygenase encoded by the first DNA fragment.
According to still another aspect of the present invention, there is provided a transformant obtainable by introducing a recombinant DNA into a host microorganism, the recombinant DNA comprising a vector which can replicate or maintained in the host and ligated to a DNA fragment of about 5.3 Kb containing a toluene monooxygenase gene, having 3 BamHI, 1 ClaI, 1 EcoRI, 3 KpnI, 2 NcoI, 2 NspV, 2 ScaI, 2 SmaI, 2 SphI, 1 StuI, 0 DraI, 0 EcoRV, 0 HindIII, OHpaI, 0 NdeI, 0 PvuII, 0 ScaI, 0 Sse83871, 0 XbaI, 0 XhoI restriction sites, and having a restriction map of: 




According to still another aspect of the present invention, there is provided a transformant obtainable by introducing a recombinant DNA comprising the DNA fragment having a nucleotide sequence of SEQ ID NO: 1 and ligated to a vector which can replicate or maintained in the host.
According to still another aspect of the present invention, there is provided a transformant obtainable by introducing into a host microorganism a recombinant DNA which comprises a vector, a promoter, and a DNA fragment, wherein the vector and the promoter are functionally ligated to the DNA fragment to enable expression of the toluene monooxygenase encoded by the DNA fragment in the host,
wherein the DNA fragment comprises a region sequence of SEQ ID NO: 3, a region encoding a polypeptide TomM having an amino acid sequence of SEQ ID NO: 4, a region encoding a polypeptide TomN having an amino acid sequence of SEQ ID NO: 5, a region encoding a polypeptide TomO having an amino acid sequence of SEQ ID NO: 6, and a region encoding a polypeptide TomP having an amino acid sequence of SEQ ID NO: 7 of the Sequence Listing.
Further, according to still another aspect of the present invention, there is provided a transformant obtainable by introducing into a host microorganism a recombinant DNA comprising a vector, a promoter, a first DNA fragment, and a second DNA fragment;
wherein the first DNA encodes a toluene monooxygenase and comprises a region encoding a polypeptide TomL having an amino acid sequence of SEQ ID NO: 3, a region encoding a polypeptide TomM having an amino acid sequence of SEQ ID NO: 4, a region encoding a polypeptide TomN having an amino acid sequence of SEQ ID NO: 5, a region encoding a polypeptide TomO having an amino acid sequence of SEQ ID NO: 6, and a region encoding a polypeptide TomP having an amino acid sequence of SEQ ID NO: 7 of the Sequence Listing,
the second DNA fragment encodes a polypeptide TomK having an amino acid sequence of SEQ ID NO: 2 and a property to enhance the toluene monooxygenase activity of a protein comprised of at least TomL to TomP; or encodes a variant TomK polypeptide in which the amino acid sequence of SEQ ID NO: 2 is altered with the proviso that the property to enhance the toluene monooxygenase activity is not impaired;
the first DNA fragment is functionally linked to the promoter to express the toluene monooxygenase activity, and the second DNA fragment is functionally linked to the promoter to express the property to enhance the activity of the toluene monooxygenase encoded by the first DNA fragment.
Further, according to still another aspect of the present invention there is provided a transformant obtainable by introducing into a host microorganism a recombinant DNA comprising a vector, a first promoter and a first DNA fragment, and a second promoter and a second DNA fragment;
wherein the first DNA encodes a toluene monooxygenase and comprises a region encoding a polypeptide TomL having an amino acid sequence of SEQ ID NO: 3, a region encoding a polypeptide TomM having an amino acid sequence of SEQ ID NO: 4, a region encoding a polypeptide TomN having an amino acid sequence of SEQ ID NO: 5, a region encoding a polypeptide TomO having an amino acid sequence of SEQ ID NO: 6, and a region encoding a polypeptide TomP having an amino acid sequence of SEQ ID NO: 7 of the Sequence Listing,
the second DNA fragment encodes a polypeptide TomK having an amino acid sequence of SEQ ID NO: 2 and a property to enhance the toluene monooxygenase activity of a protein comprised of at least TomL to TomP; or encodes a variant TomK polypeptide in which the amino acid sequence of SEQ ID NO: 2 is altered with the proviso that the property to enhance the toluene monooxygenase activity is not impaired;
the first DNA fragment is functionally linked to the first promoter to express the toluene monooxygenase activity, and the second DNA fragment is functionally linked to the second promoter to express the property to enhance the activity of the toluene monooxygenase encoded by the first DNA fragment.
According to still another aspect of the present invention, there is provided a method for producing a toluene monooxygenase, which comprises a step of making an above transformant produce a toluene monooxygenase being a gene product of the DNA fragment introduced into the transformant.
According to still another aspect of the present invention, there is provided a method for degrading at least either of a chlorinated aliphatic hydrocarbon compound or an aromatic compound, which comprises a step of degrading at least either of the chlorinated aliphatic hydrocarbon compound or aromatic compound using the transformant according to any one of the aspects of the present invention mentioned above.
According to still another aspect of the present invention, there is provided a method for remedying an environment polluted with at least either of a chlorinated aliphatic hydrocarbon compound or an aromatic compound as a pollutant, comprising a step of degrading the pollutants using the transformant according to any one of the aspects of the present invention mentioned above.
According to still another aspect of the present invention, there is provided a component polypeptide having any one of amino acid sequences of SEQ ID Nos: 2-8, which can constitute a toluene monooxygenase.
According to still another aspect of the present invention, there is provided a toluene monooxygenase comprising at least component polypeptides TomL-TomP of amino acid sequences of SEQ ID NOs: 3-7.
According to still another aspect of the present invention, there is provided a variant toluene monooxygenase obtainable by mutating the above mentioned toluene monooxygenase not to loose the enzyme activity.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows a restriction map of a DNA fragment of about 5.3 Kb carrying a toluene monooxygenase gene; of about 5.3 Kb carrying a toluene monooxygenase gene;
FIG. 2 is comprised of FIGS. 2A, 2B, 2C, 2D, 2E, 2F, 2G, 2H, 2I, 2J, 2K, 2L, 2M, 2N, 2O, 2P, 2Q, 2R and 2S showing a nucleotide sequence (SEQ ID NO: 1) of a toluene monooxygenase gene of FERM BP-6933;
FIG. 3 is an amino acid sequence (TomK) (SEQ ID NO: 2) encoded by a region tomK (nucleotides 200 to 445 of SEQ ID NO: 1) in the nucleotide sequence of FIGS. 2A to 2S;
FIG. 4 is comprised of FIGS. 4A, 4B and 4C showing an amino acid sequence (TomL) (SEQ ID NO: 3) encoded by a region tomL (nucleotides 446 to 1437 of SEQ ID NO: 1) in the nucleotide sequence of FIGS. 2A to 2S;
FIG. 5 is an amino acid sequence (TomM) (SEQ ID NO: 4) encoded by a region tomM (nucleotides 1470 to 1739 of SEQ ID NO: 1) in the nucleotide sequence of FIGS. 2A to 2S;
FIG. 6 is comprised of FIGS. 6A, 6B, 6C and 6D showing an amino acid sequence (TomN) (SEQ ID NO: 5) encoded by a region tomN (nucleotides 1777 to 3324 of SEQ ID NO: 1) in the nucleotide sequence of FIGS. 2A to 2S;
FIG. 7 is an amino acid sequence (TomO) (SEQ ID NO: 6) encoded by a region tomO (nucleotides 3341 to 3697 of SEQ ID NO: 1) in the nucleotide sequence of FIGS. 2A to 2S;
FIG. 8 is comprised of FIGS. 8A, 8B and 8C showing an amino acid sequence (TomP) (SEQ ID NO: 7) encoded by a region tomP (nucleotides 3737 to 4795 of SEQ ID NO: 1) in the nucleotide sequence of FIGS. 2A to 2S;
FIG. 9 is an amino acid sequence (TomQ) (SEQ ID NO: 8) encoded by a region tomO (nucleotides 4797 to 5132 of SEQ ID NO: 1) in the nucleotide sequence of FIGS. 2A to 2S;
FIG. 10 is a nucleotide sequence (SEQ ID NO: 9) of a first primer employed in Example 6;
FIG. 11 is a nucleotide sequence (SEQ ID NO: 10) of a second primer employed in Example 6;
FIG. 12 is a nucleotide sequence (SEQ ID NO: 11) of a third primer employed in Example 6; and
FIG. 13 is a nucleotide sequence (SEQ ID NO: 12) of a fourth primer employed in Example 6.
FIG. 14 is a nucleotide sequence (SEQ ID NO: 13) of a tom-KB primer employed in Example 7.
FIG. 15 is a nucleotide sequence (SEQ ID NO: 14) of a tom-KBT primer employed in Example 7.



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
The DNA fragment containing a toluene monooxygenase gene according to the present invention is isolated from Ralstonia eutropha strain TB64 (FERM BP-6933, hereinafter referred to as Strain TB64). The microbiological characteristics and culture conditions of Strain TB64 are described later.
Strain TB64 can be cultured, for example, by inoculating an M9 liquid medium containing 0.1% yeast extract and 2 mM phenol with a colony of strain TB64 grown on an M9 agar medium supplemented with 0.2% yeast extract, followed by culture at 30° C. In this case, culture period of about 20 hours is suitable.
Isolation of the DNA fragment according to the present invention is achieved by partial digestion of the total DNA of Strain TB64 with a restriction enzyme Sau3AI. Specifically, total DNA can be prepared by the standard method, in which the above microorganism is grown in a suitable medium, for example, LB medium (containing 10 g of tryptone, 5 g of yeast extract, and 5 g of sodium chloride in 1 litter) and then cells are disrupted, for example, in the presence of sodium dodecyl sulfate (SDS) at 70° C. The total DNA is then partially digested by Sau3AI to obtain a DNA fragment containing about 5.8 Kb region carrying a toluene monooxygenase gene. The DNA fragment thus obtained is ligated to a plasmid vector completely digested by BamHI, for example, pUC18, and the recombinant vector is introduced into competent cells of, for example, E. coli JM109, prepared by the Hanahan method to obtain transformants. Then, transformants can be selected by a suitable method, for example, by culturing cells on an LB medium plate containing ampicillin.
In order to select a transformant containing a recombinant vector carrying a toluene monooxygenase gene from the above transformants, it is preferable to add cresol, phenol, or the like to LB medium for transformant selection in advance. The transformant carrying a toluene monooxygenase gene can be selected as brown colonies, since these substrates are monooxygenated by toluene monooxygenase to produce methylcatechol or catechol which is then autooxidized to develop color. Alternatively, after culturing cells on an ordinary LB medium plate, various substrates may be sprayed onto the plate to select brown colonies in a similar manner.
The isolated DNA fragment of about 5.3 Kb has the following restriction sites:
Restriction Enzyme Number of Restriction Sites
















