# Patent

## Title
Cells, nucleic acids, enzymes and use thereof, and methods for the production of sophorolipids

## Abstract

The invention relates to cells, nucleic acids, and enzymes, the use thereof for producing sophorolipids, and methods for producing sophorolipids.

## Background
FIELD OF THE INVENTION
The invention relates to nucleic acids, enzymes and cells and to their use for producing sophorolipids, and also to processes for producing sophorolipids.
PRIOR ART
Currently the production of surfactants is essentially based on the basis of petrochemical raw materials. The utilization of surfactants based on renewable raw materials is a suitable alternative due to the foreseeable shortage of petrochemical raw materials and the increasing demand for products which are based on renewable raw materials and/or which are biodegradable.
Sophorolipids have the surface-active properties required for use as a surfactant.
These lipids are currently produced using wild-type isolates of a variety of yeasts, in particular Candida bombicola. 
Performance parameters of product formation, such as carbon yield, space-time yield, product concentration, product homogeneity (degree of acetylation, fatty acid species, lactone form vs. open-chain form) have to date been improved exclusively via the optimization of the process control (pH, oxygen supply, media composition, feeding strategies, nitrogen supply, temperature, choice of substrate and the like).
The only exception is the genetic modification of Candida bombicola in as far as β-oxidation has been eliminated so that triglycerides, fatty acids, fatty alcohols and the like which are fed by way of substrate can no longer be utilized as a carbon source, in other words degraded (Van Bogaert et al. FEMS Yeast Res. 2009 June; 9(4):610-7). In this manner, it should be possible, by choosing the substrate, specifically to control the fatty acid moiety of the sophorolipids in order to influence the product properties.
Since the improvement of performance parameters in the biotechnological production of sophorolipids via optimizing the process control is possible to a limited extent only, the cells also have to be subjected to genetic modification.
This comprises, firstly, the enhancement of the enzymes involved in sophorolipid synthesis: cytochrome P450 monooxygenase, glycosyltransferase I, glycosyltransferase II, acetyltransferase, sophorolipid exporter with the aim of improving the performance parameters of product formation such as carbon yield, space-time yield, product concentration, product homogeneity (degree of acetylation, fatty acid species) and the like.
This secondly comprises attenuating some of the enzymes involved in sophorolipid synthesis: glycosyltransferase II, acetyltransferase with the aim of modifying the structure and the properties of the sophorolipids produced: glycosyltransferase II: production of monoglycosyl-sophorolipids; acetyltransferase: production of nonacetylated sophorolipids.
If sophorolipids are to be employed on a large scale as surfactants in cleaning applications, cosmetic applications and other applications, they will have to compete with the currently employed surfactants. The latter are bulk chemicals which can be produced at very low cost. Therefore, sophorolipids must be produced at the lowest possible costs. This is not possible by merely optimizing the performance parameters via process optimization.
There is therefore an increasing demand for efficient productions of sophorolipids with high product yields.
The present invention was therefore based on the problem of providing tools and/or processes with the aid of which specific sophorolipids can be synthesized in a simple manner and in large amounts.
DESCRIPTION OF THE INVENTION
Surprisingly, it has been found that the cells, nucleic acids, polypeptides and processes described hereinbelow are capable of solving the above problem.
The subject matter of the present invention are, therefore, genetically modified cells with a modified enzymatic equipment for the synthesis of sophorolipids.
A further subject matter of the invention are novel nucleic acids and vectors as described in claims 11 and 12.
Yet another subject matter of the present invention are novel enzymes which are useful in sophorolipid biosynthesis.
The advantage of the present invention is that not only are the performance parameters of sophorolipid formation, such as carbon yield and space-time yield, improved, but also that the product homogeneity as regards for example the degree of acetylation and the fatty acid species can be improved.
A subject matter of the invention is a cell which is capable of forming sophorolipids, which cell has been genetically modified in such a way that it has an activity, as specified in each case hereinbelow, of at least one of the enzymes selected from the group hereafter, which activity is modified in comparison with its wild type:
at least one enzyme E1 with the polypeptide sequence SEQ ID NO:7, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61 or SEQ ID NO:63, in particular SEQ ID NO:7, or with a polypeptide sequence where up to 25%, preferably up to 20%, especially preferably up to 15%, in particular up to 10, 9, 8, 7, 6, 5, 4, 3, 2, 1% of the amino acid residues are modified over the respective reference sequence SEQ ID NO:7, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61 or SEQ ID NO:63, in particular SEQ ID NO:7, by deletion, insertion, substitution or a combination of these and which retains at least 50%, preferably 65%, especially preferably 80%, in particular more than 90% of the enzymatic activity of the enzyme with the respective reference sequence SEQ ID NO:7, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61 or SEQ ID NO:63, where enzymatic activity for an enzyme E1 is understood as meaning the ability to convert Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid,
at least one enzyme E2 with the polypeptide sequence SEQ ID NO:8 or SEQ ID NO:11 or with a polypeptide sequence where up to 60%, preferably up to 25%, especially preferably up to 15%, in particular up to 10, 9, 8, 7, 6, 5, 4, 3, 2, 1% of the amino acid residues are modified over SEQ ID NO:8 or SEQ ID NO:11 by deletion, insertion, substitution or a combination of these and which retains at least 50%, preferably 65%, especially preferably 80%, in particular more than 90% of the enzymatic activity of the enzyme with the respective reference sequence SEQ ID NO:8 or SEQ ID NO:11, where enzymatic activity for an enzyme E2 is understood as meaning the ability to convert UDP-glucose and 17-hydroxy-Z-9-octadecenoic acid into 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid,
at least one enzyme E3 with the polypeptide sequence SEQ ID NO:11 or with a polypeptide sequence where up to 60%, preferably up to 25%, especially preferably up to 15%, in particular up to 10, 9, 8, 7, 6, 5, 4, 3, 2, 1% of the amino acid residues are modified over SEQ ID NO:11 by deletion, insertion, substitution or a combination of these and which retains at least 50%, preferably 65%, especially preferably 80%, in particular more than 90% of the enzymatic activity of the enzyme with the reference sequence SEQ ID NO:11, where enzymatic activity for an enzyme E3 is understood as meaning the ability to convert 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and UDP-glucose into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid,
at least one enzyme E4 with the polypeptide sequence SEQ ID NO:9 or with a polypeptide sequence where up to 50%, preferably up to 25%, especially preferably up to 15%, in particular up to 10, 9, 8, 7, 6, 5, 4, 3, 2, 1% of the amino acid residues are modified over SEQ ID NO:9 by deletion, insertion, substitution or a combination of these and which retains at least 50%, preferably 65%, especially preferably 80%, in particular more than 90% of the enzymatic activity of the enzyme with SEQ ID NO:9, where enzymatic activity for an enzyme E4 is understood as meaning the ability to convert 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate or 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate or 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate, with the first option being preferred,
at least one enzyme E5 with the polypeptide sequence SEQ ID NO:10 or with a polypeptide sequence where up to 45%, preferably up to 25%, especially preferably up to 15% and in particular up to 10, 9, 8, 7, 6, 5, 4, 3, 2, 1% of the amino acid residues are modified over SEQ ID NO:10 by deletion, insertion, substitution or a combination of these and which retains at least 50%, preferably 65%, especially preferably 80%, in particular more than 90% of the enzymatic activity of the enzyme with SEQ ID NO:10, where enzymatic activity for an enzyme E5 is understood as meaning the ability to transfer a sophorolipid out of a cell into the surrounding medium.
In the context of the present invention, the expression “sophorolipids” is understood as meaning compounds of the general formulae (Ia) and (Ib)




in which

    R1=H or CO—CH3,
    R2=H or CO—CH3,
    R3=a divalent organic moiety which comprises 6 to 32 carbon atoms and which is unsubstituted or substituted by hydroxyl functions, is unbranched and optionally comprises one to three double or triple bonds,
    R4=H, CH3 or a monovalent organic radical which comprises 2 to 10 carbon atoms and which is unsubstituted or substituted by hydroxyl functions, which is unbranched and which optionally comprises one to three double or triple bonds, and
    n=1 or 0.


