IP Library Granted Patent US 12,442,026
Granted Patent B2
US 12,442,026 · App. 18/421,170 · Granted Oct 14, 2025

Production of fatty acyl-CoA in yeast using a fatty acid feedstock

Inventors: Alexander Hutagalung (San Diego, CA); Jose Miguel Laplaza (San Diego, CA)
Assignee: Pyrone Systems, Inc.
C12P17/06C12N1/16C12P7/42C12Y103/03006C12Y203/01206C12Y404/01026
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Quick Facts
Patent No.
US 12,442,026
App. No.
18/421,170
Granted
Oct 14, 2025
Kind
B2
Abstract

Strains of yeasts are provided containing the genes for the production of cannabinoids from fatty acids. The enzymes that mediate cannabinoid production are localized to the cytosol, peroxisome or different compartments within the secretory pathway (e.g., endoplasmic reticulum, Golgi, vacuole) to ensure efficient production. The engineered microorganisms produce cannabinoids in a controlled fermentation process.

Claims (22)

1. A method of producing a fatty acyl-CoA in a peroxisome, the method comprising:

providing a fatty acid to a genetically modified microorganism, wherein the genetically modified organism is a yeast or a fungus, wherein the microorganism comprises a biosynthetic enzyme targeted to the peroxisome, wherein the biosynthetic enzyme is capable of catabolizing the fatty acid into the fatty acyl-CoA;

culturing the microorganism under conditions sufficient to produce the fatty acyl-CoA in the peroxisome; and

isolating the fatty acyl-CoA.

2. The method of claim 1 , wherein the fatty acyl-CoA is acetyl-CoA, malonyl-CoA, or hexanoyl-CoA.

3. The method of claim 1 , wherein the yeast is from a genus selected from the group consisting of Candida, Arxula, Pichia, Scheffersomyces, Kluyveromyces, Saccharomyces, Yarrowia , or Schizosaccharomyces.

4. The method of claim 1 , wherein the fungus is Aspergillus parasiticus, Aspergillus nidulans , Thraustochytrium, Schizochytrium, Rhizopus arrhizus, Rhizopus oryzae , or Rhizopus nigricans.

5. The method of claim 1 , wherein the biosynthetic enzyme is a fatty acyl-CoA synthetase, fatty acyl activating enzyme, acyl-CoA oxidase, acyl-CoA thioesterase, hexanoyl-CoA synthetase, acetyl-CoA carboxylase, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase, beta-ketothiolase, thiolase, acyl-CoA synthase, cannabidiolic acid synthase, tetrahydrocannabidiolic acid, olivetolic acid synthase, or polyketide synthase.

6. The method of claim 5 , wherein the polyketide synthase is a Type III polyketide synthase.

7. The method of claim 6 , wherein the Type III polyketide synthase is tetraketide synthase, TKS1, or TKS1p.

8. The method of claim 1 , wherein the biosynthetic enzyme comprises a peroxisomal targeting sequence.

9. The method of claim 8 , wherein the peroxisomal targeting sequence has a consensus sequence of [S/A/H/C/E/P/Q/V]-[K/R/H/Q]-[L/F] as set forth in SEQ ID NO: 7, or GRRAKL as set forth in SEQ ID NO: 6.

10. The method of claim 1 , wherein the enzyme is removed of its endogenous amino-terminal localization sequence and/or carboxyl-terminal localization sequence.

11. A genetically modified microorganism, comprising a biosynthetic enzyme targeted to a peroxisome in the microorganism, wherein the genetically modified microorganism is a yeast or a fungus, wherein the biosynthetic enzyme is capable of catabolizing a fatty acid into a fatty acyl-CoA.

12. The genetically modified microorganism of claim 11 , wherein the yeast is from a genus selected from the group consisting of Candida, Arxula, Pichia, Scheffersomyces, Kluyveromyces, Saccharomyces, Yarrowia , or Schizosaccharomyces.

13. The genetically modified microorganism of claim 11 , wherein the fungus is Aspergillus parasiticus, Aspergillus nidulans , Thraustochytrium, Schizochytrium, Rhizopus arrhizus, Rhizopus oryzae , or Rhizopus nigricans.

