WO2024040211A2 - Bioproduction de flavonoïdes à l'aide d'hôtes de micro-organismes - Google Patents

Bioproduction de flavonoïdes à l'aide d'hôtes de micro-organismes Download PDF

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WO2024040211A2
WO2024040211A2 PCT/US2023/072449 US2023072449W WO2024040211A2 WO 2024040211 A2 WO2024040211 A2 WO 2024040211A2 US 2023072449 W US2023072449 W US 2023072449W WO 2024040211 A2 WO2024040211 A2 WO 2024040211A2
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seq
hydroxylase
engineered host
host cell
flavonol
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WO2024040211A3 (fr
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Nicholas BRIDEAU
Jingyi Li
Joshua BRITTON
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Debut Biotechnology, Inc.
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/70—Vectors or expression systems specially adapted for E. coli
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/52—Genes encoding for enzymes or proenzymes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0071—Oxidoreductases (1.) acting on paired donors with incorporation of molecular oxygen (1.14)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P17/00—Preparation of heterocyclic carbon compounds with only O, N, S, Se or Te as ring hetero atoms
    • C12P17/02—Oxygen as only ring hetero atoms
    • C12P17/06—Oxygen as only ring hetero atoms containing a six-membered hetero ring, e.g. fluorescein
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y114/00—Oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (1.14)
    • C12Y114/11—Oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (1.14) with 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (1.14.11)
    • C12Y114/11009—Flavanone 3-dioxygenase (1.14.11.9), i.e. naringenin-3-dioxygenase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y114/00—Oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (1.14)
    • C12Y114/11—Oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (1.14) with 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (1.14.11)
    • C12Y114/11023—Flavonol synthase (1.14.11.23)

Definitions

  • the invention related to materials (including engineered cells and cell lines) and methods involved in the production of flavonoids, anthocyanins and other organic compounds.
  • Flavonoids and anthocyanins are natural products produced in plants that find a variety of roles such as antioxidants, ultraviolet (UV) defense mechanisms, and colors. Over the past several years, the health benefits of flavonoids and anthocyanins have been widely demonstrated. These compounds are capable of scavenging radicals and can act as enzyme inhibitors and antiinflammatory agents. With these recognized health and color benefits, much research has gone into understanding how these compounds are made in nature.
  • Myricetin is a common plant-derived flavonoid and is well recognized for its nutraceuticals value. It is one of the key ingredients of various foods and beverages. The compound exhibits a wide range of activities that include strong antioxidant, anticancer, antidiabetic and antiinflammatory activities.
  • Kaempferol is a polyphenol antioxidant found in fruits and vegetables. Many studies have described the beneficial effects of dietary kaempferol in reducing the risk of chronic diseases, especially cancer.
  • Quercetin a plant pigment is a potent antioxidant flavonoid, found mostly in onions, grapes, berries, cherries, broccoli, and citrus fruits. It is a versatile antioxidant known to possess protective abilities against tissue injury induced by various drug toxicities.
  • Flavonoids and anthocyanins are synthesized from phenylpropanoid starter units and malonyl-Cofactor-A (malonyl-CoA) extender units that then undergo modifications to create many polyphenol compounds such as taxifolin, naringenin, and (+)-catechin. However, in most cases, these compounds are extracted or chemically manufactured.
  • malonyl-Cofactor-A malonyl-Cofactor-A
  • the engineered cells include one or more genetic modifications that increase(s) flavonoid and anthocyanin bioproduction by increasing metabolic flux to flavonoid precursors and/or reducing carbon losses resulting from the production of byproducts.
  • the invention provides engineered host cells, wherein the engineered host cells comprise one or more genetic modifications to increase the production of flavonols through transformation by one or more enzymes of a carbon source by the engineered host cell.
  • the flavonol is selected from a group consisting of kaempferol, myricetin, and quercetin.
  • the carbon source is selected from a group consisting of naringenin, dihydrokaempferol (DHK), dihydromyricetin (DHM), dihydroquercetin (DHQ), and eriodictyol (EDL).
  • one or more genetic modifications are at least one genetic modification selected from the group consisting of: (i) one or more modifications for overexpressing one or more endogenous genes in the engineered host cells; (ii) one or more modifications for under-expressing one or more endogenous genes in the engineered host cells; (iii) one or more genetic modification is expressing one or more non-native genes in the engineered host cells; and (iv) a combination thereof.
  • the engineered host cell comprises at least one or more nucleic acid sequences selected from the group consisting of: (i) nucleic acid sequences encoding native or modified flavanone-3 -hydroxylase (F3H) or a homolog thereof, (ii) nucleic acid sequences encoding native or modified flavanone-3 ’-hydroxylase (F3’H) or a homolog thereof, (iii) nucleic acid sequences encoding native or modified flavonoid 3’,5’- hydroxylase (F3’5’H) or a homolog thereof, (iv) nucleic acid sequences encoding native or modified flavonol synthase (FLS) or a homolog thereof, and (v) any combinations thereof.
  • the engineered host cell is E. coli.
  • the production of flavonols through enzymatic transformation of a carbon source includes one or more chemical intermediates.
  • the flavonol is myricetin
  • the carbon source is dihydromyricetin (DHM)
  • the one or more enzyme is flavonol synthase (FLS).
  • the flavonol is myricetin
  • the carbon source is dihydrokaempferol (DHK)
  • the one or more enzymes are selected from a group consisting of (i) flavonoid 3 ’,5 ’-hydroxylase (F3’5’H), (ii) flavonol synthase (FLS), and (iii) any combination thereof.
  • flavonoid 3 ’,5 ’-hydroxylase (F3’5’H) has an amino acid sequence at least 80% identical to the polypeptides selected from a group consisting of: (i) SEQ ID NO. 10, (ii) SEQ ID NO. 56, and (iii) SEQ ID NO. 57.
  • the flavonol is kaempferol
  • the carbon source is dihydrokaempferol (DHK)
  • the one or more enzyme is flavonol synthase (FLS).
  • flavonol synthase (FLS) has an amino acid sequence at least 80% identical to any one of the polypeptides listed in SEQ ID NOS. 99-122.
  • the flavonol is quercetin
  • the carbon source is eriodictoyl (EDL)
  • the one or more enzyme is selected from a group consisting of (i) flavanone-3-hydroxylase (F3H), (ii) flavonol synthase (FLS), and (iii) any combination thereof.
  • the flavanone-3 -hydroxylase (F3H) has an amino acid sequence at least 80% identical to the polypeptides selected from a group consisting of: (i) SEQ ID NO. 7, (ii) SEQ ID NO. 45, (iii) SEQ ID NO. 46, (iv) SEQ ID NO. 47, and (v) SEQ ID NO. 48.
  • production of quercetin leads to formation of dihydroquercetin (DHQ) as an intermediate.
  • the flavonol is quercetin
  • the carbon source is dihydroquercetin (DHQ)
  • the one or more enzyme is flavonol synthase (FLS).
  • the flavonol is quercetin
  • the carbon source is kaempferol
  • the enzyme is flavanone-3 ’-hydroxylase (F3’H).
  • flavanone-3 ’ -hydroxylase (F3’H) has an amino acid sequence at least 80% identical to the polypeptide set forth in (i) SEQ ID NO: 8 (ii) SEQ ID NO. 49, (iii) SEQ ID NO. 50, (iv) SEQ ID NO. 51, and (v) SEQ ID NO. 52.
  • the flavonol is kaempferol
  • the carbon source is dihydrokaempferol (DHK), naringenin, or a combination thereof
  • the one or more enzyme is selected from a group consisting of (i) flavanone-3 -hydroxylase (F3H), (ii) flavonol synthase (FLS), or (iii) any combination thereof.
  • the flavonol is quercetin
  • the carbon source is dihydroquerctin (DHQ), dihydrokaempferol (DHK), eriodictyol (EDL), naringenin, kaempferol, or any combination thereof
  • the one or more enzyme is selected from a group consisting of: (i) flavonol synthase (FLS), (ii) flavanone-3 ’-hydroxylase (F3’H), (iii) flavanone-3-hydroxylase (F3H), or (iv) any combination thereof.
  • the flavonol is myricetin
  • the carbon source is dihydromyricetin (DHM), dihydroquerctin (DHQ), dihydrokaempferol (DHK), eriodictyol (EDL), naringenin, quercetin, kaempferol, or any combination thereof
  • the one or more enzyme is selected from a group consisting of: (i) flavonol synthase (FLS), (ii) flavanones’ -hydroxylase (F3’H), (iii) flavanone-3 -hydroxylase (F3H), (iv) flavonoid-3’ -5 ’-hydroxylase (F3’5’H), or (v) any combination thereof.
  • the invention provides a method of increasing the production of flavonols, comprising engineered host cells, wherein the engineered host cells comprise one or more genetic modifications to increase the production of flavonols through transformation by one or more enzymes of a carbon source by the engineered host cell.
  • the flavonol is selected from a group consisting of kaempferol, myricetin, and quercetin.
  • the carbon source is selected from a group consisting of naringenin, dihydrokaempferol (DHK), dihydromyricetin (DHM), dihydroquercetin (DHQ), and eriodictyol (EDL).
  • one or more genetic modifications are at least one genetic modification selected from the group consisting of: (i) one or more modifications for overexpressing one or more endogenous genes in the engineered host cells; (ii) one or more modifications for under-expressing one or more endogenous genes in the engineered host cells; (iii) one or more genetic modification is expressing one or more non-native genes in the engineered host cells; and (iv) a combination thereof.
  • the engineered host cell comprises at least one or more nucleic acid sequences selected from the group consisting of: (i) nucleic acid sequences encoding native or modified flavanone-3 -hydroxylase (F3H) or a homolog thereof, (ii) nucleic acid sequences encoding native or modified flavanone-3 ’-hydroxylase (F3’H) or a homolog thereof, (iii) nucleic acid sequences encoding native or modified flavonoid 3’,5’- hydroxylase (F3’5’H) or a homolog thereof, (iv) nucleic acid sequences encoding native or modified flavonol synthase (FLS) or a homolog thereof, and (v) any combinations thereof.
  • the engineered host cell is E. coli.
  • the production of flavonols through enzymatic transformation of a carbon source includes one or more chemical intermediates.
  • the flavonol is myricetin
  • the carbon source is dihydromyricetin (DHM)
  • the one or more enzyme is flavonol synthase (FLS).
  • the flavonol is myricetin
  • the carbon source is dihydrokaempferol (DHK)
  • the one or more enzymes are selected from a group consisting of (i) flavonoid 3 ’,5 ’-hydroxylase (F3’5’H), (ii) flavonol synthase (FLS), and (iii) any combination thereof.
  • flavonoid 3 ’,5 ’-hydroxylase (F3’5’H) has an amino acid sequence at least 80% identical to the polypeptides selected from a group consisting of: (i) SEQ ID NO. 10, (ii) SEQ ID NO. 56, and (iii) SEQ ID NO. 57.
  • the flavonol is kaempferol
  • the carbon source is dihydrokaempferol (DHK)
  • the one or more enzyme is flavonol synthase (FLS).
  • flavonol synthase (FLS) has an amino acid sequence at least 80% identical to any one of the polypeptides listed in SEQ ID NOS. 99-122.
  • the flavonol is quercetin
  • the carbon source is eriodictoyl (EDL)
  • the one or more enzyme is selected from a group consisting of (i) flavanone-3-hydroxylase (F3H), (ii) flavonol synthase (FLS), and (iii) any combination thereof.
  • the flavanone-3 -hydroxylase (F3H) has an amino acid sequence at least 80% identical to the polypeptides selected from a group consisting of: (i) SEQ ID NO. 7, (ii) SEQ ID NO. 45, (iii) SEQ ID NO. 46, (iv) SEQ ID NO. 47, and (v) SEQ ID NO. 48.
  • production of quercetin leads to formation of dihydroquercetin (DHQ) as an intermediate.
  • the flavonol is quercetin
  • the carbon source is dihydroquercetin (DHQ)
  • the one or more enzyme is flavonol synthase (FLS).
  • the flavonol is quercetin
  • the carbon source is kaempferol
  • the enzyme is flavanone-3 ’-hydroxylase (F3’H).
  • flavanone-3 ’-hydroxylase (F3’H) has an amino acid sequence at least 80% identical to the polypeptide set forth in (i) SEQ ID NO: 8 (ii) SEQ ID NO. 49, (iii) SEQ ID NO. 50, (iv) SEQ ID NO. 51, and (v) SEQ ID NO. 52.
  • the flavonol is kaempferol
  • the carbon source is dihydrokaempferol (DHK), naringenin, or a combination thereof
  • the one or more enzyme is selected from a group consisting of (i) flavanone-3 -hydroxylase (F3H), (ii) flavonol synthase (FLS), or (iii) any combination thereof.
  • the flavonol is quercetin
  • the carbon source is dihydroquerctin (DHQ), dihydrokaempferol (DHK), eriodictyol (EDL), naringenin, kaempferol, or any combination thereof
  • the one or more enzyme is selected from a group consisting of: (i) flavonol synthase (FLS), (ii) flavanone-3 ’-hydroxylase (F3’H), (iii) flavanone-3-hydroxylase (F3H), or (iv) any combination thereof.
  • the flavonol is myricetin
  • the carbon source is dihydromyricetin (DHM), dihydroquerctin (DHQ), dihydrokaempferol (DHK), eriodictyol (EDL), naringenin, quercetin, kaempferol, or any combination thereof
  • the one or more enzyme is selected from a group consisting of: (i) flavonol synthase (FLS), (ii) flavanone- 3 ’-hydroxylase (F3’H), (iii) flavanone-3 -hydroxylase (F3H), (iv) flavonoid-3’ -5 ’-hydroxylase (F3’5’H), or (v) any combination thereof.
  • FIG. 1 shows the metabolic pathway of flavonoid and anthocyanin bioproduction in engineered cells and methods of preparing anthocyanins described herein.
  • FTG. 2 shows structures of the flavonoid and anthocyanin molecules that may be produced using engineered cells and methods of preparing anthocyanins described herein.
  • FIG. 3 shows HPLC spectra showing peaks corresponding to the molecules prepared using engineered cells and methods of preparing anthocyanins described herein.
  • FIG. 4 shows the pathway of flavonoid and anthocyanin bioproduction in engineered cells and methods of preparing anthocyanins described herein.
  • FIG. 5 shows the pathway of production of flavonols, including myricetin, kaempferol, and quercetin.
  • FIG. 6 shows the specific carbon source, intermediate, and the enzyme combinations to generate flavonols, including kaempferol, quercetin, and myricetin.
  • FIG. 7 provides the data for bioproduction of quercetin using the methods of the invention.
  • the present application provides engineered cells for producing one or more flavonoids, cultures that include the engineered cells, and methods of producing one or more flavonoids, or at least one anthocyanin.
  • flavonoids flavonoids
  • flavonoids product or flavonoids compound
  • flavonoids compound a member of a diverse group of phytonutrients found in almost all fruits and vegetables.
  • flavonoid flavonoid product
  • flavonoid compound are used interchangeably to refer a molecule containing the general structure of a 15-carbon skeleton, which consists of two phenyl rings (A and B) and a heterocyclic ring.
  • Flavonoids may include, but are not limited to, isoflavone type (e.g., genistein), flavone type (e.g., apigenin), flavonol type (e.g., kaempferol), flavanone type (e.g., naringenin), chaicone type (e.g., phloretin), anthocyanidin type (e.g., cyanidin), catechins, flavanones, and flavanonols.
  • isoflavone type e.g., genistein
  • flavone type e.g., apigenin
  • flavonol type e.g., kaempferol
  • flavanone type e.g., naringenin
  • chaicone type e.g., phloretin
  • anthocyanidin type e.g., cyanidin
  • catechins flavanones,
  • Flavonoid compounds of interest include, without limitation, naringenin, naringenin chaicone, eriodictyol, taxifolin, dihydrokaempferol, dihydroquercetin, dihydromyricetin, leucocyanidin, leucopelargonidin, leucodelphindin, pentahydroxyflavone, cyanidin, catechin, delphinidin, pelargonidin, and kaempferol.
  • Anthocyanins are in the forms of anthocyanidin glycosides and acylated anthocyanins.
  • Anthocyanin compounds of interest include, without limitation, cyanidin glycoside, delphinidin glycoside, pelargonidin glycoside, peonidin glycoside, and petunidin glycoside.
  • precursors or ‘flavonoid precursor’ as used herein may refer to any intermediate present in the biosynthetic pathway that leads to the production of catechins or anthocyanins, flavonoid precursors may include, but are not limited to tyrosine, phenylalanine, coumaric acid, p- coumaroyl-CoA, malonyl-CoA, pyruvate, acetyl-CoA, and naringenin.
  • Cells engineered for the production of a flavonoid or an anthocyanin can have one or multiple modifications, including, without limitation, the downregulation, disruption, or deletion of endogenous genes, the upregulation of an endogenous gene, and the introduction of exogenous genes.
  • non-naturally occurring when used in reference to an enzyme is intended to mean that nucleic acids or polypeptides include at least one genetic alteration not normally found in a naturally occurring polypeptide or nucleic acid sequence.
  • Naturally occurring nucleic acids, and polypeptides can be referred to as “wild-type” or “original”.
  • a host cell, organism, or microorganism that includes at least one genetic modification generated by human intervention can also be referred to as “non-naturally occurring”, “engineered”, “genetically engineered,” or “recombinant”.
  • a host cell, organism, or microorganism engineered to express or overexpress a gene or nucleic acid sequence, or to overexpress an enzyme or polypeptide has been genetically engineered through recombinant DNA technology to include a gene or nucleic acid sequence that does not naturally encode the enzyme or polypeptide or to express an endogenous gene at a level that exceeds its level of expression in a non-altered cell.
  • a host cell, organism, or microorganism engineered to express or overexpress a gene or a nucleic acid sequence, or to overexpress an enzyme or polypeptide can have any modifications that affect a coding sequence of a gene, the position of a gene on a chromosome or regulatory elements associated with a gene.
  • Overexpression of a gene can also be by increasing the copy number of a gene in the cell or organism.
  • a host cell, organism, or microorganism engineered to under-express or to have reduced expression of a gene, nucleic acid sequence, or to under-express an enzyme or polypeptide can have any modifications that affect a coding sequence of a gene, the position of a gene on a chromosome or regulatory elements associated with a gene.
  • gene disruptions which include any insertions, deletions, or sequence mutations into or of the gene or a portion of the gene that affect its expression or the activity of the encoded polypeptide.
  • Gene disruptions include “knockout” mutations that eliminate expression of the gene.
  • Modifications to under-express a gene also include modifications to regulatory regions of the gene that can reduce its expression.
  • exogenous or “heterologous” is intended to mean that the referenced molecule or the referenced activity is introduced into the host microbial organism.
  • the molecule can be introduced, for example, by introduction of an encoding nucleic acid into the host genetic material such as by integration into a host chromosome or as non-chromosomal genetic material that may be introduced on a vehicle such as a plasmid. Therefore, the term “endogenous” refers to a referenced molecule or activity that is naturally present in the host.
  • Genes or nucleic acid sequences can be introduced stably or transiently into a host cell using techniques well known in the art including, but not limited to, conjugation, electroporation, chemical transformation, transduction, and transfection.
  • some nucleic acid sequences in the genes or cDNAs of eukaryotic nucleic acids can encode targeting signals such as an N-terminal mitochondrial or other targeting signal, which can be removed before transformation into prokaryotic host cells, if desired.
