# Patent

## Title
Method for the production of resveratrol in a recombinant oleaginous microorganism

## Abstract

Methods to produce resveratrol and/or resveratrol glucoside in a recombinant oleaginous microorganism are provided. Expression of a resveratrol synthase gene in combination with genes involved in the phenylpropanoid pathway enabled recombinant microbial production of resveratrol in significant amounts.

## Background
This application claims the benefit of U.S. Provisional Application No. 60/682,651 filed May 19, 2005.


FIELD OF THE INVENTION
The invention is in the field of molecular biology and microbiology. Specifically, the invention relates to production of resveratrol in a recombinant oleaginous microorganism. More specifically, a method to produce resveratrol is exemplified in a recombinant oleaginous yeast (Yarrowia lipolytica). Expression of genes involved in the phenylpropanoid pathway along with a resveratrol synthase gene enables production of resveratrol at concentrations exceeding 0.01% dry cell weight.
BACKGROUND OF THE INVENTION
Resveratrol (trans-3,4′,5-trihydroxystilbene) and/or its corresponding glucoside (piceid) are stilbene compounds reported to have many beneficial health effects. Resveratrol is a potent antioxidant, decreasing low density lipid (LDL) oxidation, a factor associated with the development of atherosclerosis (Manna et al., J. Immunol., 164:6509-6519 (2000)). It is also reported to lower serum cholesterol levels and the incidents of heart disease. This effect as been attributed to a phenomenon known and the “French Paradox”. French citizens that regularly consume red wine tend to have lower incidents of heart disease and serum cholesterol levels even though this same group tends to consume foods high in both fat and cholesterol. There is also evidence that resveratrol may have other cardiovascular protective effects including modulation of vascular cell function, suppression of platelet aggregation, and reduction of myocardial damage during ischemia-reperfusion (Bradamante et al., Cardiovasc. Drug. Rev., 22(3):169-188 (2004)). Resveratrol is reported to have anti-inflammatory effects associated with the inhibition of the cyclooxygenase-1 (Cox-1), an enzyme associated with the conversion of arachidonic acid to pro-inflammatory mediators. It may also aid in the inhibition of carcinogenesis (Schultz, J., J Natl Cancer Inst., 96(20):1497-1498 (2004); Scifo et al., Oncol Res., 14(9):415-426 (2004); and Kundu, J. and Surh, Y., Mutat Res., 555(1-2):65-80 (2004)).
Resveratrol is classified as a phytoalexin due to its antifungal properties. It appears that some plants produce resveratrol as natural defense mechanism against fungal infections. For example, red grapes have been reported to produce resveratrol in response to fungal infections. Fungal cell wall components can stimulate local expression of the resveratrol synthase gene in grapes. The antifungal property of resveratrol has been applied to plants that do not naturally produce the compound. Transgenic plants modified to express the resveratrol synthase gene exhibit improved resistance to fungal infections. Furthermore, it has been reported that treatment of fresh fruits and vegetables with an effective amount of resveratrol will significantly increase shelf life (Gonzalez-Urena et al., J. Agric. Food Chem., 51:82-89 (2003)).
Use of resveratrol in commercial products (e.g., pharmaceuticals, personal care products, antifungal compositions, antioxidant compositions, dietary supplements, etc.) is limited due to the current market price of the compound. Methods to extract resveratrol from plant tissues such as red grape skins, peanuts or the root tissue of Polygonum cuspidatum are not economical. Means to produce resveratrol by chemical synthesis are difficult, inefficient, and expensive. There is a need for an efficient and cost effective method to synthesize resveratrol.
Resveratrol and/or resveratrol glucoside are naturally produced in a variety of herbaceous plants (Vitaceae, Myrtaceae, and Leguminosae). The resveratrol biosynthesis pathway is well known. In plants, a single type III polyketide synthase (resveratrol synthase; E.C. 2.3.1.95) catalyzes three consecutive Claisen condensations of the acetate unit from malonyl CoA with the phenylpropanoid compound p-coumaroyl CoA, which is succeeded by (1) an aldol reaction that forms the second aromatic ring, (2) cleavage of the thioester, and (3) decarboxylation to form resveratrol.
Industrial microbial production offers a possible means to economically produce commercial quantities of resveratrol. Microbial production requires functional expression of the resveratrol synthase gene in the presence of suitable quantities of malonyl CoA and p-coumaroyl CoA. Cost-effective microbial production generally requires host cells having the ability to produce both malonyl CoA and p-coumaroyl CoA in suitable quantities from a relatively inexpensive carbon substrate.
Many naturally occurring microorganisms, such as E. coli and Saccharomyces cerevisiae, produce malonyl CoA, albeit in relatively low quantities ranging from barely detectable levels up to about 30 μM (Davis et al., J. Biol. Chem., 275:28593-28598 (2000) and Subrahmanyam, S, and Cronan, J., J. Bacteriol., 180:45964602 (1998)). Since malonyl CoA is involved in fatty acid biosynthesis, a host cell capable of synthesizing significant amounts of oil (e.g., an oleaginous microorganism) may produce suitable quantities of malonyl CoA (or may exhibit the ability to accommodate high-flux malonyl CoA production).
Recombinant microbial production of resveratrol also requires the substrate p-coumaroyl CoA. This phenylpropanoid compound is ubiquitously produced in plants, but is found in relatively low quantities (if at all) in many microbial host cells. As such, the microbial host cell selected for resveratrol production should be engineered to produce p-coumaroyl CoA.
The enzyme coumaroyl CoA ligase (E.C. 6.2.1.12) catalyzes the conversion of para-hydroxycinnamic acid (pHCA) to p-coumaroyl CoA. In the past, coumaroyl CoA ligases were generally considered to only exist in plants, however a coumaroyl CoA ligase was recently reported in the filamentous bacterium Streptomyces coelicolor (Kaneko et al., J. Bacteriol., 185(1):20-27 (2003)). Recombinant microbial expression of coumaroyl CoA ligase has been reported (Becker et al., FEMS Yeast Research, 4(1):79-85 (2003)); Keneko et al., supra; Watts et al., Chembiochem, 5:500-507 (2004); and Hwang et al., Appl. Environ. Microbiol., 69(5):2699-2706 (2003)).
Recombinant biosynthesis of coumaroyl CoA requires a suitable source of pHCA. The source of pHCA may be supplied exogenously to the host cell or it may be produced within the host cell. Preferably, the host cell can be engineered to produce suitable levels of pHCA when grown on an inexpensive carbon source, such as glucose. Recombinant microbial host cells engineered to produce and/or accumulate phenylpropanoid-derived compounds (I.e., p-hydroxycinnamic acid) have been reported (U.S. Pat. Nos. 6,368,837, 6,521,748, U.S. application Ser. Nos. 10/138,970, 10/439,479, 10/621,826; and Schroder, J. and Schroder, G., Z. Naturforsch, 45:1-8 (1990)). Recombinant expression of a coumaroyl CoA ligase in cells engineered to produce para-hydroxycinnamic acid (pHCA) results in the production of p-coumaroyl CoA (p-coumaric acid).
Microbial expression of enzymes involved in the phenylpropanoid pathway to produce the flavanone narigenin is described by Watts et al. (supra) and Hwang et al. (supra). Specifically, Watts et al. describe the simultaneous expression of a phenylalanine ammonia lyase, a tyrosine ammonia lyase, a cinnamate 4-hydroxylase (C4H), a coumaroyl CoA ligase, and a chalcone synthase (E.C. 2.3.1.74) in E. coli to produce narigenin and phloretin up to 20.8 mg/L. However, Watts et al. were not able to actively express cinnamate-4-hydroxylase (C4H) in E. coli and had to supply exogenous p-coumaric acid or 3-(4-hydroxyphenyl)propionic acid to obtain significant concentrations of the desired products. Watts et al. do not describe recombinant microbial production of resveratrol.
Hwang et al. describe recombinant bacterial (E. coli) production of the flavanones pinocembrin and narigenin by simultaneously expressing phenylalanine ammonia lyase, coumaroyl CoA ligase, and a chalcone synthase (E.C. 2.3.1.74). The bacterial coumaroyl CoA ligase used by Hwang et al. was able to convert both cinnamic acid to cinnamoyl CoA and p-coumaric acid to p-coumaroyl CoA, resulting in the production of pinocembrin (from phenylalanine) and naringenin (from tyrosine) as the PAL used also exhibited tyrosine ammonia lyase activity, resulting in the production of pHCA. In the absence of exogenously supplementing the medium with excess L-phenylalanine and/or L-tyrosine, only small amounts of each flavanone are produced (<0.3 μg/L). Hwang et al. do not describe recombinant microbial production of resveratrol.
Becker et al. (supra) describe recombinant expression of several phenylpropanoid pathway genes in Saccharomyces cerevisiae FY23 for the production of resveratrol. Genes encoding a coumaroyl CoA ligase and a resveratrol synthase were recombinantly expressed in S. cerevisiae in a culture medium supplemented with pHCA, producing resveratrol in amounts up to 1.45 μg/L in the culture volume. Becker et al. report that experiments supplementing the culture medium with additional precursors necessary for resveratrol production do not produce significantly more resveratrol. Becker et al. do not illustrate a method to produce significant quantities of resveratrol in a recombinant host cell, including production of resveratrol from a commonly used (and economical) fermentable carbon source (e.g., glucose).
The problem to be solved is to provide a method for recombinant microbial production of resveratrol in significant amounts.
SUMMARY OF THE INVENTION
The stated problem has been solved by engineering an oleaginous microorganism (e.g., oleaginous yeast) to produce resveratrol. The recombinant host cell (Yarrowia lipolytica) was genetically modified to produce resveratrol by introducing several genes from the phenylpropanoid pathway in combination with a suitable resveratrol synthase gene. The recombinant host cell produced p-coumaroyl CoA through recombinant expression of at least one nucleic acid molecule encoding an enzyme providing phenylalanine/tyrosine ammonia lyase activity and at least one nucleic acid molecule encoding an enzyme providing coumaroyl CoA ligase. This, in combination with the oleaginous host cell's natural ability to produce a suitable amount of malonyl CoA enabled production of resveratrol in significant quantities (at least 0.03% dry cell weight).
Accordingly the invention provides a method for the production of resveratrol comprising:

    
    
        a) providing an oleaginous microbial host cell comprising:
        
            1) at least one nucleic acid molecule encoding an enzyme having resveratrol synthase activity;
            2) a source of malonyl CoA and coumaroyl CoA;
        
        
        b) growing the oleaginous microbial host of (a) under conditions where malonyl CoA and coumaroyl CoA are reacted to form a product selected from the group consisting of resveratrol and resveratrol glucoside; and
        c) optionally recovering the product of step (b).
    
    


In other embodiments the invention provides methods of the invention which additionally make use of nucleic acid molecules encoding various other enzymes and their corresponding substrates such as coumaroyl CoA ligase/p-hydroxycinnamic acid; tyrosine ammonium lyase/tyrosine; cinnamate-4-hydroxylase/cinnamic acid; phenylalanine ammonium lyase/phenylalanine.
In another embodiment the invention provides a recombinant oleaginous microorganism comprising at least one nucleic acid molecule encoding an enzyme having resveratrol synthase activity which produces a product selected from the group consisting of resveratrol and resveratrol glucoside. Optionally the recombinant oleaginous microorganism of the invention may also comprise at least one nucleic acid molecule encoding an enzyme having an activity selected from the group consisting of; coumaroyl CoA ligase, tyrosine ammonium lyase, cinnamate-4-hydroxylase and phenylalanine ammonium lyase.
In another embodiment the invention provides a composition selected from the group consisting of antioxidants, anti-inflammatory agents, antifungal/antimicrobial agents, cosmetics, cosmeceuticals, nutritional/dietary supplements, feed additives, and pharmacological agents comprising 0.1 to 99 wt % recombinant oleaginous microbial biomass having at least 0.01% (dry cell weight) resveratrol and/or resveratrol glucoside.



