Patent Application
20230416789
This application claims the benefit of and priority to U.S. patent application Ser. No. 16/953,638 filed Nov. 20, 2020, the entirety of which is hereby incorporated by reference.
The present disclosure relates generally to proteins having olivetolic acid cyclase activity, useful in production of phytocannabinoids.
Phytocannabinoids are a large class of compounds with over 100 different known structures that are produced in the Cannabis sativa plant. Phytocannabinoids are known to be biosynthesized in C. sativa, or may result from thermal or other decomposition from phytocannabinoids biosynthesized in C. sativa. These bio-active molecules, such as tetrahydrocannabinol (THC) and cannabidiol (CBD), can be extracted from plant material for medical and recreational purposes. However, the synthesis of plant material is costly, not readily scalable to large volumes, and requires lengthy growing periods to produce sufficient quantities of phytocannabinoids. While the C. sativa plant is also a valuable source of grain, fiber, and other material, growing C. sativa for phytocannabinoid production, particularly indoors, is costly in terms of energy and labour. Subsequent extraction, purification, and fractionation of phytocannabinoids from the C. sativa plant is also labour and energy intensive.
Phytocannabinoids are pharmacologically active molecules that contribute to the medical and psychotropic effects of C. sativa. Biosynthesis of phytocannabinoids in the C. sativa plant scales similarly to other agricultural projects. As with other agricultural projects, large scale production of phytocannabinoids by growing C. sativa requires a variety of inputs (e.g. nutrients, light, pest control, CO, etc.). The inputs required for cultivating C. sativa must be provided. In addition, cultivation of C. sativa, where allowed, is currently subject to heavy regulation, taxation, and rigorous quality control where products prepared from the plant are for commercial use, further increasing costs.
Phytocannabinoid analogues are pharmacologically active molecules that are structurally similar to phytocannabinoids. Phytocannabinoid analogues are often synthesized chemically, which can be labour intensive and costly. As a result, it may be economical to produce the phytocannabinoids and phytocannabinoid analogues in a robust and scalable, fermentable organism. Saccharomyces cerevisiae is an example of a fermentable organism that has been used to produce industrial scales of similar molecules.
The extensive time, energy, and labour involved in growing C. sativa for production of naturally-occurring phytocannabinoids provides a motivation to produce transgenic cell lines for production of phytocannabinoids by other means. Polyketides, including olivetolic acid and its analogues are valuable precursors to phytocannabinoids.
It is desirable to find alternative enzymes and methods for the production of phytocannabinoids, and/or for the production of compounds useful in phytocannabinoid biosynthesis as intermediate or precursor compounds.
Olivetolic Acid Cyclase (OAC) variants are described herein which are capable of producing olivetolic acid (OVLa). These variants are useful in the production of olivetolic acid and relevant phytocannabinoids in a heterologous host. Methods of production are described. The described OAC variants that can produce olivetolic acid and downstream metabolites in a modified yeast cell can be applied to any host and used in phytocannabinoid production.
In certain aspects described, OAC variants comprise 6 or greater non-conservative substitution amino acid mutations relative to the wild type enzyme. Certain OAC variants described have improved activity and/or show improved ratios of olivetol to olivetolic acid compared to the wild type enzyme.
A method of producing OVLa or a phytocannabinoid derived therefrom in a heterologous host cell having OVLa-producing or phytocannabinoid-producing capacity is described. The method comprises: transforming the host cell with a nucleotide encoding a variant olivetolic acid cyclase (OAC) protein having at least 6 amino acid mutations relative to the wild type OAC protein, and culturing said transformed host cell to produce olivetolic acid and/or phytocannabinoids therefrom, wherein the variant OAC protein comprises at least 85%, at least 90%, at least 95%, or at least 99% sequence identity with the wild type OAC protein sequence according to SEQ ID NO:91.
An isolated polypeptide having olivetolic acid cyclase activity is described, comprising an amino acid sequence of at least 85%, at least 90%, at least 95%, or at least 99% sequence identity with SEQ ID NO: 92, wherein 6 or more amino acid residues comprise mutations relative to SEQ ID NO:91, located at 6 or more of residues 28, 31, 41, 43, 44, 68, 74, 84, 100 or 102 of SEQ ID NO:91.
An isolated polynucleotide is described, comprising: (a) a nucleotide sequence according to SEQ ID NO:3-SEQ ID NO:39; (b) a nucleotide sequence having at least 85%, at least 90%, at least 95%, or at least 99% identity with the nucleotide sequence of (a), or (c) a nucleotide sequence that hybridizes with the complementary strand of the nucleotide having the sequence of (a). Expression vectors comprising the polynucleotide, and host cells transformed with such expression vectors are described.
Other aspects and features of the present disclosure will become apparent to those ordinarily skilled in the art upon review of the following description of specific embodiments in conjunction with the accompanying figures.
Embodiments of the present disclosure will now be described, by way of example only, with reference to the attached Figures.