  • genes can be subjected to codon optimization with techniques well known in the art to achieve optimized expression of the proteins.
  • the percent identity (% identity) between two sequences is determined when sequences are aligned for maximum homology.
  • Algorithms well known to those skilled in the art, such as Align, BLAST, Clustal Omega, and others compare and determine a raw sequence similarity or identity, and also determine the presence or significance of gaps in the sequence which can be assigned a weight or score.
  • Such algorithms also are known in the art and are similarly applicable for determining nucleotide or amino acid sequence similarity or identity and can be useful in identifying orthologs of genes of interest.
  • Additional sequences added to a polypeptide sequence such as but not limited to immunodetection tags, purification tags, localization sequences (presence or absence), etc., do not affect the % identity.
  • a homolog is a gene or genes that have the same or identical functions in different organisms.
  • Genes that are orthologous can encode proteins with sequence similarity of about 45% to 100% amino acid sequence identity, and more preferably about 60% to 100% amino acid sequence identity.
  • Genes can also be considered orthologs if they share three-dimensional structure but not necessarily sequence similarity, of a sufficient amount to indicate that they have evolved from a common ancestor to the extent that the primary sequence similarity is not identifiable.
  • Paralogs are genes related by duplication within a genome, and can evolve new functions, even if these are related to the original one.
  • a genetic modification can be a modification for over-expressing or under-expressing one or more endogenous genes in the engineered host cell or can be a modification for expressing one or more non-native genes in the engineered host cell.
  • Engineered cells as provided herein can include multiple genetic modifications.
  • the cell cultures include engineered cells as disclosed herein in a culture medium that includes a carbon source that can also be an energy source, such as glycerol, sugar, or an organic acid.
  • the culture medium can include at least one feed molecule such as but not limited to one or more organic acids or amino acids that can be converted into a flavonoid precursor (such as tyrosine, p-coumaroyl-CoA or malonyl-CoA).
  • feed molecules include, but are not limited to, acetate, malonate, tyrosine, phenylalanine, pantothenate, coumarate, etc.
  • the feed molecules may be of reduced or low purity.
  • glycerol as a feed molecule may be crude glycerol, including a biomass comprising glycerol, for example, glycerol obtained as a byproduct of biodiesel processing.
  • the culture medium can include a supplemental compound that can be a cofactor or a precursor of a cofactor used by an enzyme that functions in a flavonoid pathway, such as, for examples, bicarbonate, biotin, thiamine, pantothenate, alpha-ketoglutarate, ascorbate, or 5-aminolevulinic acid.
  • the methods include culturing the engineered cells in a culture medium that includes at least one feed molecule or supplement such as but not limited to: tyrosine, phenylalanine, malonate, p-coumarate, bicarbonate, acetate, pantothenate, biotin, thiamine, alpha-ketoglutarate, ascorbate, and 5- aminolevulinic acid.
  • the methods can further include recovering at least one of the flavonoids from culture medium, whole culture, or the cells.
  • cells engineered to produce one or more flavonoids or anthocyanins wherein the cells include, in addition to nucleic acid sequences encoding either tyrosine ammonia lyase activity and/or phenylalanine ammonia lyase activity and cinnamate-4- hydroxylase activity, 4-coumarate-CoA ligase activity, chaicone synthase activity, chaicone isomerase activity, flavanone-3-hydroxylase activity, flavonoid 3 ’-hydroxylase activity or flavonoid 3’5’-hydroxylase activity, cytochrome P450 reductase activity, leucoanthocyanidin reductase activity, and dihydroflavonol-4- reductase activity, one or more genetic modifications for improving production of the flavonoids or anthocyanins.
  • a cell that is engineered to produce one or more of the flavonoids is engineered to include an exogenous nucleic acid sequence encoding tyrosine ammonia lyase activity that can form 4-coumaric acid using tyrosine as substrate (e.g., tyrosine ammonia lyase TAL, EC: 4.3.1.25) or, alternatively or in addition, an exogenous nucleic acid sequence encoding phenylalanine ammonia lyase activity that can convert phenylalanine to trans-cinnamic acid and an exogenous nucleic acid sequence encoding cinnamate-4-hydroxylase activity that forms 4-coumaric acid from trans-cinnamic acid, an exogenous nucleic acid sequence encoding CoA ligase activity that forms p-coumaroyl-CoA from coumaric acid (e.g., 4-coumarate— CoA ligase, 4CL, EC:
  • a cell that is engineered to produce anthocyanins is further engineered to include an exogenous nucleic acid sequence encoding anthocyanin synthase activity that forms cyanidin from catechin or leucocyanidin, forms delphinidin from leucodelphinidin, or forms pelargonidin from leucopelargonidin (e.g., anthocyanin synthase, ANS, EC: 1.14.20.4) and to include an exogenous nucleic acid sequence encoding glucosyltransferase activity that forms cyani din-3 -O-beta-D-glucoside from cyanidin, delphinidin-3 -O-beta-D-glucoside from delphinidin, or pelagonidin-3-O-beta-D-glucoside from pelagonidin (e.g., anthocyanidin 3-0- glucosyltransferase, 3GT, EC:
  • the cells provided herein that are engineered to produce flavonoids or anthocyanins are further engineered to increase the production of flavonoids or anthocyanins product, for example by increasing metabolic flux to a flavonoid or anthocyanin pathway, or by decreasing byproduct formation.
  • a cell engineered to produce a flavonoid is further engineered to increase the supply of precursor malonyl-CoA.
  • One strategy for increasing malonyl-CoA includes increasing acetyl-CoA carboxylase (ACC) activity.
  • the ACC enzyme which in most eukaryotes, including fungi, is a large single chain polypeptide, and in plant and bacteria such as E. coli is a multi-subunit enzyme, is overexpressed in the host strain.
  • Examples of acetyl-CoA carboxylase that can be expressed in a host cell engineered to produce a flavonoid or anthocyanin include, without limitation, the ACC genes of Mucor circinelloides. Rhodotorula toruloides, Lipomyces starkeyi, Ustilago maydis, and orthologs of these ACCs in other species having at least 50% amino acid identity to these ACCs.
  • Additional strategies for increasing malonyl-CoA include increasing acetyl-CoA, which is converted to malonyl-CoA by acetyl-CoA carboxylase (ACC).
  • acetyl-CoA synthase ACS
  • Cultures of engineered host cells that include overexpressed nucleic acid sequence encoding ACS can optionally include acetate in the culture medium.
  • Examples of acetyl-CoA synthase that can be expressed in a host cell engineered to produce a flavonoid or anthocyanin include, without limitation, the ACS gene of E. coli, the ACS o Salmonella typhimurium, orthologs of these ACSs in other species having at least 50% amino acid identity to these ACSs.
  • an engineered host cell that overexpresses a gene encoding pyruvate dehydrogenase (PDH), which converts pyruvate to acetyl-CoA.
  • PDH pyruvate dehydrogenase
  • a variant of the Lpd subunit of PDH can be expressed that includes a mutation (E354K) that reduces inhibition of PDH by NADH.
  • a cell engineered to produce a flavonoid, or an anthocyanin is further engineered to increase the cell’s supply of malonyl-CoA includes an exogenous nucleic acid sequence encoding a malonyl-CoA synthetase that generates malonyl-CoA from malonate.
  • malonyl-CoA synthetases examples include the malonyl-CoA synthetases of Streptomyces coelicolor, Rhodopseudomonas palustris, or a malonyl-CoA synthetase having at least 50% identity to any of these or other naturally occurring malonyl-CoA synthetases.
  • Malonate can optionally be added to the culture medium of a culture that includes a cell engineered to express a malonyl-CoA synthetase.
  • An engineered cell that includes an exogenous gene encoding a malonyl-CoA synthetase can also include an exogenous nucleic acid sequence encoding a malonate transporter, such as a malonate transporter encoded by a matC gene, for example, of Streptomyces coelicolor, or a malonate transporter encoded by DctPQM of Sinorhizobium medicae.
  • a cell engineered to produce a flavonoid or an anthocyanin is further engineered to include an exogenous nucleic acid sequence encoding malonate CoA- transferase that makes malonyl-CoA by direct transfer of the CoA from acetyl-CoA.
  • malonate CoA-transferase that can be expressed in an engineered cell as provided herein include, without limitation, the alpha subunit (mdcA) of malonate decarboxylase from Acinelobacter calcoaceticus, Geobacillus sp, or a transferase having at least 50% identity to any of these or other naturally occurring malonate CoA-transferases.
  • a cell engineered to produce flavonoids or anthocyanins is further engineered to increase the supply of coenzyme A (CoA) to increase its availability for producing acetyl-CoA, malonyl-CoA, and/or p-coumaroyl-CoA.
  • CoA coenzyme A
  • Strategies for increasing CoA supply include upregulating endogenous pantothenate kinase (PanK) (EC:2.7.1.33) that produces CoA from pantothenate.
  • a host cell can be engineered to include a nucleic acid sequence encoding type III pantothenate kinase that is not feedback inhibited by coenzyme A, such as CoaX gene of pseudomonas aeruginosa (EC:2.7.1.33).
  • Cultures of cells engineered for the production of flavonoids or anthocyanins can in some embodiments include a medium that includes pantothenate, a precursor of CoA biosynthesis, and can optionally also include cysteine, used in the CoA biosynthesis.
  • Additional strategies to increase malonyl-CoA flux to the flavonoid pathway include mutation or downregulation of one or more genes that function in fatty acid biosynthesis. Without limiting the embodiments to any particular mechanism, limiting fatty acid biosynthesis can increase the malonyl-CoA supply available for flavonoid biosynthesis.
  • the gene beta-ketoacyl-ACP synthase II (E. coli fabF) can be disrupted to reduce fatty acid biosynthesis.
  • Another example of a fatty acid biosynthesis gene of a host cell that may be mutated or downregulated is a gene encoding malonyl-CoA-ACP transacylase (E. coli fabD).
  • Other fatty acid biosynthesis genes of the engineered host cell that can be downregulated include a beta- ketoacyl-ACP synthase I enzyme (E. coli fabB) and acyl carrier protein (E. coli acpP).
  • Additional genetic modifications that may be present in a host cell engineered to produce flavonoids or anthocyanins include downregulation, disruption, or deletion of genes encoding alcohol dehydrogenase, lactate dehydrogenase, pyruvate oxidase, acetyl phosphate transferase and acetate kinase.
  • lactate dehydrogenase lactate dehydrogenase
  • pyruvate oxidase acetyl phosphate transferase and acetate kinase.
  • genes that are downregulated, disrupted, or deleted can include aldehyde-alcohol dehydrogenase (adhE), lactate dehydrogenase (IdhA), pyruvate oxidase (poxB), and enzyme acetate kinase phosphate acetyltransferase (ackA-pta).
  • adhE aldehyde-alcohol dehydrogenase
  • IdhA lactate dehydrogenase
  • poxB pyruvate oxidase
  • ackA-pta enzyme acetate kinase phosphate acetyltransferase
  • a cell engineered for the production of flavonoids or anthocyanins can have one or more genes encoding thioesterases downregulated, disrupted, or deleted to prevent hydrolysis of precursors malonyl-CoA, actetyl-CoA, and/or p-coumaryol-CoA.
  • thioesterase genes tesA, tesB, yciA, and ybgC can be downregulated, disrupted, or deleted.
  • genes encoding enzymes of the tricarboxylic acid cycle can be disrupted or downregulated to increase alphaketoglutarate supply which serves as a cofactor for one or more of the flavonoid and anthocyanin pathway enzymes.
  • TCA enzymes that can be downregulated include citrate synthase that converts acetyl-CoA to citrate.
  • an engineered host cell for the production of flavonoids or anthocyanins to upregulate the endogenous biosynthesis of amino acid tyrosine.
  • Tyrosine is one of the precursors for the flavonoid biosynthesis and its conversion to coumaric acid is the first committed step of the pathway.
  • L-tyrosine is one of the three aromatic amino acids derived from the shikimate pathway. The initial step of the shikimate pathway is catalyzed by DAHP synthase isozymes and regulated through feedback-inhibition.
  • Strategies to increase tyrosine production can include, without limitation, transcriptional deregulation, removing feedback inhibition, overexpression of rate-limiting enzymes, and/or deletion of the L- phenylalanine branch of the aromatic acid biosynthetic pathway.
  • the tyrR gene can be disrupted, feedback-inhibition-resistant versions of the DAHP synthase (aroG) and chorismate mutase (tyrA) can be introduced, and/or rate-limiting enzymes, shikimate kinase (aroK or aroL) and quinate (QUIN)/shikimate dehydrogenase (ydiB) can be overexpressed.
  • the Phosphoenolpyruvate synthase (ppsA) and transketolase (tktA) can be exogenously introduced to enhance tyrosine production.
  • an engineered host cell for the production of flavonoids or anthocyanins further engineered to upregulate the endogenous biosynthesis of cofactor heme.
  • Cytochrome P450 CYPs
  • CYPs Cytochrome P450
  • CYPs one of the exogenous genes in the engineered cells provided herein, contain heme as a cofactor. Improving heme supply can be an effective strategy to increase flavonoid biosynthesis.
  • 5-aminolevulinic acid (ALA) is the first committed precursor to the heme pathway. Strategies to increase heme supply include overexpression of the genes that synthesize the precursor ALA.
  • ALA is formed from the 5-carbon skeleton of glutamate (the C5 pathway).
  • the three enzymes involved in ALA biosynthesis are glutamyl-tRNA synthetase (gltX), glutamyl-tRNA reductase (hemA), and glutamate- 1 -semialdehyde aminotransferase (hemL).
  • the engineered cells provided herein can be further engineered to express or overexpress hemA or its variants, and/or hemL to increase the heme precursor ALA production.
  • the nonlimiting examples of hemA gene that can be overexpressed include a mutated hemA (inserting two lysine residuals between Thr-2 and Leu-3 at N terminus of hemA gene from Salmonella typhimurium (EC: 1.1.1.70).
  • heterologous ALAS gene can be introduced to produce ALA via the C4 pathway (ALS is synthesized by the condensation of glycine and succinyl-CoA).
  • ALS is synthesized by the condensation of glycine and succinyl-CoA.
  • heterologous ALAS that can be expressed in E. colt include ALAS of Bradyrhizobium Japonicum (EC: 2.3.1.37), ALAS of Rhodobacter capsidatus, or an ALAS having at least 50% sequence identity to a naturally occurring ALAS.
  • one or more of the downstream genes e.g., in E.
  • Cultures of cells engineered for the production of flavonoids or anthocyanins can in some embodiments include a medium that includes succinate and/or glycine, precursors of heme biosynthesis via the C4 pathway.
  • cell cultures that include engineered cells as provided herein in a culture medium, where the culture medium includes a carbon source that is also an energy source for the cells, where the carbon source can be, for example, glycerol, a sugar, or an organic acid, as nonlimiting examples.
  • the culture medium can further include a feed molecule that is used to produce flavonoids or anthocyanins.
  • a feed molecule can be, for example, acetate, malonate, tyrosine, pantothenate, coumarate, biotin, alpha-ketoglutarate, ascorbate, 5- aminolevulinic acid, succinate, or glycine.
  • the culture comprises a culture medium that includes a carbon source and at least one supplement that is a cofactor of an enzyme or is a precursor of an enzyme cofactor.
  • methods for producing flavonoids and anthocyanins that include incubating a culture of engineered host cell as provided herein to produce flavonoids or anthocyanins.
  • the methods can further include recovering at least one of the flavonoids from the cells, the culture medium, or the whole culture.
  • the invention provides an engineered host cell that comprises one or more genetic modifications resulting in production of flavonoid or anthocyanin from a carbon source that can also be an energy source, through multiple chemical intermediates, by the engineered host cell.
  • the production of flavonoid or anthocyanin from glycerol occurs through enzymatic transformation.
  • the production of flavonoid or anthocyanin from a carbon source that can also be an energy source occurs through enzymatic transformation.
  • the carbon source is selected from a group consisting of: (i) glycerol, (ii) a sugar, (iii) an organic acid, (iv) an amino acid, (v) a biomass comprising glycerol; and (vi) any combination thereof.
  • the engineered host cell is cultured in a medium comprising molecules selected from a group consisting of: (i) glycerol, (ii) a sugar, (iii) an organic acid, (iv) an amino acid, (v) a biomass comprising glycerol; and (vi) any combination thereof.
  • one or more genetic modifications lead to increase metabolic flux to flavonoid precursors or cofactors.
  • one or more genetic modifications cause reduction of formation of byproducts.
  • one or more genetic modifications are selected from: (i) one or more modifications for overexpressing one or more endogenous genes in the engineered host cells; (ii) one or more modifications for under-expressing one or more endogenous genes in the engineered host cells; (iii) one or more genetic modification is expressing one or more non-native genes in the engineered host cells; and (iv) a combination thereof.
  • the engineered host cell is cultured in a medium comprising molecules selected from: tyrosine, phenylalanine, malonate, p- coumarate, bicarbonate, acetate, pantothenate, biotin, thiamine, alpha-ketoglutarate, ascorbate, and 5-aminolevulinic acid, wherein one or more of the selected molecules are the chemical intermediates, including molecules in the biosynthesis pathway or cofactors.
  • the engineered host cell comprises at least one or more nucleic acid sequences selected from: (i) nucleic acid sequences encoding tyrosine ammonia lyase activity; (ii) nucleic acid sequences encoding phenylalanine ammonia lyase activity; (iii) nucleic acid sequences encoding cinnamate 4-hydroxylase activity; (iv) nucleic acid sequences encoding 4-courmarate- CoA ligase (4CL) activity; and (v) any combination thereof.
  • nucleic acid sequences selected from: (i) nucleic acid sequences encoding tyrosine ammonia lyase activity; (ii) nucleic acid sequences encoding phenylalanine ammonia lyase activity; (iii) nucleic acid sequences encoding cinnamate 4-hydroxylase activity; (iv) nucleic acid sequences encoding 4-courmarate- CoA ligase
  • the engineered host cell comprises at least one or more peptides selected from: (i) chaicone isomerase; (ii) chaicone synthase; (iii) a fusion protein comprises a chaicone synthase and a chaicone isomerase; and (iv) any combination thereof.
  • the engineered cell is E. coli.
  • one or more genetic modifications decreases fatty acid biosynthesis.
  • the engineered host cell comprises an exogenous nucleic acid sequence selected from: (i) nucleic acid sequence encoding tyrosine ammonia lyase, wherein the encoded tyrosine ammonia lyase forms 4-coumaric acid using tyrosine as a substrate; (ii) nucleic acid sequence encoding phenylalanine ammonia lyase, wherein the encoded phenylalanine ammonia lyase converts phenylalanine to trans-cinnamic acid; (iii) nucleic acid sequence encoding cinnamate-4-hydroxylase, wherein the cinnamate-4-hydroxylase produces 4-coumaric acid from trans-cinnamic acid; (iv) nucleic acid sequence encoding flavanone-3-hydroxylase, wherein flavanone-3 -hydroxylase forms dihydrokaempferol from naringenin; and (v) any combinations thereof.