In connection with the present invention, a “wild type” of a cell is preferably understood as meaning the original strain from which the cell according to the invention has been developed as the result of recombinant manipulation of the genetic elements which are responsible for the activities of the enzymes of the abovementioned Seq ID Nos.
The expression “modified activity of an enzyme” is preferably understood as meaning modified intracellular activity.
Modifications of amino acid residues of a given polypeptide sequence which do not lead to any substantial modifications of the properties and function of the given polypeptide are known to a person skilled in the art. Thus, for example, it is possible to exchange what are known as conserved amino acids for each other; examples of such suitable amino acid substitutions are: Ala for Ser; Arg for Lys; Asn for Gln or His; Asp for Glu; Cys for Ser; Gln for Asn; Glu for Asp; Gly for Pro; His for Asn or Gln; Ile for Leu or Val; Leu for Met or Val; Lys for Arg or Gln or Glu; Met for Leu or Ile; Phe for Met or Leu or Tyr; Ser for Thr; Thr for Ser; Trp for Tyr; Tyr for Trp or Phe; Val for Ile or Leu. Likewise, it is known that modifications in particular at the N- or C-terminal end of a polypeptide in the form of, for example, amino acid insertions or deletions frequently have no substantial effect on the function of the polypeptide.
The activity of an enzyme E1 can be determined by disrupting, in a manner known to the skilled worker, cells which comprise this activity, for example with the aid of a ball mill, a French press or an ultrasonic disintegrator, and intact cells, cell debris and disruption aids such as, for example, glass beads can subsequently be removed by centrifugation for 10 minutes at 13 000 rpm and 4° C. Then, enzyme assays followed by LC-ESI-MS detection of the products can be carried out with the resulting cell-free crude extract. As an alternative, the enzyme can be concentrated or else purified until homogeneous in a manner known to a person skilled in the art by chromatographic methods (such as nickel/nitrilotriacetic acid affinity chromatography, streptavidin affinity chromatography, gel filtration chromatography or ion-exchange chromatography). A standard assay can be carried out in a total volume of 200 μl of 200 mM sodium phosphate buffer (pH 7.4), 0.5 mM NADPH, 0.5 mM dithiothreitol, 3 mM glucose 6-phosphate and 0.5 U glucose-6-phosphate dehydrogenase and 50 μl of crude protein extract (approx. 1 mg of total protein) or purified protein in solution (10 μg of purified protein). The reaction is started by the addition of a) 5 μl of a 10 mM solution of the substrate (Z-9-octadecenoic acid) in ethanol or of b) 5 μl of a 10 mM solution of the substrate (Z-9-octadecenoic acid) in 0.1% Triton X-100 which had previously been pretreated by two sonication treatments for in each case 30 seconds, and incubated for 30 minutes at 30° C. Thereafter, the reaction is extracted with 200 μl of ethyl acetate. Undissolved components are sedimented, phase separation is brought about by brief centrifugation (5 minutes at 16 100 g) and the ethyl acetate phase is analyzed by means of LC-ESI-MS. The products are identified by analyzing the relevant mass trajectories and the MS2 spectra.
The activity of an enzyme E2 can be determined by disrupting, in a manner known to the skilled worker, cells which comprise this activity, for example with the aid of a ball mill, a French press or an ultrasonic disintegrator, and intact cells, cell debris and disruption aids such as, for example, glass beads can subsequently be removed by centrifugation for 10 minutes at 13 000 rpm and 4° C. Then, enzyme assays followed by LC-ESI-MS detection of the products can be carried out with the resulting cell-free crude extract. As an alternative, the enzyme can be concentrated or else purified until homogeneous in a manner known to a person skilled in the art by chromatographic methods (such as nickel/nitrilotriacetic acid affinity chromatography, streptavidin affinity chromatography, gel filtration chromatography or ion-exchange chromatography). A standard assay can consist of 185 μl of 10 mM Tris-HCl (pH 7.5), 10 μl of 125 mM UDP-glucose and 50 μl of crude protein extract (approx. 1 mg of total protein) or purified protein in solution (10 μg of purified protein). The reaction is started by the addition of a) 5 μl of a 10 mM solution of the substrate (such as, for example, 18-hydroxy-Z-9-octadecenoic acid) in ethanol or of b) 5 μl of a 10 mM solution of the substrate (such as, for example, 18-hydroxy-Z-9-octadecenoic acid) in 0.1% Triton X-100 which had previously been pretreated by two sonication treatments for in each case 30 seconds and incubated for 30 minutes at 30° C. Thereafter, the reaction is extracted with 200 μl of ethyl acetate. Undissolved components are sedimented, phase separation is brought about by brief centrifugation (5 minutes at 16 100 g) and the ethyl acetate phase is analyzed by means of LC-ESI-MS. The products are identified by analyzing the relevant mass trajectories and the MS2 spectra. In this assay it is preferred to employ, as the substrate, 18-hydroxy-Z-9-octadecenoic acid because it is commercially available and because it has already been demonstrated variously that the enzymes of the sophorolipid biosynthesis accept, as substrate, not only 18-hydroxy-Z-9-octadecenoic acid, 17-hydroxy-Z-9-octadecenoic acid and also hydroxy fatty acids of different chain lengths (saturated or unsaturated) and hydroxylated on the ω- or ω−1-carbon, but also the mono- and diglucosides generated therefrom during sophorolipid biosynthesis (Asmer, H. J., Lang, S., Wagner, F., Wray, V. (1988). Microbial production, structure elucidation and bioconversion of sophorose lipids. J. Am. Oil Chem. Soc. 65:1460-1466; Nunez, A., Ashby, R., Foglia, T. A. et al. (2001). Analysis and characterization of sophorolipids by liquid chromatography with atmospheric pressure chemical ionization. Chromatographia 53:673-677; Ashby, R. D., Solaiman, D. K., Foglia, T. A. (2008). Property control of sophorolipids: influence of fatty acid substrate and blending. Biotechnology Letters 30:1093-1100).
The activity of an enzyme E3 can be determined by disrupting, in a manner known to the skilled worker, cells which comprise this activity, for example with the aid of a ball mill, a French press or an ultrasonic disintegrator, and intact cells, cell debris and disruption aids such as, for example, glass beads can subsequently be removed by centrifugation for 10 minutes at 13 000 rpm and 4° C. Then, enzyme assays followed by LC-ESI-MS detection of the products can be carried out with the resulting cell-free crude extract. As an alternative, the enzyme can be concentrated or else purified until homogeneous in a manner known to a person skilled in the art by chromatographic methods (such as nickel/nitrilotriacetic acid affinity chromatography, streptavidin affinity chromatography, gel filtration chromatography or ion-exchange chromatography). A standard assay can consist of 185 μl of 10 mM Tris-HCl (pH 7.5), 10 μl of 125 mM UDP-glucose and 50 μl of crude protein extract (approx. 1 mg of total protein) or purified protein in solution (10 μg of purified protein). The reaction is started by the addition of a) 5 μl of a 10 mM solution of the substrate (such as, for example, 18-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid) in ethanol or of b) 5 μl of a 10 mM solution of the substrate (18-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid) in 0.1% Triton X-100 which had previously been pretreated by two sonication treatments for in each case 30 seconds or c) by addition of the reaction mixture described for the activity determination of the enzyme E2, and incubated for 30 minutes at 30° C. Thereafter, the reaction is extracted with 200 μl (substrate added, as described in a) and b)) or 400 μl (substrate added, as described in c)) of ethyl acetate. Undissolved components are sedimented, phase separation is brought about by brief centrifugation (5 minutes at 16 100 g) and the ethyl acetate phase is analyzed by means of LC-ESI-MS. The products are identified by analyzing the relevant mass trajectories and the MS2 spectra. In this assay it is preferred to employ, as the substrate, because its precursor molecule 18-hydroxy-Z-9-octadecenoic acid is commercially available and because it has already been demonstrated variously that the enzymes of the sophorolipid biosynthesis accept, as substrate, not only 18-hydroxy-Z-9-octadecenoic acid, 17-hydroxy-Z-9-octadecenoic acid and also hydroxy fatty acids of different chain lengths (saturated or unsaturated) and hydroxylated on the ω- or ω−1-carbon, but also the mono- and diglucosides generated therefrom during sophorolipid biosynthesis.
The activity of an enzyme E4 can be determined by disrupting, in a manner known to the skilled worker, cells which comprise this activity, for example with the aid of a ball mill, a French press or an ultrasonic disintegrator, and intact cells, cell debris and disruption aids such as, for example, glass beads can subsequently be removed by centrifugation for 10 minutes at 13 000 rpm and 4° C. Then, enzyme assays followed by LC-ESI-MS detection of the products can be carried out with the resulting cell-free crude extract. As an alternative, the enzyme can be concentrated or else purified until homogeneous in a manner known to a person skilled in the art by chromatographic methods (such as nickel/nitrilotriacetic acid affinity chromatography, streptavidin affinity chromatography, gel filtration chromatography or ion-exchange chromatography). A standard assay can consist of 185 μl of 10 mM Tris-HCl (pH 7.5), 2.5 μl of 100 mM acetyl-coenzyme A and 50 μl of crude protein extract (approx. 1 mg of total protein) or purified protein in solution (10 μg of purified protein). The reaction is started by the addition of a) 5 μl of a 10 mM solution of the substrate (chemically deacetylated sophorolipids) in ethanol or of b) 5 μl of a 10 mM solution of the substrate (chemically deacetylated sophorolipids) in 0.1% Triton X-100 which had previously been pretreated by two sonication treatments for in each case 30 seconds, or c) by addition of the reaction mixture described for the activity determination of the enzyme E3 (in the manner of the substrate addition described therein under c) followed by incubation for 30 minutes at 30° C.), and incubated for 30 minutes at 30° C. Thereafter, the reaction is extracted with 200 μl (substrate added as described in a) and b)) or 600 μl (substrate added as described in c)) of ethyl acetate. Undissolved components are sedimented, phase separation is brought about by brief centrifugation (5 minutes at 16 100 g) and the ethyl acetate phase is analyzed by means of LC-ESI-MS. The products are identified by analyzing the relevant mass trajectories and the MS2 spectra. It is preferred in accordance with the invention that the enzyme E4 not only accepts as substrates the lactone forms of the sophorolipids as chosen here for the reference activities, but is also capable of at least monoacetylating the acid form of the sophorolipids at suitable sites, as shown in general in formula (Ia) where R1 and R2=H.
The modified activity of an enzyme E5 in comparison with its wild type can be determined in the simplest manner indirectly via the absolute amount of enzyme E5 per cell, since it can be assumed that an increased presence causes an increased activity and a reduced presence a reduced activity based on the cell and that these relationships are directly dependent on each other. The modified presence of the enzyme E5 in comparison with the wild type can be determined by conventional methods. Thus, the protein concentration can be analyzed by Western Blot hybridization with an antibody which is specific for the protein to be detected (Sambrook et al., Molecular Cloning: a laboratory manual, 2nd Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. USA, 1989), followed by visual evaluation with suitable software for the concentration determination (Lohaus and Meyer (1989) Biospektrum, 5: 32-39; Lottspeich (1999), Angewandte Chemie 111: 2630-2647).
Cells which are preferred in accordance with the invention are microorganisms, preferably bacterial cells, yeast cells or fungal cells, with Ascomycetes of the genera Candida and Wickerhamiella, in particular Candida bombicola, Candida bogoriensis, Candida batistae, Candida apicola and Wickerhamiella domericqiae being especially preferred.
The strains Candida bombicola ATCC 22214, Candida bogoriensis NRRL Y-5980, Candida batistae CBS 8550, Candida apicola IMET 42747 and Wickerhamiella domericqiae, in particular, are especially suitable cells.
Since the sophorolipids are formed by the cell according to the invention starting from glucose and fatty acids, it is advantageous when cells according to the invention are at least partially blocked in their β-oxidation since this prevents the outflow of substrate and therefore makes possible higher product concentrations and carbon yields. Candida cells which are blocked in their β-oxidation are described for example in WO 03/100013, Candida bombicola cells which are blocked in the β-oxidation in Van Bogaert et al. FEMS Yeast Res. 2009 June; 9(4):610-7.
In cells which are preferred in accordance with the invention, the modified enzyme activity is preferably an increased enzyme activity.
In accordance with the invention, preferred cells are those which show increased activities of the following enzyme combinations:
E1E2, E1E3, E1E4, E1E5, E2E3, E2E4, E2E5, E3E4, E3E5, E4E5, E1E2E3, E1E2E4, E1E2E5, E1E3E4, E1E3E5, E1E4E5, E2E3E4, E2E4E5, E3E4E5, E1E2E3E4, E2E3E4E5, E1E3E4E5, E1E2E4E5, E1E2E3E5, E1E2E3E4 and E1E2E3E4E5,
with the combinations
E1E2, E1E3, E1E4, E1E5, E2E3, E2E4, E2E5, E3E4, E3E5, E4E5, E1E2E3, E1E2E4, E1E2E5, E1E3E4, E1E3E5, E1E4E5, E2E3E4, E2E4E5, E3E4E5 and E1E2E3E4E5,
in particular
E1E2, E1E3, E1E4, E1E5, E2E3, E2E4, E2E5, E3E4, E3E5, E4E5 and E1E2E3E4E5 
being preferred.
To prepare sophorolipids of the general formula (Ia) where n=0, as little as possible enzymatic activity of an enzyme E3 should be present in the cell. Thus, in a specific embodiment of the cell according to the invention, the modified activity of an enzyme E3 is a reduced activity.
Cells which are preferred in accordance with the invention in this context are those which show a reduced activity of an enzyme E3 and optionally simultaneously an increased activity of at least one of the enzymes E1, E2, E4 and E5 and which show in particular besides the reduced activity of an enzyme E3 an increased activity of the following enzyme combinations:
E1E2, E1E4, E1E5, E2E4, E2E5, E4E5, E1E2E4, E1E2E5, E1E4E5 and E1E2E4E5,
especially preferably
E1E2, E1E4, E1E5, E2E4, E2E5, E4E5 and E1E2E4E5.
In this context, the cell according to the invention is preferably a Candida bombicola, Candida bogoriensis, Candida batistae, Candida apicola or Wickerhamiella domericgiae cell.
Furthermore preferred in this context are cells according to the invention in which the reduction of the enzymatic activity is achieved by the modification of a gene comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO:6 and a sequence which is to at least 80%, especially preferably to at least 90%, more preferably to at least 95% and most preferably to at least 99% identical to the reference sequence SEQ ID NO:6, where the modification is selected from the group comprising, preferably consisting of,
insertion of foreign DNA into the gene, deletion of at least portions of the gene, point mutations in the gene sequence, RNA interference (siRNA), antisense RNA or modification (insertion, deletion or point mutations) of regulatory sequences which flank the gene.
A nucleic acid which is suitable for the preparation of such cells is, for example, one with the SEQ ID NO:16, which is also subject matter of the invention.
To prepare sophorolipids of the general formula (Ia) or (Ib) where R1 and R2 equal H, as little as possible enzymatic activity of an enzyme E4 should be present in the cell. Thus, in a specific embodiment of the cell according to the invention, the modified activity of an enzyme E4 is a reduced activity.
In this context, cells which are preferred in accordance with the invention are those which show a reduced activity of at least one enzyme E4 and which optionally simultaneously show an increased activity of at least one of the enzymes E1, E2, E3 and E5 and which show in particular besides the reduced activity of an enzyme E4 an increased activity of the following enzyme combinations:
E1E2, E1E3, E1E5, E2E3, E2E5, E3E5, E1E2E3, E1E2E5, E1E3E5 and E1E2E3E5,
especially preferably
E1E2, E1E3, E1E5, E2E3, E2E5, E3E5 and E1E2E3E5.
In this context, the cell according to the invention is preferably a Candida bombicola, Candida bogoriensis, Candida batistae, Candida apicola or Wickerhamiella domericgiae cell.
Furthermore preferred in this context are cells according to the invention in which the reduction of the enzymatic activity is achieved by the modification of a gene comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO:4 and a sequence which is to at least 80%, especially preferably to at least 90%, more preferably to at least 95% and most preferably to at least 99% identical to SEQ ID NO:4,
where the modification is selected from the group comprising, preferably consisting of,
insertion of foreign DNA into the gene, deletion of at least portions of the gene, point mutations in the gene sequence, RNA interference (siRNA), antisense RNA or modification (insertion, deletion or point mutations) of regulatory sequences which flank the gene.
A nucleic acid which is suitable for the preparation of such cells is, for example, one with the SEQ ID NO:14, which is also subject matter of the invention.
To prepare sophorolipids of the general formula (Ia) where n=0 and R1 equals H, as little as possible enzymatic activity of the enzymes E3 and E4 should be present in the cell. Thus, in a specific embodiment of the cell according to the invention, the modified activity of the enzymes E3 and E4 is a reduced activity.
In this context, cells which are preferred in accordance with the invention are those which show a reduced activity of in each case at least one enzyme E3 and E4 and which simultaneously show an increased activity of at least one of the enzymes E1, E2 and E5 and which show in particular besides the reduced activity of the in each case at least one enzyme E3 and E4 an increased activity of the following enzyme combinations:
E1E2, E1E5, E2E5, E1E2E5,
especially preferably
E1E2, E1E5 and E2E5.
In this context, the cell according to the invention is preferably a Candida bombicola, Candida bogoriensis, Candida batistae, Candida apicola or Wickerhamiella domericqiae cell.
Furthermore preferred in this context are cells according to the invention in which the reduction of the enzymatic activity is achieved by the modification of a gene comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO:4 and a sequence which is to at least 80%, especially preferably to at least 90%, more preferably to at least 95% and most preferably to at least 99% identical to SEQ ID NO:4 and
of a gene comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO:6 and a sequence which is to at least 80%, especially preferably to at least 90%, more preferably to at least 95% and most preferably to at least 99% identical to the reference sequence SEQ ID NO:6,
where the modification is selected from the group comprising, preferably consisting of,
insertion of foreign DNA into the gene, deletion of at least portions of the gene, point mutations in the gene sequence, RNA interference (siRNA), antisense RNA or modification (insertion, deletion or point mutations) of regulatory sequences which flank the genes.
Nucleic acids which are suitable for preparing such cells are, for example, those of SEQ ID NO:14 and 16.
What will be said hereinbelow regarding the increasing of the enzyme activity in cells applies both to increasing the activity of the enzymes E1 to E5 and to all enzymes mentioned hereinbelow whose activity may optionally be increased.
In principle, an increase of the enzymatic activity can be achieved by increasing the copy number of the gene sequence(s) which encode(s) the enzyme, by using a strong promoter, by modifying the codon usage of the gene, by increasing in various ways the half-life of the mRNA or of the enzyme, by modifying the regulation of gene expression or by using a gene or allele which encodes a suitable enzyme with an increased activity, and optionally by combining these measures. Cells which are genetically modified in accordance with the invention are generated for example by transformation, transduction, conjugation or a combination of these methods with a vector which comprises the desired gene, an allele of this gene or parts thereof and a promoter which makes possible the expression of the gene. Heterologous expression in particular is achieved by integrating the gene or the alleles into the chromosome of the cell or into an extrachromosomally replicating vector. An overview over the possibilities of increasing the enzyme activity in cells with reference to the enzyme isocitrate lyase can be found in EP0839211, which is herewith incorporated by reference and whose disclosure content in respect of the possibilities of increasing the enzyme activity in cells forms part of the disclosure of the present invention.
The expression of the enzymes or genes mentioned hereinabove, and the expression of all enzymes or genes mentioned hereinbelow, can be detected with the aid of 1- and 2-dimensional protein gel separation followed by visual identification of the protein concentration in the gel using suitable evaluation software. If the increase of an enzyme activity is based exclusively on an increase of the expression of the gene in question, the quantitative determination of the increase of the enzyme activity can be determined in a simple manner by comparing the 1- or 2-dimensional protein separations between the wild type and the genetically modified cell. A customary method of preparing the protein gels in coryneform bacteria and of identifying the proteins is the procedure described by Hermann et al. (Electrophoresis, 22: 1712.23 (2001)). The protein concentration can also be analyzed by Western Blot hybridization with an antibody which is specific for the protein to be detected (Sambrook et al., Molecular Cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. USA, 1989) followed by visual evaluation using suitable concentration determination software (Lohaus and Meyer (1989) Biospektrum, 5: 32-39; Lottspeich (1999), Angewandte Chemie 111: 2630-2647). The activity of DNA-binding proteins can be measured by means of DNA band shift assays (also referred to as gel retardation) (Wilson et al. (2001) Journal of Bacteriology, 183: 2151-2155). The effect of DNA-binding proteins on the expression of other genes can be detected by various well-described reporter gene assay methods (Sambrook et al., Molecular Cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. USA, 1989). The intracellular (specific) enzymatic activities can be determined by various described methods (Donahue et al. (2000) Journal of Bacteriology 182 (19): 5624-5627; Ray et al. (2000) Journal of Bacteriology 182 (8): 2277-2284; Freedberg et al. (1973) Journal of Bacteriology 115 (3): 816-823). Unless specific methods for determining the activity of a specific enzyme are stated in what follows, the increase of the enzyme activity, but also the reduction of an enzyme activity, are preferably determined by the methods described in Hermann et al., Electrophoresis, 22: 1712-23 (2001), Lohaus et al., Biospektrum 5 32-39 (1998), Lottspeich, Angewandte Chemie 111: 2630-2647 (1999) and Wilson et al., Journal of Bacteriology 183: 2151-2155 (2001).
If the enzyme activity is increased by mutating the endogenous gene, such mutations can either be generated in an undirected manner using traditional methods, such as, for example, by UV irradiation or by mutagenic chemicals, or in a specific fashion by means of recombinant methods such as deletion(s), insertion(s) and/or nucleotide substitution(s). These mutations give rise to modified cells. Especially preferred mutants of enzymes are, in particular, also those enzymes which are no longer feedback-inhibitable, or at least show a degree of reduced feedback inhibition in comparison with the wild-type enzyme.
If the enzyme activity is increased by increasing the synthesis of an enzyme, then for example the copy number of the genes in question is increased or the promoter region and the regulation region or the ribosomal binding site which is located upstream of the structural gene are mutated. Expression cassettes which are introduced upstream of the structural gene are active in the same manner. In addition, inducible promoters allow the expression to be increased at any desired point in time. Furthermore, the enzyme gene may also have assigned to it regulatory sequences also referred to as “enhancers”, which likewise bring about an increased gene expression via improving the interaction between RNA polymerase and DNA. Measures for extending the life of the mRNA likewise improve expression. Furthermore, the enzyme activity will also be increased by preventing enzyme degradation. Here, the genes or gene constructs are either present in plasmids with different copy numbers or else are integrated into and amplified in the chromosome. As an alternative, overexpression of the genes in question may furthermore be achieved by modifying the media composition and the culture conditions. A person skilled in the art may find information in this context in Martin et al. (Bio/Technology 5, 137-146 (1987)), in Guerrero et al. (Gene 138, 35-41 (1994)), Tsuchiya and Morinaga (Bio/Technology 6, 428-430 (1988)), in Eikmanns et al. (Gene 102, 93-98 (1991)), in EP-A-0 472 869, in U.S. Pat. No. 4,601,893, in Schwarzer and Pallier (Bio/Technology 9, 84-87 (1991)), in Reinscheid et al. (Applied and Environmental Microbiology 60, 126-132 (1994)), in LaBarre et al. (Journal of Bacteriology 175, 1001-1007 (1993)), in WO-A-96/15246, in Malumbres et al. (Gene 134, 15-24 (1993)), in JP-A-10-229891, in Jensen and Hammer (Biotechnology and Bioengineering 58, 191-195 (1998)) and in known textbooks of genetics and molecular biology, inter alia. The above-described measures result in genetically modified cells, as do the mutations.
Expression of the genes in question is increased for example by using episomal plasmids. Suitable plasmids and vectors are, in principle, all embodiments available to a person skilled in the art for this purpose. Such plasmids and vectors may be found for example in brochures from Novagen, Promega, New England Biolabs, Clontech or Gibco BRL. Other preferred plasmids and vectors may be found in: Glover, D. M. (1985), DNA cloning: a practical approach, Vol. I-III, IRL Press Ltd., Oxford; Rodriguez, R. L. and Denhardt, D. T (ed.) (1988), Vectors: a survey of molecular cloning vectors and their uses, 179-204, Butterworth, Stoneham; Goeddel, D. V. (1990), Systems for heterologous gene expression, Methods Enzymol. 185, 3-7; Sambrook, J.; Fritsch, E. F. and Maniatis, T. (1989), Molecular cloning: a laboratory manual, 2nd ed., Cold Spring Harbor Laboratory Press, New York.
The vectors, such as expression vectors, gene deletion cassettes, gene insertion cassettes or gene overexpression cassettes, which comprise the gene to be amplified or portions of the gene to be inactivated are subsequently transferred into the desired strain by means of transformation. Transformation methods, in particular electroporation, lithium-acetate-mediated transformation, freeze-thaw transformation, are described for example in Gietz, R. D., Schiestl, R. H. (2007). Frozen competent yeast cells that can be transformed with high efficiency using the LiAc/SS carrier DNA/PEG method. Nat. Protoc. 2:1-4; Suga, M., Hatakeyama, T. (2003). High-efficiency electroporation by freezing intact yeast cells with addition of calcium. Curr Genet. 43:206-211; Hubberstey, A. V., Wildeman, A. G. (1991). Transformation of Saccharomyces cerevisiae by use of frozen spheroplasts. Trends Genet. 7:41; Bröker, M. (1993). Rapid transformation of cryopreserved competent Schizosaccharomyces pombe cells. Biotechniques. 15:598-600; Gietz, R. D., Schiestl, R. H. (1989). High efficiency transformation of intact yeast cells using single stranded nucleic acids as a carrier. Curr Genet. 16:339-346 and in “Nonconventional yeast in biotechnology” (ed. Klaus Wolf, Springer-Verlag Berlin, 1996). After the transformation, the vectors, in particular gene deletion cassettes, gene insertion cassettes or gene overexpression cassettes, integrate by means of a crossover event into the chromosome of the desired strain as a result of homologous or heterologous, preferably homologous, recombination. As an alternative, the vectors, in particular expression vectors, may also replicate episomally, in other words as an independent replication unit, in cells of the desired strain. This ensures in all cases that the vectors, such as expression vectors, gene deletion cassettes, gene insertion cassettes or gene overexpression cassettes, will also be passed on to the daughter cells upon cell division.
The wording “an activity of an enzyme Ex which is increased in comparison with its wild type” used hereinabove and in what follows preferably always means an activity of the respective enzyme Ex which is increased by a factor of at least 1.5, especially preferably of at least 10, more preferably of at least 100, even more preferably of at least 1000 and most preferably of at least 10 000.
Furthermore, the cell according to the invention which shows “an activity of an enzyme Ex which is increased in comparison with its wild type” comprises in particular also a cell whose wild type shows no, or at least no detectable, activity of this enzyme Ex and which only shows a detectable activity of this enzyme Ex after increasing the enzyme activity, for example by overexpression. In this context, the term “overexpression” or the wording “increase of the expression” used in what follows also comprises the case in which a starting cell, for example a wild-type cell, shows no or at least no detectable expression and a detectable synthesis of the enzyme Ex is induced only by recombinant methods.
Accordingly, the wording “reduced activity of an enzyme Ex” used is understood as meaning an activity which is reduced preferably by a factor of at least 0.5, especially preferably of at least 0.1, more preferably of at least 0.01, even more preferably of at least 0.001 and most preferably of at least 0.0001. The wording “reduced activity” also includes no detectable activity (“zero activity”). The activity of a specific enzyme may be reduced for example by targeted mutation or by other measures of reducing the activity of a specific enzyme which are known to a person skilled in the art.
Methods of reducing enzymatic activities in microorganisms are known to a person skilled in the art.
Techniques of molecular biology, in particular, are the method of choice here. Information on modifying and reducing protein expression and the associated reduction of enzymatic activities specifically for Candida, in particular for disrupting specific genes, can be found by a person skilled in the art in WO91/006660 and WO03/100013.
Cells which are preferred in accordance with the invention are characterized in that the reduction of the enzymatic activity is achieved by modifying a gene comprising one of the abovementioned nucleic acid sequences, with the modification being selected from the group comprising, preferably from the group consisting of, insertion of foreign DNA into the gene, deletion of at least parts of the gene, point mutations in the gene sequence, RNA interference (siRNA), antisense RNA or modification (insertion, deletion or point mutations) of regulatory sequences which flank the gene.
In this context, foreign DNA is understood as meaning any DNA sequence which is “foreign” to the gene (and not to the organism), in other words Candida-bombicola-endogenous DNA sequences may in this context also act as “foreign DNA”.
In this context, it is especially preferred for the gene to be interrupted by the insertion of a selection marker gene, the foreign DNA thus being a selection marker gene, where the insertion has preferably been performed by homologous recombination into the gene locus.
Cells which are preferred in accordance with the invention are characterized in that they have been transformed with at least one nucleic acid according to the invention described hereinbelow and/or a vector according to the invention described hereinbelow.
Cells according to the invention may be used advantageously for the production of sophorolipids.
Thus, a further object of the invention is the use of cells according to the invention for the production of compounds of the general formulae (Ia) and (Ib)
in which

    R1=H or CO—CH3,
    R2=H or CO—CH3,
    R3=a divalent organic moiety which comprises 6 to 32, preferably 7 to 19 carbon atoms and which is unsubstituted or substituted by hydroxyl functions, is unbranched and optionally comprises one to three double or triple bonds,
    R4=H, CH3 or a monovalent organic radical which comprises 2 to 10 carbon atoms and which is unsubstituted or substituted by hydroxyl functions, which is unbranched and which optionally comprises one to three double or triple bonds, and
    n=0 or 1,

in particular of those compounds of the general formulae (Ia) and (Ib)

in which

    R1=H or CO—CH3,
    R2=H or CO—CH3,
    R3=a divalent organic moiety which comprises 6 to 32, preferably 7 to 19 carbon atoms and which is unsubstituted or substituted by hydroxyl functions, is unbranched and optionally comprises one to three double or triple bonds,
    R4=H, CH3 or C9H19, and
    n=0 or 1,

and very especially preferably compounds of the general formulae (Ia) and (Ib)

in which

    R1=H or CO—CH3,
    R2=H or CO—CH3,
    R3=a divalent organic moiety which comprises 6 to 32, preferably 7 to 19 carbon atoms and which is unsubstituted or substituted by hydroxyl functions, is unbranched and optionally comprises one to three double or triple bonds, in particular C8H15=C7H14,
    R4=H, CH3 or C9H19, in particular H or CH3, and
    n=1.