14. The genetically modified microorganism of claim 11 , wherein the biosynthetic enzyme is a fatty acyl-CoA synthetase, fatty acyl activating enzyme, acyl-CoA oxidase, acyl-CoA thioesterase, hexanoyl-CoA synthetase, acetyl-CoA carboxylase, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase, beta-ketothiolase, thiolase, acyl-CoA synthase, cannabidiolic acid synthase, tetrahydrocannabidiolic acid, olivetolic acid synthase, or polyketide synthase.

15. The genetically modified microorganism of claim 11 , wherein the biosynthetic enzyme comprises a peroxisomal targeting sequence.

16. The genetically modified microorganism of claim 15 , wherein the peroxisomal targeting sequence has a consensus sequence of [S/A/H/C/E/P/Q/V]-[K/R/H/Q]-[L/F] as set forth in SEQ ID NO: 7, or GRRAKL as set forth in SEQ ID NO: 6.

17. The genetically modified microorganism of claim 11 , wherein the microorganism is capable of producing in the peroxisome a fatty acyl-CoA.

18. The genetically modified microorganism of claim 17 , wherein the fatty acyl-CoA is acetyl-CoA, malonyl-CoA, or hexanoyl-CoA.

19. The genetically modified microorganism of claim 11 , wherein the enzyme is removed of its endogenous amino-terminal localization sequence and/or carboxyl-terminal localization sequence.