BamHI
3



ClaI
1



EcoRI
1



KpnI
3



NcoI
2



NspV
2



ScaI
2



SmaI
2



SphI
2



StuI
1










The DNA fragment has no DraI, EcoRV, HindIII, HpaI, NdeI, NheI, PvuII, SacI, Sse8387I, XbaI or XhoI restriction site.
The restriction map of the DNA fragment of the present invention is as shown above. Toluene monooxygenase genes derived from Burkholderia cepacia G4 5223 PR1 (U.S. Pat. No. 5,543,317), derived from Burkholderia sp. JS150 (Appl. Environ. Microbiol., 61, 3336 (1995), derived from Pseudomonas pickettii PK01 (J. Bacteriol., 176, 3749 (1994)), and derived from Pseudomonas mendocina KR1 (J. Bacteriol., 173, 3010 (1991)) were reported. Phenol hydroxylases reported to have a similar structure are derived from Acinetobacter calcoaceticus NCIIB8250 (Mol. Microbiol., 18, 13 (1995)), Pseudomonas sp. CF600 (J. Bacteriol., 172, 6826 (1990)), Pseudomonas spp. (J. Bacteriol., 177, 1485 (1995)), and Pseudomonas putida P35X (Gene, 151, 29 (1994)). The DNA fragment of the present invention has, however, a restriction map different from any of those. It is thus clear that the DNA fragment of the present invention contains a novel toluene monooxygenase gene.
Although the DNA fragment thus obtained can sufficiently enables the degradation of aromatic compounds and/or halogenated aliphatic hydrocarbon compounds even in pUC18, it can be integrated in an expression vector or a vector of a wide host range to improve the degradation ability or to be optimized for the treatment site.
The plasmid according to the present invention can be constructed from following elements:
1) Toluene monooxygenase gene;
2) Marker gene (drug-resistance, auxotrophic complement, or the like); and
3) Vector containing an autonomous replication sequence (plasmid, or the like).
As the toluene monooxygenase gene, the DNA fragment of about 5.3 kb as shown above can be employed by itself, or a constitution containing elements necessary for a toluene monooxygenase activity can be also employed, for example, with or without spacer sequences. Further, each element can be varied with the proviso that its function is not impaired. These variations can be attained by changing DNA sequences encoding them.
As the drug-resistance genes, an ampicillin resistance gene, a kanamycin (G418, neomycin) resistance gene, a tetracycline resistance gene, a chloramphenicol resistance gene, a hygromycin resistance gene can be employed. For auxotrophic complement, a gene sequence to supply the nutrient required by the host organism is used. Typically, a gene enabling the synthesis of the required amino acid is utilized.
As the autonomous replication sequences, a sequence derived from plasmid RSF1010, which can function as a wide host range replication region in most of the gram-negative bacteria, can be employed. It can be also employed vector pBBR122 (Mo Bi Tec) containing a wide host range replication region which does not belong to any incompatible groups, IncP, IncQ, or IncW or the like.
For the recombinant plasmid according to the present invention, various promoters and terminators can be employed and various factors can be further introduced to improve and control the ability of degrading aromatic compounds and/or halogenated aliphatic hydrocarbon compounds. Specifically, promoters such as lac, trc, tac T3, and T7 can be employed. As a terminator, an rrnB operon terminator or the like can be employed. Also, introduction of a repressor gene such as lacIq and a lac operator enables expression control with an inducer such as isopropyl thiogalactoside (IPTG). Alternatively, the absence of these suppressor and operator as elements, enables constitutive expression of degradation activity. In addition, a temperature-sensitive control system or the like can be employed.
For recombination of a DNA fragment containing the toluene monooxygenase gene into an expression vector containing these regulating elements, natural restriction sites can be utilized as it is, or restriction sites may be newly created by site-directed mutagenesis or a polymerase chain reaction using a primer involving base substitution. In general, recombination into an expression vector often utilizes NcoI restriction sites. It is convenient to design so as to create an NcoI restriction site in the initiation codon ATG or GTG region by site-directed mutagenesis or primer design. Known methods using an adaptor can be employed. For optimization of expression, the DNA fragment may be properly deleted using exonuclease III or Bal31 nuclease. As described above, molecular biological techniques suitable for the purpose can be employed for recombination into an expression vector.
As a method for introducing the recombinant plasmid carrying a desired gene into a host organism, any methods that can introduce a foreign gene into a host can be employed, and known methods, for example, the calcium chloride method, the electroporation method, and the conjugation transfer method can be employed.
In the present invention, any microorganisms can be used as a host organism so long as it can express the aromatic compounds and/or halogenated aliphatic hydrocarbon compounds-degrading activity after the introduction of the recombinant plasmid, including the genera Escherichia, Pseudomonas, Burkholderia, Acinetobacter, Moraxella, Alcaligenes, Vibrio, Nocardia, Bacillus, Lactobacillus, Achromobacter, Arthrobacter, Micrococcus, Mycobacterium, Methylosinus, Methylomonas, Welchia, Methylocystis, Nitrosomonas, Saccharomyces, Candida, Torulopsis, and Ralstonia. 
In addition, the aromatic compounds and/or halogenated aliphatic hydrocarbon compounds-degrading microorganisms such as strain J1, strain JM1, Pseudomonas sp. strain TL1, strain KK01, Pseudomonas alcaligenes strain KB2, Alcaliqenes sp. strain TL2, and Vibrio sp. strain KB1 can be employed as a host. These strains have been deposited in the National Institute of Bioscience and Human Technology, Agency of Industrial Science and Technology of Japan. The date of deposit, Accession No., and microbiological characteristics of these strains are shown below.
<Strain KK01 (Deposit Date: Mar. 11, 1992, Accession No. FERM BP-4235)>
A. Morphological Characteristics


    (1) Gram staining: Negative
    (2) Size and shape: Rod of 1.0-2.0 μm in length and 0.5 μm in width
    (3) Motility: Motile

B. Growth on Various Culture Media















Medium
Growth temperature (° C.)
Growth

















Blood agar medium
37
+


Lactose agar medium
37
+


Chocolate agar medium
37
++


GMA
37
−


Scyllo
37
−


Standard agar medium
4
−


Standard agar medium
25
±


Standard agar medium
37
+


Standard agar medium
41
±









C. Physiological Characteristics

    (1) Aerobic or anaerobic: Obligate aerobic
    (2) Sugar degradation mode: Oxidation
    (3) Oxidase production: +
    (4) Silver nitrate reduction: +
    (5) Hydrogen sulfide production: −
    (6) Indole production: −
    (7) Urease production: −
    (8) Gelatin liquefaction: −
    (9) Arginine hydrolysis: −
    (10) Lysine decarboxylation: +
    (11) Ornithine decarboxylation: −
    (12) Utilization of citric acid: +
    (13) Methyl carbinol acetyl reaction (VP reaction): −
    (14) Detection of tryptophan deaminase: −
    (15) ONPG:
    (16) Assimilation of carbohydrates
    
        Glucose: +
        Fructose: +
        Maltose: +
        Galactose: +
        Xylose: +
        Mannitol: ±
        Sucrose: −
        Lactose: +
        Esculin: −
        Inositol: −
        Sorbitol: −
        Rhamnose: −
        Melibiose: −
        Amygdalin: −
        L-(+)-arabinose: +

Strain J1 (Deposit Date: May 25, 1994, Accession No. FERM BP-5102)

A. Morphological Characteristics

        Gram staining: Positive
        Size and shape of cells: Polymorphous rod of 1-6
        μm in length and about 0.5-2 μm in width
        Mobility: Negative
        Colony: Cream to light pink, sticky

B. Growth on Various Media

        BHIA: Good growth
        MacConkey: No growth

C. Optimal Temperature for Growth: 25° C.>30° C.>35° C.

D. Physiological Characteristics

        Aerobic or anaerobic: aerobic
        TSI (slant/butt): Alkaline/alkaline, H2S (−)
        Oxidase: Negative
        Catalase: Positive
        Sugar fermentation
        
            Glucose: Negative
            Sucrose: Negative
            Raffinose: Negative
            Galactose: Negative
            Maltose: Negative
            Urease: Positive
            Esculin: Positive
            Nitric acid: Negative

Strain JM1 (Deposit Date: Jan. 10, 1995, Accession No. FERM BP-5352)

        
        
        Gram staining and morphology: Gram-negative rod
        Growth on various media
        
            BHIA: Good growth
            MacConkey: Possible to grow
        
        
        Colony color: Cream
        Optimal temperature for growth: 25° C.>30° C.>35° C.
        Mobility: Negative (semi-fluid medium)
        TSI (slant/butt): Alkaline/alkaline, H2S (−)
        Oxidase: Positive (weak)
        Catalase: Positive
        Sugar fermentation
        
            Glucose: Negative
            Sucrose: Negative
            Raffinose: Negative
            Galactose: Negative
            Maltose: Negative
        
        
        Urease: Positive
        Esculin hydrolysis (β-glucosidase): Positive
        Nitrate reduction: Negative
        Indole production: Negative
        Glucose acidification: Negative
        Arginine dehydrase: Negative
        Gelatin hydrolysis (protease): Negative
        β-Galactosidase: Negative
        Assimilation of compounds
        
            Glucose: Negative
            L-Arabinose: Negative
            D-Mannose: Negative
            D-Mannitol: Negative
            N-Acetyl-D-glucosamine: Negative
            Maltose: Negative
            Potassium gluconate: Negative
            n-Capric acid: Positive
            Adipic acid: Negative
            dl-Malic acid: Positive
            Sodium citrate: Positive
            Phenyl acetate: Negative

Strain TL1 (Deposit Date: Jan. 10, 1995, Accession No. FERM P-14726/FERM BP-6923.

A. Gram Staining and Morphology: Gram-Negative Rod

B. Growth on Various Media

        
        
        Standard agar: Good growth
        MacConkey agar: Poor growth

C. Optimal Temperature for Growth: 25° C.>35° C.

D. Physiological Characteristics

        Aerobic/anaerobic: Aerobic
        TSI (slant/butt): Alkaline/alkaline, H2S (−)
        Oxidase: Positive
        Catalase: Positive
        Oxidation/fermentation test: −/−
        Potassium nitrate reduction: Negative
        Indole production from L-tryptophan: Negative
        Glucose acidification: Negative
        Arginine dehydrase: Negative
        Urease: Negative
        Esculin hydrolysis (β-glucosidase): Negative
        Gelatin hydrolysis (protease): Negative
        β-Galactosidase: Negative
        Cytochrome oxidase: Positive

E. Assimilation of Sugars, Organic Acids, etc.

        Glucose: Positive
        L-Arabinose: Positive
        D-Mannose: Negative
        D-Mannitol: Positive
        N-Acetyl-D-glucosamine: Negative
        Maltose: Negative
        Potassium gluconate: Positive
        n-Capric acid: Negative
        Adipic acid: Positive
        dl-Malic acid: Negative
        Sodium citrate: Negative
        Phenyl acetate: Negative

Strain TL2 (Deposit Date on Nov. 15, 1994, Accession No. FERM BP-6913.

A. Gram Staining and Morphology: Gram-Negative Rod

B. Growth on Various Media

        Standard agar: Good growth
        MacConkey agar: Poor growth

C. Optimal Temperature for Growth: 25° C.>35° C.

D. Physiological Characteristics

        Aerobic/anaerobic: Aerobic
        TSI (slant/butt): Alkaline/alkaline, H2S (−)
        Oxidase: Positive
        Catalase: Positive
        Oxidation/fermentation test: −/−
        Potassium nitrate reduction: Positive
        Indole production from L-tryptophan: Negative
        Glucose acidification: Negative
        Arginine dehydrase: Negative
        Urease: Negative
        Esculin hydrolysis (β-glucosidase): Negative
        Gelatin hydrolysis (protease): Negative
        β-Galactosidase: Negative
        Cytochrome oxidase: Positive

E. Assimilation of Sugars, Organic Acids, etc.

        Glucose: Negative
        L-Arabinose: Negative
        D-Mannose: Negative
        D-Mannitol: Negative
        N-Acetyl-D-glucosamine: Negative
        Maltose: Negative
        Potassium gluconate: Positive
        n-Capric acid: Positive
        Adipic acid: Positive
        dl-Malic acid: Positive
        Sodium citrate: Positive
        Phenyl acetate: Positive

Strain KB1 (Deposit date: Nov. 15, 1994, Accession No. FERM BP-6914.