A further subject matter of the present invention is a process for the production of sophorolipids, preferably of compounds of the general formulae (Ia) and (Ib)
in which


    R1=H or CO—CH3,
    R2=H or CO—CH3,
    R3=a divalent organic moiety which comprises 6 to 32, preferably 7 to 19 carbon atoms and which is unsubstituted or substituted by hydroxyl functions, is unbranched and optionally comprises one to three double or triple bonds,
    R4=H, CH3 or a monovalent organic radical which comprises 2 to 10 carbon atoms and which is unsubstituted or substituted by hydroxyl functions, which is unbranched and which optionally comprises one to three double or triple bonds, and
    n=0 or 1,

in particular of those compounds of the general formulae (Ia) and (Ib)

in which

    R1=H or CO—CH3,
    R2=H or CO—CH3,
    R3=a divalent organic moiety which comprises 6 to 32, preferably 7 to 19 carbon atoms and which is unsubstituted or substituted by hydroxyl functions, is unbranched and optionally comprises one to three double or triple bonds,
    R4=H, CH3 or C9H19, and
    n=0 or 1,

and very especially preferably of compounds of the general formulae (Ia) and (Ib)

in which

    R1=H or CO—CH3,
    R2=H or CO—CH3,
    R3=a divalent organic moiety which comprises 6 to 32, preferably 7 to 19 carbon atoms and which is unsubstituted or substituted by hydroxyl functions, is unbranched and optionally comprises one to three double or triple bonds, in particular C8H15=C7H14,
    R4=H, CH3 or C9H19, in particular H or CH3, and
    n=1

comprising the process steps:



I) bringing a cell according to the invention into contact with a medium comprising a carbon source
II) culturing the cell under conditions which allow the cell to form a sophorolipid from the carbon source, and
III) optionally isolating the formed sophorolipids.
The genetically modified cells according to the invention may be brought into contact with the nutrient medium continuously or batchwise by the batch method or the fed-batch method or the repeated-fed-batch method for the purposes of producing the abovementioned products and thereby cultured. Also feasible is a semicontinuous process as described in GB-A-1009370. An overview of known cultivation methods can be found in the textbook by Chmiel (“Bioprozesstechnik 1. Einführung in die Bioverfahrenstechnik” (Gustav Fischer Verlag, Stuttgart, 1991)) or in the textbook by Storhas (“Bioreaktoren and periphere Einrichtungen”, Vieweg Verlag, Brunswick/Wiesbaden, 1994).
The culture medium to be used in each case must satisfy the demands of the strains in question in a suitable manner. The textbook “Nonconventional yeast in biotechnology” (ed. Klaus Wolf, Springer-Verlag Berlin, 1996) contains descriptions of culture media for various yeast strains. Carbon sources which can be employed are carbohydrates such as, for example, glucose, sucrose, arabinose, xylose, lactose, fructose, maltose, molasses, starch, cellulose and hemicelluloses, vegetable and animal oils and fats such as, for example, soya oil, safflower oil, groundnut oil, hemp oil, jatropha oil, coconut fat, pumpkinseed oil, linseed oil, corn oil, poppyseed oil, evening primrose oil, olive oil, palm kernel oil, palm oil, rapeseed oil, sesameseed oil, sunflower oil, grapeseed oil, walnut oil, wheatgerm oil and coconut fat, fatty acids such as, for example, caprylic acid, capric acid, lauric acid, myristic acid, palmitic acid, palmitolenic acid, stearic acid, arachidonic acid, behenic acid, oleic acid, linoleic acid, linolenic acid, gamma-linolenic acid and their methyl or ethyl esters, and fatty acid mixtures, mono-, di- and triglycerides with the fatty acids which have just been mentioned, alcohols such as, for example, glycerol, ethanol and methanol, hydrocarbons such as methane, carbon-containing gases and gas mixtures, such as CO, CO2, synthesis gas, flue gas, amino acids such as L-glutamate or L-valine or organic acids such as, for example, acetic acid. These substances may be employed singularly or as a mixture. It is especially preferred to employ carbohydrates, in particular monosaccharides, oligosaccharides or polysaccharides, as the carbon source, as is described in U.S. Pat. No. 6,01,494 and U.S. Pat. No. 6,136,576, and hydrocarbons, in particular alkanes, alkenes and alkynes and the monocarboxylic acids derived from these and the mono-, di- and triglycerides derived from these monocarboxylic acids, and glycerol and acetate. Very especially preferred are mono-, di- and triglycerides comprising the esterification products of glycerol with caprylic acid, capric acid, lauric acid, myristic acid, palmitic acid, palmitolenic acid, stearic acid, arachidonic acid, behenic acid, oleic acid, linoleic acid, linolenic acid and/or gamma-linoleic acid.
Nitrogen sources which may be used are organic compounds comprising nitrogen, such as peptones, yeast extract, meat extract, malt extract, corn steep liquor, soybean meal and urea or inorganic compounds such as ammonium sulfate, ammonium chloride, ammonium phosphate, ammonium carbonate and ammonium nitrate, ammonia, ammonium hydroxide or ammonia water. The nitrogen sources may be employed singularly or as a mixture.
Phosphorus sources which may be used are phosphoric acid, potassium dihydrogen phosphate or dipotassium hydrogen phosphate or the corresponding sodium-containing salts. The culture medium must furthermore comprise salts of metals, such as, for example, magnesium sulfate or iron sulfate, which are required for growth. Finally, essential growth factors such as amino acids and vitamins may be employed in addition to the abovementioned substances. Furthermore, suitable precursors may be added to the culture medium. The feedstock mentioned may be added to the culture as a single batch or fed in a suitable manner during culturing.
The pH of the culture is controlled by employing basic compounds such as sodium hydroxide, potassium hydroxide, ammonia or ammonia water, or acidic compounds such as phosphoric acid and sulfuric acid. Foaming may be controlled by using antifoams such as, for example, fatty acid polyglycol esters. To maintain the stability of plasmids, suitable selective substances such as, for example, antibiotics may be added to the medium. Oxygen or oxygen-containing gas mixtures such as, for example, air are introduced into the culture in order to maintain aerobic conditions.
The temperature of the culture is normally more than 20° C., preferably more than 25° C., it may also be more than 40° C., with a culture temperature of 95° C., especially preferably 90° C. and most preferably 80° C. not being exceeded.
In step III) of the process according to the invention, the sophorolipids formed by the cells may optionally be isolated from the cells and/or the nutrient medium, where all methods of isolating low-molecular-weight substances from complex compositions which are known to a person skilled in the art may be used for the isolation, such as, for example, filtration, extraction, adsorption (chromatography) or crystallization. As a rule, work-up of the sophorolipids is performed as a function of the product form. In the case of a sophorolipid which is present in the water-insoluble lactone form, the following procedure may be the procedure of choice: the product in lactone form is removed from the aqueous phase by centrifugation.
In addition, the product phase comprises biomass residues and various contaminants such as oils, fatty acids and other nutrient media components. Oil residues can be removed for example by extraction by means of suitable solvents, advantageously by means of organic solvents. An alkane such as, for example, n-hexane, is preferred by way of solvent. The product may be removed from the aqueous phase for example by means of a suitable ester, for example by means of ethyl acetate. The abovementioned extraction steps may be carried out in any order.
Alternatively, sophorolipids may be isolated from the nutrient medium by converting the lactone form into the water-soluble open acid form. For example, the conversion into the open acid form is performed by means of hydrolysis, advantageously by alkaline hydrolysis.
Thereafter, the open-chain sophorolipids are dissolved in an aqueous acid, for example aqueous sulfuric acid, in order to remove any salts which may have formed in the solution. The further purification of the product is carried out by means of extraction. Here, it is preferred to employ solvents, in particular organic solvents. n-Pentanol is preferred by way of solvent. To remove the solvent, for example a distillation is performed. Thereafter, the lyophilized product may be purified further, for example by means of chromatographic methods. Examples which may be mentioned at this point are the precipitation by means of suitable solvents, the extraction by means of suitable solvents, complexing, for example by means of cyclodextrins or cyclodextrin derivatives, crystallization, purification or isolation by means of chromatographic methods, or the conversion of the sophorolipids into derivatives which can be removed readily.
The sophorolipids produced by the process according to the invention may be employed advantageously in cleaning compositions, in cosmetic or pharmaceutical formulations and in crop protection formulations.
Thus, a further subject of the present invention is the use of the sophorolipids obtained by the process according to the invention for the preparation of cosmetic, dermatological or pharmaceutical formulations, crop protection formulations and care and cleaning compositions and surfactant concentrates.
The term “care composition” is understood here as meaning a formulation which satisfies the purpose of retaining an object in its original form, of reducing or avoiding the effects of external influences (for example time, light, temperature, pressure, soiling, chemical reaction with other reactive compounds that come into contact with the object) such as, for example, ageing, soiling, material fatigue, bleaching, or even of improving desired positive properties of the object. For the last point, mention may be made for example of improved hair shine or greater elasticity of the object under consideration.
“Crop protection formulations” are to be understood as meaning those formulations which are obviously used for the protection of plants depending on the nature of their preparation; this is the case especially if at least one compound from the classes of the herbicides, fungicides, insecticides, acaricides, nematicides, bird repellents, plant nutrients and soil conditioners is present in the formulation.
It is preferred in accordance with the invention to use sophorolipids prepared by the process according to the invention in care and cleaning compositions for domestic purposes, for industry, in particular for hard surfaces, leather or textiles.
A contribution to solve the problem is provided by an isolated DNA which is selected from among the following sequences:
A1a) a sequence according to SEQ ID NO:2, SEQ ID NO:52 or SEQ ID NO:54, in particular SEQ ID NO:2, where this sequence encodes a protein which is capable of converting Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid,
B1a) an intron-free sequence which is derived from a sequence according to A1a) and which encodes for the same protein or peptide as the sequence according to SEQ ID NO:2, SEQ ID NO:52 or SEQ ID NO:54, in particular according to SEQ ID NO:2,
C1a) a sequence which encodes a protein or peptide which comprises the amino acid sequence according to SEQ ID NO:7, SEQ ID NO:53 or SEQ ID NO:55, in particular SEQ ID NO:7, and which is preferably capable of converting Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid,
D1a) a sequence which is identical to at least 800, especially preferably to at least 90%, more preferably to at least 95% and most preferably to at least 99% to a sequence according to any of groups A1a) to C1a), especially preferably according to group A1a), where this sequence preferably encodes a protein or peptide which is capable of converting Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid,
E1a) a sequence which hybridizes, or which, taking into consideration the degeneracy of the genetic code, would hybridize with the counterstrand of a sequence according to any of groups A1a) to D1a), especially preferably according to group A1a), where this sequence preferably encodes a protein or peptide which is capable of converting Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid,
F1a) a derivative of a sequence according to any of groups A1a) to E1a), especially preferably according to group A1a), which is obtained by substitution, addition, inversion and/or deletion of at least one base, preferably of at least 2 bases, more preferably of at least 5 bases and most preferably of at least 10 bases, but preferably of no more than 100 bases, especially preferably of no more than 50 bases and most preferably of no more than 25 bases, where this derivative preferably encodes a protein or peptide which is capable of converting Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid, and

    G1a) a sequence which is complementary to a sequence according to any of groups A1a) to F1a), especially preferably according to group A1a).