BRIEF DESCRIPTION OF THE FIGURES SEQUENCE DESCRIPTIONS
The invention can be more fully understood from the following detailed description, the figures, and the accompanying sequence descriptions that form a part of this application.
FIG. 1. The resveratrol biosynthetic pathway. Phenylalanine (Phe) or tyrosine (Tyr) can be converted into para-hydroxycinnamic acid (pHCA). Phenylalanine can be converted into tyrosine using an enzyme having phenylalanine hydroxylase activity. The tyrosine is then converted into pHCA using an enzyme have PAL/TAL activity. Optionally, phenylalanine can be converted into cinnamic acid (CA) using an enzyme having PAL/TAL activity. A cytochrome P450/P450 reductase system (cinnamate 4-hydroxylase activity) converts cinnamic acid to pHCA. The pHCA is converted into p-coumaroyl CoA by coumaroyl CoA ligase. Malonyl CoA (naturally produced in suitable quantities in the oleaginous. microorganisms) and p-coumaroyl CoA are converted into resveratrol by resveratrol synthase (stilbene synthase).
FIG. 2. Plasmid maps for pZFPALs, pZTRS, pZUF4C, pKO2UGP4C, and pKO2UT4C.
FIG. 3. Plasmid maps for plasmids used to create plasmid pZG4PR.
FIG. 4. Plasmid maps for plasmids used to create plasmid pZT4PR.
FIG. 5. Plasmid maps for plasmids for pZUF-Mod-1, pEXP-MOD-1, and pZGN.
FIG. 6. Mass analysis of pZGN transformed 20362U1 cells. Using negative ion electrospray mass spectroscopy, a peak at 10.51 min contains the molecular ion of 227 that matches the molecular weight of resveratrol (top). The peak at 7.84 min contains the molecular ion of 163 that matches the molecular weight of pHCA (bottom).
The following sequences conform with 37 C.F.R. 1.821-1.825 (“Requirements for Patent Applications Containing Nucleotide Sequences and/or Amino Acid Sequence Disclosures—the Sequence Rules”) and consistent with World Intellectual Property Organization (WIPO) Standard ST.25 (1998) and the sequence listing requirements of the European Patent Convention (EPC) and PCT (Rules 5.2 and 49.5(a-bis), and Section 208 and Annex C of the Administrative Instructions). The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. §1.822.
A Sequence Listing is provided herewith on Compact Disk. The contents of the Compact Disk containing the Sequence Listing are hereby incorporated by reference in compliance with 37 CFR 1.52(e). The Compact Discs are submitted in duplicate and are identical to one another. The discs are labeled “Copy 1—Sequence Listing” and “Copy 2 Sequence listing” The discs contain the following file: CL2033 US NA.ST25 having the following size: 379,000 bytes and which was created May 16, 2006.
SEQ ID NO:1 is the nucleotide sequence of the phenylalanine ammonia lyase coding sequence from Rhodotorula glutinis (herein also referred to as Rhodosporidium toruloides; GenBank® Accession No. X12702).
SEQ ID NO:2 is the deduced amino acid sequence of the phenylalanine ammonia lyase from Rhodotorula glutinis (GenBank® Accession No. X12702).
SEQ ID NO:3 is the nucleotide sequence of the phenylalanine ammonia lyase coding sequence from Rhodotorula glutinis (GenBank® Accession No. X12702) codon-optimized for expression in Yarrowia lipolytica. 
SEQ ID NO:4 is the nucleotide sequence of the coumaroyl CoA ligase coding sequence from Streptomyces coelicolor (GenBank® Accession No. AL939119).
SEQ ID NO:5 is the deduced amino acid sequence of the coumaroyl CoA ligase from Streptomyces coelicolor (GenBank® Accession No. AL939119).
SEQ ID NO:6 is the nucleotide sequence of the coumaroyl CoA ligase coding sequence from Streptomyces coelicolor (GenBank® Accession No. AL939119) codon-optimized for expression in Yarrowia lipolytica. 
SEQ ID NO:7 is the nucleotide sequence of a resveratrol synthase coding sequence isolated from Vitis sp.
SEQ ID NO:8 is the deduced amino acid sequence of a resveratrol synthase isolated from Vitis sp.
SEQ ID NO:9 is the nucleotide sequence of a resveratrol synthase coding sequence isolated from Vitis sp. codon-optimized for expression in Yarrowia lipolytica. 
SEQ ID NO:10 is the nucleotide sequence of the FBAIN promoter from Yarrowia lipolytica (U.S. Ser. No. 10/987,548).
SEQ ID NO:11 is the nucleotide sequence of primer pY331.
SEQ ID NO:12 is the nucleotide sequence of primer pY332.
SEQ ID NO:13 is the nucleotide sequence of primer TEF5′.
SEQ ID NO:14 is the nucleotide sequence of primer TEF3′.
SEQ ID NO:15 is the nucleotide sequence of the XPR2 transcriptional terminator.
SEQ ID NO:16 is the nucleotide sequence of primer XPR5′.
SEQ ID NO:17 is the nucleotide sequence of primer XPR3′.
SEQ ID NO:18 is the nucleotide sequence of 5′ end part of the codon-optimized coumaroyl CoA ligase gene.
SEQ ID NO:19 is the nucleotide sequence of primer YL539.
SEQ ID NO:20 is the nucleotide sequence of primer YL540.
SEQ ID NO:21 is the nucleotide sequence of the FBAIN promoter::4CL::Pex20 chimeric gene (GenBank® AF054613).
SEQ ID NO:22 is the nucleotide sequence of primer YL27.
SEQ ID NO:23 is the nucleotide sequence of primer YL28.
SEQ ID NO:24 is the nucleotide sequence of primer YL61.
SEQ ID NO:25 is the nucleotide sequence of primer YL62.
SEQ ID NO:26 is the nucleotide sequence of the Mortierella alpina Δ 5 desaturase gene (U.S. Pat. No. 6,075,183).
SEQ ID NO:27 is the nucleotide sequence of primer YL11.
SEQ ID NO:28 is the nucleotide sequence of primer YL12.
SEQ ID NO:29 is the nucleotide sequence of primer YL224.
SEQ ID NO:30 is the nucleotide sequence of primer YL225.
SEQ ID NO:31 is the nucleotide sequence of primer YL232.
SEQ ID NO:32 is the nucleotide sequence of primer YL233.
SEQ ID NO:33 is the nucleotide sequence of primer YL101.
SEQ ID NO:34 is the nucleotide sequence of primer YL102.
SEQ ID NO:35 is the nucleotide sequence of primer YL95.
SEQ ID NO:36 is the nucleotide sequence of primer YL266.
SEQ ID NO:37 is the nucleotide sequence of primer YL263.
SEQ ID NO:38 is the nucleotide sequence of primer YL265.
SEQ ID NO:39 is the nucleotide sequence of primer YL285.
SEQ ID NO:40 is the nucleotide sequence of primer YL286.
SEQ ID NO:41 is the nucleotide sequence of primer YL259.
SEQ ID NO:42 is the nucleotide sequence of primer YL260.
SEQ ID NO:43 is the nucleotide sequence of the Yarrowia GPAT promoter (U.S. Ser. No. 11/225,354; hereby incorporated by reference).
SEQ ID NO:44 is the nucleotide sequence of primer YL497
SEQ ID NO:45 is the nucleotide sequence of primer YL498
SEQ ID NO:46 is the nucleotide sequence of primer YL103
SEQ ID NO:47 is the nucleotide sequence of primer YL104
SEQ ID NO:48 is the nucleotide sequence of plasmid pKO2UFkF2.
SEQ ID NO:49 is the nucleotide sequence of 730-bp 5′ part of the Yarrowia Δ12 desaturase gene.
SEQ ID NO:50 is the nucleotide sequence of 573-bp 3′ part of the Yarrowia Δ12 desaturase gene.
SEQ ID NO:51 is the nucleotide sequence of a modified FBAIN promoter designated as the FBAINm promoter.
SEQ ID NO:52 is the nucleotide sequence of Δ12 desaturase gene (Δ12DS) from Fusarium moniliforme. 
SEQ ID NO:53 is the nucleotide sequence of the Pex20 terminator sequence of the Yarrowia Pex20 gene (GenBank® AF054613).
SEQ ID NO:54 is the nucleotide sequence of Yarrowia Ura3 gene (GenBank® AJ306421).
SEQ ID NO: 55 is the nucleotide sequence of plasmid pZG4PR.
SEQ ID NO: 56 is the nucleotide sequence of plasmid pZT4PR.
SEQ ID NO: 57 is the nucleotide sequence of plasmid pZUF-MOD-1.
SEQ ID NO: 58 is the nucleotide sequence of primer pZUF-mod1.
SEQ ID NO: 59 is the nucleotide sequence of primer pZUF-mod2.
SEQ ID NO: 60 is the nucleotide sequence of the multiple cloning site used in making pZUF-MOD-1.
SEQ ID NO: 61 is the nucleotide sequence of the EXP promoter from Yarrowia lipolytica gene YALI-CDS5725.1.
SEQ ID NO: 62 is the nucleotide sequence of primer EP-Promoter-F.
SEQ ID NO: 63 is the nucleotide sequence of primer EP-Promoter-R.
SEQ ID NO: 64 is the nucleotide sequence of plasmid pEXP-MOD-1.
SEQ ID NO: 65 is the nucleotide sequence of plasmid pZGN.
SEQ ID NO: 66 is the nucleotide sequence comprising a phenylalanine ammonia lyase coding sequence from Rhodotorula mucilaginosa. 
SEQ ID NO: 67 is the nucleotide sequence comprising a phenylalanine ammonia lyase coding sequence from Amanita muscaria. 
SEQ ID NO: 68 is the nucleotide sequence comprising a phenylalanine ammonia lyase coding sequence from Ustilago maydis. 
SEQ ID NO: 69 is the nucleotide sequence comprising a phenylalanine ammonia lyase coding sequence from Arabidopsis thaliana. 
SEQ ID NO: 70 is the nucleotide sequence comprising a phenylalanine ammonia lyase coding sequence from Rubus idaeus. 
SEQ ID NO: 71 is the nucleotide sequence comprising a phenylalanine ammonia lyase coding sequence from Medicago sativa. 
SEQ ID NO: 72 is the nucleotide sequence comprising a phenylalanine ammonia lyase coding sequence from Rehmannia glutinosa. 
SEQ ID NO: 73 is the nucleotide sequence comprising a phenylalanine ammonia lyase coding sequence from Lactuca savita. 
SEQ ID NO: 74 is the nucleotide sequence comprising a phenylalanine ammonia lyase coding sequence from Petroselinium crispum. 
SEQ ID NO: 75 is the nucleotide sequence comprising a phenylalanine ammonia lyase coding sequence from Prunus avium. 
SEQ ID NO: 76 is the nucleotide sequence comprising a phenylalanine ammonia lyase coding sequence from Lithospernum erythrorhizon. 
SEQ ID NO: 77 is the nucleotide sequence comprising a phenylalanine ammonia lyase coding sequence from Citrus limon. 
SEQ ID NO: 78 is the nucleotide sequence comprising a phenylalanine ammonia lyase coding sequence from Rhodotorula glutinis. 
SEQ ID NO: 79 is the nucleotide sequence comprising a phenylalanine ammonia lyase coding sequence from Rhodobacter sphaeroides. 
SEQ ID NO: 80 is the nucleotide sequence comprising a phenylalanine ammonia lyase coding sequence from Trichosporon cutaneum (U.S. Pat. No. 6,951,751).
SEQ ID NO: 81 is the nucleotide sequence comprising a coumaroyl CoA ligase coding sequence from Streptomyces coelicolor. 
SEQ ID NO: 82 is the nucleotide sequence comprising a coumaroyl CoA ligase coding sequence from Allium cepa. 
SEQ ID NO: 83 is the nucleotide sequence comprising a coumaroyl CoA ligase coding sequence from Streptomyces avermitilis. 
SEQ ID NO: 84 is the nucleotide sequence comprising a coumaroyl CoA ligase coding sequence from Populus tremuloides. 
SEQ ID NO: 85 is the nucleotide sequence comprising a coumaroyl CoA ligase coding sequence from Oryza sativa. 
SEQ ID NO: 86 is the nucleotide sequence comprising a coumaroyl CoA ligase coding sequence from Amorpha fruticosa. 
SEQ ID NO: 87 is the nucleotide sequence comprising a coumaroyl CoA ligase coding sequence from Populus tomentosa. 
SEQ ID NO: 88 is the nucleotide sequence comprising a coumaroyl CoA ligase coding sequence from Nicotiana tabacum. 
SEQ ID NO: 89 is the nucleotide sequence comprising a coumaroyl CoA ligase coding sequence from Pinus taeda. 
SEQ ID NO: 90 is the nucleotide sequence comprising a coumaroyl CoA ligase coding sequence from Glycine max. 
SEQ ID NO: 91 is the nucleotide sequence comprising a coumaroyl CoA ligase coding sequence from Arabidopsis thaliana. 
SEQ ID NO: 92 is the nucleotide sequence comprising a coumaroyl CoA ligase coding sequence from Arabidopsis thaliana. 
SEQ ID NO: 93 is the nucleotide sequence comprising a coumaroyl CoA ligase coding sequence from Rubus idaeus. 
SEQ ID NO: 94 is the nucleotide sequence comprising a coumaroyl CoA ligase coding sequence from Lithospermum erythrorhizon. 
SEQ ID NO: 95 is the nucleotide sequence comprising a coumaroyl CoA ligase coding sequence from. Zea mays. 
SEQ ID NO: 96 is the nucleotide sequence comprising a resveratrol synthase (stilbene synthase) coding sequence from Vitis sp.
SEQ ID NO: 97 is the nucleotide sequence comprising a resveratrol synthase (stilbene synthase) coding sequence from Vitis vinifera. 
SEQ ID NO: 98 is the nucleotide sequence comprising a resveratrol synthase (stilbene synthase) coding sequence from Vitis vinifera. 
SEQ ID NO: 99 is the nucleotide sequence comprising a resveratrol synthase (stilbene synthase) coding sequence from Arachis hypogaea. 
SEQ ID NO: 100 is the nucleotide sequence comprising a resveratrol synthase (stilbene synthase) coding sequence from Cissus rhombifolia. 
SEQ ID NO: 101 is the nucleotide sequence comprising a resveratrol synthase (stilbene synthase) coding sequence from Parthenocissus henryana. 
SEQ ID NO: 102 is the nucleotide sequence comprising a resveratrol synthase (stilbene synthase) coding sequence from Parthenocissus quinquefolia. 
SEQ ID NO: 103 is the nucleotide sequence comprising a resveratrol synthase (stilbene synthase) coding sequence from Vitis riparia. 
SEQ ID NO: 104 is the nucleotide sequence comprising a resveratrol synthase (stilbene synthase) coding sequence from Vitis labrusca. 
SEQ ID NO: 105 is the nucleotide sequence comprising a resveratrol synthase (stilbene synthase) coding sequence from Vitis sp. cv. “Norton”.
SEQ ID NO: 106 is the nucleotide sequence comprising a cinnamate 4-hydroxylase coding sequence from Cicer arietinum. 
SEQ ID NO: 107 is the nucleotide sequence comprising a cinnamate 4-hydroxylase coding sequence from Populus tremuloides. 
SEQ ID NO: 108 is the nucleotide sequence comprising a cinnamate 4-hydroxylase coding sequence from Oryza sativa. 
SEQ ID NO: 109 is the nucleotide sequence comprising a cinnamate 4-hydroxylase coding sequence from Camellia sinensis. 
SEQ ID NO: 110 is the nucleotide sequence comprising a cinnamate 4-hydroxylase coding sequence from Vigna radiata. 
SEQ ID NO: 111 is the nucleotide sequence comprising a cinnamate 4-hydroxylase coding sequence from Helianthus tuberosus. 
SEQ ID NO: 112 is the nucleotide sequence comprising a cinnamate 4-hydroxylase coding sequence from Camptotheca acuminata. 
SEQ ID NO: 113 is the nucleotide sequence comprising a cinnamate 4-hydroxylase coding sequence from Arabidopsis thaliana. 
SEQ ID NO: 114 is the nucleotide sequence comprising a cinnamate 4-hydroxylase coding sequence from Ruta graveolens. 
SEQ ID NO: 115 is the nucleotide sequence comprising a cinnamate 4-hydroxylase coding sequence from Glycine max. 
SEQ ID NO: 116 is the nucleotide sequence comprising a cinnamate 4-hydroxylase coding sequence from Citrus sinensis. 
SEQ ID NO: 117 is the nucleotide sequence comprising a phenylalanine hydroxylase coding sequence from Chromobacterium violaceum. 
SEQ ID NO: 118 is the nucleotide sequence comprising a phenylalanine hydroxylase coding sequence from Pseudomonas aeruginosa. 
SEQ ID NO: 119 is the nucleotide sequence comprising a phenylalanine hydroxylase coding sequence from Geodia cydonium. 
SEQ ID NO: 120 is the nucleotide sequence comprising a phenylalanine hydroxylase coding sequence from Xanthomonas axonopodis. 
SEQ ID NO: 121 is the nucleotide sequence comprising a phenylalanine hydroxylase coding sequence from Xanthomonas campestris. 
SEQ ID NO: 122 is the nucleotide sequence comprising a phenylalanine hydroxylase coding sequence from Nocardia farcinica. 
SEQ ID NO: 123 is the nucleotide sequence comprising a phenylalanine hydroxylase coding sequence from Gallus gallus. 
SEQ ID NO: 124 is the nucleotide sequence comprising a acetyl CoA carboxylase coding sequence from Saccharomyces cerevisiae. 
SEQ ID NO: 125 is the nucleotide sequence comprising a acetyl CoA carboxylase coding sequence from Saccharomyces cerevisiae. 
SEQ ID NO: 126 is the nucleotide sequence comprising a acetyl CoA carboxylase coding sequence from Kluyveromyces lactis. 
SEQ ID NO: 127 is the nucleotide sequence comprising a acetyl CoA carboxylase coding sequence from Debaryomyces hansenii. 
SEQ ID NO: 128 is the nucleotide sequence comprising a acetyl CoA carboxylase coding sequence from Yarrowia lipolytica. 
SEQ ID NO: 129 is the nucleotide sequence comprising a acetyl CoA carboxylase coding sequence from Aspergillus nidulans. 
SEQ ID NO: 130 is the nucleotide sequence comprising a acetyl CoA carboxylase coding sequence from Schizosaccharomyces pombe. 
SEQ ID NO: 131 is the nucleotide sequence comprising a acetyl CoA carboxylase coding sequence from Ustilago maydis. 
SEQ ID NO: 132 is the nucleotide sequence comprising a acetyl CoA carboxylase coding sequence from Gallus gallus. 
SEQ ID NO: 133 is the nucleotide sequence comprising a β-glucosidase coding sequence from Mesoplasma florum. 
SEQ ID NO: 134 is the nucleotide sequence comprising β-glucosidase coding sequence from Oryza sativa. 
SEQ ID NO: 135 is the nucleotide sequence comprising a β-glucosidase coding sequence from Pseudomonas putida. 
SEQ ID NO: 136 is the nucleotide sequence comprising β-glucosidase coding sequence from Pseudomonas syringae. 
SEQ ID NO: 137 is the nucleotide sequence comprising a β-glucosidase coding sequence from Streptomyces coelicolor. 
SEQ ID NO: 138 is the nucleotide sequence comprising β-glucosidase coding sequence from Caulobacter crescentus. 
SEQ ID NO: 139 is the nucleotide sequence comprising a β-glucosidase coding sequence from Candida wickerhamii. 



DETAILED DESCRIPTION OF THE INVENTION
The present invention describe a method for microbial production of resveratrol and/or resveratrol glucoside (piceid) in a recombinant oleaginous microorganism. In another embodiment, the present invention provides microorganisms genetically modified to produce resveratrol and/or resveratrol glucoside. Both compounds can be isolated and purified for a variety of commercial applications. In one aspect, resveratrol can be obtained from resveratrol glucoside by removing the glucose moiety using chemical or enzymatic hydrolysis to release the aglycone (i.e., non-glycosylated resveratrol).
In one aspect, the recombinant host cell is oleaginous microorganism that produces suitable amounts of malonyl CoA. In a preferred aspect, the recombinant host cell is oleaginous yeast that produces suitable amounts of malonyl CoA. In another preferred aspect, the recombinant oleaginous yeast is engineered to product both resveratrol/resveratrol glucoside and at least one ω-3 polyunsaturated fatty acid. In a further aspect, the recombinant host cell is Yarrowia lipolytica. 
In the following disclosure, a number of terms and abbreviations are used. The following definitions are provided.
As used herein, the term “about” modifying the quantity of an ingredient or reactant of the invention employed refers to variation in the numerical quantity that can occur, for example, through typical measuring and liquid handling procedures used for making concentrates or use solutions in the real world; through inadvertent error in these procedures; through differences in the manufacture, source, or purity of the ingredients employed to make the compositions or carry out the methods; and the like. The term “about” also encompasses amounts that differ due to different equilibrium conditions for a composition resulting from a particular initial mixture. Whether or not modified by the term “about”, the claims include equivalents to the quantities. In one embodiment, the term “about” means within 10% of the reported numerical value, preferably with 5% of the reported numerical value.
As used herein the term “invention” or “present invention” is not meant to be limiting to any specific aspect or embodiment of the invention but shall be read to refer to all embodiments of the invention as described in the claims and the specification.
As used herein, the term “resveratrol” is used to describe the compound 3,4′,5-trihydroxystilbene as shown below.




