US20030135879A1 - Methods and materials for making and using transgenic dicamba-degrading organisms - Google Patents

Abstract

The invention provides isolated and at least partially-purified dicamba-degrading enzymes, isolated DNA molecules coding for dicamba-degrading enzymes, DNA constructs coding for dicamba-degrading enzymes, transgenic host cells comprising DNA coding for dicamba-degrading enzymes, and transgenic plants and plant parts comprising one or more cells comprising DNA coding for dicamba-degrading enzymes. Expression of the dicamba-degrading enzymes results in the production of dicamba-degrading organisms, including dicamba-tolerant plants. The invention further provides a method of controlling weeds in a field containing the transgenic dicamba-tolerant plants of the invention and a method of decontaminating a material containing dicamba comprising applying an effective amount of a transgenic microorganism or dicamba-degrading enzyme(s) of the invention to the material. Finally, the invention provides a method of selecting transformed plants and plant cells based on dicamba tolerance and a method of selecting or screening transformed host cells, intact organisms and parts of organisms based on the fluorescence of 3,6-dichlorosalicylic acid produced as a result of dicamba degradation.

Description

• This application is a continuation-in-part of application Ser. No. 09/055,145, filed Apr. 3, 1998, and claims benefit of provisional applications 60/042,666 and 60/042,941, both filed Apr. 4, 1997, the complete disclosures of all three of which are incorporated herein by reference.[0001]
FIELD OF THE INVENTION
• The present invention relates to transgenic organisms that are able to degrade the herbicide dicamba, including transgenic plants that have been made tolerant to dicamba. The invention also relates to dicamba-degrading enzymes and to DNA molecules and DNA constructs coding for dicamba-degrading enzymes. The invention further relates to a method of controlling weeds in fields of dicamba-tolerant transgenic plants and to a method of removing dicamba from materials contaminated with it (bioremediation). Finally, the invention relates to methods of selecting transformants based on dicamba tolerance or on detecting the fluorescence of 3,6-dichlorosalicylic acid which is generated as a result of dicamba degradation.[0002]
BACKGROUND
• Herbicides are used routinely in agricultural production. Their effectiveness is often determined by their ability to kill weed growth in crop fields and the tolerance of the cash crop to the herbicide. If the cash crop is not tolerant to the herbicide, the herbicide will either diminish the productivity of the cash crop or kill it altogether. Conversely, if the herbicide is not strong enough, it may allow too much weed growth in the crop field which will, in turn, lessen the productivity of the cash crop. Therefore, it is desirable to produce economically important plants which are tolerant to herbicides. To protect the water and environmental quality of agricultural lands, it is also desirable to develop technologies to degrade herbicides in cases of accidental spills of the herbicide or in cases of unacceptably high levels of soil or water contamination.[0003]
• Genes encoding enzymes which inactivate herbicides and other xenophobic compounds have previously been isolated from a variety of procaryotic and eucaryotic organisms. In some cases, these genes have been genetically engineered for successful expression in plants. Through this approach, plants have been developed which are tolerant to the[0004]herbicides 2,4-dichlorophenoxyacetic acid (Streber and Willmitzer (1989)Bio/Technology7:811-816; 2,4-D), bromoxynil (Stalker et al. (1988)Science242:419-423; tradename Buctril), glyphosate (Comai et al. (1985)Nature317:741-744; tradename Round-Up) and phosphinothricin (De Block et al. (1987)EMBO J.6:2513-2518; tradename Basta).
• Dicamba (tradename Banvel) is used as a pre-emergent and post-emergent herbicide for the control of annual and perennial broadleaf weeds and several grassy weeds in corn, sorghum, small grains, pasture, hay, rangeland, sugarcane, asparagus, turf and grass seed crops. See[0005]Crop Protection Reference,pages 1803-1821 (Chemical & Pharmaceutical Press, Inc., New York, N.Y., 11th ed., 1995). Unfortunately, dicamba can injure many commercial crops (including beans, soybeans, cotton, peas, potatoes, sunflowers, tomatoes, tobacco, and fruit trees), ornamental plants and trees, and other broadleaf plants when it comes into contact with them. Id. Dicamba is chemically stable and can sometimes be persistent in the environment.
• Dicamba is in the class of benzoic acid herbicides. It has been suggested that plants tolerant to benzoic acid herbicides, including dicamba, can be produced by incorporating a 1-aminocyclopropane-1-carboxylic acid (ACC) synthase antisense gene, an ACC oxidase antisense gene, an ACC deaminase gene, or combinations thereof, into the plants. See Canadian Patent Application 2,165,036 (published Jun. 16, 1996). However, no experimental data are presented in this application which demonstrate such tolerance.[0006]
• Bacteria that metabolize dicamba are known. See U.S. Pat. No. 5,445,962; Krueger et al.,[0007]J. Agric. Food Chem.,37, 534-538 (1989); Cork and Krueger,Adv. Appl. Microbiol.,38, 1-66 (1991); Cork and Khalil,Adv. Appl. Microbiol.,40, 289-320 (1995). It has been suggested that the specific genes responsible for dicamba metabolism by these bacteria could be isolated and used to produce dicamba-resistant plants and other organisms. See id. and Yang et al.,Anal. Biochem.,219:37-42 (1994). However, prior to the present invention, no such genes had been identified or isolated.
SUMMARY OF THE INVENTION
• The invention provides an isolated and at least partially purified dicamba-degrading O-demethylase, an isolated and at least partially purified dicamba-degrading oxygenase, an isolated and at least partially purified dicamba-degrading ferredoxin, and an isolated and at least partially purified dicamba-degrading reductase, all as defined and described below.[0008]
• The invention also provides an isolated DNA molecule comprising a DNA sequence coding for a dicamba-degrading oxygenase, an isolated DNA molecule comprising a DNA sequence coding for a dicamba-degrading ferredoxin, and an isolated DNA molecule comprising a DNA sequence coding for a dicamba-degrading reductase. The invention further provides a DNA construct comprising a DNA sequence coding for a dicamba-degrading oxygenase, a DNA sequence coding for a dicamba-degrading ferredoxin, or a DNA sequence coding for a dicamba-degrading reductase, each DNA coding sequence being operatively linked to expression control sequences. In addition, the invention provides a DNA construct comprising a DNA sequence coding for a dicamba-degrading oxygenase, a DNA sequence coding for a dicamba-degrading ferredoxin, and a DNA sequence coding for a dicamba-degrading reductase, each DNA coding sequence being operatively linked to expression control sequences.[0009]
• The invention further provides a transgenic host cell comprising DNA coding for a dicamba-degrading oxygenase, DNA coding for a dicamba-degrading ferredoxin, or DNA coding for a dicamba-degrading reductase, each DNA being operatively linked to expression control sequences. In addition, the invention provides a transgenic host cell comprising DNA coding for a dicamba-degrading oxygenase and DNA coding for a dicamba-degrading ferredoxin, DNA coding for a dicamba-degrading reductase, or DNA coding for a dicamba-degrading ferredoxin and DNA coding for a dicamba-degrading reductase, each DNA being operatively linked to expression control sequences. The transgenic host cell may be a plant cell or a prokaryotic or eukaryotic microorganism.[0010]
• The invention also provides a transgenic plant or plant part comprising one or more cells comprising DNA coding for a dicamba-degrading oxygenase, DNA coding for a dicamba-degrading ferredoxin, or DNA coding for a dicamba-degrading reductase, each DNA being operatively linked to expression control sequences. The invention further provides a transgenic plant or plant part comprising one or more cells comprising DNA coding for a dicamba-degrading oxygenase and DNA coding for a dicamba-degrading ferredoxin, DNA coding for a dicamba-degrading reductase, or DNA coding for a dicamba-degrading ferredoxin and DNA coding for a dicamba-degrading reductase, each DNA being operatively linked to expression control sequences. The transgenic plant or plant part is preferably tolerant to dicamba or has had its tolerance to dicamba increased as a result of the expression of the dicamba-degrading enzyme(s).[0011]
• The invention also provides a method of controlling weeds in a field containing transgenic dicamba-tolerant plants. The method comprises applying an amount of dicamba to the field which is effective to control the weeds.[0012]
• The invention further provides methods of decontaminating a material containing dicamba. In one embodiment, the method comprises applying an effective amount of a transgenic dicamba-degrading microorganism to the material. In another embodiment, the method comprises applying an effective amount of a dicamba-degrading O-demethylase or of a combination of a dicamba-degrading oxygenase, a dicamba-degrading ferredoxin and a dicamba-degrading reductase to the material.[0013]
• The invention also provides a method of selecting transformed plant cells and transformed plants using dicamba tolerance as the selection marker. In one embodiment, the method comprises transforming at least some of the plant cells in a population of plant cells so that they are tolerant to dicamba and growing the resulting population of plant cells in a culture medium containing dicamba at a concentration selected so that transformed plant cells will grow and untransformed plant cells will not grow. In another embodiment, the method comprising applying dicamba to a population of plants suspected of comprising plants that have been transformed so that they are tolerant to dicamba, the dicamba being applied in an amount selected so that transformed plants will grow, and the growth of untransformed plants will be inhibited.[0014]
• Finally, the invention provides a method of selecting, or screening for, transformed host cells, intact organisms, and parts of organisms. The method comprises providing a population of host cells, intact organisms, or parts of organisms suspected of comprising host cells, intact organisms, or parts of organisms that have been transformed so that they are able to degrade dicamba, contacting the population of host cells, intact organisms, or parts of organisms with dicamba, and ascertaining the presence or level of fluorescence due to 3,6-dichlorosalicylic acid. The 3,6-dichlorosalicyclic acid is generated in transformed host cells, intact organisms, or parts of organisms as a result of the degradation of dicamba, but will not be generated in untransformed host cells, intact organisms, or parts of organisms.[0015]
BRIEF DESCRIPTION OF THE DRAWINGS
• FIG. 1. A diagram of the proposed electron transport scheme for dicamba O-demethylase. Electrons from NADH are transferred sequentially from reductase[0016]_DICto ferredoxin_DICand then to oxygenase_DIC. The reaction of oxygen with the substrate dicamba to form 3,6-dichlorosalicylic acid is catalyzed by oxygenase_DIC. ox, oxidized; red, reduced.
• FIG. 2. Comparison of the derived amino acid sequence of the ferredoxin component of dicamba O-demethylase to the amino acid sequences of members of the adrenodoxin family of ferredoxins. In FIG. 2, ferr di6=ferredoxin component of dicamba O-demethylase from[0017]Pseudomonas maltophiliaDI-6[SEQ ID NO: 5]; fer6 rhoca=ferredoxin fromRhodobacter capsulatus[SEQ ID NO: 10]; fer caucr=ferredoxin fromCaulobacter crescentus [SEQ ID NO: 11]; thcc rhocr=ferredoxin fromRhodococcus erythropolis [SEQ ID NO: 12]; putx psepu=ferredoxin fromPseudomonas putida [SEQ ID NO: 13]; terp psesp=ferredoxin from Pseudomonas sp. [SEQ ID NO: 14]. Also in FIG. 2, the numbers 1-3 designate the three conserved motifs of the adrenodoxin family of bacterial ferredoxins.
• FIG. 3. Comparison of the derived amino acid sequence of the two reductase components of dicamba O-demethylase to the amino acid sequences of members of the family of FAD-dependent pyridine nucleotide reductases. In FIG. 3, red1 di6=reductase component of dicamba O-demethylase from[0018]P. maltophiliaDI-6[SEQ ID NO: 7]; red2 di6=reductase component of dicamba O-demethylase fromP. maltophiliaDI-6[SEQ ID NO: 9]; AJ002606=reductase from Sphingomonas sp. [SEQ ID NO: 15]; thcd rhoer=reductase fromR. erythropolis [SEQ ID NO: 16]; cama psepu=reductase fromP. putida [SEQ ID NO: 17]; tera pscsp=reductase from Pseudomonas sp. [SEQ ID NO: 18]. Also in FIG. 3, the numbers 1-5 designate the five conserved motifs of FAD-dependent pyridine nucleotide reductases.
DETAILED DESCRIPTION OF THE PRESENTLY PREFERRED EMBODIMENTS OF THE INVENTION
• Prior studies (Cork and Kreuger,[0019]Advan. Appl. Microbiol.36:1-56 and Yang et al. (1994)Anal. Biochem.219:37-42) have shown that the soil bacterium,Pseudomonas maltophilia,strain DI-6, is capable of destroying the herbicidal activity of dicamba through a single step reaction in which dicamba (3,6-dichloro-2-methoxybenzoic acid) is converted to 3,6-dichlorosalicylic acid (3,6-DCSA). 3,6-DCSA has no herbicidal activity and has not been shown to have any detrimental effects on plants. In addition, 3,6-DCSA is readily degraded by the normal bacterial flora present in soil.
• The experiments described herein confirm the hypothesis of Yang et al. (see id.) that an O-demethylase is responsible for the conversion of dicamba to 3,6-DCSA by[0020]P. maltophiliastrain DI-6 and establish that the O-demethylase is a three-component enzyme system consisting of a reductase, a ferredoxin, and an oxygenase. See Examples 1 and 3 which describe in detail the isolation, purification and characterization of theP. maltophiliaO-demethylase and its three components. The reaction scheme for the reaction catalyzed by the three components of dicamba O-demethylase is presented in FIG. 1. As illustrated in FIG. 1, electrons from NADH are shuttled through a short electron chain consisting of the reductase and ferredoxin to the terminal oxygenase which catalyzes the oxidation of dicamba to produce 3,6-DCSA.
• In a first embodiment, the invention provides isolated and at least partially purified dicamba-degrading enzymes. “Isolated” is used herein to mean that the enzymes have at least been removed from the cells in which they are produced (i.e., they are contained in a cell lysate). “At least partially purified” is used herein to mean that they have been separated at least partially from the other components of the cell lysate. Preferably, the enzymes have been purified sufficiently so that the enzyme preparations are at least about 70% homogenous.[0021]
• In particular, the invention provides an isolated and at least partially purified dicamba-degrading O-demethylase. “Dicamba-degrading O-demethylase” is defined herein to mean a combination of a dicamba-degrading oxygenase, a dicamba-degrading ferredoxin and a dicamba-degrading reductase, all as defined below.[0022]
• The invention also provides an isolated and at least partially purified dicamba-degrading oxygenase. “Dicamba-degrading oxygenase” is defined herein to mean the oxygenase purified from[0023]P. maltophiliastrain DI-6 and oxygenases which have an amino acid sequence which is at least about 65% homologous, preferably at least about 85% homologous, to that of theP. maltophiliaoxygenase and which can participate in the degradation of dicamba. “Dicamba-degrading oxygenases” include mutant oxygenases having the amino acid sequence of theP. maltophiliaoxygenase wherein one or more amino acids have been added to, deleted from, or substituted for, the amino acids of theP. maltophiliaoxygenase sequence. Activity of dicamba-degrading oxygenases can be determined as described in Examples 1 and 3.
• The invention further provides an isolated and at least partially purified dicamba-degrading ferredoxin. “Dicamba-degrading ferredoxin” is defined herein to mean the ferredoxin purified from[0024]P. maltophiliastrain DI-6 and ferredoxins which have an amino acid sequence which is at least about 65% homologous, preferably at least about 85% homologous, to that of theP. maltophiliaferredoxin and which can participate in the degradation of dicamba. “Dicamba-degrading ferredoxins” include mutant ferredoxins having the amino acid sequence of theP. maltophiliaferredoxin wherein one or more amino acids have been added to, deleted from, or substituted for, the amino acids of theP. maltophiliaferredoxin sequence. Activity of dicamba-degrading ferredoxins can be determined as described in Examples 1 and 3.
• Finally, the invention provides an isolated and at least partially purified dicamba-degrading reductase. “Dicamba-degrading reductase” is defined herein to mean the reductases purified from[0025]P. maltophiliastrain DI-6 and reductases which have an amino acid sequence which is at least about 65% homologous, preferably at least about 85% homologous, to that of one of theP. maltophiliareductases and which can participate in the degradation of dicamba. “Dicamba-degrading reductases” include mutant reductases having the amino acid sequence of one of theP. maltophiliareductases wherein one or more amino acids have been added to, deleted from, or substituted for, the amino acids of theP. maltophiliareductase sequence. Activity of dicamba-degrading reductases can be determined as described in Examples 1 and 3.
• Methods of determining the degree of homology of amino acid sequences are well known in the art. For instance, the FASTA program of the Genetics Computing Group (GCG) software package (University of Wisconsin, Madison, Wis.) can be used to compare sequences in various protein databases such as the Swiss Protein Database.[0026]
• The dicamba-degrading enzymes of the invention can be isolated and purified as described in Examples 1 and 3 from[0027]P. maltophiliaor other organisms. Suitable other organisms include bacteria other thanP. maltophiliastrain DI-6 that degrade dicamba. Several strains of such bacteria are known. See U.S. Pat. No. 5,445,962; Krueger et al.,J. Agric. Food Chem.,37, 534-538 (1989); Cork and Krueger,Adv. Appl. Microbiol.,38, 1-66 (1991); Cork and Khalil,Adv. Appl. Microbiol.,40, 289-320 (1995). Other dicamba-degrading bacterial strains can be isolated as were these strains by methods well known in the art.
• Preferably, however, the dicamba-degrading enzymes of the invention are prepared using recombinant DNA techniques (see below). In particular, mutant enzymes having the amino acid sequence of the[0028]P. maltophiliaenzyme wherein one or more amino acids have been added to, deleted from, or substituted for, the amino acids of theP. maltophiliasequence are prepared in this manner using, for example, oligonucleotide-directed mutagenesis, linker-scanning mutagenesis, mutagenesis using the polymerase chain reaction, and the like. See Ausubel et al. (eds.),Current Protocols In Molecular Biology(Wiley Interscience 1990) and McPherson (ed.),Directed Mutagenesis: A Practical Approach(IRL Press 1991).
• In a second embodiment, the invention provides isolated DNA molecules coding for dicamba-degrading enzymes of the invention. “Isolated” is used herein to mean that the DNA molecule has been removed from its natural environment or is not a naturally-occurring is DNA molecule. Methods of preparing these DNA molecules are well known in the art. See, e.g., Maniatis et al.,[0029]Molecular Cloning: A Laboratory Manual,Cold Spring Harbor, N.Y. (1982), Sambrook et al.,Molecular Cloning: A Laboratory Manual,Cold Spring Harbor, N.Y. (1989).
• For instance, the DNA molecules of the invention may be isolated cDNA or genomic clones. The identification and isolation of clones coding for the dicamba-degrading enzymes of[0030]P. maltophiliastrain DI-6 are described in Examples 2 and 4-5. Additional clones coding for dicamba-degrading enzymes can be obtained in a similar manner. The isolated clones, or portions of them, can be used as probes to identify and isolate additional clones from organisms other than the ones from which the clones were originally isolated. Suitable organisms include bacteria that degrade dicamba. As noted above, in addition toP. maltophiliastrain DI-6, several strains of bacteria are known that degrade dicamba. See U.S. Pat. No. 5,445,962; Krueger et al.,J. Agric. Food Chem.,37, 534-538 (1989); Cork and Krueger,Adv. Appl. Microbiol.,38, 1-66(1991); Cork and Khalil,Adv. Appl. Microbiol.,40, 289-320 (1995).
• The DNA molecules of the invention can also be chemically synthesized using the sequences of isolated clones. Such techniques are well known in the art. For instance, DNA sequences may be synthesized by phosphoamidite chemistry in an automated DNA synthesizer. Chemical synthesis has a number of advantages. In particular, chemical synthesis is desirable because codons preferred by the host in which the DNA sequence will be expressed may be used to optimize expression. Not all of the codons need to be altered to obtain improved expression, but preferably at least the codons rarely used in the host are changed to host-preferred codons. High levels of expression can be obtained by changing greater than about 50%, most preferably at least about 80%, of the codons to host-preferred codons. The codon preferences of many host cells are known. See, e.g.,[0031]Maximizing Gene Expression,pages 225-85 (Reznikoff & Gold, eds., 1986), PCT WO 97/31115, PCT WO 97/11086, EP 646643, EP 553494, and U.S. Pat. Nos. 5,689,052, 5,567,862, 5,567,600, 5,552,299 and 5,017,692. The codon preferences of other host cells can be deduced by methods known in the art. Also, using chemical synthesis, the sequence of the DNA molecule or its encoded protein can be readily changed to, e.g., optimize expression (e.g., eliminate mRNA secondary structures that interfere with transcription or translation), add unique restriction sites at convenient points, delete protease cleavage sites, etc.
• In a third embodiment, the present invention provides DNA constructs comprising DNA coding for a dicamba-degrading enzyme operatively linked to expression control sequences or a plurality of DNA coding sequences, each coding for a dicamba-degrading enzyme and each being operatively linked to expression control sequences. “DNA constructs” are defined herein to be constructed (non-naturally occurring) DNA molecules useful for introducing DNA into host cells, and the term includes chimeric genes, expression cassettes, and vectors.[0032]
• As used herein “operatively linked” refers to the linking of DNA sequences (including the order of the sequences, the orientation of the sequences, and the relative spacing of the various sequences) in such a manner that the encoded proteins are expressed. Methods of operatively linking expression control sequences to coding sequences are well known in the art. See, e.g. Maniatis et al.,[0033]Molecular Cloning: A Laboratory Manual,Cold Spring Harbor, N.Y. (1982), Sambrook et al.,Molecular Cloning: A Laboratory Manual,Cold Spring Harbor, N.Y. (1989).
• “Expression control sequences” are DNA sequences involved in any way in the control of transcription or translation in prokaryotes and eukaryotes. Suitable expression control sequences and methods of making and using them are well known in the art.[0034]
• The expression control sequences must include a promoter. The promoter may be any DNA sequence which shows transcriptional activity in the chosen host cell or organism. The promoter may be inducible or constitutive. It may be naturally-occurring, may be composed of portions of various naturally-occuring promoters, or may be partially or totally synthetic. Guidance for the design of promoters is provided by studies of promoter structure, such as that of Harley and Reynolds,[0035]Nucleic Acids Res.,15, 2343-61 (1987). Also, the location of the promoter relative to the transcription start may be optimized. See, e.g., Roberts, et al.,Proc. Natl Acad. Sci. USA,76, 760-4 (1979). Many suitable promoters for use in prokaryotes and eukaryotes are well known in the art.