A. Gram Staining and Morphology: Gram-Negative Rod

B. Growth Conditions on Various Media

        Standard agar: Good growth
        MacConkey agar: Good growth

C. Optimal Temperature for Growth: 25° C.>35° C.

D. Physiological Characteristics

        Aerobic/anaerobic: Aerobic
        TSI (slant/butt): Alkaline/alkaline, H2S (−)
        Catalase: Positive
        Oxidation/fermentation test: −/−
        Potassium nitrate reduction: Positive
        Indole productivity from L-tryptophan: Negative
        Glucose acidification: Negative
        Arginine dehydrase: Positive
        Urease: Positive
        Esculin hydrolysis (β-glucosidase): Negative
        Gelatin hydrolysis (protease): Negative
        β-Galactosidase: Negative
        Cytochrome oxidase: Positive

E. Assimilation of Sugars, Organic Acids, etc.

        Glucose: Negative
        L-Arabinose: Negative
        D-Mannose: Negative
        D-Mannitol: Negative
        N-Acetyl-D-glucosamine: Positive
        Maltose: Negative
        Potassium gluconate: Positive
        n-Capric acid: Positive
        Adipic acid: Positive
        dl-Malic acid: Positive
        Sodium citrate: Negative
        Phenyl acetate: Positive

Strain KB2 (Deposit Date: Nov. 15, 1994, Accession No. FERM BP-5354)

A. Gram Staining and Morphology: Gram-Negative Rod

B. Growth on Various Media

        Standard agar: Good growth
        MacConkey agar: Good growth

C. Optimal Temperature for Growth: 25° C.>35° C.

        Growth at 42° C.: Good

D. Physiological Characteristics

        Aerobic/anaerobic: Aerobic
        TSI (slant/butt): Alkaline/alkaline, H2S (−)
        Catalase: Positive
        Oxidation/fermentation test: −/−
        Potassium nitrate reduction: Positive
        Indole production from L-tryptophan: Negative
        Glucose acidification: Negative
        Arginine dehydrase: Negative
        Urease: Negative
        Esculin hydrolysis (β-glucosidase): Negative
        Gelatin hydrolysis (protease): Negative
        β-Galactosidase: Negative
        Cytochrome oxidase: Positive

E. Assimilation of Sugars, Organic Acids, etc.

        Glucose: Negative
        L-Arabinose: Negative
        D-Mannose: Negative
        D-Mannitol: Negative
        N-Acetyl-D-glucosamine: Negative
        Maltose: Negative
        Potassium gluconate: Positive
        n-Capric acid: Negative
        Adipic acid: Positive
        dl-Malic acid: Positive
        Sodium citrate: Negative
        Phenyl acetate: Negative
    
    


Burkholderia cepacia strain KK01 was once classified into genus Pseudomonas but reclassified into genus Burkholderia since Pseudomonas cepacia has been taxonomically changed to Burkholderia cepacia. The deposited strain KK01 itself, however, is the same.
Strain J1 is an aromatic compound-assimilating bacterium which degrades organic halogenated compounds with the participation of oxygenase. In spite of its excellent ability of degrading organic halogenated compounds that it can almost completely degrade about 20 ppm of TCE at a low temperature of 15° C. close to natural environment such as soil, it requires aromatic compounds such as phenol, toluene, and cresol as a degradation inducer. Strain JM1 was obtained by nitrosoguanidine mutagenization of strain J1, and has the same microbiological characteristics as the parental strain J1 except that it can degrade organic halogenated compounds in the absence of aromatic compounds such as phenol, toluene, and cresol as a degradation inducer.
In order to exploit the microbial degrading ability more effectively, it is preferable to select the host microorganism for recombinants from the microorganisms isolated to the environment to be treated, more preferably a dominant microorganism in the environment, considering environmental adaptation of the recombinant. Generally, in the natural world, microorganisms that have existed in an environment will adapt to the environment most probably, and the probability of the survival of foreign microorganisms introduced into the environment is not high. On the other hand, when a very strong microorganism is introduced from outside, it may disturb the existing ecosystem. Thus, the use of the indigenous microorganisms as a host is a superior method in environmental adaptability, survival, and safety.
A transformant to which a recombinant plasmid has been introduced may be cultured in the conditions suitable for the growth of the host. For example, a carbon and nitrogen source such as yeast extract, tryptone, and peptone, and a inorganic salt such as sodium chloride and potassium chloride can be used. An M9 medium (containing 6.2 g of Na2HPO4, 3.0 g of KH2PO4, 0.5 g of NaCl, and 1.0 g of NH4Cl in 1 litter) supplemented with various minerals and suitable carbon sources such as sodium malate, sodium succinate, sodium lactate, sodium pyruvate, sodium glutamate, sodium citrate, etc. can also be employed. Further, yeast extract, tryptone, peptone, etc. can be used in combination. The pH of the growth medium and culture temperature can be adjusted to those suitable for the host microorganism, although pH of about 5-9 and culture temperature of 15-37° C. are generally preferable.
A transformant containing a recombinant DNA carrying a toluene monooxygenase gene can be suitably employed for the treatment to degrade at least either halogenated aliphatic hydrocarbon compounds or aromatic compounds (hereinafter referred to as “pollution compounds”) contained in a medium. In other words, the degradation treatment for the pollution compounds according to the present invention can be carried out by bringing the transformant into contact with the pollution compounds in an aqueous medium, soil, or a gas phase. Any method can be used to contact the degrading transformant with the pollution compounds so long as the transformant can express the degrading activity. Various methods such as a batch method, semi-continuous method, and continuous method can be employed. Semi-immobilized or immobilized transformant on an appropriate carrier can be also used. The environments such as polluted water, drainage, waste water, soil, and gas phase can be treated by various methods, as required. These treatment methods are described below.
The degradation treatment of the pollution compounds in an aqueous medium according to the present invention can be carried out by contacting the degrading transformant with the pollution compounds in the aqueous medium. The representative treating methods are described below. However, the method according to the present invention is not limited thereto.
The simplest method is, for example, to introduce the degrading transformant directly into an aqueous medium contaminated with the pollution compounds. In this case, it is preferable to optimize the pH, salt temperature of the aqueous medium, and the concentrations of the pollution compounds in accordance with the degrading transformant.
As another application mode, the degrading transformant is grown in a culture vessel, and an aqueous medium containing the pollution compounds is introduced into the vessel at a predetermined flow rate for degradation of these compounds. The aqueous medium can be introduced and discharged, continuously, intermittently or batch-wise according to the treatment capacity. It is preferable to optimize the system by a system control in accordance to the concentrations of the pollution compounds.
Alternatively, the degrading microorganism may be first attached to a carrier such as soil particles and the filled in a reactor vessel, to which an aqueous medium containing the pollution compounds is introduced for degradation treatment. In this case, any carrier can be employed not restricted to soil particles, but carriers having a high capacity to retain the transformant and not preventing aeration are preferable. To provide the transformant with habitats, it can be used various bioreactor carriers, for example, those conventionally employed in the pharmaceutical industry, food industry, and wastewater treatment systems. More specifically, there can be used inorganic particulate carries such as porous glass, ceramics, metal oxides, activated carbon, kaolinite, bentonite, zeolite, silica gel, alumina, and anthracite; gel carries such as starch, agar, chitin, chitosan, polyvinyl alcohol, alginic acid, polyacrylamide, carrageenan, and agarose; ion-exchange cellulose, ion-exchange resins, cellulose derivatives, glutaraldehyde, polyacrylic acid, polyurethane, polyester, or the like. As natural materials, cellulose materials such as cotton, hemp, and papers, and lignin materials such as saw dust and barks can be employed.
The degradation treatment of the pollution compounds in soil according to the present invention can be carried out by bringing the degrading transformant in contact with the pollution compounds in the soil. The representative treating methods are described below. However, the method according to the present invention is not limited thereto.
The simplest method is, for example, to introducing degrading transformant directly into the soil polluted with the pollution compounds. Introduction of the transformant may be carried out by spraying it on the surface of the soil and, for the treatment of rather deeper underground, by introducing it through the well arranged in the underground, wherein the application of pressure of air, water, etc. allows the transformant to spread over the wide area of the soil and makes the process more effective. When the transformant is introduced into soil, it is necessary to adjust various conditions of the soil so that they are suitable for the transformant used for the process.
Further, there is such a method that first the transformant is attached to a carrier, next the carrier is put in a reaction vessel, and then the reaction vessel is introduced into, primarily, the aquifer of the contaminated soil, to undergo degradation treatment. The form of the reaction vessel is desirably like a fence or a film which can cover the wide area of the soil. Any carrier can be used, but it is preferable to use those having an excellent retention of transformant and not inhibiting aeration. As a material of the carrier, which can provide suitable habitats for the transformant, for example, it can be used various bioreactor carriers, for example, those conventionally employed in the pharmaceutical industry, food industry, and wastewater treatment systems.
According to the present invention, the degradation treatment of the pollution compounds in gas phase can be achieved by contacting the transformant with the contaminants in the gas phase. The representative modes are shown below, but are not intended to limit the present invention.
One mode is, for example, such that the degradation transformant is cultured in a culture vessel, and then the gas containing the pollution compounds is introduced into the vessel at a given flow rate to undergo degradation treatment. The method for introducing the gas is not limited specifically, but it is desirably such that introduction of the gas causes agitation of the culture medium and promote its aeration. Introduction and discharge of the gas may be carried out continuously, or it may be carried out intermittently according to the degradation capacity. A batch method is also applicable. Preferably such control is systematized in accordance with the concentrations of the pollution compounds to give optimum results.
Another mode is such that the transformant is attached to a carrier like soil particles, next the carrier is put into a reaction vessel, and then the gas containing the pollution compounds is introduced into the vessel to undergo degradation treatment. Besides particles of soil, any carrier can be used, however, it is desirable to use those having an excellent retention of transformant and not inhibiting aeration. As a material of the carrier, which can provide suitable habitats for transformant, for example, it can be used various bioreactor carriers, for example, those conventionally employed in the pharmaceutical industry, food industry, and wastewater treatment systems.
As materials which can retain the degrading transformant and supply it with nutrient, many examples can be found in the compost used in the agriculture, forestry and fisheries. Specifically, dry materials from plants, such as straw of grains, sawdust, rice bran, bean curd lees, bagasse and so on, and seafood wastes, such as shells of crabs and lobster and so on are applicable.
In cleaning of contaminated gas, the degrading transformant may be introduced after the carrier material is packed. To make the degradation reaction efficient, it is preferable that the above-mentioned nutrient, water content, oxygen concentration, etc. are kept in desirable conditions for the growth of the transformant. The ratio of the carrier to water in a reaction vessel may be determined considering the growth of the transformant and aeration. The shape of the vessel may be selected considering the amount and concentration of the gas to be treated, but preferably it is designed to enhance the contact of the gas with the transformant held on the carrier. For example, column, tube, tank and box type can be used as the reaction vessel. The vessel of these forms may be joined together with an exhaust duct and a filter to form one unit, or plural vessels may be connected according to the capacity.
Polluted gas is sometimes adsorbed by the carrier material in the beginning of the reaction and there is very few case where the effect of utilizing transformant may not be exhibit. After a certain period of time, however, it is said that the pollutants adhered to the carrier material is degraded, and further contaminants can be adsorbed by the surface of the carrier material which has restored adsorption capacity. Thus, a constant decomposition rate is expected without saturation of the pollutant-eliminating ability.
The method according to the present invention is applicable for the treatment of waste liquid, soil and air in a closed system or open system. Moreover, transformant may be immobilized on a carrier, or various methods promoting their proliferation may be employed in combination.
The present invention is explained more specifically by means of the following examples.
The complete taxonomical description of Strain TB64 (FERM BP-6933) is as follows:
1. Morphological Characteristics


    Shape and dimension: Rod (0.3 to 0.5 μm in width, 1.0 to 2.0 μm in length)
    Sporulation: No spore
    Flagellation: Peritrichous flagella
    Gram stain: Negative (18 hr, 24 hr, 36 hr)

2. Physiological and Biological Properties:

    Anaerobic growth: Negative
    Catalase: Positive
    oxidase: Negative
    Litmus milk: Alkali
    Reduction of Nitrate: Negative
    V-P reaction: Negative
    pH of V-P medium: pH 7.76
    Casein hydrolysis: Negative
    Gelatin digestion: Negative
    Starch hydrolysis: Negative
    DNA hydrolysis: Negative
    Urea hydrolysis: Negative
    Tween 20 hydrolysis: Negative
    Tween 40 hydrolysis: Negative
    Tween 60 hydrolysis: Negative
    Tyrosine hydrolysis: Positive
    Utilization of organic acids
    Citric acid: Positive
    Propionic acid: Positive
    Acetic acid: Positive
    Fumaric acid: Positive
    L-malic acid: Positive
    Succinic acid: Positive

Utilization of inorganic nitrogen:

    Ammonium salts: positive
    Nitrates: Positive
    Indole production: Negative
    H2S production: Negative

Pigment production on various media:

    P agar: Negative
    F agar: Negative
    King A agar: Negative
    King B agar: Negative

Growth in the presence of NaCl:

    2%: Positive
    5%: Negative
    7%: Negative
    Growth pH: 5.0-9.0
    Growth temperature: 10° C.-40° C.
    Growth in the presence of 0.02% sodium azide: negative
    Growth in the presence of 0.001% lysozyme: positive
    OF test: negative

Production of acid from sugars:
    
        Glucose: negative
        Arabinose: negative
        Fructose: negative
        Galactose: negative
        Maltose: negative
        Lactose: negative
        Sucrose: negative
        Xylose: negative
        Trehalose: negative
        Glycerol: negative
        Mannitol: negative
        Sorbitol: negative
        Sorbose: negative
        Mannose: negative
        Rhamnose: negative
        Adonitol: negative

Gas production:

        Glucose: negative
        Arabinose: negative
        Xylose: negative
        Mannitol: negative.