A method of producing olivetolic acid (OVLa) or a phytocannabinoid produced therefrom is described herein. A heterologous host cell comprising OVLa-producing or phytocannabinoid-producing capacity is transformed with a nucleotide encoding a variant olivetolic acid cyclase (OAC) protein having at least 6 amino acid mutations relative to the wild type OAC protein and culturing said transformed host cell to produce olivetolic acid and/or phytocannabinoids therefrom, wherein the variant OAC protein comprises at least 85%, at least 90%, at least 95%, or at least 99% sequence identity with the wild type OAC protein sequence according to SEQ ID NO: 91. Exemplary variant proteins may result in improved OVLa or phytocannabinoid production over wild type according to the method described.
In some embodiments, at least 4 of the at least 6 amino acid mutations of the OAC protein are in residues 28, 31, 41, 43, 44, 68, 74, 84, 100 or 102 of the wild type OAC protein (SEQ ID NO:91), with other mutations being located elsewhere in the sequence. When a mutation is present at residue 28, 31, 41, 43, 44, 68, 74, 84, 100 or 102, it can be either a conservative or non-conservative amino acid substitution, but may advantageously be a non-conservative amino acid substitution. While at least 4 of the 6 amino acid mutations are present in the specified residue locations, in exemplary embodiments, more than 4 may be present in the specified residues, such as 6, 7, 8, 9 or 10 of the amino acid mutations may be found at positions 28, 31, 41, 43, 44, 68, 74, 84, 100 or 102, relative to the wild type sequence. In certain embodiments, mutations other than those located at residue 28, 31, 41, 43, 44, 68, 74, 84, 100 or 102 may be limited to conservative amino acid substitutions, such that the variant OAC protein remains within at least 85%, at least 90%, at least 95%, or at least 99% sequence identity with the wild type OAC protein.
The method may encompass transformation of the host cell with a nucleotide encoding the variant olivetolic acid cyclase (OAC) protein, which nucleotide has a sequence comprising: (a) a nucleotide sequence according to SEQ ID NO:3-SEQ ID NO:39; (b) a nucleotide sequence having at least 85%, at least 90%, at least 95%, or at least 99% identity with the sequence of (a); or (c) a nucleotide sequence that hybridizes with the complementary strand of the nucleotide having the sequence of (a). For example, the variant OAC protein may comprise a according to any one of SEQ ID NO:40 to SEQ ID NO:76.
In certain embodiments, at least 4 of the at least 6 amino acid mutations relative to the wild type OAC protein are selected from the group consisting of: V28A; V31G; Y41T, Y41S or Y41V; K44V; T68L or T68R; 174E, 174R, 174D or 174G; V84R; R100M or R100E; and G102R, G102S, or G102STOP. For example, in some embodiments at least 10, at least 9, at least 8, at least 7, at least 6, or at least 5 of these amino acid mutations relative to wild type may be present.
In the method, the production of a phytocannabinoid by the transformed host cell may involve production of phytocannabinoids including but not limited to cannabigerol (CBG), cannabigerolic acid (CBGa), cannabigerovarin (CBGV), cannabigerovarinic acid (CBGVa), cannabigerocin (CBGO), cannabigerocinic acid (CBGOa), a cannabivarin, tetrahydrocannabinol (THC), or tetrahydrocannabinolic acid (THCa). Further, using the OAC variants described, in combination with a divarinic acid synthase within the host cell, the host cell may produce a cannabivarin, such as divarinic acid.
The host cell may be transformed with a nucleotide encoding variant olivetolic acid cyclase (OAC) protein with at least 85%, at least 90%, at least 95%, at least 99%, or 100% sequence identity of any one of the following sequences with the indicated substitutions from OAC wild type (SEQ ID NO:91) being present:
The host cell transformed in the method described may be a bacterial cell, a fungal cell, a protist cell, or a plant cell. Exemplary organisms include S. cerevisiae, E. coli, Yarrowia lipolytica, or Komagataella phaffii, as well as others described herein. The transformed host cell may additionally comprise, or be transformed with, other enzymes useful in phytocannabinoid production. For example, a polynucleotide encoding a polyketide synthase enzyme and/or a polynucleotide encoding a prenyltransferase enzyme may also be included in the host cell. Further options for polynucleotides and methods, such as described in Applicant's co-pending International Application No. PCT/CA2020/050687 (hereby incorporated by reference) are envisioned.
An isolated polypeptide is described herein, which has olivetolic acid cyclase (OAC) activity. The polypeptide activity comprises an amino acid sequence according to SEQ ID NO: 92, wherein 6 or more amino acid residues comprise mutations relative to SEQ ID NO: 91 (wild type OAC) which are mutations at residues 28, 31, 41, 43, 44, 68, 74, 84, 100 or 102 of SEQ ID NO:91. The isolated polypeptide may have an amino acid sequence according to one of SEQ ID NO:40 to SEQ ID NO:76.
An isolated polynucleotide is described, which may have (a) a nucleotide sequence according to SEQ ID NO:3-SEQ ID NO:39; (b) a nucleotide sequence having at least 85% identity with the nucleotide sequence of (a), or (c) a nucleotide sequence that hybridizes with the complementary strand of the nucleotide having the sequence of (a).
