Patent Grant
11345936
The present invention relates to methods for effectively producing frambinone from tyrosine using fungal microorganisms and suitable culture conditions.
Raspberry flavor (Rubus idaeus) is linked to more than 200 compounds, but frambinone, a natural phenolic compound, is the compound with the greatest impact, defining its characteristic taste (Klesk et al., 2004, J. Agric. Food Chem. 52, 5155-61; Larsen et al., 1991, Acta Agric. Scand. 41, 447-54). It can also be found in other fruits and vegetables, including peaches, apples and rhubarb (Beekwilder et al., 2007, Biotechnol. J. 2, 1270-79). As it is present only in small amounts in raspberries (1-4 mg per kg of fruit), natural frambinone is highly valuable (Larsen et al., 1991). Because it has limited natural availability, producing it by means of biotechnology is highly desirable.
Frambinone (CAS no: 5471-51-2), also called raspberry ketone or 4-(4-hydroxyphenyl)butane-2-one, has the following structure:
Frambinone can be used in many applications, notably in the food business and for cosmetics (as fragrance), for agriculture (as bait/trap for insects), in the health industry (as a weight-loss product) or in medicine (as a melanogenisis inhibitor).
Frambinone can be obtained from a 4-step biosynthesis, starting with aromatic amino acid L-tyrosine as substrate (
An alternative substrate for the production of frambinone is coumaric acid, an intermediate in the path described above (denoted (2) in
L-phenylalanine (denoted (7) in
Biosynthesis of two other compounds of biotechnological interest, resveratrol and naringenin, show many similarities to the path proposed for frambinone (Jeandet et al., 2012, J. Biomed. Biotechnol. 2012, 1-14; Lussier et al., 2012, Comput. Struct. Biotechnol. J. 3, 1-11.). TAL and 4CL are used to convert tyrosine and coumaric acid into coumaroyl-CoA. A stilbene synthase (STS) or chalcone synthase (CHS) then catalyzes the consecutive condensation with three malonyl-CoA units to form resveratrol or chalcone naringenin, respectively.
In light of the interest in an alternative production to the chemical synthesis of frambinone, transposing these ways of synthesizing recombinant microorganisms has been attempted, in particular in Escherichia coli and Saccharomyces cerevisiae.
GB 2 416 769 in particular describes the possibility of producing frambinone using a microorganism (particularly bacteria and yeast) containing a 4CL coding sequence and BAS, at least one from heterologous source. It can additionally include a BAR, C4H, PAL and/or CHS coding sequence, the BAR coding sequence being advantageously endogenic. In the examples, this document reports:
Based on the assumption that CHS has BAS activity, GB 2 416 770 describes the possibility of producing benzalacetone and frambinone with a microorganism comprising a 4CL coding sequence (tobacco, for example) and CHS (raspberry bush or petunia), at least one being a heterologous source. It can additionally include a BAR coding sequence (raspberries for example), C4H and PAL. In the examples, this document reports:
Similarly, Beekwilder et al. (2007, Biotechnol. J. 2, 1270-79) only report the successful production of frambinone from coumaric acid in E. coli with CHS and 4CL but with a yield of 0.3 mg/L. There has been no convincing data reported for production with yeast.
Recently, Lee et al. (2016, Microb. Cell Factories 15. doi:10.1186/s12934-016-0446-2) have demonstrated the synthesis of frambinone from coumaric acid by expressing a 4CL gene and BAS in S. cerevisiae (up to 8 mg/L). Furthermore, the expression of PAL/TAL and C4H made de novo production of frambinone possible (up to 4 mg/L).
Moreover, Rodriguez et al. (2015, Metabolic Engineering 31, 181-188) described a genetically modified yeast for the production of coumaric acid, the precursor of flavonoids like resveratrol and naringenin. So it is reported that inactivation of genes PDC5 and ARO10 coding a pyruvate decarboxylase and a phenylpyruvate decarboxylase, respectively, leads to overproduction of coumaric acid.
There is, then, an obvious need to develop new technical solutions offering effective production of frambinone.
The definitions below correspond to the meaning generally used in the context of the invention and should be taken into account, unless another definition is explicitly indicated.
Within the meaning of the invention, the articles “a” and “an” are used to refer to one or more (for example, at least one) units of the grammatical subject of the article. As an example, “an element” refers to at least one element, i.e., one or more elements.
The terms “about” or “approximately”, used in reference to a measurable value such as a quantity, a duration, and other similar values, must be understood as encompassing measurement uncertainties of ±20% or ±10%, preferably ±5%, still more preferably ±1%, and particularly preferably ±0.1% of the specified value.
Intervals: throughout the present description, the various features of the invention may be presented in the form of intervals of values. It must be understood that the description of values in the form of intervals is intended solely to make reading easier and must not be interpreted as a rigid limitation of the scope of the invention. As a result, the description of an interval of values should be considered as specifically disclosing all of the possible intermediate intervals as well as each of the values within this interval. For example, the description of an interval from 1 to 6 should be considered as specifically describing each of the intervals that it comprises, such as the intervals from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6, etc., as well as each of the values in this interval, for example 1, 2, 2.7, 3, 4, 5, 5.3 and 6. This definition is valid independently of the scope of the interval.
The term “isolated” must be understood in the context of the invention as being synonymous with withdrawn or removed from its natural environment or state. For example, an isolated nucleic acid or peptide is a nucleic acid or peptide taken out of the natural environment in which it is typically found, whether it involves a plant or a living animal, for example. Thus, a nucleic acid or a peptide naturally present in a living animal is not an isolated nucleic acid or peptide within the meaning of the present invention, while the same nucleic acid or peptide, partially or completely separated from the other elements present in its natural context, is in turn “isolated” within the meaning of the invention. An isolated nucleic acid or peptide may exist in a substantially purified form, or may exist in a non-native environment, for example a host cell.
In the context of the invention, the following abbreviations are used for the most common nucleic acid bases. “A” refers to adenosine, “C” refers to cytosine, “G” refers to guanosine, “T” refers to thymidine, and “U” refers to uridine.
Unless otherwise indicated, within the meaning of the invention, a “sequence of nucleotides coding for a sequence of amino acids” refers to all of the nucleotide sequences that code for the amino acid sequence, including the degenerated nucleotide sequences making it possible to obtain said sequence of amino acids. The nucleotide sequence that codes for a protein or an RNA or a cDNA may optionally comprise introns.
The terms “coding” or “coding for”, “code” or “code for” refer to the property inherent to the specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA or a mRNA, to serve as a matrix for the synthesis of other polymers and macromolecules in biological processes, having either a defined sequence of nucleotides (for example rRNA, tRNA and mRNA), or a defined sequence of amino acids, and the biological properties resulting therefrom. Thus, a gene codes for a protein if the transcription and the translation of the mRNA corresponding to this gene produce the protein in a cell or another biological system. Both the coding strand, whose nucleotide sequence is identical to the mRNA sequence and which is generally described in the listings of sequences and databases, and the non-coding strand, used as matrix for the transcription of a gene or cDNA, can be designated as coding for the protein or another product of this gene or cDNA.
The term “polynucleotide” as used in the context of the invention is defined as a chain of nucleotides. Furthermore, the nucleic acids are nucleotide polymers. Thus, the terms nucleic acids and polynucleotides as used in the scope of the invention are interchangeable. It is well known in the field of molecular biology and genetic engineering that nucleic acids are polynucleotides, which can be hydrolyzed into monomers. Nucleotides in monomer form can be hydrolyzed into nucleosides. As used in the context of the invention, the term polynucleotide refers, non-limitingly, to any type of nucleic acid molecules, i.e., where the nucleic acid molecules can be obtained by any means available in the art, including by recombinant means, namely the cloning of sequences of nucleic acids from a recombinant library or the genome of a cell, by using ordinary cloning technologies such as PCR, or by synthesis.