  • the engineered host cell comprises an exogenous nucleic acid sequence selected from the group consisting of: (i) nucleic acid sequences encoding tyrosine ammonia lyase, wherein the encoded tyrosine ammonia lyase forms 4-coumaric acid using tyrosine as a substrate; (ii) nucleic acid sequence encoding phenylalanine ammonia lyase, wherein the encoded phenylalanine ammonia lyase converts phenylalanine to trans-cinnamic acid; (iii) nucleic acid sequence encoding cinnamate-4-hydroxylase, wherein the cinnamate-4-hydroxylase produces 4-coumaric acid from trans-cinnamic acid; (iv) nucleic acid sequence encoding 4-courmarate-CoA ligase activity, wherein 4-courmarate-CoA ligase forms p-coumaroyl-Co
  • the invention provides a method of increasing the production of flavonoids or anthocyanins, the method comprising: providing an engineered host cell that comprises one or more genetic modifications resulting in production of flavonoid or anthocyanin from a carbon source that can also be an energy source, through multiple chemical intermediates, by the engineered host cell.
  • the production of flavonoid or anthocyanin from a carbon source that can also be an energy source occurs through enzymatic transformation.
  • the carbon source is selected from a group consisting of: (i) glycerol, (ii) a sugar, (iii) an organic acid, (iv) an amino acid, (v) a biomass comprising glycerol; and (vi) any combination thereof.
  • the engineered host cell is cultured in a medium comprising molecules selected from a group consisting of: (i) glycerol, (ii) a sugar, (iii) an organic acid, (iv) an amino acid, (v) a biomass comprising glycerol; and (vi) any combination thereof.
  • one or more genetic modifications lead to increase metabolic flux to flavonoid precursors or cofactors.
  • one or more genetic modifications cause increased metabolic flux to flavonoid precursors. In certain embodiments, one or more genetic modifications cause reduction in the formation of byproducts. In certain embodiments, one or more genetic modifications are selected from: (i) one or more modifications for over-expressing one or more endogenous genes in the engineered host cells; (ii) one or more modifications for under-expressing one or more endogenous genes in the engineered host cells; (iii) one or more genetic modification is expressing one or more non-native genes in the engineered host cells; and (iv) a combination thereof.
  • the engineered host cell is cultured in a medium comprising molecules selected from: tyrosine, phenylalanine, malonate, p-coumarate, bicarbonate, acetate, pantothenate, biotin, thiamine, alpha-ketoglutarate, ascorbate, and 5- aminolevulinic acid, wherein one or more of the selected molecules are the chemical intermediates, including molecules in the biosynthesis pathway or cofactors.
  • the engineered host cell comprises at least one or more nucleic acid sequences selected from: (i) a nucleic acid sequences encoding tyrosine ammonia lyase activity; (ii) a nucleic acid sequences encoding phenylalanine ammonia lyase activity; (iii) cinnamate 4-hydroxylase; and (iv) any combination thereof.
  • the engineered host cell comprises at least one or more peptides selected from: (i) chaicone isomerase; (ii) chaicone synthase; (iii) a fusion protein comprises a chaicone synthase and a chaicone isomerase; and (iv) any combination thereof.
  • the engineered cell is E. Coll.
  • one or more genetic modifications decreases fatty acid biosynthesis.
  • the engineered host cell comprises an exogenous nucleic acid sequence selected from: (i) nucleic acid sequences encoding tyrosine ammonia lyase, wherein the encoded tyrosine ammonia lyase forms 4-coumaric acid using tyrosine as a substrate; (ii) nucleic acid sequence encoding phenylalanine ammonia lyase, wherein the encoded phenylalanine ammonia lyase converts phenylalanine to trans-cinnamic acid; (iii) nucleic acid sequence encoding cinnamate-4-hydroxylase, wherein the cinnamate-4-hydroxylase produces 4-coumaric acid from trans-cinnamic acid; (iv) nucleic acid sequence encoding flavanone-3 -hydroxylase, wherein flavanone-3-hydroxylase forms dihydrokaempferol from naringenin; and (v) any combinations thereof.
  • the engineered host cell comprises an exogenous nucleic acid sequence selected from the group consisting of: (i) nucleic acid sequence encoding tyrosine ammonia lyase, wherein the encoded tyrosine ammonia lyase forms 4-coumaric acid using tyrosine as a substrate; (ii) nucleic acid sequence encoding phenylalanine ammonia lyase, wherein the encoded phenylalanine ammonia lyase converts phenylalanine to trans-cinnamic acid; (iii) nucleic acid sequence encoding cinnamate-4- hydroxylase, wherein the cinnamate-4-hydroxylase produces 4-coumaric acid from trans-cinnamic acid; (iv) nucleic acid sequence encoding 4-courmarate-CoA ligase activity, wherein 4- courmarate-CoA ligase forms p-coumaroyl-CoA
  • the invention provides a plurality of engineered host cells, wherein each of the plurality of the engineered host cells comprises one or more genetic modifications resulting in production of flavonoid or anthocyanin from a carbon source that can also be an energy source, through multiple chemical intermediates.
  • the production of flavonoid or anthocyanin from a carbon source that can also be an energy source occurs through enzymatic transformation.
  • the carbon source is selected from a group consisting of: (i) glycerol, (ii) a sugar, (iii) an organic acid, (iv) an amino acid, (v) a biomass comprising glycerol; and (vi) any combination thereof.
  • the engineered host cell is cultured in a medium comprising molecules selected from a group consisting of: (i) glycerol, (ii) a sugar, (iii) an organic acid, (iv) an amino acid, (v) a biomass comprising glycerol; and (vi) any combination thereof.
  • a medium comprising molecules selected from a group consisting of: (i) glycerol, (ii) a sugar, (iii) an organic acid, (iv) an amino acid, (v) a biomass comprising glycerol; and (vi) any combination thereof.
  • one or more genetic modifications lead to increase metabolic flux to flavonoid precursors or cofactors.
  • one or more genetic modifications lead to increase metabolic flux to flavonoid precursors or cofactors.
  • one or more genetic modifications cause reduction of formation of byproducts
  • one or more genetic modifications are selected from: (i) one or more modifications for over-expressing one or more endogenous genes in the engineered host cells; (ii) one or more modifications for under-expressing one or more endogenous genes in the engineered host cells; (iii) one or more genetic modification is expressing one or more non-native genes in the engineered host cells; and (iv) a combination thereof.
  • At least one of the engineered cells from the plurality of the engineered host cells is cultured in a medium comprising molecules selected from: tyrosine, phenylalanine, malonate, p-coumarate, bicarbonate, acetate, pantothenate, biotin, thiamine, alpha-ketoglutarate, ascorbate, and 5-aminolevulinic acid, wherein one or more of the selected molecules are the chemical intermediates, including molecules in biosynthesis pathway or cofactors Tn
  • at least one of the engineered cells from the plurality of the engineered host cells comprise at least one or more nucleic acid sequences selected from: (i) nucleic acid sequences encoding tyrosine ammonia lyase activity; (ii) nucleic acid sequences encoding phenylalanine ammonia lyase activity; (iii) nucleic acid sequences encoding cinnamate 4-hydroxylase activity; (iv)
  • At least one of the engineered host cell from the plurality of engineered host cells comprise at least one or more peptides selected from: (i) chaicone isomerase; (ii) chaicone synthase; (iii) a fusion protein comprises a chaicone synthase and a chaicone isomerase; and (iv) any combination thereof.
  • at least one the engineered host cell is E. coll.
  • one or more genetic modifications decreases fatty acid biosynthesis.
  • At least one of the engineered host cell from the plurality of the engineered host cells comprises an exogenous nucleic acid sequence selected from: (i) nucleic acid sequence encoding tyrosine ammonia lyase, wherein the encoded tyrosine ammonia lyase forms 4-coumaric acid using tyrosine as a substrate; (ii) nucleic acid sequence encoding phenylalanine ammonia lyase, wherein the encoded phenylalanine ammonia lyase converts phenylalanine to trans-cinnamic acid; (iii) nucleic acid sequence encoding cinnamate-4-hydroxylase, wherein the cinnamate-4-hydroxylase produces 4-coumaric acid from trans-cinnamic acid; (iv) nucleic acid sequence encoding flavanone-3- hydroxylase, wherein flavanone-3 -hydroxylase forms dihydrokaempferol from n
  • the engineered host cell comprises an exogenous nucleic acid sequence selected from the group consisting of: (i) nucleic acid sequence encoding tyrosine ammonia lyase, wherein the encoded tyrosine ammonia lyase forms 4-coumaric acid using tyrosine as a substrate; (ii) nucleic acid sequence encoding phenylalanine ammonia lyase, wherein the encoded phenylalanine ammonia lyase converts phenylalanine to trans- cinnamic acid; (iii) nucleic acid sequence encoding cinnamate-4-hydroxylase, wherein the cinnamate-4-hydroxylase produces 4-coumaric acid from trans-cinnamic acid; (iv) nucleic acid sequence encoding 4-courmarate-CoA ligase activity, wherein 4-courmarate-CoA ligase forms p- coumaroyl-Co
  • the invention provides a method of increasing the production of flavonoids or anthocyanins, the method comprising: providing a plurality of engineered host cells, wherein each of the plurality of the engineered host cell comprises one or more genetic modifications resulting production of flavonoid or anthocyanin from a carbon source that can also be an energy source, through multiple chemical intermediates, by the engineered host cell.
  • the production of flavonoid or anthocyanin from a carbon source that can also be an energy source occurs through enzymatic transformation.
  • the carbon source is selected from a group consisting of: (i) glycerol, (ii) a sugar, (iii) an organic acid, (iv) an amino acid, (v) a biomass comprising glycerol; and (vi) any combination thereof.
  • the engineered host cell is cultured in a medium comprising molecules selected from a group consisting of: (i) glycerol, (ii) a sugar, (iii) an organic acid, (iv) an amino acid, (v) a biomass comprising glycerol; and (vi) any combination thereof.
  • one or more genetic modifications lead to increase metabolic flux to flavonoid precursors or cofactors.
  • one or more genetic modifications lead to increase metabolic flux to flavonoid precursors or cofactors. In certain embodiments, one or more genetic modifications cause reduction of formation of byproducts. In certain embodiments, one or more genetic modifications are selected from: (i) one or more modifications for over-expressing one or more endogenous genes in the engineered host cells; (ii) one or more modifications for under-expressing one or more endogenous genes in the engineered host cells; (iii) one or more genetic modification is expressing one or more non-native genes in the engineered host cells; and (iv) a combination thereof.
  • At least one of the engineered cells from the plurality of the engineered host cells is cultured in a medium comprising molecules selected from: tyrosine, phenylalanine, malonate, p-coumarate, bicarbonate, acetate, pantothenate, biotin, thiamine, alphaketoglutarate, ascorbate, and 5-aminolevulinic acid, wherein one or more of the selected molecules are the chemical intermediates, including molecules in biosynthesis pathway or cofactors.
  • At least one of the engineered cells from the plurality of the engineered host cells comprise at least one or more nucleic acid sequences selected from: (i) nucleic acid sequences encoding tyrosine ammonia lyase activity; (ii) nucleic acid sequences encoding phenylalanine ammonia lyase activity; (iii) nucleic acid sequences encoding cinnamate 4-hydroxylase activity; (iv) nucleic acid sequences encoding 4-courmarate-CoA ligase (4CL) activity; and (v) any combination thereof.
  • At least one of the engineered host cell from the plurality of engineered host cells comprise at least one or more peptides selected from: (i) chaicone isomerase; (ii) chaicone synthase; (iii) a fusion protein comprises a chaicone synthase and a chaicone isomerase; and (iv) any combination thereof.
  • at least one the engineered host cell is E. coll.
  • one or more genetic modifications decreases fatty acid biosynthesis.
  • At least one of the engineered host cell from the plurality of the engineered host cells comprises an exogenous nucleic acid sequence selected from: (i) nucleic acid sequence encoding tyrosine ammonia lyase, wherein the encoded tyrosine ammonia lyase forms 4-coumaric acid using tyrosine as a substrate; (ii) nucleic acid sequence encoding phenylalanine ammonia lyase, wherein the encoded phenylalanine ammonia lyase converts phenylalanine to trans-cinnamic acid; (iii) nucleic acid sequence encoding cinnamate-4-hydroxylase, wherein the cinnamate-4-hydroxylase produces 4-coumaric acid from trans-cinnamic acid; (iv) nucleic acid sequence encoding flavanone-3 -hydroxylase, wherein flavanone-3 -hydroxylase forms dihydrokaempferol from n
  • the engineered host cell comprises an exogenous nucleic acid sequence selected from the group consisting of: (i) nucleic acid sequence encoding tyrosine ammonia lyase, wherein the encoded tyrosine ammonia lyase forms 4-coumaric acid using tyrosine as a substrate; (ii) nucleic acid sequence encoding phenylalanine ammonia lyase, wherein the encoded phenylalanine ammonia lyase converts phenylalanine to trans-cinnamic acid; (iii) nucleic acid sequence encoding cinnamate-4-hydroxylase, wherein the cinnamate-4-hydroxylase produces 4-coumaric acid from trans-cinnamic acid; (iv) nucleic acid sequence encoding 4-courmarate-CoA ligase activity, wherein 4-courmarate-CoA ligase forms p-coumaroyl-CoA
  • the flavonoid is catechin.
  • the engineered host cell comprises one or more genetic modifications to increase the production and/or availability of malonyl-CoA.
  • the production and/or availability of malonyl-CoA is increased by transformation of acetyl-CoA to malonyl-CoA.
  • the engineered host cell comprises one or more genetic modifications selected from: (i) expression of acetyl-CoA carboxylase (ACC); and (ii) overexpression of acetyl-CoA carboxylase.
  • the engineered host cell is an E. coll.
  • the E. coli cell further comprises genes from fungi.
  • the acetyl-CoA carboxylase is from: Mucor circinelloides, Rhodotorula toruloides, Lipomyces starkeyi, and Ustilago maydis, and orthologs of acetyl-CoA carboxylase having at least 50% amino acid identity to the acetyl-CoA carboxylase of these aforementioned species.
  • one or more genetic modification is deletion or attenuation of one or more fatty biosynthetic genes resulting in decrease in fatty acid biosynthesis.
  • one or more genetic modification is overexpression of acetyl-CoA synthase (ACS).
  • the acetyl-CoA synthase is selected from: acetyl-CoA synthase gene of E. coli, acetyl-CoA synthase gene of Salmonella typhimurium, and orthologs of acetyl-CoA synthase gene in any other species having at least 50% amino acid identity to the acetyl-CoA synthase gene of E. coli and Salmonella typhimurium.
  • one or more genetic modification is selected from a group consisting of: (i) overexpression a gene encoding pyruvate dehydrogenase (PDH), wherein the PDH may include E354K mutation; (ii) exogenous nucleic acid sequence encoding a malonyl-CoA synthetase; (iii) upregulation of endogenous pantothenate kinase (PanK), wherein PanK is not feedback inhibited by coenzyme A; (iv) exogenous nucleic acid sequence encoding a malonate transporter; and (v) any combinations thereof.
  • PDH pyruvate dehydrogenase
  • PanK pantothenate kinase
  • the malonyl-CoA synthetase is selected from of malonyl-CoA synthetases of Streptomyces coelicolor, Rhodopseudomonas palustris, or a malonyl-CoA synthetase having at least 50% identity to any of these or other naturally occurring malonyl-CoA synthetases.
  • one or more genetic modifications to decrease fatty acid biosynthesis is selected from: (i) mutation or downregulation of a gene encoding malonyl-CoA-ACP transacylase (E. coli fabD); (ii) modifications to the gene beta-ketoacyl-ACP synthase II (E.
  • E. coli fabF downregulation of beta-ketoacyl-ACP synthase I enzyme
  • E coli fabB downregulation of acyl carrier protein
  • E. coli acpP acyl carrier protein
  • the engineered host cell comprises peptides selected from: (i) acetyl-CoA carboxylase (ACC) having an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO: 15 or SEQ ID NO: 16; (ii) malonate CoA-transferase having an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO: 19; (iii) acetyl-CoA synthase (ACS) having an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO: 16; (iv) malonyl-CoA synthase having an amino acid sequence at least 80% identical SEQ ID NO: 77, SEQ ID NO: 78, or SEQ ID NO: 79; (v) malonate transporter having an amino acid sequence at least 80% identical to SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 80,
  • the invention provides a method of increasing the production of flavonoids comprising an engineered host cell, wherein the one or more engineered host cells comprise one or more genetic modifications to increase the production and/or availability of malonyl-CoA.
  • the production and/or availability of malonyl-CoA is increased by transformation of acetyl-CoA to malonyl-CoA.
  • the engineered host cell comprises one or more genetic modifications selected from: (i) expression of acetyl-CoA carboxylase (ACC); and (ii) overexpression of acetyl-CoA carboxylase.
  • the engineered host cell is an E. coll.
  • the E. coll cell further comprises genes from fungi.
  • the acetyl-CoA carboxylase is from: Mucor circinelloides, Rhodotorula toruloides, Lipomyces starkeyi, and Ustilago maydis, and orthologs of acetyl-CoA carboxylase having at least 50% amino acid identity to the acetyl-CoA carboxylase of these aforementioned species.
  • one or more genetic modification is deletion or attenuation of one or more fatty biosynthetic genes resulting in decrease in fatty acid biosynthesis.
  • one or more genetic modification is overexpression of acetyl-CoA synthase (ACS).
  • the acetyl-CoA synthase is selected from: acetyl-CoA synthase gene of E. coli, acetyl-CoA synthase gene of Salmonella typhimurium, and orthologs of acetyl-CoA synthase gene in any other species having at least 50% amino acid identity to the acetyl-CoA synthase gene of E. coli and Salmonella typhimurium.
  • one or more genetic modification is selected from a group consisting of: (i) overexpression a gene encoding pyruvate dehydrogenase (PDH), wherein the PDH may include E354K mutation; (ii) exogenous nucleic acid sequence encoding a malonyl-CoA synthetase; (iii) upregulation of endogenous pantothenate kinase (PanK), wherein PanK is not feedback inhibited by coenzyme A; (iv) exogenous nucleic acid sequence encoding a malonate transporter; and (v) any combinations thereof.
  • PDH pyruvate dehydrogenase
  • PanK pantothenate kinase
  • the malonyl-CoA synthetase is selected from of malonyl-CoA synthetases of Streptomyces coelicolop Rhodopsetidomonas palustris, or a malonyl-CoA synthetase having at least 50% identity to any of these or other naturally occurring malonyl-CoA synthetases.
  • one or more genetic modifications to decrease fatty acid biosynthesis is selected from: (i) mutation or downregulation of a gene encoding malonyl-CoA- ACP transacylase (E coli fabD); (ii) modifications to the gene beta-ketoacyl-ACP synthase II (E.
  • the engineered host cell comprises peptides selected from: (i) acetyl-CoA carboxylase (ACC) having an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO: 15 or SEQ ID NO: 16; (ii) malonate CoA-transferase having an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO: 19; (iii) acetyl-CoA synthase (ACS) having an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO: 16; (iv) malonyl-CoA synthase having an amino acid sequence at least 80% identical SEQ ID NO: 77, SEQ ID NO: 78, or SEQ ID NO: 79; (v) malonate transporter having an amino acid sequence at least 80% identical to SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 80,
  • the invention provides an engineered host cell, wherein the engineered host cell comprises one or more genetic modifications to increase endogenous biosynthesis of tyrosine.
  • one or more genetic modifications comprises upregulation of 3- deoxy-D-arabino-heptulosonate synthase.
  • one or more genetic modifications are selected from: (i) upregulation of chorismate mutase; (ii) upregulation of prephenate dehydrogenase; (iii) overexpression of shikimate kinase; (iv) overexpression of shikimate dehydrogenase; and (v) any combinations thereof.
  • one or more genetic modifications comprises downregulation of L-phenylalanine biosynthetic pathway.