Assignments (2)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jan 24, 2024
From: LAPLAZA, JOSE M.; HUTAGALUNG, ALEXANDER
To: LEVADURA BIOTECHNOLOGY, INC.
Reel/Frame 066234/0118 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jan 24, 2024
From: LEVADURA BIOTECHNOLOGY, INC.
To: PYRONE SYSTEMS, INC.
Reel/Frame 066234/0153 →
Continuity (6)
Continuation 17449847 · Oct 4, 2021
Continuation 16783122 · Feb 5, 2020
Continuation PCTUS2019051357 · Sep 16, 2019
Provisional Application 62731978 · Sep 17, 2018
Provisional Application 62731980 · Sep 17, 2018
Related Publication 20240384314A1 · Nov 21, 2024
References Cited (145)
US 4683195A · Mullis · 1987 [cited by applicant]
US 4683202A · Mullis · 1987 [cited by applicant]
US 4965188A · Mullis · 1990 [cited by applicant]
US 5232841A · Hashimoto · 1993 [cited by applicant]
US 5268273A · Buckholz · 1993 [cited by applicant]
US 5389529A · Panayotatos · 1995 [cited by applicant]
US 5470719A · Meng · 1995 [cited by applicant]
US 5648247A · Picataggio · 1997 [cited by applicant]
US 5656493A · Mullis · 1997 [cited by applicant]
US 5712114A · Mankovich · 1998 [cited by applicant]
US 5766891A · Shuman · 1998 [cited by applicant]
US 5846818A · Robinson · 1998 [cited by applicant]
US 5888732A · Hartley · 1999 [cited by applicant]
US 5932474A · Tsien · 1999 [cited by applicant]
US 6008378A · Tsien · 1999 [cited by applicant]
US 6054271A · Tsien · 2000 [cited by applicant]
US 6143557A · Hartley · 2000 [cited by applicant]
US 6171861B1 · Hartley · 2001 [cited by applicant]
US 6270969B1 · Hartley · 2001 [cited by applicant]
US 6277608B1 · Hartley · 2001 [cited by applicant]
US 6288302B1 · Yu · 2001 [cited by applicant]
US 6451569B1 · Tsien · 2002 [cited by applicant]
US 6518488B1 · Agarwal · 2003 [cited by applicant]
US 6720140B1 · Hartley · 2004 [cited by applicant]
US 7851199B2 · Bailey et al. · 2010 [cited by applicant]
US 8884100B2 · Page et al. · 2014 [cited by applicant]
US 9546362B2 · Page et al. · 2017 [cited by applicant]
US 9611460B2 · Page et al. · 2017 [cited by applicant]
US 9765308B2 · Page et al. · 2017 [cited by applicant]
US 9822384B2 · Poulos et al. · 2017 [cited by applicant]
US 10059971B2 · Page et al. · 2018 [cited by applicant]
US 10287557B2 · Geysens et al. · 2019 [cited by applicant]
US 11136605B2 · Hutagalung · 2021 [cited by examiner]
US 11884948B2 · Hutagalung · 2024 [cited by examiner]
US 20020007051A1 · Cheo · 2002 [cited by applicant]
US 20030083373A1 · Tsien · 2003 [cited by applicant]
US 20050032176A1 · Khosla · 2005 [cited by applicant]
US 20050112590A1 · Boom · 2005 [cited by applicant]
US 20050287592A1 · Kless · 2005 [cited by applicant]
US 20060057689A1 · Otto et al. · 2006 [cited by applicant]
US 20080026421A1 · Sagt et al. · 2008 [cited by applicant]
US 20120077252A1 · Picataggio · 2012 [cited by applicant]
US 20120122180A1 · Austin · 2012 [cited by applicant]
US 20140004598A1 · Picataggio et al. · 2014 [cited by applicant]
US 20140228586A1 · Beardslee et al. · 2014 [cited by applicant]
US 20160010126A1 · Poulos et al. · 2016 [cited by applicant]
US 20160298151A1 · Butt et al. · 2016 [cited by applicant]
US 20170211049A1 · Page et al. · 2017 [cited by applicant]
US 20170233779A1 · Page et al. · 2017 [cited by applicant]
US 20180030486A1 · Beardslee et al. · 2018 [cited by applicant]
US 20180073043A1 · Poulos et al. · 2018 [cited by applicant]
US 20180155748A1 · Butt et al. · 2018 [cited by applicant]
US 20180334692A1 · Barr et al. · 2018 [cited by applicant]
US 20190078098A1 · Alper · 2019 [cited by applicant]
US 20190169661A1 · Page · 2019 [cited by applicant]
JP 2000078979 · 2000 [cited by applicant]
JP 2001029082 · 2001 [cited by applicant]
WO WO1996019497A1 · 1996 [cited by applicant]
WO WO1998056943A1 · 1998 [cited by applicant]
WO WO1999021013A1 · 1999 [cited by applicant]
WO WO2017139496A1 · 2017 [cited by applicant]
WO WO2017160801A1 · 2017 [cited by applicant]
WO WO2018148848A1 · 2018 [cited by applicant]