A further contribution to the solution of the problem is provided by an isolated DNA which is selected from among the following sequences:
A1b) a sequence according to SEQ ID NO:56, SEQ ID NO:58 or SEQ ID NO:60, where this sequence encodes a protein which is capable of converting Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid,
B1b) an intron-free sequence which is derived from a sequence according to A1b) and which encodes for the same protein or peptide as the sequence according to SEQ ID NO:56, SEQ ID NO:58 or SEQ ID NO:60,
C1b) a sequence which encodes a protein or peptide which comprises the amino acid sequence according to SEQ ID
NO:57, SEQ ID NO:59 or SEQ ID NO:61, and which is preferably capable of converting Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid,
D1b) a sequence which is identical to at least 800, especially preferably to at least 86%, more preferably to at least 95% and most preferably to at least 99% to a sequence according to any of groups A1b) to C1b), especially preferably according to group A1b), where this sequence preferably encodes a protein or peptide which is capable of converting Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid,
E1b) a sequence which hybridizes, or which, taking into consideration the degeneracy of the genetic code, would hybridize with the counterstrand of a sequence according to any of groups A1b) to D1b), especially preferably according to group A1b), where this sequence preferably encodes a protein or peptide which is capable of converting Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid,
F1b) a derivative of a sequence according to any of groups A1b) to E1b), especially preferably according to group A1b), which is obtained by substitution, addition, inversion and/or deletion of at least one base, preferably of at least 2 bases, more preferably of at least 5 bases and most preferably of at least 10 bases, but preferably of no more than 100 bases, especially preferably of no more than 50 bases and most preferably of no more than 25 bases, where this derivative preferably encodes a protein or peptide which is capable of converting Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid, and
G1b) a sequence which is complementary to a sequence according to any of groups A1b) to F1b), especially preferably according to group A1b).
A further contribution to the solution of the problem is provided by an isolated DNA which is selected from among the following sequences:
A1c) a sequence according to SEQ ID NO:62, where this sequence encodes a protein which is capable of converting Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid,
B1c) an intron-free sequence which is derived from a sequence according to A1c) and which encodes for the same protein or peptide as the sequence according to SEQ ID NO:62,
C1c) a sequence which encodes a protein or peptide which comprises the amino acid sequence according to SEQ ID NO:63, and which is preferably capable of converting Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid,
D1c) a sequence which is identical to at least 60%, especially preferably to at least 85%, more preferably to at least 90% and most preferably to at least 99% to a sequence according to any of groups A1c) to C1c), especially preferably according to group A1c), where this sequence preferably encodes a protein or peptide which is capable of converting Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid,
E1c) a sequence which hybridizes, or which, taking into consideration the degeneracy of the genetic code, would hybridize with the counterstrand of a sequence according to any of groups A1c) to D1c), especially preferably according to group A1c), where this sequence preferably encodes a protein or peptide which is capable of converting Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid,
F1c) a derivative of a sequence according to any of groups A1c) to E1c), especially preferably according to group A1c), which is obtained by substitution, addition, inversion and/or deletion of at least one base, preferably of at least 2 bases, more preferably of at least 5 bases and most preferably of at least 10 bases, but preferably of no more than 100 bases, especially preferably of no more than 50 bases and most preferably of no more than 25 bases, where this derivative preferably encodes a protein or peptide which is capable of converting Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid, and
G1c) a sequence which is complementary to a sequence according to any of groups A1c) to F1c), especially preferably according to group A1c).
A further subject of the invention is an isolated DNA which is selected from among the following sequences:
A2) a sequence according to SEQ ID NO:3, where this sequence encodes a protein which is capable of converting UDP-glucose and 17-hydroxy-Z-9-octadecenoic acid into 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid,
B2) an intron-free sequence which is derived from a sequence according to A2) and which encodes for the same protein or peptide as the sequence according to SEQ ID NO:3,
C2) a sequence which encodes a protein or peptide which comprises the amino acid sequence according to SEQ ID NO:8 and which is preferably capable of converting UDP-glucose and 17-hydroxy-Z-9-octadecenoic acid into 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid,
D2) a sequence which is to at least 80%, especially preferably to at least 90%, more preferably to at least 95% and most preferably to at least 99% identical to a sequence according to any of groups A2) to C2), especially preferably according to group A2), where this sequence preferably encodes a protein or peptide which is capable of converting UDP-glucose and 17-hydroxy-Z-9-octadecenoic acid into 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid,
E2) a sequence which hybridizes or which, taking into consideration the degeneracy of the genetic code, would hybridize to the counterstrand of a sequence according to any of groups A2) to D2), especially preferably according to group A2), where this sequence preferably encodes a protein or peptide which is capable of converting UDP-glucose and 17-hydroxy-Z-9-octadecenoic acid into 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid,
F2) a derivative of a sequence according to any of groups A2) to E2), especially preferably according to group A2), which is obtainable by substitution, addition, inversion and/or deletion of at least one base, preferably of at least 2 bases, more preferably of at least 5 bases and most preferably of at least 10 bases, but preferably of no more than 100 bases, especially preferably of no more than 50 bases and most preferably of no more than 25 bases, where this derivative preferably encodes a protein or peptide which is capable of converting UDP-glucose and 17-hydroxy-Z-9-octadecenoic acid into 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid, and
G2) a sequence which is complementary to a sequence according to any of groups A2) to F2), especially preferably according to group A2).
A further subject matter of the invention is an isolated DNA which is selected from among the following sequences:
A3) a sequence according to SEQ ID NO:4, where this sequence encodes a protein which is capable of converting 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate or 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate or 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate, with the first option being preferred,
B3) an intron-free sequence which is derived from a sequence according to A3) and which encodes for the same protein or peptide as the sequence according to SEQ ID NO:4,
C3) a sequence which encodes a protein or peptide which comprises the amino acid sequence according to SEQ ID NO:9 and which is preferably capable of converting 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate or 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate or 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate, with the first option being preferred,
D3) a sequence which is identical to at least 80%, especially preferably to at least 90%, more preferably to at least 95% and most preferably to at least 99% to a sequence according to any of groups A3) to C3), especially preferably according to group A3), where this sequence preferably encodes a protein or peptide which is capable of converting 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate or 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate or 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate, with the first option being preferred,
E3) a sequence which hybridizes or, taking into consideration the degeneracy of the genetic code, would hybridize with the counterstrand of a sequence according to any of groups A3) to D3), especially preferably according to group A3), where this sequence preferably encodes a protein or peptide which is capable of converting 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate or 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate or 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate, with the first option being preferred,
F3) a derivative of a sequence according to any of groups A3) to E3), especially preferably according to group A3), which has been obtained by substitution, addition, inversion and/or deletion of at least one base, preferably of at least 2 bases, more preferably of at least 5 bases and most preferably of at least 10 bases, but preferably of no more than 100 bases, especially preferably of no more than 50 bases and most preferably of no more than 25 bases, where this derivative preferably encodes a protein or peptide which is capable of converting 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate or 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate or 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate, with the first option being preferred, and
G3) a sequence which is complementary to a sequence according to any of groups A3) to F3), especially preferably according to group A3).
A further subject matter of the invention is an isolated DNA which is selected from among the following sequences:
A4) a sequence according to SEQ ID NO:5, where this sequence encodes a protein which is capable of transferring a sophorolipid out of a cell into the surrounding medium,
B4) an intron-free sequence which is derived from a sequence according to A4) and which encodes for the same protein or peptide as the sequence according to SEQ ID NO:5,
C4) a sequence which encodes a protein or peptide which comprises the amino acid sequence according to SEQ ID NO:10 and which is preferably capable of transferring a sophorolipid out of a cell into the surrounding medium,
D4) a sequence which is to at least 80%, especially preferably to at least 90%, more preferably to at least 95% and most preferably to at least 99% identical to a sequence according to any of groups A4) to C4), especially preferably according to group A4), where this sequence preferably encodes a protein or peptide which is capable of transferring a sophorolipid out of a cell into the surrounding medium,
E4) a sequence which hybridizes, or which, taking into consideration the degeneracy of the genetic code, would hybridize with the counterstrand of a sequence according to any of groups A4) to D4), especially preferably according to group A4), where the sequence preferably encodes a protein or peptide which is capable of transferring a sophorolipid out of a cell into the surrounding medium,
F4) a derivative of a sequence according to any of groups A4) to E4), especially preferably according to group A4), which has been obtained by substitution, addition, inversion and/or deletion of at least one base, preferably of at least 2 bases, more preferably of at least 5 bases and most preferably of at least 10 bases, but preferably of no more than 100 bases, especially preferably of no more than 50 bases and most preferably of no more than 25 bases, where this derivative preferably encodes a protein or peptide which is capable of transferring a sophorolipid out of a cell into the surrounding medium, and
G4) a sequence which is complementary to a sequence according to any of groups A4) to F4), especially preferably according to group A4).
A further subject matter of the invention is an isolated DNA which is selected from among the following sequences:
A5) a sequence according to SEQ ID NO:6, where this sequence encodes a protein which is capable of converting UDP-glucose and 17-hydroxy-Z-9-octadecenoic acid into 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid or 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and UDP-glucose into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid, with the latter option being preferred,
B5) an intron-free sequence which is derived from a sequence according to A5) and which encodes for the same protein or peptide as the sequence according to SEQ ID NO:6,
C5) a sequence which encodes a protein or peptide which comprises the amino acid sequence according to SEQ ID NO:11 and which is preferably capable of converting UDP-glucose and 17-hydroxy-Z-9-octadecenoic acid into 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid or 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and UDP-glucose into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid, with the latter option being preferred,
D5) a sequence which is to at least 80%, especially preferably to at least 90%, more preferably to at least 95% and most preferably to at least 99% identical to a sequence according to any of groups A5) to C5), especially preferably according to group A5), where this sequence preferably encodes a protein or peptide which is capable of converting UDP-glucose and 17-hydroxy-Z-9-octadecenoic acid into 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid or 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and UDP-glucose into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid, with the latter option being preferred,
E5) a sequence which hybridizes or which, taking into consideration the degeneracy of the genetic code, would hybridize to the counterstrand of a sequence according to any of groups A5) to D5), especially preferably according to group A5), where this sequence preferably encodes a protein or peptide which is capable of converting UDP-glucose and 17-hydroxy-Z-9-octadecenoic acid into 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid or 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and UDP-glucose into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid, with the latter option being preferred,
F5) a derivative of a sequence according to any of groups A5) to E5), especially preferably according to group A5), which has been obtained by substitution, addition, inversion and/or deletion of at least one base, preferably of at least 2 bases, more preferably of at least 5 bases and most preferably of at least 10 bases, but preferably of no more than 100 bases, especially preferably of no more than 50 bases and most preferably of no more than 25 bases, where this derivative preferably encodes a protein or peptide which is capable of converting UDP-glucose and 17-hydroxy-Z-9-octadecenoic acid into 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid or 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and UDP-glucose into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid, with the latter option being preferred, and
G5) a sequence which is complementary to a sequence according to any of groups A5) to F5), especially preferably according to group A5).
The “nucleotide identity” or “amino acid identity” here is determined with the aid of known methods. In general, one uses special computer programs with algorithms, taking into consideration specific requirements.
Preferred methods of determining the identity first generate the largest match between the sequences to be compared. Computer programs for determining the identity comprise, but are not limited to, the GCG software package, including GAP (Deveroy, J. et al., Nucleic Acid Research 12 (1984), page 387, Genetics Computer Group University of Wisconsin, Medicine (Wi), and BLASTP, BLASTN and FASTA (Altschul, S. et al., Journal of Molecular Biology 215 (1990), pages 403-410. The BLAST program can be obtained from the National Center For Biotechnology Information (NCBI) and from other sources (BLAST Handbuch, Altschul S. et al., NCBI NLM NIH Bethesda ND 22894; Altschul S. et al., hereinabove).
Likewise, the known Smith-Waterman algorithm may be used for determining the nucleotide identity.
Preferred parameters for determining the “nucleotide identity” when using the BLASTN program (Altschul, S. et al., Journal of Molecular Biology 215 (1990), pages 403-410) are:

    Expect Threshold: 10
    Word size: 28
    Match Score: 1
    Mismatch Score: −2
    Gap costs: Linear


The above parameters are the default parameters for comparing nucleotide sequences.
The GAP program is likewise suitable for use with the above parameters.
Preferred parameters for determining the “amino acid identity” when using the BLASTP program (Altschul, S. et al., Journal of Molecular Biology 215 (1990), pages 403-410) are:

    Expect Threshold: 10
    Word size: 3
    Matrix: BLOSUM62
    Gap costs: Existence: 11; Extension: 1
    Compositional adjustments: Conditional compositional score matrix adjustment


The above parameters are the default parameters when comparing amino acid sequences.
The GAP program is likewise suitable for use with the above parameters.
An identity of 80% according to the above algorithm means 80% identity in connection with the present invention. The same applies to higher identities.
The feature “sequence which hybridizes or which, taking into consideration the degeneracy of the genetic code, would hybridize to the counterstrand of a sequence” indicates a sequence which hybridizes or which, taking into consideration the degeneracy of the genetic code, would hybridize with the counterstrand of a reference sequence under preferably stringent conditions. For example, the hybridizations may be carried out at 68° C. in 2×SSC or according to the protocol of the digoxigenin labeling kit from Boehringer (Mannheim). Preferred hybridization conditions are, for example, incubation at 65° C. overnight in 7% SDS, 1% BSA, 1 mM EDTA, 250 mM sodium phosphate buffer (pH 7.2), followed by washing at 65° C. with 2×SSC; 0.1% SDS.
The derivatives of the isolated DNA according to the invention which, according to alternative F1a), F1b), F1b), F1c), F2), F3), F4) or F5), can be obtained by substitution, addition, inversion and/or deletion of one or more bases of a sequence according to any of groups A1a) to E1a), A1b) to E1b), A1c) to E1c), A2) to E2), A3) to E3), A4) to E4) and A5) to E5), include in particular the sequences which, in the protein which they encode, result in conservative amino acid substitutions such as, for example, the substitution of glycine for alanine or of aspartic acid for glutamic acid. Such function-neutral mutations are referred to as sense mutations and do not lead to any major modification of the activity of the polypeptide. Furthermore, it is known that modifications of the N- and/or C-terminal end of a polypeptide do not have a profound adverse effect on its function and indeed are even capable of stabilizing it, so that, accordingly, DNA sequences in which bases are added at the 3′-end or at the 5′-end of the sequence with the nucleic acids according to the invention are comprised by the present invention, too. Information in this context can be found by a person skilled in the art in, inter alia, Ben-Bassat et al. (Journal of Bacteriology 169:751-757 (1987)), in O'Regan et al. (Gene 77:237-251 (1989)), in Sahin-Toth et al. (Protein Sciences 3:240-247 (1994)), in Hochuli et al. (Bio/Technology 6:1321-1325 (1988)) and in known textbooks of genetics and molecular biology.
A contribution to solving the problems specified at the outset is furthermore provided by a vector, preferably an expression vector, a gene deletion cassette, gene insertion cassette or gene overexpression cassette, comprising a DNA with a sequence according to any of groups A1a) to G1a), A1b) to G1b), A1c) to G1c), A2) to G2), A3) to G3), A4) to G4) and A5) to G5), as defined hereinabove. Suitable vectors are all the vectors which are known to a person skilled in the art and which are conventionally employed for introducing DNA into a host cell. These vectors are not only capable of autonomous replication since they have origins of replication such as for example those of the 2μ plasmid or of the ARS (autonomously replicating sequences) but are also capable of integration into the chromosomes (nonreplicating plasmids). Vectors are also understood as meaning linear DNA fragments which have no origins of replication whatsoever, such as, for example, gene deletion cassettes, gene insertion cassettes or gene overexpression cassettes. Gene deletion cassettes are usually composed of a selection marker and DNA fragments which flank the region to be deleted. Gene insertion cassettes are usually composed of a marker and fragments of the gene to be inactivated. Gene overexpression cassettes are usually composed of a marker, the gene to be overexpressed and regulatory regions which are relevant for the expression of the gene, such as, for example, promoter and terminator. Preferred vectors are selected from the group comprising plasmids and cassettes, such as, for example E. coli yeast shuttle plasmids; especially preferred are expression vectors, gene deletion cassettes, gene insertion cassettes or gene overexpression cassettes, in particular the gene deletion cassettes described hereinbelow with SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15 and SEQ ID NO:16 and the expression cassettes with SEQ ID NO:70, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73 and SEQ ID NO:74. According to a preferred embodiment of the vector according to the invention, the DNA with a sequence according to any of groups A1) to F5) is under the control of a constitutive promoter or a promoter capable of being regulated, which promoter is suitable for expressing the polypeptide encoded by these DNA sequences in the cell of a microorganism, preferably a bacterial cell, a yeast cell or a fungal cell, especially preferably a yeast cell, most preferably a Candida bombicola, Candida bogoriensis, Candida batistae, Candida apicola or Wickerhamiella domericqiae cell. Examples of such constitutive promoters are for example the TSC3 promoter, the ENO1 promoter, the FBA1 promoter, the GPD promoter, the GPM promoter, the FBA1 promoter, the ICL1 promoter or the ACT1 promoter. Examples of such promoters which are capable of being regulated are for example the GAL1 promoter, the GAL2 promoter, the GAL7 promoter, the MEL1 promoter, the GAL10 promoter, the SBG1 promoter, the SBG2 promoter, the SBG3 promoter, the SBG4 promoter, the SBG5 promoter or the MAL2 promoter.
Besides a promoter, the vector according to the invention should preferably comprise a ribosome binding site and a terminator. In this context, it is especially preferred that the DNA according to the invention is incorporated into an expression cassette of the vector comprising the promoter, the ribosome binding site and the terminator. Besides the abovementioned structural elements, the vector may furthermore comprise selection marker genes which are known to a person skilled in the art.
The nucleic acids SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, IntEx-CbSBG1 (SEQ ID NO:70), IntEx-CbSBG2 (SEQ ID NO:71), IntEx-CbSBG3 (SEQ ID NO:72), IntEx-CbSBG4 (SEQ ID NO:73) and IntEx-CbSBG5 (SEQ ID NO:74) described in the examples are vectors which are preferred in accordance with the invention.
A further contribution to the solution of the problem is provided by the novel enzymes E1 to E5.
Thus, a further subject matter of the invention is an isolated polypeptide selected from the group consisting of an enzyme E1 with the polypeptide sequence SEQ ID NO:7, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61 or SEQ ID NO:63, especially SEQ ID NO:7, or with a polypeptide sequence where up to 25%, preferably up to 20%, especially preferably up to 15%, in particular up to 10, 9, 8, 7, 6, 5, 4, 3, 2, 1% of the amino acid residues are modified over the respective reference sequence SEQ ID NO:7, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61 or SEQ ID NO:63, especially SEQ ID NO:7, by deletion, insertion, substitution or a combination of these and which retains at least 50%, preferably 65%, especially preferably 80%, in particular more than 90% of the enzymatic activity of the enzyme with the respective reference sequence, where enzymatic activity for an enzyme E1 is understood as meaning the ability to convert Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid,
an enzyme E2 with the polypeptide sequence SEQ ID NO:8 or SEQ ID NO:11 or with a polypeptide sequence where up to 60%, preferably up to 25%, especially preferably up to 15%, in particular up to 10, 9, 8, 7, 6, 5, 4, 3, 2, 1% of the amino acid residues are modified over SEQ ID NO:8 or SEQ ID NO:11 by deletion, insertion, substitution or a combination of these and which retains at least 50%, preferably 65%, especially preferably 80%, in particular more than 90% of the enzymatic activity of the enzyme with the respective reference sequence No. 8 or 11, where enzymatic activity for an enzyme E2 is understood as meaning the ability to convert UDP-glucose and 17-hydroxy-Z-9-octadecenoic acid into 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid,
an enzyme E3 with the polypeptide sequence SEQ ID NO:11 or with a polypeptide sequence where up to 60%, preferably up to 25%, especially preferably up to 15%, in particular up to 10, 9, 8, 7, 6, 5, 4, 3, 2, 1% of the amino acid residues are modified over SEQ ID NO:11 by deletion, insertion, substitution or a combination of these and which retains at least 50%, preferably 65%, especially preferably 80%, in particular more than 90% of the enzymatic activity of the enzyme with the respective reference sequence No. 11, where enzymatic activity for an enzyme E3 is understood as meaning the ability to convert 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and UDP-glucose into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid,
an enzyme E4 with the polypeptide sequence SEQ ID NO:9 or with a polypeptide sequence where up to 50%, preferably up to 25%, especially preferably up to 15%, in particular up to 10, 9, 8, 7, 6, 5, 4, 3, 2, 1% of the amino acid residues are modified over SEQ ID NO:9 by deletion, insertion, substitution or a combination of these and which retains at least 50%, preferably 65%, especially preferably 80%, in particular more than 90% of the enzymatic activity of the enzyme with SEQ ID NO:9, where enzymatic activity for an enzyme E4 is understood as meaning the ability to convert 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate or 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate or 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate, with the first option being preferred,
and
an enzyme E5 with the polypeptide sequence SEQ ID NO:10 or with a polypeptide sequence where up to 45%, preferably up to 25%, especially preferably up to 15% and in particular up to 10, 9, 8, 7, 6, 5, 4, 3, 2, 1% of the amino acid residues are modified over SEQ ID NO:10 by deletion, insertion, substitution or a combination of these and which retains at least 50%, preferably 65%, especially preferably 80%, in particular more than 90% of the enzymatic activity of the enzyme with SEQ ID NO:10, where enzymatic activity for an enzyme E5 is understood as meaning the ability to transfer a sophorolipid out of a cell into the surrounding medium.
In the examples given hereinbelow, the present invention is described by way of example without it being intended to limit the invention, whose scope is clear from all of the description and the claims, to the embodiments mentioned in the examples.



The following figures are part of the examples:
FIG. 1: Accurate mass trajectory for 17-L-[(6′-O-acetyl-2′-O-β-D-glucopyranosyl-6′′-O-acetyl-β-D-glucopyranosyl)oxy]-Z-9-octadecene 4′′-O-lactone
FIG. 2: Accurate mass trajectory for 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecene 4′′-O-lactone



EXAMPLES
Example 1
Generation of Uracil-Auxotrophic Mutants of Candida bombicola ATCC 22214
A uracil-auxotrophic mutant of Candida bombicola ATCC 22214 was generated as described hereinabove (van Bogaert et al. Yeast. 2007. 24(3):201-8). This strain was named C. bombicola ATCC 22214 ura−.
Example 2
Inactivation of the Structural Genes of the Enzymes Involved in Sophorolipid Biosynthesis in Candida bombicola ATCC 22214
In order to be able to identify enzymes involved in sophorolipid biosynthesis, the genome of Candida bombicola ATCC 22214 was first sequenced by means of GLS Flex Titanium technology. Upon inspection of the genetic information of Candida bombicola ATCC 22214, a cluster of five genes (SEQ ID NO:01) was identified whose coding regions (SEQ ID NO:02, SEQ ID NO:03, SEQ ID NO:04, SEQ ID NO:05, SEQ ID NO:06) encode gene products (SEQ ID NO:07, SEQ ID NO:08, SEQ ID NO:09, SEQ ID NO:10, SEQ ID NO:11).
The five genes were named SBG1 (SEQ ID NO:02), SBG2 (SEQ ID NO:03), SBG3 (SEQ ID NO:04), SBG4 (SEQ ID NO:05) and SBG5 (SEQ ID NO:06) (SBG stands for Sophorolipid Biosynthesis Gene).
They encode the following proteins: Sbg1p (SEQ ID NO:07), Sbg2p (SEQ ID NO:08), Sbg3p (SEQ ID NO:09), Sbg4p (SEQ ID NO:10) and Sbg1p (SEQ ID NO:11).







