Patent Application
20180251796
The present invention concerns a method of producing enantiomerically pure alpha-ionone. Further, the invention concerns a nucleic acid, which comprises a sequence, which encodes a lycopene-epsilon-cyclase (EC), plasmids, which encode components of the alpha-ionone biosynthesis, and a microorganism, which contains heterologous nucleotide sequences, which encode the enzymes geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI), phytoene synthase (crtB), and lycopene-epsilon-cyclase (EC) or geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI), phytoene synthase (crtB), lycopene-epsilon-cyclase (EC) and carotenoid-cleavage-dioxygenase (CCD1). Additionally, the invention concerns a method of producing highly pure epsilon-carotene.
Nowadays fragrances are used in many products, such as detergents and cleaning agents, but also in numerous cosmetic skin and body care products, deodorants and perfumes. These fragrances do not only have to be produced in sufficient amounts and affordably, but also have to be available in highly pure form. The latter is necessary to prevent unwanted side effects, but also to have maximal freedom with regard to the formulation of fragrance mixtures.
The ionones are a group of ubiquitous natural products that belong to the terpenes, which are produced in many plants through the conversion of carotenoids. Ionones are used in the fragrance industry in great amounts as fragrances. The substance group comprises the individual substances alpha-, beta-, and gamma-ionone, which differ in the position of the double bond in the ionone-ring structure. For both alpha- and gamma-ionone two enantiomers exist: (R)-alpha-ionone and (S)-alpha-ionone or (R)-gamma-ionone and (S)-gamma-ionone (
In natural sources the ionones always exist as mixtures of different composition. The most common representatives are alpha- and beta-ionone wherein beta-ionone is the main product and alpha-ionone exists in lower amounts as additional component. Gamma-ionone is produced only by a few plants. Therefore, to obtain the individual substances in pure form from nature and to provide them for industrial use laborious and costly enrichment and purification steps are necessary. This is particularly true for the industrially highly relevant but very rare (R)-alpha-ionone.
In plants the formation of the ionones occurs through a multistep synthetic pathway: initially the linear carotenoid lycopene is produced, which is subsequently transformed in different further mono- or bi-cyclic carotenoids through the activity of different lycopene-cyclases (
In plants, the transformation of different carotenes through carotenases (CCD) leads to the formation of alpha-ionone (
Alpha-ionone can also be chemically synthesized. A method of synthesizing alpha- and beta-ionone from citral has already been developed and patented in 1893. This chemically synthesized alpha-ionone exists as racemic mixture and thus contains enantiomers with different scent. The utility for the fragrance industry is therefore limited. More recently enantio-selective synthetic methods for (S)-alpha-ionone (Bovolenta et al., 2004) or (R)-alpha-ionone (Soorukram and Knochel, 2004) have been described. The enantiomeric purity of the so produced (R)-alpha-ionone is 97%. Thus, substantial amounts of the (5)-enantiomer are still contained. The yield is 61%.
For a sustainable and environment friendly ionone-production fermentative production systems, in particular involving the use of the recombinant microorganisms, are preferred.
In general, recombinant delta-carotene and epsilon-carotene producing microorganisms are suitable for the production of alpha-ionone. The use of delta-carotene as starting material for an efficient alpha-ionone production is however not sensible, since only one molecule ionone per starting molecule can be obtained from this monocyclic substrate. A biosynthesis using epsilon-carotene is preferred, since the yield of alpha-ionone per starting molecule epsilon-carotene can be doubled.
The recombinant systems described so far with proven ionone-synthesis mostly resulted from the biochemical characterization of different CCD1-enzymes. The natural processes were imitated by additionally inserting the CCD1-enzymes to be tested in recombinant bacterial strains, in which prior to this the synthetic genes for different carotenoids had been implemented (Misawa et al., 1990, Cunningham et al., 1996). In doing so it has been shown that CCD1-enzymes have a broad spectrum of substrates and that they transform the substrates with different preferences. Preferably, CCD1-enzymes were tested in strains that provide lycopene, beta-carotene or zeaxanthin.
Carotenoids are ubiquitous lipophilic pigments that belong to the class of tetraterpenes. Most carotenoids can be formally derived from acyclic lycopene and are formed through cyclization of the end groups, hydrogenation or dehydrogenation or also through the introduction of oxygen.
Starting materials of the carotenoid synthesis are the isoprene derivative isopentenyl-diphosphate (IPP) and the corresponding isomer dimethyl-allyl-diphosphate (DMAPP), which, depending on the host organism, are produced via the so called non-mevalonate pathway (MEP-pathway) and/or the so called mevalonate pathway (MVA-pathway). In plants, both synthetic pathways are active. Through the coupling of multiple IPP and DMAPP-molecules initially the important intermediate geranylgeranyl-diphosphate (GGPP) is formed. Through the condensation of 2 GGPP-units the first tetraterpene compound is formed, phytoene. The colorless phytoene is then through repeated desaturation and isomerisation transformed into the red lycopene, which is the essential intermediate, from which through different cyclization reactions the carotenoids alpha-, beta-, gamma-, delta- and epsilon-carotene are formed. An overview is depicted in
Carotenoid biosynthesis pathways have not only been identified for plants, but also for different microorganisms (bacteria and yeast) and the corresponding genes or gene clusters have been isolated. As early as 1986 a corresponding bacterial gene cascade was cloned by Perry and coworkers from Erwinia herbicola for the expression in E. coli (Perry et al, 1986). The analogous expression cassette from Erwinia uredovora was described for the first time in 1990 (Misawa et al., 1990). Subsequently, Cunningham and coworkers described a recombinant microbial system for the synthesis of carotenoids in E. coli, which used the biosynthesis genes of the above mentioned known Erwinia species, E. uredovora and E. herbicola (Cunningham et al., 1996).
Since then many research groups have used the plasmid described by Perry et al (1986) as basis for investigating the functionality of individual bacterial or plant enzymes of the carotenoid biosynthesis through complementation experiments (Cunningham et al., 1994, 1996). In doing so always the original cassette from E. herbicola with the original promoter, terminator and the transitions between the individual genes including original ribosome binding sites (Shine-Dalgarno-sequences; SD) were used.
Recently, an additional gene cluster for carotenoid-synthesis was reported which is expressed in E. coli. The heterologous expression of the genes of Cronobacter sakazakii leads to a yellow coloration of the colonies. The individual genes have been identified as idi, crtE, crtX, crtY, crtI, crtB and crtZ (Zhang et al., 2014). These have been cloned in different combinations with optimized SD-sequences in the target vector pWSK29.
To date different clusters have been identified and heterologously expressed; however, the publications do not report optimizing the yields of carotenes.
Several essential enzymes are involved in the synthesis of epsilon-carotene from lycopene and the release of ionones from carotenoids, which are described in the following.
Lycopene-epsilon-cyclases catalyze the formation of alpha-ionone-ring structures at the ends of the lycopene molecule, wherein initially the monocyclic delta-carotene is produced as an intermediate, which is then transformed to epsilon-carotene through several lycopene-epsilon-cyclases (EC) under formation of a second alpha-ionone ring. Accordingly, two classes of lycopene-epsilon-cyclases can be distinguished: one class of which can only produce a single ring and therefore exclusively synthesize delta-carotene. The epsilon-cyclase of Arabidopsis thaliana and the absolute majority of plant EC-enzymes that have been investigated and described to date belong to this class. The second EC-class can also generate a second ring at the same molecule (or the monocyclic intermediate) and thus can also produce epsilon-carotene. The EC-enzyme of Lactuca sativa (salad) belongs to this class. It predominantly produces epsilon-carotene.
The described EC-enzymes of Zea mays (corn) and Adonis aestivalis synthesize a mixture of equal amounts of delta-carotene and epsilon-carotene (Bai et al., 2009; Cunningham und Gantt, 2001).
Cunningham und Gantt (2001) were able to show that the exchange of a single amino acid leads to a change in the product of the enzymatic reaction. For the enzyme of salad (Lactuca sativa) the exchange of histidine of leucine at position 457 leads to the formation of a monocyclic product, while the complementary mutation at the corresponding position in the EC-enzyme of A. thaliana (L448H) leads to a bicyclic product, i.e. the formation of epsilon-carotene is preferred. This work also showed the introduction of a hexapeptide sequence from the salad-EC in the enzyme of Arabidopsis, which leads to an exchange of four amino acids in this enzyme (A447F/L448H/Q451L/F452M). This mutated enzyme synthesized the bicyclic epsilon-carotene as main product.
More recent work also shows for the EC of corn that the change of the amino acid sequence at one position (L461H) leads to an increase in the fraction of bicyclic epsilon-carotene to 80%. A mutation of alanine to serine at position 502, however, leads to an increased fraction of the monocyclic delta-carotene (Bai et al., 2009).
Carotenases are plant enzymes that are able to cleave mono and bicyclic carotenoids in the area of the linear central molecule structure. The reaction occurs under O2 consumption. According to the reaction mechanism, the enzymes are also referred to as carotenoid-cleaving-dioxygenases, CCD. The respective CCD-enzyme determines in which position the substrate molecules are cleaved—this is a fundamental enzyme characteristic. Only CCD-enzymes that are able to cleave carotene substrates between the positions 9, 10 and 9′, 10′ are able to release ionones.
The carotenoid-cleavage-dioxygenase 1 of A. thaliana (AtCCD1) accepts a broad spectrum of linear and cyclic carotenoid-substrates, as do its homologues of corn and tomato, and can cleave lycopene in addition to alpha- and beta-carotene (Vogel et al., 2008). The authors also show the cleavage of ζ-carotene for the corn-CCD1. For CCD1 of Osmanthus fragrans (OfCCD1) it has been shown that it in vitro transforms alpha- and beta-carotene and in doing so produces beta- and alpha-ionone (Baldermann et al., 2010). The CCD of Daucus carota has greater substrate specificity and cannot transform lycopene, phytoene or GGPP, but is able to transform zeaxanthin, beta-carotene and delta-carotene (Yahyaa et al., 2013).
As described above, alpha-ionone and in particular (R)-alpha-ionone is an important raw material for the fragrance industry. The presently available methods of producing alpha-ionone by means of isolation from natural sources or chemical synthesis provide only insufficient access to this important raw material in insufficient quantity and purity. Furthermore, against the background of an environment friendly and sustainable production an alternative to classical chemical synthesis is desirable.
Accordingly, it is a problem of the present invention to produce alpha-ionone and in particular (R)-alpha-ionone by means of an environment friendly and sustainable method in sufficient quantity and purity.
The above formulated problem is solved by the provision of a method of producing enantiomerically pure alpha-ionone, comprising the culturing of a microorganism, which contains heterologous nucleotide sequences, which encode the following enzymes: geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI), phytoene synthase (crtB), lycopene-epsilon-cyclase (EC) and carotenoid-cleavage-dioxygenase (CCD1).