As used herein, the term “comprising” means the presence of the stated features, integers, steps, or components as referred to in the claims, but that it does not preclude the presence or addition of one or more other features, integers, steps, components or groups thereof.
As used herein, the terms “para-hydroxycinnamic acid”, “p-hydroxycinnamic acid”, and “4-hydroxycinnamic acid” are used interchangeably and are abbreviated as “pHCA”.
As used herein, “resveratrol glucoside” and “piceid” are used interchangeably to describe resveratrol 3-O-β-D-glucoside. In many eukaryotic host cells, compounds produced during secondary metabolism are glycosylated using an endogenous glycosyl transferase. As used herein, “resveratrol glycosylating activity” and “endogenous resveratrol glycosylating activity” will be used to describe the endogenous enzymatic activity observed in many host cells that adds at least one sugar moiety to resveratrol. In one aspect, the endogenous resveratrol glycosylating activity adds a single glucose moiety to resveratrol. In another aspect, the glucose moiety can be chemically hydrolyzed and/or enzymatically hydrolyzed to produce the aglycone (free resveratrol).
As used herein, the terms “trans-cinnamic acid”, “cinnamic acid”, and “trans-cinnamate” are used interchangeably.
As used herein, the terms “phenylalanine” and “L-phenylalanine” are used interchangeably.
As used herein, the terms “tyrosine” and “L-tyrosine” are used interchangeably.
As used herein, the terms “stilbene synthase” and “resveratrol synthase” are used interchangeably arid are abbreviated as RS. Resveratrol synthase is a type III polyketide synthase (E. C. 2.3.1.95) that condenses one molecule of p-coumaroyl CoA with 3 molecules of malonyl CoA to produce 1 molecule of resveratrol.
As used herein, the terms “para-coumaroyl CoA” and “p-coumaroyl CoA” are used interchangeably.
As used herein, the term “coumaroyl CoA ligase” is used to described an enzyme that converts pHCA into p-coumaroyl CoA (E.C. 6.2.1.12).
As used herein, the term “phenylalanine hydroxylase” is abbreviated PAH. The term “PAH” activity” or “PAH enzyme” refers to an enzyme that hydroxylates phenylalanine to produce tyrosine (E.C. 1.14.16.1).
As used herein, the term “cinnamate 4-hydroxylase” is used to describe one or more enzymes having an enzyme activity (E.C. 1.14.13.11) that converts trans-cinnamic acid to p-hydroxycinnamic acid and is abbreviated C4H.
As used herein, the term “tyrosine ammonia lyase” or “TAL enzyme” is abbreviated TAL (EC 4.3.1.). As used herein, the term “TAL activity” refers to the ability of a protein to catalyze the direct conversion of tyrosine to p-hydroxycinnamic acid (pHCA). “taf” represents a gene that encodes an enzyme with TAL activity. TAL enzymes typically have some PAL activity.
As used herein, the term “phenylalanine ammonia-lyase” or “PAL enzyme” is abbreviated PAL (EC 4.3.1.5). As used herein, the term “PAL activity” refers to the ability of a protein to catalyze the conversion of phenylalanine to trans-cinnamic acid. “pal” represents a gene that encodes an enzyme with PAL activity. The phenylalanine ammonia lyase used in the present examples has significant TAL activity. As used herein, the term “phenylalanine ammonia lyase” will be also be referred to as a “phenylalanine/tyrosine ammonia lyase”, “phenylalanine/tyrosine enzyme”, “an enzyme having phenylalanine/tyrosine ammonia lyase activity”, and “PAL/TAL enzyme”. In one aspect, the PAL/TAL enzyme has a ratio of TAL specific activity:PAL specific activity ranging from 0.001 to 1000, preferably 0.1 to 100.
As used herein, “phenylalanine/tyrosine ammonia lyase activity” and “PAL/TAL activity” refers to an enzyme that has both PAL activity and TAL activity, converting phenylalanine to trans-cinnamic acid and tyrosine to p-hydroxycinnamic acid.
As used herein, the term “modified PAL/TAL” or “mutant PAL/TAL” refers to a protein which has been derived from a wild type PAL enzyme which has greater TAL activity than PAL activity (U.S. Pat. No. 6,368,837; hereby incorporated by reference). As such, a modified PAL/TAL protein has a greater substrate specificity (or at least greatly improved in comparison to the non-modified enzyme from which it is derived) for tyrosine than for phenylalanine.
As used herein, the terms “significant amount” and “significant amount of resveratrol” are used to describe the amount of resveratrol and/or resveratrol glucoside produced using the present method. In one aspect, a significant amount produced by the present method is a resveratrol titer of at least 0.5 mg/L within the culture volume, preferably at least 1 mg/L within the culture volume, and most preferably at least 1.4 mg/L within the culture volume. In one aspect, “significant amount” is defined as at least 0.01% dry cell weight (dcw), preferably at least 0.03% (dcw) and more preferably at least 0.1% (dcw), and most preferably at least 1.0% (dcw).
As used herein, the terms “suitable amount” and “suitable substrate amount” are used to describe an amount of available substrate that enables recombinant microbial production of resveratrol and/or resveratrol glucoside at concentrations exceeding 0.01% (dcw) within the culture volume using the present method. In another aspect, the suitable amount enables production of resveratrol and/or resveratrol glucoside at concentrations exceeding 0.03% (dcw) within the culture volume using the present method. In yet another aspect, the suitable amount enables production of resveratrol and/or resveratrol glucoside at concentrations of about 0.1% (dcw) or more within the culture volume. In still yet another aspect, the suitable amount enable production of resveratrol and/or resveratrol glucoside at concentrations of at least 1.0% (dcw). In one aspect, the recombinant microbial host cell can produce suitable amounts of the necessary substrates for resveratrol production from the fermentable carbon source supplied to the fermentation media. In another aspect, one or more substrates useful for the biosynthesis of resveratrol may be exogenously supplemented to the fermentation media to enable production resveratrol and/or resveratrol glucoside in significant quantities. In yet another aspect, the exogenously supplied substrate is selected from the group consisting of acetate, malonate or malonic acid, phenylalanine, tyrosine, p-hydroxycinnamic acid, and trans-cinnamic acid. In a preferred aspect, the exogenously supplied substrate is p-hydroxycinnamic acid.
As used herein, the terms “P450/P-450 reductase system” and “cytochrome P450/P450 reductase system” refers to a protein system responsible for the catalytic conversion of trans-cinnamic acid to pHCA. The P450/P450 reductase system is one of several enzymes or enzyme systems known in the art that performs a cinnamate 4-hydroxylase function. As used herein, the term “cinnamate 4-hydroxylase” will refer to the general enzymatic activity that results in the conversion of trans-cinnamic acid to pHCA, whereas the term “P450/P450 reductase system” will refer to a specific binary protein system that has cinnamate 4-hydroxylase activity.
As used herein, the term “aromatic amino acid biosynthesis” means the biological processes and enzymatic pathways internal to a cell needed for the production of an aromatic amino acid (i.e., L-phenylalanine and/or L-tyrosine).
As used herein, the term “oleaginous” or “oleaginous microorganism” refers to those microorganisms that tend to store their energy source in the form of lipid (Weete, In: Fungal Lipid Biochemistry, 2nd Ed., Plenum, 1980). In one aspect, oleaginous microorganisms are those microorganisms that store lipids/oils in amounts greater than 20% of their dry cell weight. Many species of oleaginous microalgae, oleaginous diatoms and oleaginous fungi have the ability to store lipids to >20% of the dry cell weight. Examples of oleaginous microorganisms include those belonging to the genera Mortierella, Conidiobolus, Pythium, Phytophathora, Penicillium, Porphyridium, Coidosporium, Mucor, Fusarium, Aspergillus, Rhodotorula, and Entomophthora. Within the genus Porphyridium, of particular interest is P. cruentum. Within the genus Mortierella, of particular interest are M. elongata, M. exigua, M. hygrophila, M. ramanniana var. angulispora, and M. alpina. Within the genus Mucor, of particular interest are M. circinelloides and M. javanicus. 
As used herein, the term “oleaginous yeast” refers to those microorganisms classified as yeasts (and modified versions thereof) that can accumulate at least 20% of their dry cell weight as oil. Genera typically identified as oleaginous yeast include, but are not limited to: Yarrowia, Candida, Rhodotorula, Rhodosporidium, Cryptococcus, Trichosporon and Lipomyces. More specifically, illustrative oil-synthesizing yeasts include: Rhodosporidium toruloides, Liopmyces starkeyii, L. lipoferus, Candida revkaufl, C. pulcherrima, C. tropicalis, C. utilis, Trichosporon pullans, T. cutaneum, Rhodotorula glutinus, R. graminis, and Yarrowia lipolytica (formerly classified as Candida lipolytica). In another aspect, the oleaginous yeast is Yarrowia lipolytica; and, in a further aspect, the Y. lipolytica strains are designated as ATCC #20362, ATCC #8862, ATCC #18944, ATCC #76982 and/or LGAM S(7)1 (Papanikolaou S., and Aggelis G., Bioresour. Technol., 82(1):43-9 (2002)). In a preferred aspect, the oleaginous yeast is capable of producing at least one ω-3 polyunsaturated fatty acid (PUFA). In a further preferred aspect, the oleaginous yeast is a Yarrowia lipolytica strain genetically modified to produce at least one ω-3 PUFA select from the group consisting of eiscosatetraenoic acid (ETA), eicosapentaenoic acid (EPA), docasapentaenoic acid (DPA), and docasahexaenoic acid (DHA).
As used herein, the term “fermentable carbon substrate” refers to a carbon source capable of being metabolized by host organisms of the present invention and particularly carbon sources selected from the group consisting of monosaccharides (e.g., glucose, fructose), disaccharides (e.g., lactose, sucrose), oligosaccharides, polysaccharides (e.g., starch, cellulose or mixtures thereof), sugar alcohols (e.g., glycerol) or mixtures from renewable feedstocks (e.g., cheese whey permeate, cornsteep liquor, sugar beet molasses, barley malt). Additionally, carbon sources may include alkanes, fatty acids, esters of fatty acids, monoglycerides, diglycerides, triglycerides, phospholipids and various commercial sources of fatty acids including vegetable oils (e.g., soybean oil) and animal fats. Additionally, the carbon source may include one-carbon sources (e.g., carbon dioxide, methanol, formaldehyde, formate, carbon-containing amines) for which metabolic conversion into key biochemical intermediates has been demonstrated. Hence, it is contemplated that the source of carbon utilized in the present invention may encompass a wide variety of carbon-containing sources and will only be limited by the choice of the host organism. Although all of the above mentioned carbon sources and mixtures thereof are expected to be suitable in the present invention, preferred carbon sources are sugars and/or fatty acids. Most preferred is glucose and/or fatty acids containing between 10-22 carbons and mixtures thereof.
As used herein, the term “complementary” is used to describe the relationship between nucleotide bases that are capable of hybridizing to one another. For example, with respect to DNA, adenosine is complementary to thymine and cytosine is complementary to guanine. Accordingly, the instant invention also includes isolated nucleic acid fragments that are complementary to the complete sequences as reported in the accompanying Sequence Listing as well as those substantially similar nucleic acid sequences.
As used herein, “gene” refers to a nucleic acid fragment that expresses a specific protein, including regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. “Native gene” or “wild type gene” refers to a gene as found in nature with its own regulatory sequences. “Chimeric gene” refers any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. “Endogenous gene” refers to a native gene in its natural location in the genome of an organism. A “foreign” gene refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes.
As used herein, an “nucleic acid molecule” is a polymer of RNA or DNA that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases. A nucleic acid molecule in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA or synthetic DNA.
As used herein, “coding sequence” refers to a DNA sequence that codes for a specific amino acid sequence.
As used herein, “suitable regulatory sequences” refer to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, and polyadenylation recognition sequences.
As used herein, “promoter” refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3′ to a promoter sequence. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions. Promoters which cause a gene to be expressed in most cell types at most times are commonly referred to as “constitutive promoters”. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of different lengths may have identical promoter activity.
As used herein, the term “FBA1” refers to a fructose-bisphosphate aldolase enzyme (E.C. 4.1.2.13) encoded by the fba1 gene and which converts D-fructose 1,6-bisphosphate into dihydroxyacetone phosphate (DHAP) plus D-glyceraldehyde 3-phosphate (U.S. Ser. No. 10/987,548; hereby incorporated by reference).
As used herein, the term “FBA promoter” or “FBA promoter region” refers to the 5′ upstream untranslated region in front of the ‘ATG’ translation initiation codon of fba1 and that is necessary for expression (U.S. Ser. No. 10/987,548).
As used herein, the term “FBAIN promoter” or “FBAIN promoter region” or “FBAIN” refers to the 5′ upstream untranslated region in front of the ‘ATG’ translation initiation codon and that is necessary for expression, plus a portion of 5′ coding region that has an intron of a fba1 gene (U.S. Ser. No. 10/987,548). An example of a suitable FBAIN promoter region is provided as SEQ ID NO: 10, but this is not intended to be limiting in nature.
As used herein, the term “FBAINm promoter” or “FBAINm promoter region” or “FBAINm” refers to a modified version of the FBAIN promoter (U.S. Ser. No. 10/987,548) as represented by SEQ ID NO: 51.
As used herein, the term “promoter activity” will refer to an assessment of the transcriptional efficiency of a promoter. This may, for instance, be determined directly by measurement of the amount of mRNA transcription from the promoter (e.g., by Northern blotting or primer extension methods) or indirectly by measuring the amount of gene product expressed from the promoter.
As used herein, the term “operably linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.
As used herein, “introns” are sequences of non-coding DNA found in gene sequences (either in the coding region, 5′ non-coding region, or 3′ non-coding region) in most eukaryotes. Their full function is not known; however, some enhancers are located in the introns (Giacopelli, F. et al., Gene Expr., 11:95-104 (2003)). These intron sequences are transcribed, but removed from within the pre-mRNA transcript before the mRNA is translated into a protein. This process of intron removal occurs by self-splicing of the sequences (exons) on either side of the intron.
As used herein, the term “expression”, as used herein, refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from the nucleic acid fragment of the invention. Expression may also refer to translation of mRNA into a polypeptide. “Antisense inhibition” refers to the production of antisense RNA transcripts capable of suppressing the expression of the target protein. “Overexpression” refers to the production of a gene product in transgenic organisms that exceeds levels of production in normal or non-transformed organisms. “Co-suppression” refers to the production of sense RNA transcripts capable of suppressing the expression of identical or substantially similar foreign or endogenous genes (U.S. Pat. No. 5,231,020).
As used herein, “transformation” refers to the transfer of a nucleic acid molecule into the genome of a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as “transgenic” or “recombinant” or “transformed” organisms. In the present application, the nucleic acid molecule(s) transferred into the genome of host organism are operably linked to suitable regulatory sequences (e.g., promoters, terminators, etc.) that facilitate expression in the host.
As used herein, the terms “plasmid”, “vector” and “cassette” refer to an extra chromosomal element often carrying genes which are not part of the central metabolism of the cell, and usually in the form of circular double-stranded DNA molecules. Such elements may be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear or circular, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing a promoter fragment and DNA sequence for a selected gene product along with appropriate 3′ untranslated sequence into a cell. “Transformation cassette” refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that facilitate transformation of a particular host cell. “Expression cassette” refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that allow for enhanced expression of that gene in a foreign host.
As used herein, “pQZ-PAL” refers to the name of the plasmid comprised of the codon optimized phenylalanine ammonia lyase coding sequence (SEQ ID NO: 3) inserted into plasmid pUC57 (GenScript Corporation, Piscataway, N.J.).
As used herein, “pQZ-4CL” refers to the name of the plasmid comprised of the codon optimized coumaroyl CoA ligase coding sequence (SEQ ID NO: 6) inserted into plasmid pUC57 (GenScript Corporation, Piscataway, N.J.).
As used herein, “pQZ-RS” refers to the name of the plasmid comprised of the codon optimized resveratrol synthase coding sequence (SEQ ID NO: 9) inserted into plasmid pUC57 (GenScript Corporation, Piscataway, N.J.).
As used herein, “pZT4FP” refers to the name of a plasmid comprised of codon-optimized versions of the resveratrol synthase, phenylalanine ammonia lyase, and coumaroyl CoA ligase genes.
As used herein, “pZT4PR” refers to the name of a plasmid comprised of codon-optimized versions of the chimeric resveratrol synthase, phenylalanine ammonia lyase, and coumaroyl CoA ligase genes.
As used herein, “pZUF-MOD-1” refers to an vector comprising the FBA-1 promoter, a multiple cloning site (MCS also referred to herein as “MCR-stuffer”), and the Pex20 terminator.
As used herein, “pEXP-MOD-1” refers to an vector comprising the EXP promoter, a multiple cloning site (MCS or “MCR-stuffer”), and the Pex20 terminator.
As used herein, “pZGN” refers to a vector comprising comprised of codon-optimized versions of the chimeric resveratrol synthase, phenylalanine lyase, and coumaroyl CoA ligase genes. Transformation of the oleaginous microorganism using the pZGN vector resulted in the production of resveratrol.
As used herein, the term “fatty acids” refers to long chain aliphatic acids (alkanoic acids) of varying chain lengths, from about C12 to C22 (although both longer and shorter chain-length acids are known). The predominant chain lengths are between C16 and C22. The structure of a fatty acid is represented by a simple notation system of “X:Y”, where X is the total number of carbon (C) atoms in the particular fatty acid and Y is the number of double bonds. Additional details concerning the differentiation between “saturated fatty acids” versus “unsaturated fatty acids”, “monounsaturated fatty acids” versus “polyunsaturated fatty acids” (or “PUFAs”), and “omega-6 fatty acids” (ω-6 or n-6) versus “omega-3 fatty acids” (ω-3 or n-3) are provided in WO2004/101757. “PUFAs” can be classified into two major families (depending on the position (n) of the first double bond nearest the methyl end of the fatty acid carbon chain). Thus, the “ω-6 fatty acids” (ω-6 or n-6) have the first unsaturated double bond six carbon atoms from the omega (methyl) end of the molecule and additionally have a total of two or more double bonds, with each subsequent unsaturation occurring 3 additional carbon atoms toward the carboxyl end of the molecule. In contrast, the “co-3 fatty acids” (ω-3 or n-3) have the first unsaturated double bond three carbon atoms away from the omega end of the molecule and additionally have a total of three or more double bonds, with each subsequent unsaturation occurring 3 additional carbon atoms toward the carboxyl end of the molecule.
As used herein, the terms “triacylglycerol”, “oil” and “TAGs” refer to neutral lipids composed of three fatty acyl residues esterified to a glycerol molecule (and such terms will be used interchangeably throughout the present disclosure herein). Such oils can contain long chain PUFAs, as well as shorter saturated and unsaturated fatty acids and longer chain saturated fatty acids. Thus, “oil biosynthesis” generically refers to the synthesis of TAGs in the cell. “Microbial oils” or “single cell oils” are those oils naturally produced by microorganisms during their lifespan.
As used herein, “percent (%) PUFAs in the total lipid and oil fractions” refers to the percent of PUFAs relative to the total fatty acids in those fractions. The term “total lipid fraction” or “lipid fraction” both refer to the sum of all lipids (i.e., neutral and polar) within an oleaginous organism, thus including those lipids that are located in the phosphatidylcholine (PC) fraction, phosphatidyletanolamine (PE) fraction and triacylglycerol (TAG or oil) fraction. However, the terms “lipid” and “oil” will be used interchangeably throughout the specification.
As used herein, the term “amino acid” will refer to the basic chemical structural unit of a protein or polypeptide. The following abbreviations will be used herein to identify specific amino acids:
















Three-Letter
One-Letter



Amino Acid
Abbreviation
Abbreviation









Alanine
Ala
A



Arginine
Arg
R



Asparagine
Asn
N



Aspartic acid
Asp
D



Asparagine or aspartic acid
Asx
B



Cysteine
Cys
C



Glutamine
Gln
Q



Glutamine acid
Glu
E



Glutamine or glutamic acid
Glx
Z



Glycine
Gly
G



Histidine
His
H



Leucine
Leu
L



Lysine
Lys
K



Methionine
Met
M



Phenylalanine
Phe
F



Proline
Pro
P



Serine
Ser
S



Threonine
Thr
T



Tryptophan
Trp
W



Tyrosine
Tyr
Y



Valine
Val
V










As used herein, the term “chemically equivalent amino acid” will refer to an amino acid that may be substituted for another in a given protein without altering the chemical or functional nature of that protein. For example, it is well known in the art that alterations in a gene which result in the production of a chemically equivalent amino acid at a given site, but do not effect the functional properties of the encoded protein are common. For the purposes of the present invention substitutions are defined as exchanges within one of the following five groups:

    
    
        1. Small aliphatic, nonpolar or slightly polar residues: Ala, Ser, Thr (Pro, Gly);
        2. Polar, negatively charged residues and their amides: Asp, Asn, Glu, Gin;
        3. Polar, positively charged residues: His, Arg, Lys;
        4. Large aliphatic, nonpolar residues: Met, Leu, Ile, Val (Cys); and
        5. Large aromatic residues: Phe, Tyr, Trp.
    
    