• For instance, suitable constitutive promoters for use in plants include: the promoters from plant viruses, such as the 35S promoter from cauliflower mosaic virus (Odell et al.,[0036]Nature313:810-812 (1985), promoters of Chlorella virus methyltransferase genes (U.S. Pat. No. 5,563,328), and the full-length transcript promoter from figwort mosaic virus (U.S. Pat. No. 5,378,619); the promoters from such genes as rice actin (McElroy et al.,Plant Cell2:163-171 (1990)), ubiquitin (Christensen et al.,Plant Mol. Biol.12:619-632 (1989) and Christensen et al.,Plant Mol. Biol.18:675-689 (1992)), pEMU (Last et al.,Theor. Appl. Genet.81:581-588 (1991)), MAS (Velten et al.,EMBO J.3:2723-2730 (1984)), maize H3 histone (Lepetit et al.,Mol. Gen. Genet.231:276-285 (1992) and Atanassova et al.,Plant Journal2(3):291-300 (1992)),Brassica napusALS3 (PCT application WO 97/41228); and promoters of various Agrobacterium genes (see U.S. Pat. Nos. 4,771,002, 5,102,796, 5,182,200, 5,428,147).
• Suitable inducible promoters for use in plants include: the promoter from the ACE1 system which responds to copper (Mett et al.[0037]PNAS90:4567-4571 (1993)); the promoter of the maize In2 gene which responds to benzenesulfonamide herbicide safeners (Hershey et al.,Mol. Gen. Genetics227:229-237 (1991) and Gatz et al.,Mol. Gen. Genetics243:32-38 (1994)), and the promoter of the Tet repressor from Tn10 (Gatz et al.,Mol. Gen. Genet.227:229-237(1991). A particularly preferred inducible promoter for use in plants is one that responds to an inducing agent to which plants do not normally respond. An exemplary inducible promoter of this type is the inducible promoter from a steroid hormone gene, the transcriptional activity of which is induced by a glucocorticosteroid hormone. Schena et al.,Proc. Natl. Acad. Sci. USA88:10421 (1991). Other inducible promoters for use in plants are described in EP 332104, PCT WO 93/21334 and PCT WO 97/06269.
• Suitable promoters for use in bacteria include the promoter of the[0038]Bacillus stearothermophilusmaltogenic amylase gene, theBacillus licheniformisalpha-amylase gene, theBacillus amyloliquefaciensBAN amylase gene, theBacillus subtilisalkaline protease gene, theBacillus pumilusxylosidase gene, the phage lambda P_Rand P_Lpromoters, and theEscherichia colilac, trp and tac promoters. See PCT WO 96/23898 and PCT WO 97/42320.
• Suitable promoters for use in yeast host cells include promoters from yeast glycolytic genes, promoters from alcohol dehydrogenase genes, the TPI1 promoter, and the ADH2-4c promoter. See PCT WO 96/23898.[0039]
• Suitable promoters for use in filamentous fungi include the ADH3 promoter, the tpiA promoter, the promoters of the genes encoding[0040]Aspergillus oryzaeTAKA amylase,Rhizomucor mieheiaspartic proteinase,Aspergillus nigerneutral alpha-amylase,A. nigeracid stable alpha-amylase,A. nigerorAspergillus awamoriglucoamylase,R. mieheilipase,A. oryzaealkaline protease,A. oryzaetriose phosphate isomerase, andAspergillus nidulansacetamidase. See PCT WO 96/23898.
• Suitable promoters for use in mammalian cells are the SV40 promoter, metallothionein gene promoter, murine mammary tumor virus promoter,[0041]Rous sarcomavirus promoter, andadenovirus 2 major late promoter. See PCT WO 96/23898 and PCT WO 97/42320.
• Suitable promoters for use in insect cells include the polyhedrin promoter, P10 promoter, the[0042]Autographa californicapolyhedrosis virus basic protein promoter, the baculovirus immediateearly gene 1 promoter and the baculovirus 39K delayed-early gene promoter. See PCT WO 96/23898.
• Finally, promoters composed of portions of other promoters and partially or totally synthetic promoters can be used. See, e.g., Ni et al.,[0043]Plant J.,7:661-676(1995)and PCT WO 95/14098 describing such promoters for use in plants.
• The promoter may include, or be modified to include, one or more enhancer elements. Preferably, the promoter will include a plurality of enhancer elements. Promoters containing enhancer elements provide for higher levels of transcription as compared to promoters which do not include them. Suitable enhancer elements for use in plants include the 35S enhancer element from cauliflower mosaic virus (U.S. Pat. Nos. 5,106,739 and 5,164,316) and the enhancer element from figwort mosaic virus (Maiti et al.,[0044]Transgenic Res.,6, 143-156 (1997)). Other suitable enhancers for use in other cells are known. See PCT WO 96/23898 andEnhancers And Eukaryotic Expression(Cold Spring Harbor Press, Cold Spring Harbor, N.Y., 1983).
• For efficient expression, the coding sequences are preferably also operatively linked to a 3′ untranslated sequence. The 3′ untranslated sequence contains transcription and/or translation termination sequences. The 3′ untranslated regions can be obtained from the flanking regions of genes from bacterial, plant or other eukaryotic cells. For use in prokaryotes, the 3′ untranslated region will include a transcription termination sequence. For use in plants and other eukaryotes, the 3′ untranslated region will include a transcription termination sequence and a polyadenylation sequence. Suitable 3′ untranslated sequences for use in plants include those of the cauliflower mosaic virus 35S gene, the phaseolin seed storage protein gene, the pea ribulose biphosphate carboxylase small subunit E9 gene, the soybean 7S storage protein genes, the octopine synthase gene, and the nopaline synthase gene.[0045]
• In plants and other eukaryotes, a 5′ untranslated sequence is also employed. The 5′ untranslated sequence is the portion of an mRNA which extends from the 5′ CAP site to the translation initiation codon. This region of the mRNA is necessary for translation initiation in eukaryotes and plays a role in the regulation of gene expression. Suitable 5′ untranslated regions for use in plants include those of alfalfa mosaic virus, cucumber mosaic virus coat protein gene, and tobacco mosaic virus.[0046]
• As noted above, the DNA construct may be a vector. The vector may contain one or more replication systems which allow it to replicate in host cells. Self-replicating vectors include plasmids, cosmids and viral vectors. Alternatively, the vector may be an integrating vector which allows the integration into the host cell's chromosome of the sequences coding for the dicamba-degrading enzymes of the invention. The vector desirably also has unique restriction sites for the insertion of DNA sequences. If a vector does not have unique restriction sites, it may be modified to introduce or eliminate restriction sites to make it more suitable for further manipulations.[0047]
• The DNA constructs of the invention can be used to transform a variety of host cells (see below). A genetic marker must be used for selecting transformed host cells (“a selection marker”). Selection markers typically allow transformed cells to be recovered by negative selection (i.e., inhibiting growth of cells that do not contain the selection marker) or by screening for a product encoded by the selection marker.[0048]
• The most commonly used selectable marker gene for plant transformation is the neomycin phosphotransferase II (nptII) gene, isolated from Tn5, which, when placed under the control of plant regulatory signals, confers resistance to kanamycin. Fraley et al.,[0049]Proc. Natl. Acad. Sci. USA,80:4803 (1983). Another commonly used selectable marker gene is the hygromycin phosphotransferase gene which confers resistance to the antibiotic hygromycin. Vanden Elzen et al.,Plant Mol. Biol.,5:299 (1985).
• Additional selectable marker genes of bacterial origin that confer resistance to antibiotics include gentamycin acetyl transferase, streptomycin phosphotransferase, aminoglycoside-3′-adenyl transferase, and the bleomycin resistance determinant. Hayford et al.,[0050]Plant Physiol.86:1216 (1988), Jones et al.,Mol. Gen. Genet.210:86 (1987), Svab et al.,Plant Mol. Biol.14:197 (1990), Hille et al., Plant Mol. Biol. 7:171 (1986). Other selectable marker genes confer resistance to herbicides such as glyphosate, glufosinate or bromoxynil. Comai et al.,Nature317:741-744 (1985), Gordon-Kamm et al.,Plant Cell2:603-618 (1990) and Stalker et al.,Science242:419-423 (1988).
• Other selectable marker genes for plant transformation are not of bacterial origin. These genes include, for example, mouse dihydrofolate reductase, plant 5-enolpyruvylshikimate-3-phosphate synthase and plant acetolactate synthase. Eichholtz et al.,[0051]Somatic Cell Mol. Genet.13:67 (1987), Shah et al.,Science233:478 (1986), Charest et al.,Plant Cell Rep.8:643 (1990).
• Commonly used genes for screening presumptively transformed cells include β-glucuronidase (GUS), β-galactosidase, luciferase, and chloramphenicol acetyltransferase. Jefferson, R. A.,[0052]Plant Mol. Biol. Rep.5:387 (1987)., Teeri et al.,EMBO J.8:343 (1989), Koncz et al.,Proc. Natl. Acad. Sci. USA84:131 (1987), De Block et al.,EMBO J.3:1681 (1984), green fluorescent protein (GFP) (Chalfie et al.,Science263:802 (1994), Haseloff et al.,TIG11:328-329 (1995) and PCT application WO 97/41228). Another approach to the identification of relatively rare transformation events has been use of a gene that encodes a dominant constitutive regulator of theZea maysanthocyanin pigmentation pathway. Ludwig et al.,Science247:449 (1990).
• Suitable selection markers for use in prokaryotes and eukaryotes other than plants are also well known. See, e.g., PCT WO 96/23898 and PCT WO 97/42320. For instance, resistance to antibiotics (ampicillin, kanamycin, tetracyline, chloramphenicol, neomycin or hygromycin) may be used as the selection marker.[0053]
• According to another aspect of the present invention, tolerance to dicamba can be used as a selection marker for plants and plant cells. “Tolerance” means that transformed plant cells are able to grow (survive and regenerate into plants) when placed in culture medium containing a level of dicamba that prevents untransformed cells from doing so. “Tolerance” also means that transformed plants are able to grow after application of an amount of dicamba that inhibits the growth of untransformed plants.[0054]
• Methods of selecting transformed plant cells are well known in the art. Briefly, at least some of the plant cells in a population of plant cells (e.g., an explant or an embryonic suspension culture) are transformed with a DNA construct or combination of DNA constructs providing for dicamba degradation. The resulting population of plant cells is placed in culture medium containing dicamba at a concentration selected so that transformed plant cells will grow, whereas untransformed plant cells will not. Suitable concentrations of dicamba can be determined empirically as is known in the art.[0055]
• Methods of selecting transformed plants are also known in the art. Briefly, dicamba is applied to a population of plants suspected of comprising a DNA construct or a combination of DNA constructs providing for dicamba degradation. The amount of dicamba is selected so that transformed plants will grow, and the growth of untransformed plants will be inhibited. The level of inhibition must be sufficient so that transformed and untransformed plants can be readily distinguished (i.e., inhibition must be statistically significant). Such amounts can be determined empirically as is known in the art.[0056]
• Further, the generation of 3,6-DCSA as a result of the degradation of dicamba can be used for selection and screening. The generation of 3,6-DCSA can be readily ascertained by observing the fluorescence of this compound, allowing selection and screening of transformed host cells, intact organisms, and parts of organisms (e.g., microorganisms, plants, plant parts, and plant cells). In this regard, the invention allows for selection and screening of transformed host cells, intact organisms, and parts of organisms in the same manner as for green fluorescent protein (GFP). See U.S. Pat. Nos. 5,162,227 and 5,491,084 and PCT applications WO 96/27675, WO 97/11094, WO 97/41228 and WO 97/42320, all of which are incorporated herein by reference. In particular, 3,6-DCSA can be detected in transformed host cells, intact organisms, and parts of organisms using conventional spectrophotometric methods. For instance, microscopes can be fitted with appropriate filter combinations for fluorescence excitation and detection. A hand-held lamp may be used for benchtop work or field work (see Example 1). Fluorescence-activated cell sorting can also be employed. 3,6-DCSA is excited at a wavelength of 312-313 nm, with a maximum emission wavelength of 424 nm.[0057]
• “Parts” of organisms include organs, tissues, or any other part. “Plant parts” include seeds, pollen, embryos, flowers, fruits, shoots, leaves, roots, stems, explants, etc.[0058]
• Selection based on dicamba tolerance or dicamba degradation can be used in the production of dicamba-tolerant plants or dicamba-degrading microorganisms, in which case the use of another selection marker may not be necessary. Selection based on dicamba tolerance or dicamba degradation can also be used in the production of transgenic cells or organisms that express other genes of interest. Many such genes are known and include genes coding for proteins of commercial value and genes that confer improved agronomic traits on plants (see, e.g., PCT WO 97/41228, the complete disclosure of which is incorporated herein by reference).[0059]
• The DNA constructs of the invention can be used to transform a variety of host cells, including prokaryotes and eukaryotes. The DNA sequences coding for the dicamba-degrading enzyme(s) and the selection marker, if a separate selection marker is used, may be on the same or different DNA constructs. Preferably, they are arranged on a single DNA construct as a transcription unit so that all of the coding sequences are expressed together. Also, the gene(s) of interest and the DNA sequence(s) coding for the dicamba-degrading enzyme(s), when dicamba-tolerance or dicamba degradation is being used as a selection marker, may be on the same or different DNA constructs. Such constructs are prepared in the same manner as described above.[0060]
• Suitable host cells include prokaryotic and eukaryotic microorganisms (e.g., bacteria (including[0061]Agrobacterium tumefaciensandEscherichia coli), yeast (includingSaccharomyces cerevisiae) and other fungi (including Aspergillus sp.), plant cells, insect cells, and mammalian cells. Preferably, the host cell is one that does not normally degrade dicamba. However, the present invention can also be used to increase the level of dicamba degradation in host cells that normally degrade dicamba.
• Thus, the “transgenic” cells and organisms of the invention include cells and organisms that do not normally degrade dicamba, but which have been transformed according to the invention so that they are able to degrade this herbicide. The “transgenic” cells and organisms of the invention also include cells and organisms that normally degrade dicamba, but which have been transformed according to the invention so that they are able to degrade more of this herbicide or to degrade the herbicide more efficiently.[0062]
• Methods of transforming prokaryotic and eukaryotic host cells are well known in the art. See, e.g., Maniatis et al.,[0063]Molecular Cloning: A Laboratory Manual,Cold Spring Harbor, N.Y. (1982), Sambrook et al.,Molecular Cloning: A Laboratory Manual,Cold Spring Harbor, N.Y. (1989); PCT WO 96/23898 and PCT WO 97/42320.
• For instance, numerous methods for plant transformation have been developed, including biological and physical transformation protocols. See, for example, Miki et al., “Procedures for Introducing Foreign DNA into Plants” in[0064]Methods in Plant Molecular Biology and Biotechnology,Glick, B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton, 1993) pp. 67-88. In addition, vectors and in vitro culture methods for plant cell or tissue transformation and regeneration of plants are available. See, for example, Gruber et al., “Vectors for Plant Transformation” inMethods in Plant Molecular Biology and Biotechnology,Glick, B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton, 1993) pp. 89-119.
• The most widely utilized method for introducing an expression vector into plants is based on the natural transformation system of Agrobacterium. See, for example, Horsch et al.,[0065]Science227:1229 (1985).A. tumefaciensandA. rhizogenesare plant pathogenic soil bacteria which genetically transform plant cells. The Ti and Ri plasmids ofA. tumefaciensandA. rhizogenes,respectively, carry genes responsible for genetic transformation of the plant. See, for example, Kado, C. I.,Crit. Rev. Plant. Sci.10:1 (1991). Descriptions of Agrobacterium vector systems and methods for Agrobacterium-mediated gene transfer are provided by numerous references, including Gruber et al., supra, Miki et al., supra, Moloney et al.,Plant Cell Reports8:238 (1989), and U.S. Pat. Nos. 4,940,838 and 5,464,763.
• A generally applicable method of plant transformation is microprojectile-mediated transformation wherein DNA is carried on the surface of microprojectiles. The expression vector is introduced into plant tissues with a biolistic device that accelerates the microprojectiles to speeds sufficient to penetrate plant cell walls and membranes. Sanford et al.,[0066]Part. Sci. Technol.5:27 (1987), Sanford, J. C.,Trends Biotech.6:299 (1988), Sanford, J. C.,Physiol. Plant79:206 (1990), Klein et al.,Biotechnology10:268 (1992).
• Another method for physical delivery of DNA to plants is sonication of target cells. Zhang et al.,[0067]Bio/Technology9:996 (1991). Alternatively, liposome or spheroplast fusion have been used to introduce expression vectors into plants. Deshayes et al.,EMBO J.,4:2731 (1985), Christou et al.,Proc Natl. Acad. Sci. USA84:3962 (1987). Direct uptake of DNA into protoplasts using CaCl₂precipitation, polyvinyl alcohol or poly-L-ornithine have also been reported. Hain et al.,Mol. Gen. Genet.199:161 (1985) and Draper et al.,Plant Cell Physiol.23:451 (1982). Electroporation of protoplasts and whole cells and tissues have also been described. Donn et al., In Abstracts of VIIth International Congress on Plant Cell and Tissue Culture IAPTC, A2-38, p. 53 (1990); D'Halluin et al.,Plant Cell4:1495-1505 (1992) and Spencer et al.,Plant Mol. Biol.24:51-61 (1994).
• Transgenic dicamba-tolerant plants of any type may be produced according to the invention. In particular, broadleaf plants (including beans, soybeans, cotton, peas, potatoes, sunflowers, tomatoes, tobacco, fruit trees, and ornamental plants and trees) that are currently known to be injured by dicamba can be transformed so that they become tolerant to the herbicide. Other plants (such as corn, sorghum, small grains, sugarcane, asparagus, and grass) which are currently considered tolerant to dicamba can be transformed to increase their tolerance to the herbicide. “Tolerant” means that the transformed plants can grow in the presence of an amount of dicamba which inhibits the growth of untransformed plants[0068]
• It is anticipated that the dicamba-degrading oxygenases of the invention can function with endogenous reductases and ferredoxins found in transgenic host cells and organisms to degrade dicamba. Plant chloroplasts are particularly rich in reductases and ferredoxins. Accordingly, a preferred embodiment for the production of transgenic dicamba-tolerant plants is the use of a sequence coding for a peptide that will direct the dicamba-degrading oxygenase into chloroplasts (“a chloroplast targeting sequence”). DNA coding for the chloroplast targeting sequence is preferably placed upstream (5′) of the sequence coding for the dicamba-degrading oxygenase, but may also be placed downstream (3′) of the coding sequence, or both upstream and downstream of the coding sequence. Exemplary chloroplast targeting sequences include the maize cab-m7 signal sequence (see Becker et al.,[0069]Plant Mol. Biol.20:49 (1992) and PCT WO 97/41228) and the pea glutathione reductase signal sequence (Creissen et al.,Plant J.2:129 (1991) and PCT WO 97/41228). An alternative preferred embodiment is the direct transformation of chloroplasts using a construct comprising a promoter functional in chloroplasts to obtain expression of the oxygenase in chloroplasts. See, e.g., PCT application WO 95/24492 and U.S. Pat. No. 5,545,818. Of course, if a selected transgenic host cell or organism does not produce sufficient endogenous reductase, ferredoxin, or both, the host cell or organism can be transformed so that it produces one or both of these enzymes as well as the oxygenase.
• In yet another embodiment, the invention provides a method of controlling weeds in a field where transgenic dicamba-tolerant plants are growing. The method comprises applying an effective amount of dicamba to the field to control the weeds. Methods of applying dicamba and amounts of dicamba effective to control various types of weeds are known. See[0070]Crop Protection Reference, pages 1803-1821 (Chemical & Pharmaceutical Press, Inc., New York, N.Y., 11th ed., 1995).
• In another embodiment, the invention provides a method of degrading dicamba present in a material, such as soil, water, or waste products of a dicamba manufacturing facility. Such degradation can be accomplished using the dicamba-degrading enzymes of the invention. The enzymes can be purified from microorganisms naturally expressing them (see Examples 1 and 3) or can be purified from transgenic host cells producing them. If the enzymes are used in such methods, then appropriate cofactors must also be provided (see Example 1). Effective amounts can be determined empirically as is known in the art (see Example 1). Alternatively, transgenic prokaryotic and eukaryotic microorganisms can be used to degrade dicamba in such materials. Transgenic prokaryotic and eukaryotic microorganisms can be produced as described above, and effective amounts can be determined empirically as is known in the art.[0071]
• Dicamba is introduced into the environment in large quantities on a continuing basis. The elimination of dicamba is dependent in large part on the action of enzyme systems which are found in microorganisms inhabiting the soil and water of the planet. An understanding of these enzyme systems, including dicamba-degrading O-demethylases and their three components, is important in efforts to exploit natural and genetically modified microbes for bioremediation and the restoration of contaminated soil, water and other materials. Thus, the dicamba-degrading enzymes, DNA molecules, DNA constructs, etc., of the invention can be used as research tools for the study of dicamba degradation and bioremediation.[0072]
• Finally, the dicamba-degrading enzymes of the invention can be used in an assay for dicamba. A sample suspected of containing dicamba is mixed with a dicamba-degrading O-demethylase or a combination of a dicamba-degrading oxygenase, a dicamba-degrading ferredoxin and a dicamba-degrading reductase. Suitable assays are described in Examples 1 and 3. In particular, detecting or quantitating the fluorescence due to the generation of 3,6-DCSA makes for a convenient assay.[0073]
EXAMPLESExample 1Purification and Characterization of the Components of Dicamba O-Demethylase ofPseudomonas maltophiliaDI-6Methods and Materials
• Bacterium and growth conditions.[0074]Pseudomonas maltophilia,strain DI-6 (Kreuger, et al., (1989)J. Agric. Food Chem.,37:534-538) was isolated from a soil site persistently contaminated with dicamba. The bacterium was provided by Dr. Douglas Cork of the Illinois Institute of Technology (Chicago, Ill.), and was maintained on reduced chloride medium (Kreuger, J. P., (1989) Ph.D. thesis, Illinois Institute of Technology, Chicago, Ill.), supplemented with either dicamba (2 mg/ml) or a mixture of glucose (2 mg/ml) and Casamino Acids (2 mg/ml). The carbon sources were filter-sterilized and added to the medium after it was autoclaved. Solid media were prepared by the addition of 1% (wt/vol) Gelrite (Scott Laboratories, West Warwick, R.I.).