  • one or more genetic modifications comprises expression of exogenous phosphoenolpyruvate synthase (ppsA). In certain embodiments, one or more genetic modifications comprises expression of exogenous transketolase (tktA). In certain embodiments, wherein the one or more genetic modifications comprises disruption of tyrR gene.
  • one or more genetic modifications are selected from a group consisting of: (i) expression or overexpression of (D146N) variant of phospho-2-dehydro-3 -deoxyheptonate aldolase; (ii) expression or overexpression of variant of 3-dehydroquinate synthase (aroB); (iii) overexpression of transketolase tktA; (iv) deletion of shikimate kinase (aroK); (v) deletion of tyrR; (vi) expression or overexpression of A354V variant of chorismate mutase (tyrA); (vi) and any combination thereof.
  • the invention provides a method of increasing endogenous biosynthesis of tyrosine comprising an engineered cell, wherein the engineered host cell comprises one or more genetic modifications to increase endogenous biosynthesis of tyrosine.
  • one or more genetic modifications comprises upregulation of 3-deoxy-D-arabino-heptulosonate synthase.
  • one or more genetic modifications are selected from: (i) upregulation of chorismate mutase; (ii) upregulation of prephenate dehydrogenase; (iii) overexpression of shikimate kinase; (iv) overexpression of shikimate dehydrogenase; and (v) any combinations thereof.
  • one or more genetic modifications comprises downregulation of L-phenylalanine biosynthetic pathway. In certain embodiments, one or more genetic modifications comprises expression of exogenous phosphoenolpyruvate synthase (ppsA). In certain embodiments, one or more genetic modifications comprises expression of exogenous transketolase (tktA). In certain embodiments, wherein the one or more genetic modifications comprises disruption of tyrR gene.
  • one or more genetic modifications are selected from a group consisting of: (i) expression or overexpression of (D146N) variant of phospho-2-dehydro-3-deoxyheptonate aldolase; (ii) expression or overexpression of variant of 3- dehydroquinate synthase (aroB); (iii) overexpression of transketolase tktA; (iv) deletion of shikimate kinase (aroK); (v) deletion of tyrR; (vi) expression or overexpression of A354V variant of chorismate mutase (tyrA); (vi) and any combination thereof.
  • the invention provides an engineered host cell, wherein the engineered host cell comprises one or more genetic modifications to increase transformation of leucocyanidin or catechin to cyani din-3 -glucoside (Cy3G).
  • one or more genetic modifications comprises overexpression of anthocyanin synthase.
  • the anthocyanin synthase is selected from: (i) anthocyanin synthase of Carica papaya (SEQ ID NO: 13); (ii) the anthocyanin synthase has an amino acid sequence at least 80% identical to SEQ. ID NO: 66, SEQ. ID NO: 67, SEQ. ID NO: 68, or SEQ.
  • one or more engineered host cells comprises flavonoid-3 -glucosyl transferase (3GT).
  • flavonoid-3 -glucosyl transferase is selected from: (i) flavonoid-3-glucosyl transferase in Vitis labrusca (SEQ. ID NO: 14); (ii) the flavonoid-3-glucosyl transferase has an amino acid sequence at least 80% identical to SEQ. ID NO: 70, SEQ. ID NO: 71, SEQ. ID NO: 72, or SEQ.
  • one or more genetic modifications comprises overexpression of anthocyanin synthase and flavonoid-3 -glucosyl transferase (3GT). In certain embodiments, the one or more genetic modifications comprises overexpression of anthocyanin synthase and flavonoid-3-glucosyl transferase (3GT). In certain embodiments, the one or more genetic modifications are selected from a group consisting of: (i) anthocyanin synthase, (ii) flavonoid-3 -glucosyl transferase (3GT), and (iii) a combination thereof.
  • the invention provides a method for increasing the production of flavonoids comprising an engineered host cell, wherein the engineered host cell comprises one or more genetic modifications to increase transformation of leucocyanidin or catechin to cyanidin-3- glucoside (Cy3G).
  • one or more genetic modifications comprises overexpression of anthocyanin synthase.
  • the anthocyanin synthase is selected from: (i) anthocyanin synthase of Carica papaya (SEQ. ID NO: 13); (ii) the anthocyanin synthase has an amino acid sequence at least 80% identical to SEQ. ID NO: 66, SEQ. ID NO: 67, SEQ.
  • one or more engineered host cells comprises flavonoid-3 -glucosyl transferase (3GT).
  • flavonoid-3 -glucosyl transferase is selected from: (i) flavonoid-3- glucosyl transferase in Vitis labrusca (SEQ. ID NO: 14); (ii) the flavonoid-3 -glucosyl transferase has an amino acid sequence at least 80% identical to SEQ. ID NO: 70, SEQ.
  • one or more genetic modifications comprises overexpression of anthocyanin synthase and flavonoid-3- glucosyl transferase (3 GT).
  • the one or more genetic modifications comprises overexpression of anthocyanin synthase and flavonoid-3 -glucosyl transferase (3GT).
  • the one or more genetic modifications are selected from a group consisting of: (i) anthocyanin synthase, (ii) flavonoid-3 -glucosyl transferase (3GT), and (iii) a combination thereof.
  • the invention provides a method of increasing the transformation of leucocyanidin or catechin to cyani din-3 -glucoside (Cy3G), delphinidin or gallocatechin to delphindin-3 -glucoside (De3G), or afzelechin or pelargonidin to pelargoni din-3 -glucoside (Pe3G) comprising anthocyanin synthase, wherein the anthocyanin synthase is selected from: (i) anthocyanin synthase of Carica papaya (SEQ. ID NO: 13); (ii) the anthocyanin synthase has an amino acid sequence at least 80% identical to SEQ. ID NO: 66, SEQ.
  • one or more genetic modifications comprises overexpression of anthocyanin synthase and flavonoid-3- glucosyl transferase (3GT).
  • the one or more genetic modifications are selected from a group consisting of: (i) anthocyanin synthase, (ii) flavonoid-3 -glucosyl transferase (3 GT), and (iii) a combination thereof.
  • the invention provides a method of increasing the transformation of cyanidin to cyanidin-3-glucoside (Cy3G), delphindin to delphindin-3 -glucoside (De3G), or pelargonidin to pelagonidin-3 -glucoside (Pe3G), comprising flavonoid-3 -glucosyl transferase (3GT), wherein the flavonoid-3 -glucosyl transferase is selected from: (i) flavonoid-3-glucosyl transferase in Vitis labrusca (SEQ. ID NO: 14); (ii) the flavonoid-3 -glucosyl transferase has an amino acid sequence at least 80% identical to SEQ. ID NO: 70, SEQ. ID NO: 71, SEQ. ID NO: 72, or SEQ. ID NO: 73; and (iii) any combinations thereof.
  • the invention provides an engineered host cell comprises one or more genetic modifications to increase the production of dihydroquercetin (DHQ), dihydromyricein (DHM), eriodictoyl (EDL), and/or pentahydroxyflayaone (PHF), wherein the engineered host cell comprises cytochrome P450 reductase (CPR) and at least one of flavanone-3-hydroxylase (F3H), flavanone-3’ -hydroxylase (F3’H), or flavonoid 3 ’,5 ’-hydroxylase (F3’5’H).
  • DHQ dihydroquercetin
  • DLM dihydromyricein
  • EDL eriodictoyl
  • PHF pentahydroxyflayaone
  • the engineered host cell comprises cytochrome P450 reductase (CPR) and at least one of flavanone-3-hydroxylase (F3H), flavanone-3’ -hydroxylase (F3’H), or flavonoid 3 ’,
  • the precursor for increase in production of dihydroquercetin (DHQ), dihydromyricein (DHM), eriodictoyl (EDL), and/or pentahydroxyflayanone (PHF) is naringenin and/or dihydrokaempferol (DHK).
  • the engineered host cell further comprises peptides selected from a group consisting of: (i) flavonoid 3 ’-hydroxylase (F3’H); (ii) cytochrome P450 reductase (CPR); and (iii) any combination thereof.
  • the engineered host cell produces eriodictyol or taxifolin.
  • the engineered host cell further comprises flavonoid 3 ’,5 ’-hydroxylase (F3’5’H).
  • the engineered host cell produces pentahydroxyflavone or dihydromyricetin.
  • flavonoid 3 ’-hydroxylase (F3’H) is truncated to remove the N-terminal leader sequence.
  • cytochrome P450 reductase (CPR) is truncated to remove the N-terminal leader sequence.
  • flavonoid 3 ’-hydroxylase (F3’H) is fused with cytochrome P450 reductase (CPR).
  • flavonoid 3 ’,5 ’-hydroxylase (F3’5’H) is fused with cytochrome P450 reductase (CPR).
  • flavanone-3 -hydroxylase (F3H) has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 7.
  • flavanone-3 ’-hydroxylase (F3’H) has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 8.
  • cytochrome P450 reductase (CPR) has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 9.
  • flavonoid 3’,5’-hydroxylase (F3’5’H) has an amino acid sequence at least 80% identical to the polypeptides selected from a group consisting of: (i) SEQ ID NO. 10, (ii) SEQ ID NO. 56, and (iii) SEQ ID NO. 57.
  • the engineered host cell further comprises cytochrome bs.
  • cytochrome b has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 98.
  • the flavanone-3 -hydroxylase (F3H) has an amino acid sequence at least 80% identical to the polypeptides selected from a group consisting of: (i) SEQ ID NO. 7, (ii) SEQ ID NO. 45, (iii) SEQ ID NO. 46, (iv) SEQ ID NO. 47, and (v) SEQ ID NO. 48
  • the invention provides method of increasing the production of dihydroquercetin (DHQ), dihydromyricein (DHM), eriodictoyl (EDL), and/or pentahydroxyflayaone (PHF) comprising an engineered host cell, wherein the engineered host cell comprises cytochrome P450 reductase (CPR) and at least one of flavanone-3-hydroxylase (F3H), flavanone-3 ’-hydroxylase (F3’H), or flavonoid 3 ’,5 ’-hydroxylase (F3’5’H).
  • DHQ dihydroquercetin
  • DLM dihydromyricein
  • EDL eriodictoyl
  • PPF pentahydroxyflayaone
  • the precursor for increase in production of dihydroquercetin (DHQ), dihydromyricein (DHM), eriodictoyl (EDL), and/or pentahydroxyflayanone (PHF) is naringenin and/or dihydrokaempferol (DHK).
  • the engineered host cell further comprises peptides selected from a group consisting of: (i) flavonoid 3 ’-hydroxylase (F3’H); (ii) cytochrome P450 reductase (CPR); and (iii) any combination thereof.
  • the engineered host cell produces eriodictyol or taxifolin.
  • the engineered host cell further comprises flavonoid 3 ’,5 ’-hydroxylase (F3’5’H).
  • the engineered host cell produces pentahydroxyflavone or dihydromyricetin.
  • flavonoid 3 ’-hydroxylase (F3’H) is truncated to remove the N-terminal leader sequence.
  • cytochrome P450 reductase (CPR) is truncated to remove the N-terminal leader sequence.
  • flavonoid 3 ’-hydroxylase (F3’H) is fused with cytochrome P450 reductase (CPR).
  • flavonoid 3 ’,5 ’-hydroxylase (F3’5’H) is fused with cytochrome P450 reductase (CPR).
  • flavanone-3 -hydroxylase (F3H) has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 7.
  • flavanone-3 ’-hydroxylase (F3’H) has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 8.
  • cytochrome P450 reductase (CPR) has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 9.
  • flavonoid 3’,5’-hydroxylase has an amino acid sequence at least 80% identical to the polypeptides selected from a group consisting of: (i) SEQ ID NO. 10, (ii) SEQ ID NO. 56, and (iii) SEQ ID NO. 57.
  • the engineered host cell further comprises cytochrome bs.
  • cytochrome bs has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 98.
  • the flavanone-3 -hydroxylase (F3H) has an amino acid sequence at least 80% identical to the polypeptides selected from a group consisting of: (i) SEQ ID NO. 7, (ii) SEQ ID NO. 45, (iii) SEQ ID NO. 46, (iv) SEQ ID NO. 47, and (v) SEQ ID NO. 48
  • An engineered cell for producing flavonoids include an exogenous nucleic acid sequence encoding tyrosine ammonia lyase (TAL) activity (alternatively or in addition, an exogenous nucleic acid encoding phenylalanine ammonia-lyase (PAL) activity and an exogenous nucleic acid encoding cinnamate-4-hydroxylase (C4H) activity), an exogenous nucleic acid sequence encoding 4-coumarate-CoA ligase (4CL) activity, an exogenous nucleic acid sequence encoding chaicone synthase (CHS) activity, and an exogenous nucleic acid sequence encoding chaicone isomerase (CHI) activity.
  • TAL exogenous nucleic acid sequence encoding tyrosine ammonia lyase
  • PAL phenylalanine ammonia-lyase
  • C4H cinnamate-4-hydroxylase
  • 4CL 4-coumarate-Co
  • the engineered cell can further include an exogenous nucleic acid sequence encoding an exogenous nucleic acid sequence encoding flavanone-3 -hydroxylase (F3H) activity, an exogenous nucleic acid sequence encoding flavonoid 3’-hydroxlase (F3’H) activity or flavonoid 3 ’,5 ’-hydroxylase (F3’5’H), an exogenous nucleic acid sequence encoding cytochrome P450 reductase (CPR) activity, an exogenous nucleic acid sequence encoding dihydroflavonol-4- reductase (DFR) activity, and/or an exogenous nucleic acid sequence encoding leucoanthocyanidin reductase (LAR) activity.
  • F3H flavanone-3 -hydroxylase
  • F3H flavonoid 3’-hydroxlase
  • F3’5 flavonoid 3 ’,5 ’-hydroxylase
  • CPR cytochrome P450 reduct
  • Tyrosine ammonia-lyase can be, for example, a member of the aromatic amino acid deaminase family that catalyzes the elimination of ammonia from L-tyrosine to yield p-coumaric acid.
  • An exemplary tyrosine ammonia lyase is the Saccharothrix espanaensis tyrosine ammonia lyase (TAL; SEQ ID NO: 1).
  • TALs with SEQ ID NOS: 23-26 are also considered for use in the engineered cells provided herein, TALs with SEQ ID NOS: 23-26, TALs listed in Table 1, TAL homologs and variants having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ ID: 1 that have the activity of a tyrosine ammonia lyase that produces p-coumaric acid from tyrosine.
  • phenylalanine ammonia-lyase can be a member of the aromatic amino acid deaminase family that catalyzes the non-oxidative deamination of L- phenylalanine to form trans-cinnamic acid.
  • An exemplary phenylalanine ammonia-lyase is the Brevibacilhis laterosporus phenylalanine ammonia-lyase (PAL; SEQ ID NO :2).
  • PALs with SEQ ID NOS: 27-29 PAL homologs and variants having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ TD NO: 2 that have the activity of a phenylalanine ammonia lyase that produces trans-cinnamic acid from phenylalanine.
  • Cinnamate-4-hydroxylase belongs to the cytochrome P450-dependent monooxygenase family and catalyzes the formation of p-coumaric acid from trans-cinnamic acid. Considered for use in the engineered cells provided herein are C4H of Helianthus annuus L.
  • C4H SEQ ID NO: 3
  • C4Hs with SEQ ID NOS: 30-32 C4H homologs of other species, as well as variants of naturally occurring C4Hs having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to the SEQ ID NO: 3 (C4H, Helianthus annuus L.) that have the activity of a C4H.
  • SEQ ID NO: 3 C4H, Helianthus annuus L.
  • 4-coumarate-CoA ligase (4CL) catalyzes the activation of 4-coumarate to its CoA ester.
  • 4CLs of Petroselinum crispum SEQ ID NO: 4
  • 4CLs with SEQ ID NOS: 33-36 4CL homologs of other species, as well as variants of naturally occurring 4CLs having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to SEQ ID No: 4 (4CL, Petroselinum crispum) that have the activity of a 4CL.
  • the chaicone synthase can be, for example, a type III polyketide synthase that sequentially condenses three molecules of malonyl-CoA with one molecule of p-coumaryol-CoA to produce the naringenin precursor naringenin chaicone or naringenin.
  • An exemplary chaicone synthase is the chaicone synthase of Petunia x hybrida (CHS, SEQ ID NO: 5).
  • CHSs with SEQ ID: 37- 40 are also considered for use in the engineered cells provided herein.
  • CHSs with SEQ ID: 37- 40 are also considered for use in the engineered cells provided herein.
  • CHS homologs and variants having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to SEQ ID NO: 5 (CHS, Petunia x hybrida) that have the activity of a chaicone synthase.
  • CHS Petunia x hybrida
  • Chaicone isomerase (CHI, also referred to as chaicone flavonone isomerase) catalyzes the stereospecific and intramolecular isomerization of naringenin chaicone into its corresponding (2S)-flavanones.
  • CHI of Medicago saliva SEQ ID NO: 6
  • CHI of Table 4 CHIs with SEQ ID NOS: 41-44, and CHI homologs of other species, as well as variants of naturally occurring CHI having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to SEQ ID NO: 6 (CHI, Medicago sativa) that have the activity of a chaicone isomerase.
  • a nucleic acid sequence encoding a CHI can in some embodiments be fused to a nucleic acid sequence encoding a CHS in an engineered cell as provided herein, such that the CHI activity is fused to the chaicone synthase activity, i.e., a fusion protein is produced in the engineered cell that has both condensing and cyclization activities.
  • Flavanone 3-hydroxylase catalyzes the stereospecific hydroxylation of (2S)- naringenin to form (2R,3R)-dihydrokaempferol.
  • Other substrates include (2S)-eriodictyol, (2S)- dihydrotricetin and (2S)-pinocembrin.
  • Some F3H enzymes are bifunctional and also catalyzes as flavonol synthase (EC: 1.14.20.6).
  • F3H oi Rubus occidentalis SEQ ID NO: 7
  • F3Hs with SEQ ID NOS: 45-48 F3Hs listed in Table 5
  • other F3H homologs and variants having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to SEQ ID NO: 7 (F3H, Rubus occidentalis) that have the activity of a F3H.
  • Table 5 Flavanone 3 -hydroxylases
  • Flavonoid 3 ’-hydroxylases belongs to the cytochrome P450 family with systematic name of flavonoid, NADPH:oxygen oxidoreductase (3 ’-hydroxylating).
  • F3’H converts dihydrokaempferol to dihydroquercetin (taxifolin) or naringenin to eriodictyol.
  • flavonoid 3 ’ -hydroxylases F3 ’H may be used to convert kaempferol to quercetin.
  • F3’H of Brassica napus F3’H; SEQ ID NO: 8
  • F3’H with SEQ ID NOS: 49-52 those listed in Table 6, and homologs and variants having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to these F3’H.
  • F3’H is a cytochrome P450 enzyme that requires a cytochrome P450 reductase (CPR) to function.
  • CPR cytochrome P450 reductase
  • Cytochrome P450 reductases are diflavin oxidoreductases that supply electrons to F3’Hs.
  • the P450 reductase can be from the same species as F3’H or different species from F3’H.
  • CPR of Catharanthus roseus SEQ ID NO: 9
  • additional CPRs listed in Table 7, CPRs with SEQ ID NOS: 53-55, CPR homologs of other species, and variants of naturally occurring CPRs having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to these CPRs that have the activity of a CPR.
  • the N-terminal nucleic acid sequences in the genes of F3’H and/or CPR originated from eukaryotic cells can encode targeting leader peptides, which can be removed before introduction into prokaryotic host cells, if desired.