Thus, alanine, a hydrophobic amino acid, may be substituted by another less hydrophobic residue (such as glycine) or a more hydrophobic residue (such as valine, leucine, or isoleucine). Similarly, changes which result in substitution of one negatively charged residue for another (such as aspartic acid for glutamic acid) or one positively charged residue for another (such as lysine for arginine) can also be expected to produce a functionally equivalent product. Additionally, in many cases, alterations of the N-terminal and C-terminal portions of the protein molecule would also not be expected to alter the activity of the protein.
A nucleic acid molecule is “hybridizable” to another nucleic acid molecule, such as a cDNA, genomic DNA, or RNA molecule, when a single-stranded form of the nucleic acid molecule can anneal to the other nucleic acid molecule under the appropriate conditions of temperature and solution ionic strength. Given the nucleic acid sequences described herein, one of skill in the art can identify substantially similar nucleic acid fragments that may encode proteins having similar activity. Hybridization and washing conditions are well known and exemplified in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y. (1989), particularly Chapter 11 and Table 11.1 therein. The conditions of temperature and ionic strength determine the “stringency” of the hybridization. Stringency conditions can be adjusted to screen for moderately similar fragments (such as homologous sequences from distantly related organisms), to highly similar fragments (such as genes that duplicate functional enzymes from closely related organisms). Post-hybridization washes determine stringency conditions. One set of preferred conditions uses a series of washes starting with 6×SSC, 0.5% SDS at room temperature for 15 min, then repeated with 2×SSC, 0.5% SDS at 45° C. for 30 min, and then repeated twice with 0.2×SSC, 0.5% SDS at 50° C. for 30 min. A more preferred set of stringent conditions uses higher temperatures in which the washes are identical to those above except for the temperature of the final two 30 min washes in 0.2×SSC, 0.5% SDS was increased to 60° C. Another preferred set of highly stringent conditions uses two final washes in 0.1×SSC, 0.1% SDS at 65° C. An additional set of stringent conditions include hybridization at 0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS at 65° C. followed by 0.1×SSC, 0.1% SDS at 65° C., for example.
Hybridization requires that the two nucleic acids contain complementary sequences, although depending on the stringency of the hybridization, mismatches between bases are possible. The appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the greater the value of Tm for hybrids of nucleic acids having those sequences. The relative stability (corresponding to higher Tm) of nucleic acid hybridizations decreases in the following order: RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100 nucleotides in length, equations for calculating Tm have been derived (see Sambrook et al., supra, 9.50-9.51). For hybridizations with shorter nucleic acids, i.e., oligonucleotides, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see Sambrook et al., supra, 11.7-11.8). In one aspect the length for a hybridizable nucleic acid is at least about 10 nucleotides. Preferably a minimum length for a hybridizable nucleic acid is at least about 15 nucleotides; more preferably at least about 20 nucleotides; and most preferably the length is at least about 30 nucleotides. Furthermore, the skilled artisan will recognize that the temperature and wash solution salt concentration may be adjusted as necessary according to factors such as length of the probe.
As used herein, a “substantial portion” of an amino acid or nucleotide sequence is that portion comprising enough of the amino acid sequence of a polypeptide or the nucleotide sequence of a gene and/or a nucleic acid fragment to putatively identify that polypeptide or gene and/or nucleic acid fragment, either by manual evaluation of the sequence by one skilled in the art, or by computer-automated sequence comparison and identification using algorithms such as BLAST (Basic Local Alignment Search Tool; Altschul, S. F., et al., J. Mol. Biol. 215:403-410 (1993). In general, a sequence of ten or more contiguous amino acids or thirty or more nucleotides is necessary in order to identify putatively a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene-specific oligonucleotide probes comprising 20-30 contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12-15 bases may be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a “substantial portion” of a nucleotide sequence comprises enough of the sequence to specifically identify and/or isolate a nucleic acid fragment comprising the sequence.
The instant specification teaches partial or complete amino acid and nucleotide sequences encoding one or more particular proteins and promoters. The skilled artisan, having the benefit of the sequences as reported herein, may now use all or a substantial portion of the disclosed sequences for purposes known to those skilled in this art. Accordingly, the instant invention comprises the complete sequences as reported in the accompanying Sequence Listing, as well as substantial portions of those sequences as defined above.
The term “complementary” is used to describe the relationship between nucleotide bases that are capable of hybridizing to one another. For example, with respect to DNA, adenosine is complementary to thymine and cytosine is complementary to guanine. Accordingly, the instant invention also includes isolated nucleic acid fragments that are complementary to the complete sequences as reported in the accompanying Sequence Listing, as well as those substantially similar nucleic acid sequences.
The term “percent identity”, as known in the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences. In the art, “identity” also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences. “Identity” and “similarity” can be readily calculated by known methods, including but not limited to those described in: 1.) Computational Molecular Biology (Lesk, A. M., Ed.) Oxford University: NY (1988); 2.) Biocomputing: Informatics and Genome Projects (Smith, D. W., Ed.) Academic: NY (1993); 3.) Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., Eds.) Humana: NJ (1994); 4.) Sequence Analysis in Molecular Biology (von Heinje, G., Ed.) Academic (1987); and 5.) Sequence Analysis Primer (Gribskov, M. and Devereux, J., Eds.) Stockton: NY (1991). Preferred methods to determine identity are designed to give the best match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Sequence alignments and percent identity calculations may be performed using the Megalign program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). Multiple alignment of the sequences is performed using the Clustal method of alignment (Higgins and Sharp, CABIOS, 5:151-153 (1989)) with default parameters (GAP PENALTY=10, GAP LENGTH PENALTY=10). Default parameters for pairwise alignments using the Clustal method are: KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5.
In one aspect, suitable nucleic acid fragments encode polypeptides that are at least about 70% identical to the amino acid sequences reported herein. In another aspect, the nucleic acid fragments encode amino acid sequences that are about 85% identical to the amino acid sequences reported herein. In a further aspect, the nucleic acid fragments encode amino acid sequences that are at least about 90% identical to the amino acid sequences reported herein. In yet a further aspect, the nucleic acid fragments encode amino acid sequences that are at least about 95% identical to the amino acid sequences reported herein. In even yet a further aspect, the nucleic acid fragments encode amino acid sequences that are at least 99% identical to the amino acid sequences reported herein. Suitable nucleic acid fragments not only have the above homologies but typically encode a polypeptide having at least 50 amino acids, preferably at least 100 amino acids, more preferably at least 150 amino acids, still more preferably at least 200 amino acids, and most preferably at least 250 amino acids.
Likewise, suitable promoter regions encode promoter regions that are at least about 70% identical to the nucleotide sequences reported herein. In one aspect, the nucleic acid fragments are about 85% identical to the nucleotide sequences reported herein, in another aspect they are at least about 90% identical, and in a further aspect the nucleic acid fragments are at least about 95% identical to the nucleotide sequences reported herein. In yet a further aspect, the promoter regions are at least 99% identical to the nucleic acid sequences reported herein. Suitable promoter regions not only have the above homologies but typically are at least 50 nucleotides in length, more preferably at least 100 nucleotides in length, more preferably at least 250 nucleotides in length, and more preferably at least 500 nucleotides in length.
“Codon degeneracy” refers to the nature in the genetic code permitting variation of the nucleotide sequence without affecting the amino acid sequence of an encoded polypeptide. The skilled artisan is well aware of the “codon-bias” exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a gene for improved expression in a host cell, it is desirable to design the gene such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell. In one aspect, the recombinantly expressed genes are codon optimized for expression in the oleaginous microorganism. In another aspect, the recombinantly expressed genes are codon optimized for expression in an oleaginous yeast strain. In yet another aspect, the recombinantly expressed genes are codon optimized for expression in Yarrowia lipolytica (Table 2).
As used herein, the term “sequence analysis software” refers to any computer algorithm or software program that is useful for the analysis of nucleotide or amino acid sequences. “Sequence analysis software” may be commercially available or independently developed. Typical sequence analysis software will include, but is not limited to: 1.) the GCG suite of programs (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.); 2.) BLASTP, BLASTN, BLASTX (Altschul et al., J. Mol. Biol. 215:403-410 (1990)); 3.) DNASTAR (DNASTAR, Inc. Madison, Wis.); and 4:) the FASTA program incorporating the Smith-Waterman algorithm (W. R. Pearson, Comput. Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992, 111-20. Editor(s): Suhai, Sandor. Plenum: New York, N.Y.). Within the context of this application it will be understood that where sequence analysis software is used for analysis, that the results of the analysis will be based on the “default values” of the program referenced, unless otherwise specified. As used herein, “default values” will mean any set of values or parameters (as set by the software manufacturer) which originally load with the software when first initialized.
Standard recombinant DNA and molecular cloning techniques used here are well known in the art and are described by Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual, 2nd ed.; Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y., 1989 (hereinafter “Maniatis”); and by Silhavy, T. J., Bennan, M. L. and Enquist, L. W. Experiments with Gene Fusions; Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y., 1984; and by Ausubel, F. M. et al., In Current Protocols in Molecular Biology, published by Greene Publishing and Wiley-Interscience, 1987.
Engineering pHCA Production in a Recombinant Host Cell
The present method describes production of pHCA in the recombinant host. In one embodiment, p-hydroxycinnamic acid can be produced by expressing a phenylalanine ammonia lyase in combination with a cinnamate 4-hydroxylase (C4H), harnessing the endogenous production of the aromatic amino acid phenylalanine to produce pHCA (FIG. 1). Phenylalanine ammonia lyase (EC 4.3.1.5) is widely distributed in plants, fungi, yeast, and Streptomyces, but it has not been found in Escherichia coli or mammalian cells. PAL catalyzes the removal of the (pro-3S)-hydrogen and —NH3+ from L-phenylalanine to form trans-cinnamic acid. Subsequently, the enzyme cinnamic acid 4-hydroxylase (C4H; E.C. 1.14.13.11) catalyzes the conversion of trans-cinnamic acid to 4-hydroxycinnamate. Coumaroyl CoA ligase (4CL) converts 4-hydroxycinnamate (and other substituted cinnamic acids) into the corresponding CoA thiol esters (i.e., p-coumaroyl CoA), which are used for the biosynthesis of flavonoids, isoflavonoids, lignin, suberins, and coumarins (Ehlting et al., Plant J., 19(1):9-20 (1999)).
L-tyrosine can also be converted to para-hydroxycinnamic acid by using an enzyme having tyrosine ammonia lyase activity (“TAL”; EC 4.3.1.-). A tyrosine ammonia lyase directly converts L-tyrosine to pHCA without the intermediacy of cinnamate (trans-cinnamic acid).
Phenylalanine ammonia lyases will, to some extent, also accept tyrosine as a substrate, converting tyrosine directly to p-hydroxycinnamic acid. As such, PAL enzymes (especially those exhibiting significant TAL activity) can alternatively be referred to a phenylalanine/tyrosine ammonia lyases (Rosier et al., Plant Physiol., 113:175-179 (1997); Hwang et al., supra). Conversely, naturally-occurring TAL enzymes will have some PAL activity, converting L-phenylalanine to trans-cinnamic acid (Kyndt et al., FEBS Letters, 512:240-244 (2002); Watts et al., supra). Enzymes having PAL and/or TAL activity are defined by the substrate preference of the enzyme. TAL enzymes are defined as those that preferentially use L-tyrosine as a substrate. The source of the TAL in the present invention can be obtained or derived from any naturally-occurring source. In one aspect, an enzyme having TAL activity can be obtained by mutating a naturally-occurring PAL gene into one that encodes an enzyme that preferentially uses L-tyrosine as a substrate (U.S. Pat. No. 6,368,837, hereby incorporated by reference; Kyndt et al., supra). In another aspect, L-phenylalanine is converted to L-tyrosine using an enzyme having phenylalanine hydroxylase (PAH) activity. The L-tyrosine produced using a phenylalanine hydroxylase is then subsequently converted to pHCA using an enzyme having tyrosine ammonia lyase activity (Watts et al., supra; FIG. 1).
In one embodiment, pHCA is exogenously supplemented to the fermentor medium and/or produced by the recombinant host cell. In a further aspect, L-phenylalanine and/or trans-cinnamate can be exogenously supplied to a recombinant host cell expressing a phenylalanine ammonia lyase and/or a cinnamate 4-hydroxylase.
In another aspect, a phenylalanine hydroxylase (PAH) can be recombinantly expressed in a host cell capable of producing phenylalanine to increase L-tyrosine production in the recombinant host cell (assuming that a tyrosine ammonia lyase activity is present to convert the tyrosine into pHCA). In another aspect, the host cell is engineered to recombinantly express genes required to convert a portion of the aromatic amino acids endogenously produced by the host cell (L-phenylalanine and/or L-tyrosine) into pHCA by recombinantly expressing genes in the phenylpropanoid pathway. One of skill in the art will recognize that there is a need to balance the carbon flow from aromatic amino acid production into pHCA production (and eventually resveratrol production) so that a decrease in concentration of the free aromatic amino acids is not detrimental to the viability or health of the recombinant host cell. In another aspect, L-phenylalanine and/or L-tyrosine can be exogenously supplemented to the culture medium to increase resveratrol and/or resveratrol glucoside production. In yet another aspect, the genes involved in aromatic amino acid biosynthesis can be upregulated to increase the production of L-phenylalanine and/or L-tyrosine.
Microbial expression of a phenylalanine ammonia lyase and/or a tyrosine ammonia lyase is known in the art. Use of an enzyme having PAL/TAL activity in the present methods is exemplified by recombinant expression of the Rhodotorula glutinis (also referred to herein as Rhodosporidium toruloides) PAL (SEQ ID NOs: 2 and 3) in an oleaginous yeast. Other PAL/TAL genes are publicly available and known in the art (for example, see Table 1). One of skill in the art can select and recombinantly express one or more genes encoding enzyme(s) having PAL/TAL activity using the present methods.
Production of p-Coumaroyl CoA from pHCA
The pHCA produced by the recombinant host cell is converted into p-coumaroyl CoA by expressing an enzyme having coumaroyl CoA ligase activity. The coumaroyl CoA ligase can be endogenous to the host cell or can be recombinantly expressed within the host cell to increase p-coumaroyl CoA production. Microbial expression of plant and/or bacterial coumaroyl CoA ligases has previously been reported. The coumaroyl CoA ligase presently exemplified was isolated from Streptomyces coelicolor(SEQ ID NOs: 5 and 6). However, one of skill in the art can select and recombinantly expression any of the publicly available coumaroyl CoA ligases (see for example, Table 1 for a non-limited list). In one aspect, the coumaroyl CoA ligase is chosen based on its ability to convert pHCA into p-coumaroyl CoA. In another aspect, a plurality of coumaroyl CoA ligases are coexpressed to increase the production of resveratrol and/or resveratrol glucoside. In yet another aspect, the coumaroyl CoA ligase activity is derived from Streptomyces coelicolor or Acinectobactersp. ADP1.
Production of Malonyl COA
Resveratrol synthase (stilbene synthase) catalyzes the formation of resveratrol by combining 3 molecules of malonyl CoA with 1 molecule coumaroyl CoA. In one aspect, the recombinant host cell endogenously produces suitable amounts of malonyl CoA (for example, oleaginous microorganisms, presently exemplified by an oleaginous yeast). In another aspect, the host cell is engineered to produce increased amounts of malonyl CoA by recombinantly expressing acetyl CoA carboxylase (Davis et al., J. Biol. Chem., 275:28593-28598 (2000)).). Acetyl CoA carboxylase catalyzes the production of malonyl CoA from acetyl CoA. Acetyl CoA carboxylases are known in the art (Table 1; Davis et al., supra).
In yet another aspect, the host cell is capable of high flux biosynthesis of fatty acids. The synthesis of malonyl-CoA is the first committed step of fatty acid biosynthesis, which takes place in the cytoplasm. Malonyl-CoA is produced via carboxylation of acetyl-CoA by acetyl-CoA carboxylase (“ACC”). Fatty acid synthesis is catalyzed by a multi-enzyme fatty acid synthase complex (“FAS”) and occurs by the condensation of eight two-carbon fragments (acetyl groups from acetyl-CoA) to form a 16-carbon saturated fatty acid, palmitate (Smith, S., FASEB J., 8(15):1248-59 (1994)). Since malonyl CoA is used as precursor for fatty acid biosynthesis, organisms capable of producing significant amounts of fatty acids (oleaginous microorganisms) have the capability to produce significant amounts of malonyl CoA. In yet a further aspect, the host cell is an oleaginous yeast, capable of producing suitable amounts of malonyl CoA (i.e., an organism capable of high flux malonyl CoA production). In another aspect, the oleaginous yeast is a Yarrow sp. In a further aspect, the oleaginous yeast is Yarrowia lipolytica. 
In another embodiment, the recombinant host cell is engineered to recombinantly express an enzyme having malonyl CoA synthetase activity (E.C. 6.2.1.-). Malonyl CoA synthetases catalyzes the synthesis of malonyl CoA from malonate and CoA (Kim and Yang, Biochem. J. 297:327-333 (1994)). Genes encoding enzymes having malonyl CoA synthetase activity are known in the art. Recombinant expression of malonyl CoA synthetases has been reported (An, J. H., and Kim, Y. S., Eur. J. Biochem. 257:395-402 (1998)). In one embodiment, the recombinant host cell recombinantly expresses at least one malonyl CoA synthetase in order to produce suitable amounts of malonyl CoA when grown on an inexpensive carbon source (i.e., the cell produces malonate and CoA). In another embodiment, malonic acid or malonate is supplemented to the fermentation medium to increase resveratrol production.
Uptake of exogenous supplied malonic acid/malonate may be improved by coexpressing at least one nucleic acid molecule encoding an enzyme having dicarboxylate carrier protein activity. Dicarboxylate carrier proteins are membrane bound proteins that facilitate cellular update of dicarboyxlates. Interestingly, malonyl CoA biosynthesis operons have been reported to contain coding regions for both malonyl CoA synthetase (matB) and a dicarboxylate carrier protein (malonate transporter; matC). Recombinant expression of matB and matC genes has been reported (An, J. H., and Kim, Y. S., supra). In one embodiment, host cells grown in the presence of endogenously supplemented malonate/malonic acid recombinantly express at least one nucleic acid molecule encoding a protein having dicarboxylate carrier protein (malonic acid transporter) activity.
In one embodiment, the recombinant host cell engineered for resveratrol production expresses at least one nucleic acid molecule encoding an enzyme having malonyl CoA synthetase activity and at least one nucleic acid molecule encoding a dicarboxylate carrier protein.
Hydrolysis of Resveratrol Glucoside to Free Resveratrol
The recombinant host cell is engineered to produce resveratrol in significant amounts. In one aspect, the host cell endogenously glycosylates the resveratrol to produce resveratrol glucoside (piceid). The glucose moieties (one or more) attached to the resveratrol glucoside can hydrolyzed to produce free resveratrol (i.e., the aglycone). In one aspect, the glucose moieties are removed from the piceid using a non-enzymatic process such as acid or base hydrolysis (Jencks, William, P., in Catalysis in Chemistry and Enzymology, Dover Publications, New York, 1987). In another aspect, the recombinantly produced glycoside is treated with a α-glucosidase (E.C. 3.2.1.21) to release the sugar moieties bound to resveratrol (Example 8). In a further aspect, the gene(s) encoding the endogenous glucosyltransferase(s) is/are disrupted to block the production of the resveratrol glycoside (assuming this is not detrimental to the growth characteristics and/or viability of the host cell). In yet another aspect, a β-glucosidase is recombinantly expressed in the host cell to increase production of the aglycone.
In one aspect, the resveratrol and/or resveratrol glycoside is accumulated within the recombinant host cell. In this instance, the resveratrol and/or resveratrol glycoside can be purified from the recombinant host cells. In a further aspect, the recombinant host cell can be further modified so that the resveratrol (or resveratrol glycoside) produced is secreted from the host cell into the fermentation medium where it can be purified in batch or continuously removed from the fermentation medium.
In yet another aspect, the resveratrol glycoside produced by the recombinant host cell is the desired end product (i.e., for use in personal care products). Resveratrol glycoside may be the produced using the present methods by simply omitting the final hydrolysis step used to produce the aglycone.
Genes Useful for Resveratrol Biosynthesis
The key enzymatic activities used in the present invention are encoded by a number of genes known in the art. The principal enzymes used in the conversion of L-phenylalanine and/or L-tyrosine into resveratrol are phenylalanine/tyrosine ammonia lyases (PAL/TAL), cinnamate 4-hydroxylase (when converting phenylalanine to cinnamate using PAL activity), coumaroyl CoA ligase, and resveratrol synthase (FIG. 1). Additional enzymes useful for the production of resveratrol in the transformed microorganisms may also include acetyl CoA carboxylase (carboxylates acetyl CoA to make malonyl CoA), phenylalanine hydroxylase (used to convert phenylalanine to tyrosine), malonyl CoA synthetase (catalyzes formation of malonyl CoA from malonate and CoA), and β-glucosidase (used to remove sugar moieties from resveratrol glycoside) (FIG. 1). In another aspect, the genes useful to produce resveratrol and/or resveratrol glycoside by the present methods are expressed in multiple copies, optionally having divergent amino acid and/or nucleic acid sequences to create a more genetically stable production host (i.e., reduce or eliminate probability of homologous recombination events). In yet another aspect, the one or more of the genes used to produce resveratrol and/or resveratrol glucoside are chromosomally expressed. In another aspect, one or more of the genes used to produced resveratrol and/or resveratrol glucoside are expressed extrachromosomally (i.e., on an expression vector).
The current methods are exemplified using genes isolated from specific sources. However, one of skill in the art recognizes that homologs for each of the exemplified genes are known in the art as illustrated by the non-limited list provided in Table 1.







TABLE 1







Examples of Alternative Sources for Genes Useful


for Recombinant Production of Resveratrol










GenBank ® Accession No., Source



Gene
Organism
SEQ ID NO.:












pal, tal
X13094, Rhodotorula mucilaginosa
66


(phenylalanine
AAJ10143, Amanita muscaria
67


ammonia
XM397693, AF306551, Ustilago
68


lyases and/or
maydis


tyrosine
AY079363, Arabidopsis thaliana
69


ammonia
AF237955, Rubus idaeus
70


lyases)
X58180, Medicago sativa
71



AF401636, Rehmannia glutinosa
72



AF299330, Lactuca savita
73



P14913, Petroselinium crispum
74



AF036948, Prunus avium
75



D83075, Lithospernum
76



erythrorhizon



U43338, Citrus limon
77



AAP01719, Rhodotorula glutinis
78



from U.S. Pat. No. 6,521,748



ZP_00005404, Rhodobacter
79



sphaeroides



AR722988, Trichosporon cutaneum
80



from U.S. Pat. No. 6,951,751


Coumaroyl CoA
CAB95894, AL939119, for
81


ligase (4CL)
Streptomyces coelicolor



AY541033, Allium cepa
82



AP005036, Streptomyces avermitilis
83



AF041049, Populus tremuloides



XM_482683, Oryza sativa
84



AF435968, Amorpha fruticosa
85



AY043495, Populus tomentosa
86



D43773, Nicotiana tabacum
87



U12013, Pinus taeda
88



AF279267, Glycine max
89



NM_113019, Arabidopsis thaliana
90



AY376731, Arabidopsis thaliana
91



AF239687, Rubus idaeus
92



D49367, Lithospermum
93



erythrorhizon
94



AY566301, Zea mays
95


Resveratrol
S63225, Vitis sp.
96


Synthase (RS)
AF274281, Vitis vinifera
97


(Stilbene
X76892.1, Vitis vinifera
98


synthase)
AB027606, Arachis hypogaea
99



AY094616.1, Cissus rhombifolia
100



AY094615.1, Parthenocissus
101



henryana



AY094617.1, Parthenocissus
102



quinquefolia



AB046373.1, Vitis riparia
103



AB046374.1, Vitis labrusca
104



AF418566, Vitis sp. cv. “Norton”
105


Cinnamate 4-
O81928, AJ007449, Cicer arietinum
106


hydroxylase
O24312, U47293, Populus
107


(C4H)
tremuloides



XP_465542, Oryza sativa
108



AAT68775, AY641731, Camellia
109



sinensis



P37115, L07634, Vigna radiata
110



Q04468, Z17369, Helianthus
111



tuberosus



AAT39513, AY621152,
112



Camptotheca acuminata



P92994, U71081, Arabidopsis
113



thaliana



AAN63028, AF548370, Ruta
114



graveolens



Q42797, X92437, Glycine max
115



AAF66065, AF255013, Citrus
116



sinensis


Phenylalanine
AAA23115, M55915,
117


hydroxylase
Chromobacterium violaceum


(PAH)
AAA25938, M88627, Pseudomonas
118



aeruginosa



CAA76184, Y16353, Geodia
119



cydonium



AAM35066, AE011641,
120



Xanthomonas axonopodis



AAM39475, AE012111,
121



Xanthomonas campestris



BAD55786, AP006618 Nocardia
122



farcinica



NP_001001298, Gallus gallus
123


Acetyl CoA
NP_014413, NC_001146,
124


carboxylase
Saccharomyces cerevisiae



M92156, Saccharomyces cerevisiae
125



XM_455355, Kluyveromyces lactis
126



XM_457211, Debaryomyces
127



hansenii



XM_501721, Yarrowia lipolytica
128



Y15996, Aspergillus nidulans
129



D78169, Schizosaccharomyces
130



pombe



Z46886, Ustilago maydis
131



J03541, Gallus gallus
132


β-Glucosidase
YP_053668, NC_006055
133



Mesoplasma florum



AAV32242, AC135927 Oryza sativa
134



NP_743562, NC_002947
135



Pseudomonas putida



NP_793101, NC_004578
136



Pseudomonas syringae



NP_630676, NC_003888
137



Streptomyces coelicolor A3(2)



NP_420939, NC_002696
138



Caulobacter crescentus



2107160A, U13672, Candida
139



wickerhamii









In one embodiment, the present method comprises at least one nucleic acid molecule encoding an enzyme providing resveratrol synthase activity is selected from the group consisting of:

    
    
        (1) a nucleic acid molecule encoding a polypeptide having resveratrol synthase activity, said polypeptide having an amino acid sequence SEQ ID NO: 8;
        (2) a nucleic acid molecule encoding a polypeptide having resveratrol synthase activity, said polypeptide having 95% identity to SEQ ID NO: 8; and
        (3) a nucleic acid molecule that hybridizes with (1) under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS, at 65° C.; followed by 0.1×SSC, 0.1% SDS, at 65° C.
    