The above formulated problem is also solved by the provision of a nucleic acid, which comprises a sequence, which encodes a lycopene-epsilon-cyclase (EC), which catalyzes the transformation of lycopene to epsilon-carotene, wherein the lycopene-epsilon-cyclase (EC) leads to a greater epsilon-carotene yield than a reference lycopene-epsilon-cyclase (EC) with a sequence according to SEQ ID No. 26. Further, the problem is solved by the provision of the lycopene-epsilon-cyclase (EC) itself that is encoded by the nucleic acid.
Further, the provided plasmid contributes to the solution of the problem, wherein the plasmid is characterized in that it comprises nucleotide sequences that encode the enzymes geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI) and phytoene synthase (crtB), wherein the heterologous expression of the lycopene-biosynthetic pathway that is encoded by the plasmid leads to a grater lycopene-yield compared to the heterologous expression of the lycopene-biosynthetic pathway that is encoded by the plasmid pACBETAipi-ΔcrtY (SEQ ID No. 28).
Further, the microorganism provided by the invention contributes to the solution of the problem, wherein the microorganism comprises heterologous nucleotide sequences that encode the following enzymes: geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI), phytoene synthase (crtB), and lycopene-epsilon-cyclase (EC) or geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI), phytoene synthase (crtB), lycopene-epsilon-cyclase (EC) and carotenoid-cleavage-dioxygenase (CCD1).
The method of producing highly pure epsilon-carotene provided by the present invention also contributes to the solution of the problem, wherein the method comprises the culturing of a microorganism, which comprises heterologous nucleotide sequences, which encode the following enzymes: geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI), phytoene synthase (crtB) and lycopene-epsilon-cyclase (EC).
Finally, the provided plasmid also contributes to the solution of the problem, wherein the plasmid is characterized in that it comprises nucleotide sequences that encode the following enzyme: 1-desoxy-D-xylulose-5-phosphate-synthase (DXS) and isopentenyl-pyrophosphate-isomerase (CwIPI).
The nucleic acids, lycopene-epsilon-cyclases, plasmids, microorganisms and methods according to the present invention enable the efficient fermentative production of lycopene with clearly improved yields compared to the state of the art, as well as epsilon-carotene, with clearly improved yields of epsilon-carotene compared to the state of the art. Both, lycopene as well as epsilon-carotene are intermediates in the production of alpha-ionone.
The present invention is, among other things, characterized by an improved production of the two intermediates of the alpha-ionone biosynthesis compared to the state of the art, lycopene and epsilon-carotene (
A further advantage of the present invention compared to the state of the art is the provision of (R)-alpha-ionone in enantiomerically pure form in sufficient quantity and purity.
Further, the fermentative methods of the present invention are more environment friendly and more sustainable than the traditional chemical synthetic methods of the state of the art.
The present invention is not limited to the specifically mentioned products and methods herein, but provides a general technical teaching, which enables the skilled person to achieve the advantages described herein. The used terminology should not limit the general technical teaching described herein in any form, but serves merely to describe the specific embodiments.
The used EC-classification numbers (EC-numbers) classify enzymes according to the reactions that they catalyze. These EC-numbers are issued by the International Union of Biochemistry and Molecular Biology (UIBMB) and can be searched by the skilled person on the internet.
The “accession numbers” used herein (GenBank accession number—GenBank) serve for the unambiguous characterization of nucleotide sequences or amino acid sequences and are taken from the webpage of the NCBI (National Center for Biotechnology Information).
The term “AtEC” as used herein describes the Arabidopsis thaliana lycopene-epsilon-cyclase (EC) with the GenBank accession number GenBank: AAL85102.1.
The term “LsEC” as used herein describes the Lactuca sativa lycopene-epsilon-cyclase (EC) with the GenBank accession number GenBank: AAK07434.1.
The term “ZmEC” as used herein describes the Zea mays lycopene-epsilon-cyclase (EC) with the GenBank accession number GenBank: ABU93262.1.
The term “lycopene” as used herein describes a linear carotenoid that is known to the skilled person, which is also known to the skilled person under the name “lycopin” and “leukopin” or “all-trans-lycopene”. These terms can be used interchangeably.
The term “lycopene-biosynthetic pathway” as used herein describes the combination of the enzymes geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI) and phytoene synthase (crtB).
The term “AtECmut” as used herein describes the mutants of the Arabidopsis thaliana lycopene-epsilon-cyclase according to the present invention, wherein the term may refer to the entire protein or only to the specific mutation, which is appended to the term as a number (e.g. AtECmut3). The meaning of the term follows for the skilled person unambiguously from the respective context. The term “AtECmut” is used herein equivalently with the term “ECmut”.
The term “yield” as used herein describes the amount of a produced material based on a determined culture volume (liquid culture of a microorganism) or the isolated dry matter from a determined culture volume or based on a different reference value. The term “amount” as used herein describes the amount of substance of a material or a different measure, whose value is directly dependent on the amount of substance of the material, for example the peak area of an HPLC absorption chromatogram.
The term “sequence identity” as used herein describes the agreement of two nucleotide sequences or amino acid sequences, given in percent, and depends on the number of identical positions between the two sequences, wherein the number and length of gaps that need to be introduced to achieve an optimal sequence alignment is taken into account. As used herein, the sequence identity is determined according to the BLAST-algorithm (Altschul et al., 1990). As known to the skilled person, the sequence identity can be determined according to the BLAST-algorithm for nucleotide sequences (blastn) or amino acid sequences (blastp) simply on the NCBI webpage (http://blast.ncbi.nlm.nih.gov/Blast.cgi).
The term “geranylgeranyl-diphosphate-synthase” as used herein describes an enzyme with the EC-number EC 2.5.1.29, which catalyzes the condensation of farnesyl-diphosphate and isopentenyl-diphosphate to geranylgeranyl-diphosphate. Preferred embodiments are the geranylgeranyl-diphosphate-synthase crtE and idsA.
The term “1-desoxy-D-xylulose-5-phosphate-synthase (DXS)” as used herein describes an enzyme with EC-number EC 2.2.1.7, which catalyzes the condensation of pyruvate and glycerinaldehyd-3-phosphate to 1-desoxy-D-xylulose-5-phosphate (DXP).
The term “isopentenyl-diphosphate-isomerase (IPI)” as used herein describes an enzyme with the EC-number EC 5.3.3.2, which catalyzes the rearrangement of isopentenyl-diphosphate (IPP) to dimethylallyl-diphosphate (DMAPP), or the converse reaction. Also the enzymes CwIPI or the codon-optimized variant CwIPI-co2 are isopentenyl-diphosphate-isomerases with an enzymatic activity according to the EC-number EC 5.3.3.2.
The term “phytoene-desaturase/dehydrogenase (crtI)” as used herein describes an enzyme with the EC-number EC 1.3.99.31, which catalyzes the desaturation (oxidation) of phytoene to all-trans-lycopene.
The term “phytoene synthase (crtB)” as used herein describes an enzyme with the EC-number EC 2.5.1.32, which catalyzes the condensation of two molecules of geranylgeranyl-diphosphate to phytoene.
Lycopene-Epsilon-Cyclase
An aspect of the invention concerns a nucleic acid, which encodes lycopene-epsilon-cyclase.
The nucleic acid according to the present invention is characterized in that it comprises a sequence which encodes lycopene-epsilon-cyclase (EC), which catalyzes the transformation of lycopene to epsilon-carotene, wherein the lycopene-epsilon-cyclase (EC) leads to a greater epsilon-carotene yield as a reference lycopene-epsilon-cyclase with a sequence according to SEQ ID NO: 26 (AtECmut1).
In a preferred embodiment of the nucleic acid according to the present invention, which may be combined with any of the preceding or subsequent embodiments, the lycopene-epsilon-cyclase (EC) leads to a greater epsilon-carotene yield, wherein the lycopene-epsilon-cyclase (EC) is a expressed in a microorganism. To be able to compare the lycopene yield of the lycopene-epsilon-cyclase (EC) with the reference lycopene-epsilon-cyclase, both cyclases are expressed in the same microorganism under the same conditions. For the expression of the lycopene-epsilon-cyclase (EC) and the reference lycopene-epsilon-cyclase in the microorganism, a plasmid that encodes the lycopene-epsilon-cyclase (EC) or a reference lycopene-epsilon-cyclase can be introduced into a microorganism by means of transformation.
In a preferred embodiment of the nucleic acid according to the present invention, which can be combined with any of the preceding or subsequent embodiments, the encoded lycopene-epsilon-cyclase has a sequence with at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with the sequence according to SEQ ID NO: 19 (AtEC-del).
SEQ ID NO: 19 (AtEC-del) defines the sequence of the lycopene-epsilon-cyclase of Arabidopsis thaliana having the N-terminal 44 amino acids (not including the N-terminal methionine) of the wildtype sequence removed. This N-terminal peptide is a chloroplast import signal (transit peptide) which affects the transport of the newly synthesized proteins into the chloroplasts in the plant. The positions of the amino acids of the mutations according to the present invention of the different lycopene-epsilon-cyclase variants are indicated relative to this N-terminal truncated version of the lycopene-epsilon-cyclase of A. thaliana (SEQ ID NO: 19). The corresponding positions in the wildtype sequence of the lycopene-epsilon-cyclase of A. thaliana are therefore shifted by 44 positions. Thus, position 403 in the truncated version (SEQ ID NO: 19) corresponds to position 447 in the wildtype sequence (AAL85102.1), position 404 corresponds to position 448, and position 445 corresponds to position 489.
In a further embodiment of the nucleic acid according to the invention, which can be combined with any of the preceding or subsequent embodiments, the sequence of the encoded lycopene-epsilon-cyclase differs in at least one of the positions 403, 404 and 445 from the sequence according to SEQ ID NO: 19 (AtEC-del).