WO WO2018148849A1 · 2018 [cited by applicant]
WO WO2018200888A1 · 2018 [cited by applicant]
WO WO2018219995A1 · 2018 [cited by applicant]
WO WO2019071000A1 · 2019 [cited by applicant]
Accession Q33DR0. Dec. 6, 2005 (Year: 2005). [cited by applicant]
Agarwal et al. 2001 “Gene isolation and characterization of two acyl CoA oxidases from soybean with broad substrate specificities and enhanced expression in the growing seedling axis.” Plant Mol Biol. Nov. 2001;47(4):51… [cited by applicant]
Aizpurua-Olaizola et al. “Identification and quantification of cannabinoids in [cited by applicant]
Akbergenov et al., ARC-1, a sequence element complementary to an internal 18S rRNA segment, enhances translation efficiency in plants when present in the leader or intercistronic region of mRNAs Nucleic Acids Research 3… [cited by applicant]
Alani et al., “A method for gene disruption that allows repeated use of URA3 selection in the construction of multiply disrupted yeast strains”, Genetics 116(4):541-545 Aug. 1987. [cited by applicant]
Alconado and Juarez 2006. “Acyl-CoA oxidase activity from Beauveria bassiana, an entomopathgenic fungus”. J Basic Microbiol. 2006;46(6):435-43. [cited by applicant]
Arie et al., “Phylogenetic identification of n-alkane assimilating Candida yeasts based on nucleotide divergence in the 5 end of LSU rDNA gene” J. Gen. Appl. Microbiol., 46, 257-262 (2000). [cited by applicant]
Austin, M. B. and J. P. Noel., “The chalcone synthase superfamily of type III polyketide synthases”, Natural Product Reports, 2002.20(1): p. 79-110. [cited by applicant]
Backer et al. “Innovative development and validation of an HPLC/DAD method for the qualitative and quantitative determination of major cannabinoids in cannabis plant material.” J Chromatogr B Analyt Technol Biomed Life … [cited by applicant]
Bakke et al. “N-ethylmaleimide-resistant acyl-coenzyme A oxidase from Arthrobacter ureafaciens NBRC 12140: molecular cloning, gene expression and characterization of the recombinant enzyme.” Biochim Biophys Acta. Jan. 2… [cited by applicant]
Barth and Gaillardin. “Physiology and genetics of the dimorphic fungus Yarrowia lipolytica.” FEMS Microbiol Rev. Apr. 1997;19(4):219-37. [cited by applicant]
Beggah et al. “Intra- and intermolecular events direct the propeptide-mediated maturation of the Candida albicans secreted aspartic proteinase Sap1p.” Microbiology. Nov. 2000;146 ( Pt 11):2765-73. [cited by applicant]
Brocard and Hartig. “Peroxisome targeting signal 1: is it really a simple tripeptide?” Biochim Biophys Acta. Dec. 2006;1763(12):1565-73. [cited by applicant]
Brown et al. Aspergillus has distinct fatty acid synthases for primary and secondary metabolism.: Proc Natl Acad Sci U S A. Dec. 10, 1996;93(25):14873-7. [cited by applicant]
Capone et al., “Amber, ochre and opal suppressor tRNA genes derived from a human serine tRNA gene”, EMBO J. 4:213, 1985. [cited by applicant]
Carvalho et al. “Designing microorganisms for heterologous biosynthesis of cannabinoids.” FEMS Yeast Res. Jun. 1, 2017;17(4). [cited by applicant]
Chica et al. Curr Opin Biotechnol. Aug. 2005; 16(4):378-84. (Year: 2005). [cited by applicant]
Current Protocols in Molecular Biology, John Wiley & Sons, N.Y., 6.3.1-6.3.6 (1989). [cited by applicant]
Deshpande, Mukund V., Appl. Biochem. Biotechnol., 36:227 (1992). [cited by applicant]
Eggertsson, et al., “Transfer ribonucleic acid-mediated suppression of termination codons in [cited by applicant]
Engleerg-Kukla, et al. (1996) in [cited by applicant]
Gagne et al. “Identification of olivetolic acid cyclase from Cannabis sativa reveals a unique catalytic route to plant polyketides.” Proc Natl Acad Sci U S A. Jul. 31, 2012;109(31):12811-6. [cited by applicant]
Gajewski et al. “Engineering fungal de novo fatty acid synthesis for short chain fatty acid production.” Nat Commun. Mar. 10, 2017;8:14650. [cited by applicant]