Within the meaning of the invention, the terms “peptide”, “polypeptide” and “protein” are used interchangeably and refer to a compound made up of amino acid residues covalently bonded by peptide bonds. By definition, a protein contains at least two amino acids, without limitation regarding the maximum number of amino acids. Polypeptides indifferently comprise several peptides and/or proteins, which in turn comprise two or more amino acids linked to one another by peptide bonds. As used here, the term refers both to short chains, which are also commonly referred to in the art as peptides, oligopeptides and oligomers, for example, and longer chains, which are generally referred to in the art as proteins, many types of which exist. “Polypeptides” for example comprise biologically active fragments, substantially homologous polypeptides, oligopeptides, homodimers, heterodimers, polypeptide variants, modified polypeptides, derivatives, analogs, fusion proteins, among others. Polypeptides comprise natural peptides, recombinant peptides, synthetic peptides, or a combination thereof.
The terms “homologous” and “identical” refer to the similarity of sequence or identity of sequence between two polypeptides or between two nucleic acid molecules. When a position in each of the two compared sequences is occupied by the same amino acid monomer base or sub-unit (for example, when a position in each of the two DNA molecules is occupied by an adenine), then the molecules are homologous or identical for this position. The percentage of identity between two sequences depends on the number of corresponding positions shared by the two sequences, and corresponds to this number divided by the number of positions compared and multiplied by 100. For example, if 6 out of 10 of the positions in two paired sequences are identical, then the two sequences are 60% identical. As a general rule, the comparison is done by aligning the two sequences so as to provide maximal homology/identity.
A “vector” within the meaning of the invention is a molecular construct that comprises an isolated nucleic acid and that can be used to deliver the isolated nucleic acid to the inside of a cell. Many vectors are known in the art, including, but not limited to, linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids and viruses. Thus, the term “vector” for example refers to a plasmid with autonomous replication or a virus. The term must also be interpreted as comprising non-plasmid or non-viral compounds that facilitate the transfer of nucleic acids into the cells, for example compounds of polylysine, liposomes, and the like.
The term “expression vector” refers to a vector comprising a recombinant polynucleotide, which comprises expression control sequences operationally linked to a nucleotide sequence to be expressed. An expression vector in particular comprises cis-acting expression elements; other elements for the expression can be provided by the host cell or by an in vitro expression system. The expression vectors within the meaning of the invention include all those known in the art, such as cosmids, plasmids (for example naked or contained in liposomes) and viruses (for example lentiviruses, retroviruses, adenoviruses and adeno-associated viruses), which incorporate the recombinant polynucleotide.
The term “promoter” as used here is defined as a DNA sequence recognized by the synthesis machinery of the cell, or the introduced synthesis machinery, necessary to initiate the specific transcription of a sequence of polynucleotides.
Within the meaning of the invention, the terms “promoter/regulator sequence” refer to a nucleic acid sequence, necessary for the expression of the polynucleotide linked operationally to the promoter/regulator sequence. In some cases, this sequence may be the base sequence of the promoter, while in other cases, this sequence may also comprise an activator sequence and other regulator elements, useful for the expression of the polynucleotide. The promoter/regulator sequence may for example be a sequence allowing the expression of the polynucleotide that is specific to a tissue, i.e., preferably being produced in that tissue.
Within the meaning of the invention, a “constitutive” promoter is a nucleotide sequence which, when operationally linked to a polynucleotide, leads to an expression of the polynucleotide under most or all of the physiological conditions of the cell.
Within the meaning of the invention, an “inducible” promoter is a nucleotide sequence which, when operationally linked to a polynucleotide, leads to an expression of the polynucleotide only when an inducer of the promoter is present in the cell.
The present invention concerns a genetically modified fungal microorganism for the production of frambinone, said microorganism having the following characteristics:
Within the scope of the invention, the expression “genetically modified microorganism” means that the microorganism according to the invention is not found in nature and is modified by introducing new genetic elements and/or deleting or modifying endogenous genetic elements of the microorganism. Such a microorganism can be subject to selection pressure, combining directed mutagenesis and being cultured in the selection medium.
In what follows and for reasons of simplification, the term “genetic element” is equivalent to “gene” or “sequence”. A nucleic acid sequence, then, can have any type of functionality. For example, it could be a coding sequence (coding specifically for an enzyme from the synthesis or degradation pathway of interest), or a regulatory sequence, particularly a promoter or a terminator. Especially when a coding sequence is concerned, it is optimizable, that is, modifiable to integrate the preferred codons of the host, here a fungal microorganism, wherein this sequence is expressed. According to another preferred embodiment, only the coding sequence in the gene of interest, or ORF (“Open Reading Frame”) is isolated and implemented.
According to an initial phase, the new genetic elements introduced in the microorganism target of the invention are genetic elements called exogenous or heterologous elements, which can also be synthetic or come from other organisms (or sources). In particular, a microorganism can express exogenous or heterologous genes if they are introduced into the aforesaid microorganism with all the elements needed to express in the host microorganism.
According to another embodiment, the endogenous genes can be modified to modulate their expression and/or their activity, for example by introducing mutations into their coding sequence to modify the genetic product or modify the regulating sequences, for example, further introducing heterologous sequences or replacing endogenous regulating sequences. Modulating the endogenous genes can result in over-expression or increased activity of the endogenous gene produced or, on the other hand, decreased expression or activity.
What is more, supernumerary or additional copies of an endogenous gene can also be introduced into the microorganism thereby increasing the level of expression and thus the activity of the product coded by the gene.
The techniques used to introduce DNA into a host (or transformation) are well known to the person skilled in the art and include permeabilization of the membranes by applying an electric field (electroporation) with heat (application of a thermal shock) or chemically, using lithium acetate, for instance.
The genetic elements introduced can be integrated into the genome of the host, notably by homologous recombination or chromosomal integration, advantageously with the use of integrative cassettes, or expressed extrachromosomically assisted by plasmids or vectors. Different types of plasmids, advantageously self-replicating, are well known by the person skilled in the art, differing notably by the origin of replication, the promoter (inducible or constitutive), the marker (for instance resistance to antibiotics or capacity to grow in a selective medium) and the number of copies per cell.
Advantageously in a fungal microorganism, genetic chromosomal integration, notably of expression cassettes bearing heterologous genes or supernumerary copies of endogenous genes, is done using the technique called “modular cassette integration technique.” According to a particular embodiment, the gene(s) are integrated at the HO locus. In the event of the integration of several cassettes, they are chosen for having extremities with homologous sequences, called recombination regions (RR) permitting homologous recombination and integration in the order desired and the position desired for different cassettes. Advantageously, one of the cassettes called “cassette marker” codes a marker, for example resistance to an antibiotic or capacity to grow in a selective medium, making it possible to select or identify microorganisms in which chromosomal integration has taken place. Advantageously, an expression cassette comprises the coding part or ORF of a gene of interest, notably the enzymes involved in the biosynthetic path to frambinone from tyrosine, placed under control of regulator sequences, advantageously at least one promoter and one terminator, which can be the native regulator sequences of this gene or heterologous sequences chosen for their functionality and/or effectiveness in a host microorganism.
Inactivation of the endogenous genes can be done for instance by introducing by homologous recombination at the target gene level, a cassette, either at the regulator regions level, thus inhibiting gene expression, or the level of sequence coding resulting in inactivation of the gene produced. According to a particular embodiment, the cassette is a cassette marker, advantageously comprising a dominant gene marker controlled by a promoter and a terminator. Even more advantageously, said cassette comprises at its 5′ and 3′ extremities homologous regions in the 5′ and 3′ regions of the targeted gene, for example, corresponding to 5′ in the promoter of the targeted gene and corresponding to 3′ in the terminator of the targeted gene. The cassette can also contain loxP sites making it possible to excise said cassette from the genome due to the action of cre recombinase.