    


In another embodiment, the present method comprises at least one nucleic acid molecule encoding an enzyme providing coumaroyl CoA ligase activity is selected from the group consisting of:

    
    
        (1) a nucleic acid molecule encoding a polypeptide having coumaroyl CoA ligase activity, said polypeptide having an amino acid sequence SEQ ID NO: 5;
        (2) a nucleic acid molecule encoding a polypeptide having coumaroyl CoA ligase activity, said polypeptide having 95% identity to SEQ ID NO: 5; and
        (3) a nucleic acid molecule that hybridizes with (1) under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS, at 65° C.; followed by 0.1×SSC, 0.1% SDS, at 65° C.
    
    


In another embodiment, the present method optionally comprises at least one nucleic acid molecule encoding an enzyme providing phenylalanine/tyrosine ammonia lyase activity is selected from the group consisting of:

    
    
        (1) a nucleic acid molecule encoding a polypeptide having phenylalanine/tyrosine ammonia lyase activity, said polypeptide having an amino acid sequence SEQ ID NO: 2;
        (2) a nucleic acid molecule encoding a polypeptide having phenylalanine/tyrosine ammonia lyase activity, said polypeptide having 95% identity to SEQ ID NO: 2; and
        (3) a nucleic acid molecule that hybridizes with (1) under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS, at 65° C.; followed by 0.1×SSC, 0.1% SDS, at 65° C.
    
    


In another embodiment, the present invention provides a resveratrol-producing and/or resveratrol glucoside-producing recombinant oleaginous microorganism comprising at least one isolated nucleic acid molecule encoding an enzyme having resveratrol synthase activity and at least one isolated nucleic acid molecule encoding an enzyme providing coumaroyl CoA ligase activity and optionally at least one nucleic acid molecule encoding an enzyme having phenylalanine/tyrosine ammonia lyase activity. In a further embodiment, the recombinant oleaginous microorganism further comprises at least one nucleic acid molecule encoding an enzyme having phenylalanine/tyrosine ammonia lyase activity. Preferably, the enzyme having phenylalanine/tyrosine ammonia lyase activity will have a tyrosine ammonia lyase activity to phenylalanine ammonia lyase activity (TAL specific activity:PAL specific activity) of at least 0.1, more preferably at least 1, even more preferably at least 10, and most preferably at least 1000.
In yet another embodiment, an isolated recombinant oleaginous microorganism capable of producing resveratrol or resveratrol glucoside is provided comprising:

    
    
        a) at least one nucleic acid molecule encoding an enzyme having resveratrol synthase activity selected from the group consisting of:
        
            i) a nucleic acid molecule encoding a polypeptide having an amino acid sequence SEQ ID NO: 8;
            ii) a nucleic acid molecule encoding a polypeptide having 95% identity to SEQ ID NO: 8; and
            iii) a nucleic acid molecule that hybridizes with (a)(i) under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS, at 65° C.; followed by 0.1×SSC, 0.1% SDS, at 65° C.;
        
        
        b) at least one nucleic acid molecule encoding an enzyme having coumaroyl CoA ligase activity selected from the group consisting of:
        
            i) a nucleic acid molecule encoding a polypeptide having an amino acid sequence SEQ ID NO: 5;
            ii) a nucleic acid molecule encoding a polypeptide having 95% identity to SEQ ID NO: 5; and
            iii) a nucleic acid molecule that hybridizes with (b)(i) under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS, at 65° C.; followed by 0.1×SSC, 0.1% SDS, at 65° C.; and
        
        
        c) optionally at least one nucleic acid molecule encoding an enzyme having phenylalanine/tyrosine ammonia lyase activity selected from the group consisting of:
        
            i) a nucleic acid molecule encoding a polypeptide having an amino acid sequence SEQ ID NO: 2;
            ii) a nucleic acid molecule encoding a polypeptide having 95% identity to SEQ ID NO: 2; and
            iii) a nucleic acid molecule that hybridizes with (c)(i) under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS, at 65° C.; followed by 0.1×SSC, 0.1% SDS, at 65° C.
        
        
    
    