  • the hydroxylase complex HpaBC from E. coll was used to hydroxylate naringenin to eriodictyol or dihydrokaempferol to dihydroquercetin (taxifolin). Table 6. Flavonoid 3 ’-hydroxylases
  • a nucleic acid sequence encoding a F3’H can in some embodiments be fused to a nucleic acid sequence encoding a CPR in an engineered cell as provided herein, such that the F3 ’H activity is fused to the CPR activity.
  • flavonoid 3’, 5 ’-hydroxylase (F3’5’H) can be used to convert dihydrokaempferol to dihydromyricetin or naringenin to pentahydroxyflavone, which is further converted to dihydromyricetin by a F3H.
  • F3’5’H has the systematic name flavanone, NADPH:oxygen oxidoreductase and catalyzes the formation of 3’, 5’- dihydroxyflavanone from flavanone.
  • Tn cells engineered to enhance production of myricetin, flavonoid 3’, 5 ’-hydroxylase may be used to convert kaempferol and quercetin to myricetin.
  • An exemplary F3’5’H is the Delphinium grandiflorum F3’5’H (SEQ ID NO: 10), Also considered for use in the engineered cells provided herein include F3’5’H with SEQ ID NOS:56-57, F3’5’H homologs of other species, and variants of naturally occurring F3’5’H having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to SEQ ID NOS: 10 that have the activity of a F3’5’H.
  • Flavonol synthase catalyzes the oxidation of dihydroflavonol to produce flavonol.
  • flavonol synthase In cells engineered to enhance production of myricetin, kampferol, and/or quercetin, flavonol synthase (FLS) may be used for catalyzing the conversion of dihydromyricetin (DHM) to myricetin; conversion of dihydrokaempferol (DHK) to kampferol; and conversion of dihydroquercetin (DHQ) to quercetin.
  • DHM dihydromyricetin
  • DHQ dihydroquercetin
  • An exemplary flavonol synthase (FLS) is FLS from Petroselinum crispum (EC: 1.14.11.23).
  • FLS of Petroselinum crispum SEQ ID NO: 99
  • other FLS homologs and variants having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to SEQ ID NOS: 99-122 that have the activity of FLS.
  • Dihydroflavonol 4-reductase acts on (+) - dihydrokaempferol (DHK), (+)- dihydroquercetin (Taxifolin, DHQ), or dihydromyricein (DHM) to reduce those compounds to the corresponding cis-flavan-3,4-diol (DHK to leucopelargonidin; Taxifolin to leucocyanidin; DHM to leucodelphinidin).
  • An exemplary DFR is the Anthurium andraeanum DFR (SEQ ID NO: 11).
  • DFRs in Table 8 DFRs with SEQ ID NOS: 58-61, and DFR homologs of other species, as well as variants of naturally occurring DFR having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to SEQ ID NO: 11.
  • LAR Leucoanthocyanidin reductase catalyzes the synthesis of catechin from 3,4-cis- leucocyanidin. LAR also synthesizes afzelechin and gallocatechin.
  • LAR oiDesmodium uncinatum SEQ ID NO: 12
  • LARs with SEQ ID NOS: 62-65 SEQ ID NOS: 62-65
  • LAR homologs of other species as well as variants of naturally occurring LAR having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to SEQ ID NO: 12 (LAR, Desmodium uncinatum) that have the activity of a LAR.
  • the cells are further engineered to include an anthocyanin synthase (ANS) which catalyzes the conversion of leucoanthocyanidin or catechin to anthocyanidin, leucopelargonidin to pelargonidin, or leucodelphinidin to delphinidin.
  • ANS anthocyanin synthase
  • ANS of Carica papaya SEQ ID NO: 13
  • ANS with SEQ ID NOS: 66-69 and ANS homologs of other species, as well as variants of naturally occurring ANS having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to SEQ ID NO: 13 (ANS, Carica papaya) that have the activity of a ANS.
  • the cells are further engineered to include a flavonoid-3 -glucosyl transferase (3 GT) to generate anthocyanins by transfer of a sugar moiety such as, without limitation, UDP-a- D-glucose to anthocyanidins to form glycosylated anthocyanins.
  • a flavonoid-3 -glucosyl transferase 3 GT
  • UDP-a- D-glucose to anthocyanidins to form glycosylated anthocyanins.
  • 3GT of Vitis labrusca (SEQ ID NO: 14), 3GT with SEQ ID NOS: 70-73, and 3GT homologs of other species, as well as variants of naturally occurring 3GT having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to SEQ ID NO: 14 (3GT, Vitis labrusca) that have the activity of a 3GT.
  • host cells may be engineered for enhanced production of flavonoids or anthocyanins by introducing additional exogenous pathways and/or modifying endogenous metabolic pathways to remove or downregulate competitive pathways to reduce carbon loss, increase precursor supply, improve cofactor availability, reduce byproduct formation, or improve cell fitness. Enhancing or improving production of flavonoids or anthocyanins can be increasing yield, titer, or rate of production.
  • a host cell engineered for the production of a flavonoid or anthocyanin can be engineered to include any or any combination of: overexpression of an acetyl-CoA carboxylase (ACC) or an ACC variant; expression or overexpression of at least one enzyme for increasing cell’s malonyl-CoA supply that does not rely on the ACC step; expression or overexpression of at least one enzyme to increase tyrosine supply; expression or overexpression of at least one enzyme to increase CoA availability for synthesizing precursors malonyl-CoA or p-coumaryol-CoA; expression or overexpression at least one enzyme to increase heme biosynthesis; deletion or downregulation of at least one fatty acid synthesis enzyme; at least one alcohol dehydrogenase, lactate dehydrogenase, pyruvate oxidase, phosphate acetyl transferase, or acetate kinase; at least one enzyme of a fatty acid degradation pathway, at least one thi
  • Malonyl-CoA is the direct precursor for chaicone synthase to perform sequential condensations with p-coumaryol-CoA. Malonyl-CoA supply can be increased by one or more modifications. Malonyl-CoA is synthesized by acetyl-CoA carboxylase (ACC) via the ATP- dependent carboxylation of acetyl-CoA in a multistep reaction. First, the biotin carboxylase domain catalyzes the ATP-dependent carboxylation of biotin using bicarbonate as a CO2 donor. In the second reaction, the carboxyl -group is transferred from biotin to acetyl-CoA to form malonyl- CoA.
  • ACC acetyl-CoA carboxylase
  • Host cells can be engineered for example to express an exogenous acetyl-CoA carboxylase or a variant ACC to increase malonyl-CoA synthesis from acetyl-CoA.
  • Mucor circinelloides SEQ ID NO: 15
  • acetyl-CoA carboxylase can be introduced into the host cells.
  • ACC genes that may be used in the engineered cells provided herein include, without limitation, the genes listed in Table 9, genes with SEQ ID NOS: 74-76, naturally occurring orthologs of these ACCs, or variants having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to referenced genes.
  • naturally occurring acetyl-CoA carboxylase genes can be further engineered to introduce single or multiple amino acid mutations to increase catalytic activity and/or remove feedback inhibition.
  • Additional strategies for increasing malonyl-CoA include increasing acetyl-CoA, which is converted to malonyl-CoA by acetyl-CoA carboxylase (ACC).
  • Acetyl-CoA can be synthesized from acetate by an acyl-CoA ligase in an ATP-dependent reaction.
  • Acetyl-CoA synthetase (ACS) or acetate-CoA ligase catalyzes the formation of a new chemical bond between acetate and CoA coenzyme A (CoA).
  • ACSs with native activity on acetate will provide the function of increasing acetyl-CoA supply when cells are either supplied with acetate as a co-feed, or where acetate is produced as a by-product.
  • Other acyl-CoA ligases having their main activity on other acid substrates, may also have substantial activity on acetate, and are viable candidates for providing acetate-CoA ligase activity in the engineered cells provided herein.
  • the ACSs expressed in the host cells can be prokaryotic or eukaryotic. Cultures of engineered host cells that overexpress a nucleic acid sequence encoding ACS can optionally include acetate in the culture medium.
  • acetyl-CoA synthase that can be expressed in a host cell engineered to produce a flavonoid or anthocyanin include, without limitation, the ACS gene of E. colt, the ACS of Salmonella typhimurium (SEQ ID NO: 16), and orthologs of these ACSs in other species having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to these ACSs.
  • the ACS gene of E. colt the ACS of Salmonella typhimurium (SEQ ID NO: 16)
  • orthologs of these ACSs in other species having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%,
  • an engineered host cell can overexpress a gene encoding pyruvate dehydrogenase (PDH), which converts pyruvate to acetyl-CoA, to increase acetyl-CoA supply.
  • PDH catalyzes an irreversible metabolic step, and the control of its activity is complex and involves control by its substrates and products.
  • Nicotinamide adenine dinucleotide hydrogen (NADH) is a competitive inhibitor of the PDH complex.
  • the NADH sensitivity of the PDH complex has been demonstrated to reside in LPD, the enzyme that interacts with NAD+ as a substrate.
  • a variant of the Lpd subunit of PDH can be expressed that includes one or more mutations that reduces inhibition of PDH by NADH.
  • a LPD variant in E. coli that contains E354K mutation, and the mutated enzyme was less sensitive to NADH inhibition than the native LPD.
  • a cell engineered to produce a flavonoid or an anthocyanin as provided herein can include an exogenous nucleic acid sequence encoding a malonyl-CoA synthetase (EC 6.2.1.14) that generates malonyl-CoA from malonate.
  • Acyl-CoA synthetase catalyzes the conversion of a carboxylic acid to its acyl-CoA thioester through an ATP- dependent two-step reaction.
  • the free fatty acid is converted to an acyl-AMP intermediate with the release of pyrophosphate.
  • the activated acyl group is coupled to the thiol group of CoA, releasing AMP and the acyl-CoA product.
  • malonyl-CoA synthetases include the malonyl-CoA synthetases of Streptomyces coelicolor (SEQ ID NO: 17), matB of Rhodopseudomonas palustris (SEQ ID NO: 77), matB of Rhizobium sp, BUS003 (SEQ ID NO: 78), matB of Ochrobacrum sp.
  • Malonate can optionally be added to the culture medium of a culture that includes a cell engineered to express a malonyl-CoA synthetase.
  • the matB gene is part of the matABC operon, with matA encoding a malonyl-CoA decarboxylase and matC encoding a putative dicarboxylate carrier protein or malonate transporter.
  • An engineered cell that includes an exogenous gene encoding a malonyl- CoA synthetase can also include an exogenous nucleic acid sequence encoding a malonate transporter, such as a malonate transporter encoded by a matC gene, for example of Streptomyces coelicolor (SEQ ID NO: 18), of Rhizobiales bacterium (SEQ ID NO: 80), of Rhizobium leguminosarum (SEQ ID NO:81), of Agrobacterium vitis (SEQ ID NO: 82), of Neorhizobium sp.
  • SEQ ID NO: 18 Streptomyces coelicolor
  • SEQ ID NO: 80 Rhizobiales bacterium
  • SEQ ID NO:81 Rhizobium leguminosarum
  • Agrobacterium vitis SEQ ID NO: 82
  • Cell cultures of a host cell engineered to express a malonyl-CoA synthetase and a malonate transporter can include a culture medium that includes malonate.
  • a cell engineered to produce a flavonoid or an anthocyanin is further engineered to include an exogenous nucleic acid sequence encoding malonate CoA- transferase (EC:2.8.3.3; also referred to as the alpha subunit of malonate decarboxylase) that makes malonyl-CoA by direct transfer of the CoA from acetyl-CoA.
  • malonate CoA- transferase EC:2.8.3.3; also referred to as the alpha subunit of malonate decarboxylase
  • the alpha subunit of malonate decarboxylase from the mdcACDE gene cluster in Acinetobacter calcoaceticus has the malonate CoA-transferase activity.
  • the mdcA gene product, the a subunit, is malonate CoA-transferase
  • mdcD gene product, the subunit is a malonyl-CoA decarboxylase.
  • the mdcE gene product, the y subunit may play a role in subunit interaction to form a stable complex or as a codecarboxylase.
  • the mdcC gene product, the 8 subunit was an acyl-carrier protein, which has a unique CoA-like prosthetic group.
  • the engineered cells can include a nucleic acid encoding a malonate CoA-transferase to increase malonyl-CoA supply.
  • mdcAs that can be expressed in an engineered cell as provided herein include, without limitation, mdcA of Acinetobacter calcoaceticus (SEQ ID NO: 19), mdcAs of Table 10, mdcAs with SEQ ID NOS: 84-87, or a transferase having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to any of these or other naturally occurring malonate CoA- transferases.
  • a cell engineered to produce flavonoids or anthocyanins is further engineered to increase the supply of coenzyme A (CoA) to increase its availability for producing acetyl-CoA, malonyl-CoA, and/or p-coumaroyl-CoA.
  • CoA coenzyme A
  • Strategies for increasing CoA supply include expressing or overexpressing at least one enzyme of a CoA biosynthesis pathway.
  • Pantothenate kinase (EC 2.7.1.33, PanK; CoaA) is the first enzyme in the coenzyme CoA biosynthetic pathway.
  • pantothenate (vitamin B5) to form 4'- phosphopantothenate at the expense of a molecule of adenosine triphosphate (ATP). It is the ratelimiting step in the biosynthesis of CoA.
  • PanK- I found in bacteria
  • PanK -II mainly found in eukaryotes, but also in the Staphylococci'
  • PanK-III also known as CoaX (found in bacteria).
  • pantothenate kinase is competitively inhibited by CoA itself, as well as by some CoA esters.
  • the type III enzymes CoaX are not subject to feedback inhibition by CoA.
  • a host cell can be engineered to include a nucleic acid sequence encoding type III pantothenate kinase that is not feedback inhibited by coenzyme A, such as, without limitation, CoaX gene of Pseudomonas aeruginosa (EC:2.7.1.33, SEQ ID NO: 20), CoaX of Streptomyces sp.
  • a nucleic acid sequence encoding type III pantothenate kinase that is not feedback inhibited by coenzyme A, such as, without limitation, CoaX gene of Pseudomonas aeruginosa (EC:2.7.1.33, SEQ ID NO: 20), CoaX of Streptomyces sp.
  • Cultures of cells engineered for the production of flavonoids or anthocyanins can in some embodiments include a medium that includes pantothenate, a precursor of CoA biosynthesis, and can optionally also include cysteine, used in the CoA biosynthesis.
  • Additional strategies to increase malonyl-CoA flux to the flavonoid pathway include mutation or downregulation of one or more genes that function in fatty acid biosynthesis. Fatty acid biosynthesis directly competes with flavonoid biosynthesis for the precursor malonyl-CoA and thus limits flavonoid formation. Without limiting the embodiments to any particular mechanism, limiting fatty acid biosynthesis can increase the malonyl-CoA supply available for flavonoid biosynthesis.
  • the gene beta-ketoacyl-ACP synthase II (E. coli fabF) can be disrupted, attenuated or deleted to reduce fatty acid biosynthesis.
  • a fatty acid biosynthesis gene of a host cell that may be mutated or downregulated is a gene encoding malonyl-CoA-ACP transacylase (E. coli fabD).
  • Other fatty acid biosynthesis genes of the engineered host cell that can be downregulated include a beta-ketoacyl-ACP synthase I enzyme (E. coli fabB) and/or acyl carrier protein (E coli acpP).
  • Additional genetic modifications that may be present in a host cell engineered to produce flavonoids or anthocyanins include downregulation, disruption, or deletion of the gene targets that divert carbon flux to form byproducts such as ethanol, acetate, and lactate.
  • genes that are downregulated, disrupted, or deleted can include adhE, IdhA, poxB, and ackA-pta.
  • a cell engineered for the production of flavonoids or anthocyanins can have one or more genes encoding thioesterases downregulated, disrupted, or deleted to prevent hydrolysis of precursors malonyl-CoA, acetyl-CoA, and/or p-coumaryol-CoA.
  • Acyl-CoA thioesterase enzymes ACOTs catalyze the hydrolysis of acyl-CoAs (short-, medium-, long- and very long- chain), bile acid-CoAs, and methyl branched-CoAs, to the free fatty acid and coenzyme A.
  • ACOTs Acyl-CoA thioesterase enzymes
  • acyl-CoAs short-, medium-, long- and very long- chain
  • bile acid-CoAs bile acid-CoAs
  • methyl branched-CoAs methyl branched-CoAs
  • a cell engineered for the production of flavonoids or anthocyanins can have one or more of fatty acid degradation genes downregulated, disrupted, or deleted to improve precursor supply to the flavonoid pathway.
  • the acyl-coenzyme A dehydrogenase (fade) gene encoding acyl-CoA dehydrogenase, adhesion A (fadA) gene encoding 3-ketoacyl-CoA thiolase, and/or gene encoding fatty acid oxidation complex subunit alpha (fadB) can be downregulated, disrupted, or deleted.
  • genes encoding enzymes of the tricarboxylic acid cycle can be disrupted or downregulated to increase alphaketoglutarate supply which serves as a cofactor for the flavonoid and anthocyanin pathway enzymes.
  • TCA enzymes that can be downregulated include citrate synthase that converts acetyl-CoA to citrate.
  • an engineered host cell for the production of flavonoids or anthocyanins to upregulate the endogenous biosynthesis of amino acid tyrosine.
  • Tyrosine is one of the precursors for the flavonoid biosynthesis and its conversion to 4-coumaric acid is the first committed step of the pathway. Efficient biosynthesis of L-tyrosine from feedstock such as glucose or glycerol is necessary to make biological production economically viable.
  • L- tyrosine is one of the three aromatic amino acids derived from the shikimate pathway.
  • the shikimate pathway is the central metabolic route leading to formation of tryptophan (TRP), tyrosine (TYR), and phenylalanine (PHE), this pathway exclusively exists in plants and microorganisms. It starts with the condensation of intermediates of glycolysis and pentosephosphate-pathway, phosphoenolpyruvate (PEP), and erythrose-4-phosphate (E4P), respectively, which enter the pathway through a series of condensation and redox reactions via 3- deoxy-d-arabino-heptulosonate-7-phosphate (DAEIP), 3-dehydroquinate (DHQ), 3- dehydroshikimate (DHS) to shikimate.
  • DAEIP 3- deoxy-d-arabino-heptulosonate-7-phosphate
  • DHQ 3-dehydroquinate
  • DHS 3- dehydroshikimate
  • metabolite chorismate is obtained via shikimate-3 -phosphate under ATP hydrolysis and introduction of a second PEP.
  • the initial step of the shikimate pathway is catalyzed by DAHP synthase isozymes and regulated through feedback-inhibition.
  • DAHP synthase isozymes exist (aroF, aroG, aroH), which are each feedback inhibited by one of the three aromatic amino acids (TYR, PHE, TRP), in contrast the two DAHP synthases of plants are not subject to feedback-inhibition.
  • the subsequent five steps are catalyzed by single enzymes.
  • coli host the tyrR gene can be disrupted, feedback- inhibition-resistant versions of the DAHP synthase (aroG) and chorismate mutase (tyrA) can be introduced, and/or rate-limiting enzymes, shikimate kinase (aroK or aroL) and quinate (QUIN)/shikimate dehydrogenase (ydiB) can be overexpressed. Further, the ppsA, aroG, and/or transketolase (tktA) can be overexpressed or exogenously introduced to enhance tyrosine production.
  • an engineered host cell for the production of flavonoids or anthocyanins further engineered to upregulate the endogenous biosynthesis of cofactor heme.
  • Cytochrome P450 CYPs
  • CYPs Cytochrome P450
  • heme as a cofactor. Improving heme supply can be an effective strategy to increase flavonoid biosynthesis.