Within the scope of the invention, adapted markers are the genes conferring resistance to antibiotics that are then introduced into the culture medium of the genetically modified microorganism to ensure selection and maintenance of the genetic modification. Numerous markers are available to the person skilled in the art, for example:
A good introduction and functionality of the genetic modifications desired can be verified by any technique known by the person skilled in the art, notably:
As previously stated, the important elements to control gene expression are the promoters, placed upstream of the coding sequence whose expression is governed by the promoter. The genes can be thus expressed using inducible or constitutive promoters of variable force. According to a particular embodiment, the promoters used in the invention are constitutive promoters. These promoters can be homologous or heterologous. Within the context of the invention, the promoters commonly used by the person skilled in the art are, for example:
Other important elements to control gene expression are termination sequences, also called terminators, placed downstream of the coding sequence to be expressed. There again, they can be homologous terminators from the microorganism in question, or heterologous terminators, that is, artificial sequences or terminators from a source other than the host microorganism. Numerous termination sequences are available to the person skilled in the art, for example:
In the context of the invention, the term “fungal microorganism” advantageously designates a yeast or a mushroom.
In the context of the invention, the term “fungal microorganism” means a “strain of fungal microorganism”. Indeed, advantageously, the genetically modified fungal microorganism, object of the present invention, is obtained from an isolated strain and at least partially characterized.
Illustratively and in reference to yeasts, “yeast” is understood to be a commercial product obtained by implementing a method for producing a yeast strain. Thus, yeasts having different properties can be obtained from a single strain, where these differences are connected with the production method implemented.
More precisely, the invention targets a yeast strain, in other words, a strain belonging to the phyla ascomycetes or basidiomycetes. Advantageously, the strain belongs to the genus Saccharomycetales, even more advantageously to the families Debaryomycetaceae, Dipodascaceae, or Saccaromycetaceae. According to a preferred embodiment, the strain belongs to the genus Yarrowia, Debaryomyces, Arsula, Scheffersomyces, Geotrichum, Pichia or Saccharomyces. For example, it can be of the species Yarrowia lipolytica, Debaryomyces hansenii or Saccharomyces cerevisiae.
According to a particular embodiment, the strain used for constructing a strain according to the invention or for constructing a process according to the invention is strain called “industrial”, as opposed to a strain called “laboratory”. Industrial yeast strains are those producible using industrial substrates as a carbon source. As an example, said carbon source can be molasses from sugar cane or sugar beet.
According to an advantageous embodiment, the microorganism is chosen with at least one of the following characteristics:
Regarding the first characteristic, the microorganism to be genetically modified can have at least one endogenous enzymatic activity involved in the conversion of tyrosine into frambinone. According to a particular embodiment, 4-hydroxybenzalacetone can be converted into frambinone and naturally present a BAR activity, as detailed below:
The microorganism can be chosen for other characteristics of interest, notably for its biotechnological application (knowledge of the genome, tools available for genetic manipulation, etc.), its metabolism (notably respiratory and lipid favoring production of malonyl-CoA or acetyl-CoA, co-substrates for synthesis of frambinone), or conditions for its industrial use (aerobic growth, tolerance to stress and toxic compounds, etc.)
According to a particular embodiment, a microorganism of interest is chosen from the following list: Beauveria bassiana, Candida boidinii, Galactomyces candidum (Geotrichum candidum), Kloeckera saturnus, Kodamaea ohmeri (Pichia ohmeri), Komagataella pastoris (Pichia pastoris), Mucor nederlandicus (Mucor subtilissimus), Pichia membranifaciens, Schwanniomyces etchellsii (Pichia etchellsii), Torulaspora delbrueckii (Saccharomyces fermentati), Wickerhamomyces anomalus (Hansenula anomala), Yarrowia lipolytica (Candida lipolytica), Saccharomyces cerevisiae, Debaryomyces hansenii. Advantageously, it is Saccharomyces cerevisiae, Yarrowia lipolytica or Debaryomyces hansenii.
Fungal microorganisms of particular interest are Yarrowia lipolytica or Debaryomyces hansenii.
A microorganism according to the invention intended to produce frambinone using tryosine. Advantageously, such a microorganism has an improved capacity to produce frambinone from tyrosine, notably compared with strains already described or compared with the same microorganism that has not been genetically modified.
Frambinone is known to be produced from other substrates but tyrosine is clearly of interest from an economic point of view. In addition, it has been shown that adding tyrosine into a culture medium, advantageously a fermentation medium, was possible in terms of solubility and showed no noteworthy toxicity. In an appropriate manner and as seen in more detail in relation to the process according to the invention, the production of frambinone is done from tyrosine exogenous to the microorganism according to the invention, advantageously by addition into its culture medium. Typically, the concentration of tyrosine in the culture medium is greater than or equal to 50 mg/L, even greater than or equal to 100, 150, 200, 250, 300, 350, 400 or even 450 mg/L. In addition, it is advantageously less than or equal to 1 g/L, or even less than or equal to 950, 900, 850, 800, 750, 700, 650, 600, 550, 500 or even 450 mg/L.
According to another aspect, the invention also concerns the use of a microorganism as defined within the scope of the present application for the production of frambinone from tyrosine. Within the scope of the invention, production levels of frambinone by a microorganism never yet achieved are intended, advantageously a concentration in the culture medium of the microorganism greater than 4 mg/L, more advantageously greater than or equal to 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or even 20, 25 or 30 mg/L. In these concentrations and under the conditions of the process according to the invention, frambinone remains soluble with no toxicity vis-a-vis the microorganisms according to the invention.
According to a first characteristic, a microorganism according to the invention or implemented in a process according to the invention is genetically modified to have the capacity to produce or synthesize frambinone from tyrosine, or even an improved capacity to produce or synthesize frambinone from tyrosine.
According to the invention, the microorganism can naturally have the capacity to synthesize frambinone from tyrosine and the purpose of the genetic modifications is to improve this capacity. Alternatively, the organism does not naturally have the capacity to synthesize frambinone from tyrosine, and the purpose of the genetic changes is to confer this capacity.
As stated and shown in
According to an advantageous embodiment, the microorganism according to the invention is genetically modified to ensure or improve the production of frambinone from tyrosol. Advantageously the genetic changes permit at least one of the four aforementioned enzymatic activities to increase. For example:
Concerning TAL, the enzymes of the family of lyases having a predominant activity for tyrosine (tyrosine ammonia-lyase, EC 4.3.1.23) are rare. It often shows at least equal or even greater affinity for the substrate phenylalanine (phenylalanine/tyrosine ammonia-lyase, PAL/TAL, EC 4.3.1.25).
In certain cases, it may be desirable to choose a TAL enzyme with no or very little PAL activity so as to avoid the accumulation of the cinnamic acid intermediate, which can present a certain toxicity. Where the TAL enzyme chosen has well-known PAL activity, it may be advantageous to ensure that the microorganism additionally has C4H and/or CPR activity, and possibly to modify it to introduce sequences encoding the enzymatic activities useful in converting cinnamic acid to coumaric acid. Alternatively, one might mutate the TAL coding sequence to decrease the possibly associated PAL activity. In addition, an accumulation of cinnamic acid can exert negative feedback on TAL possibly necessitating a balanced expression of 4CL.
Note that enzymatic tests to evaluate TAL and PAL activities are well known to the person skilled in the art and are described in documents by Berner et al. (J. Microbiol., 2006, 188, 2666-73), Kyndt et al. (FEBS Lett., 2002 512, 240-44) and Rosier et al. (Plant Physiol., 1997, 113, 175-79).
Genes of interest that can be implemented within the scope of the invention are listed in Table 1 below:
Rhodotorula
glutinis/
Rhodospor-
idium
toruloides
Rhodobacter
sphaeroides
Rhodobacter
capsulatus
Saccharothrix
espanaensis
Chitinophaga
pinensis
Trichosporon
cutaneum
According to a particular embodiment, the TAL protein encoded by the gene introduced in the microorganism according to the invention has the sequence SEQ ID NO: 18, or a protein sequence with at least 70%, or even 80, 85, 90, 95 or even 99% homology or sequence identity SEQ ID NO: 18 and possessing TAL activity.