3. Compositional Analysis of Quinones

    
    
    Ubiquinone 8: 95.4%


EXAMPLE 1
Cloning of Toluene Monooxygenase Gene of Strain TB64
Cells of strain TB64 (FERM BP-6933) which can assimilate toluene were cultured in 100 ml of LB medium (containing 10 g of tryptone, 5 g of yeast extract, and 5 g of sodium chloride in 1 liter) overnight, harvested and washed with 100 mM phosphate buffer (pH 8.0). To the cells thus obtained, 10 ml of STE (10 mM tris (pH 8.0)/1 mM EDTA/100 mM sodium chloride) and 1 ml of 10% sodium dodecyl sulfate (final concentration of about 1%) were added. After the cells were incubated at 70° C. for 30 minutes for lysis, phenol treatment and ethanol sedimentation were carried out. DNA thus obtained was dissolved in a 10 mM tris (pH 8.0)/1 mM EDTA buffer (TE).
The DNA thus obtained was dissolved at various concentrations and treated with a restriction enzyme Sau3AI (Takara Shuzo Co., Ltd.) at 37° C. for 15 minutes for partial digestion. Aliquots of the partial digestion products were applied to gel electrophoresis on 0.8% agarose gel to identify the samples almost digested to about 5-10 kb. These samples were applied to spin column HR-400 (Amarsham-Pharmacia) to purify DNA fragments.
The DNA fragments were ligated to plasmid pUC18 (Takara Shuzo Co., Ltd.) completely digested with a restriction enzyme BamHI (Takara Shuzo Co., Ltd.) and dephosphorylated with bovine alkaline phosphatase (Takara Shuzo Co., Ltd.), using DNA Ligation Kit Ver. 2 (Takara Shuzo Co., Ltd.). Recombinant plasmids thus prepared were then introduced into the host E. coli HB101 (Takara Shuzo Co., Ltd.), and the cells were cultured on LB agar plates containing 100 μg/ml of ampicillin as a selection agent and 200 ppm phenol as an indicator for toluene monooxygenase activity. About 15,000 colonies of transformants grew on the plates.
Three brown colonies were found in these colonies and picked up. Recombinant plasmid DNA carrying toluene monooxygenase gene was extracted from the cells of each brown colony and the restriction map thereof was determined. It was found that all recombinant plasmids derived from the three colonies had a common insertion fragment of 5.3 kb. A plasmid containing only the common fragment of 5.3 kb was designated as pTB64 and a restriction map of the inserted DNA fragment was made (See FIG. 1). A recombinant E. coli HB101 carrying a plasmid containing a 6.1 kb insertion fragment containing this common 5.3 kb fragment was deposited in the National Institute of Bioscience and Human Technology, Agency of Industrial Science and Technology in accordance with the Budapest Treaty under the accession No. FERM BP-6942. Its microbiological characteristics were identical to those of E. coli HB101 except that it can degrade aromatic compounds and halogenated aliphatic hydrocarbon compounds.
In order to confirm that the inserted DNA fragment of pTB64 was derived from strain TB64, southern hybridization was performed. DNA was extracted from strain TB64 and completely digested with NcoI (Takara Shuzo Co., Ltd.) or KpnI (Takara Shuzo Co., Ltd.), and then subjected to southern hybridization. The inserted DNA fragment of pTB64 was digested with EcoRI-SphI (Takara Shuzo Co., Ltd.) to obtain a DNA fragment of about 0.8 kb, and this was used as a probe. As a result, a strong signal was observed around 1.8 kb with the NcoI-digested DNA, and around 0.8 and 1.5 kb with the KpnI digested DNA, in a good agreement with the lengths of the fragments predicted from the restriction map. Consequently, it was confirmed that the toluene monooxygenase gene contained in pTB64 was derived from the strain TB64.
EXAMPLE 2
Monooxygenation by E. coli HB101(pTB64)
The cells of E. coli HB101(pTB64) were inoculated in 100 ml of LB medium, cultured at 37° C. overnight, harvested, washed, and then resuspended in 100 ml of M9 medium (6.2 g of Na2HPO4, 3.0 g of KH2PO4, 0.5 g of NaCl, and 1.0 g of NH4Cl per liter) supplemented with a mineral stock solution of the following composition (3 ml/liter of M9 medium)(referred to as M9+mineral solution).
Composition of Mineral Stock Solution


    Nitrilotriacetic acid: 1.5 g
    MgSO4: 3.0 g
    CaCl2: 0.1 g
    Na2MoO4: 0.1 g
    FeSO4: 0.1 g
    MnSO4: 0.5 g
    NaCl: 1.0 g
    ZnSO4: 0.1 g
    CuSO4: 0.1 g
    AlK(SO4)2: 0.1 g
    H3BO3: 0.1 g
    NiCl2: 0.1 g
    Distilled water (to 1,000 ml)


Then, 27.5 ml vials were prepared, and 10 ml aliquot of the above suspension was placed in each vial, which was then tightly sealed with a teflon-coated butyl rubber stopper and aluminum seal. Gaseous toluene or benzene was introduced into each vial with a syringe to a concentration of 100 ppm (a concentration supposing all toluene or benzene completely dissolved in the aqueous phase in the vial). After incubation at 30° C. for 3 hours, 1 ml aliquot was taken from each vial, and cells were removed by centrifugation and substances of 10,000 or higher in molecular weight were removed by ultrafiltration. Production of ortho-cresol and 3-methylcatechol from toluene and phenol and catechol from benzene was confirmed by HPLC, to show that toluene and benzene are monooxygenated by toluene monooxygenase encoded by the cloned DNA fragment.
EXAMPLE 3
Degradation of Aromatic Compounds and Halogenated Aliphatic Hydrocarbon Compounds by E. coli HB101(pTB64)
The cells of E. coli HB101(pTB64) cultured as described in Example 2 were suspended in M9+mineral solution. 10 ml aliquots of the suspension were placed in 27.5 ml vials. Each vial was tightly sealed with a teflon-lined butyl rubber stopper and an aluminum seal. Gaseous trichloroethylene (TCE), cis-1,2-dichloroethylene (cis-1,2-DCE), trans-1,2-dichloroethylene (trans-1,2-DCE), 1,1-dichloroethylene (1,1-DCE), toluene, and benzene were injected into respective vials to a concentration of 25 ppm (a concentration supposing the introduced substance completely dissolved in the aqueous phase in the vial). The vials were shaken and incubated at 30° C. The concentrations of the respective compounds in the gas phase were measured by gas chromatography after 6 hours. The results are shown in Table 1. E. coli HB101 harboring pUC18 (E. coli HB101(pUC18)) was employed as a control and degradation was evaluated in the same manner.
Similarly, phenol, ortho-cresol, meta-cresol and para-cresol were introduced into respective 27.5 ml vials each containing 10 ml of the cell suspension at a concentration of 50 ppm. Each vial was tightly sealed with a butyl rubber stopper and aluminum seal. The vials were shaken and incubated at 30° C. The quantities of the respective compounds in the liquid phase were determined by the amino antipyrine method with a spectrophotometer to obtain their concentrations after 6 hours. The results are shown in Table 2. E. coli HB101(pUC18) was employed as a control and degradation was evaluated in the same manner.
The above results show that E. coli HB101(pTB64) had an excellent ability to degrade aromatic compounds and halogenated aliphatic hydrocarbon compounds.
EXAMPLE 4
Definition of Toluene Monooxygenase Region
The toluene monooxygenase region was defined further by stepwise deletion or subcloning of plasmid pTB64 obtained in Example 1 using restriction sites thereof. Toluene monooxygenase activity was evaluated by the method in Example 3, and 25 ppm toluene was employed as a substrate.
First, a subclone pTB64 ΔBamHI in which a top 0.7-kb fragment was deleted was prepared from pTB64 using the Scal sites at 0.7 kb and 5.3 kb. More specifically, pTB64 was completely digested by restriction enzymes ScaI (Takara Shuzo Co., Ltd.) to obtain three fragments of about 0.9 kb, 2.4 kb and 4.6 kb. The fragments were separated by agarose gel electrophoresis, and the 4.6 kb fragment was cut out and recovered from the gel and purified with a spin column HR-400 (Amarsham-Pharmacia). The fragment was ligated to pUC18 previously completely digested by HincII enzymes, and E. coli HB101 was transformed with the recombinant plasmid according to the conventional method. E. coli HB101 cells were then applied on an LB plate containing 100 μg/ml of ampicillin to select transformants. From the cells grown overnight in LB medium, plasmid DNA was extracted by an alkaline method to confirm the presence of pTB64ΔScaI, and a transformant carrying pTB64 ΔScaI was isolated. E. coli HB101 (pTB64ΔScaI) cells were evaluated for toluene monooxygenase activity. No degradation of toluene was observed, indicating that the 0.7-kb fragment is essential for toluene monooxygenase activity.
Then, a subclone pTB64ΔEcoRI was prepared by deleting a 0.3 kb fragment from pTB64 using the 0.3 kb EcoRI restriction site of pTB64. More specifically, pTB64 was partially digested by restriction enzyme EcoRI, and then self-ligated to transform E. coli HB101. The E. coli HB101 transformants were then selected on an LB plate containing 100 μg/ml of ampicillin. After the transformants were cultured in LB medium overnight, the plasmid DNA was extracted from the cells by the alkaline method to confirm the presence of pTB64ΔEcoRI and a transformant carrying pTB64ΔEcoRI was isolated. E, coli HB101(pTB64ΔEcoRI) was evaluated for toluene monooxygenase activity. Degradation of toluene was observed, but the activity was lower than that of E. coli HB101(pTB64), indicating that the 0.3 kb fragment was not essential for toluene monooxygenase activity but necessary for full expression of the activity.
Further, the stepwise deletion method was employed to restrict the toluene monooxygenase region from the opposite direction. More specifically, stepwise deletion was introduced from the XbaI restriction site using XbaI (Takara Shuzo Co., Ltd.) restriction site and Sse8387I (Takara Shuzo Co., Ltd.) restriction site of pUC18. The stepwise deletion was carried out using Deletion Kit for Kilo-Sequence (Takara Shuzo Co., Ltd.) according to the attached protocol. The results of the activity evaluation of various deletion clones thus obtained show that the region up to 4.8 kb is essential for expression of the activity and a region from 4.8 kb to 5.3 kb is not especially required for degradation activity.
EXAMPLE 5
Sequencing of Toluene Monooxygenase Gene
The nucleotide sequence of pTB64 was determined as follows. pTB64 was digested by various restriction enzymes and subcloned into pUC18 plasmid. Deletion clones were prepared from pTB64 or subclones of partial pTB64 using Deletion Kit for Kilo-Sequence (Takara Shuzo Co., Ltd.) to determine the nucleotide sequence of the 5.3 kb fragment encoding toluene monooxygenase by the dideoxy method. The dideoxy method was carried out using ABI PRISM Cycle Sequencing Kit (Perkin Elmer Corporation) according to the attached protocol for reaction conditions, etc. DNA recombination and Kilo-Sequence method were also performed according to the conventional methods or the manufacturer's protocols attached. The results of sequencing show that the DNA encoding toluene monooxygenase is contained in 5,331 bases comprised of 7 coding regions as shown by SEQ ID NO: 1; a region tomK encoding the amino acid sequence TomK of SEQ ID NO: 2; a region tomL encoding the amino acid sequence TomL of SEQ ID NO: 3; a region tomM encoding an amino acid sequence TomM of SEQ ID NO: 4; a region tomN encoding an amino acid sequence TomN of SEQ ID NO: 5; a region tomO encoding an amino acid sequence TomO of SEQ ID NO: 6; a region tomP encoding an amino acid sequence TomP of SEQ ID NO: 7 and a region tomO encoding an amino acid sequence TomQ encoding an amino acid sequence TomQ of SEQ ID NO: 8.
Here, considering the results of Example 4 together, the polypeptide (TomK)(SEQ ID NO: 2) encoded by tomK is not essential for expression of the activity but the presence of TomK clearly enhances the toluene monooxygenase activity. It is, therefore, desirable for sufficient expression of the activity that TomK is present as a component of toluene monooxygenase. The polypeptide (TomQ)(SEQ ID NO: 8) encoded by tomQ is not essential for expression of the activity. In addition, the toluene monooxygenase activity is not affected by the presence of TomQ. Thus, it is not essential to contain TomQ as a component of toluene monooxygenase.
In other words, any DNA fragment containing segments encoding the amino acid sequences of SEQ ID NOs: 3-7 as the components of toluene monooxygenase where these segments are aligned so that expressed TomL to TomP having the amino acid sequences of SEQ ID NOs: 3-7 can form a protein with a toluene monooxygenase activity is included in the preferred DNA fragment of the present invention. DNA fragments with variation in at least one segment of the DNA fragment with the proviso that the activity of toluene monooxygenase is not impaired are included in the preferred DNA fragments of the present invention.
DNA fragments further containing a region encoding the amino acid sequence TomK of SEQ ID NO: 2 or a variant in which the amino acid sequence of SEQ ID NO: 2 is altered with the proviso that it does not impair the property to enhance a toluene monooxygenase activity are also included in the preferred embodiment of the present invention.
EXAMPLE 6
Recombination of Toluene Monooxygenase Gene into Expression Vectors-(1)
As expression vectors, pSE280 (Invitrogen), and pSE380 (Invitrogen) were employed. They contain an ampicillin-resistant gene as a marker, and pSE280 and pSE380 have a sequence derived from ColE1 as ori. All these two vectors contain a trc promoter and a rrnB terminator, and a ribosome-binding site is located before the NcoI restriction site. lacIq is contained in pSE380 but not in pSE280.
To incorporate the toluene monooxygenase gene into these vectors, NcoI restriction sites were introduced in tomK and tomL. The following 4 primers (Amarsham-Pharmacia) were prepared to introduce the NcoI restriction site by PCR:









1) tom-K
SEQ ID NO:9










5′-AGCGACCCATTCACCATGGCCCTGCAGACCCCAG-3′
34 mer










2) tom-L
SEQ ID NO:10










5′-CTCAGGAGCAACCCATGGCAATCGAGCTGAAAAC-3′
34 mer










3) tomΔNcoI
SEQ ID NO:11










5′-TACTTCCAGTACGCGTCGATGGTCAGGCGGAACG-3′
34 mer










4) tail
SEQ ID NO:12










5′-GCCCAGCTTTGCCATGGCGGCGAGCAGCGATTCG-3′
34 mer







The tom-K was designed to introduce the NcoI restriction site at the first ATG site (bases 200-202 in the Sequence Listing) of tomK. Similarly, tom-L was designed to introduce the NcoI site at the first GTG site (bases 446-448 in the SEQ ID NO: 1) of tomL. The tomΔNcoI was designed to perish the NcoI site in the toluene monooxygenase gene (about 1.95 kb). Using primer combinations of the primer (3) with the respective primers (1) and (2) and the recombinant plasmid DNA of FERM BP-6942 as the template, PCR was performed. PCR was carried out by using Takara LA PCR Kit Ver. 2 (Takara Shuzo Co., Ltd.) with a reaction volume of 50 μl, and the reaction was started at 94° C. for 1 minute and then a reaction cycle of 98° C. for 20 seconds followed by 72° C. for 5 minutes was repeated for 30 times (shuttle PCR), and then followed by reaction at 72° C. for 10 minutes. The reaction conditions were according to the manufacturer's protocol.
As a result, the combinations of the primers (1) and (3), and (2) and (3) gave the PCR products of about 1.8 kb, and about 1.5 kb, respectively. Then, using these products as the primer in combination with the primer (4) respectively, PCR was carried out. The reaction conditions were the same as the above. As a result, the combinations of the primers ((1)-(3)) and (4), and ((2)-(3)) and (4) gave the PCR products of about 4.8 kb, and about 4.5 kb, respectively. The respective DNA fragments were digested with the restriction enzyme NcoI (Takara Shuzo Co., Ltd.). It was confirmed that the NcoI site in the oxygenase had completely disappeared. These NcoI-digested products were purified using a spin column HR-4000 (Amarsham-Pharmacia) and used for the following ligation reaction.
The above-mentioned expression vector were completely digested with the restriction enzyme NcoI, dephosphorylated, subjected to phenol treatment, and purified with a spin column HR-400 (Amarsham-Pharmacia). The vectors were then ligated to NcoI-digested PCR products to transform E. coli HB101 (Takara Shuzo Co., Ltd.) according to the conventional method. The transformed E. coli HB101 cells were then grown on LB plate containing 100 μg/ml of ampicillin for transformant selection. After the transformants were cultured in LB liquid medium at 37° C. overnight, plasmid DNA was extracted by the alkaline method to examine the recombinant plasmids. Transformants in which the respective PCR fragments were accurately inserted into the NcoI restriction site of the respective expression vectors were obtained.
A list of the obtained recombinant plasmids are shown in Table 3.
EXAMPLE 7
Recombination of Toluene Monooxygenase Gene into Expression Vectors-(2)
A recombinant vector to express only TomK was constructed using pSTV28 (TaKaRa) as the expression vector. Since pSTV28 contains a chloramphenicol resistance gene as a marker and an ori derived from pACYC, it is compatible with pSE280 or pSE380 in the same cell. pSTV28 does not contain lacIq. BamHI sites were introduced upstream and downstream tomK in order to incorporate a gene encoding TomK into this vector. Two primers (Amarsham-Pharmacia Biotec) were prepared to introduce BamHI sites by PCR.









5) tom-KB
SEQ ID NO: 13












5′-CAATGAAAGGGGATCCGAGGCGACATCGAC-3′
30 mer










6) tom-KBT
SEQ ID NO: 14












5′-ATGTCGACGGGATCCAGCTCGATTGTCACG-3′
30 mer







Here, tom-KB was designed to introduce a BamHI site upstream SD sequence of tomK, tom-KBT was designed to introduce a BamHI site downstream the termination codon of tomK.