Gallie et al., “The 5′-leader sequence of tobacco mosaic virus RNA enhances the expression of foreign gene transcripts in vitro and in vivo”, Nucleic Acids Research 15: 3257-3273 (1987). [cited by applicant]
Gallie, The 5′-leader of tobacco mosaic virus promotes translation through enhanced recruitment of elF4F Nucleic Acids Research 30: 3401-3411 (2002). [cited by applicant]
Gao et al. “Iterative integration of multiple-copy pathway genes in Yarrowia lipolytica for heterologous β-carotene production”. Metab Eng. May 2017;41:192-201. [cited by applicant]
Ghaedi et al. Journal of Sciences, Islamic Republic of Iran (2009), 20(3), 205-211. Abstract. (Year: 2009). [cited by applicant]
Gietz and Woods “Transformation of Yeast by Lithium Acetate/Single-Stranded Carrier DNA/Polyethylene Glycol Method”. Methods Enzymol. 2002;350:87-96. [cited by applicant]
Hiltunen et al. (JBC, vol. 267, No. 10, Apr. 5, 1992, pp. 6646-6653). [cited by applicant]
Hong et al. “Engineering Yarrowia lipolytica to express secretory invertase with strong FBA1IN promoter”. Yeast. Feb. 2012;29(2):59-72. [cited by applicant]
Hooks et al. “Long-chain acyl-CoA oxidases of [cited by applicant]
Hooks et al., Biochem J., 320:607-614 (1996). [cited by applicant]
Hunkova and Fenci. “Toxic effects of fatty acids on yeast cells: dependence of inhibitory effects on fatty acid concentration.” Biotechnol Bioeng. Nov. 1977;19(11):1623-41. [cited by applicant]
Kistler and Broz “Cellular compartmentalization of secondary metabolism” Front. Microbiology Feb. 2015. [cited by applicant]
Kizer et al. Appl Environ Microbial. May 2008;74(10):3229-41. (Year: 2008). [cited by applicant]
Klionsky et al. “Intracellular sorting and processing of a yeast vacuolar hydrolase: proteinase A propeptide contains vacuolar targeting information.” Mol Cell Biol. May 1988;8(5):2105-16. [cited by applicant]
Krink-Koutsoubelis et al.“Engineered Production of Short-Chain Acyl-Coenzyme A Esters in [cited by applicant]
Lametschwandtner et al. “The difference in recognition of terminal tripeptides as peroxisomal targeting signal 1 between yeast and human is due to different affinities of their receptor Pex5p to the cognate signal and t… [cited by applicant]
Landy, Curr. Opin. Biotech. 3:699-707 (1993). [cited by applicant]
Ledesma-Amaro and Nicaud. “Yarrowia lipolytica as a biotechnological chassis to produce usual and unusual fatty acids.” Prog Lipid Res. Jan. 2016;61:40-50. [cited by applicant]
Liang et al. “Structure, mechanism and function of prenyltransferase.” Eur J Biochem. Jul. 2002;269(14):3339-54. [cited by applicant]
Lim et al., “Exploiting the Biosynthetic Potential of Type III Polyketide Synthases”, Molecules, 2016.21(6): p. 806. [cited by applicant]
Lui et al. “Membrane stress caused by octanoic acid in [cited by applicant]
Luo et al.2019 “Complete biosynthesis of cannabinoids and their unnatural analogues in yeast.” Nature. Mar. 2019;567(7746):123-126. [cited by applicant]
Luo et al.2002 “The acyl-CoA oxidases from the yeast Yarrowia lipolytica: characterization of Aox2p.” Arch Biochem Biophys. Nov 1;407(1):32-8. [cited by applicant]
Marks M D, et al. (2009) Identification of candidate genes affecting Delta9-tetrahydrocannabinol biosynthesis in Cannabis sativa. J Exp Bot. 60, 3715-3726. [cited by applicant]
Meyers & Miller, Cabios 4: 11-17 (1988). [cited by applicant]
Mignone et al., “Untranslated regions of mRNAs”, Genome Biology 3(3): reviews 0004.1-0001.10 (2002). [cited by applicant]
Mignone et al., “UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs”, Nucleic Acids Research 33: D141-D146 (2005). [cited by applicant]
Morimoto et al. (1998) Purification and characterization of cannabichromenic acid synthase from Cannabis sativa. Phytochemistry. 49: 1525-1529. [cited by applicant]
Needleman & Wunsch, J. Mol. Biol. 48: 444-453 (1970). [cited by applicant]
Nelson Biochemistry Jun. 1996. 25; 35(25):8429-38. [cited by applicant]