In an embodiment of the nucleic acid according to the present invention, which can be combined with any of the preceding or subsequent embodiments, the encoded lycopene-epsilon-cyclase comprises one of the following mutations or mutation combinations: ECmut2 (A445S), ECmut9 (L404S), ECmut3 (L404H/A445S), ECmut3.10 (A403C/A445S), ECmut3.12 (L404T/A445S), ECmut4 (A403S/L404H), ECmut5 (A403F/L404W), ECmut6 (A403G/L404G), ECmut7 (A403K/L404D), ECmut8 (A403W/L404R), ECmut10 (A403S/L404T), ECmut11 (A403F/L404S), ECmut12 (A403C/L404S), ECmut13 (A403I/L404T), ECmut14 (A403T/L404R), ECmut15 (A403F/L404R), ECmut16 (A403W/L404G), ECmut17 (A403C/A404C), ECmut18 (A403L/L404V), ECmut19 (A403K/L404R), ECmut20 (A403Y/L404K), ECmut21 (A403Q/L404K), ECmut22 (A403G/L404Q), ECmut3.1 (A403S/L404H/A445S), ECmut3.2 (A403C/L404C/A445S), ECmut3.3 (A403E/L404A/A445S), ECmut3.4 (A403W/L404R/A445S), ECmut3.5 (A403M/L404A/A445S), ECmut3.6 (A403N/L404T/A445S), ECmut3.7 (A403N/L404A/A445S), ECmut3.8 (A403H/L404S/A445S), ECmut3.9 (A403E/L404G/A445S), ECmut3.11 (A403K/L404G/A445S), ECmut3.13 (A403R/L404S/A445S), ECmut3.14 (A403G/L404R/A445S), ECmut3.15 (A403F/L404V/A445S) and ECmut3.16 (A403G/L404G/A445S).
In a preferred embodiment of the nucleic acid according to the present invention, which can be combined with any of the preceding or subsequent embodiments, the encoded lycopene-epsilon-cyclase comprises one of the mutations or mutation combinations: ECmut16 (A403W/L404G), ECmut3.12 (L404T/A445S), ECmut3.3 (A403E/L404A/A445S), ECmut3.5 (A403M/L404A/A445S), ECmut3.8 (A403H/L404S/A445S), ECmut3.9 (A403E/L404G/A445S), ECmut3.16 (A403G/L404G/A445S), ECmut9 (L404S), ECmut10 (A403S/L404T) and ECmut3.2 (A403C/L404C/A445S).
In a particularly preferred embodiment of the nucleic acid according to the present invention, which can be combined with any of the preceding or subsequent embodiments, the encoded lycopene-epsilon-cyclase comprises one of the following mutations or mutation combinations: ECmut9 (L404S), ECmut10 (A403S/L404T) and ECmut3.2 (A403C/L404C/A445S).
In a further particularly preferred embodiment of the nucleic acid according to the present invention, which can be combined with any of the preceding or subsequent embodiments, the encoded lycopene-epsilon-cyclase consists of a sequence according to SEQ ID NO: 19 and has one of the above-mentioned mutations or mutation combinations. Particularly preferred in this context are embodiments with a mutation combination selected from the group consisting of ECmut16 (A403W/L404G), ECmut3.12 (L404T/A445S), ECmut3.3 (A403E/L404A/A445S), ECmut3.5 (A403M/L404A/A445S), ECmut3.8 (A403H/L404S/A445S), ECmut3.9 (A403E/L404G/A445S) and ECmut3.16 (A403G/L404G/A445S) and particularly preferred are embodiments with a mutation or a mutation combination selected from the group consisting of ECmut9 (L404S), ECmut10 (A403S/L404T) and ECmut3.2 (A403C/L404C/A445S).
A further aspect of the invention concerns the lycopene-epsilon-cyclase itself.
The lycopene-epsilon-cyclase according to the present invention is characterized in that it is encoded by one of the above-described nucleic acids.
In a particularly preferred embodiment of the nucleic acid according to the present invention, which can be combined with any of the preceding or subsequent embodiments, the encoded lycopene-epsilon-cyclase consists of a sequence according to SEQ ID NO: 19 and has one of the mutations or mutation combinations according to the present invention. Particularly preferred in this context are embodiments with a mutation combination selected from the group consisting of ECmut16 (A403W/L404G), ECmut3.12 (L404T/A445S), ECmut3.3 (A403E/L404A/A445S), ECmut3.5 (A403M/L404A/A445S), ECmut3.8 (A403H/L404S/A445S), ECmut3.9 (A403E/L404G/A445S) and ECmut3.16 (A403G/L404G/A445S) and particularly preferred are embodiments with a mutation or a mutation combination selected from the group consisting of ECmut9 (L404S), ECmut10 (A403S/L404T) and ECmut3.2 (A403C/L404C/A445S).
Plasmids
Part of the invention also are different plasmids, which comprise nucleotide sequences which encode the components of the present invention of the lycopene, epsilon-carotene and/or alpha-ionone biosynthesis. Particularly preferred embodiments of these plasmids according to the present invention are listed in
Part of the invention is a plasmid which comprises nucleotide sequences which encode components according to the present invention of the lycopene biosynthesis geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI) and phytoene synthase (crtB) (“Lyc-synthesis” plasmid). Part of the invention is further a plasmid which comprises a nucleotide sequence which encodes components according to the present invention of the epsilon-carotene biosynthesis, geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI), phytoene synthase (crtB) and lycopene-epsilon-cyclase (EC) (“eCaro-synthesis” plasmid). Further, part of the invention is a plasmid which comprises nucleotide sequences which encode the components according to the present invention for cleaving epsilon-carotene to alpha-ionone carotenoid-cleavage-dioxygenase (CCD1) (“eCaro-cleavage” plasmid). Part of the invention is also a plasmid which comprises nucleotide sequences which encode the components according to the present invention of the alpha-ionone biosynthesis geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI), phytoene synthase (crtB), lycopene-epsilon-cyclase (EC) and carotenoid-cleavage-dioxygenase (CCD1) (“ionone synthesis” plasmid). Equally part of the invention is a plasmid which comprises nucleotide sequences which encode the components according to the present invention for connecting the non-mevalonate pathway (MEP pathway) to the lycopene, epsilon-carotene and/or alpha-ionone biosynthesis, namely 1-desoxy-D-xylulose-5-phosphat-synthase (DXS) (“MEP pathway” plasmid).
In a preferred embodiment of the plasmids according to the present invention, which can be combined with any of the preceding or subsequent embodiments, the heterologous expression of the lycopene biosynthetic pathway that is encoded by the plasmid (geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-Isomerase (IPI), phytoen-desaturase/dehydrogenase (crtI) and phytoene synthase (crtB)) leads to an increased lycopene yield in a microorganism, preferably a bacterium. A preferred bacterium is E. coli. Particularly preferred in this context are the E. coli strains, XL1-blue, TOP10, XL10 blue, DH5-alpha, JM109, C41, BL21gold (DE3) and W3110. In particular, the microorganism according to the present invention can be the E. coli strain TOP10. Particularly preferred is the E. coli strain BL21gold (DE3).
In a preferred embodiment of the plasmids according to the present invention, which can be combined with any of the preceding or subsequent embodiments, the enzymes geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-Isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI) and phytoene synthase (crtB) are the corresponding enzymes of Erwinia herbicola.
In a preferred embodiment of the plasmids according to the present invention, which can be combined with any of the preceding or subsequent embodiments, the enzymes encoded by the plasmid are under the control of an inducible promoter. Particularly preferred are the inducible promoters pTet, pBAD, pLac, and pXyl, which are also described in more detail in Example 10 and
In a preferred embodiment of the plasmids according to the present invention, which can be combined with any of the preceding or subsequent embodiments, the enzymes encoded by the plasmid are under the control of a constitutive promoter. Particularly preferred are the constitutive promoters according to the present invention aP5, aP12, aP15, aP32 and aP47.2 (Example 10 and
“Lyc-Synthesis” Plasmid
The “Lyc-synthesis” plasmid according to the present invention is characterized in that it comprises nucleotide sequences that encode the following enzymes: geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-Isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI) and phytoene synthase (crtB), wherein the heterologous expression of the lycopene-biosynthetic pathway that is encoded by the plasmid leads to an increased lycopene yield compared to the heterologous expression of the lycopene biosynthetic pathway that is encoded by the plasmid pAC-BETAipi-ΔcrtY (SEQ ID Nr. 28).
In a further embodiment of the plasmid according to the present invention, which can be combined with any of the previous or subsequent embodiments, the plasmid comprises a sequence or preferably consists of this sequence, which has at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a reference sequence.
In a further embodiment of the plasmid according to the present invention, which can be combined with any of the previous or subsequent embodiments, the reference sequence is a sequence according to SEQ ID Nr. 28, wherein the reference sequence has a deletion of the bases 984-1394 and 3432-4198 relative to the sequence according to SEQ ID Nr. 28 (pAC-BETAipi-ΔcrtY).
In a further embodiment of the plasmid according to the present invention, which can be combined with any of the previous and subsequent embodiments, the reference sequence has a deletion of the bases 984-1394, 3432-4198 and 6605-7242 relative to the sequence according to SEQ ID Nr. 28 (pAC-BETAipi-ΔcrtY).
In a preferred embodiment of the plasmid according to the present invention, which can be combined with any of the previous and subsequent embodiments, the reference sequence is a sequence according to SEQ ID Nr. 11 (pGT1036). Particularly, the sequence of the plasmid according to the invention can comprise a sequence, which is identical to the sequence according to SEQ ID Nr. 11. In a particularly preferred embodiment, the plasmid consists of a sequence that is identical to the sequence according to SEQ ID Nr. 11.
“eCaro-Synthesis” Plasmid
The “eCaro-synthesis” plasmid according to the present invention is characterized in that it comprises nucleotide sequences that encode the following enzymes: geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-Isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI) and phytoene synthase (crtB) and lycopene-epsilon-cyclase (EC), wherein the heterologous expression of the lycopene biosynthetic pathway that is encoded by the plasmid leads to an increased lycopene yield compared to the heterologous expression of the lycopene biosynthetic pathway that is encoded by the plasmid pAC-BETAIPI-ΔcrtY (SEQ ID Nr. 28).
The “eCaro-synthesis” plasmid according to the present invention comprises particularly also all embodiments of the “Lyc-synthesis” plasmids according to the present invention and of the lycopene-epsilon-cyclase (EC) according to the present invention.
In a preferred embodiment of the “eCaro-synthesis” plasmid according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the reference sequence (characterized in the passage “Lyc-synthesis” plasmid) is a sequence according to SEQ ID Nr. 18 (pGT1066*, corresponding to pGT1066, however with n, corresponding to a, t, c or g, for the nucleotides of the codons that encode for amino acid positions 403, 404 and 445 of the AtEC-del-enzyme). In particular, the sequence of the plasmid according to the present invention can also comprise a sequence that is identical to the sequence according to SEQ ID Nr. 18. In a particularly preferred embodiment, the plasmid consists of a sequence that is identical to the sequence according to SEQ ID Nr. 18.