Using primer combinations of the primers (5) and (6) and the recombinant plasmid DNA of FERM BP-6942 as the template, PCR was performed. PCR was carried out by using Takara LA PCR Kit Ver. 2 (Takara Shuzo Co., Ltd.) with a reaction volume of 50 μl, and the reaction was started at 94° C. for 1 minute and then a reaction cycle of 98° C. for 20 seconds followed by 72° C. for 5 minutes was repeated for 30 times (shuttle PCR), and then followed by reaction at 72° C. for 10 minutes. The reaction conditions were according to the manufacturer's protocol.
As a result, a 0.3 kb PCR product was obtained. Then, the product was completely digested by BamHI (Takara Shuzo Co., Ltd.) and purified using a spin column HR-4000 (Amarsham-Pharmacia) and used for the following ligation reaction.
The above-mentioned pSTV28 was completely digested with the restriction enzyme BamHI, dephosphorylated, subjected to phenol treatment, and purified with a spin column HR-400 (Amarsham-Pharmacia). The vector was then ligated to BamHI-digested PCR product to transform E. coli HB101 (Takara Shuzo Co., Ltd.) according to the conventional method. The transformed E. coli HB101 cells were then grown on LB plate containing 25 μg/ml chloramphenicol for transformant selection. After the transformants were cultured in LB liquid medium at 37° C. overnight, plasmid DNA was extracted by the alkaline method to examine the recombinant plasmids. Transformants in which the PCR fragment was accurately inserted into the BamHI restriction site of pSTV28 were obtained. The obtained recombinant plasmid was designated as pKS-64.
EXAMPLE 8
Ability of E. coli HB101 Recombinants to Degrade Aromatic Compounds and Halogenated Aliphatic Hydrocarbon Compounds (without Induction with IPTG)
The cells of the E. coli strains, each harboring one of the 4 recombinant plasmids obtained as described in Example 6, were inoculated in 100 ml of LB medium, cultured at 37° C. overnight, harvested, washed, and suspended in an M9+mineral solution. 10 ml aliquots of the suspension were put in 27.5 ml vials, and each vial was tightly sealed with a Teflon-coated butyl rubber stopper and aluminium seal. Then, gaseous trichloroethylene (TCE), cis-1,2-dichloroethylene (cis-1,2-DCE), trans-1,2-dichloroethylene (trans-1,2-DCE), 1,1-dichloroethylene (1,1-DCE), toluene, and benzene were added to respective vials with a syringe to a concentration of 50 ppm (supposing all of the introduced substance dissolved in the aqueous phase in the vial). The vials were shaken and incubated at 30° C. The concentrations of the respective compounds in the gas phase after 6 hour incubation were measured by gas chromatography. The results are shown in Table 4. E. coli HB101 harboring no plasmid was employed as a control and degradation was evaluated in the same manner.
Similarly, phenol, ortho-cresol, meta-cresol and para-cresol were introduced into respective 27.5 ml vials each containing 10 ml of the cell suspension at a concentration of 50 ppm. Each vial was tightly sealed with a butyl rubber stopper and aluminum seal. The vials were shaken and incubated at 30° C. The quantities of the respective compounds in the liquid phase were determined by the aminoantipyrine method with a spectrophotometer to determine their concentrations after 6 hours. The results are shown in Table 5. E. coli HB101 harboring no plasmid was employed as a control and degradation was evaluated in the same manner.
The above results confirm that E. coli HB101 recombinants containing toluene monooxygenase gene have an excellent ability to degrade the aromatic compounds and halogenated aliphatic hydrocarbon compounds. It is shown that transformants harboring pSE380-derived monooxygenase expression vectors express a lower degrading activity in a system not containing IPTG than those harboring pSE280-derived plasmids, since pSE280 lacks lacIq.
EXAMPLE 9
Ability of E. coli HB101 Recombinants to Degrade Aromatic Compounds and Halogenated Aliphatic Hydrocarbon Compounds (with Induction with IPTG)
Each E. coli HB101 transformant strain harboring one of the four recombinant plasmids obtained as described in Example 6, was inoculated in 100 ml of LB medium, cultured at 37° C. to reach OD600 of about 0.8, and then IPTG was added to 1 mM concentration followed by further incubation at 37° C. for 5 hours. Then the cells were harvested, washed and suspended in an M9+mineral solution. Ten ml aliquots of the suspension were placed in 27.5 ml vials, and each vial was tightly sealed with a Teflon-coated butyl rubber stopper and aluminium seal. Then, gaseous trichloroethylene (TCE), cis-1,2-dichloroethylene (cis-1,2-DCE), trans-1,2-dichloroethylene (trans-1,2-DCE), 1,1-dichloroethylene (1,1-DCE), toluene, and benzene were added to respective vials with a syringe to a concentration of 50 ppm (supposing all of the introduced substance dissolved in the aqueous phase in the vial). The vials were shaken and incubated at 30° C. The concentrations of the respective compounds in the gas phase after 6 hour incubation were measured by gas chromatography. The results are shown in Table 6. E. coli HB101 harboring no plasmid was employed as a control and degradation was evaluated in the same manner. Similarly, phenol, ortho-cresol, meta-cresol and para-cresol were introduced into respective 27.5 ml vials each containing 10 ml of the cell suspension, at a concentration of 50 ppm. Each vial was tightly sealed with a butyl rubber stopper and aluminum seal. The vials were shaken and incubated at 30° C. The quantities of the respective compounds in the liquid phase were determined by the amino antipyrine method with a spectrophotometer to determine their concentrations after 6 hours. The results are shown in Table 7. E. coli HB101 harboring no plasmid was employed as a control and degradation was evaluated in the same manner.
The above results confirm that E. coli HB101 recombinants containing toluene monooxygenase gene have an excellent ability to degrade aromatic compounds and halogenated aliphatic hydrocarbon compounds. It is shown that transformants harboring pSE380-derived expression vectors for the monooxygenase show more excellent degrading activity by IPTG induction.
EXAMPLE 10
Ability of E. coli HB101 Recombinants to Degrade Aromatic Compounds and Halogenated Aliphatic Hydrocarbon Compounds (without Induction with IPTG)(2)
Two E. coli HB101 transformants harboring pL2-64 and pL3-64 recombinant plasmids respectively obtained in Example 6 were treated by the calcium chloride method to further transform them with pKS-64 obtained in Example 7.
Transformation was carried conventionally and transformants were selected by spreading the cells onto an LB agar medium containing 25 μg chloramphenicol and 100 μg/ml ampicillin. The cells of each transformant were inoculated in 100 ml of LB medium, cultured at 37° C. overnight, harvested, washed, and suspended in an M9+mineral solution. 10 ml aliquots of the suspension were placed in 27.5 ml vials, and each vial was tightly sealed with a Teflon-coated butyl rubber stopper and aluminium seal. Then, gaseous trichloroethylene (TCE), cis-1,2-dichloroethylene (cis-1,2-DCE), trans-1,2-dichloroethylene (trans-1,2-DCE), 1,1-dichloroethylene (1, -DCE), toluene, and benzene were added to respective vials with a syringe to a concentration of 50 ppm (supposing all of the introduced substance dissolved in the aqueous phase in the vial). The vials were shaken and incubated at 30° C. The concentrations of the respective compounds in the gas phase after 6 hour incubation were measured by gas chromatography. The results are shown in Table 8. E. coli HB101 harboring no plasmid was employed as a control and degradation was evaluated in the same manner.
Similarly, phenol, ortho-cresol, meta-cresol and para-cresol were introduced into respective 27.5 ml vials each containing 10 ml of the cell suspension at a concentration of 50 ppm. Each vial was tightly sealed with a butyl rubber stopper and aluminum seal. The vials were shaken and incubated at 30° C. The quantities of the respective compounds in the liquid phase were determined by the aminoantipyrine method with a spectrophotometer to determine their concentrations after 6 hours. The results are shown in Table 9. E. coli HB101 harboring no plasmid was employed as a control and degradation was evaluated in the same manner.
The above results confirm that E. coli HB101 recombinants containing the toluene monooxygenase gene have an excellent ability to degrade the aromatic compounds and volatile halogenated aliphatic hydrocarbon compounds. It has been also shown that excellent degradation of the pollution compound can be achieved when TomK and TomLMNOP are expressed from different systems. It is shown that transformants harboring pSE380(tomLMNOP) plasmid express a lower degrading activity in a system not containing IPTG than those harboring pSE280(tomLMNOP) plasmid, since pSE380 contains lacIq.
EXAMPLE 11
Ability of E. coli HB101 Recombinants to Degrade Aromatic Compounds and Halogenated Aliphatic Hydrocarbon Compounds (with Induction with IPTG)(2)
Each E. coli HB101 transformant strain harboring combination of two plasmids obtained in Example 10 was inoculated in 100 ml of LB medium, cultured at 37° C. to reach OD600 of about 0.8, and then IPTG was added to 1 mM concentration followed by further incubation at 37° C. for 5 hours. Then the cells were harvested, washed and suspended in an M9+mineral solution. 10 ml aliquots of the suspension were placed in 27.5 ml vials, and each vial was tightly sealed with a Teflon-coated butyl rubber stopper and aluminium seal. Then, gaseous trichloroethylene (TCE), cis-1,2-dichloroethylene (cis-1,2-DCE), trans-1,2-dichloroethylene (trans-1,2-DCE), 1,1-dichloroethylene (1,1-DCE), toluene, and benzene were added to respective vials with a syringe to a concentration of 50 ppm (supposing all of the introduced substance dissolved in the aqueous phase in the vial). The vials were shaken and incubated at 30° C. The concentrations of the respective compounds in the gas phase after 6 hour incubation were measured by gas chromatography. The results are shown in Table 10. E. coli HB101 harboring no plasmid was employed as a control and degradation was evaluated in the same manner.
Similarly, phenol, ortho-cresol, meta-cresol and para-cresol were introduced into respective 27.5 ml vials each containing 10 ml of the cell suspension, at a concentration of 50 ppm. Each vial was tightly sealed with a butyl rubber stopper and aluminum seal. The vials were shaken and incubated at 30° C. The quantities of the respective compounds in the liquid phase were determined by the amino antipyrine method with a spectrophotometer to determine their concentrations after 6 hours. The results are shown in Table 11. E. coli HB101 harboring no plasmid was employed as a control and degradation was evaluated in the same manner.
The above results confirm that E. coli HB101 recombinants containing the monooxygenase gene have an excellent ability to degrade the aromatic compounds and volatile halogenated aliphatic hydrocarbon compounds. It has been also shown that excellent degradation of the pollution compound can be achieved when TomK and TomLMNOP are expressed from different systems. It is shown that transformants harboring pSE380(tomLMNOP) plasmid express higher degrading activity in a system containing IPTG.
EXAMPLE 12
TCE Degradation by E. coli HB101(pK2-64) and HB101(pK3-64) Recombinants in Soil (without IPTG Induction)
E. coli HB101(pK2-64) and HB101(pK3-64) recombinant strains as described in Example 6 were respectively inoculated in 10 ml of LB medium and cultured at 37° C. overnight. 50 g of Sawara sieved sand (unsterilized) was placed in 68 ml vials each. 5 ml of LB medium inoculated with the above seed culture to 100:1, was then added to the sand in each vial. Each vial was cotton-plugged, and incubated at 37° C. for 8 hours without shaking. After that, each vial was tightly sealed with a Teflon-coated butyl rubber stopper and aluminum seal. Gaseous TCE was introduced into the vials with a syringe to 50 ppm (supposing all TCE dissolved into the aqueous phase in the vial). The vials were incubated at 30° C. Quantitative analysis of TCE in the gas phase were carried out by gas chromatography after 6 hours to determine TCE concentrations. The results are shown in Table 12. E. coli HB101 harboring no plasmid was employed as a control and evaluated in the same manner.
The above results confirm that E. coli HB101 transformants harboring pK2-64 and pK3-64 also show an excellent TCE-degrading ability in soil. It is shown that transformant harboring pK3-64 (pSE380-based) expresses a lower degrading activity in a system not containing IPTG than that harboring pSE280-derived plasmid pK2-64, since the former contains lacIq.
EXAMPLE 13
TCE Degradation by E. coli Recombinants HB101(pK2-64) and HB101(pK3-64) in Soil (with IPTG Induction)
The cells of E. coli HB101(pK2-64) and HB101(pK3-64) recombinant strains as described in Example 6 were respectively inoculated in 10 ml of LB medium and cultured at 37° C. overnight. Fifty grams of Sawara sieved sand (unsterilized) were placed in 68 ml vials each. 5 ml of LB medium inoculated with the above seed culture to 100:1, was then added to the sand. Each vial was cotton-plugged, and incubated at 37° C. for 4 hours without shaking. Then 1 ml of a 10 mM IPTG solution was added to each vial. After that, each vial was tightly sealed with a Teflon-coated butyl rubber stopper and aluminum seal. Gaseous TCE was introduced into the vials with a syringe to 50 ppm (supposing all TCE dissolved into the aqueous phase in the vial). The vials were incubated at 30° C. Quantitative analysis of TCE in the gas phase were carried out by gas chromatography after 6 hours to determine TCE concentrations. The results are shown in Table 13. E. coli HB101 harboring no plasmid was employed as a control and evaluated in the same manner.
The above results confirm that E. coli recombinants HB101(pK2-64) and HB101(pK3-64) also show an excellent TCE-degrading ability in soil. It is shown that the recombinant harboring pK3-64 (pSE380-based) expresses higher degrading activity with IPTG induction.
EXAMPLE 14
TCE Degradation by Recombinants E. coli HB101(pK2-64) and HB101(pK3-64) in Gas Phase (without IPTG Induction)
The cells of respective recombinant strains, E. coli HB101(pK2-64) and HB101(pK3-64) as described in Example 6, were inoculated in 100 ml of LB medium and cultured at 37° C. overnight. Aliquots (30 ml) of each seed culture were transferred into 68 ml vials, into which air which had passed through a saturation TCE solution was introduced at a flow rate of 20 ml/min for 10 minutes. Each vial was tightly sealed with a Teflon-coated butyl rubber stopper and aluminum seal, and shaking culture was conducted at 30° C. Quantitative analysis of TCE in the gas phase were carried out by gas chromatography to determine its concentration after 6 hours. The results are shown in Table 14. E. coli HB101 harboring no plasmid was employed as a control and degradation was evaluated in the same manner.
The above results confirm that recombinants E. coli HB101(pK2-64) and HB101(pK3-64) show an excellent TCE-degrading ability also in the gas phase. It is shown that the recombinant harboring pK3-64 (pSE380-based) expresses a lower degrading activity in a system not containing IPTG than that harboring pSE280-derived plasmid pK2-64, since the former contains lacIq.
EXAMPLE 15
TCE Degradation by Recombinants E. coli HB101(pK2-64) and HB101(pK3-64) in Gas Phase (with IPTG Induction)
E. coli (HB101) recombinant strains each harboring pK2-64 or pK3-64 as described in Example 6 were respectively inoculated into 100 ml of LB medium and cultured at 37° C. to reach OD600 of about 0.8, and then IPTG was added to 1 mM concentration followed by further incubation at 37° C. for 5 hours. Aliquots (30 ml) of the cell suspension were transferred into 68 ml vials, into which air which had passed through in a saturated TCE solution was introduced at a flow rate of 20 ml/min for 10 minutes. Each vial was tightly sealed with a Teflon-coated butyl rubber stopper and aluminum seal, and shaking culture was conducted at 30° C. Quantitative analysis of TCE in the gas phase were carried out by gas chromatography to determine its concentration after 6 hours. The results are shown in Table 15. E. coli HB101 harboring no plasmid was employed as a control and degradation was evaluated in the same manner.
The above results confirm that recombinants E. coli HB101(pK2-64) and HB101(pK3-64) show an excellent TCE-degrading ability also in the gas phase, and it is shown that the recombinant harboring pK3-64 (pSE380-based) expresses higher degrading activity with IPTG induction.
EXAMPLE 16
Introduction of Recombinant Plasmid containing Toluene Monooxygenase Gene into Alcaligenes sp. strain TL2 (FERM BP-6913)
The toluene monooxygenase gene beginning from the first ATG of tomK (base number 200-202) was transferred from a recombinant plasmid pK2-64 of Example 6 (recombinant pSE280 containing the gene) into a vector pBBR122 (Mo Bi Tec) having a wide host range replication region not belonging to an incompatible group of IncP, IncQ, and IncW. This recombinant plasmid was introduced in Alcaligenes sp. strain TL2 (FERM BP-6913), and its ability to degrade aromatic compounds and halogenated aliphatic hydrocarbon compounds was evaluated.
First, a wide host range recombinant plasmid was constructed. An about 6.8-kb fragment containing the toluene monooxygenase gene, a trc promoter, and a rrnB terminator was cut out from pK2-64 by complete digestion by the restriction enzyme HpaI (Takara Shuzo Co., Ltd.) followed by partial digestion by ScaI (Takara Shuzo Co., Ltd.). This fragment of 6.8 kb does not contain the lacIq sequence. As a vector of a wide host range, pBBR122 was employed. pBBR122 was completely digested with the restriction enzyme SmaI (Takara Shuzo Co., Ltd.). The 6.8 kb fragment containing the toluene monooxygenase gene, a trc promoter, and an rrnB terminator prepared as described above was ligated to the SmaI restriction site of the pBBR122 using DNA Ligation Kit Ver. 2 (Takara Shuzo Co., Ltd.) and the recombinant plasmid thus constructed was introduced into E. coli HB101 (Takara Shuzo Co., Ltd.). The cells of the E. coli thus treated were applied on LB plate containing 50 μg/ml of chloramphenicol as a selection agent. When the colonies on the plate grew to an appropriate size, the colonies were transferred by replica printing onto an LB plate containing 50 μg/ml of kanamycin as a selection agent. Transformants that could proliferate on the plate with chloramphenicol but not on the plate with kanamycin were selected, and cultured in LB medium at 37° C. overnight, to extract plasmid DNA from the cells by the alkaline method. After checking the plasmids, transformants harboring a recombinant plasmid where the 6.8 kb fragment was correctly inserted into the SmaI site of the pBBR122 were obtained. The recombinant plasmid thus obtained was about 12.1 kb in length and designated as pK2-64bbr.
The SOB medium shown below was employed for liquid culture of Alcaligenes sp. strain TL2. Chloramphenicol was used at a concentration of 50 μg/ml as a selection agent and the culture temperature was 30° C. The recombinant plasmid pK2-64 was introduced into Alcaligenes sp. strain TL2 cells by electroporation using a gene pulsar (Bio-Rad). The recombinant plasmid pK2-64bbr was stably retained after introduction into Alcaligenes sp. strain TL2.
SOB medium:
Tryptone: 20 g
Yeast extract: 5 g
NaCl: 0.5 g
250 mM KCl: 10 ml
Distilled water (to 990 ml)
pH 7.0
The above solution was sterilized by autoclaving and cooled to room temperature, to which 10 ml of a 2 M magnesium solution (1 M MgSO4.7H2O+1 M MgCl2.6H2O) separately sterilized by autoclaving was added.
EXAMPLE 17
Ability of Alcaligenes sp. TL2(pK2-64bbr) to Degrade Aromatic Compounds and Halogenated Aliphatic Hydrocarbon Compounds
The cells of Alcaligenes sp. TL2(pK2-64bbr) were inoculated in 100 ml of SOB medium, cultured at 30° C. overnight, harvested, washed, and then suspended in 100 ml of M9 (containing 6.2 g of Na2HPO4, 3.0 g of KH2PO4, 0.5 g of NaCl, and 1.0 g of NH4Cl per liter) supplemented with a mineral stock solution (3 ml to 1 liter of M9 medium).
10 ml of the suspension was placed in respective 27.5 ml vials and each vial was tightly sealed with a Teflon-coated butyl rubber stopper and aluminum seal. Then, gaseous trichloroethylene (TCE), cis-1,2-dichloroethylene (cis-1,2-DCE), trans-1,2-dichloroethylene (trans-1,2-DCE), 1,1-dichloroethylene (1,1-DCE), toluene, and benzene were added to respective vials with a syringe to a concentration of 50 ppm (supposing all of the introduced substance dissolved in the aqueous phase in the vial). The vials were shaken and incubated at 30° C. The concentrations of the respective compounds in the gas phase after 6 hour incubation were measured by gas chromatography. The results are shown in Table 16. Alcaligenes sp. TL2 not containing pK2-64bbr was tested as a control and degradation was evaluated in the same manner.
Similarly, to 10 ml of the prepared cell suspension in a 27.5-ml vial, phenol, ortho-cresol, meta-cresol, and para-cresol were added to 50 ppm, respectively. The vial was tightly sealed with a butyl rubber stopper and aluminum seal, and then shaken and incubated at 30° C. The quantities of the respective compounds in the liquid phase were measured by the aminoantipyrine method with a spectrophotometer to obtain their concentrations after 6 hours. The results are shown in Table 17. Alcaligenes sp. strain TL2 not containing pK2-64bbr was employed as a control and degradation was evaluated in a similar system.
The above results show that the recombinant Alcaligenes sp. strain TL2 harboring pK2-64bbr can constitutively express the ability to degrade aromatic compounds and halogenated aliphatic hydrocarbon compounds.
EXAMPLE 18
Degradation of TCE by Recombinant Alcaligenes sp. TL2(pK2-64bbr) in Soil
Recombinant Alcaligenes sp. TL2(pK2-64bbr) as described in Example 16 was inoculated in 10 ml of SOB medium and cultured at 30° C. overnight. Fifty grams of Sawara sieved sand (unsterilized) was placed in each 68 ml vial. Five milliliter of SOB medium inoculated with the above seed culture to 100:1 was then added to the sand in each vial. Each vial was cotton-plugged and incubated at 30° C. for 12 hours without shaking. After that, each vial was tightly sealed with a Teflon-coated butyl rubber stopper and aluminum seal. Gaseous TCE was introduced into the vials with a syringe to 50 ppm (supposing all TCE dissolved into the aqueous phase in degradation was evaluated in the same manner.
The above results show that the recombinant Alcaligenes sp. TL2(pK2-64bbr) can constitutively express the ability to degrade TCE also in the gas phase.
According to the present invention, a DNA fragment carrying a toluene monooxygenase gene with an excellent ability to degrade aromatic compounds and halogenated aliphatic hydrocarbon compounds can be obtained. In addition, a novel recombinant plasmid containing the DNA fragment as a whole or a part thereof that can be utilized to obtain a transformant capable of degrading aromatic compounds and/or halogenated aliphatic hydrocarbon compounds can be obtained. Further, a transformant harboring the plasmid and can be utilized to degrade aromatic compounds and/or halogenated aliphatic hydrocarbon compounds can be obtained. Furthermore, a method for environmental remediation that can efficiently degrade either aromatic compounds and/or halogenated aliphatic hydrocarbon compounds by utilizing the transformant.