According to another particular embodiment, the TAL protein coding sequence introduced into the microorganism according to the invention has the sequence SEQ ID NO: 5, or a sequence with at least 60%, even 70, 80, 85, 90, 95 or even 99% sequence identity SEQ ID NO: 5. Its expression may be placed under the control of regulatory sequences SEQ ID NO.: 4 or SEQ ID NO: 6.
Concerning 4CL, it is a priori an enzyme that is not present in the fungal microorganisms considered in the present invention. Thus and advantageously, at least one copy of at least one heterologous gene is introduced.
Note that enzymatic tests to evaluate 4CL activities are well known to the person skilled in the art and are described in documents by Ehlting et al. (Plant J., 1999, 19, 9-20), Knobloch and Hahlbrock (Arch. Biochem. Biophys., 1977, 184, 237-48) and Lee and Douglas (Plant Physiol., 1996, 112, 193-205).
The majority of the 4-coumarate:CoA ligases (4CL; EC6.2.1.12) are found in plants. Genes of interest that can be implemented within the invention are listed in Table 2 below:
Arabidopsis
thaliana
Nicotiana
tabacum
Petroselinum
crispum
Lithospermum
erythrorhizon
Populus
trichocarpa ×
P. deltoides
Glycine
max
Streptomyces
coelicolor
Chitinophaga
pinensis
According to a particular embodiment, the 4CL protein encoded by the gene introduced in the microorganism according to the invention has the sequence SEQ ID NO: 19, or a protein sequence with at least 70%, or even 80, 85, 90, 95 or even 99% homology or identity with sequence SEQ ID NO: 19 and possessing 4CL activity.
According to another particular embodiment, the 4CL protein coding sequence introduced into the microorganism according to the invention has the sequence SEQ ID NO: 8, or a sequence with at least 60%, even 70, 80, 85, 90, 95 or even 99% sequence identity SEQ ID NO: 8. Its expression may be placed under the control of regulatory sequences SEQ ID NO.: 7 and/or SEQ ID NO: 9.
It should be noted that the accumulation of coumaryl-CoA generated under 4CL action can engender the undesirable formation of phloretic acid and inhibit TAL activity. It is therefore important that the microorganism according to the invention has appropriate BAS activity (catalyzing the next step in synthesizing frambinone).
Concerning BAS, it is a priori an enzyme that is not present in the fungal microorganisms considered in the present invention. Thus and advantageously, at least one copy of at least one heterologous gene is introduced.
Note that enzymatic tests to evaluate BAS activities are well known to the person skilled in the art and are described in documents by Abe et al. (Eur. J. Biochem., 2001, 268, 3354-59 and Morita et al., 2010). Morita et al. (Acad. Sci. 2010, 107, 669-673).
Benzalacetone synthases (BAS; EC2.3.1.212) are part of the PKS (PolyKetone synthase) family that also includes chalcone synthases (CHS; involved for example in the synthesis of naringenin) and stilbene synthases (STS; involved for example in the synthesis of resveratrol). These enzymes accept coumaroyl-CoA and other substrates and catalyze a condensation with malonyl-CoA. Malonyl-CoA is an intermediate in the synthesis of fatty acids and its formation requires ATP. While CHS and STS add three malonyl-CoA units, BAS adds only one. However, the BAS enzymes described also have CHS activity. Genes of interest that can be implemented within the invention are listed in Table 3 below:
Rheum
palmatum
Rubus
idaeus
Wachendorfia
thyrsiflora
Polygonum
cuspidatum
Polygonum
cuspidatum
According to a particular embodiment, the protein BAS encoded by the gene introduced into the microorganism according to the invention has the sequence SEQ ID NO: 20, or a protein sequence with at least 70%, or even 80, 85, 90, 95 or even 99% homology or identity with sequence SEQ ID NO: 20 and possessing BAS activity.
According to another particular embodiment, the BAS protein coding sequence introduced into the microorganism according to the invention has the sequence SEQ ID NO: 11, or a sequence with at least 60%, even 70, 80, 85, 90, 95 or even 99% identity with sequence SEQ ID NO: 11. Its expression may be placed under the control of regulatory sequences, particularly a sequence promoter for SEQ ID NO.: 10 or SEQ ID NO: 13 and/or sequence terminator SEQ ID NO: 12 or SEQ ID NO: 14.
According to another particular embodiment, at least two BAS coding sequences, for example two copies of the same sequence, are introduced into the microorganism according to the invention. It should be noted that they can be placed under the control of various regulatory sequences.
The last step in synthesizing frambinone is the reduction of the α,β-double bond in p-hydroxybenzalacetone, which requires NADPH, catalyzed by benzalacetone reductase (BAR; EC 1.3.1.x). Only two enzymes with this activity have been identified to date. However, certain microorganisms have been reported to have endogenous BAR activity, E. coli and S. cerevisiae for example (Beekwilder et al., 2007, Biotechnol. J. 2, 1270-79). The first enzyme is described in document GB 2 416 769: a protein of 309 amino acids was isolated from raspberry protein fractions with BAR activity. It is homologous with isoflavone reductases (EC 1.3.1.45) and is capable of converting p-hydroxybenzalacetone into frambinone in in vitro tests carried out with purified enzyme. In 2011, Koeduka et al. (Biochem. Biophys. Res. Common. 412, 104-108) have identified a ketone/zingerone synthase of R. idaeus with BAR activity (RiRZS1, Uniprot G1FCG0). The purified protein effectively converts p-hydroxybenzalacetone into frambinone in an enzymatic test.
Note that enzymatic tests to evaluate BAR activity are well known to the person skilled in the art and are described in Koeduka et al. document (Biochem. Biophys. Res. Commun., 2011, 412, 104-108).
According to a particular embodiment, the protein BAR is encoded by a gene introduced into the microorganism according to the invention and with the sequence SEQ ID NO: 21, or a protein sequence with at least 70%, or even 80, 85, 90, 95 or even 99% homology or sequence identity SEQ ID NO: 21 and possessing BAR activity.
According to another particular embodiment, the BAR protein coding sequence is introduced into the microorganism according to the invention has the sequence SEQ ID NO: 2, or a sequence with at least 60%, even 70, 80, 85, 90, 95 or even 99% identity with sequence SEQ ID NO: 2. Its expression may be placed under the control of regulatory sequences, particularly sequences SEQ ID NO.: 1 and/or SEQ ID NO: 3.
According to a particular embodiment, the fungal microorganism according to the invention is naturally devoid of at least one enzymatic activity among 4CL and BAS, or even the 2.
Advantageously, the fungal microorganism according to the invention includes at least one heterologous sequence encoding the enzyme 4-coumarate:CoA ligase (4CL) or benzalacetone synthase (BAS), advantageously enzymes 4CL and BAS.
According to a preferred embodiment, said sequence codes a 4CL enzyme having the sequence SEQ ID NO: 19, or a protein sequence with at least 70%, or even 80, 85, 90, 95 or even 99% homology or identity with sequence SEQ ID NO: 19 and possessing 4CL activity. Preferably, this sequence comprises the sequence SEQ ID NO: 8, or a sequence with at least 60%, even 70, 80, 85, 90, 95 or even 99% sequence identity SEQ ID NO: 8. It can also comprise the sequence SEQ ID NO: 7, advantageously located upstream of the 4CL coding sequence, and/or the sequence SEQ ID NO: 9, advantageously located downstream of the 4CL coding sequence.
According to another preferred embodiment, said sequence encodes a BAS enzyme showing the sequence SEQ ID NO: 20, or a protein sequence with at least 70%, or even 80, 85, 90, 95 or even 99% homology or identity with sequence SEQ ID NO: 20 and possessing BAS activity. Preferably, said sequence includes sequence SEQ ID NO: 11 or a sequence with at least 60%, even 70, 80, 85, 90, 95 or even 99% sequence identity SEQ ID NO: 11. It can also comprise the sequence SEQ ID NO: 10 or SEQ ID NO: 13, advantageously located upstream of the BAS coding sequence, and/or the sequence SEQ ID NO: 12 or SEQ ID NO: 14, advantageously located downstream of the BAS coding sequence.