• Chemicals and reagents. Dicamba, 3,6-DCSA, and [[0075]¹⁴C]dicamba (U-phenyl-¹⁴C, 42.4 mCi/mmol, radiochemical purity greater than 98%) were supplied by Sandoz Agro, Inc. (Des Plaines, Ill). To increase solubility, the dicamba and 3,6-DCSA stock solutions were prepared by titration with KOH to pH 7.0. All chemicals were purchased from Sigma Chemical Co. (St. Louis, Mo.), unless otherwise stated.Superose 12, Mono Q, Q-Sepharose (Fast Flow) and Phenyl-Sepharose (CL-4B) column packings for the FPLC (fast performance liquid chromatography) apparatus were obtained from Pharmacia (Milwaukee, Wis.). Ampholyte pH 4-6 and ampholyte pH 4-9 were purchased from Serva (Heidelberg, FRG). Acrylamide, β-mercaptoethanol, N,N,N′,N′-tetramethylethylenediamine (TEMED) and ammonium persulfate (APS) were from Bio-Rad Laboratories (Hercules, Calif.). Thin layer chromatography (TLC) plates were silica gel (250 μm thickness) with UV 254 indicator, and were purchased from J. T. Baker Chemical Co. (Phillipsburg, N.J.).
• Enzyme assays. Dicamba O-demethylase activity was assayed by measuring the formation of [[0076]¹⁴C]3,6-DCSA from [¹⁴C]dicamba. Briefly, the activity in mixtures of enzyme components was measured at 30° C. in a standard 300 μl reaction mixture containing 25 mM potassium phosphate buffer (pH 7.0), 10 mM MgCl₂, 0.5 mM NADH (beta-nicotinamide adenine dinucleotide, reduced form), 0.5 mM ferrous sulfate, 50 μM cold dicamba, 2.5 μM [¹⁴C]dicamba (the final specific activity of the radioactive dicamba was 1.9 mCi/mmol), and different amounts of cell lysate or partially purified enzyme. All enzyme assays during the final purification steps were conducted in phosphate buffer because the pH optimum for dicamba O-demethylase activity was found to be in the mid range of phosphate buffers, and higher enzyme activity was observed with phosphate buffer compared to Tris-HCl [tris(hydroxymethyl)aminomethane hydrochloride] buffer at pH 7.0. Reactions were initiated by the addition of the substrate, dicamba. At specific times, the reactions were stopped by adding 50 μl of 5% (vol/vol) H₂SO₄. Dicamba and dicamba metabolites were then extracted twice with one volume of ether, and the extracts were evaporated to dryness. The efficiencies of recovery (means±standard deviations) for the extraction procedure were 87%±2% for dicamba and 85%±3% for 3,6-DCSA (Yang et al.,Anal. Biochem.219:37-42 (1994)).
• [[0077]¹⁴C]dicamba and¹⁴C-labeled metabolites were separated by thin layer chromatography (TLC). The ether-extracted dicamba and its metabolites were redissolved in 50 μl of ether prior to being spotted onto a TLC plate. The solvent system for running the TLC was chloroform-ethanol-acetic acid (85:10:5 [vol/vol/vol]). The resolved reaction products were visualized and quantified by exposing the TLC plate to a phosphor screen for 24 hours and then scanning the screen in a PhosphorImager SF (Molecular Dynamics, Sunnyvale, Calif.). Estimates of the amount of radioactivity in a particular spot on the TLC plate were determined by comparing the total pixel count in that spot relative to a spot on the same plate containing a known amount of [¹⁴C]dicamba. One unit of activity was defined as the amount of enzyme that catalyzes the formation of 1 nmol of3,6-DCSA from dicamba per minute at 30° C. Specific activities were based on the total protein concentration of the assay mixture.
• The activity of the reductase component of dicamba demethylase was assayed by measuring reduction of 2,6-dichlorophenolindophenol (DCIP) with a Hitachi U-2000 spectrophotometer. The reaction contained 0.5 mM NADH, 0.2 mM FAD (flavin adenine dinucleotide), 50 μM DCIP, 20 mM Tris buffer (pH 8.0), and 10-100 μl of enzyme sample in a total volume of 1 ml. The change in absorbance at 600 nm with time was measured at room temperature. Specific activity was calculated using an extinction coefficient at 600 nm of 21.0 mM[0078]⁻¹cm⁻¹for reduced DCIP. Specific activity was expressed as nmol DCIP reduced min⁻¹mg⁻¹of protein.
• In addition, an in situ DCIP assay was used to detect and locate the reductase activity in protein preparations separated on isoelectric focusing (IEF) gels. After electrophoresis of the proteins on an IEF gel, lanes sliced from the gel were washed with 20 ml of cold 20 mM Tris-HCl buffer (pH 8.0). Low melting agarose was dissolved by heating in 10 ml of 20 mM Tris-HCl buffer (pH 8.0) at a final concentration of 1.5% (w/v). When the agarose cooled to near room temperature, it was supplemented with 0.2 mM FAD, 50 μM DCIP, and 0.5 mM NADH. The assay mixture was poured onto a glass plate and allowed to solidify. The gel piece was placed on top of the solidified reaction mixture and allowed to set at room temperature for 15 minutes. If the gel slice contained a protein with reductase activity, a colorless band of reduced DCIP was generated in the blue background of DCIP.[0079]
• Cell lysates. Cells were grown to an optical density at 550 nm of 1.3 to 1.5 in liquid reduced chloride medium containing a mixture of glucose and Casamino Acids on a rotary shaker (250 rpm at 30° C.). The cells were harvested by centrifugation, washed twice with cold 100 mM MgCl[0080]₂, and centrifuged again. Cell pastes were either used immediately or quickly frozen in liquid nitrogen and stored at −80° C. At the time of enzyme purification, 25 g of frozen cells were thawed and resuspended in 50 ml of isolation buffer containing 25 mM Tris buffer (pH 7.0), 10 mM MgCl₂, and 0.5 mM EDTA. Phenylmethylsulfonyl fluoride and dithiothreitol were added to final concentrations of 0.5 mM and 1 mM, respectively. After addition of 10 mg of lysozyme and 1 mg of DNase, cells were stirred for 10 min on ice and broken by sonication (model XL2020 sonicator; Heat Systems) on ice at a medium setting (setting 5) with twelve 20-second bursts and 40-second resting intervals. The resulting cell lysates were diluted to 90 ml with isolation buffer and centrifuged at 76,000×g for 1 h at 4° C. The supernatant was used as the source of cleared cell lysate.
• Enzyme purification. All procedures were performed at 4° C., unless otherwise stated. Solid ammonium sulfate was slowly added to a 90-ml volume of cleared cell lysate to 40% (wt/vol) saturation, with constant stirring. After 15 minutes of stirring, the mixtures were centrifuged at 15,400×g for 15 minutes, and the precipitate was discarded. Additional solid ammonium sulfate was added to 70% (wt/vol) saturation, with constant stirring of the supernatant. After 15 min of stirring, the mixtures were centrifuged under the conditions described above. The supernatant was discarded, and the precipitate was resuspended in a minimal volume of buffer A (20 mM Tris [pH 8.0], 2.5 mM MgCl[0081]₂, 0.5 mM EDTA, 5% (vol/vol) glycerol, and 1 mM dithiothreitol).
• The 40%-70% ammonium sulfate cut was then loaded onto a Phenyl-Sepharose column (2.5 by 10 cm) connected to a FPLC apparatus (Pharmacia) and eluted with a decreasing linear gradient of (NH[0082]₄)₂SO₄from 10% (w/v) to 0% (w/v). The column was preequilibrated with buffer A containing 10% (wt/vol) armonium sulfate. The flow rate was 1 ml/min. Protein concentrations were continuously monitored at A₂₈₀during column elution. The column was washed with 120 ml of buffer A containing 10% (wt/vol) ammonium sulfate until baseline A₂₈₀readings were obtained. Bound proteins were eluted with a decreasing gradient of (NH₄)₂SO₄in buffer A [10 to 0% (wt/vol) (NH₄)₂SO₄in a total volume of 210 ml]. Fractions of 2 ml were collected. Aliquots of 10 μl were taken from each fraction and added to the standard dicamba O-demethylase assay mixture (see above), except that nonradioactive dicamba was used as the substrate. Dicamba O-demethylase activity was detected by monitoring the conversion of dicamba to the highlyfluorescent reaction product 3,6-DCSA with a hand-held UV lamp (312 nm, Fotodyne) in a darkened room.
• This procedure allowed resolution of dicamba O-demethylase into three pools containing the separated components (designated components I, II and III). Each component was essential for dicamba O-demethylase activity (see below). When a single component was assayed, the other two components were provided in excess. Fractions containing a single type of activity were pooled (component I, fractions 128-145; component II, unbound fractions 12-33; component III, fractions 62-92).[0083]
• (i) Purification of component I. Fractions containing component I activity (eluting from a Phenyl-Sepharose column at 0 M (NH[0084]₄)₂SO₄, fractions 128-145) were pooled to provide a total volume of 34 ml. The pooled samples were concentrated to 10 ml by centrifugation in a Centriprep-10 device (Amicon) and then applied to a Q-Sepharose (Fast Flow) FPLC column (Pharmacia) (2.5 by 6 cm) equilibrated with buffer A and washed with 80 ml of buffer A. Proteins bound to the column were eluted with a 100 ml linear gradient of 0 to 0.6 M KCl in buffer A at a flow rate of 1 ml/min. Fractions were collected at 1.5 minute intervals. Those fractions exhibiting component I activity (fractions 29-37) were pooled, dialyzed against buffer A overnight at 4° C. and applied to aMono Q HR 5/5 FPLC anion-exchange column in buffer A. Proteins were eluted at 1 ml/min by using a 50 ml gradient of increasing KCl concentration (0 to 0.5 M). Fractions showing component I activity (fractions 19 to 25) were pooled and concentrated to 0.4 ml by centrifugation in a Centricon-10 device. The concentrated sample was then subjected to chromatography on a Superose 12 FPLC column (1.6 by 50 cm) at a flow rate of 0.2 ml/min with buffer A containing 100 mM KCl. Fractions 7-10 showing component I activity were pooled and concentrated by centrifugation in a Centricon-10 device.
• The partially purified component I was diluted with cold 1% (w/v) glycine and concentrated by centrifugation in a Centricon-10 device three more times to desalt it in preparation for IEF electrophoresis. The desalted and concentrated sample was then applied to a 6% (w/v) IEF (pH 4-6) gel and subjected to electrophoresis for 1.5 hours at 4° C. (see below). After electrophoresis, the gel was washed with 25 mM cold phosphate buffer (pH 7.0) for 5 minutes and then each slice of the gel lane was diced into small (6 mm×4 mm) pieces. Protein was eluted from the diced gel fragments by grinding them with a pipette tip in the presence of 10 μl of 25 mM phosphate buffer (pH 7.0). Protein from each segment was mixed with an excess of components II and III and assayed for dicamba O-demethylase activity. The gel segment which showed component I activity (which was also reddish brown in color) was loaded onto a 12.5% (w/v) sodium dodecyl sulfate polyacrylamide gel (SDS-PAGE) to check sample purity.[0085]
• (ii) Purification of component II Component II obtained by Phenyl-Sepharose column chromatography was dialyzed against buffer A overnight at 4° C. and applied to a FPLC Q-Sepharose column (2.5 by 6 cm). Sample elution conditions were identical to those described above for component I except that the elution gradient was 0 to 1 M KCl in buffer A. Fractions exhibiting component II activity (fractions 30-37) were pooled, dialyzed against buffer A, concentrated to 0.4 ml and applied to a[0086]FPLC Superose 12 column (1.6 by 50 cm). The procedures for sample application and elution were identical to those described above for component I. Fractions exhibiting component II activity (fractions 3-6) were pooled, diluted with an equal volume of buffer A, and applied to a FPLC Mono Q column. Proteins were eluted from the column using the same KCl gradient as for component I. Fractions 20-25 showed component II activity. Partially purified component II was further purified by IEF (pH 4-6) electrophoresis using the same conditions as described for component I. The gel segment which showed component II activity was loaded onto a 12.5% (w/v) SDS-PAGE for further analysis.
• (iii) Purification of component III. Component III obtained by Phenyl-Sepharose column chromatography was dialyzed against buffer A overnight at 4° C. and applied to a FPLC Q-Sepharose column (2.5 by 6 cm). Conditions were identical to those described above for component I. Fractions exhibiting component III activity (fractions 26-38) were dialyzed against buffer B [10 mM Tris-HCl (pH 7.5), 2.5 mM MgCl[0087]₂, 5% (v/v) glycerol, 1 mM dithiothreitol] and concentrated to 5 ml. Blue dye affinity matrix [Cibacron Blue 3GA type 3000 (Sigma)] was packed into a FPLC column (1×5 cm) and pre-equilibrated with 20 ml of buffer B. Concentrated component III was loaded onto the blue dye column and washed with 20 ml of buffer B at a flow rate of 0.2 ml/min until the A₂₈₀of the column effluent reached baseline levels. Bound protein was then eluted with 5 mM NADH in buffer B. Fractions containing reductase activity were detected by assaying for dicamba O-demethylase activity in the presence of an excess of components I and II and also by the ability of each fraction to reduce DCIP in the presence of NADH. Fractions having strong reductase activity in both assays were pooled, dialyzed against buffer A containing 100 mM KCl, concentrated to 0.2 ml, and applied to aFPLC Superose 12 column. The same conditions were used for running the Superose column as described for component I. Fractions containing proteins which catalyzed DCIP reduction were pooled, dialyzed against buffer A and applied to a FPLC Mono Q column. Proteins were eluted using the same conditions as for component I. Partially purified component III was further purified by IEF (pH 4-6) gel electrophoresis. The reductase activity of proteins within the IEF gel was detected by assaying for DCIP reduction in an agarose gel overlay as described above. The gel segment which showed component II activity was loaded onto a 12.5% (w/v) SDS-PAGE for further analysis.
• Determination of NH[0088]₂-terminal amino acid sequences. Protein bands were excised from IEF gels and placed in the wells of a 12.5% (w/v) SDS polyacrylamide gel. After electrophoresis, the gel slices containing the purified proteins were transblotted onto a PVDF (polyvinylidene difluoride) membrane (Millipore) in a Trans-Blot cell (Bio-Rad, Richmond, Calif.) at 25 volts for 16 hours. The blotting buffer was a solution of 20% (v/v) methanol with 10 mM CAPS [3-(cyclohexylamino)-1-propanesulfonic acid], pH 10.0. Sequencing was performed using an Applied Biosystems Inc. 420 H machine by Edman degradation (Edman and Henschen (1975) pages 232-279 in S. B. Needleman (ed.),Protein sequence determination,2nd ed., Springer-Verlage, N.Y.).
• Determination of protein concentration. Protein concentrations were determined by the method of Bradford (1976)[0089]Anal. Biochem.72:248-254, with bovine serum albumin as the standard.
• SDS-PAGE. Sodium dodecyl sulfate-polyacrylamide gel eletrophoresis (SDS-PAGE) was performed according to modified methods of Laemmli (Laemmli (1970)[0090]Nature,227:680-685). 12.5% (w/v) SDS gels of 85×65×0.75 mm were made as follows: running gel: 2.5 ml 40% (w/v) acrylamide/bis solution (37:5:1), 1 ml running buffer solution [3M Tris-CHl (pH 8.8), 0.8% (w/v) SDS], 4.5 ml H₂O, 5 μl TEMED, and 40 μl 10% (w/v) APS; stacking gel: 0.5 ml 40% (w/v) acrylamide/bis, 0.5 ml stacking buffer solution [1 M Tris-HCl (pH 6.8), 0.8% (w/v) SDS], 3 ml H₂O, 5 μl TEMED, and 12.5 μl 10% (w/v) APS. The composition of the running buffer was 25 mM Tris-HCl (pH 8.3), 0.2 M glycine, and 0.1% (w/v) SDS. The sample buffer contained 0.25 ml stacking buffer, 0.6 ml 20% (w/v) SDS, 0.2 ml β-mercaptoethanol, and 0.95 ml 0.1% bromphenol blue (w/v) in 50% (v/v) glycerol. Electrophoresis was performed at 80 volts in a Bio-Rad Mini Gel apparatus until the tracking dye was 0.5 cm from the anode end of the gel. Proteins were stained with 0.1% (w/v) Coomassie Brilliant Blue R-250 in a mixture of isopropanol, water, and acetic acid at a ratio of 3:6:1 (v/v/v). Destaining was performed in a mixture of methanol, water, and acetic acid at a ratio of 7:83:10 (v/v/v). Standard proteins (Gibco BRL) included: myosin (214.2 kDa), phosphorylase B (111.4 kDa), bovine serum albumin (74.25 kDa), ovalbumin (45.5 kDa), carbonic anhydrase (29.5 kDa), β-lactoglobulin (18.3 kDa), and lysozyme (15.4 kDa).
• Determination of molecular weight. The molecular weight (M[0091]_r) of peptides under denaturing conditions was estimated using SDS-PAGE analysis. The molecular weights of the native components I, II and III were estimated by gel filtration through a Superose 12 HR 10/30 FPLC column (Pharmacia) at a flow rate of 0.2 ml/min in buffer A containing 100 mM KCl. Calibration proteins were gel filtration standards from Bio-Rad. They were: bovine thyroglobulin (670 kDa), bovine gamma globulin (158 kDa), chicken ovalbumin (44 kDa), horse myoglobin (17 kDa) and vitamin B-12 (1.35 kDa). The void volume of theSuperose 12 column was calculated using Blue Dextran (M_r2,000,000, Sigma).
• IEF. Isoelectric focusing (IEF) gel electrophoresis was performed in a vertical mini-gel apparatus (Model #MGV-100) from C.B.S. Scientific Co. (Del Mar, Calif.). IEF gels with 6% (w/v) polyacrylamide (70×90×1 mm) were made by mixing the following: 1.6 ml 30% (w/v) acrylamide/bis (37:5:1), 0.8 g glycerol, 0.32 ml ampholyte pH 4-6 (Serva), 0.08 ml ampholyte pH 4-9 (Serva), 5.2 ml H[0092]₂O, 10 μl TEMED, and 80 μl 10% (w/v) APS. The cathode buffer was 100 mM β-alanine and the anode buffer was 100 mM acetic acid. Protein samples in approximately 1 to 10 μl of 1% (w/v) glycine were mixed with an equal volume of sample buffer [50% (v/v) glycerol, 1.6% (v/v) ampholyte pH 4-9, 2.4% (v/v) ampholyte pH 4-6]. Samples were loaded at the cathode end of the gel and allowed to migrate at 200 volts for 1.5 hours and 400 volts for another 1.5 hours. Proteins were stained with Coomassie Brilliant Blue R-250 using the procedure described above for SDS polyacrylamide gels. IEF markers (Sigma) were: amyloglucosodase, pI 3.6; glucose oxidase, pI 4.2; trypsin inhibitor, pI 4.6; β-lactoglobulin A, pI 5.1; carbonic anhydrase II, pI 5.4; carbonic anhydrase II, pI 5.9 and carbonic anhydrase I, pI 6.6
• Kinetic analysis. The kinetics of the demethylation reaction catalyzed by dicamba O-demethylase were studied by analyzing the initial rates of the reaction in the presence of a constant concentration of the enzyme and increasing concentrations of the substrate, dicamba. Reaction mixtures contained 25 mM potassium phosphate buffer (pH 7.0), 10 mM MgCl[0093]₂, 0.5 mM NADH, 0.5 mM FeSO₄, 25 μg of partially purified O-demethylase enzyme [the 40%-70% (w/v) (NH₄)₂SO₄fraction from a cleared cell lysate], various concentrations (0.5 to 50 μM) of dicamba and various concentrations (0.025 to 2.5 μM) of [¹⁴C]dicamba (U-phenyl-¹⁴C, 42.4 mCi/mmol) in a total volume of 300 μl. For assays with dicamba concentrations of 0.5 μM and 1 μM, the reaction volume was increased to 900 μl to ensure that sufficient amounts of radioactive dicamba and its metabolites were present to allow detection. In these reactions, the amounts of all other components in the reaction were tripled. The conversion of [¹⁴C]dicamba to [¹⁴C]3,6-DCSA was determined for different time points at each concentration of dicamba using a PhosphorImager SF to scan radioactivity on phosphor screens which had been exposed to TLC plates for 24 hours. One unit of activity was defined as the amount of enzyme that forms 1 nmol of 3,6-DCSA per minute at 30° C. The initial rates of each reaction were determined by plotting the reaction rate versus time at each substrate concentration. Data were modeled to Michaelis-Menten kinetics and values of K_mand V_maxwere determined by fitting to Lineweaver-Burk plots using SigmaPlot® (Jandel Scientific, Corte Madera, Calif.).
• Oxygen requirement. Preliminary experiments using a Clark oxygen electrode indicated oxygen consumption during a standard dicamba O-demethylase assay with dicamba as a substrate. To verify a requirement for oxygen in the O demethylation of dicamba by dicamba O-demethylase, reactions were conducted in an anaerobic chamber which contained less than 1 ppm of oxygen. The procedures for displacement of oxygen from the reaction mixture were performed at 4° C. Reaction mixtures lacking enzyme were placed in a vial and sealed with a rubber stopper. For displacement of oxygen, the vial was evacuated twice by vacuum and flushed each time with nitrogen. After a third evacuation, the vial was flushed with 90% nitrogen plus 10% hydrogen. The enzyme solution was likewise purged of oxygen (with care taken not to bubble the enzyme solution). Both the reaction mixtures and enzyme solutions were transferred into an anaerobic chamber (95% N[0094]₂-5% H₂atmosphere). Two hundred forty microliters of cleared cell lysate was injected through the rubber stopper with a microsyringe and gently mixed with 960 μl of oxygen-free reaction mixture. Reactions were carried out at 30° C.
• An examination of the reaction products on TLC plates showed that the rate of [[0095]¹⁴C]3,6-DCSA production from [¹⁴C]dicamba under anaerobic conditions was significantly lower than the rate of reactions with the same amount of enzyme under aerobic conditions. Under anaerobic conditions, there was virtually no conversion of dicamba to 3,6-DCSA within 1 hour. However, when a parallel reaction mixture was taken from the anaerobic chamber after 30 min and incubated with air, a significant quantity of one of the components of the dicamba O-demethylase enzyme complex was an oxygenase.
• It may be noted that the in vitro conversion of [[0096]¹⁴C]dicamba to [¹⁴C]3,6-DCSA mimics the in vivo conversion pathway documented earlier (Cork and Kreuger,Adv. Appl. Microbiol.36:1-66 (1991); Yang et al.,Anal. Biochem.219:37-42 (1994)). In these studies, DCSA was identified as a reaction product by both TLC and capillary electrophoresis. Stringent identification of the first major product of dicamba degradation as DCSA both in vivo and in vitro has been obtained by gas chromatography-mass spectrometry analyses.
• Component and cofactor requirements. After the initial separation of the three components of dicamba O-demethylase by phenyl-Sepharose column chromatography, the partially purified preparations were taken individually through one additional purification on a Q-Sepharose column (2.5 by 6 cm). Samples were applied to a Q-Sepharose (Fast Flow) fast protein liquid chromatography column (Pharmacia) in buffer A and eluted with a 100-ml linear gradient of 0 to 0.6 M KCl (for the oxygenase component) or 0 to 1.0 M KCl (for the ferredoxin and reductase components) in 1.5-ml fractions. Appropriate pooled fractions from separate columns for oxygenase purification (fractions 29 to 37), for ferredoxin purification (fractions 30 to 37), or for reductase purification (fractions 26 to 38) were used for the determination of component and cofactor requirements.[0097]
• The three components were assayed for O-demethylase activity in various combinations to determine component requirements.[0098]
• To determine cofactor requirements, O-demethylase activity was assayed using a mixture of the three components with [[0099]¹⁴C]dicamba for 30 minutes at 30° C. The amounts of partially purified protein (provided in an optimized ratio) in the reaction mixtures were 85 μg of oxygenase, 55 μg of ferredoxin and 50 μg of reductase. The concentration of cofactors used in the reaction mixtures were 0.5 mM NADH, 0.2 mM FAD, 0.5 mM FeSO₄, 10 mM MgCl₂, 0.5 mM NADPH, and 0.2 mM FMN.
Results
• Component I. The component of dicamba O-demethylase which bound most tightly to the Phenyl-Sepharose column (designated initially as component I and subsequently identified as an oxygenase) was distinctly reddish brown in color. This indicated the potential presence of a protein(s) containing an iron-sulfur cluster(s) or a heme group(s). The fractions with component I activity from the Phenyl-Sepharose column were subjected to further purification by Q-Sepharose (Fast Flow) and Mono Q chromatography and then to separation on a Superose 12 size exclusion column. The component I protein was then further purified on an IEF gel.[0100]
• Protein from the major band on the IEF gel (with an apparent pI of approximately 4.6) was excised and separated from any remaining minor contaminants by SDS-PAGE. The major component I protein obtained after purification by IEF was greater than 90% pure as judged by densitometric analysis of this SDS-polyacrylamide gel stained with Coomassie Blue.[0101]
• The N-terminal amino acid sequence of the dominant protein with an apparent molecular mass of approximately 40,000 Daltons was determined. Results of amino acid sequencing indicated that the first 29 amino acids of the N-terminal region were present in the following sequence (residues in parentheses are best guesses):[0102]