In another embodiment, the present invention provides an isolated oleaginous microbial biomass comprising at least 0.03 wt % (dcw) resveratrol and/or resveratrol glucoside for inclusion in an animal feed, a pharmaceutical composition, an antifungal composition, or a dietary supplement.
Phenylalanine Ammonia Lyase (PAL) and Cinnamate 4-hydroxylase (C4H)
Phenylalanine ammonia-lyase (PAL) (EC 4.3.1.5) is widely distributed in plants (Koukol et al., J. Biol. Chem., 236:2692-2698 (1961)), fungi (Bandoni et al., Phytochemistry, 7:205-207 (1968)), yeast (Ogata et al., Agric. Biol. Chem., 31:200-206 (1967)), and Streptomyces (Emes et al., Can. J. Biochem., 48:613-622 (1970)), but it has not been found in Escherichia coli or mammalian cells (Hanson and Havir In The Enzymes, 3rd ed.; Boyer, P., Ed.; Academic: New York, 1967; pp 75-167). PAL is the first enzyme of phenylpropanoid metabolism and catalyzes the removal of the (pro-3S)-hydrogen and —NH3+ from L-phenylalanine to form trans-cinnamic acid. In the presence of a P450 enzyme system (cinnamate 4-hydroxylase activity), trans-cinnamic acid can be converted to para-hydroxycinnamic acid (pHCA), which serves as the common intermediate in plants for production of various secondary metabolites such as lignin and isoflavonoids. In microbes however, trans-cinnamic acid (not pHCA) acts as the precursor for secondary metabolite formation.
Phenylalanine ammonia lyases will, to some extent, also accept tyrosine as a substrate, converting tyrosine directly to p-hydroxycinnamic acid. As such, PAL enzymes (especially those having a PAL/TAL activity ratio of at least 0.1) can alternatively be referred to an phenylalanine/tyrosine ammonia lyases. Preferably, phenylalanine/tyrosine ammonia lyases having significant tyrosine ammonia lyase activity are used in the present methods to converted tyrosine directly to p-hydroxycinnamic acid. In one embodiment, the TAL specific activity of the PAL/TAL enzyme is at least 0.02 S−1, preferably at least 0.1 s−1, more preferably at least 0.5 S−1, even more preferably at least 1 S−1, and most preferably at least 3 S−1.
Tyrosine Ammonia LVase (TAL) to Convert Tyrosine to pHCA
Another biosynthetic pathway leading to the production of pHCA is based on the use of an enzyme having tyrosine ammonia lyase activity. Instead of the two enzyme reactions used to convert phenylalanine to pHCA, an enzyme tyrosine ammonia lyase activity converts L-tyrosine directly into pHCA. A coumaroyl CoA ligase then converts pHCA into p-coumaroyl CoA. In one aspect, an enzyme classified as a tyrosine ammonia lyase can be recombinantly expressed in the host cell. The classification of tyrosine ammonia lyases and phenylalanine ammonia lyases is primarily determined by the enzyme's activity towards each substrate, where classification is assigned based on the preferred substrate. However, these enzymes normally accept both L-tyrosine and L-phenylalanine as substrates, albeit to varying degrees. As such, an in another embodiment as defined herein, tyrosine ammonia lyases will also be referred to as “phenylalanine/tyrosine ammonia lyases”. One exception is bacterial tyrosine ammonia lyases from Rhodobacter capsulatus and Rhodobacter sphaeroides. These TAL enzymes are specific towards tyrosine, with very low activity towards phenylalanine. But these TAL enzymes have relatively low overall activity, e.g., Rhodobacter sphaeroides TAL has a kcat of 0.02 S-1. Kyndt et al. (supra) report the TAL activity for Rhodobacter capsulatus is 27 S−1, but we were unable to reproduce this data (actually measured activity was 0.02 S−1; unpublished results).
Mutating Phenyalanine Ammonia Lyase to Create Tyrosine Ammonia Lyase (TAL)
In nature, genes encoding phenylalanine ammonia-lyase are known to convert phenylalanine to trans-cinnamate which may then be converted to para-hydroxycinnamic acid (pHCA) via a p450/p450 reductase enzyme system (FIG. 1). Phenylalanine ammonia lyases have dual substrate specificity, acting on L-phenylalanine principally, but also having some affinity for L-tyrosine. For example, the PAL enzyme isolated from parsley (Appert et al., Eur. J. Biochem., 225:491 (1994)) and corn ((Havir et al., Plant Physiol., 48:130 (1971)) both demonstrate the ability to use tyrosine as a substrate. Similarly, the PAL enzyme isolated from Rhodosporidium (Hodgins D S, J. Biol. Chem., 246:2977 (1971)) also may use L-tyrosine as a substrate. Such enzymes are referred to herein as “PAL/TAL” enzymes or activities. Where it is desired to create a recombinant organism expressing a wild type gene encoding PAL/TAL activity, genes isolated from maize, wheat, parsley, Rhizoctonia solani, Rhodosporidium, Sporobolomyces pararoseus, and Rhodosporidium may be used as discussed in Hanson and Havir, The Biochemistry of Plants; 
Academic: New York, 1981; Vol. 7, pp 577-625.
It is possible to increase the substrate specificity of the PAL/TAL enzyme via various forms of mutagenesis and protein engineering. In one aspect, a phenylalanine ammonia lyase can be protein engineered to have increased activity towards L-tyrosine as a substrate for the production of pHCA (U.S. Pat. No. 6,521,748; hereby incorporated by reference). A variety of approaches may be used for the mutagenesis of the PAL/TAL enzyme. Suitable approaches for mutagenesis include error-prone PCR (Leung et al., Techniques, 1:11-15 (1989) and Zhou et al., Nucleic Acids Res., 19:6052-6052 (1991) and Spee et al., Nucleic Acids Res., 21:777-778 (1993)), in vitro mutagenesis, and in vivo mutagenesis. Protein engineering may be accomplished by the method commonly known as “gene shuffling” (U.S. Pat. Nos. 5,605,793; 5,811,238; 5,830,721; and 5,837,458), by recombinogenic methods as described in U.S. Ser. No. 10/374,366, or by rationale design based on three-dimensional structure and classical protein chemistry.
The process of protein engineering an enzyme classified as a phenylalanine ammonia lyase into an mutant enzyme with increased activity for L-tyrosine as a substrate (hence tyrosine ammonia lyase activity) has previously been reported (U.S. Pat. No. 6,368,837; hereby incorporated by reference).
Phenylalanine Hydroxylase (PAH) to Increase Tyrosine Production
In another aspect, phenylalanine hydroxylase (PAH) activity can be endogenous or introduced into the host cell to increase production of tyrosine (FIG. 1). The PAH enzyme hydroxylates L-phenylalanine to produce L-tyrosine. This enzyme is well known in the art and has been reported in Proteobacteria (Zhao et al., In Proc. Natl. Acad. Sci. USA., 91:1366 (1994)). For example Pseudomonas aeruginosa possesses a multi-gene operon that includes phenylalanine hydroxylase which is homologous with mammalian phenylalanine hydroxylase, tryptophan hydroxylase, and tyrosine hydroxylase (Zhao et al., supra). The enzymatic conversion of L-phenylalanine to L-tyrosine is known in eukaryotes. Human phenylalanine hydroxylase is specifically expressed in the liver to convert L-phenylalanine to L-tyrosine (Wang et al., J. Biol. Chem., 269 (12): 9137-46 (1994)). Although any gene encoding a PAH activity will be useful, and genes isolated from Proteobacteria will be particularly suitable A PAH gene encoding such activity has been isolated from Chromobacterium violaceum and recombinantly expressed (U.S. Ser. No. 10/138,970; hereby incorporated by reference).
Coumaroyl CoA Ligase (4CL) for the Synthesis of p-Coumaroyl-CoA from pHCA
Coumaroyl CoA ligases catalyze the conversion of 4-coumaric acid (pHCA) and other substituted cinnamic acids into the corresponding CoA thiol esters. In the present invention, coumaroyl CoA ligase is used to convert pHCA into p-coumaroyl CoA, one of the substrates used by resveratrol synthase to make resveratrol. Coumaroyl CoA ligases are well-known in the art and have been recombinantly expressed in microorganisms (Watts et al., supra; Hwang et al., supra; and Kaneko et al., supra). A non-limited list of additional, publicly available coumaroyl CoA ligases is provided in Table 1.
Resveratrol Synthase (Stilbene Synthase)
Resveratrol synthase, also referred to as stilbene synthase, catalyzes the formation of resveratrol from p-coumaroyl CoA and malonyl CoA. Specifically, resveratrol is formed by three consecutive Claisen condensations of the acetate unit from malonyl CoA with p-coumaroyl CoA, which is succeeded by an aldol reaction that forms the second aromatic ring, cleaves the thioester, and decarboxylates to produce resveratrol.
The present methods were exemplified using the resveratrol synthase isolated from Vitis sp. (SEQ ID NOs: 8 and 9). However, resveratrol synthases appear to be highly conserved in both structure and function based on comparisons to publicly available sequences. As such, one of skill in the art would expect that the present method is not limited to the particular resveratrol synthase exemplified in the present examples. A non-limited list of additional, publicly available, resveratrol synthases is provided in Table 1.
Synthesis of Malonyl CoA
Synthesis of resveratrol and/or resveratrol glucoside is dependent upon an available pool of malonyl CoA. In one aspect, the oleaginous host cell produces a suitable amount of malonyl CoA. In another aspect, the selected host cell is genetically modified to increase the amount of available malonyl CoA. In yet a further aspect, the host cell is engineered for increased expression of acetyl CoA carboxylase (Davis et al., supra). A non-limited list of additional, publicly available acetyl CoA carboxylases is provided in Table 1.
Microbial Hosts—Oleaginous Microorganisms
Many species of oleaginous microalgae, oleaginous diatoms, and oleaginous fungi/yeasts have the ability to store lipids (i.e. oils) to >20% of the dry cell weight. In one aspect, suitable oleaginous microorganisms useful for the present methods include oleaginous microalgae, oleaginous diatoms, and oleaginous fungi/yeast. In another aspect, suitable oleaginous microorganisms useful for the present methods include oleaginous fungi. Examples of oleaginous microorganisms include those belonging to the genera Mortierella, Conidiobolus, Pythium, Phytophathora, Penicillium, Porphyridium, Coidosporium, Mucor, Fusarium, Aspergillus, Rhodotorula, Yarrowia, and Entomophthora. Within the genus Porphyridium, of particular interest is P. cruentum. Within the genus Mortierella, of particular interest are M. elongata, M. exigua, M. hygrophila, M. ramanniana var. angulispora, and M. alpina. Within the genus Mucor, of particular interest are M. circinelloides and M. javanicus. The fungus Mortierella alpina, for example, can accumulate oil to more than half it weight, as can the yeast Yarrowia lipolytica. For an organism to produce large quantities of oil, the flux through the fatty acid biosynthetic pathway must be substantially higher than non-oleaginous organisms. Thus, these organisms have the ability to produce substantial amounts of malonyl-CoA Since the biosynthesis of resveratrol requires malonyl-CoA, oleaginous microorganisms have a clear advantage over non-oleaginous microorganisms when producing resveratrol, especially if one can genetically engineer the organism such that the production of fatty acid is reduced, redirecting the accumulated malonyl-CoA towards resveratrol biosynthesis.
Oleaginous Yeasts
In one aspect, the production host is an oleaginous yeast.
Oleaginous yeasts are defined as those organisms (and derivatives thereof) that are naturally capable of oil synthesis and accumulation, wherein oil accumulation ranges from at least about 20% of the cellular dry weight. These oleaginous organisms are naturally capable of oil synthesis and accumulation, wherein the oil can comprise greater than about 20% of the cellular dry weight, more preferably greater than 25% of the cellular dry weight, even more preferably greater than about 30% of the cellular dry weight, and most preferably greater than about 40% of the cellular dry weight. Genera typically identified as oleaginous yeast include, but are not limited to: Yarrowia, Candida, Rhodotorula, Rhodosporidium, Cryptococcus, Trichosporon, and Lipomyces. More specifically, illustrative oil-synthesizing yeasts include: Rhodosporidium toruloides, Liopmyces starkeyii, L. lipoferus, Candida revkaufi, C. pulcherrima, C. tropicalis, C. utilis, Trichosporon pullans, T. cutaneum, Rhodotorula glutinus, R. graminis, and Yarrowia lipolytica (formerly classified as Candida lipolytica).
In one particular aspect, the oleaginous yeast is Yarrowia lipolytica. In a further aspect, the Y. lipolytica strains designated as ATCC #20362, ATCC #8862, ATCC #18944, ATCC #76982 and/or LGAM S(7)1 (Papanikolaou S., and Aggelis G., Bioresour. Technol., 82(1):43-9 (2002)) are used. In yet a further aspect, the Yarrowia lipolytica strains is an ω-3 and/or ω-6 polyunsaturated fatty acid-producing derivative of ATCC #20362, ATCC #8862, ATCC #18944, ATCC #76982 and/or LGAM S(7).
The technology for growing oleaginous yeast with high oil content is well developed (for example see EP 0 005 277B1; Ratledge, C., Prog. Ind. Microbiol. 16:119-206 (1982)). In addition, these organisms have been commercially used for a variety of purposes in the past. For example, various strains of Yarrowia lipolytica have historically been used for the manufacture and production of: isocitrate lyase (DD259637); lipases (SU 1454852, WO2001083773, DD279267); polyhydroxyalkanoates (WO2001088144); citric acid (RU2096461, RU2090611, DD285372, DD285370, DD275480, DD227448, PL160027); erythritol (EP770683); 2-oxoglutaric acid (DD267999); γ-decalactone (U.S. Pat. No. 6,451,565, FR2734843); γ-dodecalactone (EP578388); and pyruvic acid (JP09252790). Most recently, the natural abilities of oleaginous yeasts have been enhanced by advances in genetic engineering, resulting in organisms capable of producing polyunsaturated fatty acids (“PUFAs”). Specifically, is has demonstrated that Yarrowia lipolytica can be engineered for production of ω-3 and ω-6 fatty acids, by introducing and expressing genes encoding the (ω-3/ω-6 biosynthetic pathway (U.S. Ser. Nos. 10/840,579, 10/840,478, 10/840,579, 10/840,325, 10/869,630, 10/882,760, 10/985,109, 10/985,691, 10/987,548, 11/024,545, 11/024,544, 11/166,993, 11/183,664, 11/185,301, 11/190,750, 11/198,975, 11/225,354, 11/251,466, 11/254,173, 11/253,882, 11/264,784, 11/264,737, and 11/265,761; each hereby incorporated by reference).
Recombinant Microbial Expression
Microbial expression systems and expression vectors containing regulatory sequences that direct high level expression of foreign proteins are well known to those skilled in the art. Any of these could be used to construct chimeric genes for production of resveratrol and/or resveratrol glucoside. These chimeric genes could then be introduced into appropriate microorganisms via transformation to allow for expression of high level of the enzymes.
Vectors or cassettes useful for the transformation of suitable microbial host cells are well known in the art. Typically the vector or cassette contains sequences directing transcription and translation of the relevant gene, a selectable marker, and sequences allowing autonomous replication or chromosomal integration. Suitable vectors comprise a region 5′ of the gene which harbors transcriptional initiation controls and a region 3′ of the DNA fragment which controls transcriptional termination. It is most preferred when both control regions are derived from genes homologous to the transformed host cell, although it is to be understood that such control regions need not be derived from the genes native to the specific species chosen as a production host.
Initiation control regions or promoters, which are useful to drive expression of the relevant genes in the desired host cell are numerous and familiar to those skilled in the art. Expression in a host cell can be accomplished in a transient or stable fashion. Transient expression can be accomplished by inducing the activity of a regulatable promoter operably linked to the gene of interest. Stable expression can be achieved by the use of a constitutive promoter operably linked to the gene of interest. Virtually any promoter capable of driving these genes is suitable for the present invention including, but not limited to FBAIN, FBAINm, EXP, FBA1, GPAT, CYC1, HIS3, GAL1, GAL10, ADH1, PGK, PHO5, GAPDH, ADCI, TRP1, URA3, LEU2, ENO, TPI; AOXI (particularly useful for expression in Pichia); and lac, trp, IPL, IPRR, T7, tac, and trc (particularly useful for expression in Escherichia coli).
In another aspect, when the host cell is yeast, transcriptional and translational regions functional in yeast cells are provided, particularly from the host species (e.g., see U.S. Ser. No. 11/265,761 and WO 2004/101757 for preferred transcriptional initiation regulatory regions for use in Yarrowia lipolytica). The transcriptional initiation regulatory regions can be obtained, for example, from: 1.) genes in the glycolytic pathway, such as alcohol dehydrogenase, glyceraldehyde-3-phosphate-dehydrogenase (U.S. Ser. No. 10/869,630, hereby incorporated by reference), glyceraldehyde-3-phosphate O-acyltransferase (U.S. Ser. No. 11/225,354;hereby incorporated by reference), phosphoglycerate mutase (U.S. Ser. No. 10/869,630), fructose-bisphosphate aldolase (U.S. Ser. No. 10/987,548, hereby incorporated by reference), phosphoglucose-isomerase, phosphoglycerate kinase, etc.; or, 2.) regulatable genes such as acid phosphatase, lactase, metallothionein, glucoamylase, the translation elongation factor EF1-α (TEF) protein (U.S. Pat. No. 6,265,185), ribosomal protein S7 (U.S. Pat. No. 6,265,185), etc. Any one of a number of regulatory sequences can be used, depending upon whether constitutive or induced transcription is desired, the efficiency of the promoter in expressing the ORF of interest, the ease of construction and the like.
Nucleotide sequences surrounding the translational initiation codon ‘ATG’ have been found to affect expression in yeast cells. If the desired polypeptide is poorly expressed in yeast, the nucleotide sequences of exogenous genes can be modified to include an efficient yeast translation initiation sequence to obtain optimal gene expression. For expression in yeast, this can be done by site-directed mutagenesis of an inefficiently expressed gene by fusing it in-frame to an endogenous yeast gene, preferably a highly expressed gene. Alternatively, as demonstrated in Yarrowia lipolytica, one can determine the consensus translation initiation sequence in the host and engineer this sequence into heterologous genes for their optimal expression in the host of interest.
Termination control regions may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary, however, it is most preferred if included. The termination region can be derived from the 3′ region of the gene from which the initiation region was obtained or from a different gene. A large number of termination regions are known and function satisfactorily in a variety of hosts (when utilized both in the same and different genera and species from where they were derived). The termination region usually is selected more as a matter of convenience rather than because of any particular property. Preferably, the termination region is derived from a yeast gene, particularly Saccharomyces, Schizosaccharomyces, Candida, Yarrowia or Kluyveromyces. The 3′-regions of mammalian genes encoding γ-interferon and α-2 interferon are also known to function in yeast. Termination control regions may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary; however, it is most preferred if included. In one embodiment, the terminator is the terminator is selected from the group consisting of LIP2, PEX20, and XPR2.
Suitable Coding Regions of Interest
Coding regions of interest to be expressed in the recombinant yeast host may be either endogenous to the host or heterologous and must be compatible with the host organism. Genes encoding proteins of commercial value are particularly suitable for expression. For example, suitable coding regions of interest may include (but are not limited to) those encoding viral, bacterial, fungal, plant, insect, or vertebrate coding regions of interest, including mammalian polypeptides.
The coding regions of the present invention are those encoding proteins useful for the production of resveratrol and/or resveratrol glucoside. The coding regions of interest may be optionally codon-optimized using the preferred codon usage of the host cell selected. The present methods are exemplified using specific genes as described by the accompanying sequence listing. However, many of the genes used to recombinantly produce resveratrol and/or resveratrol glucoside are available from alternative sources. For example, a non-limited list of alternative, publicly available genes of the present invention are provided in Table 1. One of skill in the art can operably link a suitable coding region of interest to suitable regulatory sequences. In a further aspect, one or more of the genes used to recombinantly produce resveratrol can be optionally codon optimized using the preferred codon usage of the host cell selected. In yet a further aspect, the genes selected for recombinant expression in Yarrowia lipolytica can be optionally codon optimized using the preferred codon usage described in Table 2.
Components of Vectors/DNA Cassettes
Vectors or DNA cassettes useful for the transformation of suitable host cells are well known in the art. The specific choice of sequences present in the construct is dependent upon the desired expression products, the nature of the host cell, and the proposed means of separating transformed cells versus non-transformed cells. Typically, however, the vector or cassette contains sequences directing transcription and translation of the relevant gene(s), a selectable marker, and sequences allowing autonomous replication or chromosomal integration. Suitable vectors comprise a region 5′ of the gene that controls transcriptional initiation and a region 3′ of the DNA fragment that controls transcriptional termination. It is most preferred when both control regions are derived from genes from the transformed host cell, although it is to be understood that such control regions need not be derived from the genes native to the specific species chosen as a production host.
As one of skill in the art is aware, merely inserting a chimeric gene into a cloning vector does not ensure that it will be successfully expressed at the level needed. In response to needs for high expression rates, many specialized expression vectors have been created by manipulating a number of different genetic elements that control aspects of transcription, translation, protein stability, oxygen limitation and secretion from the host cell. More specifically, some of the molecular features that have been manipulated to control gene expression include: 1.) the nature of the relevant transcriptional promoter and terminator sequences; 2.) the number of copies of the cloned gene and whether the gene is plasmid-borne or integrated into the genome of the host cell; 3.) the final cellular location of the synthesized foreign protein; 4.) the efficiency of translation in the host organism; 5.) the intrinsic stability of the cloned gene protein within the host cell; and 6.) the codon usage within the cloned gene, such that its frequency approaches the frequency of preferred codon usage of the host cell. Each of these types of modifications are encompassed in the present invention as means to further optimize expression of a chimeric gene.
Transformation of Yeast Cells
Once an appropriate chimeric gene has been constructed that is suitable for expression in a yeast cell, it is placed in a plasmid vector capable of autonomous replication in a host cell or it is directly integrated into the genome of the host cell. Integration of expression cassettes can occur randomly within the host genome or can be targeted through the use of constructs containing regions of homology with the host genome sufficient to target recombination with the host locus (Example 8). Where constructs are targeted to an endogenous locus, all or some of the transcriptional and translational regulatory regions can be provided by the endogenous locus.
Where two or more genes are expressed from separate replicating vectors, it is desirable that each vector has a different means of selection and should lack homology to the other constructs to maintain stable expression and prevent reassortment of elements among constructs. Judicious choice of regulatory regions, selection means and method of propagation of the introduced construct can be experimentally determined so that all introduced genes are expressed at the necessary levels to provide for synthesis of the desired products.
Constructs comprising a coding region of interest may be introduced into a host cell by any standard technique. These techniques include transformation (e.g., lithium acetate transformation [Guthrie, C., Methods in Enzymology, 194:186-187 (1991)]), protoplast fusion, biolistic impact, electroporation, microinjection, or any other method that introduces the gene of interest into the host cell. More specific teachings applicable for oleaginous yeast (i.e., Yarrowia lipolytica) include U.S. Pat. No. 4,880,741, U.S. Pat. No. 5,071,764, and Chen, D. C. et al. (Appl Microbiol Biotechnol., 48(2):232-235 (1997)).
For convenience, a host cell that has been manipulated by any method to take up a DNA sequence (e.g., an expression cassette) will be referred to as “transformed” or “recombinant” herein. The transformed host will have at least one copy of the expression construct and may have two or more, depending upon whether the gene is integrated into the genome, amplified, or is present on an extrachromosomal element having multiple copy numbers. The transformed host cell can be identified by selection for a marker contained on the introduced construct.
Alternatively, a separate marker construct may be co-transformed with the desired construct, as many transformation techniques introduce many DNA molecules into host cells. Typically, transformed hosts are selected for their ability to grow on selective media. Selective media may incorporate an antibiotic or lack a factor necessary for growth of the untransformed host, such as a nutrient or growth factor. An introduced marker gene may confer antibiotic resistance or encode an essential growth factor or enzyme, thereby permitting growth on selective media when expressed in the transformed host. Selection of a transformed host can also occur when the expressed marker protein can be detected, either directly or indirectly. The marker protein may be expressed alone or as a fusion to another protein. The marker protein can be detected by: 1.) its enzymatic activity (e.g., β-galactosidase can convert the substrate X-gal [5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside] to a colored product; luciferase can convert luciferin to a light-emitting product); or 2.) its light-producing or modifying characteristics (e.g., the green fluorescent protein of Aequorea victoria fluoresces when illuminated with blue light). Alternatively, antibodies can be used to detect the marker protein or a molecular tag on, for example, a protein of interest. Cells expressing the marker protein or tag can be selected, for example, visually, or by techniques such as FACS or panning using antibodies. For selection of yeast transformants, any marker that functions in yeast may be used. Preferred for use herein are resistance to kanamycin, hygromycin and the aminoglycoside G418, as well as ability to grow on media lacking uracil or leucine.
Industrial Production Using Transformed Oleaginous Microorganisms Expressing Suitable Coding Regions of Interest
In general, media conditions which may be optimized for high-level expression of a particular coding region of interest include the type and amount of carbon source, the type and amount of nitrogen source, the carbon-to-nitrogen ratio, the oxygen level, growth temperature, pH, length of the biomass production phase and the time of cell harvest. Microorganisms of interest, such as oleaginous yeast, are grown in complex media (e.g., yeast extract-peptone-dextrose broth (YPD)) or a defined minimal media that lacks a component necessary for growth and thereby forces selection of the desired expression cassettes (e.g., Yeast Nitrogen Base (DIFCO Laboratories, Detroit, Mich.)).
Fermentation media in the present invention must contain a suitable carbon source for the production of resveratrol and/or resveratrol glucoside. Suitable carbon sources may include, but are not limited to: monosaccharides (e.g., glucose, fructose), disaccharides (e.g., lactose, sucrose), oligosaccharides, polysaccharides (e.g., starch, cellulose or mixtures thereof), sugar alcohols (e.g., glycerol) or mixtures from renewable feedstocks (e.g., cheese whey permeate, cornsteep liquor, sugar beet molasses, barley malt). Additionally, carbon sources may include alkanes, fatty acids, esters of fatty acids, monoglycerides, diglycerides, triglycerides, phospholipids and various commercial sources of fatty acids including vegetable oils (e.g., soybean oil) and animal fats. Additionally, the carbon source may include one-carbon sources (e.g., carbon dioxide, methanol, formaldehyde, formate, carbon-containing amines) for which metabolic conversion into key biochemical intermediates has been demonstrated. Hence, it is contemplated that the source of carbon utilized in the present invention may encompass a wide variety of carbon-containing sources and will only be limited by the choice of the host organism. Although all of the above mentioned carbon sources and mixtures thereof are expected to be suitable in the present invention, preferred carbon sources are sugars and/or fatty acids. Most preferred is glucose and/or fatty acids containing between 10-22 carbons.
Nitrogen may be supplied from an inorganic (e.g., (NH4)2SO4) or organic source (e.g., urea or glutamate). In addition to appropriate carbon and nitrogen sources, the fermentation media must also contain suitable minerals, salts, cofactors, buffers, vitamins, and other components known to those skilled in the art suitable for the growth of the microorganism.
Preferred growth media in the present invention are common commercially prepared media, such as Yeast Nitrogen Base (DIFCO Laboratories, Detroit, Mich.). Other defined or synthetic growth media may also be used and the appropriate medium for growth of the particular microorganism will be known by one skilled in the art of microbiology or fermentation science. A suitable pH range for the fermentation is typically between about pH 4.0 to pH 8.0, wherein pH 5.5 to pH 7.0 is preferred as the range for the initial growth conditions. The fermentation may be conducted under aerobic or anaerobic conditions, wherein microaerobic conditions are preferred.
Host cells comprising a suitable coding region of interest operably linked to the promoters of the present invention may be cultured using methods known in the art. For example, the cell may be cultivated by shake flask cultivation, small-scale or large-scale fermentation in laboratory or industrial fermentors performed in a suitable medium and under conditions allowing expression of the coding region of interest.
Where commercial production of resveratrol and/or resveratrol glucoside is desired a variety of fermentation methodologies may be applied. For example, large-scale production of a specific gene product over-expressed from a recombinant host may be produced by a batch, fed-batch or continuous fermentation process.
A batch fermentation process is a closed system wherein the media composition is fixed at the beginning of the process and not subject to further additions beyond those required for maintenance of pH and oxygen level during the process. Thus, at the beginning of the culturing process the media is inoculated with the desired organism and growth or metabolic activity is permitted to occur without adding additional sources (i.e., carbon and nitrogen sources) to the medium. In batch processes the metabolite and biomass compositions of the system change constantly up to the time the culture is terminated. In a typical batch process, cells proceed through a static lag phase to a high growth log phase and finally to a stationary phase, wherein the growth rate is diminished or halted. Left untreated, cells in the stationary phase will eventually die. A variation of the standard batch process is the fed-batch process, wherein the source is continually added to the fermentor over the course of the fermentation process. A fed-batch process is also suitable in the present invention. Fed-batch processes are useful when catabolite repression is apt to inhibit the metabolism of the cells or where it is desirable to have limited amounts of source in the media at any one time. Measurement of the source concentration in fed-batch systems is difficult and therefore may be estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen and the partial pressure of waste gases (e.g., CO2). Batch and fed-batch culturing methods are common and well known in the art and examples may be found in Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, 2nd ed., (1989) Sinauer Associates Sunderland, Mass.; or Deshpande, Mukund V., Appl. Biochem. Biotechnol., 36:227 (1992).
Commercial production of resveratrol and/or resveratrol glucoside may also be accomplished by a continuous fermentation process, wherein a defined media is continuously added to a bioreactor while an equal amount of culture volume is removed simultaneously for product recovery. Continuous cultures generally maintain the cells in the log phase of growth at a constant cell density. Continuous or semi-continuous culture methods permit the modulation of one factor or any number of factors that affect cell growth or end product concentration. For example, one approach may limit the carbon source and allow all other parameters to moderate metabolism. In other systems, a number of factors affecting growth may be altered continuously while the cell concentration, measured by media turbidity, is kept constant. Continuous systems strive to maintain steady state growth and thus the cell growth rate must be balanced against cell loss due to media being drawn off the culture. Methods of modulating nutrients and growth factors for continuous culture processes, as well as techniques for maximizing the rate of product formation, are well known in the art of industrial microbiology and a variety of methods are detailed by Brock, supra.
Methods to Isolate Resveratrol and/or Resveratrol Glucoside
Resveratrol can be extracted from plant or other sources by extraction with organic solvents, such as methanol or methanol/water (80:20) (Adrian et al., J. Agric. Food Chem., 48:6103-6105 (2000)) and methanol:acetone:water:formic acid (40:40:20:0.1) (Rimando et al., J. Agric. Food Chem., 52:4713-4719 (2004)). Dried or freeze-dried extracts are dissolved in methanol, or water, or acetone, before reverse phase HPLC analysis. In one study in which resveratrol glucoside is produced in transgenic alfalfa (Hipskind, J. D., and Paiva, N. L, Molecular plant-microbe interactions, 13(5):551-562 (2000)), resveratrol and other metabolites are extracted in 100% acetone, followed by drying completely in nitrogen, and dissolving in 70% methanol in water. The extract is then analyzed by reverse phase HPLC. It is also possible to extract resveratrol using ethanol, dimethylsulfoxide, or other polar solvents. In the study in which resveratrol is produced in the yeast Saccharomyces cerevisiae at  ̃1.4 μg/L (Becker et al., supra), resveratrol was extracted by breaking cells open by glass beads in 100% ice cold methanol and incubating at 37° C. for a few hours. Upon glycosidase treatment, the sample was dried and dissolved in 50% acetonitrile and analyzed by HPLC and mass spectroscopy. It is also possible to extract resveratrol using ethanol, dimethylsulfoxide, acetonitrile or other polar solvents. Resveratrol or resveratrol glucoside can also be detected by 1H-NMR.
Uses of Resveratrol and/or Resveratrol Glucoside
The microbially produced resveratrol and/or resveratrol glucoside of the present invention may be used as an antioxidant, anti-inflammatory agent, antimicrobial/antifungal agent, a dietary supplement, or as a pharmacological agent used to treat such conditions as hypercholesterolemia or cancer, to name a few. The resveratrol and/or resveratrol glucoside can be used for formulating cosmetics, cosmeceuticals, nutritional supplements, one or more components of a pharmaceutical composition, compositions applied fresh foods and or agricultural crops to deter and/or inhibit microbial/fungal growth. In another embodiment, the isolated resveratrol-producing and/or resveratrol glucoside-producing microbial biomass is used as an additive in a composition selected from the group consisting of antioxidants, anti-inflammatory agents, antifungal/antimicrobial agents, cosmetics, cosmeceuticals, nutritional/dietary supplements, feed additives, and pharmacological agents, to name a few. The isolated oleaginous biomass may be in the form of whole cells, homogenized cells, or partially-purified cell extracts.
In one aspect of the invention, a composition selected from the group consisting of antioxidants, anti-inflammatory agents, antifungal/antimicrobial agents, cosmetics, cosmeceuticals, nutritional/dietary supplements, feed additives, and pharmacological agents is provided comprising 0.1 to 99 wt %, preferably from 0.1 to 30 wt %, recombinant oleaginous microbial biomass comprising at least 0.01% (dry cell weight) resveratrol and/or resveratrol glucoside.
In another embodiment, resveratrol and/or resveratrol glucoside is used as an antioxidant to stabilize other antioxidants such as carotenoids (including xanthophylls) and polyunsaturated fatty acids, especially ω-3 polyunsaturated fatty acids. In one embodiment, the recombinantly produced stilbene is added to compositions comprising at least one ω-3 PUFA. In a preferred embodiment, the oleaginous microorganism is engineered to produce both resveratrol/resveratrol glucoside and at least one ω-3 polyunsaturated fatty acid whereby either compounds, preferably the ω-3 PUFA, exhibits increased stability to oxidation.
EXAMPLES
The present invention is further defined in the following Examples. It should be understood that these Examples, while indicating preferred aspects of the invention, are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various usages and conditions.
Unless otherwise specified, all referenced United States patents and patent applications are hereby incorporated by reference.
General Methods
Standard recombinant DNA and molecular cloning techniques used in the Examples are well known in the art and are described by Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor,
(1989) (Maniatis) and by T. J. Silhavy, M. L. Bennan, and L. W. Enquist, Experiments with Gene Fusions, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1984) and by Ausubel, F. M. et al., Current Protocols in Molecular Biology, pub. by Greene Publishing Assoc. and Wiley-Interscience (1987).
Materials and methods suitable for the maintenance and growth of bacterial cultures are well known in the art. Techniques suitable for use in the following examples may be found as set out in Manual of Methods for General Bacteriology (Phillipp Gerhardt, R. G. E. Murray, Ralph N. Costilow, Eugene W. Nester, Willis A. Wood, Noel R. Krieg and G. Briggs Phillips, eds), American Society for Microbiology, Washington, D.C. (1994)) or by Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition, Sinauer Associates, Inc., Sunderland, Mass. (1989).
All reagents, restriction enzymes and materials used for the growth and maintenance of bacterial cells were obtained from Aldrich Chemicals (Milwaukee, Wis.), DIFCO Laboratories (Detroit, Mich.), GIBCO/BRL (Gaithersburg, Md.), or Sigma Chemical Company (St. Louis, Mo.) unless otherwise specified.
The meaning of abbreviations is as follows: “sec” means second(s), “min” means minute(s), “h” or “hr” means hour(s), “psi” means pounds per square inch, “nm” means nanometers, “d” means day(s), “μL” means microliter, “mL” means milliliters, “L” means liters, “mm” means millimeters, “nm” means nanometers, “mM” means millimolar, “M” means molar, “mmol” means millimole(s), “pmole” mean micromole”, “g” means gram, “μg” means microgram and “ng” means nanogram, “U” means units, “mU” means milliunits, “U mg−1” means units per mg, “PEG” mean (poly)ethylene glycol, and “DTT” means dithiothreitol.
Example 1
Determining the Preferred Codon Usage in Yarrowia lipolytica
Approximately 100 genes of Yarrowia lipolytica were found in the National Center for Biotechnology Information public database. The coding regions of these genes, comprising 121,167 bp, were translated by the EditSEQ program of DNAStar to the corresponding 40,389 amino acids and were tabulated to determine the Y. lipolytica codon usage profile shown in Table 2. The column titled “No.” refers to the number of times a given codon encodes a particular amino acid in the sample of 40,389 amino acids. The column titled “%” refers to the frequency that a given codon encodes a particular amino acid. Entries shown in bold text represent the codons favored in Yarrowia lipolytica.