According to a particular embodiment, the fungal microorganism according to the invention comprises at least two heterologous sequences encoding the enzyme benzalacetone synthase (BAS), advantageously from the same source, even more advantageously of the same coding sequence but possibly placed under the control of different regulatory sequences.
According to another embodiment, the fungal microorganisms within the present invention do not present at least one of the following activities: TAL, 4CL, BAS and/or BAR.
Advantageously, the fungal microorganism according to the invention comprises at least one heterologous or supernumerary sequence encoding the enzyme tyrosine ammonia lyase (TAL) or benzalacetone reductase (BAR), advantageously enzymes TAL and BAR.
According to a preferred embodiment, said sequence encodes a TAL enzyme with the sequence SEQ ID NO: 18, or a protein sequence with at least 70%, or even 80, 85, 90, 95 or even 99% homology or sequence identity SEQ ID NO: 18 and possessing TAL activity. Preferably, this sequence comprises the sequence SEQ ID NO: 5, or a sequence with at least 60%, even 70, 80, 85, 90, 95 or even 99% sequence identity SEQ ID NO: 5. It can also comprise the sequence SEQ ID NO: 4, advantageously located upstream of the TAL coding sequence, and/or the sequence SEQ ID NO: 6, advantageously located downstream of the TAL coding sequence.
According to a preferred embodiment, said sequence encodes a BAR enzyme with the sequence SEQ ID NO: 21, or a protein sequence with at least 70%, or even 80, 85, 90, 95 or even 99% homology or sequence identity SEQ ID NO: 21 and possessing BAR activity. Preferably, this sequence comprises the sequence SEQ ID NO: 2, or a sequence with at least 60%, even 70, 80, 85, 90, 95 or even 99% identity with sequence SEQ ID NO: 2. It can also comprise the sequence SEQ ID NO: 1, advantageously located upstream of the BAR coding sequence, and/or the sequence SEQ ID NO: 3, advantageously located downstream of the BAR coding sequence.
According to a particular embodiment, the fungal microorganisms referred to by the present invention include at least one heterologous sequence encoding the enzymes 4-coumarate:CoA ligase (4CL) and benzalacetone synthase (BAS), and at least one heterologous or supernumerary sequence encoding the enzyme tyrosine ammonia-lyase (TAL) and benzalacetone reductase (BAR).
A particular strain of Saccharomyces cerevisiae with these characteristics, and thus a path to converting tyrosine into functional frambinone and appropriate for the target applications, is the industrial strain RK4, registered with the CNCM (National Collection of Microorganism Cultures, Pasteur Institute, 25 rue du Docteur Roux, 75724 Paris Cedex 15) dated Jun. 1, 2016 under number I-5101. This was obtained by chromosomal integration, at the level of HO locus of the strain registered with the CNCM dated Sep. 4, 2008 under number I-4071, expression cassettes encoding these 4 enzymes, as described below (See examples).
Another particular strain of Saccharomyces cerevisiae with these same characteristics is the industrial strain RK5, registered with the CNCM on Apr. 26, 2017 under number I-5199. This was obtained from strain RK4, by excising the kanMX 4 gene into the expression cassette (see examples below).
With respect to the path of synthesizing frambinone, the fungal microorganisms according to the invention may undergo other genetic modifications, such as for example:
Thus and according to a particular embodiment, the microorganism used according to the invention comprises at least one heterologous or supernumerary sequence encoding the enzyme phenylalanine ammonia lyase (TAL) or 4-(C4H), advantageously TAL and C4H enzymes.
According to a second advantageous characteristic, one target fungal microorganism of the invention is earmarked in its path to break down tyrosine as illustrated in
It is evident, in the scope of the present application, that the predominant path to breaking down tyrosine into the fungal microorganisms of interest was the path for breaking tyrosine down into tyrosol, as shown in
Said capacity can be evaluated as described in the section “Examples of Implementation” below, cultivating of fungal microorganisms potentially of interest in the production of frambinone, genetically modified or not, in the presence of tyrosine and following the production of tyrosol, for example by HPLC. Typically, a microorganism may prove to be of interest if in the conditions described in the experimental part, namely in conditions of aerobic fermentation conducted in the medium, advantageously an inorganic medium, for example composed of 1.7 g/L of YNB (Difco™), 5 g/L of ammonium sulfate, 2.7 g/L potassium phosphate and 20 g/L of dextrose, and containing tyrosine, advantageously at a level of 300 mg/L, the quantity of tyrosol produced is less than or equal to 150 mg/L, advantageously less than or equal to 100 mg/L, even 50, 40, 30, 20 mg/L or even 10 mg/L.
Alternatively and as is clear from
Advantageously, the HPPDC activity in the microorganism according to the invention is less than or equal to 2×10−6 KAT per g of protein, advantageously less than or equal to 1×10−6 KAT per g of protein, or even to 5×10−7 KAT per g of protein. In the scope of the invention, it refers to the proteins extracted from the microorganism.
More specifically, the HPPDC activity measured in a microorganism according to the invention is preferentially less than or equal to 10−5 KAT per g of protein, advantageously less than or equal to 5×10−6, 4×10−6, 3×10−6, 2×10−6, 1×10−6 KAT per g of protein, or even less than or equal to 9×10−7, 8×10−7, 7×10−7, 6×10−7, 5×10−7 KAT per g of protein. According to a particular embodiment, it is less than or equal to 4×10−7 KAT per g of protein, advantageously less than or equal to 3×10−7 KAT per g of protein, even more advantageously less than or equal to 2×10−7, 1.5×10−7, 1×10−7, or even 0.5×10−7 KAT per g of protein.
Thus and according to the invention, the microorganism is selected for its low or nil capacity to break down tyrosine, assessed according to one of the two methods mentioned above. As already said, this selection of adapted microorganisms can be performed before or after the genetic modification of the said microorganism.
According to a first embodiment, the microorganism is selected for its naturally limited capacity or incapacity to break tyrosine down into tyrosol, p-hydroxyphenylacetaldehyde and/or p-hydroxyphenylacetate.
Alternatively, a microorganism of interest, in particular for its capacity to synthesize frambinone, is subjected to genetic modifications to reduce or even eliminate its capacity to break tyrosine down into tyrosol, p-hydroxyphenylacetaldehyde and/or p-hydroxyphenylacetate.
As shown in
As already stated, different means are available to the person skilled in the art to achieve this inhibition or inactivation by genetic modification of the microorganism, including the chromosomal insertion of genetic elements either exogenous at the level of the regulatory regions in such a way as to interfere with the expression of the target gene, either at the level of the coding sequence in a manner to prevent the production of the product of the gene or to lead to the production of a truncated and/or inactive protein. It is also possible to mutate the target gene at the level of critical sequences for its expression or its activity.
According to a particular embodiment, the target gene is inactivated using a cassette capable of expressing a marker (Goldstein and McCusker, 1999, Yeast Chichester Engl. 15, 1541-53; Güldener et al., 2002, Nucleic Acids Res. 30, e23; Güldener et al., 1996, Nucleic Acids Res. 24, 2519-24.; Janke et al., 2004, Yeast 21, 947-62.; Sauer, 1987, Mol. Cell. Biol. 7, 2087-96), at the ends of which the 5′ and 3′ regions of the target gene are inserted so as to allow the homologous recombination and replace the coding portion of the gene by the expression cassette of the marker.