  Thr Phe Val Arg Asn Ala Trp Tyr Val Ala Ala Leu Pro Glu Glu Leu Ser Glu Lys Pro	[SEQ ID NO:1]
  Leu Gly Arg Thr Ile Leu Asp (Asp or Thr) (Pro).

• Comparison with amino acid sequences in various databases indicated little or no homology with NH[0103]₂-terminal sequences reported for other monoxygenases or dioxygenases.
• Component II. The protein fraction which did not bind to a Phenyl-Sepharose column was designated as component II. Because this yellowish colored fraction could be replaced by ferredoxin from[0104]Clostridium pasteurianum(but with slower reaction rates) when assays were performed in combination with components I and III, it was tentatively designated as a ferredoxin-containing fraction. The Clostridium ferredoxin clearly functioned in place of component II, but given the highly impure nature of the component II used in these experiments, the efficiency of the Clostridium enzyme was significantly lower than that of the putative ferredoxin from strain DI-6. In particular, 55 μg of partially purified component II mixed with excess amounts of components I and III catalyzed the conversion of dicamba to 3,6-DCSA at a rate of approximately 5 nmol min⁻¹mg⁻¹, while 100 μg of highly purified ferredoxin from Clostridium resulted in an activity of only 0.6 nmol min⁻¹mg⁻¹.
• Purification steps involving Q-Sepharose (Fast Flow) chromatography,[0105]Superose 12 gel filtration and Mono Q chromatography yielded approximately one milligram of purified protein from an initial 25 grams of cell paste. This fraction was purified in a similar manner to the oxygenase component by electrophoresis on an IEF gel and subsequent electrophoresis of the active IEF fraction on an SDS-polyacrylamide gel.
• Analysis of component II activity in proteins eluted from segments of the IEF gel indicated that a fraction with a pI of approximately 3.0 contained the active protein in component II. Protein from this gel slice was eluted and subjected to SDS-PAGE. Staining of the gel with Coomassie Blue revealed one prominent band of protein (molecular weight of about 28,000 Daltons) along with a smear of lower molecular weight proteins.[0106]
• Component III. Component III of dicamba O-demethylase was retained on a Phenyl-Sepharose column in high concentrations of (NH[0107]₄)₂SO₄and eluted at approximately 4% (w/v) (NH₄)₂SO₄. This light yellow fraction was tentatively identified as a reductase-containing fraction based on its ability to reduce oxidized cytochrome c and DCIP in the presence of NADH and because it could be replaced by cytochrome c reductase from porcine heart (Type 1, Sigma) in assays with components I and II. In this set of reactions, the use of 50 μg of partially purified component III produced a reaction rate of approximately 5 nmol min⁻¹mg⁻¹when mixed with an excess of components I and II. The highly purified cytochrome c reductase showed a specific activity of approximately 2.5 nmol min⁻¹mg⁻¹in the reaction, an activity well below that provided by component III when one considers the impurity of the crude component III used in these assays. In addition, component III exhibited reductase activity when incubated with cytochrome c or 2,6-dichlorophenol-indophenol (DCPIP) in the presence of NADH. Neither component I nor component II showed activity in either of these two reductase assays.
• Additional purification of this fraction by chromatography on columns containing Q-Sepharose (Fast Flow), blue dye affinity matrix,[0108]Superose 12, and Mono Q packings resulted in low amounts of protein in the fractions with reductase activity. The component III protein was about 70% pure as judged by densitometric analysis of the active protein fraction after separation by SDS-PAGE and staining with Coomassie Blue.
• To further exacerbate purification of component III, it was found that two different protein fractions from the Mono Q column step contained reductase activity when assayed with the ferredoxin and oxygenase components. Further purification of these two fractions by eletrophoresis on an IEF gel revealed that the reductase activities of the two fractions had distinctly different isoelectric points. This was demonstrated by excising lanes containing each of the two reductase fractions from the IEF gel and laying the slices on top of a pad of low melt agarose containing a DCIP reaction mixture. Reductase activity in both gel slices was identified by the NADH-dependent reduction of DCIP to its colorless, reduced form. The reductase in[0109]fraction 35 had an apparent pI of approximately 5.6 while the reductase in fraction 27 possessed an apparent pI of approximately 4.8.
• Both reductase activities isolated from the IEF gel slices were unstable and present in low amounts. Indeed, only the reductase from[0110]fraction 35 from the Mono Q column fractionation retained sufficient protein concentration and activity to allow further purification and characterization. A slice from an IEF gel containing this reductase activity was eluted and separated from contaminating proteins by SDS-PAGE. The predominant protein in this gel was one with a mass of approximately 45,000 Daltons. Size exclusion chromatography had indicated an approximate molecular mass of 50,000 Daltons for component III in its native state.
• Biochemical characteristics of dicamba O-demethylase. Dicamba O-demethylase activity was measured during incubations in vitro at temperatures ranging from 20° C. to 50° C. and at pH values from approximately 6 to 9. Activity peaked sharply at 30° C. and broadly at pH values between 6.5 and 7.5. Enzymatic activity was dependent on the type of pH buffer employed. At pH 7, for example, activity was approximately 40% lower in Tris-containing buffers than in phosphate-containing buffers.[0111]
• Values for K[0112]_mand V_maxfor dicamba O-demethylase were estimated using SigmaPlot® to generate best fit curves from Michaelis-Menten and Lineweaver-Burk plots of data from duplicate experiments. The K_mfor dicamba was estimated to be approximately 9.9±3.9 μM and the V_maxfor the reaction was estimated to be approximately 108±12 nmol/min/mg.
• The three components were assayed for dicamba O-demethylase activity in various combinations. None of the components showed enzyme activity when assayed alone. Indeed, a significant amount of O-demethylase activity could be detected only when all three components were combined. A mixture of components I and II exhibited small amounts of enzyme activity, probably due to traces of component III contaminating the component I fractions.[0113]
• Both NADH and NADPH supported enzyme activity, with NADH being markedly more effective than NADPH. Mg[0114]²⁺ was necessary for enzyme activity. Fe²⁺, flavin adenine dinucleotide (FAD), and flavin mononucleotide (FMN) produced little or no stimulation of enzymatic activity with the partially purified protein preparations in these experiments. The highest activity was obtained using a combination of NADH, Fe²⁺, Mg²⁺, and FAD.
• Discussion[0115]
• Dicamba O-demethylase from[0116]Pseudomonas maltophilia,strain DI-6, is a three component oxygenase (Wang, X -Z (1996) Ph.D. thesis, University of Nebraska-Lincoln, Lincoln, Nebr.) responsible for the conversion of the herbicide, dicamba (2-methoxy-3,6-dichlorobenzoic acid), to 3,6-dichlorosalicylic acid (3,6-DCSA; 2-hydroxy-3,6-dichlorobenzoic acid). Purification schemes have been devised which have allowed the isolation of each of the three components to a homogeneous or near-homogeneous state.
• Initial separation of the three components was achieved by chromatography on a Phenyl-Sepharose column. Enzymatic activities and other characteristics of the partially purified components allowed a tentative identification of the components as a reductase, a ferredoxin and an oxygenase—a composition similar to that found in a number of other previously studied heme-containing and nonheme-containing, multicomponent oxygenases (Batie, et al. (1992) pages 543-565, In F. Müller (ed.),[0117]Chemistry and biochemistry of flavoenzymes,vol. 111, CRC Press, Boca Raton; Harayama, et al. (1992)Annu. Rev. Microbiol.46:565-601; Mason and Cammack (1992)Annu. Rev. Microbiol.46:277-305; Rosche et al. (1995)Biochem. Biophys. Acta1252:177-179). Component III isolated from the Phenyl-Sepharose column catalyzed the NADH-dependent reduction of both cytochrome c and the dye, DCIP. In addition, its ability to support conversion of dicamba to 3,6-DCSA when combined with components I and II could be replaced in part by cytochrome c reductase. Component II could be replaced by the addition of ferredoxin fromClostridium pasteurianumto reactions containing components I and III. The absolute need for molecular oxygen to support the O-demethylation reaction indicated that the remaining component was an oxygenase.
• Oxygenase[0118]_DIC. ComponentI of dicamba O-demethylase (designated as oxygenase_DIC) has been purified to homogeneity and subjected to N-terminal amino acid sequencing. The resulting sequence of twenty nine amino acid residues showed no significant homology to other protein sequences in the various data banks. However, the information obtained from this amino acid sequence permitted the design of degenerate oligonucleotide probes which have been successfully used to detect and clone the component I gene (see Example 2). Furthermore, a comparison of the amino acid sequence derived from the nucleotide sequence of this clone with that of the protein sequences in the data base showed strong homology to other oxygenases (see Example 2).
• The apparent molecular mass of oxygenase[0119]_DIC, estimated from its migration in SDS-polyacrylamide gels, is approximately 40,000 Daltons. Purified preparations of the oxygenase exhibited only one major band on SDS-polyacrylamide gels stained with Coomassie Blue and Edman degradation of the protein contained in that band indicated the presence of only one N-terminal species. Estimates derived from the behavior of native oxygenase_DICon size exclusion columns suggests a molecular size of approximately 90,000 Daltons. All of these results suggest that the native oxygenase exists as a homodimer.
• The oxygenase/hydroxylase component of a number of multicomponent systems is composed of an (αβ)[0120]_n-type subunit arrangement in which the larger α subunit is approximately 50,000 Daltons in size and the smaller β subunit is approximately 20,000 Daltons in molecular mass (Harayama, et al. (1992)Annu. Rev. Microbiol.46:565-601). In contrast, the oxygenase component of dicamba O-demethylase appears to possess a single subunit of approximately 40 kDa in molecular mass which may exist as a dimer in its native state. This (α)_n-type subunit arrangement is similar to that found in other well characterized oxygenases such as 4-chlorophenylacetate 3,4-dioxygenase from Pseudomonas sp. strain CBS (Markus, et al. (1986)J. Biol. Chem.261:12883-12888), phthalate dioxygenase fromPseudomonas cepacia(Batie, et al. (1987)J. Biol. Chem.262:1510-1518),4-sulphobenzoate 3,4-dioxygenase fromComamonas testosteroni(Locher, et al. (1991)Biochem. J.,274:833-842), 2-oxo-1,2-dihydroquinoline 8-monooxygenase fromPseudomonas putida86 (Rosche et al. (1995)Biochem. Biophys. Acta1252:177-179), 4-carboxydiphenyl ether dioxygenase fromPseudomonas pseudoalcaligenes(Dehmel, et al. (1995)Arch. Microbiol.163:35-41), and 3-chlorobenzoate 3,4-dioxygenase fromPseudomonas putida,(Nakatsu, et al. (1995)Microbiology(Reading) 141:485-495).
• Ferredoxin[0121]_DIC. Component II (ferredoxin_DIC) of dicamba O-demethylase was purified by several steps of column chromatography and IEF. Final purification by SDS-PAGE produced one major band of protein (M_r˜28,000) and a smear of slightly smaller proteins.
• The N-terminal amino acid sequence of the protein with an apparent molecular weight of approximately 28,000 Daltons was determined. This amino acid sequence permitted the preparation of degenerate oligonucleotide probes, and these probes were used to isolate a genomic clone coding for this protein. Although the protein produced by this clone was a ferredoxin (ferrodoxin[0122]_28kDa), it was subsequently determined not to be active in the degradation of dicamba when combined with the other two components of dicamba O-demethylase (data not shown).
• Other evidence supports the conclusion that ferrodoxin[0123]_28kDais not the ferredoxin component of dicamba O-demethylase. First, the molecular mass of this protein(28 kDa) protein is significantly higher than that of the other ferredoxins found in multicomponent oxygenases from bacteria (i.e., 8-13 kDa) (Batie, et al. (1992) pages 543-565, In F. Müller (ed.),Chemistry and biochemistry of flavoenzymes,vol. III, CRC Press, Boca Raton; Harayama, et al. (1992)Annu. Rev. Microbiol.46:565-601).
• Second, a comparison of the N-terminal sequence of 20 amino acid residues obtained from ferredoxin[0124]_28kDato other amino acid sequences in the various protein data banks using Genetics Computing Group (GCG) software package (University of Wisconsin, Madison, Wis.) revealed strong homology (80-85% identity compared to the most likely N-terminal sequence of ferredoxin_28kDa) to a number of dicluster bacterial ferredoxins (those fromPseudomonas stutzeri, Pseudomonas putida, Rhodobacter capsulatusandAzotobacter vinelandii). The four dicluster ferredoxins which showed strong homology to ferredoxin_28kDahave a [3Fe-4S] cluster followed by a [4Fe-4S] cluster at the N-terminus of the protein. This suggests that ferredoxin_28kDais distinctly different from the ferredoxin components with [2Fe-2S] clusters which are usually associated with non-heme multicomponent oxygenases (Harayama, et al. (1992)Annu. Rev. Microbiol.46:565-601; Mason and Cammack (1992)Annu. Rev. Microbiol.46:277-305; Rosche, et al. (1995)Biochem. Biophys. Acta1252:177-179).
• Reductase[0125]_DIC. Component III of dicamba O-demethylase (designated as reductase_DIC) has been the most recalcitrant of the three components to purify. This is due in part to its apparent instability and low abundance in lysates of strain DI-6. Nonetheless, sufficient protein has been purified to assign a tentative molecular mass of 45,000 Daltons. This is similar to the molecular mass of approximately 50,000 Daltons obtained from size exclusion chromatography and suggests that reductase_DICexists in its native form as a monomer. The purification of the reductase component has been further complicated by the fact that chromatography on a Mono Q column and IEF resolves purified reductase preparations into two activities with apparently distinct pI values. Both fractions from the Mono Q column functioned in combination with purified ferredoxin_DICand oxygenase_DICto produce dicamba O-demethylase activity. The presence in Sphingomonas sp. strain RW1 of two similar flavoproteins which function equally well as reductase components in the threecomponent dibenzofuran 4,4a-dioxygenase has recently been reported by Bünz and Cook (Bünz and Cook (1993)J. Bacteriol.175:6467-6475). Interestingly, both reductases were 44,000 Daltons in molecular mass, quite similar to that of the 45,000 Dalton reductase_DIC. Multiple components of leghemoglobin reductase have also been observed in lupin root nodules using isoelectric focusing techniques (Topunov, et al. (1982)Biokhimiya(English edition) 162:378-379). In this case, IEF revealed four separate components with NADH-dependent reductase activity. The resolution of the question of whether there is only one reductase_DICwhich exists in two forms or two distinct reductases in strain DI-6 will rely on the development of improved procedures for isolating larger quantities of the proteins and/or on the cloning and sequencing of the gene(s) involved (see Examples 3 and 5).
• Dicamba O-demethlylase characteristics. In addition to the physical and biochemical properties of the individual components noted above, analyses of enzymatic activity have shown that the O-demethylase system has a strong affinity (K[0126]_m=˜10 μM) for its substrate and a V_maxof approximately 100-110 nmol/min/mg. As expected for a soil bacterium collected in a temperate climatic zone, the maximal enzymatic activity was observed at temperatures near 30° C. While the pH optima for the enzyme system was in the range from pH 6.5 to pH 7.5, the activity measured with a given preparation of enzyme was strongly affected by the type of pH buffering system employed. Activity in the presence of Tris buffers was at least 40% lower than with phosphate buffers at the same pH.
• The reaction scheme for the reaction catalyzed by the three components of dicamba O-demethylase is presented in FIG. 1. Electrons from NADH are shuttled through a short electron chain consisting of the reductase and ferredoxin to the terminal oxygenase which catalyzes the oxidation of dicamba. The similarities between dicamba O-demethylase and several multicomponent dioxygenases suggest that dicamba O-demethylase may potentially possess cryptic dioxygenase activity. It is clear, however, that this enzyme is not in the class of dioxygenases which split O[0127]₂and incorporate one atom of oxygen into the major substrate and the other into a small organic substrate such as α-ketoglutarate (Fukumori and Hausinger (1993)J. Biol. Chem.268:24311-24317). Indeed, combinations of highly purified reductase_DIC, ferredoxin_DIC, and oxygenase_DICrequire only O₂, NADH, Mg²⁺, Fe²⁺, and dicamba for activity.
Example 2Identification and Sequencing of a Clone Coding for the Oxygenase of Dicamba O-Demethylase ofPseudomonas maltophiliaDI-6
• As noted in Example 1, the first 29 amino acids of the N-terminal amino acid sequence of oxygenase[0128]_DIChad been determined to be (residues in parentheses are best guesses):

  Thr Phe Val ArgAsn Ala Trp Tyr Val AlaAla Leu Pro Glu Glu Leu Ser Glu Lys	[SEQ ID NO:1]
  Pro Leu Gly Arg Thr Ile Leu Asp (Asp or Thr) (Pro).