TABLE 1







E.




coliHB101(pTB64)
HB101(pUC18)




















TCE
0
25.0



cis-1,2-DCE
0
26.0



trans-1,2-DCE
0
25.0



1,1-DCE
0
24.8



Toluene
0
27.1



Benzene
0
24.1







(Unit: ppm) 
















TABLE 2







E. coli
E. coli



HB101(pTB64)
HB101(pUC18)




















Phenol
0
49



Ortho-cresol
0
53



Meta-cresol
0
51



Para-cresol
0
49







(Unit: ppm) 
















TABLE 3







tom-K
tom-L


















pSE280
pK2-64
pL2-64


pSE380
pK3-64
pL3-64






















TABLE 4







pK2-64
pL2-64
pK3-64
pL3-64
HB101





















TCE
0
42.1
47.3
49.7
52.1


cis-1,2-DCE
0
37.3
46.7
52.1
51.2


trans-1,2-DCE
0
39.2
47.2
52.0
55.2


1,1-DCE
0
50.2
52.3
52.8
49.9


Toluene
0
36.7
40.8
48.7
52.5


Benzene
0
44.7
42.5
49.0
50.9





(Unit: ppm) 



















TABLE 5







pK2-64
pL2-64
pK3-64
pL3-64
HB101





















Phenol
0
0
0
0
48.1


Orthocresol
0
0
0
0
53.1


Methacresol
0
2.1
7.9
16.0
52.5


Paracresol
0
7.5
15.2
21.2
53.2





(Unit: ppm) 



















TABLE 6







pK2-64
pL2-64
pK3-64
pL3-64
HB101





















TCE
0
0
0
0
48.8


cis-1,2-DCE
0
0
0
0
54.1


trans-1,2-DCE
0
0
0
0
52.5


1,1-DCE
0
10.2
0
8.3
52.2


Toluene
0
0
0
0
49.8


Benzene
0
0
0
0
51.0





(Unit: ppm) 



















TABLE 7







pK2-64
pL2-64
pK3-64
pL3-64
HB101





















Phenol
0
0
0
0
49.9


Orthocresol
0
0
0
0
50.2


Methacresol
0
0
0
0
50.9


Paracresol
0
1.8
0
5.2
48.0





(Unit: ppm) 

















TABLE 8







pL2-64 + pKS-64
pL3-64 + pKS-64
HB101



















TCE
0
42.2
53.5


cis-1,2-DCE
0
46.1
51.1


trans-1,2-DCE
0
45.5
49.8


1,1-DCE
0
49.8
51.1


Toluene
0
38.3
50.2


Benzene
0
42.1
51.1





(Unit: ppm) 

















TABLE 9







pL2-64 + pKS-64
pL3-64 + PKS-64
HE101



















Phenol
0
0
50.0


Orthocresol
0
0
52.9


Methacresol
0
12.8
49.0


Paracresol
0
19.8
50.9





(Unit: ppm) 

















TABLE 10







pL2-64 + pKS-64
pL3-64 + pKS-64
HB101



















TCE
0
0
50.5


cis-1,2-DCE
0
0
47.9


trans-1,2-
0
0
48.9


DCE


1,1-DCE
0
0
49.2


Toluene
0
0
47.9


Benzene
0
0
52.0





(Unit: ppm) 

















TABLE 11







pL2-64 + pKS-64
pL3-64 + pKS-64
HB101



















Phenol
0
0
52.7


Orthocresol
0
0
50.1


Methacresol
0
0
50.3


Paracresol
0
0
51.3





(Unit: ppm) 

















TABLE 12







pK2-64
pK3-64
HB101





















TCE
0
38.2
48.1







(Unit: ppm) 

















TABLE 13







pK2-64
pK3-64
HB101





















TCE
0
0
48.0







(Unit: ppm) 

















TABLE 14







pK2-64
pK3-64
HB101





















TCE
0
37.2
55.0







(Unit: ppm) 

















TABLE 15







pK2-64
pK3-64
HB101





















TCE
0
0
52.9







(Unit: ppm) 
















TABLE 16







TL2 (pK2-64bbr)
TL2




















TCE
0
52.2



cis-1,2-DCE
0
47.2



trans-1,2-DCE
0
52.0



1-1,DCE
0
55.2



Toluene
0
47.6



Benzene
0
50.0







(Unit: ppm) 
















TABLE 17







TL2 (pK2-64bbr)
TL2




















Phenol
0
50.8



Ortho-cresol
0
54.4



Meta-cresol
0
52.1



Para-cresol
0
52.0







(Unit: ppm) 
















TABLE 18







TL2 (pK2-64bbr)
TL2




















TCE
0
49.9







(Unit: ppm) 
















TABLE 19







TL2 (pK2-64bbr)
TL2 (pBBR122)




















TCE
0
51.3







(Unit: ppm)

## Claims

1. An isolated DNA fragment containing a portion encoding a toluene monooxygenase, the portion comprising a region encoding a polypeptide TomL having an amino acid sequence of SEQ ID NO: 3, a region encoding a polypeptide TomM having an amino acid sequence of SEQ ID NO: 4, a region encoding a polypeptide TomN having an amino acid sequence of SEQ ID NO: 5, a region encoding a polypeptide TomO having an amino acid sequence of SEQ ID NO: 6, and a region encoding a polypeptide TomP having an amino acid sequence of SEQ ID NO: 7 of the Sequence Listing, and the regions are aligned in the order of TomL-TomM-TomN-TomO-TomP so that expressed TomL-TomP polypeptides can form an active monooxygenase protein.

2. The isolated DNA fragment according to claim 1, wherein no spacer sequence is present between the regions or at least one spacer sequence is present between the regions.

3. The isolated DNA fragment according to claim 1, further comprising a region encoding a polypeptide TomQ having an amino acid sequence of SEQ ID NO: 8 in the Sequence Listing.

4. A DNA fragment having a mutation in at least one region of the DNA fragment according to claim 1, and encoding a protein having a toluene monooxygenase activity.