In a particularly preferred embodiment of the “eCaro-synthesis” plasmid according to the present invention, which can be combined with any of the previous and subsequent embodiments, the reference sequence is a sequence according to SEQ ID No. 29 (pGT1066-AtEC-del), wherein the lycopene-epsilon-cyclase (EC) that is encoded by the plasmid comprises or has one of the following mutations or mutation combinations: ECmut2 (A445S), ECmut9 (L404S), ECmut3 (L404H/A445S), ECmut3.10 (A403C/A445S), ECmut3.12 (L404T/A445S), ECmut4 (A403S/L404H), ECmut5 (A403F/L404W), ECmut6 (A403G/L404G), ECmut7 (A403K/L404D), ECmut8 (A403W/L404R), ECmut10 (A403S/L404T), ECmut11 (A403F/L404S), ECmut12 (A403C/L404S), ECmut13 (A403I/L404T), ECmut14 (A403T/L404R), ECmut15 (A403F/L404R), ECmut16 (A403W/L404G), ECmut17 (A403C/A404C), ECmut18 (A403L/L404V), ECmut19 (A403K/L404R), ECmut20 (A403Y/L404K), ECmut21 (A403Q/L404K), ECmut22 (A403G/L404Q), ECmut3.1 (A403S/L404H/A445S), ECmut3.2 (A403C/L404C/A445S), ECmut3.3 (A403E/L404A/A445S), ECmut3.4 (A403W/L404R/A445S), ECmut3.5 (A403M/L404A/A445S), ECmut3.6 (A403N/L404T/A445S), ECmut3.7 (A403N/L404A/A445S), ECmut3.8 (A403H/L404S/A445S), ECmut3.9 (A403E/L404G/A445S), ECmut3.11 (A403K/L404G/A445S), ECmut3.13 (A403R/L404S/A445S), ECmut3.14 (A403G/L404R/A445S), ECmut3.15 (A403F/L404V/A445S) and ECmut3.16 (A403G/L404G/A445S). Particularly preferred mutation combinations are ECmut16 (A403W/L404G), ECmut3.12 (L404T/A445S), ECmut3.3 (A403E/L404A/A445S), ECmut3.5 (A403M/L404A/A445S), ECmut3.8 (A403H/L404S/A445S), ECmut3.9 (A403E/L404G/A445S) and ECmut3.16 (A403G/L404G/A445S). Particularly preferred are the mutations or mutation combinations ECmut9 (L404S), ECmut10 (A403S/L404T) and ECmut3.2 (A403C/L404C/A445S).
In a particularly preferred embodiment of “eCaro-Synthese” plasmid according to the present invention, which can be combined with any of the previous and subsequent embodiments, the plasmid consists of a sequence according to SEQ ID No. 29 (pGT1066-AtEC-del), wherein the lycopene-epsilon-cyclase (EC) that is encoded by the plasmid has one of the following mutations or mutation combinations: ECmut9 (L404S), ECmut10 (A403S/L404T), ECmut3.2 (A403C/L404C/A445S) and ECmut3.3 (A403E/L404A/A445S).
In a particularly preferred embodiment of “eCaro-synthesis” plasmid according to the present invention, which can be combined with any of the previous and subsequent embodiments, the plasmid has at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% oder 100% sequence identity with a sequence according to SEQ ID No. 30, 31, 32, 33, 34, 35 or 36.
“eCaro-Cleavage” Plasmid
The “eCaro-cleavage” plasmid according to the present invention is characterized in that it comprises a nucleotide sequence that encodes the enzyme carotenoid-cleavage-dioxygenase (CCD1).
In a preferred embodiment of the “eCaro-cleavage” plasmid according to the present invention, the carotenoid-cleavage-dioxygenase (CCD1) is a carotenoid-cleavage-dioxygenase 30 (CCD1) of Arabidopsis thaliana or Osmanthus fragrans.
In a preferred embodiment of the “eCaro-cleavage” plasmid according to the present invention, which can be combined with any of the previous and subsequent embodiments, the plasmid has at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a sequence according to SEQ ID No. 21, 24, 37, 38, 39, 40, 41 or 42. Particularly preferred are the sequences according to SEQ ID No. 37 and 41.
“Ionone Synthesis” Plasmid
The “ionone synthesis” plasmid according to the present invention characterized in that it comprises nucleotide sequences that encode the following enzymes: geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-Isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI) and phytoene synthase (crtB) and lycopene-epsilon-cyclase (EC) and carotenoid-cleavage-dioxygenase (CCD1), wherein the heterologous expression of the lycopene biosynthetic pathway that is encoded by the plasmid leads to an increased lycopene yield compared to heterologous expression of the lycopene biosynthetic pathway that is encoded by the plasmid pAC-BETAIPI-ΔcrtY (SEQ ID No. 28).
The “ionone synthesis” plasmid according to the present invention comprises also in particular all embodiments of the “Lyc-synthesis” plasmids according to the present invention, the lycopene-epsilon-cyclase (EC) according to the present invention and the “eCaro-Synthesis” plasmids according to the present invention.
In a preferred embodiment of the “ionone synthesis” plasmid according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the plasmid has at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a sequence according to SEQ ID No. 43 or 44, wherein die sequence according to SEQ ID No. 44 is particularly preferred. In particular preferred is a plasmid that has a sequence according to SEQ ID No. 44.
“MEP Pathway” Plasmid
The “MEP pathway” plasmid according to the present invention is characterized in that it comprises nucleotide sequences that encode the following enzyme: 1-desoxy-D-xylulose-5-phosphate-synthase (DXS).
In a preferred embodiment of the “MEP pathway” plasmid according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the plasmid comprises nucleotide sequences that encode the isopentenyl-diphosphate-Isomerase (CwIPI) of Curcuma wenyujin. Particularly preferred is a codon optimized synthetic gene sequence of the isopentenyl-diphosphate-Isomerase (CwIPI-co2). The isopentenyl-diphosphate-Isomerase (CwIPI) is per se not necessary for the coupling of the lycopene-epsilon-carotene and/or alpha-ionone biosynthesis to the MEP pathway. In a particularly preferred embodiment of the “MEP pathway” plasmid according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the “MEP pathway” plasmid has at least 80% or at least 85%, 90% 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a sequence according to SEQ ID No. 45, 46 or 47, wherein the sequence according to SEQ ID No. 45 is particularly preferred. Particularly preferred is a plasmid that has a sequence according to SEQ ID No. 45.
A further aspect of the invention concerns the expression cassettes according to the present invention, which the skilled person can take from the figures, in particular
The expression cassettes according to the present invention comprise particularly the expression cassettes as listed in
In particular, the expression cassettes according to the present invention, which preferably are present in the genome of a microorganism, such as E. coli, comprise expression cassettes that have at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with the expression cassettes according to
In a preferred embodiment of the expression cassettes according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the enzymes that are encoded by the expression cassettes according to the present invention are under the control of a constitutive promoter. The particularly preferred constitutive promoters according to the present invention are aP5, aP12, aP15, aP32 and aP47.2.
In a preferred embodiment of the expression cassettes according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the enzymes that are encoded by the expression cassettes are under the control of an inducible promoter. Particularly preferred are the inducible promoters pTet, pBAD, pLac, and pXyl, which are also described in detail in Example 10. Particularly preferred are the inducible promoters pTet-m1, pXyl0, pXyl1 and pXyl2 (Example 10).
Microorganisms
The microorganism according to the present invention is characterized in that it contains heterologous nucleotide sequences that encode the following enzymes: geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-Isomerase (IPI), phytoene- desaturase/dehydrogenase (crtI), phytoene synthase (crtB) and lycopene-epsilon-cyclase (EC), or geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-Isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI), phytoene synthase (crtB), lycopene-epsilon-cyclase (EC) and carotenoid-cleavage-dioxygenase (CCD1).
In a preferred embodiment of the microorganism according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the enzymes are encoded on one or more plasmids. Particularly preferred embodiments of the microorganism according to the present invention contain one or multiple plasmids according to the present invention. Particularly preferred are the “Lyc-synthesis”, “eCaro-synthesis”, “eCaro-cleavage”, “ionone-synthesis” and “MEP pathway” plasmids.
In a further preferred embodiment of the microorganism according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the enzymes geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-Isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI) and phytoene synthase (crtB) are the corresponding enzymes of Erwinia herbicola.
In a preferred embodiment of the microorganism according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the plasmid or the plasmids are present in the microorganism as individual structures or are integrated into the genome of the microorganism.
In a further preferred embodiment of the microorganism according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the expression of the carotenoid-cleavage-dioxygenase (CCD1) is under the transcriptional control of an inducible promoter. In a further preferred embodiment, which can be combined with any of the preceding and subsequent embodiments, the inducible promoter is the arabinose inducible promoter pBAD. Particularly preferred are furthermore the constitutive and/or inducible promoters pXYL1, pXYL2, aP5 and aP15.
In a further preferred embodiment of the microorganism according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism contains the nucleic acid according to the present invention that encodes a lycopene-epsilon-cyclase.
In a further preferred embodiment of the microorganism according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the carotenoid-cleavage-dioxygenase (CCD1) oxidatively cleaves the 9, 10- and 9′, 10′-double bonds of the epsilon-carotene.
In a particularly preferred embodiment of the microorganism according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism contains the “eCaro-synthesis” plasmid according to the present invention, which comprises a sequence or consists of it, which has at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a sequence according to SEQ ID No. 29 (pGT1066-AtEC-del), wherein the lycopene-epsilon-cyclase (EC) that is encoded by the plasmid has one of the following mutations or mutation combinations: ECmut16 (A403W/L404G), ECmut3.12 (L404T/A445S), ECmut3.3 (A403E/L404A/A445S), ECmut3.5 (A403M/L404A/A445S), ECmut3.8 (A403H/L404S/A445S), ECmut3.9 (A403E/L404G/A445S), ECmut3.16 (A403G/L404G/A445S), ECmut9 (L404S), ECmut10 (A403S/L404T) and ECmut3.2 (A403C/L404C/A445S). Particularly preferred are the mutations or mutation combinations ECmut9 (L404S), ECmut10 (A403S/L404T) andECmut3.2 (A403C/L404C/A445S).
In a particularly preferred embodiment of the microorganism according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism contains the “eCaro-synthesis” plasmid according to the present invention, which consists of a sequence according to SEQ ID No. 29, wherein the lycopene-epsilon-cyclase (EC) that is encoded by the plasmid has one of the following mutations or mutation combinations: ECmut9 (L404S), ECmut10 (A403S/L404T) and ECmut3.2 (A403C/L404C/A445S).
In a particularly preferred embodiment of the microorganism according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism is an E. coli strain. Particularly preferred in this context are the E. coli strains XL1-blue, TOP10, XL10 blue, DH5-alpha, JM109, C41, BL21gold (DE3) and W3110. In particular, the microorganism according to the present invention can be the E. coli strain TOP10. Particularly preferred is the E. coli strain BL21gold (DE3).