• This sequence permitted the design of degenerate oligonucleotide probes which were synthesized by Operon, Alameda, Calif. In particular, a mixture of 32 probes, each of which was 17 nucleotides in length, and contained all of the possible nucleotide sequences which could encode the amino acid sequence highlighted in bold above, was used. The oligonucleotide probes were 3′-end-labeled with digoxigenin (DIG) according to instructions provided by Boehringer Mannheim, Indianapolis, Ind.[0129]
• The DIG-labeled probes were first hybridized to[0130]P. maltophiliaDI-6 genomic DNA which had been digested with various combinations of restriction enzymes, resolved on a 1% agarose gel, and blotted to a nylon filter. Based on these results, a size-fractionated genomic library was constructed in the pBluescript II KS+ vector and transformed intoEscherichia coliDH5α competent cells. The genomic library contained 1-2 kb Xho I/Hind III fragments. The DIG-labeled oligonucleotide probes were hybridized to an array of bacterial colonies streaked on nylon filters. Plasmid DNA was isolated from positive colonies and subcloned. Both strands of each subclone were sequenced by the DNA Sequencing Facility at the University of Nebraska-Lincoln. Hybridization and detection of DIG-labeled probes were performed according to protocols provided by Boehringer Mannheim.
• A genomic DNA clone coding for the oxygenase[0131]_DICwas identified. The nucleotide sequence and the deduced amino acid sequence of the entire oxygenase_DICare given in the Sequence Listing below as SEQ ID NO: 2 and SEQ ID NO: 3, respectively.
• A comparison of the amino acid sequence derived from the nucleotide sequence of this clone with that of the protein sequences in the Swiss Protein Database showed homology to other oxygenases. Homology was determined using the FASTA program of the GCG software package. The strongest homology was with the oxygenase component of vanillate demethylase (from Pseudomonas sp., ATCC strain 19151) which showed 33.8% identity.[0132]
Example 3Purification and Characterization of Components of Dicamba O-Demethylase ofPseudomonas maltophiliaDI-6
• Bacterial cultures and preparation of cleared cell lysates.[0133]Pseudomonas maltophilia,strain DI-6, was inoculated into six two-liter Erlenmeyer flasks containing one liter of reduced chloride medium (Kreuger, J. P. 1989. Ph.D. thesis. Illinois Institute of Technology, Chicago) supplemented with glucose (2.0 mg/ml) and Casamino acids (2.0 mg/ml) as the carbon sources. Cultures were incubated on an orbital shaker (225 rpm at 30° C.). Cells were harvested at an A₆₀₀ranging from 1.5 to 2.0 using a JLA-10.500 rotor in a Beckman Avanti J-251 Centrifuge at 4,000×g for 20 minutes. Pelleted cells were stored at −80° C. The frozen cells were resuspended in 40 ml of 100 mM MgCl₂, pelleted again using the same conditions as above, and then resuspended in breaking buffer (100 mM 3-[N-morpholino]propanesulfonic acid (MOPS) (pH 7.2), 1 mM dithiothreitol, 5% glycerol) in a ratio of 2 ml breaking buffer per gram of cells wet weight. Lysozyme was added in a ratio of 80 μl per gram of cells along with a Protease Inhibitor Cocktail for bacterial extracts (Sigma, P 8465) in a ratio of 5 ml per 20 grams of cells wet weight. Finally, phenylmethylsulfonyl fluoride (0.1 M stock solution in 100% ethanol) was added in a ratio of 250 μl per 50 ml of breaking buffer. The cells were disrupted with a sonicator (Sonics and Materials Inc., Model VCX 600) in 9.0 second bursts, with 3.0 second resting periods, for 30 minutes at an amplitude of 50%. Lysed cells were centrifuged for 75 minutes at 56,000×g in a JA-25.50 rotor of a Beckman Avanti J-251 Centrifuge at 4° C. The supernatant (cleared cell lysate) was decanted and glycerol was added to a final concentration of 15% prior to storage at −80° C.
• Initial purification of dicamba O-demethylase components. An aliquot of the cleared cell lysate containing approximately 2.7 grams of protein was applied to a Pharmacia XK 26/60 column containing 25 ml of DEAE-Sepharose Fast Flow equilibrated with 50 mM MOPS (pH7.2), 1 mM dithiothreitol, and 15% (v/v) glycerol (buffer A). The column was connected to a Bio-CAD Perfusion Chromatography Workstation (USDA NRICGP Grant #9504266) and run at a flow rate of 5.0 ml/min. After the column was loaded, it was washed with buffer A until the absorbance reading at 280 nm decreased to below 0.1. All three components of dicamba O-demethylase were bound to the DEAE column under these conditions. The column was developed with a linear gradient of 0 to 500 mM NaCl in buffer A. This resulted in the elution of the ferredoxin at 400 mM NaCl and the co-elution of the reductase and oxygenase components at 250 mM NaCl.[0134]
• Purification of the ferredoxin[0135]_DIC. Fractions containing the ferredoxin_DICeluted from the DEAE-Sepharose column were pooled and buffer exchanged into 50 mM MOPS (pH 7.2), 5% glycerol (v/v) and 200 mM NaCl (buffer B). They were then concentrated to approximately 2 ml using a Amicon Cell Concentrator with a YM10 membrane and a Centricon 10 concentrator. This sample was then applied to a pre-packed Pharmacia HiPrep 26/60 Sephacryl S-100 column equilibrated with buffer B and run at a flow rate of 0.5 ml/min on a Pharmacia FPLC apparatus. Fractions that showed activity were pooled and buffer exchanged into 50 mM MOPS (pH 7.2), 1 mM dithiothreitol and 5% glycerol (v/v) (buffer C). The fractions were concentrated to approximately 2 ml and then loaded onto a PharmaciaMono Q HR 5/5 column equilibrated in buffer C. The column was developed with a linear gradient of 0-2.0 M NaCl in buffer C. Fractions that contained ferredoxin activity were assayed for protein content and stored at −80° C.
• Purification of the reductase[0136]_DIC. Fractions from the initial DEAE-Sepharose column containing the oxygenase/reductase components were pooled, and ammonium sulfate was added to a final concentration of 1.5 M. After incubating at 4° C. for 1.5 hours, the samples were centrifuged for 75 minutes at 56,000×g at 4° C. in a JA-25.50 rotor of a Beckman Avanti J-25I centrifuge. The supernatant was retained and loaded at a flow rate of 5.0 ml/min onto a Pharmacia XK 26/20 column containing 25 ml of Phenyl-Sepharose 6 Fast Flow (high sub) that was equilibrated in buffer A containing 1.5 M (NH₄)₂SO₄. Fractions that contained the reductase component were pooled, buffer exchanged into buffer B, and concentrated to approximately 2 ml using the Amicon concentrator with an YM30 membrane and a Centricon10 concentrator. The 2 ml sample was applied to a pre-packed Pharmacia HiPrep 26/60 Sephacryl S-100 column equilibrated in buffer B and run at 0.5 ml/min. Fractions containing reductase activity were pooled, buffer exchanged into buffer C, and concentrated down to approximately 2 ml. The 2 ml sample was loaded onto a pre-packed PharmaciaMono Q HR 5/5 column that was equilibrated in buffer C. The column was developed with a linear gradient of 0-2.0 M NaCl in buffer C at a flow rate of 0.5 ml/min. Fractions that showed reductase activity were assayed for protein content and stored at −80° C.
• Rapid enzyme assays. Activity for each of the three individual components was monitored in reactions using[0137]¹⁴C-labeled dicamba in a reaction containing an excess of the remaining two components. For each reaction, a buffer solution composed of 24 mM potassium phosphate (KP_i) buffer (pH 7.0), 0.48 mM NADH, 0.48 mM FeSO₄and 9.6 mM MgCl₂was added to 200 μl of protein sample along with 30 μl of master mix (562.4 μl sterile water, 12.0 μl 50 mM dicamba and 25.6 μl¹⁴C-dicamba stock solution [1.28 μCi]) for a total volume of 311 μl and a¹⁴C-dicamba specific activity of 4.12 μC_i/ml. After 60 min, each reaction was stopped by the addition of 50μl 5% H₂SO₄(v/v) and 500 μl ether. Reaction tubes were vortexed and centrifuged in a microfuge (Eppendorf, Model 5415C) at 14,000×g for 2 minutes. For a quick visual appraisal of enzymatic activity, each reaction tube was placed under a hand-held UV light (Fotodyne Inc., Model 3-6000) to detect fluorescence of the reaction product, DCSA. For more accurate, semi-quantitative measurements of enzymatic activities, reaction products were separated using thin layer chromatography as described in Example 1.
• Protein concentration determinations. The fractions obtained at different stages of the purification protocol were-assayed for protein concentration using the Bradford assay (standard protocol; Bio-Rad; see Example 1).[0138]
Example 4Identification and Sequencing of a Clone Coding for Ferredoxin_DIC
• The N-terminal sequence obtained from the purified ferredoxin protein (purification described in Example 3) was 29 amino acids in length (sequencing of proteins was performed by the Protein Core Facility at the University of Nebraska-Lincoln using a standard Edman degradation procedure; see Example 1). A comparison of this sequence to the Genbank database showed that it was 35% identical in a 26 amino acid overlap to a terpredoxin from Pseudomonas sp., a bacterial [2Fe-2S] ferredoxin in the adrenodoxin family. The sequence information was used to design three degenerate oligonucleotide primers (two forward and one reverse). The sequence of the two 17 mer forward primers was based on the N-terminal amino acid sequence obtained from the purified ferredoxin protein. The sequence of the 17 mer reverse primer was based on a conserved sequence of six amino acids near the C-terminal end of six previously sequenced bacterial adrenodoxin-type ferredoxins. The primers were used in a nested PCR reaction to amplify a 191 bp product from total[0139]P. maltophiliaDNA. The product was cloned into the pGEM-T Easy vector (Promega, Madison, Wis.) and sequenced. DNA sequencing was performed by the DNA Sequencing Core Facility at the University of Nebraska-Lincoln using a standard dideoxy-mediated chain termination procedure. An analysis of the predicted amino acid sequence of this clone confirmed that it matched the N-terminal and internal amino acid sequence previously obtained from the purified ferredoxin protein. Furthermore, the derived amino acid sequence had 48% identity over its entire length with a [2Fe-2S] ferredoxin fromRhodobacter capsulatus.The cloned fragment was labeled with digoxigenin (DIG) (Roche Diagnostics) using a standard PCR protocol (DIG/Genius System User's Guide) and hybridized by a Southern blot to totalP. maltophiliaDNA that had been digested with a number of restriction enzymes. A map of the restriction sites surrounding the gene was constructed based on the sizes of the restriction fragments that hybridized to the probe. This initial experiment showed that the gene was contained on a Xho I/Pst I fragment that was approximately 1 kb in length. Subsequently, totalP. maltophiliaDNA was digested with Xho I and Pst I, and the restriction fragments were resolved on a gel. Fragments between 0.5 and 1.5 kb in length were excised from the gel, ligated into the vector pBluescript II KS+ (Stratagene, Inc.) and transformed into DH5α cells (Gibco BRL, Inc.). Bacterial colonies containing the size-fractionated library were screened with the DIG-labeled probe and a 900 bp Xho I/Pst I fragment was identified. Sequence analysis showed that this clone contained a full-length 318 bp ferredoxin gene [SEQ ID NO: 4] that encoded an 11.4 kDa protein composed of 105 amino acid residues [SEQ ID NO: 5]. The amino acid sequence predicted by the cloned gene matched the N-terminal and internal amino acid sequence previously obtained from the purified ferredoxin protein. Furthermore, the predicted amino acid sequence was homologous over its entire length to five other members of the adrenodoxin family of [2Fe-2S] bacterial ferredoxins, ranging from 42% identity with a ferredoxin fromRhodobacter capsulatusto 35% identity with a ferredoxin from Pseudomonas (see FIG. 2). The other three ferredoxins were fromCaulobacter crescentus, Rhodococcus erythropolis,andPseudomonas putida.Proteins in this family bind a single 2Fe-2S iron-sulfur cluster and have three conserved motifs.Motif 1 includes three conserved cysteines which are 2Fe-2S ligands.Motif 2 contains a cluster of negatively charged residues.Motif 3 includes the fourth conserved cysteine of the 2Fe-2S cluster.
Example 5Identification and Sequencing of Clones Coding Reductase_DIC
• Two reductase genes were cloned by the same approach that was used in Example 4 to clone the ferredoxin gene. The N-terminal sequence obtained from the purified reductase protein (purification described in Example 3) was 25 amino acids in length. A comparison of this sequence to the Genbank database showed that it was 90% identical in a 20 amino acid overlap to a cytochrome P450-type reductase component of dioxin dioxygenase, a three component enzyme previously isolated from Sphingomonas sp. RW1. An internal sequence of 10 amino acid residues was also obtained from tryptic digests of the purified protein. The internal sequence had 87.5% identity with residues 62 through 69 of the same cytochrome P450-type reductase from Sphingomonas sp. RW1. This sequence information was used to design three degenerate oligonucleotide primers (two forward and one reverse). The sequence of the two 17 mer forward primers was based on the N-terminal amino acid sequence and the sequence of the 17 mer reverse primer was based on the internal amino acid sequence. The primers were used in a nested PCR reaction to amplify a 180 bp product from total[0140]P. maltophiliaDNA. The product was cloned into the pGEM-T Easy vector and sequenced. An analysis of the predicted amino acid sequence of this clone confirmed that it encoded a protein that matched the N-terminal and internal amino acid sequence obtained from the purified reductase protein. Furthermore, the predicted sequence had 80% identity over its entire length with the cytochrome P-450 type reductase component of the dioxin dioxygenase from Sphingomonas sp. RW1.
• The cloned fragment was labeled with DIG and hybridized by a Southern blot to total[0141]P. maltophiliaDNA that had been digested with a number of restriction enzymes. The Southern blot showed that the DIG-labeled probe recognized two distinct loci in the various restriction digests ofP. maltophiliatotal DNA. This observation suggested that there are two reductase genes located at different positions in the genome ofP. maltophilia.It was possible that the two genes are identical duplications that encode identical reductase proteins. Alternatively, one of the genes could encode a truncated protein with no activity or a full-length protein with low activity in our dicamba O-demethylase assay. Because it was necessary to clone the gene that encodes a protein with optimal activity, the DIG-labeled probe was used to retrieve both reductase genes.
• When total[0142]P. maltophiliaDNA was digested with Kpn I and EcoR I, the DIG-labeled probe hybridized to one restriction fragment that was approximately 4.0 kb in length and to another larger fragment with a size of approximately 20 kb. A map of a number of restriction sites surrounding the gene located on the 4.0 kb Kpn I/EcoR I fragment was constructed based on the sizes of different restriction fragments that hybridized to the probe. The restriction map indicated that the entire gene should be located on this 4.0 kb fragment. Subsequently, totalP. maltophiliaDNA was digested with Kpn I and EcoR I, and the restriction fragments were resolved on a gel. Fragments between 3.0 and 5.0 kb in length were excised from the gel, ligated into the vector pBluescript II KS+, and transformed into DH5α cells. Bacterial colonies containing the size-fractionated library were screened with the DIG-labeled probe and a 4.3 kb Kpn I/EcoR I fragment was identified. Sequence analysis showed that this clone contained a full-length 1224 bp reductase gene [SEQ ID NO: 6] and encoded a 43.7 kDa protein consisting of 408 amino acids [SEQ ID NO: 7]. The amino acid sequence predicted by the cloned gene matched the N-terminal and internal amino acid sequence previously obtained from the purified reductase protein. Furthermore, the predicted amino acid sequence was homologous over its entire length to at least four other FAD-dependent pyridine nucleotide reductases, ranging from 69% identity with a cytochrome P450-type reductase component of dioxin dioxygenase from Sphingomonas sp. RW1 to 36% identity with the terpredoxin reductase from a Pseudomonas species (see FIG. 3). The two other FAD-dependent pyridine nucleotide reductases were fromR. erythropolisandP. putida.Proteins in this family of FAD-dependent pyridine nucleotide reductases have five conserved motifs.Motifs 1 and 3 contain three conserved glycine residues and correspond to the ADP binding site for FAD and NAD(P) respectively.Motif 5 corresponds to the site binding the FAD flavin moiety.