According to an advantageous embodiment, the fungal microorganism according to the invention is deactivated at the level of the activity involved in the decarboxylation of the hydroxyphenyl pyruvate. In particular, and concerning S. cerevisiae, at least 3 genes have been described as being involved in this activity, i.e., ARO10, PDC5 and PDC6 (Hazelwood et al., 2008; Appl. Environ. Microbiol. 74, 2259-66; Kneen et al., 2011, FEBS J. 278, 1842-53; Vuralhan et al., 2005, Appl. Environ. Microbiol. 71, 3276-84.; Vuralhan et al., 2003, Appl. Environ. Microbiol. 69, 4534-41). Advantageously, at least one of the genes encoding phenylpyruvate decarboxylase Aro10, pyruvate decarboxylase PDC5 and pyruvate decarboxylase PDC6 is deactivated. According to a particular embodiment, genes encoding phenylpyruvate decarboxylase Aro10, pyruvate decarboxylase PDC5 and pyruvate decarboxylase PDC6 are deactivated.
Alternatively, the deaminase(s) involved in the first step of the path of breaking down tyrosine are deactivated. In relation to S. cerevisiae, this can be deaminase Aro8 and/or deaminase Aro9, or their equivalents in other fungal microorganisms.
Similarly, the alcohol dehydrogenase(s) (denoted ADH) involved in the third step of the path to break tyrosine down into tyrosol can be targeted.
Thus and according to a particular aspect, the present invention seeks a fungal microorganism comprising at least one mutation or deletion in at least one of the genes encoding the following enzymes: deaminase Aro8, deaminase Aro9, decarboxylase Aro10, decarboxylase PDC5, decarboxylase PDC6, alcohol dehydrogenase (ADH). In the scope of the invention, the aforesaid mutations and/or deletion entail a reduction or even the elimination of the capacity of the organism to break tyrosine down into tyrosol, p-hydroxyphenylacetaldehyde and/or p-hydroxyphenylacetate. Advantageously, the aforesaid microorganism also has a capacity to synthesize frambinone from tyrosine, possibly through the introduction of genetic modifications as described above.
According to a particular embodiment, such a microorganism is a strain of Saccharomyces cerevisiae which has the capacity to produce frambinone and to inactivate the gene ARO10 encoding a decarboxylase. This microorganism therefore has a path for converting tyrosine into functional frambinone and a limited capacity or no capacity to break tyrosine down into tyrosol, p-hydroxyphenylacetaldehyde and/or p-hydroxyphenylacetate as described above.
For example, this could be the industrial strain RK8, filed with the CNCM on Apr. 26, 2017 under number I-5200. This was obtained from strain RK5, by inserting a cassette allowing inactivation of the ARO10 gene (see examples of implementation below).
According to another aspect, the present invention relates to the use of a fungal microorganism with the capacity to produce the frambinone from tyrosine and a limited capacity or no capacity to break tyrosine down into tyrosol, p-hydroxyphenylacetaldehyde and/or p-hydroxyphenylacetate, advantageously as described above and notably strain I-5200, for the production of frambinone, advantageously by aerobic fermentation.
In other words, the invention also relates to a process for the production of frambinone comprising the culture of a fungal microorganism with the capacity to produce frambinone from tyrosine and a limited capacity or no capacity to break tyrosine down into tyrosol, p-hydroxyphenylacetaldehyde and/or p-hydroxyphenylacetate, advantageously as described above, particularly strain I-5200, in a medium comprising tyrosine. According to a particular embodiment, tyrosine is added into the culture medium at a concentration of between 50 and 450 or 500 mg/L, for example on the order of 300 mg/L. Optionally, the culture medium can also be fortified with coumaric acid and/or phenylalanine.
Alternatively, the microorganism implemented within the invention naturally has a certain capacity to break tyrosine down into tyrosol, p-hydroxyphenylacetaldehyde and/or p-hydroxyphenylacetate, but this path for breaking it down is inhibited by the addition of a repressor to this path, an inhibitor of one of the enzymes involved in this path for instance.
Thus and according to another aspect, the invention relates to a process for the production of frambinone comprising a fungal microorganism culture with the capacity to produce frambinone from tyrosine in a medium consisting of tyrosine and at least one repressor of the path for breaking tyrosine down into tyrosol, p-hydroxyphenylacetaldehyde and/or p-hydroxyphenylacetate. Optionally, it is a microorganism genetically modified to confer or increase the capacity of the organism to produce the frambinone from tyrosine, as described above.
According to a particular embodiment, the microorganism implemented is the industrial strain Saccharomyces cerevisiae RK4, registered with the CNCM (National Collection of Microorganism Cultures, Pasteur Institute, 25 rue du Docteur Roux, 75724 Paris Cedex 15) on Jun. 1, 2016 under number I-5101.
Alternatively, the microorganism implemented is the industrial strain Saccharomyces cerevisae RK5, registered with the CNCM (National Collection of Microorganism Cultures, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15) on Apr. 26, 2017 under number I-5199.
According to a particular embodiment, the repressor of the path for breaking tyrosine down into tyrosol, p-hydroxyphenylacetaldehyde and/or p-hydroxyphenylacetate is chosen from among glutamate, glutamine, or one of their derivatives, advantageously glutamate. According to a particular embodiment, said repressor, particularly glutamate, is added into the culture medium at a concentration greater than or equal to 0.5 g/L, even 1, 2 or 3 g/L, on the order of 2 g/L for example.
In the scope of the invention, the fungal microorganism is placed in a culture under conditions favoring the production of frambinone. Conditions particularly suitable for the culture are the following:
As previously stated and under these conditions, production levels of frambinone were observed that had not previously been achieved, the culture medium showing a concentration of frambinone advantageously greater than 4 mg/L, more advantageously greater than or equal to 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or even 20, 25 or 30 mg/L.
In a manner known by the person skilled in the art, the frambinone thus produced can be isolated from the culture medium.
The invention will be described in greater detail in the following examples of implementation, supported by the attached figures. These examples of the invention are non-limiting and provided for illustrative purposes only.
Without more precision, it is deemed that the person skilled in the art, using descriptions and examples, will be able to implement and use the microorganisms according to the invention and the methods claimed.
(1) L-tyrosine (2) p-coumaric acid (3) coumaroyl-CoA (4) p-hydroxybenzalacetone (5) frambinone (6) malonyl-CoA (7) phenylalanine (8) cinnamic acid
TAL: tyrosine ammonia-lyase, 4CL: 4-coumarate-CoA ligase, BAS: benzalacetone synthase, BAR: benzalacetone reductase, PAL: phenylalanine ammonia-lyase, C4H: cinnamate 4 hydroxylase
This consists of the deamination (Aro8/9) and decarboxylation (Aro10/PDC5/PDC6) steps leading to the formation of p-hydroxyphenylacetaldehyde. The latter may be reduced using an alcohol dehydrogenase (ADH) into tyrosol or oxidized to p-hydroxyphenylacetate. Possible inactivation of the path is indicated by a cross.
The concentration of frambinone (mg/L) was determined after 7 days of culture as a function of the substrate (tyrosine synthesized by the cell from glucose and ammonium sulfate (called de novo process), tyrosine or coumaric acid added to the culture medium).
The concentration of frambinone (mg/L) was determined after 7 days of culture as a function of the substrate (tyrosine synthesized by the cell from glucose and ammonium sulfate (called de novo process), tyrosine or coumaric acid added to the culture medium).
The hydroxy-phenylpyruvate (HDPPC) activity (expressed in nmol/min/mg protein) was determined in the cell extract after 16 hours of fermentation in a synthetic medium containing 0.3 g/L of tyrosine and optionally 2 g/L of glutamate.
The present invention will be further illustrated with respect to a strain of Saccharomyces cerevisiae genetically modified to express 4 heterologous genes encoding enzymes TAL, 4CL, BAS and BAR integrated at its HO locus and effectively producing frambinone from tyrosine in a medium enriched by glutamate, or with a derived strain showing an inactivated ARO10 gene. These examples are in no way limiting.
Generation of Expression Cassettes and Recombinant Strains
To synthesize frambinone from tyrosine, it was chosen to express four heterologous genes in Saccharomyces cerevisiae as shown in the Table 4 below:
Rhodotorula
glutinis
Arabidopsis
thaliana
Rheum
palmatum
Rubus
idaeus
The encoding sequences were “codon-optimized” with S. cerevisiae. The corresponding sequences are shown in Table 4 above.