TABLE 2







Codon Usage in Yarrowia lipolytica













Amino





Codon
Acid
No.
%
















GCA
Ala (A)
359
11.4



GCC
Ala (A)
1523
48.1



GCG
Ala (A)
256
8.1



GCU
Ala (A)
1023
32.3



AGA
Arg (R)
263
13.2



AGG
Arg (R)
91
4.6



CGA
Arg (R)
1133
56.8



CGC
Arg (R)
108
5.4



CGG
Arg (R)
209
1.0



CGU
Arg (R)
189
9.5



AAC
Ans (N)
1336
84.0



AAU
Ans (N)
255
16.0



GAC
Asp (D)
1602
66.8



GAU
Asp (D)
795
33.2



UGC
Cys (C)
268
53.2



UGU
Cys (C)
236
46.8



CAA
Gln (Q)
307
17.0



CAG
Gln (Q)
1490
83.0



GAA
Glu (E)
566
23.0



GAG
Glu (E)
1893
77.0



GGA
Gly (G)
856
29.7



GGC
Gly (G)
986
34.2



GGG
Gly (G)
148
5.1



GGU
Gly (G)
893
31.0



CAC
His (H)
618
65.5



CAU
His (H)
326
34.5



AUA
Ile (I)
42
2.1



AUC
Ile (I)
1106
53.7



AUU
Ile (I)
910
44.2



CUA
Leu (L)
166
4.7



CUC
Leu (L)
1029
29.1



CUG
Leu (L)
1379
38.9



CUU
Leu (L)
591
16.7



UUA
Leu (L)
54
1.5



UUG
Leu (L)
323
9.1



AAA
Lys (K)
344
14.8



AAG
Lys (K)
1987
85.2



AUG
Met (M)
1002
100



UUC
Phe (F)
996
61.1



UUU
Phe (F)
621
38.9



CCA
Pro (P)
207
9.6



CCC
Pro (P)
1125
52.0



CCG
Pro (P)
176
8.2



CCU
Pro (P)
655
30.2



AGC
Ser (S)
335
11.3



AGU
Ser (S)
201
6.8



UCA
Ser (S)
221
7.5



UCC
Ser (S)
930
31.5



UCG
Ser (S)
488
16.5



UCU
Ser (S)
779
26.4



UAA
Term
38
46.9



UAG
Term
30
37.0



UGA
Term
13
16.1



ACA
Thr (T)
306
12.7



ACC
Thr (T)
1245
51.6



ACG
Thr (T)
269
11.1



ACU
Thr (T)
595
24.6



UGG
Trp (W)
488
100



UAC
Tyr (Y)
988
83.2



UAU
Tyr (Y)
200
16.8



GUA
Val (V)
118
4.2



GUC
Val (V)
1052
37.3



GUG
Val (V)
948
33.6



GUU
Val (V)
703
24.9










For further optimization of gene expression in Y. lipolytica, the consensus sequence around the ‘ATG’ initiation codon of 79 genes was examined. The ‘A’ of the ATG translation codon is referenced as the +1 position. Seventy seven percent of the genes analyzed had an “A” in the −3 position, indicating a strong preference for “A” at this position. There was also preference for ‘A’ or ‘C’ at the −4, −2 and −1 positions, an ‘A’, ‘C’ or ‘T’ at position +5, and a ‘G’ or ‘C’ at position +6 (see FIG. 4 of U.S. Ser. No. 10/840,478; hereby incorporated by reference).
Example 2
Design of A Codon-optimized Phenylalanine Ammonia Lyase Gene
The phenylalanine ammonia lyase gene of Rhodotorula glutinis (SEQ ID NO:1-2) is 2151 bp in length (GenBank® Accession No: X12702). As with other phenylalanine ammonia lyases, the enzyme encoded by the phenylalanine ammonia lyase gene also has tyrosine ammonia lyase activity, converting tyrosine into pHCA. A codon-optimized phenylalanine ammonia lyase gene was designed, based on the R. glutinis DNA sequence, according to the Yarrowia codon usage pattern, the consensus sequence around the ATG translation initiation codon, and the general rules of RNA stability (Guhaniyogi, G. and J. Brewer, Gene, 265(1-2):11-23 (2001)). In addition to modifying the translation initiation site, 357 bp of the 2151 bp coding region corresponding to 342 codons were also codon-optimized. The GC content was reduced from 64.8% of the wild type coding region to 56.4% of the codon optimized coding region (SED ID NO: 3) of the phenylalanine ammonia lyase gene.
None of the modifications in the codon-optimized gene changed the amino acid sequence of the encoded protein (SEQ ID NO:2). The codon optimized gene was synthesized and inserted into pUC57 by GenScript Corparation (Piscataway, N.J.) to generate pQZ-PAL.
Example 3
Design of A Codon-optimized Coumaroyl CoA Ligase Gene
The coumaroyl CoA ligase gene of Streptomyces coelicolor (SEQ ID NOs:4-5) is 1569 bp in length (GenBank® Accession No: AL939119). A codon-optimized coumaroyl CoA ligase gene was designed, based on the Streptomyces DNA sequence, according to the Yarrowia codon usage pattern, the consensus sequence around the ATG translation initiation codon, and the general rules of RNA stability (Guhaniyogi, G. and J. Brewer, supra). In addition to modifying the translation initiation site, 278 bp of the 1569 bp coding region corresponding to 260 codons were also codon-optimized. The GC content was reduced from 72.7% of the wild type coding region to 59% of the codon optimized coding region (SED ID NO. 6) of the coumaroyl CoA ligase gene. None of the modifications in the codon-optimized gene changed the amino acid sequence of the encoded protein (SEQ ID NO:5), except the first codon from GTG (SEQ ID NO: 4) to ATG (SEQ ID NO. 6). The codon optimized gene was synthesized and inserted into pUC57 by GenScript Corparation (Piscataway, N.J.) to generate pQZ-4CL.
Example 4
Design of A Codon-optimized Resveratrol Synthase Gene
The resveratrol synthase gene of grape (SEQ ID NOs:7-8) is 1179 bp in length (clone: vlb1c.pk013.c4; E. I. du Pont de Nemours and Company, Inc., Wilmington, Del.). A codon-optimized resveratrol synthase gene was designed, based on the grape DNA sequence, according to the Yarrowia codon usage pattern, the consensus sequence around the ATG translation initiation codon, and the general rules of RNA stability (Guhaniyogi, G. and J. Brewer, supra). In addition to modifying the translation initiation site, 229 bp of the 1179 bp coding region corresponding to 203 codons were also codon-optimized. The GC content was increased from 45.4% of the wild type coding region to 56% of the codon optimized coding region (SED ID NO. 9) of the resveratrol synthase gene. None of the modifications in the codon-optimized gene changed the amino acid sequence of the encoded protein (SEQ ID NO:8). The codon optimized gene was synthesized and inserted into pUC57 by GenScript Corparation (Piscataway, N.J.) to generate pQZ-RS
Example 5
Construction of Chimeric Genes for Expression of Resveratrol Biosynthesis Genes in Yarrowia lipolytica 
In general, codon-optimized genes were either isolated by restriction digestion or amplified by PCR and inserted into appropriate vectors for expression. Each PCR amplification was carried out in a 50 μL total volume, comprising PCR buffer containing: 10 ng template, 10 mM KCl, 10 mM (NH4)2 SO4, 20 mM Tris-HCl (pH 8.75), 2 mM MgSO4, 0.1% Triton X-100, 100 μg/mL BSA (final concentration), 200 μM each deoxyribonucleotide triphosphate, 10 pmole of each primer and 1 μL of PfuTurbo DNA polymerase (Stratagene, San Diego, Calif.). Amplification was carried out as follows (unless otherwise specified): initial denaturation at 95° C. for 3 min, followed by 35 cycles of the following: 95° C. for 1 min, 56° C. for 30 sec, 72° C. for 1 min. A final extension cycle of 72° C. for 10 min was carried out, followed by reaction termination at 4° C.
Construction of pZFPAL plasmid containing FBAIN::PAL::Lip2 chimeric gene The 2154 bp NcoI/NotI fragment of pQZ-PAL which contains the codon-optimized coding region of phenylalanine ammonia lyase gene was inserted into the NcoI/NotI sites of pZF17T to generate PZFPAL (FIG. 2). pZF17T is a derivative plasmid of pDMW214 (U.S. Ser. No. 10/987,548), which contains a FBAIN promoter::codon optimized coding region of Saprolegia diclina Δ17 desaturase (U.S. Ser. No. 10/840,579)::terminator of Yarrowia lipase2 gene (GenBank® AJ012632).
The FBAIN promoter (U.S. Ser. No. 10/987,548, SEQ ID NO: 10) includes 826 bp upstream DNA sequence and 169 bp downstream sequence from the putative translation start codon of Yarrowia fructose-bisphosphate aldolase gene (fba1). There is a 102 bp intron located between +60 and +163 nucleotides of the 169 bp downstream sequence from the translation start codon (the nucleotide A of the ATG translation codon was designated as +1 position).
Construction of pZTRS Plasmid Containing TEF::RS::XPR2 Chimeric Gene
The 1179 bp NcoI/NotI fragment of PQZ-RS which contains the codon-optimized coding region of resveratrol synthase gene was inserted into the NcoI/NotI sites of pY54-PCB to generate pZTRS (FIG. 2). pY54-PCB is a derivative plasmid of pY54-PC (U.S. Ser. No. 10/840,579). A SbfI site was introduced into pY54-PC to generate pY54-PCB by in vitro mutagenesis using pY331 (SEQ ID NO: 11) and pY332 (SEQ ID NO: 12) as primers. Plasmid pZTRS contains a TEF promoter:RS::XPR2 chimeric gene. The TEF promoter (Muller, S., et al., Yeast, 14: 1267-1283 (1998)) was amplified from Yarrowia lipolytica genomic DNA by PCR using TEF5′ (SEQ ID NO: 13) and TEF3′ (SEQ ID NO: 14) primers. The XPR2 transcriptional terminator (SEQ ID NO: 15) was amplified by PCR using pINA532 (a gift from Dr. Claude Gaillardin, Institut National Agronomics, Centre de Biotechnologie Agro-Industrielle, laboratoire de Genetique Moleculaire et Cellularie INRA-CNRS, F-78850 Thiverval-Grignon, France (U.S. Ser. No. 10/840,579)) as template and XPR5′ (SEQ ID NO: 16) and XPR3′ (SEQ ID NO: 17) as primers.
Construction of PZUF4C Plasmid Containing FBAIN::4CL::Pex20 Chimeric Gene
The 788 bp of the 5′ end part of the codon-optimized 4CL gene (SEQ ID NO. 18) was amplified by PCR using pQZ-4CL as template, YL539 (SEQ ID NO. 19) and YL540 (SEQ ID NO. 20) as primers. The 5′ end of the Primer YL539 contains a NcoI site, The 5′ end of YL540 has an XmnI site. The PCR product was digested with NcoI/XmnI, and the fragment was isolated after separation of agarose gel electrophoresis. Plasmid pQZ4CL was also digested with XmnI/NotI, and the 792 bp XmnI/NotI fragment was isolated after separation by agarose gel electrophoresis. The gel purified NcoI/XmnI digested fragment and the XmnI/NotI digested fragment were then ligated with NcoI/NotI digested pZUF17 to generate pZUF4C. The pZUF4C (FIG. 2) contains a FBAIN promoter:4CL::Pex20 (GenBank® AF054613) chimeric gene (SEQ ID NO. 21).
Construction of pZUF17
Yarrowia ura3 gene (GenBank® AJ306421; SEQ ID NO: 54) was amplified using genomic DNA as template and ologouncleotides YL27 (SEQ ID NO. 22) and YL28 (SEQ ID NO. 23) as primers. The PCR product was digested with SalI/PacI, and then inserted into SalI/PacI-digested pY5-9 (U.S. Ser. No. 10/840,579) to generate pY21(Ura). A Bs/WI site was introduced into pY21 (Ura) to generate pY22(Ura) by in vitro mutagenesis using pY21 as template and oligonucleotides YL61 (SEQ ID NO. 24) and YL62 (SEQ ID NO. 25) as primers. The M. alpina A5 desaturase gene (SEQ ID NO. 26; U.S. Pat. No. 6,075,183; hereby incorporated by reference) was amplified by PCR using oligonucleotides YL11 and YL12 (SEQ ID NOs: 27, 28) as primers and plasmid pCGR4 (U.S. Pat. No. 6,075,183) as template. The 1357 bp PCR product was digested with NcoI/NotI and ligated to NcoI/NotI-digested pY5-2 to generate pYMA5. The NcoI/NotI fragment of pYMA5 was used to replace the NcoI/NotI fragment of pY22(Ura) to generate pYZT5U. A SwaI was introduced into pYZT5U to generate pYZT5U-S by in vitro mutagenesis using pZYT5U as template and oligonucleotides YL224NYL225 as primers (SEQ ID NOs. 29 and 30). A ClaI site was introduced into pYZT5U-S to generate pYZT5U-SC by in vitro mutagenesis using pZYT5U-S as template and oligonucleotides YL232/YL233 (SEQ ID NO. 31, 32) as primers.
pYSD17S-C was a derivative plasmid of pYSD17S (U.S. Ser. No. 10/840,579; incorporated herein by reference). A ClaI site was introduced into pYSD17S to generate pYSD1 7S-C by in vitro mutagenesis using pYSD17S as template and oligonucleotides YL101/YL102(SEQ ID NO. 33, 34) as primers. The GPM promoter was amplified by PCR using pT-GML as template and oligonucleotides YL95 and YL266 (SEQ ID NOs. 35 and 36) as primers. The PCR product was digested with PmeI/NcoI, and then used to replace the PmeI/NcoI fragment of pYSD1 7S-C to generate pZGM17S. The transcriptional terminator of Lip2 gene (GenBank®#: AF054613) was amplified by PCR using Yarrowia genomic DNA as template and oligonucleotides YL263 and YL265 (SEQ ID NOs. 37 and 38) as primers. The PCR product was digested with NotI/ClaI, and then used to replace the NotI/ClaI fragment of pZGM17S to generate pZGM17T. pZGM17T-S was produced by elimination of the SphI site in the Lip2 terminator of pZGM17T through in vitro mutagenesis using pZGM17T as template, oligonucleotides YL285 and YL286 (SEQ ID NOs. 39 and 40) as primers. The PmeI/NcoI fragment containing the FBAIN promoter of pDMW214 (U.S. Ser. No. 10/987,548), NcoI/NotI fragment containing the coding region of synthetic Δ17 desaturase gene of pZGM17S and the PmeI/NotI digested pZGM17T-S vector, were three way directionally ligated together to produce pZF17T. The transcriptional terminator of Pex20 gene (SEQ ID NO: 53) was PCR amplified using Yarrowia genomic DNA as template and oligonucleotides YL259 and YL260 (SEQ ID NO. 41, 42) as primers. The PCR product was digested with NotI/BsiWI. The pZUF17 was then produced by three way ligation using MfeI/NotI digested pYZT5U-SC as vector, MfeI/NotI fragment containing FBAIN::D17 of pZF17T and the NotI/BsiWI fragment containing Pex20 terminator (GenBank® AF054613).
Example 6
Construction of Plasmids PZG4PR and pZT4PR
Construction of pZG4PR
The Yarrowia GPAT promoter (SEQ ID NO. 43) was PCR amplified using pYGPAT-GUS (U.S. Ser. No. 11/225,354) as template, and oligonucleotides YL497 and YL498 (SEQ ID NOs. 44 and 45) as primers. The PCR product was digested with SwaI/NcoI. The SwaI/NcoI fragment containing the GPAT promoter, the NcoI/NotI fragment of pZUF4C, and the SwaI/NotI-digested pKO2UFkF2 were directionally ligated together to produce pKO2UGP4C. The PmeI/ClaI fragment of pZFPAL was used to replace the PmeI/ClaI fragment of pKO2UGP4C to generate pZG4FP. The ClaI/PacI fragment of pZTRS was used to replace the ClaI/PacI fragment of pZG4FP to produce pZG4PR (SEQ ID NO: 55; FIG. 3).
Construction of pZT4PR
A PmeI site was introduced into pYSD17S-C to generate pYSD17S-CP by in vitro mutagenesis using oligonucleotides YL103 and YL104 (SEQ ID NOs. 46 and 47) as primers. The PmeI/NcoI fragment of pYSD17S-CP, the NcoI/NotI fragment of pZUF4C, and the SwaI/NotI-digested pKO2UFkF2 (FIG. 4) were directionally ligated together to produce pKO2UT4C. Plasmid pKO2UFkF2 (SEQ ID NO. 48) contained the following components as described in Table 3:







TABLE 3







Description of Plasmid pKO2UFkF2








Restriction Enzyme



Sites And


Nucleotides Within


SEQ ID NO: 48
Description Of Fragment And Chimeric Gene


pKO2UF2PE
Components





AscI/BsiWI
730 bp 5′ part of Yarrowia Δ12 desaturase


92459-1722)
gene (SEQ ID NO: 49)


SalI/SphI
556 bp 3′ part of Yarrowia Δ12 desaturase


(5742-5167)
gene (SEQ ID NO: 50)


SwaI/BsiWI/
FBAINm::F. moniliforme Δ12DS::Pex20,


(7638-1722)
comprising:



FBAINm promoter (SEQ ID NO: 51)



F moniliforme.b12 DS: Fusarium moniliforme



Δ12 desaturase gene (SEQ ID NO: 52)



Pex20: Pex20 terminator sequence (SEQ ID NO.