• To clone the second gene, total[0143]P. maltophiliaDNA was digested with Kpn I and EcoR I and the resulting restriction fragments were resolved on an agarose gel. Fragments with a size of approximately 20 kb were excised from the gel, digested with a number of restriction enzymes, and then hybridized by Southern blot to the DIG-labeled probe. A map of the restriction sites surrounding the second gene was constructed based on the sizes of the restriction fragments that hybridized to the probe. These experiments showed that the full-length second reductase gene was contained on an Apa I fragment that was approximately 3.0 kb in length. Subsequently, totalP. maltophiliaDNA was digested with Apa I and the restriction fragments were resolved on a gel. Fragments between 2.0 and 4.0 kb in length were excised from the gel, ligated into the vector pBluescript II KS+, and transformed into DH5α cells. Bacterial colonies containing the size-fractionated library were screened with the DIG-labeled probe and a 3.0 kb Apa I fragment was identified. Sequence analysis showed that the 3.0 kb clone contained an open reading frame of 1227 bp [SEQ ID NO: 8] and encoded a 43.9 kDa protein consisting of 409 amino acids [SEQ ID NO: 9]. The amino acid sequence encoded by the second reductase gene is almost identical (98.8% identity) to the sequence of the first gene.
Example 6Transformation of Plants
• In order to place each of the three genes that encode the components of dicamba O-demethylase individually into cassettes suitable for expression in plants, the following steps were taken. Oligonucleotide primers were designed to generate a Nco I site at the 5′ end and an Xba I site at the 3′ end of each of the three genes by PCR amplification. The authenticity of the resulting PCR products was confirmed by sequencing, and each gene was then cloned individually into the pRTL2 vector (provided by Dr. Tom Clemente of the Plant Transformation Core Research Facility, University of Nebraska, Lincoln, Nebr.). This vector contains a 144 bp translation enhancer sequence from tobacco etch virus (TEV) (Carrington and Freed,[0144]J. Virology,64:1590-1597(1990)) at the 5′ end of the polylinker. The oxygenase, reductase, and ferredoxin genes, each with a 5′ translation enhancer, were then cloned individually as Xho I/Xba I fragments into the plant expression vector pKLP36 (obtained from Indu Maiti, University of Kentucky, Lexington, Ky.) (Maiti and Shepard,Biochem. Biophys. Res. Commun.,244:440-444 (1998)). This binary vector contains the peanut chlorotic virus full-length promoter (PCISV FLt36) with a duplicated enhancer domain for constitutive expression in plants and thepea rbcS 3′ sequence for efficient transcript termination (Maiti and Shepherd,Biochem. Biophys. Res. Commun.,244:440-444 (1998)). Constructs with all three genes on one binary vector can be produced using combinations of the three genes in a number of different orders and orientations.
• The following methods were employed to move the oxygenase, ferredoxin, and reductase constructs individually into[0145]Agrobacterium tumefaciensand to transform each construct into Arabidopsis and tobacco. The three constructs were moved into theA. tumefaciensstrain C58C1 by a modified triparental mating procedure routinely used by the Plant Transformation Core Research Facility. This involved incubatingEscherichia colicells carrying each construct with a mixture ofA. tumefacienscells andE. colicells carrying the helper plasmid pRK2013 (for plasmid mobilization).A. tumefacienscells containing each of the constructs were then used to transform tobacco and Arabidopsis with the assistance of the Plant Transformation Core Research Facility. For tobacco, leaf explants were incubated with a suspension ofA. tumefacienscells containing each of the constructs, and shoots were regenerated on solid medium containing kanamycin (Horsch et al.,Science,227:1229-1231 (1985)). Ten shoots were selected from each of the three transformation experiments, placed on rooting medium for a few weeks, and then moved to pots in the greenhouse. For Arabidopsis, a pot of plants with flowers was incubated with a suspension ofA. tumefacienscells containing each of the constructs, and the plants were then allowed to set seed (Bechtold et al.,C.R. Acad. Sci. Paris, Sciences de la vie/Life sciences,316:1194-1199 (1993); Clough and Bent,Plant J.,16(6):735-743 (1998)). The seed was collected and germinated on medium with kanamycin. After the seedlings had developed an adequate root system, several plants were selected from each transformation experiment and moved to pots in a growth chamber.
• For evaluation of the expression of each gene in the transformed plants, Western blots of leaf lysates from several transformed plants were prepared and probed with polyclonal antibodies that detect the three components of dicamba O-demethylase. To determine enzyme activities for each enzyme in plant extracts, the approach was to combine leaf lysates from transformed plants expressing the oxygenase, ferredoxin or reductase proteins with excess amounts of the other O-demethylase components purified from[0146]P. maltophiliastrain DI-6. These mixtures were tested for dicamba O-demethylase activity with both the standard¹⁴C-labeled dicamba assay (see Examples 1 and 3) and an HPLC assay employing nonradioactive dicamba as substrate (dicamba and 3,6-DCSA elute at different points from the HPLC and can be quantitated).
• To test expression of gene products in the chloroplast compartment, constructs were made with a transit peptide sequence at the 5′ end of the oxygenase, ferredoxin, and reductase genes. Such an approach was successful for introducing tolerance to the sulfonylurea herbicides into tobacco plants (O'Keefe et al.,[0147]Plant Physiol.,105:473-478 (1994)).
• To test the possibility that the codon usage of the bacterial ferredoxin gene was not fully optimal for efficient translation in a plant cell, a synthetic ferredoxin gene encoding the same amino acid sequence as the[0148]P. maltophiliastrain DI-6 ferredoxin, but with optimized codon bias for dicot plants was synthesized by Entelechon, GmbH (Regensberg, Germany). It has been well documented that changes in codon usage are essential for optimal expression of the bacterial B.t. toxin genes in plant cells (see, e.g., Diehn et al.,Genetic Engineering,18:83-99 (1996)).
• 118129PRTPseudomonas maltophilia DI-6unsure(28)..(28)Best guess for Xaa = Asp or Thr 1 Thr Phe Val Arg Asn Ala Trp Tyr Val Ala Ala Leu Pro Glu Glu Leu 1 5 10 15 Ser Glu Lys Pro Leu Gly Arg Thr Ile Leu Asp Xaa Xaa 20 2521020DNAPseudomonas maltophilia DI-6CDS(1)..(1020) 2 atg acc ttc gtc cgc aat gcc tgg tat gtg gcg gcg ctg ccc gag gaa 48 Met Thr Phe Val Arg Asn Ala Trp Tyr Val Ala Ala Leu Pro Glu Glu 1 5 10 15 ctg tcc gaa aag ccg ctc ggc cgg acg att ctc gac aca ccg ctc gcg 96 Leu Ser Glu Lys Pro Leu Gly Arg Thr Ile Leu Asp Thr Pro Leu Ala 20 25 30 ctc tac cgc cag ccc gac ggt gtg gtc gcg gcg ctg ctc gac atc tgt 144 Leu Tyr Arg Gln Pro Asp Gly Val Val Ala Ala Leu Leu Asp Ile Cys 35 40 45 ccg cac cgc ttc gcg ccg ctg agc gac ggc atc ctc gtc aac ggc cat 192 Pro His Arg Phe Ala Pro Leu Ser Asp Gly Ile Leu Val Asn Gly His 50 55 60 ctc caa tgc ccc tat cac ggg ctg gaa ttc gat ggc ggc ggg cag tgc 240 Leu Gln Cys Pro Tyr His Gly Leu Glu Phe Asp Gly Gly Gly Gln Cys 65 70 75 80 gtc cat aac ccg cac ggc aat ggc gcc cgc ccg gct tcg ctc aac gtc 288 Val His Asn Pro His Gly Asn Gly Ala Arg Pro Ala Ser Leu Asn Val 85 90 95 cgc tcc ttc ccg gtg gtg gag cgc gac gcg ctg atc tgg atc tgg ccc 336 Arg Ser Phe Pro Val Val Glu Arg Asp Ala Leu Ile Trp Ile Trp Pro 100 105 110 ggc gat ccg gcg ctg gcc gat cct ggg gcg atc ccc gac ttc ggc tgc 384 Gly Asp Pro Ala Leu Ala Asp Pro Gly Ala Ile Pro Asp Phe Gly Cys 115 120 125 cgc gtc gat ccc gcc tat cgg acc gtc ggc ggc tat ggg cat gtc gac 432 Arg Val Asp Pro Ala Tyr Arg Thr Val Gly Gly Tyr Gly His Val Asp 130 135 140 tgc aac tac aag ctg ctg gtc gac aac ctg atg gac ctc ggc cac gcc 480 Cys Asn Tyr Lys Leu Leu Val Asp Asn Leu Met Asp Leu Gly His Ala 145 150 155 160 caa tat gtc cat cgc gcc aac gcc cag acc gac gcc ttc gac cgg ctg 528 Gln Tyr Val His Arg Ala Asn Ala Gln Thr Asp Ala Phe Asp Arg Leu 165 170 175 gag cgc gag gtg atc gtc ggc gac ggt gag ata cag gcg ctg atg aag 576 Glu Arg Glu Val Ile Val Gly Asp Gly Glu Ile Gln Ala Leu Met Lys 180 185 190 att ccc ggc ggc acg ccg agc gtg ctg atg gcc aag ttc ctg cgc ggc 624 Ile Pro Gly Gly Thr Pro Ser Val Leu Met Ala Lys Phe Leu Arg Gly 195 200 205 gcc aat acc ccc gtc gac gct tgg aac gac atc cgc tgg aac aag gtg 672 Ala Asn Thr Pro Val Asp Ala Trp Asn Asp Ile Arg Trp Asn Lys Val 210 215 220 agc gcg atg ctc aac ttc atc gcg gtg gcg ccg gaa ggc acc ccg aag 720 Ser Ala Met Leu Asn Phe Ile Ala Val Ala Pro Glu Gly Thr Pro Lys 225 230 235 240 gag cag agc atc cac tcg cgc ggt acc cat atc ctg acc ccc gag acg 768 Glu Gln Ser Ile His Ser Arg Gly Thr His Ile Leu Thr Pro Glu Thr 245 250 255 gag gcg agc tgc cat tat ttc ttc ggc tcc tcg cgc aat ttc ggc atc 816 Glu Ala Ser Cys His Tyr Phe Phe Gly Ser Ser Arg Asn Phe Gly Ile 260 265 270 gac gat ccg gag atg gac ggc gtg ctg cgc agc tgg cag gct cag gcg 864 Asp Asp Pro Glu Met Asp Gly Val Leu Arg Ser Trp Gln Ala Gln Ala 275 280 285 ctg gtc aag gag gac aag gtc gtc gtc gag gcg atc gag cgc cgc cgc 912 Leu Val Lys Glu Asp Lys Val Val Val Glu Ala Ile Glu Arg Arg Arg 290 295 300 gcc tat gtc gag gcg aat ggc atc cgc ccg gcg atg ctg tcg tgc gac 960 Ala Tyr Val Glu Ala Asn Gly Ile Arg Pro Ala Met Leu Ser Cys Asp 305 310 315 320 gaa gcc gca gtc cgt gtc agc cgc gag atc gag aag ctt gag cag ctc 1008 Glu Ala Ala Val Arg Val Ser Arg Glu Ile Glu Lys Leu Glu Gln Leu 325 330 335 gaa gcc gcc tga 1020 Glu Ala Ala3339PRTPseudomonas maltophilia DI-6 3 Met Thr Phe Val Arg Asn Ala Trp Tyr Val Ala Ala Leu Pro Glu Glu 1 5 10 15 Leu Ser Glu Lys Pro Leu Gly Arg Thr Ile Leu Asp Thr Pro Leu Ala 20 25 30 Leu Tyr Arg Gln Pro Asp Gly Val Val Ala Ala Leu Leu Asp Ile Cys 35 40 45 Pro His Arg Phe Ala Pro Leu Ser Asp Gly Ile Leu Val Asn Gly His 50 55 60 Leu Gln Cys Pro Tyr His Gly Leu Glu Phe Asp Gly Gly Gly Gln Cys 65 70 75 80 Val His Asn Pro His Gly Asn Gly Ala Arg Pro Ala Ser Leu Asn Val 85 90 95 Arg Ser Phe Pro Val Val Glu Arg Asp Ala Leu Ile Trp Ile Trp Pro 100 105 110 Gly Asp Pro Ala Leu Ala Asp Pro Gly Ala Ile Pro Asp Phe Gly Cys 115 120 125 Arg Val Asp Pro Ala Tyr Arg Thr Val Gly Gly Tyr Gly His Val Asp 130 135 140 Cys Asn Tyr Lys Leu Leu Val Asp Asn Leu Met Asp Leu Gly His Ala 145 150 155 160 Gln Tyr Val His Arg Ala Asn Ala Gln Thr Asp Ala Phe Asp Arg Leu 165 170 175 Glu Arg Glu Val Ile Val Gly Asp Gly Glu Ile Gln Ala Leu Met Lys 180 185 190 Ile Pro Gly Gly Thr Pro Ser Val Leu Met Ala Lys Phe Leu Arg Gly 195 200 205 Ala Asn Thr Pro Val Asp Ala Trp Asn Asp Ile Arg Trp Asn Lys Val 210 215 220 Ser Ala Met Leu Asn Phe Ile Ala Val Ala Pro Glu Gly Thr Pro Lys 225 230 235 240 Glu Gln Ser Ile His Ser Arg Gly Thr His Ile Leu Thr Pro Glu Thr 245 250 255 Glu Ala Ser Cys His Tyr Phe Phe Gly Ser Ser Arg Asn Phe Gly Ile 260 265 270 Asp Asp Pro Glu Met Asp Gly Val Leu Arg Ser Trp Gln Ala Gln Ala 275 280 285 Leu Val Lys Glu Asp Lys Val Val Val Glu Ala Ile Glu Arg Arg Arg 290 295 300 Ala Tyr Val Glu Ala Asn Gly Ile Arg Pro Ala Met Leu Ser Cys Asp 305 310 315 320 Glu Ala Ala Val Arg Val Ser Arg Glu Ile Glu Lys Leu Glu Gln Leu 325 330 335 Glu Ala Ala4318DNAPseudomonas maltophilia DI-6CDS(1)..(318) 4 atg ccg cag att acc gtc gtc aac cag tcg ggt gaa gaa tcc agc gtc 48 Met Pro Gln Ile Thr Val Val Asn Gln Ser Gly Glu Glu Ser Ser Val 1 5 10 15 gag gcg agt gaa ggc cgc acc ctg atg gaa gtc atc cgc gac agc ggt 96 Glu Ala Ser Glu Gly Arg Thr Leu Met Glu Val Ile Arg Asp Ser Gly 20 25 30 ttt gac gaa ctc ctg gcg ctt tgc ggc ggc tgc tgc tcg tgc gcg acc 144 Phe Asp Glu Leu Leu Ala Leu Cys Gly Gly Cys Cys Ser Cys Ala Thr 35 40 45 tgc cac gtc cac atc gac ccg gcc ttc atg gac aag ctg ccg gag atg 192 Cys His Val His Ile Asp Pro Ala Phe Met Asp Lys Leu Pro Glu Met 50 55 60 agc gaa gac gag aac gac ctg ctc gac agc tcg gac cac cgc aac gag 240 Ser Glu Asp Glu Asn Asp Leu Leu Asp Ser Ser Asp His Arg Asn Glu 65 70 75 80 tac tcg cgt ctc tcg tgc cag att ccg gtc acc ggc gcc ctc gaa ggc 288 Tyr Ser Arg Leu Ser Cys Gln Ile Pro Val Thr Gly Ala Leu Glu Gly 85 90 95 atc aag gtg acg atc gcg cag gaa gac tga 318 Ile Lys Val Thr Ile Ala Gln Glu Asp 100 1055105PRTPseudomonas maltophilia DI-6 5 Met Pro Gln Ile Thr Val Val Asn Gln Ser Gly Glu Glu Ser Ser Val 1 5 10 15 Glu Ala Ser Glu Gly Arg Thr Leu Met Glu Val Ile Arg Asp Ser Gly 20 25 30 Phe Asp Glu Leu Leu Ala Leu Cys Gly Gly Cys Cys Ser Cys Ala Thr 35 40 45 Cys His Val His Ile Asp Pro Ala Phe Met Asp Lys Leu Pro Glu Met 50 55 60 Ser Glu Asp Glu Asn Asp Leu Leu Asp Ser Ser Asp His Arg Asn Glu 65 70 75 80 Tyr Ser Arg Leu Ser Cys Gln Ile Pro Val Thr Gly Ala Leu Glu Gly 85 90 95 Ile Lys Val Thr Ile Ala Gln Glu Asp 100 10561227DNAPseudomonas maltophilia DI-6CDS(1)..(1227) 6 atg agc aag gca gac gtc gta atc gtg gga gcc ggg cat ggc ggc gca 48 Met Ser Lys Ala Asp Val Val Ile Val Gly Ala Gly His Gly Gly Ala 1 5 10 15 cag tgc gcg atc gcc ctt cgc cag aac ggc ttc gaa gga acc atc acc 96 Gln Cys Ala Ile Ala Leu Arg Gln Asn Gly Phe Glu Gly Thr Ile Thr 20 25 30 gtc atc ggt cgt gag ccg gaa tat ccc tat gag cgt ccg ccg ctc tcg 144 Val Ile Gly Arg Glu Pro Glu Tyr Pro Tyr Glu Arg Pro Pro Leu Ser 35 40 45 aag gaa tat ttc gcg cgc gag aag acc ttc gac cgc ctc tac atc cgt 192 Lys Glu Tyr Phe Ala Arg Glu Lys Thr Phe Asp Arg Leu Tyr Ile Arg 50 55 60 ccg ccg acg ttc tgg gcc gag aag aac atc gag ttc aag ctt ggc acc 240 Pro Pro Thr Phe Trp Ala Glu Lys Asn Ile Glu Phe Lys Leu Gly Thr 65 70 75 80 gaa gtc acc aag gtc gat ccc aag gcg cac gaa ctg acg ctc tcc aac 288 Glu Val Thr Lys Val Asp Pro Lys Ala His Glu Leu Thr Leu Ser Asn 85 90 95 ggc gag agc tac ggt tat ggc aag ctc gtc tgg gcc acc ggc ggc gat 336 Gly Glu Ser Tyr Gly Tyr Gly Lys Leu Val Trp Ala Thr Gly Gly Asp 100 105 110 ccg cgt cgc ctt tct tgc cag ggg gcc gac ctc acc ggc atc cac gcc 384 Pro Arg Arg Leu Ser Cys Gln Gly Ala Asp Leu Thr Gly Ile His Ala 115 120 125 gtg cgc acc cgc gag gac tgc gac acg ctg atg gcc gaa gtc gat gcg 432 Val Arg Thr Arg Glu Asp Cys Asp Thr Leu Met Ala Glu Val Asp Ala 130 135 140 ggc acg aag aac atc gtc gtc atc ggc ggc ggc tac atc ggt ctg gaa 480 Gly Thr Lys Asn Ile Val Val Ile Gly Gly Gly Tyr Ile Gly Leu Glu 145 150 155 160 gcc gct gcg gtg ctg tcc aag atg ggc ctc aag gtc acc ctg ctc gaa 528 Ala Ala Ala Val Leu Ser Lys Met Gly Leu Lys Val Thr Leu Leu Glu 165 170 175 gcg ctt ccg cgc gtg ctg gcg cgc gtt gcg ggt gaa gac ctc tcg acc 576 Ala Leu Pro Arg Val Leu Ala Arg Val Ala Gly Glu Asp Leu Ser Thr 180 185 190 ttc tac cag aag gaa cat gtc gat cac ggc gtc gac ctg cgc acc gaa 624 Phe Tyr Gln Lys Glu His Val Asp His Gly Val Asp Leu Arg Thr Glu 195 200 205 gtc atg gtc gac agc ctc gtc ggc gaa aac ggc aag gtc acc ggc gtg 672 Val Met Val Asp Ser Leu Val Gly Glu Asn Gly Lys Val Thr Gly Val 210 215 220 cag ctt gcc ggc ggc gaa gtg atc ccg gcc gaa ggc gtc atc gtc ggc 720 Gln Leu Ala Gly Gly Glu Val Ile Pro Ala Glu Gly Val Ile Val Gly 225 230 235 240 atc ggc atc gtg cct gcc gtc ggt ccg ctg atc gcg gcc ggc gcg gcc 768 Ile Gly Ile Val Pro Ala Val Gly Pro Leu Ile Ala Ala Gly Ala Ala 245 250 255 ggt gcc aac ggc gtc gac gtg gac gag tac tgc cgc acc tcg ctg ccc 816 Gly Ala Asn Gly Val Asp Val Asp Glu Tyr Cys Arg Thr Ser Leu Pro 260 265 270 gac atc tat gcg atc ggc gac tgt gcg gct ttc gcc tgc gac tac gcc 864 Asp Ile Tyr Ala Ile Gly Asp Cys Ala Ala Phe Ala Cys Asp Tyr Ala 275 280 285 ggc ggc aac gtg atg cgc gtg gaa tcg gtc cag aac gcc aac gac atg 912 Gly Gly Asn Val Met Arg Val Glu Ser Val Gln Asn Ala Asn Asp Met 290 295 300 ggc acc tgc gtg gcc aag gcg atc tgc ggc gac gag aag ccc tac aag 960 Gly Thr Cys Val Ala Lys Ala Ile Cys Gly Asp Glu Lys Pro Tyr Lys 305 310 315 320 gcg ttc ccg tgg ttc tgg tcc aac cag tac gac ctc aag ctg cag acc 1008 Ala Phe Pro Trp Phe Trp Ser Asn Gln Tyr Asp Leu Lys Leu Gln Thr 325 330 335 gcc ggc atc aac ctg ggc ttc gac aag acc gtg atc cgc ggc aat ccg 1056 Ala Gly Ile Asn Leu Gly Phe Asp Lys Thr Val Ile Arg Gly Asn Pro 340 345 350 gag gag cgc agc ttc tcg gtc gtc tat ctc aag gac ggc cgc gtg gtc 1104 Glu Glu Arg Ser Phe Ser Val Val Tyr Leu Lys Asp Gly Arg Val Val 355 360 365 gcg ctg gac tgc gtg aac atg gtc aag gat tac gtg cag ggc cgc aag 1152 Ala Leu Asp Cys Val Asn Met Val Lys Asp Tyr Val Gln Gly Arg Lys 370 375 380 ctg gtc gaa gcc ggg gcc acc ccc gac ctc gaa gcg ctg gcc gat gcc 1200 Leu Val Glu Ala Gly Ala Thr Pro Asp Leu Glu Ala Leu Ala Asp Ala 385 390 395 400 ggc aag ccg ctc aag gaa ctg ctc tag 1227 Gly Lys Pro Leu Lys Glu Leu Leu 4057408PRTPseudomonas maltophilia DI-6 7 Met Ser Lys Ala Asp Val Val Ile Val Gly Ala Gly His Gly Gly Ala 1 5 10 15 Gln Cys Ala Ile Ala Leu Arg Gln Asn Gly Phe Glu Gly Thr Ile Thr 20 25 30 Val Ile Gly Arg Glu Pro Glu Tyr Pro Tyr Glu Arg Pro Pro Leu Ser 35 40 45 Lys Glu Tyr Phe Ala Arg Glu Lys Thr Phe Asp Arg Leu Tyr Ile Arg 50 55 60 Pro Pro Thr Phe Trp Ala Glu Lys Asn Ile Glu Phe Lys Leu Gly Thr 65 70 75 80 Glu Val Thr Lys Val Asp Pro Lys Ala His Glu Leu Thr Leu Ser Asn 85 90 95 Gly Glu Ser Tyr Gly Tyr Gly Lys Leu Val Trp Ala Thr Gly Gly Asp 100 105 110 Pro Arg Arg Leu Ser Cys Gln Gly Ala Asp Leu Thr Gly Ile His Ala 115 120 125 Val Arg Thr Arg Glu Asp Cys Asp Thr Leu Met Ala Glu Val Asp Ala 130 135 140 Gly Thr Lys Asn Ile Val Val Ile Gly Gly Gly Tyr Ile Gly Leu Glu 145 150 155 160 Ala Ala Ala Val Leu Ser Lys Met Gly Leu Lys Val Thr Leu Leu Glu 165 170 175 Ala Leu Pro Arg Val Leu Ala Arg Val Ala Gly Glu Asp Leu Ser Thr 180 185 190 Phe Tyr Gln Lys Glu His Val Asp His Gly Val Asp Leu Arg Thr Glu 195 200 205 Val Met Val Asp Ser Leu Val Gly Glu Asn Gly Lys Val Thr Gly Val 210 215 220 Gln Leu Ala Gly Gly Glu Val Ile Pro Ala Glu Gly Val Ile Val Gly 225 230 235 240 Ile Gly Ile Val Pro Ala Val Gly Pro Leu Ile Ala Ala Gly Ala Ala 245 250 255 Gly Ala Asn Gly Val Asp Val Asp Glu Tyr Cys Arg Thr Ser Leu Pro 260 265 270 Asp Ile Tyr Ala Ile Gly Asp Cys Ala Ala Phe Ala Cys Asp Tyr Ala 275 280 285 Gly Gly Asn Val Met Arg Val Glu Ser Val Gln Asn Ala Asn Asp Met 290 295 300 Gly Thr Cys Val Ala Lys Ala Ile Cys Gly Asp Glu Lys Pro Tyr Lys 305 310 315 320 Ala Phe Pro Trp Phe Trp Ser Asn Gln Tyr Asp Leu Lys Leu Gln Thr 325 330 335 Ala Gly Ile Asn Leu Gly Phe Asp Lys Thr Val Ile Arg Gly Asn Pro 340 345 350 Glu Glu Arg Ser Phe Ser Val Val Tyr Leu Lys Asp Gly Arg Val Val 355 360 365 Ala Leu Asp Cys Val Asn Met Val Lys Asp Tyr Val Gln Gly Arg Lys 370 375 380 Leu Val Glu Ala Gly Ala Thr Pro Asp Leu Glu Ala Leu Ala Asp Ala 385 390 395 400 Gly Lys Pro Leu Lys Glu Leu Leu 40581230DNAPseudomonas maltophilia DI-6CDS(1)..