  • 5-aminolevulinic acid ALA is the first committed precursor to the heme pathway. There exist two known alternate routes by which this committed intermediate is generated.
  • C4 pathway Shemin pathway
  • AAS ALA synthase
  • the C4 pathway is restricted to mammals, fungi and purple nonsulfur bacteria.
  • the second route is the C5 pathway, which involves three enzymatic reactions resulting in the biosynthesis of ALA from the five- carbon skeleton of glutamate.
  • the C5 pathway is active in most bacteria, all archaea and plants. Seven additional reactions, including assembly of eight ALA molecules into a cyclic tetrapyrrole, modification of the side chains, and incorporation of reduced iron into the molecule, are required to convert ALA to heme.
  • E E.
  • the three enzymes involved in ALA biosynthesis are glutamyl-tRNA synthetase (GltX), glutamyl-tRNA reductase (hemA), and glutamate- 1- semialdehyde aminotransferase (hemL).
  • GltX glutamyl-tRNA synthetase
  • hemA glutamyl-tRNA reductase
  • hemL glutamate- 1- semialdehyde aminotransferase
  • the engineered cells provided herein can be further engineered to express or overexpress hemA or its variants, and/or hemL to increase the heme precursor ALA production.
  • the nonlimiting examples of hemA gene that can be overexpressed include, without limitation, a mutated hemA gene from Salmonella typhimurium (EC: 1.1.1.70, SEQ ID NO: 21) and hemA with SEQ ID NOS: 91-93.
  • heterologous ALAS gene can be introduced to produce ALA via the C4 pathway.
  • heterologous ALAS that can be expressed in E. coli include ALAS of Rhodobacter capsulatus (SEQ ID:22), ALAS with SEQ ID NOS: 94-97, or an ALAS having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to any of these or other naturally-occurring ALAS.
  • one or more of the downstream genes E.
  • Cultures of cells engineered for the production of flavonoids or anthocyanins can in some embodiments include a medium that includes succinate and/or glycine, precursors of heme biosynthesis via the C4 pathway.
  • Engineered cells that produce a flavonoid can be engineered to include multiple pathways to enhance flavonoid production.
  • Those skilled in the art will recognize that the embodiments described herein can be combined in multiple ways. Examples of engineered cells having multiple genetic modifications are exemplary only and do not limit the scope of the invention.
  • a host cell as provided herein can be a prokaryotic cell or a eukaryotic cell.
  • Eukaryotic cells may be microbial eukaryotic cells, such as, for example, fungal cells or yeast cells.
  • Prokaryotic cells that can be engineered as provided herein include bacterial cells and cyanob acteri al cells.
  • Host can be selected based on their ability to take up and utilize particular carbon sources, nitrogen sources, or precursor molecules or may be engineered to take up and utilize molecules that may be added to the culture medium.
  • Nonlimiting examples of suitable microbial hosts for the bio-production of a flavonoid include, but are not limited to, any gram-negative organisms, more particularly a member of the family Enterobacteriaceae, such as A. coH, any gram-positive microorganism, for example Bacillus subtilis, Lactobacillus sp. or Lactococcus sp. a yeast, for example Saccharomyces cerevisiae, Pichia pastoris or Pichia stipitis; and other groups or microbial species.
  • any gram-negative organisms more particularly a member of the family Enterobacteriaceae, such as A. coH, any gram-positive microorganism, for example Bacillus subtilis, Lactobacillus sp. or Lactococcus sp. a yeast, for example Saccharomyces cerevisiae, Pichia pastoris or Pichia stipitis; and other groups or microbial species.
  • suitable microbial hosts for the bio-production of a flavonoid generally include, but are not limited to, members of the genera Clostridium, Zymomonas, Escherichia, Salmonella, Rhodococcus, Pseudomonas, Bacillus, Lactobacillus, Enterococcus, Alcaligenes, Klebsiella, Paenibacillus, Arthrobacter, Corynebacterium, Brevibacterium, Pichia, Candida, Hansenula, and Saccharomyces.
  • methods for producing a flavonoid or an anthocyanin that include incubating a culture of an engineered host cell as provided herein to produce a flavonoid or an anthocyanin.
  • the methods can further include recovering the flavonoid or anthocyanin from the culture medium, whole culture, or cells.
  • the culture comprises cells engineered for the production of flavonoids or anthocyanins in a culture medium.
  • the engineered cells can be prokaryotic or eukaryotic cells.
  • the culture medium includes at least one carbon source that is also an energy source.
  • Exemplary carbon sources include glucose, glycerol, sucrose, fructose, and xylose.
  • Such carbon sources may be purified or crude, including a biomass comprising glycerol, for example, crude glycerol produced as a byproduct of biodiesel production from com waste.
  • the culture medium can include one or more other carbon sources or compounds to increase precursor generation or cofactor supply such as, without limitation, tyrosine, phenylalanine, coumaric acid, acetate, malonate, succinate, glycine, bicarbonate, biotin, naringenin, 5-aminolevulinic acid, thiamine, pantothenate, alpha-ketoglutarate, and ascorbate.
  • tyrosine and coumaric acid are provided in the culture medium.
  • tyrosine, alpha- ketoglutarate, 5-aminolevulinic acid, and ascorbate are provided in the culture medium.
  • Culture conditions can include aerobic, microaerobic or any combination alternating aerobic/microaerobic growth conditions. Further, culture conditions can include shake flasks, fermentation, and other large scale culture procedures.
  • An exemplary growth condition for achieving a flavonoid product include aerobic or microaerobic fermentation conditions.
  • the culture conditions can be scaled up and grown continuously for manufacturing flavonoid product.
  • Exemplary growth procedures include, for example, fed-batch fermentation and batch separation.
  • the cells are grown in a bioreactor that is well controlled for growth temperature, oxygen, pH, carbon sources, and other compounds.
  • the desired temperature can be from, for example, 20-37 °C, depending on the growth characteristics of the production cells and desired conditions for the fermented products.
  • the pH of the bioreactor can be controlled to range from 5-8 or left uncontrolled in some cases.
  • the batch fermentation period can last in the range of several hours to several days, for examples, 8 to 96 hours.
  • the fermenter contents can be passed through a cell separation unit to remove cells and cell debris.
  • the cells can be lysed or disrupted enzymatically or chemically prior to or after separation of cells from the fermentation broth, as desired, in order to release additional product.
  • a method of producing a flavonoid or an anthocyanin comprises culturing an engineered cell disclosed herein in a culture medium to produce a flavonoid or an anthocyanin.
  • glycerol is used as a carbon feedstock.
  • the glycerol is crude glycerol.
  • the method comprises isolating naringenin, dihydrokaempferol, taxifolin, eriodictyol, leucocyanidin, leucodelphinidin, leucopelargonidin, (+)-catechin, cyanidin, delphinidin, pelargonidin, cyanidin glucoside, delphinidin glucoside or pelargonidin glucoside.
  • the naringenin, dihydrokaempferol, taxifolin, eriodictyol, leucocyanidin, leucodelphinidin, leucopelargonidin, (+)-catechin, cyanidin, delphinidin, pelargonidin, cyanidin glucoside, delphinidin glucoside or pelargonidin glucoside may be isolated at a purity of greater than 50%, greater than 55%, greater than 60%, greater than 65%, greater than 70%, greater than 75%, greater than 80%, greater than 85%, greater than 90%, or greater than 95%.
  • the naringenin, dihydrokaempferol, taxifolin, eriodictyol, leucocyanidin, leucodelphinidin, leucopelargonidin, (+)-catechin, cyanidin, delphinidin, pelargonidin, cyanidin glucoside, delphinidin glucoside or pelargonidin glucoside may be isolated at a purity of from about 50% to about 99%, e.g., from about 50% to about 95% (for example from: about 50%, 55%, 60%, 65%, 70%, 75%, 80% to about: 85%, 90%, 95%, 97.5%, 99% or 99.9%).
  • the naringenin, dihydrokaempferol, taxifolin, eriodictyol, leucocyanidin, leucodelphinidin, leucopelargonidin, (+)-catechin, cyanidin, delphinidin, pelargonidin, cyanidin glucoside, delphinidin glucoside or pelargonidin glucoside may be isolated at a purity of from about 50% to: about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 99%.
  • the naringenin, dihydrokaempferol, taxifolin, eriodictyol, leucocyanidin, leucodelphinidin, leucopelargonidin, (+)-catechin, cyanidin, delphinidin, pelargonidin, cyanidin glucoside, delphinidin glucoside or pelargonidin glucoside may be isolated at a purity of from about 55% to: about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 99%.
  • the naringenin, dihydrokaempferol, taxifolin, eriodictyol, leucocyanidin, leucodelphinidin, leucopelargonidin, (+)-catechin, cyanidin, delphinidin, pelargonidin, cyanidin glucoside, delphinidin glucoside or pelargonidin glucoside may be isolated at a purity of from about 60% to: about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 99%.
  • the naringenin, dihydrokaempferol, taxifolin, eriodictyol, leucocyanidin, leucodelphinidin, leucopelargonidin, (+)-catechin, cyanidin, delphinidin, pelargonidin, cyanidin glucoside, delphinidin glucoside or pelargonidin glucoside may be isolated at a purity of from about 65% to: about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 99%.
  • the naringenin, dihydrokaempferol, taxifolin, eriodictyol, leucocyanidin, leucodelphinidin, leucopelargonidin, (+)-catechin, cyanidin, delphinidin, pelargonidin, cyanidin glucoside, delphinidin glucoside or pelargonidin glucoside may be isolated at a purity of from about 70% to: about 75%, about 80%, about 85%, about 90%, about 95%, or about 99%.
  • the naringenin, dihydrokaempferol, taxifolin, eriodictyol, leucocyanidin, leucodelphinidin, leucopelargonidin, (+)-catechin, cyanidin, delphinidin, pelargonidin, cyanidin glucoside, delphinidin glucoside or pelargonidin glucoside may be isolated at a purity of from about 75% to: about 80%, about 85%, about 90%, about 95%, or about 99%, from about 80% to about 85%, about 90%, about 95%, or about 99%.
  • the naringenin, dihydrokaempferol, taxifolin, eriodictyol, leucocyanidin, leucodelphinidin, leucopelargonidin, (+)-catechin, cyanidin, delphinidin, pelargonidin, cyanidin glucoside, delphinidin glucoside or pelargonidin glucoside may be isolated at a purity of from about 85% to: about 90%, about 95%, or about 99%.
  • the naringenin, dihydrokaempferol, taxifolin, eriodictyol, leucocyanidin, leucodelphinidin, leucopelargonidin, (+)-catechin, cyanidin, delphinidin, pelargonidin, cyanidin glucoside, delphinidin glucoside or pelargonidin glucoside may be isolated at a purity of from about 90% to about 95%, or about 99%, or from about 95% to about 99% or greater.
  • E. coli cell derived from MG1655 was engineered to overexpress ACC (SEQ ID NO: 15), TAL (SEQ ID NO: 1), 4CL (SEQ ID NO: 4), CHS (SEQ ID NO: 5), and CHI (SEQ ID NO: 6) to produce naringenin when substrates tyrosine and coumaric acid were supplied in culture medium.
  • ACC was expressed on a medium-copy plasmid (15-20 copies) while TAL, 4CL, CHS, and CHI were expressed on the chromosome.
  • Cells of an OD 2.5 were cultured in a 48-well plate at 30 degree for 24 hours with a shaking speed of 600 RPM in minimal medium supplied with trace element, vitamins, 1 mM tyrosine,!
  • Variants of the foregoing host cell may be prepared using one or more of ACC (SEQ ID NO: 15), TAL (SEQ ID NO: 1), 4CL (SEQ ID NO: 4), CHS (SEQ ID NO: 5), and CHI (SEQ ID NO: 6) with one or more homologs of ACC (SEQ ID NO: 15), TAL (SEQ ID NO: 1), 4CL (SEQ ID NO: 4), CHS (SEQ ID NO: 5), or CHI (SEQ ID NO: 6), or combinations of two or more thereof, wherein the homologous enzymes have at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the referenced enzymes.
  • E. coli cell derived from MG1655 was engineered to overexpress F3H (SEQ ID NO: 7) on the chromosome to produce dihydrokaempferol when substrate naringenin was supplied in culture medium.
  • Cells of an OD 0.5-0.7 were cultured in a 24-well plate at 30 degree for 18 hours with a shaking speed of 200 RPM in minimal medium supplied with 2% glycerol, trace elements, 0.8 mM naringenin, 65 mg/L 5-aminoleuvinic acid, 0.1 mM ferrous sulfate, 0.1 mM 2- oxoglutarate, and 2.5 mM ascorbic acid.
  • Cell cultures were extracted with DMSO and centrifuged for 15 minutes. The supernatant was analyzed for dihydrokaempferol with HPLC. The cells produced 315 pM dihydrokaempferol.
  • Variants of the foregoing host cell may be prepared using a homolog of F3H (SEQ ID NO: 7), wherein the homologous enzyme has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the referenced enzyme.
  • the homologous enzyme has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the referenced enzyme.
  • An E. coli strain derived from MG1655 was engineered to overexpress F3H (SEQ ID NO: 7), F3’H (SEQ ID NO: 8), and CPR (SEQ ID NO: 9) to produce taxifolin when the substrate naringenin was supplied in culture medium.
  • F3H was overexpressed on the chromosome while F3’H and CPR were overexpressed on a medium-copy plasmid.
  • Cells of an OD 0.5-0.7 were cultured in a 24-well plate at 30 degree for 18 hours with a shaking speed of 200 RPM in minimal medium supplied with 2% glucose, 0.8 mM naringenin, 65 mg/L 5-aminoleuvinic acid, 0.1 mM ferrous sulfate, 0.1 mM 2-oxoglutarate, and 2.5 mM ascorbic acid.
  • Cell cultures were extracted with 50% DMSO and centrifuged for 15 minutes. The supernatant was analyzed for taxifolin with HPLC. The cells produced 500 pM taxifolin.
  • Variants of the foregoing host cell may be prepared using one or more of F3H (SEQ ID NO: 7), F3’H (SEQ ID NO: 8), and CPR (SEQ ID NO: 9) along with one or more homologs of F3H (SEQ ID NO: 7), F3’H (SEQ ID NO: 8), and CPR (SEQ ID NO: 9), or combinations of two or more thereof, wherein the homologous enzymes have at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the referenced enzymes.
  • An E. coli strain derived from MG1655 was engineered to overexpress ANS (SEQ ID NO: 13) and 3GT (SEQ ID NO: 14) to produce cyanidin-3-O-glucoside when the substrate (+)-catechin was supplied in culture medium.
  • ANS and 3GT were overexpressed on the chromosome.
  • Cells of an OD 0.5-0.7 were cultured in a 24-well plate at 30 °C for 18 hours with a shaking speed of 200 RPM in minimal medium supplied with 1.0% glucose, 2.0 mM (+)-catechin, 0.1 mM 2- oxoglutarate, and 2.5 mM ascorbic acid.
  • Cell cultures were acidified with 2M HCL and extracted with 100% Ethanol.
  • the supernatant was analyzed for cyanidin-3-O-glucoside by HPLC.
  • the cells produced 50 mg/L cyanidin-3-O-glucoside.
  • Variants of the foregoing host cell may be prepared using one or both of ANS (SEQ ID NO: 13) and 3GT (SEQ ID NO: 14) along with a homolog of ANS (SEQ ID NO: 13), 3GT (SEQ ID NO: 14), or both, wherein the homologous enzymes have at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the referenced enzymes.
  • An E. coli cell derived from MG1655 was engineered to overexpress ACC (SEQ ID NO: 15), TAL (SEQ ID NO: 1), 4CL (SEQ ID NO: 4), CHS (SEQ ID NO: 5), CHI (SEQ ID NO: 6), F3H (SEQ ID NO: 7), F3’H (SEQ ID NO: 8), CPR (SEQ ID NO: 9), and FLS (SEQ ID NO: 99) to produce quercetin when the substrate glycerol was supplied in culture medium.
  • ACC, TAL, 4CL, CHS, CHI, F3H, F3’H, CPR, and FLS were expressed on the chromosome.
  • Variants of the foregoing host cell may be prepared using one or more of ACC (SEQ ID NO: 15), TAL (SEQ ID NO: 1), 4CL (SEQ ID NO: 4), CHS (SEQ ID NO: 5), CHI (SEQ ID NO: 6) F3H (SEQ ID NO: 7), F3’H (SEQ ID NO: 8), CPR (SEQ ID NO: 9), and FLS (SEQ ID NO: 99) with one or more homologs of ACC (SEQ ID NO: 15), TAL (SEQ ID NO: 1), 4CL (SEQ ID NO: 4), CHS (SEQ ID NO: 5), CHI (SEQ ID NO: 6), F3H (SEQ ID NO: 7), F3’H (SEQ ID NO: 8), CPR (SEQ ID NO: 9), and FLS (SEQ ID NO: 99) or combinations of two or more thereof, wherein the homologous enzymes have at least 50%, at least 55%, at least 60%, at least 65%, at 15 least 70%, at
  • the HPLC method was as follows: An Agilent 1200 HPLC was fitted with an Ascentis C18 Column 150 mm X 4.6 mm, 3 pm, equipped with a R-18 (3 pm) guard column. The column was heated to 30 °C with the sample block being maintained at 25 °C. For each sample, 5 pL was injected and the product was eluted at a flow rate of 1.5 mL/min using 0.1% phosphoric acid in water (solvent A), acetonitrile (solvent B), and methanol (solvent C) with the following gradient:
  • the run time was a total of 15 minutes with naringenin, eriodictyol, dihydrokaempferol and taxifolin eluting at 12.50, 11.56, 10.20, and 8.85 minutes respectively.
  • a diode array detector (DAD) was used for the detection of the molecule of interest at 288 nm.
  • the reaction fluid was acidified with 13 M HC1 (1 :40 v/v), and extracted with 100% ethanol followed by mixing, centrifugation and filtration through a 0.45 pm filter.
  • the HPLC method was as follows: An Agilent 1200 HPLC was fitted with a LiChrospher RP-8 Column 250 mm X 4.6 mm, 5 pm, equipped with a LiChrospher 100 RP-8 (5 pm) LiChroCART 4-4 guard column. The column was heated to 25 °C with the sample block being maintained at 25 °C.
  • the example provides a combination of modifications to the E.coli host genome including deletions and overexpression of enzymes from other organisms to recapitulate the bioproduction pathway described in Figure 4.
  • the invention provides an engineered host cell that comprises one or more genetic modifications (as shown in FIG. 4 and described in this Example 8 and herein above in this application) that result in production of flavonoid or anthocyanin from a carbon source that can also be an energy source, through multiple chemical intermediates, by the engineered host cell Tn certain embodiments, the production of flavonoid or anthocyanin from a carbon source that can also be an energy source occurs through enzymatic transformation.
  • the carbon source is selected from a group consisting of: (i) glycerol, (ii) a sugar, (iii) an organic acid, (iv) an amino acid, and (v) any combination thereof.
  • the engineered host cell is cultured in a medium comprising molecules selected from a group consisting of: (i) glycerol, (ii) a sugar, (iii) an organic acid, (iv) an amino acid, and (v) any combination thereof.
  • one or more genetic modifications lead to increase in metabolic flux to flavonoid precursors or cofactors.
  • one or more of the genetic modifications cause reduction of formation of byproducts.