An expression vector is described, comprising a polynucleotide encoding a variant olivetolic acid cyclase (OAC) protein having the sequence of SEQ ID NO: 92, in which 6 or more amino acid mutations are present relative to the wild type OAC protein. In such an expression vector, the polynucleotide encoding the variant OAC protein may have at least 85% sequence identity with any one of SEQ ID NO:3 to SEQ ID NO:39.
A host cell transformed with the above-described expression vector is also encompassed herein. Such a host cell may additionally comprise a polynucleotide encoding other enzymes useful in synthesis of olivetolic acid and/or phytocannabinoids, such as encoding a polyketide synthase enzyme and/or a prenyltransferase enzyme. Such a host cell may be a bacterial cell, a fungal cell, a protist cell, or a plant cell, for example: S. cerevisiae, E. coli, Yarrowia lipolytica, or Komagataella phaffii.
Certain terms used herein are described below.
The term “cannabinoid” as used herein refers to a chemical compound that shows direct or indirect activity at a cannabinoid receptor. Non limiting examples of cannabinoids include tetrahydrocannabinol (THC), cannabidiol (CBD), cannabinol (CBN), cannabigerol (CBG), cannabichromene (CBC), cannabicyclol (CBL), cannabivarin (CBV), tetrahydrocannabivarin (THCV), cannabidivarin (CBDV), cannabichromevarin (CBCV), cannabigerovarin (CBGV), and cannabigerol monomethyl ether (CBGM).
The term “phytocannabinoid” as used herein refers to a cannabinoid that typically occurs in a plant species. Exemplary phytocannabinoids produced according to the invention include cannabigerol (CBG), cannabigerolic acid (CBGa), cannabigerovarin (CBGV), cannabigerovarinic acid (CBGVa), cannabigerocin (CBGo), or cannabigerocinic acid (CBGoa).
Cannabinoids and phytocannabinoids may contain or may lack one or more carboxylic acid functional groups. Non limiting examples of such cannabinoids or phytocannabinoids containing carboxylic acid function groups or phytocannabinoids include tetrahydrocannabinolic acid (THCA), cannabidiolic acid (CBDA), and cannabichromenic acid (CBCA).
The term “homologue” includes homologous sequences from the same and other species and orthologous sequences from the same and other species, without necessarily reference to biological origins. Different polynucleotides or polypeptides having homology may be referred to as homologues.
The term “homology” may refer to the level of similarity between two or more polynucleotide and/or polypeptide sequences in terms of percent of positional identity (i.e., sequence similarity or identity), without necessarily pertaining to genetic origins. Homology also refers to the concept of similar functional properties among different polynucleotide or polypeptides. Thus, the compositions and methods herein may further comprise homologues to the polypeptide and polynucleotide sequences described herein.
The term “orthologous,” as used herein, refers to homologous polypeptide sequences and/or polynucleotide sequences in different species that arose from a common ancestral gene during speciation.
As used herein, a “homologue” may be a sequence with specified functionality, whether referencing percent identity or percent homology, with a significant sequence identity (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% and/or 100%) to the polynucleotide sequences herein.
As used herein “sequence identity” refers to the extent to which two optimally aligned polynucleotide or peptide sequences are invariant throughout a window of alignment of components, e.g., nucleotides or amino acids. “Identity” can be readily calculated by known methods.
As used herein, the term “percent sequence identity” or “percent identity” refers to the percentage of identical nucleotides in a linear polynucleotide sequence of a reference (“query”) polynucleotide molecule (or its complementary strand) as compared to a test (“subject”) polynucleotide molecule (or its complementary strand) when the two sequences are optimally aligned. In some embodiments, “percent identity” can refer to the percentage of identical amino acids in an amino acid sequence.
The terms “fatty acid-CoA”, “fatty acyl-CoA”, or “CoA donors” as used herein may refer to compounds useful in polyketide synthesis as primer molecules which react in a condensation reaction with an extender unit (such as malonyl-CoA) to form a polyketide. Examples of fatty acid-CoA molecules (also referred to herein as primer molecules or CoA donors), useful in the synthetic routes described herein include but are not limited to: acetyl-CoA, butyryl-CoA, hexanoyl-CoA. These fatty acid-CoA molecules may be provided to host cells or may be synthesized by the host cells for biosynthesis of polyketides, as described herein.
Two nucleotide sequences can be considered to be substantially “complementary” when the two sequences hybridize to each other under stringent conditions. In some examples, two nucleotide sequences considered to be substantially complementary hybridize to each other under highly stringent conditions.
The terms “stringent hybridization conditions” and “stringent hybridization wash conditions” in the context of nucleic acid hybridization experiments, for example in Southern hybridizations and Northern hybridizations are sequence dependent, and are different under different environmental parameters. In some examples, generally, highly stringent hybridization and wash conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH.
In some examples, polynucleotides include polynucleotides or “variants” having at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to any of the reference sequences described herein, typically where the variant maintains at least one biological activity of the reference sequence.