Page and Nagel, “Biosynthesis of terpenophenolics in hop and cannabis”, In J T Romeo, ed, Integrative Plant Biochemistry, vol. 40. Elsevier, Oxford, pp. 179-210, 2006. [cited by applicant]
Pamplaniyi “Identification, isolation, and functional characterization of prenyltransferases in cannabis sativa ”Dissertation Dortmund 2016. [cited by applicant]
Papanikolaou S., and Aggelis G., Bioresour. Technol. 82(1):43-9 (2002). [cited by applicant]
Paulous et al., “Comparison of the capacity of different viral internal ribosome entry segments to direct translation initiation in poly(A)-dependent reticulocyte lysates”, Nucleic Acids Research 31: 722-733 (2003). [cited by applicant]
Prather et al. Curr Opin Biotechnol. Oct. 2008; 19(5):468-7 4. (Year: 2008). [cited by applicant]
Reiser et al 2009 “AoxA is a major peroxisomal long chain fattyacyl-CoA oxidase required for beta-oxidation in A. nidulans”. Curr Genet. Apr. 2010;56(2):139-50. [cited by applicant]
Sauer, B., Curr. Opin. Biotech. 5:521-527 (1994). [cited by applicant]
Sekiguchi and Shuman, Nucl. Acids Res. 22:5360-5365, 1994. [cited by applicant]
Setoyama et. al 1995 “Functional expression of two forms of rat acyl-CoA oxidase and their substrate specificities” Dec. 14;217(2):482-7. [cited by applicant]
Shimiu et al. Type III Polyketide Synthases: Functional Classification and Phylogenomics. Chembiochem. Jan. 3, 2017;18(1):50-65. [cited by applicant]
Shuman, “Site-specific Interaction of Vaccinia Virus Topoisomerase I with Duplex DNA”, J. Biol. Chem. 266:11372-11379, 1991. [cited by applicant]
Singh et al. Curr Protein Pept Sci. 2017, 18, 1-11 (Year: 2017). [cited by applicant]
Sirikantaramas S. et al. (2005) Tetrahydrocannabinolic acid synthase, the enzyme controlling marijuana psychoactivity, is secreted into the storage cavity of the glandular trichomes. Plant Cell Physiol. 46: 1578-1582. [cited by applicant]
Stout et al. “The hexanoyl-CoA precursor for cannabinoid biosynthesis is formed by an acyl-activating enzyme in Cannabis sativa trichomes.” Plant J. Aug. 2012;71(3):353-65. [cited by applicant]
Tan et al. “Synthetic Pathway for the Production of Olivetolic Acid in [cited by applicant]
Taura et al. “Characterization of olivetol synthase, a polyketide synthase putatively involved in cannabinoid biosynthetic pathway.” FEBS Lett. Jun. 18, 2009;583(12):2061-6. [cited by applicant]
Taura F. et al. (1996) Purification and characterization of cannabidiolic-acid synthase from [cited by applicant]
Taura F. et al. (2007) Cannabidiolic-acid synthase, the chemotype-determining enzyme in the fiber-type Cannabis sativa. FEBS Lett. 581: 2929-2934. [cited by applicant]
Taura F. et al.(1995) First direct evidence for the mechanism of 1-tetrahydrocannabinolic acid biosynthesis. J Am Chem Soc. 117: 9766-9767. [cited by applicant]
Tjalsma et al., “Signal Peptide-Dependent Protein Transport in Bacillus subtilis: a Genome-Based Survey of the Secretome”, Microbiol. Molec. Biol. Rev. 64: 515-547 (2000). [cited by applicant]
Vincent et al., “Helicase-dependent isothermal DNA amplification”. EMBO reports 5 (8): 795-800 (2004). [cited by applicant]
Yang et al “Structural basis for olivetolic acid formation by a polyketide cyclase from Cannabis sativa.” FEBS J. Mar. 2016;283(6):1088-106. [cited by applicant]
Yu et al. “Type III Polyketide Synthases in Natural Product Biosynthesis”, IUBMB Life, 2012. 64(4): p. 285-295. [cited by applicant]
Zirpel “Recombinant Expression and Functional Characterization of Cannabinoid Producing Enzymes in Komagataella phaffii” Dissertation Dortmund 2018. [cited by applicant]
Zirpel et al. “Optimization of Δ9-tetrahydrocannabinolic acid synthase production in Komagataella phaffii via post-translational bottleneck identification.” J Biotechnol. Apr. 20, 2018;272-273:40-47. [cited by applicant]
Zirpel et al. “Production of Δ9-tetrahydrocannabinolic acid from cannabigerolic acid by whole cells of Pichia (Komagataella) pastoris expressing Δ9-tetrahydrocannabinolic acid synthase from [cited by applicant]