In a particularly preferred embodiment of the microorganism according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism contains the “eCaro-synthesis” plasmid according to the present invention and the “eCaro-cleavage” plasmid, which has at least 80% or at least 85%, 90%, 91%, 92 according to SEQ ID No. 21 (pGT1069) or according to SEQ ID No. 24 (pGT1070). Particularly preferred embodiments of the microorganism contain the “eCaro-synthesis” plasmid according to the present invention and the “eCaro-cleavage” plasmid with a sequence according to SEQ ID Nr. 21 (pGT1069) or according to SEQ ID Nr. 24 (pGT1070), wherein the “eCaro-synthesis” plasmid according to the present invention preferably consists of a sequence according to SEQ ID No. 29 (pGT1066-AtEC-del), wherein the lycopene-epsilon-cyclase (EC) that is encoded by the plasmid has one of the following mutations or mutation combinations: ECmut9 (L404S), ECmut10 (A403S/L404T) and ECmut3.2 (A403C/L404C/A445S).
In a further particularly preferred embodiment of the microorganism according to the present invention, the microorganism corresponds to the microorganism that is cultivated in the method according to the present invention of producing a highly epsilon-carotene or in the method according to the present invention of producing enantiomerically pure alpha-ionone.
Method of Producing Highly Pure Epsilon-Carotene
The method of producing highly pure epsilon-carotene from lycopene according to the present invention comprises the culturing of a microorganism that contains heterologous nucleotide sequences that encode the following enzymes: geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-Isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI), phytoene synthase (crtB) and lycopene-epsilon-cyclase (EC).
In a particularly preferred embodiment of the method of producing highly pure epsilon-carotene from lycopene according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism according to the present invention is cultured.
In a preferred embodiment of the method of producing highly pure epsilon-carotene from lycopene according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the geranylgeranyl-diphosphate-synthase is the geranylgeranyl-diphosphate-synthase crtE or the geranylgeranyl-diphosphate-synthase idsA.
In a preferred embodiment of the method of producing highly pure epsilon-carotene from lycopene according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the lycopene-epsilon-cyclase (EC) is the lycopene-epsilon-cyclase (EC) according to the present invention. Particularly preferred in this context are embodiments, in which the lycopene-epsilon-cyclase (EC) has at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a sequence according to SEQ ID No. 19 and in which it deviates at least at one of Positions 403, 404 and 445 from the sequence according to SEQ ID No. 19. Particularly preferred are embodiments in which the lycopene-epsilon-cyclase (EC) according to the present invention comprises one of the following mutations: ECmut9 (L404S), ECmut10 (A403S/L404T), ECmut3.3 (A403E/L404A/A445S) and ECmut3.2 (A403C/L404C/A445S).
In a preferred embodiment of the method of producing highly pure epsilon-carotene from lycopene according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the enzymes are encoded on one or multiple plasmids. These plasmids can be present as individual structures in the microorganisms or be integrated into the genome of the microorganism. These enzymes can be co-expressed.
In a preferred embodiment of the method of producing highly pure epsilon-carotene from lycopene according to the present invention, which can be combined with any of the previous and subsequent embodiments, the microorganism contains a Plasmid with at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100 sequence identity with a sequence according to SEQ ID No. 30, 31, 32, 33, 34, 35 or 36.
In a preferred embodiment of the method of producing highly pure epsilon-carotene from lycopene according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism contains a plasmid with at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100 sequence identity with a sequence according to SEQ ID No. 45, 46 or 47.
In a particularly preferred embodiment of the method of producing highly pure epsilon-carotene from lycopene according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism according to the present invention is cultured, which contains the “eCaro-synthesis” plasmid according to present invention, which comprises a sequence or consists of it, which has at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a sequence according to SEQ ID No. 29 (pGT1066-AtEC-del), wherein the lycopene-epsilon-cyclase (EC) that is encoded by the plasmid comprises or has one of the following mutations or mutation combinations: ECmut2 (A445S), ECmut9 (L404S), ECmut3 (L404H/A445S), ECmut3.10 (A403C/A445S), ECmut3.12 (L404T/A445S), ECmut4 (A403S/L404H), ECmut5 (A403F/L404W), ECmut6 (A403G/L404G), ECmut7 (A403K/L404D), ECmut8 (A403W/L404R), ECmut10 (A403S/L404T), ECmut11 (A403F/L404S), ECmut12 (A403C/L404S), ECmut13 (A403I/L404T), ECmut14 (A403T/L404R), ECmut15 (A403F/L404R), ECmut16 (A403W/L404G), ECmut17 (A403C/A404C), ECmut18 (A403L/L404V), ECmut19 (A403K/L404R), ECmut20 (A403Y/L404K), ECmut21 (A403Q/L404K), ECmut22 (A403G/L404Q), ECmut3.1 (A403S/L404H/A445S), ECmut3.2 (A403C/L404C/A445S), ECmut3.3 (A403E/L404A/A445S), ECmut3.4 (A403W/L404R/A445S), ECmut3.5 (A403M/L404A/A445S), ECmut3.6 (A403N/L404T/A445S), ECmut3.7 (A403N/L404A/A445S), ECmut3.8 (A403H/L404S/A445S), ECmut3.9 (A403E/L404G/A445S), ECmut3.11 (A403C/L404C/A445S), ECmut3.13 (A403R/L404S/A445S), ECmut3.14 (A403G/L404R/A445S), ECmut3.15 (A403F/L404V/A445S) and ECmut3.16 (A403G/L404G/A445S). Particularly preferred are mutations and mutation combinations ECmut9 (L404S), ECmut10 (A403S/L404T) and ECmut3.2 (A403C/L404C/A445S).
In a particularly preferred embodiment of the method of producing highly pure epsilon-carotene from lycopene according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism according to the present invention is cultured, which contains the “eCaro-synthesis” plasmid according to the present invention, which consists of a sequence according to SEQ ID No. 29 (pGT1066-AtEC-del), wherein the lycopene-epsilon-cyclase (EC) that is encoded by the plasmid has one of the following mutations or mutation combinations: ECmut9 (L404S), ECmut10 (A403S/L404T), ECmut3.2 (A403C/L404C/A445S) and ECmut3.3 (A403E/L404A/A445S).
In a particularly preferred embodiment of the method of producing highly pure epsilon-carotene from lycopene according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism according to the present invention is E. coli. Particularly preferred in this context are the E. coli strains XL1-blue, TOP10, XL10 blue, DH5-alpha, JM109, C41, BL21gold (DE3) and W3110. In particular, the microorganism can be the E. coli strain TOP10. Particularly preferred is the E. coli strain BL21gold (DE3).
In a particularly preferred embodiment of the method of producing highly pure epsilon-carotene from lycopene according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism according to the present invention contains heterologous nucleotide sequences, which encode the enzyme 1-desoxy-D-xylulose-5-phosphate-synthase (DXS).
In a particularly preferred embodiment of the method of producing highly pure epsilon-carotene from lycopene according to the present invention, which can be combined with any of the previous and subsequent embodiments, the microorganism contains heterologous nucleotide sequences that encode the enzyme isopentenyl-diphosphate-isomerase (CwIPI).
In a particularly preferred embodiment of the method of producing highly pure epsilon-carotene from lycopene, which can be combined with any of the previous and subsequent embodiments, the microorganism contains a plasmid that has at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a sequence according to SEQ ID No. 45, 46 or 47, wherein the sequence according to SEQ ID No. 45 is particularly preferred. In particular, preferred is a plasmid that has a sequence according to SEQ ID No. 45.
Method of Producing Enantiomerically Pure Alpha-Ionone
The method of producing enantiomerically pure alpha-ionone according to the present invention comprises the culturing of a microorganism that contains heterologous nucleotide sequences, which encode the following enzymes: geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-Isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI), phytoene synthase (crtB), lycopene-epsilon-cyclase (EC) and carotenoid-cleavage-dioxygenase (CCD1).
In a preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism according to the present invention is cultured.
In a preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, (R)-alpha-ionone is produced.
In a preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the geranylgeranyl-diphosphate-synthase is the geranylgeranyl-diphosphate-synthase crtE or the geranylgeranyl-diphosphate-synthase idsA.
In a preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the lycopene-epsilon-cyclase (EC) is the lycopene-epsilon-cyclase (EC) according to the present invention. Particularly preferred in this context are embodiments in which the lycopene-epsilon-cyclase (EC) has at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a sequence according to SEQ ID No. 19 and deviates at least at one of the positions 403, 404 and 445 from the sequence according to SEQ ID No. 19. Particularly preferred are embodiments in which the lycopene-epsilon-cyclase (EC) according to the present invention comprises one of the following mutations or mutation come nations: ECmut9 (L404S), ECmut10 (A403S/L404T), ECmut3.3 (A403E/L404A/A445S) and ECmut3.2 (A403C/L404C/A445S).
In a preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the carotenoid-cleavage-dioxygenase (CCD1) is a carotenoid-cleavage-dioxygenase (CCD1) of Arabidopsis thaliana or Osmanthus fragrans.
In a preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the enzymes are encoded by one or multiple plasmids. These plasmids can be present in the microorganism as individual structures or can be integrated into the genome des microorganism. These enzymes can be co-expressed.
In a particularly preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, preferably (R)-alpha-ionone, which can be combined with any of the preceding and subsequent embodiments, the microorganism is cultured, which contains the “eCaro-synthesis” plasmid and the “eCaro-cleavage” plasmid according to the present invention, wherein the “eCaro-synthesis” plasmid according to the present invention comprises a sequence or consists of it, which has at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a sequence according to SEQ ID No. 29 (pGT1066-AtEC-del), wherein the lycopene-epsilon-cyclase (EC) that is encoded by the plasmid comprises or has one of the following mutations or mutation combinations: ECmut2 (A445S), ECmut9 (L404S), ECmut3 (L404H/A445S), ECmut3.10 (A403C/A445S), ECmut3.12 (L404T/A445S), ECmut4 (A403S/L404H), ECmut5 (A403F/L404W), ECmut6 (A403G/L404G), ECmut7 (A403K/L404D), ECmut8 (A403W/L404R), ECmut10 (A403S/L404T), ECmut11 (A403F/L404S), ECmut12 (A403C/L404S), ECmut13 (A403I/L404T), ECmut14 (A403T/L404R), ECmut15 (A403F/L404R), ECmut16 (A403W/L404G), ECmut17 (A403C/A404C), ECmut18 (A403L/L404V), ECmut19 (A403K/L404R), ECmut20 (A403Y/L404K), ECmut21 (A403Q/L404K), ECmut22 (A403G/L404Q), ECmut3.1 (A403S/L404H/A445S), ECmut3.2 (A403C/L404C/A445S), ECmut3.3 (A403E/L404A/A445S), ECmut3.4 (A403W/L404R/A445S), ECmut3.5 (A403M/L404A/A445S), ECmut3.6 (A403N/L404T/A445S), ECmut3.7 (A403N/L404A/A445S), ECmut3.8 (A403H/L404S/A445S), ECmut3.9 (A403E/L404G/A445S), ECmut3.11 (A403K/L404G/A445S), ECmut3.13 (A403R/L404S/A445S), ECmut3.14 (A403G/L404R/A445S), ECmut3.15 (A403F/L404V/A445S) and ECmut3.16 (A403G/L404G/A445S). Particularly preferred are the mutations or mutation combinations ECmut9 (L404S), ECmut10 (A403S/L404T) and ECmut3.2 (A403C/L404C/A445S). The “eCaro-cleavage” plasmid is preferably a plasmid that has at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99 or 100% sequence identity with a sequence according to SEQ ID No. 21 (pGT1069) or according to SEQ ID No. 24 (pGT1070). Particularly preferred is a further plasmid that has a sequence that is identical with a sequence according to SEQ ID Nr. 21 (pGT1069) or according to SEQ ID No. 24 (pGT1070).