As used herein, the terms “polynucleotide variant” and “variant” and the like refer to polynucleotides displaying substantial sequence identity with a reference polynucleotide sequence or polynucleotides that hybridize with a reference sequence under, for example, stringent conditions. These terms may include polynucleotides in which one or more nucleotides have been added or deleted, or replaced with different nucleotides compared to a reference polynucleotide. It will be understood that that certain alterations inclusive of mutations, additions, deletions and substitutions can be made to a reference polynucleotide whereby the altered polynucleotide retains the biological function or activity of the reference polynucleotide.
In some examples, the polynucleotides described herein may be included within “vectors” and/or “expression cassettes”.
In some embodiments, the nucleotide sequences and/or nucleic acid molecules described herein may be “operably” or “operatively” linked to a variety of promoters for expression in host cells. Thus, in some examples, the invention provides transformed host cells and transformed organisms comprising the transformed host cells, wherein the host cells and organisms are transformed with one or more nucleic acid molecules/nucleotide sequences of the invention. As used herein, “operably linked to,” when referring to a first nucleic acid sequence that is operably linked to a second nucleic acid sequence, means a situation when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably associated with a coding sequence if the promoter effects the transcription or expression of the coding sequence.
In the context of a polypeptide, “operably linked to,” when referring to a first polypeptide sequence that is operably linked to a second polypeptide sequence, refers to a situation when the first polypeptide sequence is placed in a functional relationship with the second polypeptide sequence.
The term a “promoter,” as used herein, refers to a nucleotide sequence that controls or regulates the transcription of a nucleotide sequence (i.e., a coding sequence) that is operably associated with the promoter. Typically, a “promoter” refers to a nucleotide sequence that contains a binding site for RNA polymerase II and directs the initiation of transcription. In general, promoters are found 5′, or upstream, relative to the start of the coding region of the corresponding coding sequence. The promoter region may comprise other elements that act as regulators of gene expression.
Promoters can include, for example, constitutive, inducible, temporally regulated, developmentally regulated, chemically regulated, tissue-preferred and tissue-specific promoters for use in the preparation of recombinant nucleic acid molecules, i.e., chimeric genes.
The choice of promoter will vary depending on the temporal and spatial requirements for expression, and also depending on the host cell to be transformed. Thus, for example, where expression in response to a stimulus is desired a promoter inducible by stimuli or chemicals can be used. Where continuous expression at a relatively constant level is desired throughout the cells or tissues of an organism a constitutive promoter can be chosen.
In some examples, vectors may be used.
In some examples, the polynucleotide molecules and nucleotide sequences described herein can be used in connection with vectors.
The term “vector” refers to a composition for transferring, delivering or introducing a nucleic acid or polynucleotide into a host cell. A vector may comprise a polynucleotide molecule comprising the nucleotide sequence(s) to be transferred, delivered or introduced. Non-limiting examples of general classes of vectors include, but are not limited to, a viral vector, a plasmid vector, a phage vector, a phagemid vector, a cosmid, a fosmid, a bacteriophage, or an artificial chromosome. The selection of a vector will depend upon the preferred transformation technique and the target species for transformation.
As used herein, “expression vectors” refers to a nucleic acid molecule comprising a nucleotide sequence of interest, wherein said nucleotide sequence is operatively associated with at least a control sequence (e.g., a promoter). Thus, some examples provide expression vectors designed to express the polynucleotide sequences of described herein.
An expression vector comprising a polynucleotide sequence of interest may be “chimeric”, meaning that at least one of its components is heterologous with respect to at least one of its other components. An expression cassette may also be one that is naturally occurring but has been obtained in a recombinant form useful for heterologous expression. In some examples, however, the expression vector is heterologous with respect to the host. For example, the particular polynucleotide sequence of the expression vector does not occur naturally in the host cell and must have been introduced into the host cell or an ancestor of the host cell by a transformation event.
In some examples, an expression vector may also include other regulatory sequences. As used herein, “regulatory sequences” means nucleotide sequences located upstream (5′ non-coding sequences), within or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences include, but are not limited to, promoters, enhancers, introns, 5′ and 3′ untranslated regions, translation leader sequences, termination signals, and polyadenylation signal sequences.
An expression vector may also include a nucleotide sequence for a selectable marker, which can be used to select a transformed host cell.
As used herein, “selectable marker” means a nucleotide sequence that when expressed imparts a distinct phenotype to the host cell expressing the marker and thus allows such transformed host cells to be distinguished from those that do not have the marker. Such a nucleotide sequence may encode either a selectable or screenable marker, depending on whether the marker confers a trait that can be selected for by chemical means, such as by using a selective agent (e.g., an antibiotic, a sugar, a carbon source, or the like), or on whether the marker is simply a trait that one can identify through observation or testing, such as by screening. Examples of suitable selectable markers are known in the art and can be used in the expression vectors described herein.
The vector and/or expression vectors and/or polynucleotides may be introduced in to a cell.
The term “introducing,” in the context of a nucleotide sequence of interest (e.g., the nucleic acid molecules/constructs/expression vectors), refers to presenting the nucleotide sequence of interest to cell host in such a manner that the nucleotide sequence gains access to the interior of a cell. Where more than one nucleotide sequence is to be introduced these nucleotide sequences can be assembled as part of a single polynucleotide or nucleic acid construct, or as separate polynucleotide or nucleic acid constructs, and can be located on the same or different transformation vectors. Accordingly, these polynucleotides may be introduced into host cells in a single transformation event, or in separate transformation events.