5. An isolated DNA fragment comprising a region encoding a polypeptide TomK which has an amino acid sequence of SEQ ID NO: 2 and a property to enhance the toluene monooxygenase activity of a protein comprised of at least TomL to TomP aligned in the order of TomL-TomM-TomN-TomO-TomP; or a region encoding a variant TomK in which the amino acid sequence of SEQ ID NO: 2 is altered with the proviso that the property to enhance the toluene monooxygenase activity is not impaired.

6. A recombinant DNA comprising a vector, a promoter, and a DNA fragment,
wherein the vector and the promoter are functionally ligated to the DNA fragment to enable expression of the toluene monooxygenase encoded by the DNA fragment, 
the DNA fragment comprises a region encoding a polypeptide TomL having an amino acid sequence of SEQ ID NO: 3, a region encoding a polypeptide TomM having an amino acid sequence of SEQ ID NO: 4, a region encoding a polypeptide TomN having an amino acid sequence of SEQ ID NO: 5, a region encoding a polypeptide TomO having an amino acid sequence of SEQ ID NO: 6, and a region encoding a polypeptide TomP having an amino acid sequence of SEQ ID NO: 7 of the Sequence Listing; 
wherein the regions are aligned in the order of TomL-TomM-TomN-TomO-TomP.

7. The recombinant DNA according to claim 6 wherein the promoter and the vector can function in a bacterium.

8. A recombinant DNA comprising a vector, a promoter, a first DNA fragment, and a second DNA fragment;
wherein the first DNA encodes a toluene monooxygenase and comprises a region encoding a polypeptide TomL having an amino acid sequence of SEQ ID NO: 3, a region encoding a polypeptide TomM having an amino acid sequence of SEQ ID NO: 4, a region encoding a polypeptide TomN having an amino acid sequence of SEQ ID NO: 5, a region encoding a polypeptide TomO having an amino acid sequence of SEQ ID NO: 6, and a region encoding a polypeptide TomP having an amino acid sequence of SEQ ID NO: 7 of the Sequence Listing, and 
wherein the regions are aligned in the order of TomL-TomM-TomN-TomO-TomP, 
the second DNA fragment encodes a polypeptide TomK having an amino acid sequence of SEQ ID NO: 2 and a property to enhance the toluene monooxygenase activity of a protein comprised of at least TomL to TomP aligned in the order of TomL-TomM-TomN-TomO-TomP; or encodes a variant TomK polypeptide in which the amino acid sequence of SEQ ID NO: 2 is altered with the proviso that the property to enhance the toluene monooxygenase activity is not impaired; 
the first DNA fragment is functionally linked to the promoter to express the toluene monooxygenase activity, and the second DNA fragment is functionally linked to the promoter to express the property to enhance the activity of the toluene monooxygenase encoded by the first DNA fragment.

9. A recombinant DNA comprising a vector, a first promoter and a first DNA fragment, and a second promoter and a second DNA fragment;
wherein the first DNA comprises a region encoding a polypeptide TomL having an amino acid sequence of SEQ ID NO: 3, a region encoding a polypeptide TomM having an amino acid sequence of SEQ ID NO: 4, a region encoding a polypeptide TomN having an amino acid sequence of SEQ ID NO: 5, a region encoding a polypeptide TomO having an amino acid sequence of SEQ ID NO: 6, and a region encoding a polypeptide TomP having an amino acid sequence of SEQ ID NO: 7 of the Sequence Listing, and 
wherein the regions are aligned in the order of TomL-TomM-TomN-TomO-TomP, 
the second DNA fragment encodes a polypeptide TomK having an amino acid sequence of SEQ ID NO: 2 and a property to enhance the toluene monooxygenase activity of a protein comprised of at least TomL to TomP aligned in the order of TomL-TomM-TomN-TomO-TomP; or encodes a variant TomK polypeptide in which the amino acid sequence of SEQ ID NO: 2 is altered with the proviso that the property to enhance the toluene monooxygenase activity is not impaired; 
the first DNA fragment is functionally linked to the first promoter to express the toluene monooxygenase activity, and the second DNA fragment is functionally linked to the second promoter to express the property to enhance the activity of the toluene monooxygenase encoded by the first DNA fragment.

10. The recombinant DNA according to claim 8, wherein the promoter and the vector can function in a bacterium.

11. The recombinant DNA according to claim 9, wherein the first and second promoters and the vector can function in a bacterium.

12. A transformant obtainable by introducing into a host microorganism a recombinant DNA which comprises a vector, a promoter, and a DNA fragment, wherein the vector and the promoter are functionally ligated to the DNA fragment to enable expression of a toluene monooxygenase encoded by the DNA fragment in the host, where the DNA fragment comprises a region encoding a polypeptide TomL having an amino acid sequence of SEQ ID NO: 3, a region encoding a polypeptide TomM having an amino acid sequence of SEQ ID NO: 4, a region encoding a polypeptide TomN having an amino acid sequence of SEQ ID NO: 5, a region encoding a polypeptide TomO having an amino acid sequence of SEQ ID NO: 6, and a region encoding a polypeptide TomP having an amino acid sequence of SEQ ID NO: 7 of the Sequence Listing,
wherein the regions are aligned in the order of TomL-TomM-TomN-TomO-TomP.

13. A transformant obtainable by introducing the recombinant DNA according to claim 8 or 9 into a host microorganism.

14. The transformant according to claim 12, wherein the host microorganism is a bacterium.

15. A method for producing a toluene monooxygenase, comprising: introducing a recombinant DNA comprising a vector, a promoter, and a DNA fragment into a host cell to form a transformant, wherein the vector and the promoter are functionally ligated and the transformant produces a toluene monooxygenase encoded by said DNA fragment,
wherein the DNA fragment comprises a region encoding a polypeptide TomL having an amino acid sequence of SEQ ID NO: 3, a region encoding a polypeptide TomM having an amino acid sequence of SEQ ID NO: 4, a region encoding a polypeptide TomN having an amino acid sequence of SEQ ID NO: 5, a region encoding a polypeptide TomO having an amino acid sequence of SEQ ID NO: 6, and a region encoding a polypeptide TomP having an amino acid sequence of SEQ ID NO: 7 of the Sequence Listing, 
wherein the regions are aligned in the order of TomL-TomM-TomN-TomO-TomP.

16. A method for producing a toluene monooxygenase, comprising: introducing the recombinant DNA according to claim 8 or 9 in a host to enable expression of the toluene monooxygenase encoded by the first DNA fragment.

17. A method for degrading at least one of a halogenated aliphatic hydrocarbon compound and an aromatic compound comprising a degradation of at least one of a halogenated aliphatic hydrocarbon compound and an aromatic compound by the transformant according to any one of claim 12 or 14.

18. A method for degrading at least one of a halogenated aliphatic hydrocarbon compound and an aromatic compound in a medium comprising a degradation step by a transformant obtainable by introducing into a host microorganism a recombinant DNA;
wherein the recombinant DNA comprises a vector, a promoter, and a DNA fragment where the vector and the promoter are functionally ligated to the DNA fragment to enable expression of a toluene monooxygenase encoded by the DNA fragment in the host, 
the DNA fragment comprises a region encoding a polypeptide TomL having an amino acid sequence of SEQ ID NO: 3, a region encoding a polypeptide TomM having an amino acid sequence of SEQ ID NO: 4, a region encoding a polypeptide TomN having an amino acid sequence of SEQ ID NO: 5, a region encoding a polypeptide TomO having an amino acid sequence of SEQ ID NO: 6, and a region encoding a polypeptide TomP having an amino acid sequence of SEQ ID NO: 7 of the Sequence Listing, 
wherein the regions are aligned in the order of TomL-TomM-TomN-TomO-TomP.

19. A method for degrading at least one of a halogenated aliphatic hydrocarbon compound and an aromatic compound comprising a degradation step of the compound by a transformant,
wherein the transformant is obtainable by introducing into a host microorganism the recombinant DNA according to claim 8 or 9.

20. The degradation method according to claim 18, wherein the halogenated aliphatic hydrocarbon compound is a chlorinated aliphatic hydrocarbon compound.

21. The degradation method according to claim 20, wherein the halogenated aliphatic hydrocarbon compound is either trichloroethylene (TCE) or dichloroethylene (DCE).

22. The degradation method according to claim 18, wherein the aromatic compound is at least one of toluene, benzene, phenol, and cresol.

23. A method for remedying an environment polluted with a pollutant being at least either of a halogenated aliphatic hydrocarbon compound or an aromatic compound, comprising a step of degrading the pollutant by bringing a transformant into contact with the pollutant,
wherein the transformant is obtainable by introducing into a host microorganism a recombinant DNA which comprises a vector, a promoter, and a DNA fragment where the vector and the promoter are functionally ligated to the DNA fragment to enable expression of a toluene monooxygenase encoded by the DNA fragment in the host, 
the DNA fragment comprises a region encoding a polypeptide TomL having an amino acid sequence of SEQ ID NO: 3, a region encoding a polypeptide TomM having an amino acid sequence of SEQ ID NO: 4, a region encoding a polypeptide TomN having an amino acid sequence of SEQ ID NO: 5, a region encoding a polypeptide TomO having an amino acid sequence of SEQ ID NO: 6, and a region encoding a polypeptide TomP having an amino acid sequence of SEQ ID NO: 7 of the Sequence Listing, 
wherein the regions are aligned in the order of TomL-TomM-TomN-TomO-TomP.

24. A method for remedying an environment polluted with a pollutant being at least either of a halogenated aliphatic hydrocarbon compound or an aromatic compound, comprising a step of degrading the pollutant by bringing a transformant into contact with the pollutant,
wherein the transformant is obtainable by introducing the recombinant DNA according to claim 8 or 9.

25. The remediation method according to claim 23 wherein the environment is an aqueous medium.

26. The remediation method according to claim 25 wherein the aqueous medium is brought into contact with a carrier holding the transformant.

27. The remediation method according to claim 26 wherein the aqueous medium is brought into contact with the pollutant by placing the carrier holding the transformant in a container, introducing the polluted aqueous medium from one side of the container, and discharging the remedied aqueous medium from another side.

28. The remediation method according to claim 23, wherein the environment is soil.

29. The remediation method according to claim 28 comprising the steps of:
introducing an aqueous medium containing the transformant into the polluted soil; and 
supplying nutrients and/or oxygen for proliferation of the transformant in the polluted soil.

30. The remediation method according to claim 29 wherein the transformant is introduced in the soil by applying pressure through an injection well provided in the polluted soil.

31. The remediation method according to claim 28 wherein the polluted soil is introduced in a liquid phase containing the transformant.

32. The remediation method according to claim 28 wherein the polluted soil is brought into contact with a carrier holding the transformant.

33. The remediation method according to claim 23 wherein the environment is air.

34. The remediation method according to claim 33 wherein the polluted air is introduced into a liquid phase containing the transformant.

35. The remediation method according to claim 33 wherein the polluted air is brought into contact with a carrier holding the transformant.

36. The remediation method according to claim 35 wherein contact is carried out by placing the carrier holding the transformant in a container, introducing polluted air from one side of the container, and discharging cleaned air from another side.

37. The remediation method according to claim 23 wherein the halogenated aliphatic hydrocarbon compound is either trichloroethylene (TCE) or dichloroethylene (DCE).

38. The remediation method according to claim 23 wherein the aromatic compound is at least one of toluene, benzene, phenol, and cresol.

39. A component polypeptide having an amino acid sequence of SEQ ID NO: 2 in the sequence listing, capable of being a component of a toluene monooxygenase.

40. A toluene monooxygenase comprising at least component polypeptides TomL to TomP aligned in the order of TomL-TomM-TomN-TomO-TomP having amino acid sequences of SEQ ID NOs: 3 to 7 in the Sequence Listing.

41. The toluene monooxygenase according to claim 40 further comprising a component polypeptide TomK having an amino acid sequence of SEQ ID NO: 2 in the Sequence Listing.

42. The toluene monooxygenase according to claim 41 further comprising a component polypeptide TomQ having an amino acid sequence of SEQ ID NO: 8 in the Sequence Listing.