In a particularly preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, preferably (R)-alpha-ionone, which can be combined with any of the preceding and subsequent embodiments, the microorganism according to the present invention is cultured, which contains the “eCaro-synthesis” plasmid and the “eCaro-cleavage” plasmid according to the present invention, wherein the “eCaro-synthesis” plasmid consists of a sequence according to SEQ ID No. 29 (pGT1066-AtEC-del) and the lycopene-epsilon-cyclase (EC) that is encoded by the plasmid has one of the following mutations or mutation combinations: ECmut9 (L404S), ECmut10 (A403S/L404T), ECmut3.2 (A403C/L404C/A445S) and ECmut3.3 (A403E/L404A/A445S).
In a particularly preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, preferably (R)-alpha-ionone, which can be combined with any of the preceding and subsequent embodiments, the “eCaro-cleavage” plasmid consists of a sequence according to SEQ ID NO. 21 (pGT1069) or according to SEQ ID NO. 24 (pGT1070).
In a particularly preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, preferably (R)-alpha-ionone, which can be combined with any of the preceding and subsequent embodiments, the microorganism according to the present invention is cultured, which contains the “eCaro-synthesis” plasmid and the “eCaro-cleavage” plasmid, wherein the “eCaro-cleavage” plasmid consists of a sequence according to SEQ ID No. 21 (pGT1066-AtEC-del) or according to SEQ ID Nr. 24 (pGT1070) and wherein the “eCaro-synthesis” plasmid according to the present invention consists of a sequence according to SEQ ID Nr. 29 (pGT1066-AtEC-del), wherein the lycopene-epsilon-cyclase (EC) that is encoded by the plasmid according to the present invention has one of the following mutations or mutation combinations: ECmut9 (L404S), ECmut10 (A403S/L404T), ECmut3.2 (A403C/L404C/A445S) and ECmut3.3 (A403E/L404A/A445S).
In a particularly preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism contains a plasmid with at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100 sequence identity with a sequence according to SEQ ID No. 30, 31, 32, 33, 34, 35 or 36.
In a preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism contains a plasmid with at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100 sequence identity with a sequence according to SEQ ID No. 21, 24, 37, 38, 39, 40, 41 or 42.
In a preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism contains a plasmid with at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100 sequence identity with a sequence according to SEQ ID No. 43 or 44.
In a preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism contains a plasmid with at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100 sequence identity with a sequence according to SEQ ID No. 45, 46 or 47.
In a preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism contains a plasmid with at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100 sequence identity with a sequence according to SEQ ID No. 33 and a plasmid with at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% oder 100% sequence identity with a sequence according to SEQ ID Nr. 37. In a equally preferred embodiment the microorganism contains a plasmid with at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a sequence according to SEQ ID No. 33 and a plasmid with at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a sequence according to SEQ ID No. 41. In a further particularly preferred embodiment, the microorganism contains a plasmid with at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a sequence according to SEQ ID No. 44 and a plasmid with at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a sequence according to SEQ ID No. 45.
In a particularly preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism contains a plasmid with a sequence according to SEQ ID No. 33 and a plasmid with a sequence according to SEQ ID No. 37, or a plasmid with a sequence according to SEQ ID Nr. 33 and a plasmid with a sequence according to SEQ ID No. 41, or a plasmid with a sequence according to SEQ ID No. 44 and a plasmid with a sequence according to SEQ ID Nr. 45.
In a particularly preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism is an E. coli strain. Particularly preferred in this context is die E. coli strains, XL1-blue, TOP10, XL10 blue, DH5-alpha, JM109, C41, BL21gold (DE3) and W3110. In particular, the microorganism according to the present invention can be the E. coli strain TOP10. Particularly preferred is the E. coli strain BL21gold (DE3).
In a particularly preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism contains heterologous nucleotide sequences that encode the enzyme 1-desoxy-D-xylulose-5-phosphat-synthase (DXS).
In a particularly preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism contains heterologous nucleotide sequences that encode the enzyme isopentenyl-diphosphate-Isomerase (CwIPI).
In a particularly preferred embodiment of the method of producing enantiomerically pure alpha-ionone according to the present invention, which can be combined with any of the preceding and subsequent embodiments, the microorganism contains a plasmid that has at least 80% or at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a sequence according to SEQ ID Nr. 45, 46 or 47, wherein the sequence according to SEQ ID No. 45 is particularly preferred. In particular, preferred is a plasmid that has a sequence according to SEQ ID No. 45.
In the following further embodiments of the present invention are described, which can be combined with any of the preceding and subsequent embodiments.
Embodiment 1: Nucleic acid characterized in that it comprises a sequence that encodes a lycopene-epsilon-cyclase (EC), which catalyzes the transformation of lycopene to epsilon-carotene, wherein the encoded lycopene-epsilon-cyclase (EC) leads to greater epsilon- carotene yield compared to a reference lycopene-epsilon-cyclase (EC) with a sequence according to SEQ ID No. 26.
Embodiment 2: Nucleic acid according to Embodiment 1, wherein the encoded lycopene-epsilon-cyclase (EC) has a sequence that has at least 80% sequence identity with a sequence according to SEQ ID No. 19.
Embodiment 3: Nucleic acid according to Embodiment 2, wherein the sequence of the encoded lycopene-epsilon-cyclase (EC) deviates at least at one of the Positions 403, 404 and 445 of the sequence according to SEQ ID No. 19.
Embodiment 4: Nucleic acid according to one of the Embodiments 1 to 3, wherein the encoded lycopene-epsilon-cyclase (EC) comprises one of the following mutations or mutation combinations: ECmut9 (L404S), ECmut10 (A403S/L404T), ECmut3.2 (A403C/L404C/A445S) and ECmut3.3 (A403E/L404A/A445S),
Embodiment 5: Nucleic acid according to one of the Embodiments 1 to 4, wherein the encoded lycopene-epsilon-cyclase (EC) consists of a sequence according to SEQ ID No. 19, which has one of the following mutations or mutation combinations: ECmut9 (L404S), ECmut10 (A403S/L404T), ECmut3.2 (A403C/L404C/A445S) and ECmut3.3 (A403E/L404A/A445S),
Embodiment 6: Lycopene-epsilon-cyclase (EC) encoded by a nucleic acid according to one of Embodiments 1 to 5.
Embodiment 7: Plasmid characterized in that it comprises nucleotide sequences that encode the following enzymes:
a. geranylgeranyl-diphosphate-synthase,
b. isopentenyl-diphosphate-Isomerase (IPI),
c. phytoene-desaturase/dehydrogenase (crtI) and
d. phytoene synthase (crtB),
wherein the heterologous Expression of the lycopene-biosynthetic pathway that is encoded by the plasmid leads to an increased lycopene yield compared to the heterologous expression of the lycopene-biosynthetic pathway that is encoded by the plasmid pAC-BETAIPI-ΔcrtY (SEQ ID No. 28).
Embodiment 8: Plasmid according to Embodiment 7, comprising a sequence that has at least 80% sequence identity with a reference sequence, wherein the reference sequence is a sequence according to SEQ ID No. 28, wherein the reference sequence has, relative to the sequence according to SEQ ID No. 28, a deletion of the Bases 984-1394 and 3432-4198.
Embodiment 9: Plasmid according to Embodiment 8, wherein the reference sequence relative to the sequence according to SEQ ID No. 28 has a deletion of the Bases 984-1394, 3432-4198 and 6605-7242.
Embodiment 10: Plasmid according to Embodiment 7, comprising a sequence that has at least 80% sequence identity with a reference sequence, wherein the reference sequence is a sequence according to SEQ ID No. 11.
Embodiment 11: Plasmid according to one of the Embodiments 7 to 10, wherein the plasmid further comprises a nucleic acid sequence according to one of the Embodiments 1 to 5.
Embodiment 12: Plasmid according to Embodiment 7, comprising a sequence that has at least 80% sequence identity with a reference sequence, wherein the reference sequence is a sequence according to SEQ ID No. 18.
Embodiment 13: Plasmid according to Embodiment 7, comprising a sequence that has at least 80% sequence identity with a reference sequence, wherein the reference sequence is a sequence according to SEQ ID No. 29, wherein the lycopene-epsilon-cyclase (EC) that is encoded by the plasmid has one of the following mutations or mutation combinations: ECmut9 (L404S), ECmut10 (A403S/L404T), ECmut3.2 (A403C/L404C/A445S) and ECmut3.3 (A403E/L404A/A445S).
Embodiment 14: Microorganism characterized in that it contains heterologous nucleotide sequences, which encode the following enzymes:
a. geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-Isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI), phytoene synthase (crtB), and lycopene-epsilon-cyclase (EC), or
b. geranylgeranyl-diphosphate-synthase, isopentenyl-diphosphate-Isomerase (IPI), phytoene-desaturase/dehydrogenase (crtI), phytoene synthase (crtB), lycopene-epsilon-cyclase (EC) and carotenoid-cleavage-dioxygenase (CCD1).
Embodiment 15: Microorganism according to Embodiment 14, wherein the enzymes are encoded on one or multiple plasmids.
Embodiment 16: Microorganism according to Embodiment 14 or 15, wherein the one or multiple plasmids are present in the microorganism as individual structures or are integrated into the genome of the microorganism.
Embodiment 17: Microorganism according to one of the Embodiments 14 to 16, wherein the encoded enzymes are co-expressed.
Embodiment 18: Microorganism according to one of the Embodiments 14 to 17, wherein the expression of the carotenoid-cleavage-dioxygenase (CDD1) is under the transcriptional control of an inducible promoter, preferably under the control of the arabinose inducible promoter pBAD.