As used herein, the term “contacting” refers to a process by which, for example, a compound may be delivered to a cell. The compound may be administered in a number of ways, including, but not limited to, direct introduction into a cell (i.e., intracellularly) and/or extracellular introduction into a cavity, interstitial space, or into the circulation of the organism.
The term “transformation” or “transfection” as used herein refers to the introduction of a polynucleotide or heterologous nucleic acid into a cell. Transformation of a cell may be stable or transient.
The term “transient transformation” as used herein in the context of a polynucleotide refers to a polynucleotide introduced into the cell and does not integrate into the genome of the cell.
The terms “stably introducing” or “stably introduced” in the context of a polynucleotide introduced into a cell is intended to represent that the introduced polynucleotide is stably incorporated into the genome of the cell, and thus the cell is stably transformed with the polynucleotide.
The term “host cell” includes an individual cell or cell culture which can be or has been a recipient of any recombinant vector(s) or isolated polynucleotide of the invention. Host cells include progeny of a single host cell, and the progeny may not necessarily be completely identical (in morphology or in total DNA complement) to the original parent cell due to natural, accidental, or deliberate mutation and/or change. A host cell includes cells transformed in vivo or in vitro with a recombinant vector or a polynucleotide of the invention. A host cell which comprises a recombinant vector of the invention is a recombinant host cell.
In some examples, a host cell may be a bacterial cell, a fungal cell, a protist cell, or a plant cell. Specific examples of host cells are described below.
“Conversion” refers to the enzymatic transformation of a substrate to the corresponding product. “Percent conversion” refers to the percent of the substrate that is converted to the product within a period of time under specified conditions. Thus, for example, the “activity” or “conversion rate” of a ketoreductase polypeptide can be expressed as “percent conversion” of the substrate to the product.
“Hydrophilic Amino Acid or Residue” refers to an amino acid or residue having a side chain exhibiting a hydrophobicity of less than zero according to the normalized consensus hydrophobicity scale Eisenberg et al., 1984. Genetically encoded hydrophilic amino acids include L-Thr (T), L-Ser (S), L-His (H), L-Glu (E), L-Asn (N), L-Gln (Q), L-Asp (D), L-Lys (K) and L-Arg (R).
“Acidic Amino Acid or Residue” refers to a hydrophilic amino acid or residue having a side chain exhibiting a pKa value of less than about 6 when the amino acid is included in a peptide or polypeptide. Acidic amino acids typically have negatively charged side chains at physiological pH due to loss of a hydrogen ion. Genetically encoded acidic amino acids include L-Glu (E) and L-Asp (D).
“Basic Amino Acid or Residue” refers to a hydrophilic amino acid or residue having a side chain exhibiting a pKa value of greater than about 6 when the amino acid is included in a peptide or polypeptide. Basic amino acids typically have positively charged side chains at physiological pH due to association with hydronium ion. Genetically encoded basic amino acids include L-Arg (R) and L-Lys (K).
“Polar Amino Acid or Residue” refers to a hydrophilic amino acid or residue having a side chain that is uncharged at physiological pH, but which has at least one bond in which the pair of electrons shared in common by two atoms is held more closely by one of the atoms. Genetically encoded polar amino acids include L-Asn (N), L-Gln (Q), L-Ser (S) and L-Thr (T).
“Hydrophobic Amino Acid or Residue” refers to an amino acid or residue having a side chain exhibiting a hydrophobicity of greater than zero according to the normalized consensus hydrophobicity scale (Eisenberg et al., 1984). Genetically encoded hydrophobic amino acids include L-Pro (P), L-Ile (I), L-Phe (F), L-Val (V), L-Leu (L), L-Trp (W), L-Met (M), L-Ala (A) and L-Tyr (Y).
“Aromatic Amino Acid or Residue” refers to a hydrophilic or hydrophobic amino acid or residue having a side chain that includes at least one aromatic or heteroaromatic ring. Genetically encoded aromatic amino acids include L-Phe (F), L-Tyr (Y) and L-Trp O). Although owing to the pKa of its heteroaromatic nitrogen atom L His (H) it is sometimes classified as a basic residue, or as an aromatic residue as its side chain includes a heteroaromatic ring, herein histidine is classified as a hydrophilic residue.
“Constrained amino acid or residue” refers to an amino acid or residue that has a constrained geometry. Herein, constrained residues include L-Pro (P) and L-His (H). Histidine has a constrained geometry because it has a relatively small imidazole ring. Proline has a constrained geometry because it also has a five membered ring.
“Non-polar Amino Acid or Residue” refers to a hydrophobic amino acid or residue having a side chain that is uncharged at physiological pH and which has bonds in which the pair of electrons shared in common by two atoms is generally held equally by each of the two atoms (i.e., the side chain is not polar). Genetically encoded non-polar amino acids include L-Gly (G), L-Leu (L), L-Val (V), L-Ile (I), L-Met (M) and L-Ala (A).