TABLE 1







Sbg1p, Sbg2p, Sbg3p, Sbg4p and Sbg5p and their functions in the


biosynthesis and the export of sophorolipids.











Seq






ID


NCBI



No.
Protein
PFAM domain
conserved domain
Function





07
Sbg1p
P450 (PFAM PF00067)
cytochrome P450
monooxygenase which






hydroxylates fatty






acids [ω,ω-1,ω-2,ω-3]


08
Sbg2p
UDP
glycosyltransferase
UDP-glucose: [ω,ω-




glycosyltransferase

1, ω-2,ω-3]-hydroxy




(PFAM PF00201)

fatty acid






glucosyltransferase


09
Sbg3p
none
Maltose O-acetyltransferase
acetyl-CoA:





(PRK10092)
sophorolipid






acetyltransferase


10
Sbg4p
ABC transporter
ABC transporter
Sophorolipid export




(PFAM 00667)

protein


11
Sbg5p
UDP
glycosyltransferase
UDP-glucose: [ω,ω-




glycosyltransferase

1,ω-2,ω-3]-hydroxy




(PFAM PF00201)

fatty acid






glucosyltransferase;






UDP-glucose: [ω,ω-






1,ω-2,ω-3]-(β-D-






glucopyranosyl)oxy






fatty acid






glucosyltransferase









The genes SBG1, SBG2, SBG3, SBG4 and SBG5 are inactivated individually, and the phenotype of the corresponding mutants is characterized in respect of the sophorolipid biosynthesis. To construct the corresponding mutants in C. bombicola ATCC 22214, deletion cassettes are first synthesized by GeneArt AG (Regensburg). These deletion cassettes (SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16) are composed of the above-described gene CbURA3 (van Bogaert et al. Yeast. 2007. 24(3):201-8) which encodes the C. bombicola ATCC 22214 orotidin-5-phosphate decarboxylase and which is flanked upstream and downstream by in each case approximately 1000 by of the regions flanking the genes to be inactivated. loxP-loci, which optionally permit the deletion of the CbURA3 gene by temporarily introducing the Cre-recombinase-coding gene and permit its functional expression, are inserted in each case between the flanking regions and the CbURA3 gene (for an overview see Kuhn & Torres. Methods Mol Biol. 2002. 180:175-204). In this context, the individual deletion cassettes are constructed as shown in Table 2:







TABLE 2







Structure of the deletion cassettes for the Sbg1p,


Sbg2p, Sbg3p, Sbg4p and Sbg5p encoding structural


genes of C. bombicola ATCC 22214.













SEQ

5′-



3′-


ID

flanking
loxP-

loxP-
flanking


NO:
Gene
region
locus 1
CbURA3
locus 2
region





12
SBG1
1-1003
1004-1037
1038-3106
3107-3140
3141-4143


13
SBG2
1-0999
1000-1033
1034-3102
3103-3136
3137-4143


14
SBG3
1-1002
1003-1036
1037-3105
3106-3139
3140-4140


15
SBG4
1-0997
0998-1031
1032-3100
3101-3134
3135-4130


16
SBG5
1-1002
1003-1036
1037-3105
3106-3139
3140-4141









To provide the deletion cassettes for the subsequent transformation of C. bombicola ATCC 22214 ura− in a sufficient amount, the former are amplified by PCR. The following oligonucleotides are used:
Amplification of the Deletion Cassettes for the Inactivation of CbSBG1:









SBG1-fw:



(SEQ ID NO: 17)



5′-AAT TGT TCG ATG GAT AGC TTT GGA GTC-3′



 



SBG1-rv:



(SEQ ID NO: 18)



5′-TTC GGG GCT CCT GTC GTT GTC-3′






Amplification of the Deletion Cassettes for the Inactivation of CbSBG2:









SBG2-fw:



(SEQ ID NO: 19)



5′-GAA ATC TGA TCA ATT CTG CAA ACC TG-3′



 



SBG2-rv:



(SEQ ID NO: 20)



5′-ATG ACT CCT AGA AAA GAA ATT GAC CAG-3′






Amplification of the Deletion Cassettes for the Inactivation of CbSBG3:









SBG3-fw:



(SEQ ID NO: 21)



5′-TGC AGA CAA GTT CCT GCA GCT G-3′



 



SBG3-rv:



(SEQ ID NO: 22)



5′-ATG CTT TAT TCA GGC ACG CTA CG-3′






Amplification of the Deletion Cassettes for the Inactivation of CbSBG4:









SBG4-fw:



(SEQ ID NO: 23)



5′-GGA TGA GTC GCA GTC ACG AAC-3′



 



SBG4-rv:



(SEQ ID NO: 24)



5′-TCA ATC ATT GGC TCA AGA CTA GGA AC-3′






Amplification of the Deletion Cassettes for the Inactivation of CbSBG5:









SBG5-fw:



(SEQ ID NO: 25)



5′-ATT CTG GTG CTG ACC TCG CCA C-3′



 



SBG5-rv:



(SEQ ID NO: 26)



5′-ACT CAT GTC GTA CTT GCA AGA ACT G-3′






The following parameters are employed for the PCR: 1×: initial denaturation, 98° C., 3 min; 25×: denaturation, 98° C., 0:10 min, annealing, 60° C., 0:30 min; elongation, 72° C., 2:00 min; 1×: terminal elongation, 72° C., 10 min. The PhusionTM High-Fidelity Master Mix from New England Biolabs (Frankfurt) is employed for the amplification, following the manufacturer's recommendations. The PCR products are purified using the QIAquick PCR purification kit (Qiagen, Hilden) following the manufacturer's instructions. The procedure of the PCR, the verifying of the successful amplification of the PCR by means of agarose gel electrophoresis, staining the DNA with ethidium bromide, determining the PCR fragment sizes, purification of the PCR products and determining the DNA concentration are all performed in a manner with which the skilled worker is familiar.
The transformation of C. bombicola ATCC 22214 ura− is performed as previously described (van Bogaert et al. Yeast. 2008. 25:273-278); van Bogaert et al. FEMS Yeast Res. 2009. 9:610-617).
To verify the deletion of the genes SBG1, SBG2, SBG3, SBG4 and SBG5 in C. bombicola ATCC 22214 ura− transformants following the transformation with the deletion cassettes for CbSBG1 (SEQ ID NO:12), CbSBG2 (SEQ ID NO:13), CbSBG3 (SEQ ID NO:14), CbSBG4 (SEQ ID NO:15) and CbSBG5 (SEQ ID NO:16), the respective loci of in each case 5 transformants and C. bombicola ATCC 22214 ura− are amplified by means of colony PCR. The following oligonucleotides are employed for this:
Verification of the Genomic Deletion of CbSBG1:









SBG1-KO-fw:



(SEQ ID NO: 27)



5′-GTG TCG ACT CGC CAA ATT CCA TCG GAG-3′



 



SBG1-KO-rv:



(SEQ ID NO: 28)



5′-GGT TCA TAG CGA GTT TCT TTG CAT GTG C-3′






Verification of the Genomic Deletion of CbSBG2:









SBG2-KO-fw:



(SEQ ID NO: 29)



5′-CTC CTT TAT TAA CTC CGC AGC ATG ACT G-3′



 



SBG2-KO-rv:



(SEQ ID NO: 30)



5′-CTC CTC GAA GGA CCC TCA AAA CAA AGG-3′






Verification of the Genomic Deletion of CbSBG3:









SBG3-KO-fw:



(SEQ ID NO: 31)



5′-CAA ATT TAT CTG GGA GCA CAG TTA CAT TGC-3′



 



SBG3-KO-rv:



(SEQ ID NO: 32)



5′-CAC ACA TTG CTT TAG TCC AGC AAG AAC C-3′






Verification of the Genomic Deletion of CbSBG4:







SBG4-KO-fw:


(SEQ ID NO: 33)


5′- ATT CTC CTC GCA CGT TTC TCG GGG C -3′


 


SBG4-KO-rv:


(SEQ ID NO: 34)


5′- GGT TGA AAT ACT TGT TGC CGC ACT AAA G -3′






Verification of the Genomic Deletion of CbSBG5:







SBG5-KO-fw:


(SEQ ID NO: 35)


5′- CGC TTC CTG AAT TGA GTT GGT ATC GTT AAT 


 


G -3′


 


SBG5-KO-rv:


(SEQ ID NO: 36)


5′- GAC ATT GTT GGA ATT GGC TGC TTA GTG G -3′






The following parameters are employed in the PCR: 1×: initial denaturation, 94° C., 3 min; 25×: denaturation, 94° C., 1:00 min, annealing, 60° C., 1:00 min; elongation, 72° C., 5:00 min; 1×: terminal elongation, 72° C., 10 min. The Taq PCR Master Mix Kit from Qiagen (Hilden) is employed for the amplification following the manufacturer's recommendations. In each case 10 μl of the PCR reactions are subsequently separated on a 0.8% agarose gel. The procedure of the PCR, of the agarose gel electrophoresis, staining the DNA with ethidium bromide and determining the PCR fragment sizes are all performed in a manner with which the skilled worker is familiar.
The amplification of the corresponding loci should give rise to the PCR fragment sizes specified in Table 3:







TABLE 3







Expected PCR fragment sizes for the amplification of the chromosomal


SBG1, SBG2, SBG3, SBG4 and SBG5 loci upon successful deletion


and in the wild-type situation.












Size of the PCR product
Size of the




upon chromosomal
PCR product in



Gene
deletion
the wild-type situation






SBG1
4201 bp
3678 bp



SBG2
4199 bp
3451 bp



SBG3
4199 bp
2839 bp



SBG4
4190 bp
5950 bp



SBG5
4201 bp
3360 bp









Upon amplification of the CbSBG1, CbSBG2, CbSBG3, CbSBG4 and CbSBG5 loci from C. bombicola ATCC 22214 ura−, only the fragment sizes expected when a wild-type situation is present, i.e. 3.7 kbp, 3.5 kbp, 2.8 kbp, 5.9 kbp and 3.4 kbp, respectively, are obtained.
Upon amplification of the SBG1 locus from transformants following transformation of the deletion cassettes for CbSBG1, only the fragment size to be expected after successful chromosomal deletion of CbSBG1, i.e. approximately 4.2 kbp, is obtained.
Upon amplification of the SBG2 locus from transformants following transformation of the deletion cassettes for CbSBG2, only the fragment size to be expected after successful chromosomal deletion of CbSBG2, i.e. approximately 4.2 kbp, is obtained.
Upon amplification of the SBG3 locus from transformants following transformation of the deletion cassettes for CbSBG3, only the fragment size to be expected after successful chromosomal deletion of CbSBG3, i.e. approximately 4.2 kbp, is obtained.
Upon amplification of the SBG4 locus from transformants following transformation of the deletion cassettes for CbSBG4, only the fragment size to be expected after successful chromosomal deletion of CbSBG4, i.e. approximately 4.2 kbp, is obtained.
Upon amplification of the SBG5 locus from transformants following transformation of the deletion cassettes for CbSBG5, only the fragment size to be expected after successful chromosomal deletion of CbSBG5, i.e. approximately 4.2 kbp, is obtained.
Thus, it is possible to identify in all five cases clones in which the genes CbSBG1, CbSBG2, CbSBG3, CbSBG4 or CbSBG5 have undergone chromosomal deletion. The corresponding strains are hereinbelow referred to as C. bombicola ATCC 22214 sbg1, C. bombicola ATCC 22214 sbg2, C. bombicola ATCC 22214 sbg3, C. bombicola ATCC 22214 sbg4 and C. bombicola ATCC 22214 sbg5, respectively.
Example 3
Characterization of the Sophorolipid Formation by C. bombicola ATCC 22214, C. bombicola ATCC 22214 Sbg1, C. bombicola ATCC 22214 Sbg2, C. bombicola ATCC 22214 Sbg3, C. bombicola ATCC 22214 Sbg4 and C. bombicola ATCC 22214 Sbg5
The propagation of strains C. bombicola ATCC 22214, C. bombicola ATCC 22214 sbg1, C. bombicola ATCC 22214 sbg2, C. bombicola ATCC 22214 sbg3, C. bombicola ATCC 22214 sbg4 and C. bombicola ATCC 22214 sbg5 is done on YPD agar plates. The medium referred to hereinbelow as SL production medium is used for the production of the sophorolipids. It is composed of 0.1% KH2PO4, 0.5% MgSO4×7 H2O, 0.01% FeCl3, 0.01% NaCl, 0.01% uracil, 0.4% yeast extract, 0.1% urea, 10.5% rapeseed oil and 10% glucose. The pH is brought to 4.5 and the medium is then sterilized in an autoclave (121° C., 20 min). It is not necessary to adjust the pH during the cultivation.
To study the sophorolipid production in the shake flask, a preculture is first established. To this end, 10 ml of YPD medium in a 100 ml Erlenmeyer flask are inoculated with one loop of a strain freshly plated onto a YPD agar plate. Cultivation was done overnight at 30° C. and 200 rpm. This preculture is used hereinbelow for inoculating 100 ml of SL medium in a 1000 ml Erlenmeyer flask (starting OD600 0.2). The cultures are grown for 7 days at 200 rpm and 30° C., and a sample of 2 ml of broth is taken every day, good care being taken that the culture medium was mixed thoroughly before sampling.
The samples are prepared for the subsequent chromatographic analyses as follows: using a positive-displacement pipette (Combitip), 800 μl of acetone are placed into a 2-ml reaction vessel and the reaction vessel is sealed immediately to minimize evaporation. 200 μl of broth are added. After vortexing the broth/acetone mixture, the latter is centrifuged for 1 min at 13 000 rpm, and 800 μl of the supernatant are transferred into an HPLC vessel. An evaporative light scattering detector (ELSD) is used for the detection and quantitative determination of sophorolipids and/or oleic acid. The actual measurement is performed by means of the Agilent Technologies 1200 series (Santa Clara, Calif.) and the Zorbax SB-C8 Rapid Resolution column (4.6×150 mm, 3.5 μm, Agilent). The injection volume is 5 μl, and the running time of the method is 20 min. The mobile phase used is H2O and 0.10 of TFA (trifluoroacetic acid, solution A) and methanol (solution B). The column temperature is 40° C. The detectors used were the ELSD (detector temperature 60° C.) and the DAD (diode array, 210 nm). The gradient used in the method is shown in Table 4.







TABLE 4







Description of the gradient profile of the mobile phase to be used


for the HPLC-based quantitative determination of sophorolipids.











Flow rate


t [min]
Solution B %
[ml/min]












0.00
70%
1.00


15.00
100%
1.00


15.01
70%
1.00


20.00
70%
1.00









While C. bombicola ATCC 22214 produced sophorolipids, no sophorolipid formation can be detected in the strains C. bombicola ATCC 22214 sbg1, C. bombicola ATCC 22214 sbg2 and C. bombicola ATCC 22214 sbg4. This demonstrates clearly that these genes are involved in sophorolipid formation, where they exert the functions specified above. While strains C. bombicola ATCC 22214 sbg3 and C. bombicola ATCC 22214 sbg5 are capable of forming sophorolipids, they have a modified retention time in the HPLC analysis.
It can be demonstrated by LC-MS2 that, in contrast to the sophorolipids formed by C. bombicola ATCC 22214, the sophorolipids formed by C. bombicola ATCC 22214 sbg3 correspond exclusively to compounds of the general formulae (Ia) and (Ib) in which R1=H and R2=H.
This proves the function of Sbg3p as acetyltransferase (E4) in sophorolipid biosynthesis.
Likewise, it can be demonstrated by LC-MS that, in contrast to the sophorolipids formed by C. bombicola ATCC 22214, the sophorolipids formed by C. bombicola ATCC 22214 sbg5 exclusively correspond to compounds of the general formula (Ia) in which n=0.
This demonstrates the function of Sbg5p as glycosyltransferase II (E3) in sophorolipid biosynthesis.
Example 4
Construction of Candida bombicola ATCC 22214 Strains which Overproduce Enzymes Involved in Sophorolipid Biosynthesis
To make possible the construction of Candida bombicola ATCC 22214 strains which overproduce the enzymes involved in sophorolipid biosynthesis, an integration/overexpression cassette is first synthesized by GeneArt AG (SEQ ID NO:75).
This integration/overexpression cassette comprises the components specified in Table 5:







TABLE 5







Overview over the modules present in the integration/overexpression


cassette to be developed for Candida bombicola ATCC 22214, and


important restriction cleavage sites.