Embodiment 19: Microorganism according to one of the Embodiments 14 to 18, wherein the microorganism contains a nucleic acid according to one of Embodiments 1 to 5.
Embodiment 20: Microorganism according to one of the Embodiments 14 to 19, wherein the microorganism contains the plasmid according to one of Embodiments 7 to 13.
Embodiment 21: Microorganism according to one of the Embodiments 14 to 20, wherein the carotenoid-cleavage-dioxygenase (CDD1) oxidatively cleaves the 9, 10- and 9′, 10′-double bonds of the epsilon-Carotene.
Embodiment 22: Microorganism according to one of the Embodiments 14 to 21, wherein the microorganism contains the plasmid pGT1069 (SEQ ID Nr. 21) or pGT1070 (SEQ ID Nr. 24).
Embodiment 23: Method of producing highly pure epsilon-Carotene from lycopene, characterized in that a microorganism is cultured that contains a heterologous nucleotide sequences that encode the following enzymes:
a. geranylgeranyl-diphosphate-synthase,
b. isopentenyl-diphosphate-Isomerase (IPI),
c. phytoene-desaturase/dehydrogenase (crtI),
d. phytoene synthase (crtB), and
e. lycopene-epsilon-cyclase (EC).
Embodiment 24: Method according to Embodiment 23, wherein the cultivated microorganism is a microorganism according to one of Embodiments 14 to 22.
Embodiment 25: Method of producing enantiomerically pure alpha-ionone, characterized in that a microorganism is cultured that contains heterologous nucleotide sequences that encode the following enzymes:
a. geranylgeranyl-diphosphate-synthase,
b. isopentenyl-diphosphate-Isomerase (IPI),
c. phytoene-desaturase/dehydrogenase (crtI),
d. phytoene synthase (crtB),
e. lycopene-epsilon-cyclase (EC) and
f. carotenoid-cleavage-dioxygenase (CCD1).
Embodiment 26: Method according to Embodiment 25, wherein the cultivated microorganism is a microorganism according to one of Embodiments 14 to 22.
Starting for optimizing the expression vector was the plasmid pAC-BETAipi (Cunningham et al., 2007), which carries carotenoid genes of E. herbicola (crtE, IPI, crtB and 20 crtI). Among other things, plasmid pAC-BETAipi was modified as follows, so as to produce the plasmid pGT1036 (SEQ ID No. 11) using Molecular Biology standard methods known to the skilled person (Sambrook J, Fritsch E F, Maniatis T. in: Molecular Cloning, A Laboratory Manual, 1989 (Nolan C, Ed.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.): Deletion 984-1394, Deletion 3432-5356 and Deletion 7761-25 8399. A plasmid map of the resulting plasmids pGT1036 is depicted in
The analysis of the lycopene yield was conducted analogously to the analysis described in Example 6 for the epsilon-Carotene yield. Briefly: The HPLC analysis of the bacterial carotenoid extracts was conducted using an HP-Series II 1090 liquid chromatograph (Agilent Technologies, Boblingen) with ternary pump system and diode-array-detector. For resolution, a Zorbax SB-C18 separation column (3.5 μm, 4.6×150 mm, Agilent Technologies, Boblingen) at a column temperature of 40° C. The separation of the carotenoids initially took place over a course of 2 minutes, isocratically with 20% ethyl acetate (EtAc) in acetonitrile (AcN), subsequently with a gradient of 20% EtAc in AcN to 50% EtAc in AcN for 10 minutes, and subsequently for 3 minutes isocratically at 50% EtAc in AcN with a flow rate of 1 ml per minute. The analysis was conducted with HP ChemStation for LC Version A.05.02 and was performed for lycopene at a wavelength of 450 nm. The HPLC conditions were as follows: Column—Zorbax C18 3,5 μm 150-4.6 (Agilent), column temperature—40° C., solvent A—acetonitrile, solvent B—ethyl acetate, flow rate—1 ml/min, and gradient—2 minutes isocratically at 20% B, in 10 minutes up to 50% B, 3 minutes isocratically at 50% B.
The analysis/detection was performed by means of absorption measurement. lycopene was detected at a wavelength of 450 nm.
For determining the amount of lycopene, the area of the corresponding peaks in the chromatogram is calculated. It is directly proportional to the amount of substance. For the generation of a reference curve, increasing amounts of pure reference substances in this manner. By using this reference curve, the given amount of substance (in g) can be calculated from the peak area.
The above-described changes to the plasmid pAC-BETAipi lead to a significant increase of lycopene yield. Compared to the reference plasmid pAC-BETAipi-ΔcrtY, the plasmid pGT1036 has a 4.2-fold increased lycopene yield.
Starting from the expression plasmid pGJ2720 (Jach et al. 2006) a short DNA sequence, consisting of a random sequence of 18 bp that is flanked by 10 bp inverted repeats was introduced at the 3′-end of the reporter gene RFP (Red Fluorescent Protein). The following primers were used for the PCR reaction (N=random nucleotide):
The PCR reaction (50 μl end volume) contained the following in bidest. water dissolved components: 5ng pGJ2720 plasmid (template), 20 μmol each of primers P2750 and P2751, 10 nmol each of nucleotides dATP, dCTP, dGTP, dTTP and 5 μl Q5-Puffer(10×). The following program was used: 2 minutes at 98° C., then 30 cycles each with 30 seconds at 98° C., 30 seconds at 65° C. and 90 seconds 72° C., followed by 5 minutes at 72° C.
After addition of 10 units of the restriction enzyme Dpnl, the PCR reaction was then incubated for 1 hour at 37° C. Subsequently, the resulting PCR product, in accordance with the manufacturer's instructions, was purified in a column (PCR Purification-Kit; Maschery and Nagel). For the phosphorylating the 5′-end of the PCR product, the eluate (50 μl) was combined with 2 μl 10 mM ATP and 1 μl polynucleotide-kinase and incubated for 15 minutes at 37° C. and then for 20 minutes at 65° C. 5 μl of this preparation were then added to a standard ligation reaction (Sambrook et al.; final volume 20 μl). The ligation products were then introduced into E. coli cells using standard transformation methods. The identification of functional terminator sequences was subsequent performed via the analysis of the reported gene expression of the resulting clones. A collection of functional clones was prepared, the corresponding plasmid DNA isolated and the sequence of the corresponding terminator sequence identified via DNA sequencing.
An in-silico analysis of the lycopene-epsilon-cyclase (EC) encoded by the Arabidopsis thaliana gene At5g57030 was conducted, which showed that the first 44 amino acids (excluding the N-terminal Methionine) of the protein sequence constitute a chloroplast localization signal (transit peptide). Using PCR, the determined coding region of the mature protein (AtEC-del, SEQ ID No. 19) from A. thaliana cDNA was amplified, since the genomic gene sequence contains multiple Introns and is therefore not suitable for the microbial expression of the enzyme. Subsequently, it was sub-cloned in the expression plasmid pGJ2720, and the resulting DNA sequence was verified.
Using Molecular Biology standard procedures, a lycopene-epsilon-cyclase (EC) expression cassette was generated. The generated EC-expression cassette consisting of Lac promoter (pLac), the sequence that encodes AtEC-del (SEQ ID No. 19) and the terminator aTerm5 (see Example 2), was amplified using PCR reaction and introduced into the generated plasmid pGT1036 (
The PCR reactions (50 μl final volume) contain the following in bidest. water dissolved components: 5 ng pGJ2720 plasmid (template), 20 μmol each of one of the primer combinations (SEQ ID No. 3/SEQ ID No. 4, SEQ ID No. 5/SEQ ID No. 6, SEQ ID No. 7/SEQ ID No. 8 or SEQ ID No. 9/SEQ ID No. 10), 10 μmol each of the nucleotides dATP, dCTP, dGTP, dTTP and 5 μl Q5 buffer (10×). The following program was used: 2 minutes at 98° C., then 30 cycles each with 30 seconds at 98° C., 30 seconds at 60° C. and 4 minutes at 72° C., and finally 5 minutes at 72° C. After an addition of 10 units of the restriction enzyme Dpnl, the PCR reaction was then incubated for 1 hour at 37° C. Subsequently, the resulting PCR product was purified by a column following the manufacturer's instructions (PCR Purification-Kit; Maschery and Nagel). For the PCR products, LIC reactions (ligation independent cloning) were conducted and the reaction products were transformed in E. coli XL1-blue cells using standard methods.
The screening of the AtEC-del-random mutants was performed by plating the transformants on solid medium (LB+Chloramphenicol), incubation for 24 hours at 28° C. and the subsequent selection from colonies with the most intense yellow coloration due to the epsilon-carotenoid content. For determining the resulting mutation, the plasmid DNA of the selected clone was isolated and analyzed by means of DNA sequencing.
The following mutants were selected on the basis of their intense yellow coloration:
Single Mutants:
ECmut2 (A445S), ECmut9 (L404S)
Double Mutants:
ECmut4 (A403S/L404H), ECmut5 (A403F/L404W), ECmut6 (A403G/L404G),
ECmut7 (A403K/L404D), ECmut8 (A403W/L404R), ECmut10 (A403S/L404T), ECmut11 (A403F/L404S), ECmut12 (A403C/L404S), ECmut13 (A403I/L404T), ECmut14 (A403T/L404R), ECmut15 (A403F/L404R), ECmut16 (A403W/L404G),
ECmut17 (A403C/A404C), ECmut18 (A403L/L404V), ECmut19 (A403K/L404R), ECmut20 (A403Y/L404K), ECmut21 (A403Q/L404K), ECmut22 (A403G/L404Q),
Triple Mutants:
ECmut3.1 (A403S/L404H/A445S), ECmut3.2 (A403C/L404C/A445S),
ECmut3.3 (A403E/L404A/A445S), ECmut3.4 (A403W/L404R/A445S),
ECmut3.5 (A403M/L404A/A445S), ECmut3.6 (A403N/L404T/A445S),
ECmut3.7 (A403N/L404A/A445S), ECmut3.8 (A403H/L404S/A445S),
ECmut3.9 (A403E/L404G/A445S), ECmut3.11 (A403K/L404G/A445S),
ECmut3.13 (A403R/L404S/A445S), ECmut3.14 (A403G/L404R/A445S),
ECmut3.15 (A403F/L404V/A445S), ECmut3.16 (A403G/L404G/A445S)
All expression plasmids were introduced into E. coli TOP10 cells using transformation. The transformation of host cells was conducted following standard methods (Sambrook J, Fritsch EF, Maniatis T. in: Molecular Cloning, A Laboratory Manual, 1989 (Nolan C, Ed.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.).
The recombinant strains were analyzed concerning their synthesized carotenoids using HPLC.