“Aliphatic Amino Acid or Residue” refers to a hydrophobic amino acid or residue having an aliphatic hydrocarbon side chain. Genetically encoded aliphatic amino acids include L-Ala (A), L-Val (V), L-Leu (L) and L-Ile (I).
“Small Amino Acid or Residue” refers to an amino acid or residue having a side chain that is composed of a total three or fewer carbon and/or heteroatoms (excluding the α-carbon and hydrogens). The small amino acids or residues may be further categorized as aliphatic, non-polar, polar or acidic small amino acids or residues, in accordance with the above definitions. Genetically-encoded small amino acids include L-Ala (A), L-Val (V), L-Cys (C), L-Asn (N), L-Ser (S), L-Thr (T) and L-Asp (D).
A “conservative” amino acid substitution (or mutation) refers to the substitution of a residue with a residue having a similar side chain, and thus typically involves substitution of the amino acid in the polypeptide with amino acids within the same or similar defined class of amino acids. For the following residues, the possible conservative mutations are provided in parentheses: A, L, V, I (Other aliphatic residues: A, L, V, I); A, L, V, I, G, M (Other non-polar residues: A, L, V, I, G, M); D, E (Other acidic residues: D, E); K, R (Other basic residues: K, R); P, H (Other constrained residues: P, H); N, Q, S, T (Other polar residues: N, Q, S, T); Y, W, F (Other aromatic residues: Y, W, F); and C (none).
Phytocannabinoids are a large class of compounds with over 100 different known structures that are produced in the Cannabis plant. These bio-active molecules, such as tetrahydrocannabinol (THC) and cannabidiol (CBD), can be extracted from plant material for medical and psychotropic purposes. However, the synthesis of plant material is costly, not readily scalable to large volumes, and requires lengthy growth periods to produce sufficient quantities of phytocannabinoids. A fermentable organism such as Saccharomyces cerevisiae capable of producing cannabinoids would provide an economical route to producing these compounds on an industrial scale. The extensive time, energy, and labour involved in growing C. sativa for phytocannabinoid production provides a motivation to produce transgenic cell lines for production of phytocannabinoids in yeast. One example of such efforts is provided in PCT application by Mookerjee et al WO2018/148848. Aromatic prenyltransferase from cannabis are described by Page et al. in U.S. Pat. No. 8,884,100.
The first committed step in the cannabinoid biosynthesis pathway is the biosynthesis of olivetolic acid. This is done using a polyketide synthase such as DiPKS (Ghosh et al., 2008) from D. discoideum or OAS (Taura et al., 2009) from C. sativa and also requires the use of an olivetolic acid cyclase (OAC) (Gagne et al., 2012). The process begins with the polyketide synthase condensing three units of malonyl-CoA to form a linear tetraketide. Olivetolic acid cyclase can then cyclize the tetraketide backbone to form olivetolic acid. In the absence of OAC, the tetraketide can spontaneously cyclize to form olivetol, an unwanted byproduct in the cannabinoid biosynthesis pathway. In order to improve enzyme performance in a heterologous host, the authors subjected OAC to an enzyme engineering regimen.
Enzyme engineering is the process of improving a desired phenotype of the enzyme by making modifications to the amino acid sequence of the polypeptide. As the functionality of the enzyme is dependent on the structure of the enzyme and the structure of the enzyme is dependent, partially, on the primary amino acid sequence; modification of the amino acid sequence of the enzyme could lead to a beneficial impact on the desired phenotype. This principle was applied to olivetolic acid cyclase (OAC) and modifications were made to its amino acid sequence using a directed evolution approach. This allowed for the identification of amino acid residues that improved olivetolic acid production in a strain of recombinant S. cerevisiae. Beneficial mutations were then tested in conjunction to identify combinations of mutations that improve enzyme performance.
Sequences are described herein that have multiple residues modified as compared to the wild type OAC sequence. Certain mutations produce over 2× more olivetolic acid than the wild type OAC when expressed in S. cerevisiae. Improvements to one or more enzyme properties as exhibited in the engineered OACs may include increases in enzyme activity, improved enzyme kinetics and turnover, higher tolerance to increased levels of substrate, and improved tolerance to increased product levels.
The modifications of the amino acid residues, as compared to the wild type OAC sequence may be conservative modifications or non-conservative modifications. Insertions or deletions may be used to modify the residues, relative to wild type OAC. Note that in the OAC described herein, the protein may end at position 101 instead of 102, as in other reports of wild type OAC sequences. In embodiments described herein, the residues represented as X{#} may be modified, where {#} represents the sequence position in the amino acid position of the wild type OAC sequence referenced herein as (SEQ ID NO:91). Thus, SEQ ID NO:92 comprises the option of mutations at X{28}, X{31}, X{41}, X{43}, X{44}, X{68}, X{74}, X{84}, X{100}, and X{102}, as outlined below:
SEQ ID NO:91 represents wild type OAC protein:
SEQ ID NO:92 represents the generalized variant OAC protein, wherein X
represents candidate locations for mutated residues (where X represents any amino acid):
Materials and Methods:
Genetic Manipulations:
Vector VB40 was used to construct all expression plasmids encoding enzyme proteins disclosed herein, including OAC and variants.