53) of Yarrowia Pex20 gene (GenBank ®



AF054613)


SalI/PacI
Yarrowia Ura3 gene (GenBank ® AJ306421;


(5742-7240)
SEQ ID NO. 54)









The PmeI/ClaI fragment of pZFPAL was used to replace the PmeI/ClaI fragment of pKO2UT4C to generate pZT4FP. The ClaI/PacI fragment of pZTRS was used to replace the ClaI/PacI fragment of pZT4FP to produce pZT4PR (SEQ ID NO: 56; FIG. 4).
Example 7
Construction of Plasmids Containing Strong Promoters and Suitable for the Coordinate Expression of Multiple Resveratrol Biosynthesis Pathway Genes in Yarrowia lipolytica 
Construction of pZUF-MOD-1
pZUF-MOD-1 (SEQ ID NO: 57; FIG. 5) was prepared as follows. First, primers pzuf-mod1 (5′-GATCCCATGGATCCAGGCCTGTTMCGG-3′; SEQ ID NO: 58) and pzuf-mod2 (5′-GATCGCGGCCGCAGACATGATAAGATACATTG-3′; SEQ ID NO: 59) were used to amplify a 253 bp DNA fragment containing multiple cloning sites (MCS, SEQ ID NO: 60) using pDNR-LIB (ClonTech, Palo Alto, Calif.) as template. The reaction mixture contained  ̃50 ng of template DNA in 1 μL, 1 μL of 20 μM stock solution of each primer, 22 μL of water and 25 μL of 2× premix of TaKaRa ExTaq polymerase mix (TaKaRa Bio, Inc., Mountain View, Calif.). The PCR condition was as follows: 94° C. for 1 min, 30 cycles of 94° C. 30 sec, 55° C. 30 sec and 72° C. 30 min, finish with an additional 5 min at 72° C. The amplified fragment was purified with a QIAquick PCR purification kit (Qiagen, Valencia, Calif.). This fragment was digested with NcoI-/NotI, and ligated at room temperature overnight into similarly digested pZUF17 vector (wherein the ligation consisted of 0.5 μg of the digested PCR fragment and 0.3 μg of  ̃7079 bp digested pZUF17 vector (Example 6) fragment with 2 μL of 10×T4 ligase buffer and 3 units of T4 DNA ligase (Promega, Madison, Wis.) in a total volume of 20 μL. The resulting ligation mixture was used to transform E. coli Top10 cells (Invitrogen, Carlsbad, Calif.). Plasmid DNA was purified from 4 resulting colonies, using a Qiagen QIAprep Spin Miniprep kit. The purified plasmids were digested with NcoI and NotI to confirm the presence of the  ̃250 bp fragment. The resulting plasmid was named “pZUF-MOD-1” (FIG. 5; Table 4).







TABLE 4







Description of Plasmid pZUF-MOD-1








Restriction Enzyme



Sites And Nucleotides


Within SEQ ID NO: 57
Description Of Fragment And Chimeric Gene


pZUF-MOD-1 (7323 bp)
Components





MfeI/NcoI
971 bp part of Y. lipolytica FBAIN promoter


(5798-6769)


NcoI/NotI
239 bp part of the multiple cloning site


(6769-7007)
region (MCS)


NotI/BsiWI/
316 bp fragment containing terminator region


(7007-1)
of Y. lipolytica PEX20 gene (GenBank ®



AF054613)


SalI/PacI
Yarrowia Ura3 gene (GenBank ® AJ306421;


(4213-5705)
SEQ ID NO. 54)









Construction of pEXP-MOD1

The promoter region of the Y. lipolytica gene YALI-CDS5725.1 (EXP promoter; SEQ ID NO: 61), encoding a homolog of the non-classic export protein of S. cerevisiae, was cloned by PCR using the following primers;










EP-Promoter-F




(5′-GATCCTCGAGGGAGTTTGGCGCCCGTTTTTTC-3′;



SEQ ID NO: 62)



 



EP-Promoter-R



(5′-GATCCCATGGTTGTAGATATGTCTTGTGTGTAAG-3′;



SEQ ID NO: 63)






PCR reaction was carried out using TaKaRa ExTaq polymerase 2× premix, with Y. lipolytica genomic DNA as template ( ̃100 ng). 1 μL each of 20 μM primers was added to a 50 μL PCR reaction mixture. Reaction condition was as follows: 94° C. for 2 min 30 sec followed by 30 cycles of 94° C. 30 sec, 55° C. 30 sec and 72° C. 1 min, and a final extension of 7 min at 72° C. The PCR product was purified using Qiagen PCR purification kit. Purified PCR product was digested with XhoI and NcoI, and ligated with a 6259 bp fragment resulting from a SalI and NcoI digestion of pZUF-MOD-1. This replaced the FBA-IN promoter in pZUF-MOD-1 with the EXP1 promoter. The resulting plasmid was named pEXP-MOD-1 (FIG. 5; Table 5).







TABLE 5







Description of Plasmid pEXP-MOD-1








Restriction Enzyme



Sites And


Nucleotides Within


SEQ ID NO: 64


pEXP-MOD-1 (7277
Description Of Fragment And Chimeric Gene


bp)
Components





SalI/NcoI
1017 bp Y. lipolytica EXP promoter


(6260-1)


NcoI/NotI
238 bp part of the stuffer fragment (MCS)


(1-239)


NotI/BsiWI/
316 bp fragment containing terminator


(239-556)
region of Y. lipolytica PEX20 gene



(GenBank ® AF054613)


SalI/PacI
Yarrowia Ura3 gene (GenBank ® AJ306421;


(4768-6260)
SEQ ID NO. 54)









Construction of pZGN
Plasmid pZG4PR was digested with ClaI and PacI, and a  ̃12 kb fragment was isolated. Separately, pZG4PR was also digested with NcoI and PacI, and a 1.4 kb fragment containing the resveratrol synthase and the Y. lipolytica XPR2 terminator was isolated. Finally, plasmid pEXP-MOD-1 was digested with NcoI and ClaI to obtained a  ̃860 bp fragment containing the Y. lipolytica EXP promoter. The three DNA fragments were ligated together to form plasmid pZGN (FIG. 5), where the TEF promoter in plasmid pZG4PR was replaced with the more powerful EXP promoter of Y. lipolytica (SEQ ID NO: 61).







TABLE 6







Description of Plasmid pZGN








Restriction Enzyme



Sites And Nucleotides


Within SEQ ID NO: 66
Description Of Fragment And Chimeric Gene


pZGN (14213 bp)
Components





ClaI/NcoI
838 bp fragment containing Y. lipolytica EXP


(13375-1
promoter


complementary strand)


NcoI/NotI
1182 bp resveratrol synthase (codon optimized)


(12193-13375,


complementary strand)


(10487-11980)
Yarrowia Ura3 gene (GenBank ® AJ306421)


2500-3494
994 bp region containing the Y. lipolytica


(complementary strand)
FBAIN promoter


347-2497
2150 bp Phenylalanine lyase (codon optimized)


(complementary strand)


3535-4572
1037 bp Y. lipolytica GPAT promoter


4574-6142
1568 bp coumaroyl-CoA ligase (codon



optimized)









Example 8
Integration of DNA Fragment Containing Multiple Resveratrol Biosynthesis Genes into the Genome of Yarrowia lipolytica 
The plasmid pZGN was cut with BssHII/SphI and then used to transform a Ura− derivative of Y. lipolytica ATCC# 20362, “20362U1”, according to the method of Chen, D. C. et al. (Appl Microbiol Biotechnol., 48(2):232-235-(1997)).
Briefly, 20362U1 was streaked onto a YPD plate and grown at 30° C. for approximately 18 hr. Several large loopfuls of cells were scraped from the plate and resuspended in 1-mL of transformation buffer containing:

    
    
        2.25 mL of 50% PEG, average MW 3350;
        0.125 mL of 2 M Li acetate, pH 6.0;
        0.125 mL of 2M DTT; and
        50 μg shared salmon sperm DNA.
    
    


About 500 ng of plasmid DNA was incubated in 100 μL of resuspended cells, and maintained at 39° C. for 1 hr with vortex mixing at 15 min intervals. The cells were plated onto minimal media plates lacking uracil and maintained at 30° C. for 2 to 3 days. Individual colonies were patched on to minimal media without uracil. They were then screened for resveratrol production as described in Example 9.
Example 9
Production of Resveratrol from Tyrosine in Yarrowia lipolytica Cells Harboring Phenylalanine Ammonia Lyase, Coumaroyl-CoA Ligase and Resveratrol Synthase
Three transformants from pZGN transformation of 20362U1 were grown individually in 50 mL of a medium containing 6.7 g/L yeast nitrogen base, 1 g/L proline, 20 g/L glucose, and 2 mM tyrosine at 30° C. for 3 days in the dark. Cells were harvested by centrifugation at 5,000 rpm for 10 min. Pelleted cells were resuspended in 2-mL ice cold methanol, mixed with equal volume of 0.5 mm glass beads, and shaken in a Biospec mini-beadbeater, at the setting of Homogenization, for 2 min. Three milliliters of methanol was added to the cell lysate. The whole mixture was shaken at 37° C. for 2 hr in the dark, followed by centrifugation for 2 min at 14,000 rpm to remove debris. The clarified supernatant was filtered through a 0.2 μM filter (Nylon Spin-X spin filter, CoStar, Corning Life Sciences, Acton, Mass.). The filtrates were concentrated in a Savant DNA 110 Speed Vac for 2 h to near complete dryness, re-dissolved in 250 μL 25 mM citrate-phosphate buffer, pH 5, containing 0.5 mg/mL β-glucosidase (Sigma catalog number G4511, isolated from almonds), and incubated at approximately 37° C. for 1 hr. The reaction mixture was extracted three times with 250 μL of ethyl acetate. The organic layers were combined and concentrated in Savant DNA 110 Speed Vac for 0.5 h to near complete dryness. Finally the sample was re-dissolved in 250 μL 50% acetonitrile and filtered through a 0.2 μM Nylon Spin-X spin filter (CoStar).
The filtered samples were analyzed for the presence of pHCA and resveratrol by HPLC, using an Agilent 1100 system (Agilent Technologies, Palo Alto, Calif.) with a Zorbax SB-C18 column, 4.6×150 mm, 3.5 micron. The column was eluted with a gradient of 5% to 80% acetonitrile, in 0.5% TFA (trifluoroacetic acid) for 8 min, followed by 80% acetonitrile, 0.5% TFA for 2 min. Both pHCA and resveratrol are detected at 312 nm, with typical retention time of 5.4 min (pHCA) and 6.0 min (resveratrol). The amount of pHCA and resveratrol in the samples were calculated based on a comparison of peak area with known amounts of pure pHCA and resveratrol. Table 4 showed the levels of pHCA and resveratrol in the 4 cultures tested. Resveratrol was extracted from cell pellets, and the level is represented in the amount of resveratrol detected per liter of Yarrowia cells and % dry cell weight.







TABLE 7







p-HCA and Resveratrol Titer in pZGN Transformed


Y. lipolytica 20362U1 cells.













Resveratrol
PHCA
Resveratrol


Sample
pHCA (mg/L)
(mg/L)
(% dcw)
(% dcw)





pZGN1
2.78
1.40
0.093
0.047


pZGN2
2.63
1.29
0.088
0.043


pZGN3
2.37
1.46
0.079
0.049









LC/MS analysis.

The presence of pHCA and resveratrol was further confirmed by Negative Ion Electrospray LCMS, using a Waters LCT Time of Flight mass spectrometer connected to a Waters Alliance 2790 LC system with an Agilent Zorbax SB-C18 column (2.1×150 mm). A gradient from 5% acetonitrile in H2O to 100% acetonitrile in 30 minutes, at a flow rate of 0.25 mL/minute was used to separate components in the samples. Both solvents contained 0.5% formic acid to sharpen the peaks eluding from the LC column. The mass spectrometer was set to scan from 60 to 800 Daltons in 0.9 seconds with a 0.1 second interscan delay.
Samples of pZGN transformed 20362U1 cells were analyzed as described above. The result of the analysis showed that both resveratrol and pHCA were present (FIG. 6). The presence of resveratrol was indicated by the peak at 10.51 min in the negative ion electrospray mass spectra, which contained a molecular ion of 227 Dalton, the same as resveratrol. The presence of pHCA was indicated by the peak at 7.84 min, with a molecular ion of 163 Dalton, same as pHCA. Thus, both resveratrol, and the intermediate pHCA, were present in the sample.

## Claims

1. A method for the production of resveratrol comprising:
a) providing an oleaginous microbial host cell comprising:
1) at least one nucleic acid molecule encoding an enzyme having resveratrol synthase activity;
2) a source of malonyl CoA and coumaroyl CoA;

b) growing the oleaginous microbial host of (a) under conditions where malonyl CoA and coumaroyl CoA are reacted to form resveratrol glucoside, wherein the resveratrol glucoside is hydrolyzed to resveratrol; and
c) optionally recovering the product of step (b).

2. A method according to claim 1 wherein the oleaginous microbial host cell comprises an enzyme having resveratrol glycosylating activity.

3. A method according to claim 1 wherein the oleaginous microbial host cell additionally comprises:
a) at least one nucleic acid molecule encoding an enzyme having coumaroyl CoA ligase activity; and
b) a source of p-hydroxycinnamic acid.

4. A method according to claim 3 wherein the oleaginous microbial host cell additionally comprises:
a) at least one nucleic acid molecule encoding an enzyme having tyrosine ammonium lyase activity; and
b) a source of tyrosine.

5. A method according to claim 3 wherein the oleaginous microbial host cell additionally comprises:
a) at least one nucleic acid molecule encoding an enzyme having cinnamate-4- hydroxylase activity; and
b) a source of cinnamic acid.

6. A method according to claim 5 wherein the oleaginous microbial host cell additionally comprises:
a) at least one nucleic acid molecule encoding an enzyme having phenylalanine ammonium lyase activity; and
b) a source of phenylalanine.

7. A method according to claim 1 wherein the oleaginous microbial host cell is selected from the group consisting of oleaginous algae, oleaginous fungi, and oleaginous yeast.

8. A method according to claim 7 wherein the oleaginous microbial host cell is a member of a genera selected from the group consisting of Mortierella, Conidiobolus, Pythium, Phytophathora, Penicillium, Porphyridium, Coidosporium, Mucor, Fusarium, Aspergillus, Rhodotorula, Entomophthora, Yarrowia, Candida, Rhodosporidium, Cryptococcus, Trichosporon, and Lipomyces.

9. A method according to claim 8 wherein the oleaginous microbial host cell is selected from the group consisting of Rhodosporidium toruloides, Liopmyces starkeyii, Liopmyces lipoferus, Candida revkaufi, Candida pulcherrima, Candida tropicalis, Candida utilis, Trichosporon pullans, Trichosporon cutaneum, Rhodotorula glutinus, Rhodotorula graminis, and Yarrowia lipolytica.

10. A method according to claim 1 wherein at the least one nucleic acid molecule encoding an enzyme having resveratrol synthase activity is isolated from an organism selected from the group consisting of Vitis sp., Arachis sp., Cissus sp, and Parthenocissus sp.

11. A method according to claim 3 wherein at the least one nucleic acid molecule encoding an enzyme having coumaroyl CoA ligase activity is; isolated from an organism selected from the group consisting of Streptomyces sp., Allium sp., Populus sp., Oryza sp., Amorpha sp., Nicotiana sp., Pinus sp., Glycine sp., Arabidopsis sp., Rubus sp., Lithospermum sp., and Zea sp.

12. A method according to claim 4 wherein at the least one nucleic acid molecule encoding an enzyme having tyrosine ammonium lyase activity; is isolated from an organism selected from the group consisting of Rhodotorula sp., Amanita sp., Ustilago sp., Arabidopsis sp., Rubus sp., Medicago sp, Rehmannia sp., Lactuca sp., Petroselinium sp., Prunus sp., Lithospemum sp., Citrus sp., Rhodobacter sp., and Trichosporon sp.

13. A method according to claim 5 wherein at the least one nucleic acid molecule encoding an enzyme having cinnamate-4-hydroxylase activity; is isolated from an organism selected from the group consisting of Streptomyces sp., Allium sp., Populus sp., Oryza sp., Amorpha sp., Nicotiana sp., Pinus sp., Glycine sp., Arabidopsis sp., Rubus sp., Lithospermum sp., and Zea sp.

14. A method according to claim 6 wherein at the least one nucleic acid molecule encoding an enzyme having phenylalanine ammonium lyase activity; is isolated from an organism selected from the group consisting of Rhodotorula sp., Amanita sp., Ustilago sp., Arabidopsis sp., Rubus sp., Medicago sp, Rehmannia sp., Lactuca sp., Petroselinium sp., Prunus sp., Lithospernum sp., Citrus sp., Rhodobacter sp., and Trichosporon sp.

15. A method according to claim 3 wherein the source of p-hydroxycinnamic acid is endogenous to the host cell.

16. A method according to claim 3 wherein the source of p-hydroxycinnamic acid is exogenous to the host cell.

17. A method according to claim 4 wherein the source of tyrosine is endogenous to the host cell.

18. A method according to claim 4 wherein the source of tyrosine is exogenous to the host cell.

19. A method according to claim 5 wherein the source of cinnamic acid is endogenous to the host cell.

20. A method according to claim 5 wherein the source of cinnamic acid is exogenous to the host cell.

21. A method according to claim 6 wherein the source of phenylalanine is endogenous to the host cell.

22. A method according to claim 6 wherein the source of phenylalanine is exogenous to the host cell.

23. A method according to claim 1 wherein resveratrol is produced at a concentration of at least 0.03 wt %.

24. A method according to claim 1 or 2 wherein resveratrol glucoside is produced at a concentration of at least 0.03 wt %.

25. A composition selected from the group consisting of antioxidants, anti-inflammatory agents, antifungal/antimicrobial agents, cosmetics, cosmeceuticals, nutritional/dietary supplements, feed additives, and pharmacological agents comprising 0.1 to 99 wt % recombinant oleaginous microbial biomass having at least 0.01 % (dry cell weight) resveratrol and/or resveratrol glucoside.

26. A method for the production of resveratrol comprising:
a) providing an oleaginous microbial host cell that is a member of a genera selected from the group consisting of Mortierella, Conidiobolus, Pythium, Phytophathora, Penicillium, Porphyridium, Coidosporium, Mucor, Fusarium, Aspergillus, Rhodotorula, Entomophthora, Yarrowia, Candida, Rhodosporidium, Cryptococcus, Trichosporon, and Lipomyces, the oleaginous microbial host cell comprising:
1) at least one nucleic acid molecule encoding an enzyme having resveratrol synthase activity;
2) a source of malonyl CoA and coumaroyl CoA;

b) growing the oleaginous microbial host of (a) under conditions where malonyl CoA and coumaroyl CoA are reacted to form a product selected from the group consisting of resveratrol and resveratrol glucoside; and
c) optionally recovering the product of step (b).

27. A method according to claim 26 wherein the oleaginous microbial host cell is selected from the group consisting of Rhodosporidium toruloides, Liopmyces starkeyii, Liopmyces lipoferus, Candida revkaufi, Candida puicherrima, Candida tropicalis, Candida utilis, Trichosporon pullans, Trichosporon cutaneum, Rhodotorula glutinus, Rhodotorula graminis, and Yarrowia lipolytica.

28. A method for the production of resveratrol comprising:
a) providing an oleaginous microbial host cell comprising:
1) at least one nucleic acid molecule encoding an enzyme having resveratrol synthase activity;
2) a source of malonyl CoA and coumaroyl CoA;
3) at least one nucleic acid molecule encoding an enzyme having phenylalanine ammonium lyase activity, the enzyme having phenylalanine ammonium lyase activity is isolated from an organism selected from the group consisting of Rhodotorula sp., Amanita sp., Ustilago sp., Arabidopsis sp., Rubus sp., Medicago sp, Rehmannia sp., Lactuca sp., Petroselinium sp., Prunus sp., Lithospernum sp., Citrus sp., Rhodobacter sp., and Trichosporon sp.;
4) a source of phenylalanine;

b) growing the oleaginous microbial host of (a) under conditions where malonyl CoA and coumaroyl CoA are reacted to form a product selected from the group consisting of resveratrol and resveratrol glucoside; and
c) optionally recovering the product of step (b).

29. A method for the production of resveratrol comprising:
a) providing an oleaginous microbial host cell comprising:
1) at least one nucleic acid molecule encoding an enzyme having resveratrol synthase activity;
2) a source of malonyl CoA and coumaroyl CoA;

b) growing the oleaginous microbial host of (a) under conditions where malonyl CoA and coumaroyl CoA are reacted to form a product selected from the group consisting of resveratrol and resveratrol glucoside, wherein resveratrol or resveratrol glucoside is produced at a concentration of at least 0.03 wt %; and
c) optionally recovering the product of step (b).

30. A recombinant strain of Yarrowia lipolytica comprising at least one nucleic acid molecule encoding an enzyme having resveratrol synthase activity, and optionally at least one nucleic acid molecule encoding an enzyme having an activity selected from the group consisting of; coumaroyl CoA ligase, tyrosine ammonium lyase, cinnamate-4-hydroxylase and phenylalanine ammonium lyase, which produces a product selected from the group consisting of resveratrol and resveratrol glucoside.