The recombinant strains were generated by transforming an E. coli strain with different expression plasmids, which contain, in addition to crtE, IPI, crtI and crtB, the nucleic acid for one of the different lycopene-epsilon-cyclase mutants (ECmut).
Die culturing of the recombinant strains was performed at 24 hours at 28° C. in dYT medium (+chloramphenicol and ampicillin). The cells were then pelleted using centrifugation (10 minutes, 4,000 g), the medium supernatant was removed and the formed carotenoids were quantitatively extracted from the cell pellet using acetone. The extracts were evaporated in vacuum to dryness and the resulting carotenoid pellets were dissolved in equal volumes of Acetonitril (1 ml) and directly used for HPLC analysis.
The HPLC analysis of the bacterial carotenoid extracts was performed by using the HP Series II 1090 Liquid Chromatograph (Agilent Technologies, Boblingen) with ternary pump system and diode-array-detector. For separation, a Zorbax SB-C18 separation column (3.5 μm, 4.6×150 mm, Agilent Technologies, Boblingen) was used at a column temperature of 40° C. The separation of the carotenoids was performed initially over 2 minutes isocratically with 20% ethyl acetate (EtAc) in acetonitrile (AcN), subsequently via a gradient from 20% EtAc in AcN to 50% EtAc in AcN for 10 minutes, and subsequently for 3 minutes, isocratically at 50% EtAc in AcN with a flow rate of 1 ml per minute.
The analysis was conducted using the HP ChemStation for LC Version A.05.02 and was performed for alpha-, β-, delta-, and epsilon-carotene at a wavelength of 450 nm.
The HPLC analysis indicated that with the exception of ECmut5, all generated mutants essentially completely converted the starting material lycopene and produced epsilon-Carotene as a main product (Table 1,
The mutants ECmut9, -10, -11, -12, -16, -21, -3.2, -3.3, -3.5, -3.8, -3.9, -3.12 and -3.16 are significantly better than the reference concerning the product purity and amount of product. The proportion of the epsilon-Carotene synthesized by the EC mutants compared to the total carotenoid content of the cells is 97.7% to 100% (see Table 1), whereas for the reference (ECmut1), a proportion of 94.3% was determined, which is thus slightly above the published reference value (92%; Cunningham et al., 2001).
The best mutants (ECmut9, -10, -3.2, -3.3, -3.5, -3.8, -3.9, -3.12) yielded epsilon-Carotene contents of 99.3%-100%. The ratio of epsilon-Carotene to its precursor delta-Carotene for the indicated mutants lies within 147:1 to 492:1 and is thus 3 to 10 times higher than the best amount ratios published so far, which ranged from 10:1 to 49:1 (see Table 1 and Cunningham et al., 2001, Bai et al. 2009). For ECmut3.5 the delta-Carotene amount was below the detection threshold, so that due to the total conversion, no quotient could be determined here or it is infinitely large.
Surprisingly, the analysis showed that not only the purity of the formed epsilon-Carotene, but also the amount of product depends on the used EC mutant (Table 1,
indicates data missing or illegible when filed
The first two columns name the enzyme or the enzyme mutant and the corresponding amino acid exchanges. For better comparison with the literature data, the mutations of the ECmut enzymes according to the present invention are indicated according to the full length enzymes. Positions 447, 448 and 489 of the wild type A. thaliana enzyme lycopene-epsilon-cyclase (AtEC) correspond to the positions 403, 404 and 445 of the mutants AtEC-del according to the present invention (SEQ ID No. 19) (see
Lyc=lycopene, a-Caro=alpha-Carotene, g-Caro=gamma-Carotene, d-Caro=delta-carotene, e-Caro=epsilon-Carotene; At=Arabidopsis thaliana, Ls=Latuca sativa, Zm=Zea mays, EC=lycopene-epsilon-cyclase.
For the production of alpha-ionone in shaking flask cultures initially the expression plasmids (e.g. pGT1066 coding for ECmut3 and a CCD1 expression plasmid pGT1069 or pGT1070) according to the present invention were introduced together into E. coli-TOP10 using standard transformation protocols, which were then cultured under selective conditions (selection with chloramphenicol (25 mg/L) and ampicillin (100 mg/L)) on agar plates with LB Medium (incubation for 24 hours at 28-30° C.). For the production of the substrate epsilon-carotene, liquid medium (dYT+chloramphenicol (25 mg/L) and ampicillin (100 mg/L)) was inoculated with a single colony from the obtained plates and the culture was cultured for 24 hours and 28-30° C. under shaking (200 rpm). Subsequently the expression of the carotenoid-cleavage-dioxygenase (CCD) and thus the transformation of the formed epsilon-carotene to alpha-ionone was started by addition of the induction medium (dYT+0.5% arabinose+chloramphenicol (25 mg/L) and ampicillin (100 mg/L)). ⅕ of the original volume was added. The culture was then incubated for additional 4hours at 28° C. For extracting the formed alpha-ionone the bacterial cells were separated by centrifugation (10 minutes; 5000 rpm), subsequently lysed and the lysate shaken with diethyl ether.
The produced epsilon-carotene was quantitatively transformed, which was already macroscopically visible based on the discoloration of the cells. For extracting the formed alpha-ionone the bacterial cells were separated by centrifugation (10 minutes; 5000 g), subsequently lysed and the lysate shaken with diethyl ether, as already described in Example 7. The resulting preparations were analyzed did HPLC and LC-MS (
The analysis of the fermentatively produced alpha-ionone with regard to the enantiomer distribution/purity was done by GC-mass spectrometry. For preparation, the diethyl ether extracts (see Example 8) were evaporated to dryness, to remove the diethyl ether, and the obtained dry substance was dissolved in acetonitrile. This sample was then used for GC-mass spectrometry without dilution.
Determination of the Enantiomer Distribution:
To this end, an enantiomer selective gas chromatography/mass spectrometry (GC/MS) was conducted as follows: the mass spectra were generated at a gas chromatograph Varian 3800 (Varian, Darmstadt), which was coupled to a mass spectrometer Saturn 2000 (Varian, Darmstadt). For determining the enantiomer distribution of alpha-ionone mass spectra were recorded in Cl-mode with an ionization energy of 70 eV. The following capillary column was used: BGB174, 30 m x 0.25 mm inner diameter (ID), 0.25 μm film thickness, Phenomenex. The following conditions for the GC/MS were used:
Determination of the Beta-Ionone Content:
To this end, semi quantitative gas chromatography/mass spectrometry (GC/MS) was performed with a gas chromatograph Varian 3800 (Varian, Darmstadt) that was coupled to a mass spectrometer Saturn 2000 (Varian, Darmstadt). For the semi quantitative determination of beta-ionone mass specter there recorded in El-mode with an ionization energy of 70 eV. The following capillary column was used: FFAP, 30 m x 0.25 mm inner diameter (ID), 0.25 μm film thickness, Phenomenex.
The conditions for the GC/MS were as follows:
Results:
For the alpha-ionone-sample and enantiomer distribution of 100% [R] 0% [S] was determined. The sample contains enantiomer pure (R)-alpha-ionone.
The content of beta-ionone was below the detection threshold (<2 μg/I). The sample contains pure alpha-ionone.
With the selection of the promoters the synthesis of the intermediates (lycopene, epsilon-carotene) and the end product (alpha-ionone) can be fine-tuned. To this end, inducible or constitutive promoters can be used. Depending on the construction of the microorganism with many, free plasmids or the integration of one expression cassette, respectively, in the microbial genome different promoter strengths are desirable.
Promoters of the Prior Art:
Inducible promoters according to the present invention:
Constitutive Promoters According to the Present Invention:
The used promoters were derived from a collection of constitutive expressing promoters, which were generated via a PCR-based approach. A promoter free RFP reporter construct (pGJ2720del) served in this context as template. With an inverted PCR approach the entire plasmid sequence is amplified with a proofreading polymerase, wherein the DNA fragment is extended by the additional sequences contained in the oligonucleotide primers. Primer 1 (−10-primer) binds to the template DNA in the area of the ribosome binding site before the reporter gene. Its extension consists of 9 random bases followed by the sequence TATAAT and 6 additional random bases. Primer 2 binds (in reverse orientation) directly before the binding site of primer 1. The primer 2 extension (−35-primer) consists of 9 random bases followed by the sequence TGTCAA and 6 further random bases. Primer 1 and 2 have annealing temperatures of 60° C. The primers were phosphorylated with the enzyme polynucleotide kinase (New England Biolabs) according to the manufacturer's instructions and then used for the amplification of the template with the following PCR program: 2 minutes at 98° C., followed by 30 cycles with 45 seconds at 98° C., 30 seconds at 60° C. and 2 minutes at 72° C. The resulting PCR fragment was separated electrophoretically on an agarose gel and the DNA band was isolated from the gel (PCR and gel extraction kit, Machery & Nagel). Using the enzyme T4-DNA-ligase and autoligation of the isolated DNA fragments was performed. The ligation products were transformed into E. coli XL1 cells using standard transformation methods and recombinant cells were cultured on selective media. The selection of the resulting functional promoters was done macroscopically based on the RFP reporter gene expression (red coloration) and in comparison to a corresponding microorganism, which expresses the RFP reporter gene under the control of a maximally induced pLac promoter. Loans with different expression levels were selected, the plasmid DNA isolated and the respectively obtained promoter sequence identified by DNA sequencing. The denomination was done according to the scheme aPxx according to the clone selection. The promoter number does not correlate with the expression strength.
The carotenoid-producing E. coli strain is cultured in liquid dYT medium for 18 to 48 hours at 28° C. The cell density of the resulting culture (=OD600) is determined by measuring the absorption at 600 nm in a photometer. If necessary the culture is appropriately diluted (usually 1:10) with dYT medium to give extinction values in the range of 0.1 to 0.8. Based on the results the cultures are adjusted to OD600/ml=4 (dilution with fresh medium). The cells from 1 mL of these cultures are pelleted by centrifugation (1 minute, 13,000 rpm) and the supernatant is transferred. If the pellet still contains carotenoids (coloration still visible) extraction is repeated and the supernatants of the extractions are combined. The carotenoid concentrations of the extracts are determined photometrically (in g/L) by recording absorption spectra (against acetone as reference) and by converting the measured extinctions at 474 nm (lycopene) or 442 nm (e-carotene) based on the specific extinction coefficients (lycopene: 3450 (L*g-1*cm-1); e-carotene: 2900 (L*g-1*cm-1)). The dry weight of the extracted cell mass is calculated with the following empirically determined formula from the measured cell densities: TGw (g/L)=0.35×OD600. For assessing the carotenoid synthesis performance the carotenoid amount per biomass (mg carotenoid/g TGw) is determined.
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| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2015/069751 | 8/28/2015 | WO | 00 |