  • one or more genetic modifications are selected from: (i) one or more modifications for over-expressing one or more endogenous genes in the engineered host cells; (ii) one or more modifications for under-expressing one or more endogenous genes in the engineered host cells; (iii) one or more genetic modification is expressing one or more non-native genes in the engineered host cells; and (iv) a combination thereof.
  • the engineered host cell is cultured in a medium comprising molecules selected from: tyrosine, phenylalanine, malonate, p-coumarate, bicarbonate, acetate, pantothenate, biotin, thiamine, alpha-ketoglutarate, ascorbate, and 5- aminolevulinic acid.
  • the engineered host cell comprises at least one or more nucleic acid sequences selected from: (i) a nucleic acid sequences encoding tyrosine ammonia lyase activity; (ii) a nucleic acid sequences encoding phenylalanine ammonia lyase activity; (iii) cinnamate 4-hydroxylase; and (iv) any combination thereof.
  • nucleic acid sequences selected from: (i) a nucleic acid sequences encoding tyrosine ammonia lyase activity; (ii) a nucleic acid sequences encoding phenylalanine ammonia lyase activity; (iii) cinnamate 4-hydroxylase; and (iv) any combination thereof.
  • the engineered host cell comprises at least one or more peptides selected from: (i) chaicone isomerase; (ii) chaicone synthase; (iii) a fusion protein comprises a chaicone synthase and a chai cone isomerase; and (iv) any combination thereof.
  • the engineered host cell comprises an exogenous nucleic acid sequence selected from: (i) nucleic acid sequence encoding tyrosine ammonia lyase, wherein the encoded tyrosine ammonia lyase forms 4-coumaric acid using tyrosine as a substrate; (ii) nucleic acid sequence encoding phenylalanine ammonia lyase, wherein the encoded phenylalanine ammonia lyase converts phenylalanine to trans-cinnamic acid; (iii) nucleic acid sequence encoding cinnamate-4-hydroxylase, wherein the cinnamate-4-hydroxylase produces 4-coumaric acid from trans-cinnamic acid; (iv) nucleic acid sequence encoding flavanone-3 -hydroxylase, wherein flavanone-3
  • the engineered host cell comprises at least one or more nucleic acid sequences selected from: (i) nucleic acid sequences encoding tyrosine ammonia lyase activity; (ii) nucleic acid sequences encoding phenylalanine ammonia lyase activity; (iii) nucleic acid sequences encoding cinnamate 4-hydroxylase activity; (iv) nucleic acid sequences encoding 4-courmarate-CoA ligase (4CL) activity; and (v) any combination thereof.
  • nucleic acid sequences selected from: (i) nucleic acid sequences encoding tyrosine ammonia lyase activity; (ii) nucleic acid sequences encoding phenylalanine ammonia lyase activity; (iii) nucleic acid sequences encoding cinnamate 4-hydroxylase activity; (iv) nucleic acid sequences encoding 4-courmarate-CoA ligase
  • the engineered host cell comprises an exogenous nucleic acid sequence selected from the group consisting of: (i) nucleic acid sequence encoding tyrosine ammonia lyase, wherein the encoded tyrosine ammonia lyase forms 4-coumaric acid using tyrosine as a substrate; (ii) nucleic acid sequence encoding phenylalanine ammonia lyase, wherein the encoded phenylalanine ammonia lyase converts phenylalanine to trans- cinnamic acid; (iii) nucleic acid sequence encoding cinnamate-4-hydroxylase, wherein the cinnamate-4-hydroxylase produces 4-coumaric acid from trans-cinnamic acid; (iv) nucleic acid sequence encoding 4-courmarate-CoA ligase activity, wherein 4-courmarate-CoA ligase forms p- co
  • compositions as described above can be used in methods described herein for increasing the production of flavonoids or anthocyanins. Such methods involve providing any of the compositions described above to result in enzymatic transformation by the engineered host cell of glycerol through multiple chemical intermediates into a flavonoid or anthocyanin (such as shown in part or in whole in FIG. 4). Tn yet another aspect, it is envisioned that the pathway illustrated in FIG 4 can be carried out using a plurality of engineered host cells, as opposed to a single host cell as described above.
  • the plurality of the engineered host cells have one or more genetic modifications that result in enzymatic transformation by the engineered host cell of glycerol through multiple chemical intermediates into a flavonoid or anthocyanin (as shown in FIG. 4).
  • Step 1 conversion of pyruvate to acetate. poxB is deleted to reduce carbon loss and eliminate the byproducts.
  • Step 2 conversion of pyruvate to lactate. IdhA is deleted to reduce carbon loss and eliminate the byproducts.
  • Step 3 conversion of Acetyl-CoA to acetate. ackA-pta is deleted to reduce carbon loss and eliminate the byproducts.
  • Step 4 conversion of Acetyl-CoA to ethanol (EtOH). adhE is deleted to reduce carbon loss and eliminate the byproducts.
  • Step 5 conversion of acetyl-CoA to a substrate for the tricarboxylic acid cycle (TCA).
  • Step 6 conversion of acetyl-CoA to mal-CoA.
  • Heterologous ACC is expressed to increase the concentration of available mal-CoA.
  • Heterologous ACC may be obtained from fungal species.
  • embodiments of the invention provide an engineered host cell that comprises one or more genetic modifications to increase the production and/or availability of malonyl-CoA.
  • the engineered host cell comprises one or more genetic modifications selected from: (i) expression of acetyl-CoA carboxylase (ACC); and (ii) overexpression of acetyl- CoA carboxylase.
  • the engineered host cell is an E. coli.
  • the acetyl-CoA carboxylase is from: Mucor circinelloides, Rhodotorula torukrides, Lipomyces starkeyi, and Ustilago maydis, and orthologs of acetyl-CoA carboxylase having at least 50% amino acid identity to the acetyl-CoA carboxylase of these aforementioned species.
  • one or more genetic modification is deletion or attenuation of one or more fatty biosynthetic genes resulting in decrease in fatty acid biosynthesis.
  • one or more genetic modification is overexpression of acetyl-CoA synthase (ACS).
  • the acetyl-CoA synthase is selected from: acetyl-CoA synthase gene of E. coli, acetyl-CoA synthase gene of Salmonella typhimurium, and orthologs of acetyl-CoA synthase gene in any other species having at least 50% amino acid identity to the acetyl-CoA synthase gene of E. coli and Salmonella typhimurium .
  • one or more genetic modification is selected from a group consisting of: (i) overexpression a gene encoding pyruvate dehydrogenase (PDH), wherein the PDH may include E354K mutation; (ii) exogenous nucleic acid sequence encoding a malonyl-CoA synthetase; (iii) upregulation of endogenous pantothenate kinase (PanK), wherein PanK is not feedback inhibited by coenzyme A; (iv) exogenous nucleic acid sequence encoding a malonate transporter; and (v) any combinations thereof.
  • PDH pyruvate dehydrogenase
  • PanK pantothenate kinase
  • the malonyl-CoA synthetase is selected from of malonyl-CoA synthetases of Streptomyces coelicolor, Rhodopseudomonas palustris, or a malonyl-CoA synthetase having at least 50% identity to any of these or other naturally occurring malonyl-CoA synthetases.
  • one or more genetic modifications to decrease fatty acid biosynthesis is selected from: (i) mutation or downregulation of a gene encoding malonyl-CoA-ACP transacylase (E. coli fabD); (ii) modifications to the gene beta-ketoacyl-ACP synthase II (E.
  • the engineered host cell comprises peptides selected from: (i) acetyl-CoA carboxylase (ACC) having an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO: 15 or SEQ ID NO: 16; (ii) malonate CoA-transferase having an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO: 19; (iii) acetyl-CoA synthase (ACS) having an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO: 16; (iv) malonyl-CoA synthase having an amino acid sequence at least 80% identical SEQ ID NO: 77, SEQ ID NO: 78, or SEQ ID NO: 79; (v) malonate transporter having an amino acid sequence at least 80% identical to SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 80,
  • the invention provides a method of increasing the production of flavonoids comprising an engineered host cell, wherein the one or more engineered host cells comprise one or more genetic modifications to increase production and/or availability of malonyl- CoA.
  • the engineered host cell comprises one or more genetic modifications selected from: (i) expression of acetyl-CoA carboxylase (ACC); and (ii) overexpression of acetyl-CoA carboxylase.
  • the engineered host cell is an E. coli.
  • the acetyl-CoA carboxylase is from: Mucor circinelloides, Rhodotorula toruloides, Lipomyces starkeyi.
  • one or more genetic modification is deletion or attenuation of one or more fatty biosynthetic genes resulting in decrease in fatty acid biosynthesis.
  • one or more genetic modification is overexpression of acetyl-CoA synthase (ACS).
  • the acetyl-CoA synthase is selected from: acetyl-CoA synthase gene of E.
  • acetyl-CoA synthase gene of Salmonella typhimurium and orthologs of acetyl-CoA synthase gene in any other species having at least 50% amino acid identity to the acetyl-CoA synthase gene of E. coli and Salmonella typhimurium.
  • one or more genetic modification is selected from a group consisting of: (i) overexpression a gene encoding pyruvate dehydrogenase (PDH), wherein the PDH may include E354K mutation; (ii) exogenous nucleic acid sequence encoding a malonyl-CoA synthetase; (iii) upregulation of endogenous pantothenate kinase (PanK), wherein PanK is not feedback inhibited by coenzyme A; (iv) exogenous nucleic acid sequence encoding a malonate transporter; and (v) any combinations thereof.
  • PDH pyruvate dehydrogenase
  • PanK pantothenate kinase
  • the malonyl-CoA synthetase is selected from of malonyl-CoA synthetases of Streptomyces coelicolor, Rhodopseudomonas palustris, or a malonyl-CoA synthetase having at least 50% identity to any of these or other naturally occurring malonyl-CoA synthetases.
  • one or more genetic modifications to decrease fatty acid biosynthesis is selected from: (i) mutation or downregulation of a gene encoding malonyl-CoA- ACP transacylase (E. coli fabD); (ii) modifications to the gene beta-ketoacyl-ACP synthase II (E.
  • the engineered host cell comprises peptides selected from: (i) acetyl-CoA carboxylase (ACC) having an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO: 15 or SEQ ID NO: 16; (ii) malonate CoA-transferase having an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO: 19; (iii) acetyl-CoA synthase (ACS) having an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ TD NO: 16; (iv) malonyl-CoA synthase having an amino acid sequence at least 80% identical SEQ ID NO: 77, SEQ ID NO: 78, or SEQ ID NO: 79; (v) malonate transporter having an amino acid sequence at least 80% identical to SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ
  • Step 7 conversion of mal-CoA to malonyl-ACP (acyl carrier protein).
  • malonyl-coA-ACP transacylase (fabD) is downregulated to increase carbon flux.
  • Step 8 conversion of malonyl-ACP to 3-ketyoacyl-ACP.
  • beta-ketoacyl-ACP synthase II (fabF) is downregulated to increase carbon flux.
  • Step 9 conversion to mal-CoA to naringenin chaicone; conversion of coumaryl-CoA to naringenin chaicone.
  • a heterologous CHS is overexpressed.
  • Step 10 conversion to naringenin chaicone to naringenin.
  • a heterologous CHI is overexpressed.
  • Steps 11, 12, and 13 conversion of naringenin to dihydrokaempferol (DHK); conversion of naringenin to eriodictyol (EDL); conversion of eriodictyol (EDL) to dihydroquercetin (DHQ); conversion of (DHK) to dihydroquercetin (DHQ); conversion of dihydrokaempferol (DHK) to dihydromyricetin (DHM); conversion of pentahydroxyflayaone (PHF) to dihydromyricein (DHM).
  • Heterologous F3’5’H, F3H, F3H, and/or CPR are overexpressed. Accordingly, as shown in FIG.
  • the invention provides method of increasing the production of dihydroquercetin (DHQ), dihydromyricein (DHM), eriodictyol (EDL), and/or pentahydroxyflayaone (PHF) comprising an engineered host cell, wherein the engineered host cell comprises cytochrome P450 reductase (CPR) and at least one of flavanone-3’ -hydroxylase (F3’H) or flavonoid 3 ’,5 ’-hydroxylase (F3’5’H).
  • DHQ dihydroquercetin
  • DLM dihydromyricein
  • EDL eriodictyol
  • PPF pentahydroxyflayaone
  • the precursor for increase in production of dihydroquercetin (DHQ), dihydromyricein (DHM), eriodictyol (EDL), and/or pentahydroxyflavone (PHF) is naringenin and/or dihydrokaempferol (DHK).
  • the engineered host cell further comprises peptides selected from a group consisting of: (i) flavonoid 3 ’-hydroxylase (F3’H); (ii) cytochrome P450 reductase (CPR); and (iii) any combination thereof.
  • the engineered host cell produces eriodictyol or taxifolin.
  • the engineered host cell further comprises flavonoid 3’, 5’- hydroxylase (F3’5’H).
  • the engineered host cell produces pentahydroxyflavone or dihydromyricetin.
  • flavonoid 3 ’-hydroxylase (F3’H) is truncated to remove the N-terminal leader sequence.
  • cytochrome P450 reductase (CPR) is truncated to remove the N-terminal leader sequence.
  • flavonoid 3 ’-hydroxylase (F3’H) is fused with cytochrome P450 reductase (CPR).
  • flavonoid 3 ’,5 ’-hydroxylase (F3’5’H) is fused with cytochrome P450 reductase (CPR).
  • flavanone-3 -hydroxylase (F3H) has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 7.
  • flavanone-3 ’-hydroxylase (F3’H) has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 8.
  • cytochrome P450 reductase (CPR) has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 9.
  • flavonoid 3 ’,5 ’-hydroxylase (F3’5’H) has an amino acid sequence at least 80% identical to the polypeptides selected from a group consisting of: (i) SEQ ID NO. 10, (ii) SEQ ID NO. 56, and (iii) SEQ ID NO. 57.
  • the engineered host cell further comprises cytochrome bs.
  • cytochrome bs has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 98.
  • the invention provides method of increasing the production of dihydroquercetin (DHQ), dihydromyricein (DHM), eriodictyol (EDL), and/or pentahydroxyflayaone (PHF) comprising an engineered host cell, wherein the engineered host cell comprises cytochrome P450 reductase (CPR) and at least one of flavanone-3 ’-hydroxylase (F3’H) or flavonoid 3 ’,5 ’-hydroxylase (F3’5’H).
  • DHQ dihydroquercetin
  • DLM dihydromyricein
  • EDL eriodictyol
  • PPF pentahydroxyflayaone
  • the precursor for increase in production of dihydroquercetin (DHQ), dihydromyricein (DHM), eriodictyol (EDL), and/or pentahydroxyflavone (PHF) is naringenin and/or dihydrokaempferol (DHK).
  • the engineered host cell further comprises peptides selected from a group consisting of: (i) flavonoid 3 ’-hydroxylase (F3’H); (ii) cytochrome P450 reductase (CPR); and (iii) any combination thereof.
  • the engineered host cell produces eriodictyol or taxifolin.
  • the engineered host cell further comprises flavonoid 3’,5’- hydroxylase (F3’5’H).
  • the engineered host cell produces pentahydroxyflavone or dihydromyricetin.
  • flavonoid 3 ’-hydroxylase (F3’H) is truncated to remove the N-terminal leader sequence.
  • cytochrome P450 reductase (CPR) is truncated to remove the N-terminal leader sequence.
  • flavonoid 3 ’-hydroxylase (F3’H) is fused with cytochrome P450 reductase (CPR).
  • flavonoid 3 ’,5 ’-hydroxylase (F3’5’H) is fused with cytochrome P450 reductase (CPR).
  • flavanone-3 -hydroxylase (F3H) has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 7.
  • flavanone-3 ’-hydroxylase (F3’H) has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 8.
  • cytochrome P450 reductase (CPR) has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 9.
  • flavonoid 3 ’,5 ’-hydroxylase (F3’5’H) has an amino acid sequence at least 80% identical to the polypeptides selected from a group consisting of: (i) SEQ ID NO. 10, (ii) SEQ ID NO. 56, and (iii) SEQ ID NO. 57.
  • the engineered host cell further comprises cytochrome bs.
  • cytochrome bs has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO. 98.
  • Step 14 conversion of dihydroquercetin (DHQ) to leucocyanidin (LC); conversion of dihydrokaempferol (DHK) to leucopelargonidin (LP); and conversion of dihydromyricetin (DHM) to leucodelphinidin (LD). Heterologous DFR is overexpressed.
  • Step 15 conversion of leucocyanidin (LC) to catechin; conversion of leucodelphinidin (LD) to gallocatechin; and conversion of leucopelargonidin (LP) to afzelechin.
  • Heterologous LAR is overexpressed.
  • Step 16 conversion of catechin to cyanidin; conversion of leucocyanidin (LC) to catechin; conversion to leucodelphinidin (LD) to delphinidin; conversion of gallocatechin to delphinidin; conversion of leucopelargonidin (LP) to pelargonidin; or conversion of afzelechin to pelargonidin.
  • Heterologous ANS is overexpressed. Step 16 could be carried in vivo or in a cell-free medium. Accordingly, as shown in FIG.
  • the invention provides an engineered host cell, wherein the engineered host cell comprises one or more genetic modifications to increase transformation of leucocyanidin or catechin to cyani din-3 -glucoside (Cy3G).
  • one or more genetic modifications comprises overexpression of anthocyanin synthase.
  • the anthocyanin synthase is selected from: (i) anthocyanin synthase of Carica papaya (SEQ. ID NO: 13); (ii) the anthocyanin synthase has an amino acid sequence at least 80% identical to SEQ. ID NO: 66, SEQ. ID NO: 67, SEQ. ID NO: 68, or SEQ.
  • one or more engineered host cells comprises flavonoid-3-glucosyl transferase (3GT).
  • flavonoid-3-glucosyl transferase is selected from: (i) flavonoid-3 -glucosyl transferase in Vitis labrusca (SEQ. ID NO: 14); (ii) the flavonoid-3-glucosyl transferase has an amino acid sequence at least 80% identical to SEQ. ID NO: 70, SEQ. ID NO: 71, SEQ. ID NO: 72, or SEQ.
  • one or more genetic modifications comprises overexpression of anthocyanin synthase and flavonoid-3 -glucosyl transferase (3GT). In certain embodiments, one or more genetic modifications comprises overexpression of anthocyanin synthase and flavonoid-3 -glucosyl transferase (3GT). In certain embodiments, the one or more genetic modifications comprises overexpression of anthocyanin synthase and flavonoid-3-glucosyl transferase (3GT).
  • the one or more genetic modifications are selected from a group consisting of: (i) anthocyanin synthase, (ii) flavonoid-3 -glucosyl transferase (3GT), and (iii) a combination thereof.
  • the invention provides a method for increasing the production of flavonoids comprising an engineered host cell, wherein the engineered host cell comprises one or more genetic modifications to increase transformation of leucocyanidin or catechin to cyanidin-3- glucoside (Cy3G).
  • one or more genetic modifications comprises overexpression of anthocyanin synthase.
  • the anthocyanin synthase is selected from: (i) anthocyanin synthase of Carica papaya (SEQ. ID NO: 13); (ii) the anthocyanin synthase has an amino acid sequence at least 80% identical to SEQ. ID NO: 66, SEQ. ID NO: 67, SEQ.
  • one or more engineered host cells comprises flavonoid-3 -glucosyl transferase (3GT).
  • flavonoid-3 -glucosyl transferase is selected from: (i) flavonoid-3- glucosyl transferase in Vitis labrusca (SEQ. ID NO: 14); (ii) the flavonoid-3 -glucosyl transferase has an amino acid sequence at least 80% identical to SEQ. ID NO: 70, SEQ.