(1230) 8 atg cag agg gca gac gtc gta atc gtg gga gcc ggg cat ggc ggt gca 48 Met Gln Arg Ala Asp Val Val Ile Val Gly Ala Gly His Gly Gly Ala 1 5 10 15 cag tgc gcg atc gcc ctt cgc cag aac ggc ttc gaa ggc acc atc acc 96 Gln Cys Ala Ile Ala Leu Arg Gln Asn Gly Phe Glu Gly Thr Ile Thr 20 25 30 gtc atc ggt cgt gag ccg gaa tat ccc tat gag cgt ccg ccg ctc tcg 144 Val Ile Gly Arg Glu Pro Glu Tyr Pro Tyr Glu Arg Pro Pro Leu Ser 35 40 45 aag gaa tat ttc gcg cgc gag aag acc ttc gac cgc ctc tac atc cgt 192 Lys Glu Tyr Phe Ala Arg Glu Lys Thr Phe Asp Arg Leu Tyr Ile Arg 50 55 60 ccg ccg acg ttc tgg gcc gag aag aac atc gag ttc aag ctt ggc acc 240 Pro Pro Thr Phe Trp Ala Glu Lys Asn Ile Glu Phe Lys Leu Gly Thr 65 70 75 80 gaa gtc acc aag gtc gat ccc aag gcg cac gaa ctg acg ctc tcc aac 288 Glu Val Thr Lys Val Asp Pro Lys Ala His Glu Leu Thr Leu Ser Asn 85 90 95 ggc gag agc tac ggt tat ggc aag ctc gtc tgg gcc acc ggc ggc gat 336 Gly Glu Ser Tyr Gly Tyr Gly Lys Leu Val Trp Ala Thr Gly Gly Asp 100 105 110 ccg cgt cgc ctt tct tgc cag ggg gcc gac ctc acc ggc atc cac gcc 384 Pro Arg Arg Leu Ser Cys Gln Gly Ala Asp Leu Thr Gly Ile His Ala 115 120 125 gtg cgc acc cgc gag gac tgc gac acg ctg atg gcc gaa gtc gat gcg 432 Val Arg Thr Arg Glu Asp Cys Asp Thr Leu Met Ala Glu Val Asp Ala 130 135 140 ggc acg aag aac atc gtc gtc atc ggc ggc ggc tac atc ggt ctg gaa 480 Gly Thr Lys Asn Ile Val Val Ile Gly Gly Gly Tyr Ile Gly Leu Glu 145 150 155 160 gcc gct gcg gtg ctg tcc aag atg ggc ctc aag gtc acc ctg ctc gaa 528 Ala Ala Ala Val Leu Ser Lys Met Gly Leu Lys Val Thr Leu Leu Glu 165 170 175 gcg ctt ccg cgc gtg ctg gcg cgc gtt gcg ggt gaa gac ctc tcg acc 576 Ala Leu Pro Arg Val Leu Ala Arg Val Ala Gly Glu Asp Leu Ser Thr 180 185 190 ttc tac cag aag gaa cat gtc gat cac ggc gtc gac ctg cgc acc gaa 624 Phe Tyr Gln Lys Glu His Val Asp His Gly Val Asp Leu Arg Thr Glu 195 200 205 gtc atg gtc gac agc ctc gtc ggc gaa aac ggc aag gtc acc ggc gtg 672 Val Met Val Asp Ser Leu Val Gly Glu Asn Gly Lys Val Thr Gly Val 210 215 220 cag ctt gcc ggc ggc gaa gtg atc ccg gcc gaa ggc gtc atc gtc ggc 720 Gln Leu Ala Gly Gly Glu Val Ile Pro Ala Glu Gly Val Ile Val Gly 225 230 235 240 atc ggc atc gtg cct gcc atc ggt ccg ctg atc gcg gcc ggc gcg gcc 768 Ile Gly Ile Val Pro Ala Ile Gly Pro Leu Ile Ala Ala Gly Ala Ala 245 250 255 ggc gcc aac ggc gtc gac gtg gac gag tac tgc cgc acc tcg ctg ccc 816 Gly Ala Asn Gly Val Asp Val Asp Glu Tyr Cys Arg Thr Ser Leu Pro 260 265 270 gac atc tat gcg atc ggc gac tgt gcg gct ttc gcc tgc gac tac gcc 864 Asp Ile Tyr Ala Ile Gly Asp Cys Ala Ala Phe Ala Cys Asp Tyr Ala 275 280 285 ggc ggc aac gtg atg cgc gtg gaa tcg gtc cag aac gcc aac gac atg 912 Gly Gly Asn Val Met Arg Val Glu Ser Val Gln Asn Ala Asn Asp Met 290 295 300 ggc acc tgc gtg gcc aag gcg atc tgc ggc gac gag aag ccc tac aag 960 Gly Thr Cys Val Ala Lys Ala Ile Cys Gly Asp Glu Lys Pro Tyr Lys 305 310 315 320 gcg ttc ccg tgg ttc tgg tcc aac cag tac gac ctc aag ctg cag acc 1008 Ala Phe Pro Trp Phe Trp Ser Asn Gln Tyr Asp Leu Lys Leu Gln Thr 325 330 335 gcc ggc atc aac ctg ggc ttc gac aag acc gtg atc cgc ggc aat ccg 1056 Ala Gly Ile Asn Leu Gly Phe Asp Lys Thr Val Ile Arg Gly Asn Pro 340 345 350 gag gag cgc agc ttc tcg gtc gtc tat ctc aag gac ggc cgc gtg gtc 1104 Glu Glu Arg Ser Phe Ser Val Val Tyr Leu Lys Asp Gly Arg Val Val 355 360 365 gcg ctg gac tgc gtg aac atg gtc aag gat tac gtg cag ggc cgc aag 1152 Ala Leu Asp Cys Val Asn Met Val Lys Asp Tyr Val Gln Gly Arg Lys 370 375 380 ctg gtc gaa gcc ggg gcc acc ccc gac ctc gaa gcg ctg gcc gat gcc 1200 Leu Val Glu Ala Gly Ala Thr Pro Asp Leu Glu Ala Leu Ala Asp Ala 385 390 395 400 ggc aag ccg ctc aag gaa ctg caa tac tag 1230 Gly Lys Pro Leu Lys Glu Leu Gln Tyr 4059409PRTPseudomonas maltophilia DI-6 9 Met Gln Arg Ala Asp Val Val Ile Val Gly Ala Gly His Gly Gly Ala 1 5 10 15 Gln Cys Ala Ile Ala Leu Arg Gln Asn Gly Phe Glu Gly Thr Ile Thr 20 25 30 Val Ile Gly Arg Glu Pro Glu Tyr Pro Tyr Glu Arg Pro Pro Leu Ser 35 40 45 Lys Glu Tyr Phe Ala Arg Glu Lys Thr Phe Asp Arg Leu Tyr Ile Arg 50 55 60 Pro Pro Thr Phe Trp Ala Glu Lys Asn Ile Glu Phe Lys Leu Gly Thr 65 70 75 80 Glu Val Thr Lys Val Asp Pro Lys Ala His Glu Leu Thr Leu Ser Asn 85 90 95 Gly Glu Ser Tyr Gly Tyr Gly Lys Leu Val Trp Ala Thr Gly Gly Asp 100 105 110 Pro Arg Arg Leu Ser Cys Gln Gly Ala Asp Leu Thr Gly Ile His Ala 115 120 125 Val Arg Thr Arg Glu Asp Cys Asp Thr Leu Met Ala Glu Val Asp Ala 130 135 140 Gly Thr Lys Asn Ile Val Val Ile Gly Gly Gly Tyr Ile Gly Leu Glu 145 150 155 160 Ala Ala Ala Val Leu Ser Lys Met Gly Leu Lys Val Thr Leu Leu Glu 165 170 175 Ala Leu Pro Arg Val Leu Ala Arg Val Ala Gly Glu Asp Leu Ser Thr 180 185 190 Phe Tyr Gln Lys Glu His Val Asp His Gly Val Asp Leu Arg Thr Glu 195 200 205 Val Met Val Asp Ser Leu Val Gly Glu Asn Gly Lys Val Thr Gly Val 210 215 220 Gln Leu Ala Gly Gly Glu Val Ile Pro Ala Glu Gly Val Ile Val Gly 225 230 235 240 Ile Gly Ile Val Pro Ala Ile Gly Pro Leu Ile Ala Ala Gly Ala Ala 245 250 255 Gly Ala Asn Gly Val Asp Val Asp Glu Tyr Cys Arg Thr Ser Leu Pro 260 265 270 Asp Ile Tyr Ala Ile Gly Asp Cys Ala Ala Phe Ala Cys Asp Tyr Ala 275 280 285 Gly Gly Asn Val Met Arg Val Glu Ser Val Gln Asn Ala Asn Asp Met 290 295 300 Gly Thr Cys Val Ala Lys Ala Ile Cys Gly Asp Glu Lys Pro Tyr Lys 305 310 315 320 Ala Phe Pro Trp Phe Trp Ser Asn Gln Tyr Asp Leu Lys Leu Gln Thr 325 330 335 Ala Gly Ile Asn Leu Gly Phe Asp Lys Thr Val Ile Arg Gly Asn Pro 340 345 350 Glu Glu Arg Ser Phe Ser Val Val Tyr Leu Lys Asp Gly Arg Val Val 355 360 365 Ala Leu Asp Cys Val Asn Met Val Lys Asp Tyr Val Gln Gly Arg Lys 370 375 380 Leu Val Glu Ala Gly Ala Thr Pro Asp Leu Glu Ala Leu Ala Asp Ala 385 390 395 400 Gly Lys Pro Leu Lys Glu Leu Gln Tyr 40510106PRTRhodobacter capsulatus 10 Ala Lys Ile Ile Phe Ile Glu His Asn Gly Thr Arg His Glu Val Glu 1 5 10 15 Ala Lys Pro Gly Leu Thr Val Met Glu Ala Ala Arg Asp Asn Gly Val 20 25 30 Pro Gly Ile Asp Ala Asp Cys Gly Gly Ala Cys Ala Cys Ser Thr Cys 35 40 45 His Ala Tyr Val Asp Pro Ala Trp Val Asp Lys Leu Pro Lys Ala Leu 50 55 60 Pro Thr Glu Thr Asp Met Ile Asp Phe Ala Tyr Glu Pro Asn Pro Ala 65 70 75 80 Thr Ser Arg Leu Thr Cys Gln Ile Lys Val Thr Ser Leu Leu Asp Gly 85 90 95 Leu Val Val His Leu Pro Glu Lys Gln Ile 100 10511106PRTCaulobacter crescentus 11 Met Ala Lys Ile Thr Tyr Ile Gln His Asp Gly Ala Glu Gln Val Ile 1 5 10 15 Asp Val Lys Pro Gly Leu Thr Val Met Glu Gly Ala Val Lys Asn Asn 20 25 30 Val Pro Gly Ile Asp Ala Asp Cys Gly Gly Ala Cys Ala Cys Ala Thr 35 40 45 Cys His Val Tyr Val Asp Glu Ala Trp Leu Asp Lys Thr Gly Asp Lys 50 55 60 Ser Ala Met Glu Glu Ser Met Leu Asp Phe Ala Glu Asn Val Glu Pro 65 70 75 80 Asn Ser Arg Leu Ser Cys Gln Ile Lys Val Ser Asp Ala Leu Asp Gly 85 90 95 Leu Val Val Arg Leu Pro Glu Ser Gln His 100 10512106PRTRhodococcus erythropolis 12 Pro Thr Val Thr Tyr Val His Pro Asp Gly Thr Lys His Glu Val Glu 1 5 10 15 Val Pro Thr Gly Lys Arg Val Met Gln Ala Ala Ile Gly Ala Gly Ile 20 25 30 Asp Gly Ile Val Ala Glu Cys Gly Gly Gln Ala Met Cys Ala Thr Cys 35 40 45 His Val Tyr Val Glu Ser Pro Trp Ala Asp Lys Phe Pro Ser Ile Ser 50 55 60 Glu Glu Glu Asp Glu Met Leu Asp Asp Thr Val Ser Pro Arg Thr Glu 65 70 75 80 Ala Ser Arg Leu Ser Cys Gln Leu Val Val Ser Asp Asp Val Asp Gly 85 90 95 Leu Ile Val Arg Leu Pro Glu Glu Gln Val 100 10513106PRTPseudomonas putida 13 Ser Lys Val Val Tyr Val Ser His Asp Gly Thr Arg Arg Glu Leu Asp 1 5 10 15 Val Ala Asp Gly Val Ser Leu Met Gln Ala Ala Val Ser Asn Gly Ile 20 25 30 Tyr Asp Ile Val Gly Asp Cys Gly Gly Ser Ala Ser Cys Ala Thr Cys 35 40 45 His Val Tyr Val Asn Glu Ala Phe Thr Asp Lys Val Pro Ala Ala Asn 50 55 60 Glu Arg Glu Ile Gly Met Leu Glu Cys Val Thr Ala Glu Leu Lys Pro 65 70 75 80 Asn Ser Arg Leu Cys Cys Gln Ile Ile Met Thr Pro Glu Leu Asp Gly 85 90 95 Ile Val Val Asp Val Pro Asp Arg Gln Trp 100 10514105PRTPseudomonas sp. 14 Pro Arg Val Val Phe Ile Asp Glu Gln Ser Gly Glu Tyr Ala Val Asp 1 5 10 15 Ala Gln Asp Gly Gln Ser Leu Met Glu Val Ala Thr Gln Asn Gly Val 20 25 30 Pro Gly Ile Val Ala Glu Cys Gly Gly Ser Cys Val Cys Ala Thr Cys 35 40 45 Arg Ile Glu Ile Glu Asp Ala Trp Val Glu Ile Val Gly Glu Ala Asn 50 55 60 Pro Asp Glu Asn Asp Leu Leu Gln Ser Thr Gly Glu Pro Met Thr Ala 65 70 75 80 Gly Thr Arg Leu Ser Cys Gln Val Phe Ile Asp Pro Ser Met Asp Gly 85 90 95 Leu Ile Val Arg Val Pro Leu Pro Ala 100 10515409PRTSphingomonas sp. 15 Met Arg Ser Ala Asp Val Val Ile Val Gly Ala Gly His Ala Gly Ala 1 5 10 15 Gln Cys Ala Ile Ala Leu Arg Gln Ala Gly Tyr Glu Gly Ser Ile Ala 20 25 30 Leu Val Gly Arg Glu Asn Glu Val Pro Tyr Glu Arg Pro Pro Leu Ser 35 40 45 Lys Glu Tyr Phe Ser Arg Glu Lys Ser Phe Glu Arg Leu Tyr Ile Arg 50 55 60 Pro Pro Glu Phe Trp Arg Glu Lys Asp Ile His Leu Thr Leu Gly Ile 65 70 75 80 Glu Val Ser Ala Val Asp Pro Gly Ser Lys Val Leu Thr Leu Ser Asp 85 90 95 Gly Ser Ala Phe Ala Tyr Gly Gln Leu Val Trp Ala Thr Gly Gly Asp 100 105 110 Pro Arg Lys Leu Ala Cys Pro Gly Ala Glu Leu Ser Gly Val His Ala 115 120 125 Ile Arg Thr Arg Ala Asp Cys Asp Arg Leu Met Ala Glu Ile Asp Arg 130 135 140 Gly Leu Thr Gln Val Val Val Val Gly Gly Gly Tyr Ile Gly Leu Glu 145 150 155 160 Ala Ala Ala Val Leu Thr Lys Leu Asn Cys His Val Thr Leu Leu Glu 165 170 175 Ala Met Pro Arg Val Leu Ala Arg Val Ala Gly Thr Glu Leu Ser Thr 180 185 190 Phe Tyr Glu Asn Glu His Arg Gly His Gly Val Asp Leu Arg Thr Gly 195 200 205 Ile Thr Val Ala Ala Leu Glu Gly Gln Glu Ser Val Thr Gly Val Arg 210 215 220 Leu Gly Asp Gly Ser Val Leu Pro Ala Gln Ala Val Ile Val Gly Ile 225 230 235 240 Gly Ile Val Pro Ala Val Ala Pro Leu Ile Glu Ala Gly Ala Ala Gly 245 250 255 Asp Gly Gly Val Thr Val Asp Glu Tyr Cys Arg Thr Ser Leu Pro Asp 260 265 270 Val Phe Ala Ile Gly Asp Cys Ala Ser Phe Ser Cys Ser Phe Ala Asp 275 280 285 Gly Arg Val Leu Arg Val Glu Ser Val Gln Asn Ala Asn Asp Gln Ala 290 295 300 Ser Cys Val Ala Lys Thr Ile Cys Gly Asp Pro Gln Pro Tyr Arg Ala 305 310 315 320 Phe Pro Trp Phe Trp Ser Asn Gln Tyr Asp Leu Arg Leu Gln Thr Ala 325 330 335 Gly Leu Ser Leu Gly Tyr Asp Gln Thr Val Val Arg Gly Asp Pro Ala 340 345 350 Val Arg Ser Phe Ser Val Leu Tyr Leu Lys Gln Gly Arg Val Ile Ala 355 360 365 Leu Asp Cys Val Asn Met Val Lys Asp Tyr Val Gln Gly Arg Lys Leu 370 375 380 Val Glu Ala Asn Val Cys Val Ser Pro Glu Gln Leu Val Asp Thr Gly 385 390 395 400 Leu Ala Leu Lys Asp Leu Ile Pro Val 40516427PRTRhodococcus erythropolis 16 Ser Ile Val Ile Ile Gly Ser Gly Gln Ala Gly Phe Glu Ala Ala Val 1 5 10 15 Ser Leu Arg Ser His Gly Phe Ser Gly Thr Ile Thr Leu Val Gly Asp 20 25 30 Glu Pro Gly Val Pro Tyr Gln Arg Pro Pro Leu Ser Lys Ala Tyr Leu 35 40 45 His Ser Asp Pro Asp Arg Glu Ser Leu Ala Leu Arg Pro Ala Gln Tyr 50 55 60 Phe Asp Asp His Arg Ile Thr Leu Thr Cys Gly Lys Pro Val Val Arg 65 70 75 80 Ile Asp Arg Asp Ala Gln Arg Val Glu Leu Ile Asp Ala Thr Ala Ile 85 90 95 Glu Tyr Asp His Leu Ile Leu Ala Thr Gly Ala Arg Asn Arg Leu Leu 100 105 110 Pro Val Pro Gly Ala Asn Leu Pro Gly Val His Tyr Leu Arg Thr Ala 115 120 125 Gly Glu Ala Glu Ser Leu Thr Ser Ser Met Ala Ser Cys Ser Ser Leu 130 135 140 Val Val Ile Gly Ala Gly Phe Ile Gly Leu Glu Val Ala Ala Ala Ala 145 150 155 160 Arg Lys Lys Gly Leu Asp Val Thr Val Val Glu Ala Met Asp Arg Pro 165 170 175 Met Ala Arg Ala Leu Ser Ser Val Met Ser Gly Tyr Phe Ser Thr Ala 180 185 190 His Thr Glu His Gly Val His Met Arg Leu Ser Thr Gly Val Lys Thr 195 200 205 Ile Asn Ala Ala Asp Gly Arg Ala Ala Gly Val Thr Thr Asn Ser Gly 210 215 220 Asp Val Ile His Ala Asp Ala Val Val Val Gly Ile Gly Val Val Pro 225 230 235 240 Asn Ile Glu Leu Ala Ala Leu Thr Gly Leu Pro Val Asp Asn Gly Ile 245 250 255 Val Val Asp Glu Tyr Leu Arg Thr Pro Asp Glu Asn Ile Ser Ala Ile 260 265 270 Gly Asp Cys Ala Ala Tyr Pro Ile Pro Gly Lys Ala Gly Leu Val Arg 275 280 285 Leu Glu Ser Val Gln Asn Ala Val Asp Gln Ala Arg Cys Leu Ala Ala 290 295 300 Gln Leu Thr Gly Thr Ser Thr His Tyr Arg Ser Val Pro Trp Phe Trp 305 310 315 320 Ser Glu Gln Tyr Glu Ser Lys Leu Gln Met Ala Gly Leu Thr Ala Gly 325 330 335 Ala Asp Thr His Val Val Arg Gly Ser Val Asp Ser Gly Val Phe Ser 340 345 350 Ile Phe Cys Phe Leu Gly Thr Arg Leu Leu Gly Val Glu Ser Val Asn 355 360 365 Lys Pro Arg Asp His Met Ala Ala Arg Lys Ile Leu Ala Thr Glu Met 370 375 380 Pro Leu Thr Pro Glu Gln Ala Ala Asp Thr Asp Phe Asp Leu Lys Leu 385 390 395 400 Ala Ile Ala Arg His Lys Asp Thr His Glu Lys Asp Glu Val Ala Ser 405 410 415 Ala Asp Ile Gly Glu Arg Gln Val Val Ala Ser 420 42517422PRTPseudomonas putida 17 Met Asn Ala Asn Asp Asn Val Val Ile Val Gly Thr Gly Leu Ala Gly 1 5 10 15 Val Glu Val Ala Phe Gly Leu Arg Ala Ser Gly Trp Glu Gly Asn Ile 20 25 30 Arg Leu Val Gly Asp Ala Thr Val Ile Pro His His Leu Pro Pro Leu 35 40 45 Ser Lys Ala Tyr Leu Ala Gly Lys Ala Thr Ala Glu Ser Leu Tyr Leu 50 55 60 Arg Thr Pro Asp Ala Tyr Ala Ala Gln Asn Ile Gln Leu Leu Gly Gly 65 70 75 80 Thr Gln Val Thr Ala Ile Asn Arg Asp Arg Gln Gln Val Ile Leu Ser 85 90 95 Asp Gly Arg Ala Leu Asp Tyr Asp Arg Leu Val Leu Ala Thr Gly Gly 100 105 110 Arg Pro Arg Pro Leu Pro Val Ala Ser Gly Ala Val Gly Lys Ala Asn 115 120 125 Asn Phe Arg Tyr Leu Arg Thr Leu Glu Asp Ala Glu Cys Ile Arg Arg 130 135 140 Gln Leu Ile Ala Asp Asn Arg Leu Val Val Ile Gly Gly Gly Tyr Ile 145 150 155 160 Gly Leu Glu Val Ala Ala Thr Ala Ile Lys Ala Asn Met His Val Thr 165 170 175 Leu Leu Asp Thr Ala Ala Arg Val Leu Glu Arg Val Thr Ala Pro Pro 180 185 190 Val Ser Ala Phe Tyr Glu His Leu His Arg Glu Ala Gly Val Asp Ile 195 200 205 Arg Thr Gly Thr Gln Val Cys Gly Phe Glu Met Ser Thr Asp Gln Gln 210 215 220 Lys Val Thr Ala Val Leu Cys Glu Asp Gly Thr Arg Leu Pro Ala Asp 225 230 235 240 Leu Val Ile Ala Gly Ile Gly Leu Ile Pro Asn Cys Glu Leu Ala Ser 245 250 255 Ala Ala Gly Leu Gln Val Asp Asn Gly Ile Val Ile Asn Glu His Met 260 265 270 Gln Thr Ser Asp Pro Leu Ile Met Ala Val Gly Asp Cys Ala Arg Phe 275 280 285 His Ser Gln Leu Tyr Asp Arg Trp Val Arg Ile Glu Ser Val Pro Asn 290 295 300 Ala Leu Glu Gln Ala Arg Lys Ile Ala Ala Ile Leu Cys Gly Lys Val 305 310 315 320 Pro Arg Asp Glu Ala Ala Pro Trp Phe Trp Ser Asp Gln Tyr Glu Ile 325 330 335 Gly Leu Lys Met Val Gly Leu Ser Glu Gly Tyr Asp Arg Ile Ile Val 340 345 350 Arg Gly Ser Leu Ala Gln Pro Asp Phe Ser Val Phe Tyr Leu Gln Gly 355 360 365 Asp Arg Val Leu Ala Val Asp Thr Val Asn Arg Pro Val Glu Phe Asn 370 375 380 Gln Ser Lys Gln Ile Ile Thr Asp Arg Leu Pro Val Glu Pro Asn Leu 385 390 395 400 Leu Gly Asp Glu Ser Val Pro Leu Lys Glu Ile Ile Ala Ala Ala Lys 405 410 415 Ala Glu Leu Ser Ser Ala 42018409PRTPseudomonas sp. 18 Met Gly Glu Arg Arg Asp Thr Thr Val Ile Val Gly Ala Gly His Ala 1 5 10 15 Gly Thr Ala Ala Ala Phe Phe Leu Arg Glu Phe Gly Tyr His Gly Arg 20 25 30 Val Leu Leu Leu Ser Ala Glu Thr Gln His Pro Tyr Gln Arg Pro Pro 35 40 45 Leu Ser Lys Glu Tyr Leu Leu Ala Gln His Ser Thr Pro Ser Leu Leu 50 55 60 Lys Gly Lys Asp Ser Tyr Ala Arg Ala Asp Ile Glu Leu Cys Leu Gln 65 70 75 80 Asp Asp Val Leu Ser Ile Thr Pro Ala Ser Arg Gln Val Lys Ser Ser 85 90 95 Gln Gly Ser Tyr Thr Tyr Asp His Leu Ile Leu Ala Thr Gly Ser His 100 105 110 Pro Arg Phe Met Ala Thr Leu Gly Gln Ala Asp Asn Leu Cys Tyr Leu 115 120 125 Ser Asp Trp Asp Asp Ala Gly Arg Ile Arg Gln Gln Leu Gly Glu Ala 130 135 140 Ser Arg Ile Val Val Leu Gly Gly Gly Phe Ile Gly Leu Glu Ile Ala 145 150 155 160 Ser Ser Ala Cys Lys Met Gly Lys His Val Thr Val Ile Glu Arg Ala 165 170 175 Pro Arg Leu Leu Ser Arg Val Val Ser Glu Ala Phe Ala Thr Phe Ile 180 185 190 Gly Asp Ile His Leu Gly Asn Gly Ile Glu Leu Arg Leu Gly Glu Glu 195 200 205 Val Arg Glu Val Arg Arg Cys Thr Ser Gly Val Arg Val Asp Ala Val 210 215 220 Phe Leu Ser Asp Gly Gln Leu Leu Glu Cys Asp Met Leu Val Ile Gly 225 230 235 240 Val Gly Ser Glu Pro Arg Met Glu Leu Ala Thr Ala Ala Gly Leu Ala 245 250 255 Cys Ala Ser Gly Val Leu Val Asp Glu His Cys His Thr Ser Asp Pro 260 265 270 Phe Ile Ser Ala Ile Gly Asp Cys Val Ala Val Cys Pro Ser Pro Gly 275 280 285 His Gln Leu Pro Arg Arg Glu Ser Val Gln Asn Ala Thr Glu Gln Ala 290 295 300 Arg Leu Val Ala Ala Arg Leu Ser Gly Arg Pro Val Pro Pro Val Gln 305 310 315 320 Thr Pro Trp Phe Trp Ser Asp Gln Leu Gln Ala Arg Ile Asn Leu Ala 325 330 335 Gly Glu Arg Pro Ala Gln Gly Gln Val Ile Val Arg Arg Tyr Gly Gly 340 345 350 Asp Lys Val Ser Met Leu Tyr Leu Gln Asp Gln Gln Leu Val Ala Ile 355 360 365 Glu Ala Cys Asn Met Pro Gly Asp Cys Leu Leu Ala Arg Arg Ala Ile 370 375 380 Gly Gln Asn His Ser Leu Asp Leu Ala Arg Leu Val Asp Ala Asp Val 385 390 395 400 Pro Leu Lys Asp Ala Leu His Phe Ala 405