The OAC variants were constructed in a combinatorial library using mutations that were initially selected in a site-saturation mutagenesis library screen. Plasmid VB40_OAC was used as the template in all library construction.
Site-saturation mutagenesis was conducted at each amino acid position by a PCR reaction using a forward degenerate NNK primer and a ‘back-to-back’ reverse non-mutagenic primer (
The combinatorial library was constructed by an in-house protocol. Selected mutations were combined through an overlap-extension PCR of a batch of mutagenic oligonucleotides that were generated using targeted mutagenic primers. (
The plasmids encoding OAC and variant proteins as disclosed herein were transformed and expressed in Saccharomyces cerevisiae, with the host strain HB1416. All DNA was transformed into background strains using the Gietz et al. transformation protocol (Gietz 2014).
Strain Growth and Media:
Strains were grown in yeast synthetic complete media with a composition of 1.7 g/L YNB without ammonium sulfate, 1.92 g/L URA dropout amino acid supplement, 1.5 g/L magnesium L-glutamate, with 2% w/v galactose, 2% w/v raffinose, 200 μg/l geneticin, and 200 μg/L ampicillin (Sigma-Aldrich Canada). The culture was incubated at 30° C. for four days (96 hours). Strain HB1891 and HB1892 were respectively used as wild type control and negative control in all of the screenings.
Variant Screening Conditions:
Each variant was tested in three replicates and each replicate was clonally derived from single colonies. All strains were grown in 500 μl of media for 96 hours in 96-well deepwell plates. The 96-well deepwell plates were incubated at 30° C. and shaken at 950 rpm for 96 hrs.
Metabolite extraction was performed by adding 30 μl of culture to 270 μl of 56% acetonitrile in a new 96-well microtiter plate. The solutions were mixed thoroughly, then centrifuged at 3750 rpm for 10 mins. 200 μl of the soluble layer was removed and stored in a 96-well v-bottom microtiter plate. Samples were stored at −20° C. until analysis.
Quantification Protocol:
The quantification of olivetolic acid was performed using HPLC-MS/MS on a Waters Acquity UPLC-TQD MS. The chromatography and MS conditions are described below.
HPLC Conditions
Column: ACQUITY HSS C18 UPLC 50×1 mm, 1.8 μm particle size (PN:186003529); Column temperature: 45° C.; Flow rate: 0.350 mL/min; Eluent A: Water+Formic Acid; Eluent B: Acetonitrile+0.1% Formic Acid; Gradient is shown in Table 1.
ESI-MS Conditions
The following conditions were utilized: Capillary: 2.90 (kV); Source temperature: 150° C.; Desolvation gas temperature: 250° C.; Desolvation gas flow (nitrogen): 500 L/hour; Cone gas flow (nitrogen): 1 L/hour; Detection parameters are shown in Table 2.
Strains used are described in Table 3.
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae
The following plasmids were used, as described in Table 4.
The following sequences are described herein (Table 5)
Modifications to base strains used herein are outlined below in Table 6.
niger. Accessory Protein for
enterica. Will allow greater
S. cerevisiae has demonstrated
cerevisiae terpenoid pathway
cerevisiae acetyl-coA
Results:
Identification of Variants that Demonstrate Improved Production of Olivetolic Acid (OVLa) and Downstream Cannabinoids
An OAC mutants library was constructed in a plasmid regulated by the Gall p promoter, and expressed in an olivetol-producing background strain (HB1416) harboring downstream enzymes of the cannabinoid production pathway. The strains expressing wild type OAC (HB1891) and mScarlet fluorescent protein (HB1892) were utilized as control in the screening to facilitate identification of OAC mutant hits with improved activity.
Table 7 shows production of olivetol, olivetolic acid and downstream cannabinoids in OAC wild type and engineered OACs strains.
Table 8 illustrates the ratio of OVLa or downstream metabolites (CBGa, CBDa, THCa) to OVL in OAC variants.
Table 9 provides a summary of mutational frequency data.
Use in Host Cells
Phytocannabinoids, such as tetrahydrocannabinol (THC) and cannabidiol (CBD), can be extracted from plant material for medical and psychotropic purposes. However, the synthesis of plant material is costly, not readily scalable to large volumes, and requires a lengthy grow periods to produce sufficient quantities of phytocannabinoids. An organism capable of fermentation, such as Saccharomyces cerevisiae, that is capable of producing cannabinoids would provide an economical route to producing these compounds on an industrial scale.
The early stages of the cannabinoid pathway proceeds via the generation of olivetolic acid by the type III PKS olivetolic acid synthase (OAS) and cyclase olivetolic acid cyclase (OAC). This reaction uses a hexanoyl-CoA starter as well as three units of malonyl-CoA. Olivetolic acid is the backbone of most classical cannabinoids and can be prenylated to form CBGA, which is ultimately converted to CBDA or THCA by an oxidocyclase. Production of olivetolic acid in S. cerevisiae is challenging as OAS generates significant by-products such as HTAL, PDAL and olivetol. These by-products can be reduced in a recombinant organism by the introduction of olivetolic acid cyclase (OAC) but even with this enzyme by-products can account for up to 80% of the total carbon in the reaction.