  • one or more genetic modifications comprises overexpression of anthocyanin synthase and flavonoid-3- glucosyl transferase (3GT). In certain embodiments, one or more genetic modifications comprises overexpression of anthocyanin synthase and flavonoid-3 -glucosyl transferase (3 GT). In certain embodiments, the one or more genetic modifications comprises overexpression of anthocyanin synthase and flavonoid-3 -glucosyl transferase (3GT).
  • the one or more genetic modifications are selected from a group consisting of: (i) anthocyanin synthase, (ii) flavonoid-3 -glucosyl transferase (3GT), and (iii) a combination thereof.
  • the invention provides a method of increasing the transformation of leucocyanidin or catechin to cyani din-3 -glucoside (Cy3G) comprising anthocyanin synthase, wherein the anthocyanin synthase is selected from: (i) anthocyanin synthase of Carica papaya (SEQ. ID NO: 13); (ii) the anthocyanin synthase has an amino acid sequence at least 80% identical to SEQ. ID NO: 66, SEQ. ID NO: 67, SEQ. ID NO: 68, or SEQ. ID NO: 69; (iii) the anthocyanin synthase has an amino acid sequence at least 80% identical to SEQ. ID NO: 13; and (iv) any combinations thereof.
  • anthocyanin synthase is selected from: (i) anthocyanin synthase of Carica papaya (SEQ. ID NO: 13); (ii) the anthocyanin synthase has
  • the invention provides a method of increasing the transformation of leucocyanidin or catechin to cyani din-3 -glucoside (Cy3G) comprising flavonoid-3-glucosyl transferase (3GT), wherein the flavonoid-3 -glucosyl transferase is selected from: (i) flavonoid-3- glucosyl transferase in Vitis labrusca (SEQ. ID NO: 14); (ii) the flavonoid-3 -glucosyl transferase has an amino acid sequence at least 80% identical to SEQ. ID NO: 70, SEQ. ID NO: 71, SEQ. ID NO: 72, or SEQ. ID NO: 73; and (iii) any combinations thereof.
  • Step 17 conversion of pelargonidin to callistephin; conversion of delphinidin to myrtillin (De3G); conversion of cyanidin to Cy3G. Heterologous 3 GT was overexpressed in E. coli. Step 17 could be carried in vivo or as a cell-free reaction.
  • Step 18 conversion of pyruvate to phosphoenolpyruvate (PEP).
  • ppsA is overexpressed to upregulate tyrosine.
  • Step 19 conversion of fructose-6-phosphate (F6P) to erythrose-4-phosphate (E4P).
  • F6P fructose-6-phosphate
  • E4P erythrose-4-phosphate
  • tktA is overexpressed to upregulate tyrosine.
  • Step 20 conversion of phosphoenolpyruvate (PEP) to deoxy-d-arabino-heptulosonate-7- phosphate (DAHP).
  • PEP phosphoenolpyruvate
  • DAHP deoxy-d-arabino-heptulosonate-7- phosphate
  • Step 21 conversion of deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ); conversion of erythrose-4-phosphate (E4P) to dehydroquinate (DHQ).
  • Step 22 conversion of dehydroquinate (DHQ) to 3 -dehydroshi ki mate (DHS).
  • Step 23 conversion of 3-dehydroshikimate (DHS) to shikimic acid (SHK). aroE is overexpressed to upregulate tyrosine.
  • DHS 3-dehydroshikimate
  • SHK shikimic acid
  • Step 24 conversion of shikimic acid (SHK) to shikimate-3 -phosphate (S3P).
  • Step 25 conversion of shikimate-3 -phosphate (S3P) to 5 -enolpyruvyl shikimate-3 - phosphate (EPSP).
  • Step 26 conversion of 5 -enolpyruvyl shikimate-3 -phosphate (EPSP) to chorismic acid (CHA).
  • ESP 5 -enolpyruvyl shikimate-3 -phosphate
  • CHA chorismic acid
  • Step 27 conversion of chorismic acid (CHA) to prephenate (PPA); conversion of prephenate (PPA) to 4-hydroxy-phenylpyruvate (HPP). tryA variant is overexpressed.
  • Step 28 conversion of 4-hydroxy-phenylpyruvate (HPP) to tyrosine; conversion of phenylpyruvate (POPP) to phenylalanine (Phe).
  • HPP 4-hydroxy-phenylpyruvate
  • POPP phenylpyruvate
  • Phe phenylalanine
  • embodiments of the invention provide an engineered host cell, wherein the engineered host cell comprises one or more genetic modifications to increase endogenous biosynthesis of tyrosine.
  • one or more genetic modifications comprises upregulation of 3-deoxy-D-arabino- heptulosonate synthase.
  • one or more genetic modifications are selected from: (i) upregulation of chorismate mutase; (ii) upregulation of prephenate dehydrogenase; (iii) overexpression of shikimate kinase; (iv) overexpression of shikimate dehydrogenase; and (v) any combinations thereof.
  • one or more genetic modifications comprises downregulation of L-phenylalanine biosynthetic pathway.
  • one or more genetic modifications comprises expression of exogenous phosphoenolpyruvate synthase (ppsA).
  • ppsA exogenous phosphoenolpyruvate synthase
  • tktA exogenous transketolase
  • the one or more genetic modifications comprises disruption of tyrR gene.
  • the invention provides a method of increasing endogenous biosynthesis of tyrosine comprising an engineered cell, wherein the engineered host cell comprises one or more genetic modifications to increase endogenous biosynthesis of tyrosine.
  • one or more genetic modifications comprises upregulation of 3-deoxy-D- arabino-heptulosonate synthase.
  • one or more genetic modifications are selected from: (i) upregulation of chorismate mutase; (ii) upregulation of prephenate dehydrogenase; (iii) overexpression of shikimate kinase; (iv) overexpression of shikimate dehydrogenase; and (v) any combinations thereof.
  • one or more genetic modifications comprises downregulation of L-phenylalanine biosynthetic pathway. In certain embodiments, one or more genetic modifications comprises expression of exogenous phosphoenolpyruvate synthase (ppsA). In certain embodiments, one or more genetic modifications comprises expression of exogenous transketolase (tktA). In certain embodiments, wherein the one or more genetic modifications comprises disruption of tyrR gene.
  • Step 29 conversion of tyrosine to coumaric acid. A heterologous TAL is overexpressed.
  • Step 30 conversion of courmaric acid to coumaryl-CoA. A heterologous 4CL is overexpressed.
  • Step 31 conversion of glutamate (Glut) to glutamyl-tRNA.
  • Step 32 conversion of glutamyl-tRNA to glutamate semialdehyde (GSA). hemA is overexpressed to upregulate ALA.
  • Step 33 conversion of glutamate semialdehyde (GSA) to 8 amino levulinic acid (ALA). hemL is overexpressed to upregulate ALA.
  • GSA glutamate semialdehyde
  • ALA 8 amino levulinic acid
  • Step 34 conversion of 8 amino levulinic acid (ALA) to porphobilinogen (PBG).
  • ALA 8 amino levulinic acid
  • PBG porphobilinogen
  • Step 35 conversion of porphobilinogen (PBG) to hydroxymethylbilane (HMB).
  • Step 36 conversion of hydroxymethylbilane (HMB) to uroporphyrinogen III (UPPIII).
  • Step 37 conversion of uroporphyrinogen III (UPPIII) to coproporphyrinogen III (CPPIII).
  • Step 38 conversion of coproporphyrinogen III (CPPIII) to protoporphyrinogen IX (PPPIX).
  • Step 39 conversion of protoporphyrinogen IX (PPPIX) to protoporphyrin IX, which is subsequently covered to heme.
  • PPPIX protoporphyrinogen IX
  • Step 40 conversion of prephenate (PPA) to phenylpyruvate (POPP).
  • Step 41 conversion of phenylalanine (Phe) to cinnamate. Heterologous PAL and/or TAL are overexpressed.
  • Step 42 conversion of cinnamate to coumaric acid. Heterologous C4H/CPR are overexpressed.
  • the invention provides engineered cells for increasing production of kaempferol, myricetin, and quercetin through transformation by one or more enzymes of a carbon source by the engineered host cell.
  • the enzymatic transformations described in Fig. 5 provide additional transformations to those provided in Fig. 4.
  • the enzymatic transformations in Fig. 4 are also discussed in U.S. Appl. No. 17/720,020, which is hereby incorporated by reference in its entirety.
  • the carbon source is selected from a group consisting of naringenin, dihydrokaempferol (DHK), dihydromyricetin (DHM), dihydroquercetin (DHQ), and eriodictyol (EDL).
  • one or more genetic modifications are at least one genetic modification selected from the group consisting of: (i) one or more modifications for over-expressing one or more endogenous genes in the engineered host cells; (ii) one or more modifications for under-expressing one or more endogenous genes in the engineered host cells; (iii) one or more genetic modification is expressing one or more nonnative genes in the engineered host cells; and (iv) a combination thereof.
  • the engineered host cell comprises at least one or more nucleic acid sequences selected from the group consisting of: (i) nucleic acid sequences encoding native or modified flavanone-3- hydroxylase (F3H) or a homolog thereof, (ii) nucleic acid sequences encoding native or modified flavanone-3’ -hydroxylase (F3’H) or a homolog thereof, (iii) nucleic acid sequences encoding native or modified flavonoid 3’,5’-hydroxylase (F3’5’H) or a homolog thereof, (iv) nucleic acid sequences encoding native or modified flavonol synthase (FLS) or a homolog thereof, and (v) any combinations thereof.
  • the engineered host cell is E. coll.
  • the production of flavonols through enzymatic transformation of a carbon source includes one or more chemical intermediates.
  • the flavonol is myricetin
  • the carbon source is dihydromyricetin (DHM)
  • the one or more enzyme is flavonol synthase (FLS).
  • the flavonol is myricetin
  • the carbon source is dihydrokaempferol (DHK)
  • the one or more enzymes are selected from a group consisting of (i) flavonoid 3’,5’- hydroxylase (F3’5’H), (ii) flavonol synthase (FLS), and (iii) any combination thereof.
  • flavonoid 3 ’,5 ’-hydroxylase (F3’5’H) has an amino acid sequence at least 80% identical to the polypeptides selected from a group consisting of: (i) SEQ ID NO. 10, (ii) SEQ ID NO. 56, and (iii) SEQ ID NO. 57.
  • the flavonol is kaempferol
  • the carbon source is dihydrokaempferol (DHK)
  • the one or more enzyme is flavonol synthase (FLS).
  • flavonol synthase (FLS) has an amino acid sequence at least 80% identical to any one of the polypeptides listed in SEQ ID NOS. 99-122.
  • the flavonol is quercetin
  • the carbon source is eriodictoyl (EDL)
  • the one or more enzyme is selected from a group consisting of (i) flavanone-3 -hydroxylase (F3H), (ii) flavonol synthase (FLS), and (iii) any combination thereof.
  • the flavanone-3 -hydroxylase (F3H) has an amino acid sequence at least 80% identical to the polypeptides selected from a group consisting of: (i) SEQ ID NO. 7, (ii) SEQ ID NO. 45, (iii) SEQ ID NO. 46, (iv) SEQ ID NO. 47, and (v) SEQ ID NO. 48.
  • DHQ dihydroquercetin
  • the flavonol is quercetin
  • the carbon source is dihydroquercetin (DHQ)
  • the one or more enzyme is flavonol synthase (FLS).
  • the flavonol is quercetin
  • the carbon source is kaempferol
  • the enzyme is flavanone-3 ’-hydroxylase (F3’H).
  • flavanone-3 ’ -hydroxylase (F3’H) has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO: 8.
  • the flavonol is kaempferol
  • the carbon source is dihydrokaempferol (DHK), naringenin, or any combination thereof
  • the one or more enzyme is selected from a group consisting of: (i) flavanone-3 ’-hydroxylase (F3’H), (ii) flavonol synthase (FLS), and (iii) any combination thereof.
  • the flavonol is quercetin
  • the carbon source is dihydroquerctin (DHQ), dihydrokaempferol, eriodictyol (EDL), naringenin, kaempferol, or any combination thereof
  • the one or more enzyme is selected from a group consisting of: (i) flavonol synthase (FLS), (ii) flavanone-3 ’-hydroxylase (F3’H), (iii) flavanone-3-hydroxylase (F3H), and (iv) any combination thereof.
  • the flavonol is myricetin
  • the carbon source is dihydromyricetin (DHM), dihydroquerctin (DHQ), dihydrokaempferol, eriodictyol (EDL), naringenin, quercetin, kaempferol, or any combination thereof
  • the one or more enzyme is selected from a group consisting of (i) flavonol synthase (FLS), (ii) flavanone-3 ’- hydroxylase (F3’H), (iii) flavanone-3-hydroxylase (F3H), (iv) flavonoid-3’ -5 ’-hydroxylase (F3’5’H), and (v) any combination thereof.
  • the invention provides a method of increasing the production of flavonols, comprising engineered host cells, wherein the engineered host cells comprise one or more genetic modifications to increase the production of flavonols through transformation by one or more enzymes of a carbon source by the engineered host cell.
  • the flavonol is selected from a group consisting of kaempferol, myricetin, and quercetin.
  • the carbon source is selected from a group consisting of naringenin, dihydrokaempferol (DHK), dihydromyricetin (DHM), dihydroquercetin (DHQ), and eriodictyol (EDL).
  • one or more genetic modifications are at least one genetic modification selected from the group consisting of: (i) one or more modifications for overexpressing one or more endogenous genes in the engineered host cells; (ii) one or more modifications for under-expressing one or more endogenous genes in the engineered host cells; (iii) one or more genetic modification is expressing one or more non-native genes in the engineered host cells; and (iv) a combination thereof.
  • the engineered host cell comprises at least one or more nucleic acid sequences selected from the group consisting of: (i) nucleic acid sequences encoding native or modified flavanone-3 -hydroxylase (F3H) or a homolog thereof, (ii) nucleic acid sequences encoding native or modified flavanone-3 ’-hydroxylase (F3’H) or a homolog thereof, (iii) nucleic acid sequences encoding native or modified flavonoid 3’,5’- hydroxylase (F3’5’H) or a homolog thereof, (iv) nucleic acid sequences encoding native or modified flavonol synthase (FLS) or a homolog thereof, and (v) any combinations thereof.
  • the engineered host cell is E. coli.
  • the production of flavonols through enzymatic transformation of a carbon source includes one or more chemical intermediates.
  • the flavonol is myricetin
  • the carbon source is dihydromyricetin (DHM)
  • the one or more enzyme is flavonol synthase (FLS).
  • the flavonol is myricetin
  • the carbon source is dihydrokaempferol (DHK)
  • the one or more enzymes are selected from a group consisting of (i) flavonoid 3 ’,5 ’-hydroxylase (F3’5’H), (ii) flavonol synthase (FLS), and (iii) any combination thereof.
  • flavonoid 3 ’,5 ’-hydroxylase (F3’5’H) has an amino acid sequence at least 80% identical to the polypeptides selected from a group consisting of: (i) SEQ ID NO. 10, (ii) SEQ ID NO. 56, and (iii) SEQ ID NO. 57.
  • the flavonol is kaempferol
  • the carbon source is dihydrokaempferol (DHK)
  • the one or more enzyme is flavonol synthase (FLS).
  • flavonoid synthase (FLS) has an amino acid sequence at least 80% identical to any one of the polypeptides selected from a group consisting of: SEQ ID NOS: 99-122.
  • the flavonol is quercetin
  • the carbon source is eriodictoyl (EDL)
  • the one or more enzyme is selected from a group consisting of (i) flavanone-3 -hydroxylase (F3H), (ii) flavonol synthase (FLS), and (iii) any combination thereof.
  • the flavanone-3- hydroxylase (F3H) has an amino acid sequence at least 80% identical to the polypeptides selected from a group consisting of: (i) SEQ ID NO. 7, (ii) SEQ ID NO. 45, (iii) SEQ ID NO. 46, (iv) SEQ ID NO. 47, and (v) SEQ ID NO. 48.
  • DHQ dihydroquercetin
  • the flavonol is quercetin
  • the carbon source is dihydroquercetin (DHQ)
  • the one or more enzyme is flavonol synthase (FLS).
  • the flavonol is quercetin
  • the carbon source is kaempferol
  • the enzyme is flavanone-3 ’-hydroxylase (F3’H).
  • flavanone-3’- hydroxylase (F3’H) has an amino acid sequence at least 80% identical to the polypeptide set forth in SEQ ID NO: 8.
  • the flavonol is kaempferol
  • the carbon source is dihydrokaempferol (DHK), naringenin, or any combination thereof
  • the one or more enzyme is selected from a group consisting of: (i) flavanone-3 ’-hydroxylase (F3’H), (ii) flavonol synthase (FLS), and (iii) any combination thereof.
  • the flavonol is quercetin
  • the carbon source is dihydroquerctin (DHQ), dihydrokaempferol, eriodictyol (EDL), naringenin, kaempferol, or any combination thereof
  • the one or more enzyme is selected from a group consisting of: (i) flavonol synthase (FLS), (ii) flavanone-3 ’-hydroxylase (F3’H), (iii) flavanone-3- hydroxylase (F3H), and (iv) any combination thereof.
  • the flavonol is myricetin
  • the carbon source is dihydromyricetin (DHM), dihydroquerctin (DHQ), dihydrokaempferol, eriodictyol (EDL), naringenin, quercetin, kaempferol, or any combination thereof
  • the one or more enzyme is selected from a group consisting of (i) flavonol synthase (FLS), (ii) flavanone-3 ’-hydroxylase (F3’H), (iii) flavanone-3 -hydroxylase (F3H), (iv) flavonoid- 3 ’-5 ’-hydroxylase (F3’5’H), and (v) any combination thereof.
  • Fig. 5 shows the enzymatic conversion of dihydromyricetin (DHM) to myricetin through flavonol synthase (FLS).
  • Fig. 5 also shows the enzymatic conversion of kaempferol and quercetin to myricetin through flavonoid 3’,5’-hydroxylase (F3’5’H).
  • Fig. 5 further shows the enzymatic conversion of dihydrokaempferol (DHK) to kaempferol through flavonol synthase (FLS).
  • DHK dihydrokaempferol
  • FLS flavonol synthase
  • FIG. 5 shows the enzymatic conversion of kaempferol to quercetin through flavanone-3’- hydroxylase (F3’H) and enzymatic conversion of dihydroquercetin (DHQ) to quercetin through flavonol synthase (FLS).
  • Fig. 6A and 6B show several enzymatic pathways for bioproduction of kaempferol, quercetin, and myricetin. As evident from Figs. 6A and 6B, the invention provides several pathways involving transformation of various precursors to kaempferol, quercetin, and myricetin.

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Abstract

L'invention concerne des procédés impliqués dans la production de flavonoïdes, d'anthocyanines et d'autres composés organiques. L'invention concerne des cellules modifiées pour la production de flavonoïdes, d'anthocyanines et d'autres composés organiques, les cellules modifiées comprenant une ou plusieurs modifications génétiques qui augmentent la production de flavonoïdes en augmentant le flux métabolique pour les précurseurs de flavonoïdes et/ou en réduisant les pertes de carbone résultant de la production de sous-produits.
PCT/US2023/072449 2022-08-18 2023-08-18 Bioproduction de flavonoïdes à l'aide d'hôtes de micro-organismes WO2024040211A2 (fr)

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