They were cloned between the proponents and terminators to ensure their expression. Five gene expression cassettes were built (Table 5 below) and, in addition to a cassette marker, were integrated into the genome of industrial strain S. cerevisiae filed with the CNCM Sep. 4, 2008 under number I-4071, at the HO locus using the modular cassette integration technique (
From the RK4 strain described above, the RK5 strain was obtained by elimination of the kanMX cassette marker. This was done by expressing the Cre recombinase that leads to excising the kanMX marker which is flanked by loxP sites (Steensma and Linde, 2001, Yeast, 18(5): 469-72). This is the strain registered with the CNCM on Apr. 26, 2017 under number I-5199.
An inactivation cassette of the gene ARO10 was then constructed (
The resulting strain RK8 was registered with the CNCM on Apr. 26, 2017 under number I-5200.
HPLC Measurements of the Path's Intermediates and Products
Frambinone, tyrosol and other intermediates of the path were analyzed and quantified by two HPLC methods called “long method” and “ACE_29,” respectively. HPLC devices and their parameters are summarized in Table 6 below and allow the separation of the frambinone and tyrosol from other compounds. For quantification, calibration was done with standard solutions between 0.1 and 300 mg/L. The samples of the yeast cultures were centrifuged (>15,000×g, 10 min), and the supernatant filtered through a 0.45 μm filter before injection into the HPLC.
Enzymatic Detection of Hydroxyphenyl Pyruvate Decarboxylase (HPPDC) Activity
To quantify the enzymatic activity of the decarboxylation of hydroxyphenyl pyruvate (HPPDC activity), an enzymatic test paired with a crude cell extract has been developed. The cell extract was prepared from an overnight culture (16 h) of the strain of interest in a synthetic medium composed of 1.7 g/L of YNB (Difco™), 5 g/L of ammonium sulfate, 2.7 g/L of potassium phosphate and 20 g/L of dextrose. The environment was also supplemented by 300 mg/L L-tyrosine and optionally different nitrogen sources (for example, L-glutamate). After aerobic growth at 30° C., the cells were harvested by centrifugation (5000×g, 4 min, 4° C.) and washed twice in a wash buffer (10 mM phosphate potassium, 2 mM EDTA, pH 6.8). The packed cell was taken up in an extraction buffer (100 mM potassium phosphate, 2 mM magnesium chloride, 1 mM DTT, 1× cOmplete™ proteinase inhibitors, pH 6.8) and the cells were broken with a “FastPrep” disruptor (with 0.45 mm glass beads; four 30 s to 6 m/s cycles, and 1 min on ice). The cell debris was removed by centrifugation and the supernatant used as crude cell extract. The protein concentration was determined using the “Uptima BC Assay Protein Quantification Kit” according to the manufacturer's instructions.
The enzyme assay was carried out as described by Kneen et al. (2011, FEBS J. 278, 1842-53), with minor modifications. The assay couples the HPPDC reaction (decarboxylation of hydroxyphenyl pyruvate (HPP) in hydroxyphenylacetaldehyde) with a second reaction (oxidation of hydroxyphenylacetaldehyde in hydroxyphenyl ethanol/tyrosol) catalyzed by the auxiliary enzyme alcohol dehydrogenase (ADH). The ADH activity leads to reduction of NADH to NAD+ which can be followed thanks to the decrease of absorption at 340 nm in a spectrophotometer. The reaction mixture (1 mL) contained 100 mM potassium phosphate, 1 mM magnesium chloride, 0.5 mM thiamine pyrophosphate, 0.1 mM of NADH, 0.5 U of ADH with horse liver, 4 mM of HPP and the crude cell extract equivalent to approximately 200 μg of total protein. Reactions were measured at 32° C. and pH 6.8. The reaction was initiated by the addition of the substrate HPP.
1/ Production of Frambinone and Other Metabolites from Tyrosine or Coumaric Acid as Substrate by Strain RK4.
Fermentation tests were conducted with strain RK4, cultivated in an inorganic medium composed of 1.7 g/L of YNB (Difco™), 5 g/L of ammonium sulfate, 2.7 g/L of potassium phosphate and 20 g/L of dextrose. Optionally, the medium can contain 300 mg/L of tyrosine or 100 mg/L of coumaric acid. As suggested by Ayuso et al. (2016, Microb. Cell Factories 15. doi:10.1186/s12934-016-0446-2), fermentation tests were conducted under aerobic conditions to optimize the production of frambinone.
As shown in
A last point of these results concerns the de novo synthesis of frambinone by the constructed strain RK4. Note that the frambinone concentration is approximately the same that observed in the presence of tyrosine. It has been hypothesized that this is probably linked to the regulation of the biosynthesis of tyrosine by extracellular tyrosine, and also to diverting this amino acid by a degradation pathway.
2/ Breaking Tyrosine Down into Tyrosol in Strain RK4
Breaking tyrosine down into tyrosol is a well-known method (
The production of tyrosol during the fermentation of the strain RK4 was followed.
3/ Inhibition of Hydroxyphenyl Pyruvate Decarboxylase (HPPDC) Activity.
To reduce production of tyrosol in strain RK4, it was decided to inhibit the activity of the enzyme involved in the decarboxylation of hydroxyphenyl pyruvate by adding into the fermentation compounds that reduce HPPDC activity.
Glutamate was selected to be added to the medium to reduce the HPPDC activity. To be certain that adding this supplemental amino acid yields a reduction in enzyme activity, the enzymatic test described above was performed.
HPPDC activity of strain RK8 was measured at the same time.
4/ Impact of Inhibition of Breaking Tyrosine Down on the Production of Frambinone and Tyrosol
In the first of a series of experiments, the production of tyrosol and frambinone by strain RK4 was followed by HPLC (“Long Method”) under both conditions (with or without glutamate). The concentrations of tyrosol observed demonstrate that the reduction of HPPDC activity also reduces the formation of tyrosol: a reduction of 27% in the tyrosol concentration was observed in response to glutamate, in line with the reduction of the HPPDC activity. At the same time, the production of frambinone increased by 40%. This data strongly suggests that the reduction of HPPDC activity reduces the production of tyrosol, thus rendering the tyrosine more available for the frambinone path.
In a second series of experiments, determination of the levels of frambinone (Table 7) and tyrosol (Table 8) produced by the three strains of S. cerevisiae built (RK4, RK5 and RK8) was assessed by HPLC according to the two methods described (“long method” and “ACE_29”). The ACE_29 method uses a new generation column with increased separation and compound resolution abilities, thus reducing the risk of co-elution, notably of frambinone, with other compounds as compared to the “long method”.
The results obtained with the “long method” from fermentation in a culture medium containing glutamate show an increase in the frambinone synthesis by the strain RK5 (+58%) compared with fermentation in a culture medium without glutamate, equivalent to strain RK4 under the same conditions. The increases observed equally approach the values of the first series of experiments.
The production of frambinone by strain RK8, cultivated without glutamate, was compared to strain RK5 under the same conditions. A +36% increase in the synthesis of frambinone, around the same observed for strains RK4 and RK5 cultivated with glutamate, was observed.
Determination of the levels of synthesis of frambinone by strains RK4, RK5 and RK8 by using the ACE_29 method similarly shows an increase in the production of frambinone, in proportions, however in higher proportions, that is, +100%, +95% and +129%, respectively.
The results obtained using the “long method” from fermentation in a culture medium containing glutamate show an increase in the frambinone synthesis by the strain RK5 (−20%) compared with fermentation in a culture medium without glutamate, equivalent to strain RK4 under the same conditions. The decreases observed equally approach the values of the first series of experiments.
The production of tyrosol by strain RK8, cultivated without glutamate, was compared to strain RK5 under the same conditions. A −49% decrease in the synthesis of tyrosol, around the same observed for strains RK4 and RK5 cultivated with glutamate, was observed.