Table 10 lists specific examples of host cell organisms in which the described OAC variants may be utilized for preparation of cannabinoids in the described pathways.
Escherichia coli, Streptomyces coelicolor and other species.,
Bacillus
subtilis, Mycoplasma genitalium, Synechocytis,
Zymomonas mobilis, Corynebacterium glutamicum,
Synechococcus sp., Salmonella typhi, Shigella flexneri,
Shigella sonnei, and Shigella disenteriae, Pseudomonas
putida, Pseudomonas aeruginosa, Pseudomonas
mevalonii, Rhodobacter sphaeroides, Rhodobacter
capsulatus, Rhodospirillum rubrum, Rhodococcus sp.
Saccharomyces
cerevisiae, Ogataeapolymorpha, Komagataella
phaffii, Kluyveromyceslactis, Neurosporacrassa, Aspergillus
niger, Aspergillusnidulans, Schizosaccharomycespombe,
Yarrowia
lipolytica, Myceliophthorathermophila, Aspergillus
oryzae, Trichodermareesei, Chrysosporiumlucknowense,
Fusarium sp., Fusariumgramineum, Fusariumvenenatum,
Pichia
finlandica, Pichiatrehalophila, Pichiakoclamae,
Pichia
membranaefaciens, Pichiaopuntiae, Pichia
thermotolerans, Pichiasalictaria, Pichiaguercuum, Pichia
pijperi, Pichiastipitis, Pichiamethanolica, Hansenula
polymorpha.
Chlamydomonas
reinhardtii, Dictyosteliumdiscoideum,
Chlorella sp., Haematococcuspluvialis, Arthrospiraplatensis,
Dunaliella sp., Nannochloropsisoceanica.
Cannabis
sativa, Arabidopsisthaliana, Theobromacacao, maize,
Phytocannabinoids may be produced in a host cell involving Dictyostelium discoideum polyketide synthase (DiPKS), olivetolic acid cyclase (OAC), prenyltransferases, and/or mutants of these, as described in Applicant's co-pending International Application No. PCT/CA2020/050687 (herein incorporated by reference). For example, a host cell transformed with a polyketide synthase coding sequence, an olivetolic acid cyclase coding sequence, and a prenyltransferase coding sequence may be prepared. The polyketide synthase and the olivetolic acid cyclase catalyze synthesis of olivetolic acid from malonyl CoA. The olivetolic acid cyclase may include wild type, or any of the functional mutants described herein. The host cell may include a yeast cell, a bacterial cell, a protest cell or a plant cell, selected from among those listed in Table 10.
Combinations of the methods, nucleotides, and expression vectors described herein as well as in Applicant's co-pending International Application No. PCT/CA2020/050687 may be employed together to produce phytocannabinoids, phytocannabinoid precursors such as polyketides. Depending on the desired product, selections of characteristics of the cells and methods employed may be selected to achieve production of the cannabinoid, cannabinoid precursor, or intermediate of interest.
Methods of producing a phytocannabinoid may comprising culturing a host cell under suitable culture conditions to form a phytocannabinoid, said host cell comprising: a polynucleotide encoding a polyketide synthase (PKS) enzyme; a polynucleotide encoding an olivetolic acid cyclase (OAC) enzyme mutants as described herein; and a polynucleotide encoding a prenyltransferase (PT) enzyme; and optionally comprising: a polynucleotide encoding an acyl-CoA synthase (Alk) enzyme; a polynucleotide encoding a fatty acyl CoA activating (CsAAE) enzyme; and/or a polynucleotide encoding a THCa synthase (OXC) enzyme. An expression vector can be prepared comprising a polynucleotide encoding a polyketide synthase (PKS) enzyme; a polynucleotide encoding an olivetolic acid cyclase (OAC) enzyme mutants as described herein; and a polynucleotide encoding a prenyltransferase (PT) enzyme. The expression vector can optionally comprise a polynucleotide encoding an acyl-CoA synthase (Alk) enzyme; a polynucleotide encoding CsAAE1; and/or a polynucleotide encoding a THCa synthase (OXC) enzyme.
In the preceding description, for purposes of explanation, numerous details are set forth in order to provide a thorough understanding of the embodiments. However, it will be apparent to one skilled in the art that these specific details are not required.
The embodiments described herein are intended to be examples only. Alterations, modifications and variations can be effected to the particular embodiments by those of skill in the art. The scope of the claims should not be limited by the particular embodiments set forth herein, but should be construed in a manner consistent with the specification as a whole.
The invention being thus described, it will be obvious that the same may be varied in many ways. Such variations are not to be regarded as a departure from the spirit and scope of the invention, and all such modification as would be obvious to one skilled in the art are intended to be included within the scope of the following claims.
All publications, patents and patent applications mentioned in this Specification are indicative of the level of skill those skilled in the art to which this invention pertains and are herein incorporated by reference to the same extent as if each individual publication patent, or patent application was specifically and individually indicated to be incorporated by reference.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CA2021/051626 | 11/17/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 16953638 | Nov 2020 | US |
| Child | 18253066 | US |