Position (bp)
Component





1-8
NotI recognition site


 9-507
DNA segment upstream of the C. bombicola ATCC



22214 LEU2 gene


508-513
PciI recognition site


 514-1217
Promoter region of the C. bombicola ATCC 22214



URA3 gene


1217-2005
Coding region of the C. bombicola ATCC 22214



URA3 gene


2006-2586
Terminator region of the C. bombicola ATCC



22214 URA3 gene


2587-2592
PciI recognition site


2593-2600
AsiSI recognition site


2601-3012
Promoter region of the C. bombicola ATCC 22214



TSC3 gene


3011-3016
NdeI recognition site


3025-3032
FseI recognition site


3033-3210
Terminator region of the C. bombicola ATCC



22214 TSC3 gene


3211-3218
AsiSI recognition site


3219-3224
MluI recognition site


3225-3724
DNA segment downstream of the C. bombicola ATCC



22214 LEU2 gene


3725-3732
SbfI recognition site









This integration/overexpression cassette makes possible the insertion of any desired structural genes from the start codon to the stop codon via NdeI and FseI between the promoter and the terminator region of the C. bombicola ATCC 22214 TSC3 gene, which encodes glyceraldehyde-3-phosphate dehydrogenase (van Bogaert et al.; 2008). Glyceraldehyde-3-phosphate dehydrogenase is a protein which is highly abundant in many yeasts, so that it can be assumed that a strong expression of the inserted gene can be achieved in this manner. The C. bombicola ATCC 22214 URA3 gene is selected as a selection marker so that this integration/overexpression cassette may only be used for the transformation of uracil-auxotrophic strains of C. bombicola ATCC 22214. Its generation, and the C. bombicola ATCC 22214 URA3 gene, have already been described (van Bogaert et al., 2007; van Bogaert et al., 2008). The 5′- and 3′-terminal DNA segments permit the cassette to be inserted at the C. bombicola ATCC 22214 LEU2 locus (SEQ ID NO:37), which inactivates the LEU2 gene. LEU2 encodes the only isopropylmalate dehydrogenase in C. bombicola ATCC 22214. Since isopropylmalate dehydrogenase is an essential component of leucine biosynthesis, transformants with a correct integration of the integration/overexpression cassette can be identified via their leucine auxotrophism. Various unique and redundant recognition sequences (NotI, PciI, AseSI, MluI, SbfI) permit the substitution of individual modules of the integration/overexpression cassette. The cassette is cloned by GeneArt AG into the proprietary vector pMA which comprises none of the above-described cleavage sites so that these cleavage sites may be used to their full extent.
To insert the genes CbSBG1, CbSBG3 and CbSBG5 into the integration/overexpression cassettes described, the genes are amplified by PCR from chromosomal DNA of C. bombicola ATCC 22214 and at the same time an NdeI cleavage site is introduced upstream of the start codon and an FseI cleavage site downstream of the stop codon via the oligonucleotides used. To insert the genes CbSBG2 and CbSBG4 into the integration/overexpression cassette described, the former are first synthesized de novo by GeneArt AG (Regensburg) in order to modify their sequence such that the internal FseI and NotI cleavage sites (CbSBG2) and NdeI cleavage sites (CbSBG4), respectively, are removed without modifying the amino acid sequence of the encoded protein. Thereafter, the modified genes CbSBG2 mod and CbSBG4 mod provided by GeneArt AG (Regensburg) are amplified by PCR, and an NdeI cleavage site upstream of the start codon and an FseI cleavage site downstream of the stop codon are introduced simultaneously via the oligonucleotides used. The following oligonucleotides are used:
CbSBG1:







SBG1-OE-fw:


(SEQ ID NO: 38)


5′- ATA TAT ATA CAT ATG TTA ATC AAA GAC ATT 


 


ATT CTA ACT CCA ATG-3′


 


SBG1-OE-rv:


(SEQ ID NO: 39)


5′- ATA TAT GGC CGG CCA ACT TAA GAA AAC CGC 


 


ACA ACC ACA CCG-3′






CbSBG2 mod:







SBG2-OE-fw:


(SEQ ID NO: 40)


5′- ATA TAT ATA CAT ATG AGC CCT TCA TCA CAC 


 


AAA CCC CTG -3′


 


SBG2-OE-rv:


(SEQ ID NO: 41)


5′- ATA TAT GGC CGG CCA TTC TAA GAA CTC ACC 


 


GCT AAG GCC -3′






CbSBG3:







SBG3-OE-fw:


(SEQ ID NO: 42)


5′- ATA TAT ATA CAT ATG GTT GTA AAC TCC TCG 


 


AAG GAC CC-3′


 


SBG3-OE-rv:


(SEQ ID NO: 43)


5′- ATA TAT GGC CGG CCT ACC TAG ACC TTC TGG 


 


TTA GCG GTA TTG -3′






CbSBG4 mod:







SBG4-OE-fw:


(SEQ ID NO: 44)


5′- ATA TAT ATA CAT ATG GTG GAT GAT ATA CAG 


 


GTA GAG AAG C-3′


 


SBG4-OE-rv:


(SEQ ID NO: 45)


5′- ATA TAT GGC CGG CCA CGT CAA ATC TCT CCG 


 


AGA CCT TGC AAG -3′






CbSBG5:







SBG5-OE-fw:


(SEQ ID NO: 46)


5′- ATA TAT ATA CAT ATG GCC ATC GAG AAA CCA 


 


GTG ATA GTT G -3′


 


SBG5-OE-rv:


(SEQ ID NO: 47)


5′- ATA TAT GGC CGG CCA GGT TAA GAA GCT AAT 


 


TCA CTA ATT GCC GAC -3′






The following parameters are employed for the PCR: 1×: initial denaturation, 98° C., 3 min; 25×: denaturation, 98° C., 0:10 min, annealing, 60° C., 0:30 min; elongation, 72° C., 2:00 min; 1×: terminal elongation, 72° C., 10 min. The PhusionTM High-Fidelity Master Mix by New England Biolabs (Frankfurt) is employed for the amplification, following the manufacturer's recommendations. In each case 10 μl of the PCR reactions are subsequently separated on a 0.80 agarose gel. The procedure of the PCR, of the agarose gel electrophoresis, staining the DNA with ethidium bromide and determining the PCR fragment sizes are performed in a manner known to a person skilled in the art.
In all cases it is possible to amplify PCR fragments of the expected size. These sizes are: for CbSBG1 1646 bp; for CbSBG2 1421 bp; for CbSBG3 809 bp; for CbSBG4 3929 by and for CbSBG5 1328 bp. The PCR products are digested with NdeI and FseI following the recommendations of the manufacturer of the restriction endonucleases (New England Biolabs; Frankfurt/Main) and ligated into the NdeI- and FseI-cut vector pMA-ExCat (SEQ ID NO:64). Ligation and the transformation of chemically competent E. coli DH5α cells (New England Biolabs; Frankfurt/Main) are performed in a manner known to the skilled worker. The correct insertion of the CbSBG1, CbSBG2, CbSBG3, CbSBG4 and CbSBG5 fragments into pMA-ExCat is verified and confirmed by a restriction with NdeI and FseI. The resulting vectors are named pMA_ExCat-CbSBG1 (SEQ ID NO:65), pMA_ExCat-CbSBG2 (SEQ ID NO:66), pMA_ExCat-CbSBG3 (SEQ ID NO:67), pMA_ExCat-CbSBG4 (SEQ ID NO:68) and pMA_ExCat-CbSBG5 (SEQ ID NO:69).
To provide the individual integration/overexpression cassettes and the control cassette ExCat for the subsequent transformation of C. bombicola ATCC 22214 ura− in a sufficient amount, the former are amplified by PCR. The following oligonucleotides are applied:







OEx-LEU2-fw:


(SEQ ID NO: 48)


5′- GGA CCT GCG CCC TAA AAT GGG AC -3′


 


OEx-LEU2-rv:


(SEQ ID NO: 49)


5′- ATC CTA GAA AAC AGC TGG ATA TGG ATA AAC-3′






The PCR products are purified by means of the QIAquick PCR Purification Kit (Qiagen, Hilden) following the manufacturer's information. In the procedure of the PCR, the verification of the successful amplification of the PCR by means of agarose gel electrophoresis, staining the DNA with ethidium bromide, determining the PCR fragment sizes, purification of the PCR products and determination of the DNA concentration are performed in a manner known to the skilled worker.
The resulting integration/overexpression cassettes are given the names IntEx-CbSBG1 (SEQ ID NO:70), IntEx-CbSBG2 (SEQ ID NO:71), IntEx-CbSBG3 (SEQ ID NO:72), IntEx-CbSBG4 (SEQ ID NO:73) and IntEx-CbSBG5 (SEQ ID NO:74). The control cassette ExCat (SEQ ID NO:75) is also obtained.
C. bombicola ATCC 22214 ura− is transformed as previously described (van Bogaert et al. Yeast. 2008. 25:273-278); van Bogaert et al. FEMS Yeast Res. 2009. 9:610-617).
To verify the insertion of the integration/overexpression cassettes for the overexpression CbSBG1, CbSBG2, CbSBG3, CbSBG4 and CbSBG5 and of the control cassette ExCat into the LEU2 locus of C. bombicola ATCC 22214 ura−, the LEU2 locus of in each case 5 transformants (after transformation of the integration/overexpression cassettes for CbSBG1, CbSBG2, CbSBG3, CbSBG4 and CbSBG5 and of the control cassette ExCat) and of C. bombicola ATCC 22214 ura− is amplified by colony PCR. The following oligonucleotides are employed:







LEU2-KI-fw:


(SEQ ID NO: 50)


5′- GTG CCC GAC CAC CAT GAG CTG TC -3′


 


LEU2-KI-rv:


(SEQ ID NO: 51)


5′- CCC AAG CAT GAG GGT CGT GCC GG -3′






The following parameters are employed in the PCR: 1×: initial denaturation, 94° C., 3 min; 25×: denaturation, 94° C., 1:00 min, annealing, 60° C., 1:00 min; elongation, 72° C., 5:00 min; 1×: terminal elongation, 72° C., 10 min. The Taq PCR Master Mix Kit from Qiagen (Hilden) is employed for the amplification following the manufacturer's recommendations. In each case 10 μl of the PCR reactions are subsequently separated on a 0.8% agarose gel. The procedure of the PCR, of the agarose gel electrophoresis, staining the DNA with ethidium bromide and determining the PCR fragment sizes are all performed in a manner with which the skilled worker is familiar.
The amplification of the corresponding loci should give rise to the PCR fragment sizes specified in Table 6:







TABLE 6







Expected PCR fragment sizes upon amplification of the


chromosomal LEU2 locus following homologous recombination of the


SBG1, SBG2, SBG3, SBG4 and SBG5 expression cassettes and the


control cassette ExCat into the chromosomal C. bombicola LEU2


locus and upon nonhomologous integration.












Size of the PCR





product upon





homologous
Size of the PCR product upon




integration into
nonhomologous integration at



Gene
the CbLEU2 locus
a different site of the genome






SBG1
5452 bp
2235 bp



SBG2
5227 bp
2235 bp



SBG3
4615 bp
2235 bp



SBG4
7735 bp
2235 bp



SBG5
5125 bp
2235 bp



ExCat
3844 bp
2235 bp









Upon amplification of the LEU2 locus from C. bombicola ATCC 22214 ura−, only the fragment expected when the wild-type situation is present, which has a size of 2.2 kbp, is obtained.
Upon amplification of the LEU2 locus from C. bombicola ATCC 22214 transformants after transformation with integration/overexpression cassettes for the overexpression of CbSBG1, CbSBG2 mod, CbSBG3, CbSBG4 mod and CbSBG5, only the fragment sizes expected upon successful chromosomal integration of the integration/overexpression cassettes IntEx-CbSBG1 (SEQ ID NO:70), IntEx-CbSBG2 (SEQ ID NO:71), IntEx-CbSBG3 (SEQ ID NO:72), IntEx-CbSBG4 (SEQ ID NO:73) and IntEx-CbSBG5 (SEQ ID NO:74), which are approximately 5.5 kbp, 5.2 kbp, 4.6 kbp, 7.7 kbp and 5.1 kbp, respectively, are obtained.
Thus, it is possible to identify in all five cases clones in which it was possible to bring the genes CbSBG1, CbSBG2, CbSBG3, CbSBG4 or CbSBG5 under the control of the C. bombicola ATCC 22214 TSC3 promoter so that it is possible to postulate the overexpression.
The strains in question are hereinbelow referred to as C. bombicola ATCC 22214 PTSC3-SBG1-TTSC3, C. bombicola ATCC 22214 PTSC3-SBG2-TTSC3, C. bombicola ATCC 22214 PTSC3-SBG3-TTSC3, C. bombicola ATCC 22214 PTSC3-SBG4-TTSC3 and C. bombicola ATCC 22214 PTSC3-SBG5-TTSC3.
Example 5
Characterization of the Sophorolipid Formation by C. bombicola ATCC 22214 ExCat, C. bombicola ATCC 22214 PTSC3-SBG1-TTSC3, C. bombicola ATCC 22214 PTSC3-SBG2-TTSC3, C. bombicola ATCC 22214 PTSC3-SBG3-TTSC3, C. bombicola ATCC 22214 PTSC3-SBG4-TTSC3 and C. bombicola ATCC 22214 PTSC3-SBG5-TTSC3 
The propagation of the strains C. bombicola ATCC 22214 ExCat, C. bombicola ATCC 22214 PTSC3-SBG1-TTSC3, C. bombicola ATCC 22214 PTSC3-SBG2-TTSC3, C. bombicola ATCC 22214 PTSC3-SBG3-TTSC3, C. bombicola ATCC 22214 PTSC3-SBG4-TTSC3 and C. bombicola ATCC 22214 PTSC3-SBG5-TTSC3 is performed on YPD agar plates. The medium referred to hereinbelow as SL production medium is used for producing the sophorolipids. This medium is composed of 0.1% KH2PO4, 0.5% MgSO4×7H2O, 0.01% FeCl3, 0.01% NaCl, 0.01% uracil, 0.4% yeast extract, 0.1% urea, 10.5% rapeseed oil and 10% glucose. The pH is brought to 4.5 and the medium is then sterilized in an autoclave (121° C., 20 min). It is not necessary to adjust the pH during the cultivation.
To study the sophorolipid production in the shake flask, a preculture is first established. To this end, 10 ml of YPD medium in a 100 ml Erlenmeyer flask are inoculated with one loop of a strain freshly plated onto a YPD agar plate. Cultivation was done overnight at 30° C. and 200 rpm. This preculture is used hereinbelow for inoculating 100 ml of SL medium in a 1000 ml Erlenmeyer flask (starting OD600 0.2). The cultures are grown for 7 days at 200 rpm and 30° C., and a sample of 2 ml of broth is taken every day, good care being taken that the culture medium was mixed thoroughly before sampling.
The samples are prepared for the subsequent chromatographic analyses as follows: using a positive-displacement pipette (Combitip), 800 μl of acetone are placed into a 2-ml reaction vessel and the reaction vessel is sealed immediately to minimize evaporation. 200 μl of broth are added. After vortexing the broth/acetone mixture, the latter is centrifuged for 1 min at 13 000 rpm, and 800 μl of the supernatant are transferred into an HPLC vessel. An evaporative light scattering detector (ELSD) is used for the detection and quantitative determination of sophorolipids and/or oleic acid. The actual measurement is performed by means of the Agilent Technologies 1200 series (Santa Clara, Calif.) and the Zorbax SB-C8 Rapid Resolution column (4.6×150 mm, 3.5 μm, Agilent). The injection volume is 5 μl, and the running time of the method is 20 min. The mobile phase used is H2O and 0.1% of TFA (trifluoroacetic acid, solution A) and methanol (solution B). The column temperature is 40° C. The detectors used were the ELSD (detector temperature 60° C.) and the DAD (diode array, 210 nm). The gradient used in the method is shown in Table 3.
Like the control strain C. bombicola ATCC 22214 ExCat, all strains produce sophorolipids. However, the strains C. bombicola ATCC 22214 PTSC3-SBG1-TTSC3, C. bombicola ATCC 22214 PTSC3-SBG2-TTSC3, C. bombicola ATCC 22214 PTSC3-SBG3-TTSC3, C. bombicola ATCC 22214 PTSC3-SBG4-TTSC3 and C. bombicola ATCC 22214 PTSC3-SBG5-TTSC3 show an increased space-time yield of the sophorolipid formation in comparison with C. bombicola ATCC 22214 ExCat. While C. bombicola ATCC 22214 ExCat produces approximately 2 mg of sophorolipids per liter, hour and OD600 under the conditions chosen, these parameters are between 2.5 mg and 6 mg for the strains C. bombicola ATCC 22214 PTSC3-SBG1-TTSC3, C. bombicola ATCC 22214 PTSC3-SBG2-TTSC3, C. bombicola ATCC 22214 PTSC3-SBG3-TTSC3, C. bombicola ATCC 22214 PTSC3-SBG4-TTSC3 and C. bombicola ATCC 22214 PTSC3-SBG5-TTSC3. Thus, it is possible to demonstrate that enhancing the enzymes CbSBG1, CbSBG2, CbSBG3, CbSBG4 and CbSBG5 in C. bombicola ATCC 22214 results in an increased sophorolipid formation.
Example 6
Vector pTZ_E02_His-GlcTrI for Overexpressing the Candida bombicola Gene SBG2 with N-Terminal His-tag
To overexpress the Candida bombicola ATCC22214 gene SBG2 (SEQ ID NO:03) in Escherichia coli, the plasmid pTZ_E02_His-GlcTrI was constructed. Chromosomal DNA from Candida bombicola ATCC22214 was used as the template for a PCR with the “ExpandTM High Fidelity” PCR kit from Roche Diagnostics (Mannheim), following the manufacturer's information. The SBG2 gene was amplified from the chromosomal DNA with the aid of oligonucleotides 1373_GlcTrI_BsmBI_His_fp (SEQ ID NO:76) and 1373_GlcTrI_AscI_rp (SEQ ID NO:77) (“PCR protocols. A guide to methods and applications”, 1990, Academic Press) and in this manner provided at the 5′ end with a 6-fold N-terminal histidine tag. In addition, the cleavage sites BsmBI and AscI were introduced. The following oligonucleotides were employed:







1373_GlcTrI_BsmBI_His_fp (SEQ ID NO: 76):


5′-AAACGTCTCAGATGCACCACCACCACCACCACATGGTTGTAAACTCC


 


TCG-3′


 


1373_GlcTrI_AscI_rp (SEQ ID NO: 77):


5′-AAAGGCGCGCCCTAGACCTTCTGGTTAGCG-3′






The PCR product (1435 bp) was purified by means of the QIAquick PCR purification kit (Qiagen, Hilden) following the manufacturer's instructions, cleaved with BsmBI and AscI and subsequently ligated into the expression vector pTZ_E02 (pET24d-based vector; Merck Chemicals, Darmstadt) from Trenzyme GmbH, Konstanz, which had been cleaved in the same manner. The resulting plasmid pTZ_E02_His-GlcTrI (SEQ ID NO:78) is 6700 base pairs in size. The ligation and the transformation of chemically competent E. coli DH5α cells (Gibco-BRL, Karlsruhe) were performed in the manner known to the skilled worker.
The authenticity of the insert was verified by a DNA sequence analysis.
The plasmid pTZ_E02_His-GlcTrI was introduced into the strains Escherichia coli BL21(DE3) and Escherichia coli Rosetta (DE3) (both from Merck Chemicals, Darmstadt) by means of transformation. The resulting strains were named E. coli BL21(DE3)/pTZ_E02_His-GlcTrI and E. coli Rosetta (DE3)/pTZ_E02_His-GlcTrI.
Example 7
Vector pTZ_E02_His-GlcTrII for Overexpressing the Candida bombicola Gene SBG5 with N-Terminal His-Tag
To overexpress the Candida bombicola ATCC22214 gene SBG5 SEQ ID NO:06) in Escherichia coli, the plasmid pTZ_E02_His-GlcTrII was constructed. Chromosomal DNA from Candida bombicola ATCC22214 was used as the template for a PCR with the “ExpandTM High Fidelity” PCR kit from Roche Diagnostics (Mannheim), following the manufacturer's information. The SBG5 gene was amplified from the chromosomal DNA with the aid of oligonucleotides 1373_GlcTrII_BsmBI_His_fp (SEQ ID NO:79) and 1373_GlcTrII_AscI_rp (SEQ ID NO:80) (“PCR protocols. A guide to methods and applications”, 1990, Academic Press) and in this manner provided at the 5′ end with a 6-fold N-terminal histidine tag. In addition, the cleavage sites BsmBI and AscI were introduced. The following oligonucleotides were employed:







1373_GlcTrII_BsmBI_His_fp (SEQ ID NO: 79):


5′-AAACGTCTCAGATGCACCACCACCACCACCACATGGCCATCGAGAAA


 


CCAG-3′


 


1373_GlcTrII_AscI_rp (SEQ ID NO: 80):


5′-AAAGGCGCGCCTTAAGAAGCTAATTCACTAATTGCC-3′






The PCR product (1342 bp) was purified by means of the QIAquick PCR purification kit (Qiagen, Hilden) following the manufacturer's instructions, cleaved with BsmBI and AscI and subsequently ligated into the expression vector pTZ_E02 (pET24d-based vector; Merck Chemicals, Darmstadt) from Trenzyme GmbH, Konstanz, which had been cleaved in the same manner. The resulting plasmid pTZ_E02_His-GlcTrII (SEQ ID NO:81) is 6607 base pairs in size. The ligation and the transformation of chemically competent E. coli DH5α cells (Gibco-BRL, Karlsruhe) were performed in the manner known to the skilled worker.
The authenticity of the insert was verified by a DNA sequence analysis.
The plasmid pTZ_E02_His-GlcTrII was introduced into the strains Escherichia coli BL21(DE3) and Escherichia coli Rosetta (DE3) (both from Merck Chemicals, Darmstadt) by means of transformation. The resulting strains were named E. coli BL21(DE3)/pTZ_E02_His-GlcTrII and E. coli Rosetta (DE3)/pTZ_E02_His-GlcTrII.
Example 8
Vector pTZ_E02_His-AcTr for Overexpressing the Candida bombicola Gene SBG3 with N-terminal His-Tag
To overexpress the Candida bombicola ATCC22214 gene SBG3 (SEQ ID NO:04) in Escherichia coli, the plasmid pTZ_E02_His-AcTr was constructed. Chromosomal DNA from Candida bombicola ATCC22214 was used as the template for a PCR with the “ExpandTM High Fidelity” PCR kit from Roche Diagnostics (Mannheim), following the manufacturer's information. The SBG3 gene was amplified from the chromosomal DNA with the aid of oligonucleotides 1373_AcTr_BsmBI_His_fp (SEQ ID NO:82) and 1373_AcTr_AscI_rp (SEQ ID NO:83) (“PCR protocols. A guide to methods and applications”, 1990, Academic Press) and in this manner provided at the 5′ end with a 6-fold N-terminal histidine tag. In addition, the cleavage sites BsmBI and AscI were introduced. The following oligonucleotides were employed:







1373_AcTr_BsmBI_His_fp (SEQ ID NO: 82):


5′-AAACGTCTCAGATGCACCACCACCACCACCACATGGTTGTAAACTCC


 


TCG-3′


 


1373_AcTr_AscI_rp (SEQ ID NO: 83):


5′-AAAGGCGCGCCCTAGACCTTCTGGTTAGCG-3′






The PCR product (823 bp) was purified by means of the QIAquick PCR purification kit (Qiagen, Hilden) following the manufacturer's instructions, cleaved with BsmBI and AscI and subsequently ligated into the expression vector pTZ_E02 (pET24d-based vector; Merck Chemicals, Darmstadt) from Trenzyme GmbH, Konstanz, which had been cleaved in the same manner. The resulting plasmid pTZ_E02_His-AcTr (SEQ ID NO:84) is 6088 base pairs in size. The ligation and the transformation of chemically competent E. coli DH5α cells (Gibco-BRL, Karlsruhe) were performed in the manner known to the skilled worker.
The authenticity of the insert was verified by a DNA sequence analysis.
The plasmid pTZ_E02_His-AcTr was introduced into the strains Escherichia coli BL21(DE3) and Escherichia coli Rosetta (DE3) (both from Merck Chemicals, Darmstadt) by means of transformation. The resulting strains were named E. coli BL21(DE3)/pTZ_E02_His-AcTr and E. coli Rosetta (DE3)/pTZ_E02_His-AcTr.
Example 9
Heterologous Expression of the Enzymes SBG2, SBG3 and SBG5 Involved in Sophorolipid Biosynthesis
In each case one single colony of the E. coli strains constructed under item 1-3 was first grown for 8 hours in 5 ml of LB medium (10 g/l tryptone, 5 g/l yeast extract, 10 g/l NaCl) with 50 μg/ml kanamycin at 37° C. and 175 rpm. Thereafter, 100 ml of LB medium in 500 ml shake flasks were inoculated with the first preculture and grown overnight at 37° C. and 175 rpm. On the next morning, 1 l of LB medium with a starting OD600 of 0.1 were inoculated with the second preculture (5-1 shake flask). All cultures were incubated at 37° C. and 175 rpm. The growth of the cultures was monitored with reference to the apparent optical density (OD600). When an OD600 of  ̃0.3 was reached, the culture temperature was reduced from 37° C. to 20° C. The expression of the target genes in question was induced at an OD600 of 0.6 by adding 0.5 mM IPTG (final concentration). During all of the culture steps, the relevant antibiotics were added (kanamycin 50 μg/ml). Samples for analyses were taken both before the addition of IPTG and 24 h after the induction. The cells were disrupted by Bugbuster (Merck Chemicals, Darmstadt) following the manufacturer's instructions in order to separate soluble and insoluble proteins from each other. Comparable amounts of the cell extracts were separated by means of SDS-PAGE and the gels were subsequently stained with colloidal Coomassie. An overproduction in the soluble cell extract fraction was detected for all three recombinantly produced proteins Sbg2p, Sbg3p and Sbg5p with His tags.
Example 10
Purification of the Enzymes Sbg2p, Sbg3p and Sbg5p Involved in Sophorolipid Biosynthesis
24 h after induction of the gene expression the cells were harvested by centrifugation (8000 g, 20 min, 4° C.). 1 liter of culture resulted in  ̃5 g fresh biomass. The cell pellets were resuspended in 100 ml of buffer A (100 mM Tris, pH 7.8, 50 mM NaCl, 20 mM imidazole) which additionally comprised a protease inhibitor (Roche, Order No. 11 873 580 001). The resuspended cells were disrupted by six passages through a Microfluidizer. After a further centrifugation step (10 000 g, 20 min, 4° C.), the supernatant was filtered (pore diameter: 0.45 μm) to give the soluble protein fraction. The target proteins were purified via a his-tag affinity chromatography column (GE, HisTrap FF 1 ml columns, Order No. 17-5319-01). The flow rate was 1 ml/min. A linear elution from 0-100% with buffer B (100 mM Tris, pH 7.8, 50 mM NaCl, 500 mM imidazole) was performed. To this end, 20-fold column volume of buffer B was employed, and 2 ml fractions were collected. The eluate fractions with protein were pooled and concentrated by means of a filtration unit (Amicon Ultra-15, NMWL 10 kDa Centricons, Millipore, Order No. UFC901024). Thereafter, the respective protein fractions were subjected to a buffer exchange into the final buffer (100 mM Tris, pH 7.8, 50 mM NaCl) by gel filtration with Sephadex 25 (PD-10 columns, GE, Order No. 17-0851-01). The protein purification was verified by SDS-PAGE. 3.3 mg of Sbg2p (protein concentration 1.0 μg/μl), 7.3 mg of Sbg5p (protein concentration 2.2 μg/μl) and 6.9 mg of Sbg3p (protein concentration 2.1 μg/μl) were isolated from 1 l of culture.
Example 11
Characterization of the Enzymes Sbg2p, Sbg3p and Sbg5p Involved in Sophorolipid Biosynthesis
To detect the function of the enzymes Sbg2p, Sbg3p and Sbg5p which are involved in sophorolipid biosynthesis, enzyme assays were performed with the three isolated enzymes Sbg2p, Sbg3p and Sbg5p, in each case individually and in all possible combinations. This was done in a total volume of 350 μl, following the scheme hereinbelow:







TABLE 7







Composition of the enzyme assay mixtures in μl
















1
2
3
4
5
6
7
8


















10 mM Tris-HCl (pH 7.5)
327.5
277.5
227.5
277.5
177.5
227.5
177.5
227.5


125 mM UDP-glucose
5
5
5
5
5
5
5
5


100 mM Acetyl-CoA
3.5
3.5
3.5
3.5
3.5
3.5
3.5
3.5


Sbg3p (2.1 μg/μl)
—
50
—
—
50
50
—
50


Sbg2p (1 μg/μl)
—
—
100
—
100
—
100
100


Sbg5p (2.2 μg/μl)
—
—
—
50

50
50
50


13.4 mM 18-hydroxy-z-9-
14
14
14
14
14
14
14
14


octadecenoic acid










Σ
350
350
350
350
350
350
350
350









The reaction was started by adding 14 μl of 13.4 mM solution of the substrate (18-hydroxy-Z-9-octadecenoic acid) in ethanol and incubated for 6 h at 30° C., with shaking (600 rpm). Thereafter, the reaction was stopped by adding 1.4 ml of acetone. Undissolved components were sedimented by centrifugation (16 100 g, 5 min, RT). The supernatant was subsequently transferred into a fresh container and concentrated by vacuum evaporator (25° C.) to the original reaction volume (350 μl). The samples were analyzed by LC-ESI-MS, and the products were identified by analyzing the corresponding mass trajectories and the MS spectra.
To identify the products formed, 5 μl were injected into a UPLC system Accela (Thermo Scientific, Dreieich). The substances to be studied were analyzed with a semi-UPLC column “Pursuit XRs ULTRA” (C8, 2.8 μm, 2.1×100 mm) (Varian, Darmstadt). The separation was performed within 25 min using a gradient composed of the mobile phase A1 (H2O, 0.1% (v/v) TFA) and the mobile phase B1 (methanol, 0.1% (v/v) TFA) with a flow rate of 0.3 ml/min at 40° C. The course of the gradient over time is shown in Table 8.







TABLE 8







Course of the HPLC gradient










Mobile
Mobile


Time
phase A1
phase B1


[min]
[%]
[%]












0
30
70


15
0
100


25
0
100


25.01
30
70


32
30
70









The detection was by DAD detector in the wavelength range of 200-600 nm and mass-selectively with a highly-resolving FT-ICR mass spectrometer LTQ-FT (Thermo Scientific, Dreieich) in the scanning range m/z 100-1000. Ionization was by ESI (electrospray ionization). The precise masses and the empirical chemical formulae were determined with the aid of the FT-ICR mass analyzer with a resolution of R=100 000 and a mass accuracy of ≦2 ppm.
The control reaction used was a mixture which only comprised the substrates UDP-glucose, acetyl-CoA and 18-hydroxy-Z-9-octadecenoic acid, but no enzymes (see Table 7). In this sample, only the substrate 18-hydroxy-Z-9-octadecenoic acid (C18H34O3; 298.2502 g/mol) was detected by MS.
Mixture 2 (see Table 7) comprised, besides the substrates, 105 μg of Sbg3p. As in mixture 1, only 18-hydroxy-Z-9-octadecenoic acid was detected in this sample. Mixture 3 (see Table 7) comprised, besides the substrates, 100 μg of Sbg2p. Besides the substrate 18-hydroxy-Z-9-octadecenoic acid, 18-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid (empirical formula C24H44O8; molecular weight 460.3031 g/mol) was detected. This proves that Sbg2p is capable of converting UDP-glucose and 18-hydroxy-Z-9-octadecenoic acid into 18-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid.
Mixture 4 (see Table 7) comprised, besides the substrates, in addition 110 μg of Sbg5p. Besides the substrate 18-hydroxy-Z-9-octadecenoic acid, 18-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and 18-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid (empirical formula C30H54O13; molecular weight 622.3559 g/mol) were detected. This proves that Sbg5p is capable of converting UDP-glucose and 18-hydroxy-Z-9-octadecenoic acid into 18-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and further into 18-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid.
Mixture 5 (see Table 7) comprised, besides the substrates, additionally 100 μg of Sbg2p and 105 μg of Sbg3p. Besides the substrate 18-hydroxy-Z-9-octadecenoic acid, 18-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and 18-(6-O-acetyl-β-D-glucopyranosyloxy)-Z-9-octadecenoic acid (empirical formula C26H46O9; molecular weight 502.3136 g/mol) were detected. This confirms that, as has already been demonstrated for mixture 3, Sbg2p is capable of converting UDP-glucose and 18-hydroxy-Z-9-octadecenoic acid into 18-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and it proves furthermore that Sbg3p is capable of acetylating 18-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid in the presence of acetyl-CoA to give 18-(6-O-acetyl-β-D-glucopyranosyloxy)-Z-9-octadecenoic acid.
Mixture 6 (see Table 7) comprised, besides the substrates, additionally 110 μg of Sbg5p and 105 μg of Sbg3p. Besides the substrate 18-hydroxy-Z-9-octadecenoic acid, 18-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid, 18-(6-O-acetyl-β-D-glucopyranosyloxy)-Z-9-octadecenoic acid, 18-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid, 18-L-[(6′-O-acetyl-2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid (empirical formula C32H56O14; molecular weight 664.3665 g/mol) and 18-L-[(6′-O-acetyl-2′-O-β-D-glucopyranosyl-6′′-O-acetyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid (empirical formula C34H58O15; molecular weight 706.3770 g/mol) were detected. This confirms that, as has already been demonstrated for mixture 4, Sbg5p is capable of converting UDP-glucose and 18-hydroxy-Z-9-octadecenoic acid into 18-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and further into 18-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid and furthermore proves that the formed products can be acetylated by Sb3gp in the presence of acetyl-CoA to give 18-L-[(6′-O-acetyl-2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid and/or 18-L-[(2′-O-β-D-glucopyranosyl-6′′-O-acetyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid and also 18-L-[(6′-O-acetyl-2′-O-β-D-glucopyranosyl-6′′-O-acetyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid. Mixture 7 (see Table 7) comprised, besides the substrates, additionally 100 μg of Sbg2p and 110 μg of Sbg5p. Besides the substrate 18-hydroxy-Z-9-octadecenoic acid, 18-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and 18-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid were detected. This proves that Sbg2p and Sbg5p are capable of converting, in one mixture, UDP-glucose and 18-hydroxy-Z-9-octadecenoic acid into 18-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and further into 18-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid.
Mixture 8 (see Table 7) comprised, besides the substrates, additionally 100 μg of Sbg2p, 105 μg of Sbg3p and 110 μg of Sbg5p. Besides the substrate 18-hydroxy-Z-9-octadecenoic acid, 18-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid, 18-(6-O-acetyl-β-D-glucopyranosyloxy)-Z-9-octadecenoic acid, 18-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid, 18-L-[(6′-O-acetyl-2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid and 18-L-[(6′-O-acetyl-2′-O-β-D-glucopyranosyl-6′′-O-acetyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid were detected. This confirms that, as has already been mentioned for mixture 7, Sbg2p and Sbg5p together are capable of converting UDP-glucose and 18-hydroxy-Z-9-octadecenoic acid into 18-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and further into 18-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid and also proves that, as has already been demonstrated for mixtures 5 and 6, the formed products are capable of being acetylated by Sbg3p in the presence of acetyl-CoA to give 18-L-[(6′-O-acetyl-2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid and/or 18-L-[(2′-O-β-D-glucopyranosyl-6′′-O-acetyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid and also 18-L-[(6′-O-acetyl-2′-O-β-D-glucopyranosyl-6′′-O-acetyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid.
Example 12
Alternative Route to Inactivating Acetyltransferase (SBG3) in Candida bombicola ATCC 22214
In an alternative route, the gene SBG3 was inactivated individually, and the phenotype of the corresponding mutant was characterized in terms of the sophorolipid biosynthesis. To construct the corresponding mutant in C. bombicola ATCC 22214, a deletion cassette for CbSBG3 was first synthesized by GeneArt AG (Regensburg) (SEQ ID NO:14; cf. Example 2). Thereafter, the gene CbURA3, from Trenzyme GmbH (Konstanz), which encodes the C. bombicola ATCC 22214 orotidine-5-phosphate decarboxylase (van Bogaert et al. Yeast. 2007. 24(3):201-8) was substituted by a hygromycin resistance cassette. To this end, the hygromycin cassette was amplified from the DNA of the vector p-Col-5 (SEQ ID NO:85) using the following oligonucleotides:









1390_hygR_fp_EcoRV:



(SEQ ID NO: 86)



5′- AAA GAT ATC TCT ATG CGC ACC CGT TCT



 



C -3′



 



1390_hygR_rp_Hind/Bgl:



(SEQ ID NO: 87)



5′- TTT AGA TCT AAG CTT GAG ACA CCT CAG



 



CAT GCA CCA TTC -3′






The following parameters were employed for the PCR: 1×: initial denaturation, 98° C., 3 min; 25×: denaturation, 98° C., 0:10 min, annealing, 60° C., 0:30 min; elongation, 72° C., 2:00 min; 1×: terminal elongation, 72° C., 10 min. The PhusionTM High-Fidelity Master Mix from New England Biolabs (Frankfurt) was used for the amplification following the manufacturer's recommendations. The PCR product was purified by means of the QIAquick PCR purification kit (Qiagen, Hilden) following the manufacturer's instructions. The PCR product obtained had a size of 1831 bp. The PCR procedure, the verification of the successful amplification of the PCR by means of agarose gel electrophoresis, the staining of the DNA with ethidium bromide, the determination of the PCR fragment sizes, the purification of the PCR products and the determination of the DNA concentration were carried out in a manner known to the skilled worker. The hygromycin cassette was cloned into the vector pCR4_AcTr_URA (SEQ ID NO:88) by linearizing the vector with the restriction endonucleases BglII and PmlI. The insert was prepared for the subsequent ligation using the restriction endonucleases EcoRV and BglII. The ligation and the subsequent transformation into E. coli DH5α cells were carried out in a manner known to the skilled worker. The authenticity of the insert was verified by DNA sequence analysis.
The plasmid generated was named pCR4_AcTr_HygR (SEQ ID NO:89) and has a size of 8578 bp.
The deletion cassette CbSbg3-hyg (SEQ ID NO:90) is composed of the Klebsiella pneumoniae hygromycin resistance gene (hph), which encodes the hygromycin B phosphatase (Gritz L and Davies J 1983 Plasmid-encoded hygromycin B resistance: the sequence of hygromycin B phosphotransferase gene and its expression in Escherichia coli and Saccharomyces cerevisiae. Gene 25 (2-3): 179-188). The promoter for the resistance gene is the constitutive hybrid promoter hp4d (Madzak et al. 2000, Strong hybrid promoters and integrative expression/secretion vectors for quasi-constitutive expression of heterologous proteins in the yeast Yarrowia lipolytica. J. Mol. Microbiol. Biotechnol. 2, 207-216). The resistance gene is flanked by the terminator of the XPR2 gene, which encodes an extracellular protease from Y. lipolytica (Nicaud et al. 1989a. Cloning, sequencing and amplification of the alkaline extracellular protease (XPR2) gene of the yeast Yarrowia lipolytica. J. Biotechnol. 12, 285-298). The resistance gene is flanked upstream and downstream by approximately 1000 by of the adjoining region of the gene to be inactivated.
loxP-Loci which optionally permit the deletion of the hph gene by temporarily producing the Cre-recombinase-encoding gene and permit its functional expression (for an overview, see Kühn & Torres. Methods Mol. Biol. 2002. 180:175-204) were introduced in each case between the flanking regions and the hph gene. The deletion cassette is constructed following the information in Table 9 hereinbelow:







TABLE 9







Structure of the deletion cassette for the Sbg3p-encoding


structural gene of C. bombicola ATCC 22214.