Determination of the levels of synthesis of frambinone by strains RK4, RK5 and RK8 using the ACE_29 method similarly shows a decrease in the production of tyrosol in similar proportions, that is, −19%, −19% and −52%, respectively.
In conclusion, introduction of the frambinone path as shown in
| Number | Date | Country | Kind |
|---|---|---|---|
| 1655089 | Jun 2016 | FR | national |
This application is a continuation of U.S. patent application Ser. No. 16/302,527, filed Nov. 16, 2018, which is a U.S. national phase pursuant to 35 U.S.C. § 371 of International Patent Application No. PCT/FR2017/051407, filed Jun. 2, 2017, which claims priority to French Application No. 1655089, filed Jun. 3, 2016, the disclosures of which are all herein incorporated by reference in their entireties. This application contains, as a separate part of disclosure, a Sequence Listing in computer-readable form (filename: 53662A_Seqlisting.txt; Size: 43,436 bytes; Created: Aug. 27, 2020), which is incorporated by reference in its entirety.
| Number | Name | Date | Kind |
|---|---|---|---|
| 6521748 | Tang | Feb 2003 | B2 |
| Number | Date | Country |
|---|---|---|
| 2957629 | Dec 2015 | EP |
| 2416769 | Feb 2006 | GB |
| 2416770 | Feb 2006 | GB |
| Entry |
|---|
| Abe et al., Benzalacetone synthase. A novel polyketide synthase that plays a crucial role in the biosynthesis of phenylbutanones in Rheum palmatum, Eur. J. Biochem. 268:3354-9 (2001). (2001 Abstract Only). |
| Bassard et al., Protein-protein and protein-membrane associations in the lignin pathway, Plant Cell. 24:4465-82 (2012). (2012 Abstract Only). |
| Beekwilder et al., Microbial production of natural raspberry ketone, Biotechnol. J. 2:1270-9 (2007). |
| Berner et al., Genes and enzymes involved in caffeic acid biosynthesis in the actinomycete Saccharothrix espanaensis, J. Bacteriol. 188:2666-73 (2006). (2006 Abstract Only). |
| Borejsza-Wysocki et al., Aromatic Polyketide Synthases (Purification, Characterization, and Antibody Development to Benzalacetone Synthase from Raspberry Fruits), Plant Physiol. 110:791-799 (1996). (1996 Abstract Only). |
| Ehlting et al., Three 4-coumarate:coenzyme A ligases in Arabidopsis thaliana represent two evolutionarily divergent classes in angiosperms, Plant J. 19:9-20 (1999). (1999 Abstract Only). |
| Goldstein et al., Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae, Yeast. 15:1541-53 (1999). (1999 Abstract Only). |
| Guldener et al., A new efficient gene disruption cassette for repeated use in budding yeast, Nucleic Acids Res. 24:2519-24 (1996). (1996 Abstract Only). |
| Guldener et al., A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast, Nucleic Acids Res. 30:e23 (2002). (2002 Abstract Only). |
| Hazelwood et al., The Ehrlich pathway for fusel alcohol production: a century of research on Saccharomyces cerevisiae metabolism, Appl. Environ. Microbiol. 74:2259-56 (2008). |
| International Search Report Written Opinion, PCT/FR2017/051407 (dated Sep. 11, 2017). |
| Janke et al., A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes, Yeast. 21:947-62 (2004). (2004 Abstract Only). |
| Jeandet et al., Metabolic engineering of yeast and plants for the production of the biologically active hydroxystilbene, resveratrol, J. Biomed. Biotechnol. 1-14 (2012). |
| Klesk et al., Aroma extract dilution analysis of cv. Meeker (Rubus idaeus L.) red raspberries from Oregon and Washington, J Agric. Food Chem. 52:5155-61 (2004). (2004 Abstract Only). |
| Kneen et al., Characterization of a thiamin diphosphate-dependent phenylpyruvate decarboxylase from Saccharomyces cerevisiae, FEBS. J. 278:1842-53 (2011). (2011 Abstract Only). |
| Knobloch et al., 4-Coumarate:CoA ligase from cell suspension cultures of Petroselinum hortense Hoffm. Partial purification, substrate specificity, and further properties, Arch. Biochem. Biophys. 184:237-48 (1977). (1977 Abstract Only). |
| Koeduka et al., Characterization of raspberry ketone/zingerone synthase, catalyzing the alpha, beta-hydrogenation of phenylbutenones in raspberry fruits, Biochem. Biophys. Res. Commun. 412:104-8 (2011). (2011 Abstract Only). |
| Kyndt et al., Characterization of a bacterial tyrosine ammonia lyase, a biosynthetic enzyme for the photoactive yellow protein, FEBS Lett. 512:240-4 (2002). (2002 Abstract Only). |
| Larsen et al., Relations between the Content of Aroma Compounds and the Sensory Evaluation of 10 Raspberry Varieties (Rubus idaeus L), Acta. Agric. Scand. 41:447-454 (1991). (1991 Abstract Only). |
| Lee et al., Heterologous production of raspberry ketone in the wine yeast Saccharomyces cerevisiae via pathway engineering and synthetic enzyme fusion, Microb. Cell Fact. 15:49 (2016). |
| Lee et al., Two divergent members of a tobacco 4-coumarate:coenzyme A ligase (4CL) gene family. cDNA structure, gene inheritance and expression, and properties of recombinant proteins, Plant Physiol. 112:193-205 (1996). (1996 Abstract Only). |
| Lussier et al., Engineering microbes for plant polyketide biosynthesis, Comput. Struct. Biotechnol. J. 1-11 (2012). |
| Morita et al., A structure-based mechanism for benzalacetone synthase from Rheum palmatum, Proc. Natl. Acad. Sci. USA. 107:669-73 (2010). (2010 Abstract Only). |
| Qiao et al., Engineering lipid overproduction in the oleaginous yeast Yarrowia lipolytica, Metab. Eng. 29:56-65 (2015). (2015 Abstract Only). |
| Rodriguez et al., Establishment of a yeast platform strain for production of p-coumaric acid through metabolic engineering of aromatic amino acid biosynthesis, Metab. Eng. 31:181-8 (2015). |
| Rosler et al., Maize phenylalanine ammonia-lyase has tyrosine ammonia-lyase activity, Plant Physiol. 113:175-9 (1997). |
| Sauer, Functional expression of the cre-lox site-specific recombination system in the yeast Saccharomyces cerevisiae, Mol. Cell. Biol. 7:2087-96 (1987). (1987 Abstract Only). |
| Schuckel et al., A gene-fusion approach to enabling plant cytochromes p450 for biocatalysis, Chembiochem. 13:2758-63 (2012). (2012 Abstract Only). |
| Shin et al., Production of resveratrol from tyrosine in metabolically engineered Saccharomyces cerevisiae, Enzyme Microb. Technol. 51:211-6 (2012). (2012 Abstract Only). |
| Steensma et al., Plasmids with the Cre-recombinase and the dominant nat marker, suitable for use in prototrophic strains of Saccharomyces cerevisiae and Kluyveromyces lactis, Yeast. 18:469-72 (2001). (2001 Abstract Only). |
| Vuralhan et al., Identification and characterization of phenylpyruvate decarboxylase genes in Saccharomyces cerevisiae, Appl. Environ. Microbiol. 69:4534-41 (2003). (2003 Abstract Only). |
| Vuralhan et al., Physiological characterization of the ARO10-dependent, broad-substrate-specificity 2-oxo acid decarboxylase activity of Saccharomyces cerevisiae, Appl. Environ. Microbiol. 71:3276-84 (2005). (2005 Abstract Only). |
| Winkel, Metabolic channeling in plants, Annu. Rev. Plant. Biol. 55:85-107 (2004). (2004 Abstract Only). |
| Number | Date | Country | |
|---|---|---|---|
| 20200392545 A1 | Dec 2020 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 16302527 | US | |
| Child | 17004863 | US |