Claims (108)

We claim:

1. An isolated DNA molecule comprising a DNA sequence coding for a dicamba-degrading oxygenase.

2. The DNA molecule ofclaim 1 comprising a DNA sequence coding for a dicamba-degrading oxygenase having the amino acid sequence of SEQ ID NO: 3.

3. The DNA molecule ofclaim 2 comprising the nucleotide sequence of SEQ ID NO: 2.

4. A DNA construct comprising a DNA sequence coding for a dicamba-degrading oxygenase operatively linked to expression control sequences.

5. The DNA construct ofclaim 4 comprising a DNA sequence coding for a dicamba-degrading oxygenase having the amino acid sequence of SEQ ID NO: 3.

6. The DNA construct ofclaim 5 comprising the nucleotide sequence of SEQ ID NO: 2.

7. The DNA construct ofclaim 4 which is a vector.

8. An isolated and at least partially purified dicamba-degrading oxygenase.

9. The dicamba-degrading oxygenase ofclaim 8 having the amino acid sequence of SEQ ID NO: 3.

10. An isolated DNA molecule comprising a DNA sequence coding for a dicamba-degrading ferredoxin.

11. The DNA molecule ofclaim 10 comprising a DNA sequence coding for a dicamba-degrading ferredoxin having the amino acid sequence of SEQ ID NO: 5.

12. The DNA molecule ofclaim 11 comprising the nucleotide sequence of SEQ ID NO: 4.

13. The DNA molecule ofclaim 11 comprising a nucleotide sequence which has codons selected for optimized expression in dicotyledonous plants.

14. A DNA construct comprising a DNA sequence coding for a dicamba-degrading ferredoxin operatively linked to expression control sequences.

15. The DNA construct ofclaim 14 comprising a DNA sequence coding for a dicamba-degrading ferredoxin having the amino acid sequence of SEQ ID NO: 5.

16. The DNA construct ofclaim 15 comprising the nucleotide sequence of SEQ ID NO: 4.

17. The DNA construct ofclaim 15 comprising a nucleotide sequence which has codons selected for optimized expression in dicotyledonous plants.

18. The DNA construct ofclaim 14 which is a vector.

19. An isolated and at least partially purified dicamba-degrading ferredoxin.

20. The dicamba-degrading ferredoxin ofclaim 19 which has the amino acid sequence of SEQ ID NO: 5.

21. An isolated DNA molecule comprising a DNA sequence coding for a dicamba-degrading reductase.

22. The DNA molecule ofclaim 21 comprising a DNA sequence coding for a dicamba-degrading reductase having the amino acid sequence of SEQ ID NO: 7.

23. The DNA molecule ofclaim 22 comprising the nucleotide sequence of SEQ ID NO: 6.

24. The DNA molecule ofclaim 21 comprising a DNA sequence coding for a dicamba-degrading reductase having the amino acid sequence of SEQ ID NO: 9.

25. The DNA molecule ofclaim 24 comprising the nucleotide sequence of SEQ ID NO: 8.

26. A DNA construct comprising a DNA sequence coding for a dicamba-degrading reductase operatively linked to expression control sequences.

27. The DNA construct ofclaim 26 comprising a DNA sequence coding for a dicamba-degrading reductase having the amino acid sequence of SEQ ID NO: 7.

28. The DNA construct ofclaim 27 comprising the nucleotide sequence of SEQ ID NO: 6.

29. The DNA construct ofclaim 26 comprising a DNA sequence coding for a dicamba-degrading reductase having the amino acid sequence of SEQ ID NO: 9.

30. The DNA construct ofclaim 29 comprising the nucleotide sequence of SEQ ID NO: 8.

31. The DNA construct ofclaim 26 which is a vector.

32. An isolated and at least partially purified dicamba-degrading reductase.

33. The dicamba-degrading reductase ofclaim 32 which has the amino acid sequence of SEQ ID NO: 7.

34. The dicamba-degrading reductase ofclaim 32 which has the amino acid sequence of SEQ ID NO: 9.

35. A DNA construct comprising a DNA sequence coding for a dicamba-degrading oxygenase, a DNA sequence coding for a dicamba-degrading ferredoxin, and a DNA sequence coding for a dicamba-degrading reductase, each DNA sequence being operatively linked to expression control sequences.

36. The DNA construct ofclaim 35 comprising a DNA sequence coding for a dicamba-degrading oxygenase having the amino acid sequence of SEQ ID NO: 3.

37. The DNA construct ofclaim 36 comprising the nucleotide sequence of SEQ ID NO: 2.

38. The DNA construct ofclaim 35 comprising a DNA sequence coding for a dicamba-degrading ferredoxin having the amino acid sequence of SEQ ID NO: 5.

39. The DNA construct ofclaim 38 comprising the nucleotide sequence of SEQ ID NO: 4.

40. The DNA construct ofclaim 38 comprising a nucleotide sequence which has codons selected for optimized expression in dicotyledonous plants.

41. The DNA construct ofclaim 35 comprising a DNA sequence coding for a dicamba-degrading reductase having the amino acid sequence of SEQ ID NO: 7.

42. The DNA construct ofclaim 41 comprising the nucleotide sequence of SEQ ID NO: 6.

43. The DNA construct ofclaim 35 comprising a DNA sequence coding for a dicamba-degrading reductase having the amino acid sequence of SEQ ID NO: 9.

44. The DNA construct ofclaim 43 comprising the nucleotide sequence of SEQ ID NO: 8.

45. The DNA construct ofclaim 35 which is a vector.

46. An isolated and at least partially purified dicamba-degrading O-demethylase.

47. A transgenic host cell comprising DNA coding for a dicamba-degrading oxygenase operatively linked to expression control sequences.

48. The transgenic host cell ofclaim 47 wherein the DNA codes for a dicamba-degrading oxygenase having the amino acid sequence of SEQ ID NO: 3.

49. The transgenic host cell ofclaim 48 wherein the DNA comprises the nucleotide sequence of SEQ ID NO: 2.

50. The transgenic host cell ofclaim 47 which is a plant cell.

51. The transgenic host cell ofclaim 47 which is a microorganism.

52. A transgenic host cell comprising DNA coding for a dicamba-degrading ferredoxin operatively linked to expression control sequences.

53. The transgenic host cell ofclaim 52 wherein the DNA codes for a dicamba-degrading ferredoxin having the amino acid sequence of SEQ ID NO: 5.

54. The transgenic host cell ofclaim 53 wherein the DNA comprises the nucleotide sequence of SEQ ID NO: 4.

55. The transgenic host cell ofclaim 53 wherein the DNA comprises a nucleotide sequence which has codons selected for optimized expression in dicotyledonous plants.

56. The transgenic host cell ofclaim 52 which is a plant cell.

57. The transgenic host cell ofclaim 52 which is a microorganism.

58. A transgenic host cell comprising DNA coding for a dicamba-degrading reductase operatively linked to expression control sequences.

59. The transgenic host cell ofclaim 58 wherein the DNA codes for a dicamba-degrading reductase having the amino acid sequence of SEQ ID NO: 7.

60. The transgenic host cell ofclaim 59 wherein the DNA comprises the nucleotide sequence of SEQ ID NO: 6.

61. The transgenic host cell ofclaim 58 wherein the DNA codes for a dicamba-degrading reductase having the amino acid sequence of SEQ ID NO: 9.

62. The transgenic host cell ofclaim 61 wherein the DNA comprises the nucleotide sequence of SEQ ID NO: 8.

63. The transgenic host cell ofclaim 58 which is a plant cell.

64. The transgenic host cell ofclaim 58 which is a microorganism.

65. A transgenic host cell comprising a first DNA coding for a dicamba-degrading oxygenase and a second DNA coding for a dicamba-degrading ferredoxin, a third DNA coding for a dicamba-degrading reductase, or both the second DNA and the third DNA, each DNA being operatively linked to expression control sequences.

66. The transgenic host cell ofclaim 65 wherein the first DNA codes for a dicamba-degrading oxygenase having the amino acid sequence of SEQ ID NO: 3.

67. The transgenic host cell ofclaim 66 wherein the first DNA comprises the nucleotide sequence of SEQ ID NO: 2.

68. The transgenic host cell ofclaim 65 wherein the second DNA codes for a dicamba-degrading ferredoxin having the amino acid sequence of SEQ ID NO: 5.

69. The transgenic host cell ofclaim 68 wherein the second DNA comprises the nucleotide sequence of SEQ ID NO: 4.

70. The transgenic host cell ofclaim 68 wherein the second DNA comprises a nucleotide sequence which has codons selected for optimized expression in dicotyledonous plants.

71. The transgenic host cell ofclaim 65 wherein the third DNA codes for a dicamba-degrading reductase having the amino acid sequence of SEQ ID NO: 7.

72. The transgenic host cell ofclaim 71 wherein the third DNA comprises the nucleotide sequence of SEQ ID NO: 6.

73. The transgenic host cell ofclaim 65 wherein the third DNA codes for a dicamba-degrading reductase having the amino acid sequence of SEQ ID NO: 9.

74. The transgenic host cell ofclaim 73 wherein the third DNA comprises the nucleotide sequence of SEQ ID NO: 8.

75. The transgenic host cell ofclaim 65 which is a plant cell.

76. The transgenic host cell ofclaim 65 which is a microorganism.

77. A transgenic plant or part of a plant comprising one or more cells comprising DNA coding for a dicamba-degrading oxygenase operatively linked to expression control sequences.

78. The transgenic plant or plant part ofclaim 77 wherein the DNA codes for a dicamba-degrading oxygenase having the amino acid sequence of SEQ ID NO: 3.

79. The transgenic plant or plant part ofclaim 78 wherein the DNA comprises the nucleotide sequence of SEQ ID NO: 2.

80. The transgenic plant or plant part ofclaim 77 wherein the plant is a broadleaf plant which is tolerant to dicamba.

81. A transgenic plant or part of a plant comprising one or more cells comprising DNA coding for a dicamba-degrading ferredoxin operatively linked to expression control sequences.

82. The transgenic plant or plant part ofclaim 81 wherein the DNA codes for a dicamba-degrading ferredoxin having the amino acid sequence of SEQ ID NO: 5.

83. The trangenic plant or plant part ofclaim 82 wherein the DNA comprises the nucleotide sequence of SEQ ID NO: 4.

84. The trangenic plant or plant part ofclaim 82 wherein the DNA comprises a nucleotide sequence which has codons selected for optimized expression in dicotyledonous plants.

85. The transgenic plant or plant part ofclaim 81 wherein the plant is a broadleaf plant which is tolerant to dicamba.

86. A transgenic plant or part of a plant comprising one or more cells comprising DNA coding for a dicamba-degrading reductase operatively linked to expression control sequences.

87. The transgenic plant or plant part ofclaim 86 wherein the DNA codes for a dicamba-degrading reductase having the amino acid sequence of SEQ ID NO: 7.

88. The trangenic plant or plant part ofclaim 87 wherein the DNA comprises the nucleotide sequence of SEQ ID NO: 6.

89. The transgenic plant or plant part ofclaim 86 wherein the DNA codes for a dicamba-degrading reductase having the amino acid sequence of SEQ ID NO: 9.

90. The trangenic plant or plant part ofclaim 89 wherein the DNA comprises the nucleotide sequence of SEQ ID NO: 8.

91. The transgenic plant or plant part ofclaim 86 wherein the plant is a broadleaf plant which is tolerant to dicamba.

92. A transgenic plant or part of a plant comprising one or more cells comprising a first DNA coding for a dicamba-degrading oxygenase and a second DNA coding for a dicamba-degrading ferredoxin, a third DNA coding for a dicamba-degrading reductase, or both the second DNA and the third DNA, each DNA being operatively linked to expression control sequences.

93. The transgenic plant or plant part ofclaim 92 wherein the first DNA codes for a dicamba-degrading oxygenase having the amino acid sequence of SEQ ID NO: 3.

94. The transgenic plant or plant part ofclaim 93 wherein the first DNA comprises the nucleotide sequence of SEQ ID NO: 2.

95. The transgenic plant or plant part ofclaim 92 wherein the second DNA codes for a dicamba-degrading ferredoxin having the amino acid sequence of SEQ ID NO: 5.

96. The trangenic plant or plant part ofclaim 95 wherein the second DNA comprises the nucleotide sequence of SEQ ID NO: 4.

97. The trangenic plant or plant part ofclaim 95 wherein the second DNA comprises a nucleotide sequence which has codons selected for optimized expression in dicotyledonous plants.

98. The transgenic plant or plant part ofclaim 92 wherein the third DNA codes for a dicamba-degrading reductase having the amino acid sequence of SEQ ID NO: 7.

99. The transgenic plant or plant part ofclaim 98 wherein the third DNA comprises the nucleotide sequence of SEQ ID NO: 6.

100. The transgenic plant or plant part ofclaim 92 wherein the third DNA codes for a dicamba-degrading reductase having the amino acid sequence of SEQ ID NO: 9.

101. The transgenic plant or plant part ofclaim 100 wherein the third DNA comprises the nucleotide sequence of SEQ ID NO: 8.

102. The transgenic plant or plant part ofclaim 92 wherein the plant is a broadleaf plant which is tolerant to dicamba.

103. A method of controlling weeds in a field containing a dicamba-tolerant transgenic plant, the method comprising applying an amount of dicamba to the field effective to control the weeds in the field.

104. A method of decontaminating a material containing dicamba comprising applying an amount of a dicamba-degrading transgenic microorganism to the material, the amount being effective to degrade at least some of the dicamba in the material.

105. A method of decontaminating a material containing dicamba comprising applying an amount of a dicamba-degrading O-demethylase or of a combination of a dicamba-degrading oxygenase, a dicamba-degrading ferredoxin and a dicamba-degrading reductase to the material, the amount being effective to degrade at least some of the dicamba in the material.

106. A method of selecting transformed plant cells comprising:

providing a population of plant cells;

transforming at least some of the plant cells in the population of plant cells so that they are tolerant to dicamba; and

growing the resulting population of plant cells in a culture medium containing dicamba at a concentration selected so that transformed plant cells will grow and untransformed plant cells will not grow.

107. A method of selecting transformed plants comprising:

providing a population of plants suspected of comprising plants that have been transformed so that they are tolerant to dicamba; and

applying an amount of dicamba to the population of plants, the amount of dicamba being selected so that transformed plants will grow and growth of untransformed plants will be inhibited.

108. A method of selecting, or screening for, transformed host cells, intact organisms, and parts of organisms, the method comprising:

providing a population of host cells, intact organisms, or parts of organisms suspected of comprising host cells, intact organisms, or parts of organisms that have been transformed so that they are able to degrade dicamba;

contacting the population of host cells, intact organisms, or parts of organisms with dicamba; and

ascertaining the presence or level of fluorescence due to 3,6-dichlorosalicylic acid, the 3,6-dichlorosalicyclic acid being generated in the host cells, intact organisms, or parts of organisms as a result of the degradation of dicamba.

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