SEQ

5′-



3′-


ID

flanking
loxP

loxP
flanking


NO:
Gene
region
locus 1
hph
locus 2
region





90
SBG3
1-1033
1034-1066
1067-3599
3600-3633
3634-4635









To provide the deletion cassette for the subsequent transformation of C. bombicola ATCC 22214 in a sufficient amount, it was amplified by PCR. The following oligonucleotides were used:
Amplification of the Deletion Cassette for the Inactivation of CbSBG3:









SBG3-fw:



(SEQ ID NO: 21)



5′- TGC AGA CAA GTT CCT GCA GCT G -3′



 



SBG3-rv:



(SEQ ID NO: 22)



5′- ATG CTT TAT TCA GGC ACG CTA CG -3′






The following parameters were employed for the PCR: 1×: initial denaturation, 98° C., 3 min; 25×: denaturation, 98° C., 0:10 min, annealing, 60° C., 0:30 min; elongation, 72° C., 2:00 min; 1×: terminal elongation, 72° C., 10 min. The PhusionTM High-Fidelity Master Mix from New England Biolabs (Frankfurt) was used for the amplification following the manufacturer's recommendations. The PCR product was purified by means of the QIAquick PCR purification kit (Qiagen, Hilden) following the manufacturer's instructions. The PCR procedure, the verification of the successful amplification of the PCR by means of agarose gel electrophoresis, the staining of the DNA with ethidium bromide, the determination of the PCR fragment sizes, the purification of the PCR products and the determination of the DNA concentration were carried out in a manner known to the skilled worker.
Transformation of C. bombicola ATCC 22214 was as described before (van Bogaert et al. Yeast. 2008. 25:273-278); van Bogaert et al. FEMS Yeast Res. 2009. 9:610-617). To verify the deletion of the gene SBG3 in C. bombicola ATCC 22214 transformants following transformation with the deletion cassette for CbSBG3 (SEQ ID NO:90), the respective locus was amplified from in each case 5 transformants and C. bombicola ATCC 22214 by means of colony PCR. The following oligonucleotides were used:
Verification of the Genomic Deletion of CbSBG3:







SBG3-KO-fw:


(SEQ ID NO: 31)


5′- CAA ATT TAT CTG GGA GCA CAG TTA CAT 


 


TGC -3′


 


SBG3-KO-rv:


(SEQ ID NO: 32)


5′- CAC ACA TTG CTT TAG TCC AGC AAG AAC C -3′






The following parameters were employed for the PCR: 1×: initial denaturation, 94° C., 3 min; 25×: denaturation, 94° C., 1:00 min, annealing, 60° C., 1:00 min; elongation, 72° C., 5:00 min; 1×: terminal elongation, 72° C., 10 min. The Taq PCR Master Mix Kit from Qiagen (Hilden) was used for the amplification following the manufacturer's recommendations. In each case 10 μl of the PCR reactions were subsequently separated on a 0.8% agarose gel. The procedure of the PCR, of the agarose gel electrophoresis, the staining of the DNA with ethidium bromide and the determination of the PCR fragment sizes were performed in a manner known to the skilled worker.
Upon amplification of the CbSBG3 locus from C. bombicola ATCC 22214, only the fragment sizes to be expected when the wild-type situation is present, i.e. 2839 bp, were determined.
Upon amplification of the SBG3 locus from transformants following the transformation of the deletion cassette CbSBG3-hyg, only the fragment size to be expected after the successful deletion of CbSBG3 from the chromosome, i.e. 4693 bp, was obtained.
In this manner, it was possible to identify clones in which the gene CbSBG3 had been deleted from the chromosome. The strain in question was henceforth referred to as C. bombicola ATCC 22214 sbg3-hyg.
Example 13
Characterization of the Sophorolipid Formation by C. bombicola ATCC 22214 sbg3-hyg
The strains C. bombicola ATCC 22214 and C. bombicola ATCC 22214 sbg3-hyg were propagated on YPD agar plates. The medium referred to hereinbelow as SL production medium was used for producing the sophorolipids. This medium is composed of 0.1% KH2PO4, 0.5% MgSO4×7H2O, 0.01% FeCl3, 0.01% NaCl, 0.4% yeast extract, 0.1% urea, 10.5% rapeseed oil and 10% glucose. The pH is brought to 4.5 and the medium is then sterilized in an autoclave (121° C., 20 min). It is not necessary to adjust the pH during the cultivation.
To study the sophorolipid production in the shake flask, a preculture was first established. To this end, 10 ml of YPD medium in a 100 ml Erlenmeyer flask were inoculated with one loop of a strain freshly plated onto a YPD agar plate. Cultivation was done overnight at 30° C. and 200 rpm. This preculture was used hereinbelow for inoculating 100 ml of SL medium in a 1000 ml Erlenmeyer flask (starting OD600 0.2). The cultures were grown for 7 days at 200 rpm and 30° C., and a sample of 2 ml of broth was taken every day, good care being taken that the culture medium was mixed thoroughly before sampling.
The samples were prepared for the subsequent chromatographic analyses as follows: using a positive-displacement pipette (Combitip), 800 μl of acetone were placed into a 2-ml reaction vessel and the reaction vessel was sealed immediately to minimize evaporation. 200 μl of broth were added. After vortexing the broth/acetone mixture, the latter was centrifuged for 1 min at 13 000 rpm, and 800 μl of the supernatant were transferred into an HPLC vessel.
An evaporative light scattering detector (ELSD) was used for the detection and quantitative determination of sophorolipids and/or oleic acid. The actual measurement was performed by means of the Agilent Technologies 1200 series (Santa Clara, Calif.) and the Zorbax SB-C8 Rapid Resolution column (4.6×150 mm, 3.5 μm, Agilent). The injection volume was 5 μl, and the running time of the method was 20 min. The mobile phase used was H2O and 0.1% of TFA (trifluoroacetic acid, solution A) and methanol (solution B). The column temperature was 40° C. The detectors used were the ELSD (detector temperature 60° C.) and the DAD (diode array, 210 nm). The gradient used in the method is shown in Table 10 hereinbelow.







TABLE 10







Description of the gradient profile of the mobile phase to be used


for the HPLC-based quantification of sophorolipids.











Flow rate


t [min]
Solution B %
[ml/min]












0.00
70%
1.00


15.00
100%
1.00


15.01
70%
1.00


20.00
70%
1.00









The analysis showed that both C. bombicola ATCC 22214 and C. bombicola ATCC 22214 sbg3-hyg produce sophorolipids. It was confirmed by LC-MS2 that, in contrast to the sophorolipids formed by C. bombicola ATCC 22214, the sophorolipids formed by C. bombicola ATCC 22214 sbg3-hyg exclusively correspond to compounds of the general formulae (Ia) and (Ib) in which R1=H and R2=H (see FIGS. 1 and 2) and that the concentration of these compounds is increased by the factor 10 in comparison with C. bombicola ATCC 22214. This proves the function of Sbg3p as acetyltransferase in sophorolipid biosynthesis.

## Claims

1. An isolated or purified sophorolipid-producing cell transformed with a nucleic acid encoding:
(a) the polypeptide of SEQ ID NO: 8; or
(b) a polypeptide which catalyzes the conversion of UDP-glucose and 17-hydroxy-Z-9-octadecenoic acid into 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid, wherein said polypeptide comprises a variant of the amino acid sequence of SEQ ID NO: 8 which is identical to SEQ ID NO: 8 except that at least one residue up to 5% of the amino acid residues of SEQ ID NO: 8 have been modified by deletion, substitution, and/or insertion;
wherein said cell may optionally contain a nucleic acid encoding at least one E1, E3, E4 or E5 polypeptide, or wherein said cell may optionally have a disruption in an endogenous gene encoding an E3 and/or E4 polypeptide;
wherein
E1 comprises (a) an amino acid sequence selected from the group consisting of SEQ ID NO: 7, 53, 55, 57, 59, 61 and 63; or (b) comprises a variant of the amino acid sequence of SEQ ID NO: 7, 53, 55, 57, 59, 61 or 63 which is identical to the amino acid sequence of SEQ ID NO: 7, 53, 55, 57, 59, 61 or 63 except that at least one residue up to 5% of the amino acid residues of SEQ ID NO: 7, 53, 55, 57, 59, 61 or 63 have been modified by deletion, substitution, and/or insertion, wherein the E1 polypeptide has the ability to catalyze the conversion of Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid;
E3 comprises (a) the amino acid sequence of SEQ ID NO: 11; or (b) comprises a variant of the amino acid sequence of SEQ ID NO: 11 which is identical to the amino acid sequence of SEQ ID NO: 11 except that at least one residue up to 5% of the amino acid residues of SEQ ID NO: 11 have been modified by deletion, substitution, and/or insertion, wherein the E3 polypeptide has the ability to catalyze the conversion of 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and UDP-glucose into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid;
E4 comprises the amino acid sequence of SEQ ID NO: 9; or (b) comprises a variant of the amino acid sequence of SEQ ID NO: 9 which is identical to the amino acid sequence of SEQ ID NO: 9 except that at least one residue up to 5% of the amino acid residues of SEQ ID NO: 9 have been modified by deletion, substitution, and/or insertion, wherein the E4 polypeptide has the ability to catalyze the conversion of:
(i) 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate;
(ii) 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate; or
(iii) 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate; and

E5 comprises the amino acid sequence of SEQ ID NO: 10; or (b) comprises a variant of the amino acid sequence of SEQ ID NO: 10 which is identical to the amino acid sequence of SEQ ID NO: 10 except that at least one residue up to 5% of the amino acid residues of SEQ ID NO: 10 have been modified by deletion, substitution, and/or insertion, wherein the E5 polypeptide has the ability to transfer a sophorolipid out of the sophorolipid-producing cell into the surrounding medium.

2. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell has been transformed with an extrachromosomally replicating vector carrying said nucleic acid(s).

3. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell has been transformed with more than one copy of said nucleic acid(s).

4. The isolated or purified sophorolipid-producing cell of claim 1, wherein said nucleic acid(s) are operably linked to a promoter, a regulation region, a ribosome binding site, an expression cassette or an enhancer that increases the expression of said polypeptide.

5. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell expresses more of the polypeptide of SEQ ID NO: 8 than the identical non-transformed cell.

6. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell produces more sophorolipids in greater yields than the identical non-transformed cell.

7. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell has been transformed with a nucleic acid encoding the polypeptide of SEQ ID NO: 8.

8. The isolated or purified sophorolipid-producing cell of claim 1, wherein the nucleic acid encodes a polypeptide which catalyzes the conversion of UDP-glucose and 17-hydroxy-Z-9-octadecenoic acid into 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid, wherein said polypeptide comprises a variant of the amino acid sequence of SEQ ID NO: 8 which is identical to SEQ ID NO:8 except that at least one residue up to 5% of the amino acid residues of SEQ ID NO:8 have been modified by deletion, substitution, and/or insertion.

9. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell is a yeast or fungal cell.

10. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell is selected from the group consisting of Candida bombicola, Candida bogoriensis, Candida batistae, Candida apicola and Wickerhamiella domericqiae.

11. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell has been further modified to block or partially block β-oxidation in said cell.

12. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell has been further transformed with a nucleic acid encoding at least one E1 polypeptide.

13. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell has been further transformed with a nucleic acid encoding at least one E3 polypeptide.

14. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell has been further transformed with a nucleic acid encoding at least one E4 polypeptide.

15. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell has been further transformed with a nucleic acid encoding at least one E5 polypeptide.

16. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell has been further transformed with a nucleic acid encoding at least one polypeptide selected from the group consisting of E1, E3, E4 and E5.

17. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell has been further modified to disrupt at least one endogenous gene encoding a polypeptide selected from the group consisting of E3 and E4.

18. The isolated or purified sophorolipid-producing cell of claim 16, wherein said sophorolipid-producing cell has been transformed with nucleic acids encoding a combination of polypeptides selected from the group consisting of E1E3, E1E4, E1E5, E3E4, E3E5, E4E5, E1E3E4, E1E3E5, E1E4E5, E3E4E5 and E1E3E4E5 polypeptides.

19. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell:
(a) has been further modified to disrupt an endogenous gene encoding an E3 polypeptide; and
(b) has been transformed with nucleic acids encoding combinations of E1, E4 and E5 polypeptides.

20. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell:
(a) has been further modified to disrupt an endogenous gene encoding an E4 polypeptide; and
(b) has been transformed with nucleic acids encoding combinations of E1, E3 and E5 polypeptides.

21. The isolated or purified sophorolipid-producing cell of claim 1, wherein said sophorolipid-producing cell:
(a) has been further modified to disrupt endogenous genes encoding E3 and E4 polypeptides; and
(b) has been transformed with nucleic acids encoding E1 and E5 polypeptides.

22. A process for producing a sophorolipid comprising:
(a) culturing the cell of claim 1 on a medium containing a carbon source under conditions suitable for producing a sophorolipid from the carbon source; and
(b) optionally, isolating or recovering the sophorolipid;
wherein said cell may optionally contain a nucleic acid encoding at least one E1, E3, E4 or E5 polypeptide, or wherein said cell may optionally have a disruption in an endogenous gene encoding an E3 and/or E4 polypeptide;
wherein
E1 comprises (a) an amino acid sequence selected from the group consisting of SEQ ID NO: 7, 53, 55, 57, 59, 61 and 63; or (b) comprises a variant of the amino acid sequence of SEQ ID NO: 7, 53, 55, 57, 59, 61 or 63 which is identical to the amino acid sequence of SEQ ID NO: 7, 53, 55, 57, 59, 61 or 63 except that at least one residue up to 5% of the amino acid residues of SEQ ID NO: 7, 53, 55, 57, 59, 61 or 63 have been modified by deletion, substitution, and/or insertion, wherein the E1 polypeptide has the ability to catalyze the conversion of Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid;
E3 comprises (a) the amino acid sequence of SEQ ID NO: 11; or (b) comprises a variant of the amino acid sequence of SEQ ID NO: 11 which is identical to the amino acid sequence of SEQ ID NO: 11 except that at least one residue up to 5% of the amino acid residues of SEQ ID NO: 11 have been modified by deletion, substitution, and/or insertion, wherein the E3 polypeptide has the ability to catalyze the conversion of 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and UDP-glucose into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid;
E4 comprises the amino acid sequence of SEQ ID NO: 9; or (b) comprises a variant of the amino acid sequence of SEQ ID NO: 9 which is identical to the amino acid sequence of SEQ ID NO: 9 except that at least one residue up to 5% of the amino acid residues of SEQ ID NO: 9 have been modified by deletion, substitution, and/or insertion, wherein the E4 polypeptide has the ability to catalyze the conversion of:
(i) 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate;
(ii) 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone monoacetate and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate; or
(iii) 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone and acetyl-coenzyme A into 17-L-[(2′-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-Z-9-octadecenoic acid 1′,4′′-lactone diacetate; and

E5 comprises the amino acid sequence of SEQ ID NO: 10; or (b) comprises a variant of the amino acid sequence of SEQ ID NO: 10 which is identical to the amino acid sequence of SEQ ID NO: 10 except that at least one residue up to 5% of the amino acid residues of SEQ ID NO: 10 have been modified by deletion, substitution, and/or insertion, wherein the E5 polypeptide has the ability to transfer a sophorolipid out of the sophorolipid-producing cell into the surrounding medium.

23. The process of claim 22, wherein said sophorolipid-producing cell:
(a) has been further modified to disrupt endogenous genes encoding E3 and/or E4 polypeptides; and
(b) has been transformed with nucleic acids encoding E1, E4 and/or E5 polypeptides.

24. The process of claim 23, wherein said sophorolipid-producing cell has been transformed with nucleic acids encoding a combination of polypeptides selected from the group consisting of E1E4, E1E5, E4E5, and E1E4E5.

25. The process of claim 22, wherein said sophorolipid-producing cell has been further modified to disrupt an endogenous gene encoding an E3 polypeptide.

26. The process of claim 22, wherein said sophorolipid-producing cell produces a non-acetylated sophorolipid, and wherein said sophorolipid-producing cell has been further modified to disrupt an endogenous gene encoding an E4 polypeptide.

27. An isolated or purified genetically-modified cell that produces sophorolipids which has been transformed with nucleic acids encoding enzymes E1 and E2, wherein
(a) enzyme E1 has the ability to catalyze the conversion of Z-9-octadecenoic acid into 17-hydroxy-Z-9-octadecenoic acid and comprises the amino acid sequence of SEQ ID NO: 7, or an amino acid sequence which is identical to SEQ ID NO: 7 except that at least one residue up to 5% of the amino acid residues of SEQ ID NO: 7 have been modified by deletion, substitution, and/or insertion, and
(b) enzyme E2 has the ability to catalyze the conversion of UDP-glucose and 17-hydroxy-Z-9-octadecenoic acid into 17-(β-D-glucopyranosyloxy)-Z-9-octadecenoic acid and comprises the amino acid sequence of SEQ ID NO: 8, or an amino acid sequence which is identical to SEQ ID NO: 8 except that at least one residue up to 5% of the amino acid residues of SEQ ID NO: 8 have been modified by deletion, substitution, and/or insertion.