US20070220634A1 - Plant seed oils containing polyunsaturated fatty acids - Google Patents

Plant seed oils containing polyunsaturated fatty acids Download PDF

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US20070220634A1
US20070220634A1 US11/686,872 US68687207A US2007220634A1 US 20070220634 A1 US20070220634 A1 US 20070220634A1 US 68687207 A US68687207 A US 68687207A US 2007220634 A1 US2007220634 A1 US 2007220634A1
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James G. Metz
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Martek Biosciences Corp
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Definitions

  • This invention generally relates to the production of polyunsaturated fatty acids (PUFAs) in plants, including oil seed plants, that have been genetically modified to express a PKS-like system for the production of PUFAs (a PUFA PKS system), and to the oil seeds, oils, and products comprising such oils produced by this system.
  • the oils produced by the plant contain at least one PUFA produced by the PUFA PKS system and are free of the mixed shorter-chain and less unsaturated PUFAs that are fatty acid products produced by the modification of products of the FAS system in standard fatty acid pathways.
  • PKS Polyketide synthase
  • FOS fatty acid synthase
  • PUFA PKS systems PUFA synthase systems
  • PUFA PKS pathways for PUFA synthesis in Shewanella and another marine bacteria, Vibrio marinus are described in detail in U.S.
  • U.S. Patent Application Publication No. 20040235127 published Nov. 25, 2004, discloses the detailed structural description of a PUFA PKS system in Thraustochytrium , and further detail regarding the production of eicosapentaenoic acid (C20:5, ⁇ -3) (EPA) and other PUFAs using such systems.
  • PCT Patent Publication No. WO 05/097982 describes a PUFA PKS system in Ulkenia
  • U.S. Patent Application Publication No. 20050014231 describes PUFA PKS genes and proteins from Thraustochytrium aureum .
  • PUFAs Polyunsaturated fatty acids
  • Vegetable oils derived from oil seed crops are relatively inexpensive and do not have the contamination issues associated with fish oils.
  • the PUFAs found in commercially developed plant oils are typically limited to linoleic acid (eighteen carbons with 2 double bonds, in the delta 9 and 12 positions—18:2 delta 9,12) and linolenic acid (18:3 delta 9,12,15).
  • medium chain-length saturated fatty acids products of a fatty acid synthase (FAS) system
  • FAS fatty acid synthase
  • the substrates for the elongation reaction are fatty acyl-CoA (the fatty acid chain to be elongated) and malonyl-CoA (the source of the 2 carbons added during each elongation reaction).
  • the product of the elongase reaction is a fatty acyl-CoA that has two additional carbons in the linear chain.
  • the desaturases create cis double bonds in the preexisting fatty acid chain by extraction of 2 hydrogens in an oxygen-dependant reaction.
  • the substrates for the desaturases are either acyl-CoA (in some animals) or the fatty acid that is esterified to the glycerol backbone of a PL (e.g. phosphatidylcholine).
  • PUFAs such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) may require expression of several separate enzymes to achieve synthesis. Additionally, for production of useable quantities of such PUFAs, additional engineering efforts may be required.
  • EPA eicosapentaenoic acid
  • DHA docosahexaenoic acid
  • lipids e.g., triacylglycerol (TAG) and phospholipid (PL)
  • TAG triacylglycerol
  • PL phospholipid
  • One embodiment of the invention relates to a plant or a part of the plant, wherein the total fatty acid profile in the plant or part of the plant comprises at least about 0.5% by weight of at least one polyunsaturated fatty acid (PUFA) having at least twenty carbons and four or more carbon-carbon double bonds, and wherein the total fatty acid profile in the plant or part of the plant contains less than 5% in total of all of the following PUFAs: gamma-linolenic acid (GLA; 18:3, n-6), PUFAs having 18 carbons and four carbon-carbon double bonds, PUFAs having 20 carbons and three carbon-carbon double bonds, and PUFAs having 22 carbons and two or three carbon-carbon double bonds.
  • GLA gamma-linolenic acid
  • PUFAs having 18 carbons and four carbon-carbon double bonds PUFAs having 20 carbons and three carbon-carbon double bonds
  • PUFAs having 22 carbons and two or three carbon-carbon double bonds gamma-l
  • Yet another embodiment of the invention relates to a plant or a part of the plant, wherein the total fatty acid profile in the plant or part of the plant comprises at least about 0.5% by weight of at least one polyunsaturated fatty acid (PUFA) having at least twenty carbons and four or more carbon-carbon double bonds, and wherein the total fatty acid profile in the plant or part of the plant contains less than 1% of each of the following PUFAs: gamma-linolenic acid (GLA; 18:3, n-6), PUFAs having 18 carbons and four carbon-carbon double bonds, PUFAs having 20 carbons and three carbon-carbon double bonds, and PUFAs having 22 carbons and two or three carbon-carbon double bonds.
  • GLA gamma-linolenic acid
  • PUFAs having 18 carbons and four carbon-carbon double bonds PUFAs having 20 carbons and three carbon-carbon double bonds
  • PUFAs having 22 carbons and two or three carbon-carbon double bonds gamma-lin
  • Another embodiment of the invention relates to a plant or a part of the plant, wherein the total fatty acid profile in the plant or part of the plant comprises at least about 0.5% by weight of at least one polyunsaturated fatty acid (PUFA) having at least twenty carbons and four or more carbon-carbon double bonds, and wherein the total fatty acid profile in the plant or part of the plant contains less than 2% of gamma-linolenic acid (GLA; 18:3, n-6) and dihomo-gamma-linolenic acid (DGLA or HGLA; 20:3, n-6).
  • GLA gamma-linolenic acid
  • DGLA or HGLA dihomo-gamma-linolenic acid
  • the total fatty acid profile in the plant or part of the plant contains less than 1% by weight of gamma-linolenic acid (GLA; 18:3, n-6) and dihomo-gamma-linolenic acid (DGLA or HGLA; 20:3, n-6).
  • GLA gamma-linolenic acid
  • DGLA dihomo-gamma-linolenic acid
  • Yet another embodiment of the invention relates to a plant or a part of the plant, wherein the total fatty acid profile in the plant or part of the plant comprises at least about 0.5% by weight of at least one polyunsaturated fatty acid (PUFA) having at least twenty carbons and four or more carbon-carbon double bonds, and wherein the total fatty acid profile in the plant or part of the plant contains less than 1% of gamma-linolenic acid (GLA; 18:3, n-6).
  • the total fatty acid profile in the plant or part of the plant contains less than 0.5% by weight of gamma-linolenic acid (GLA; 18:3, n-6).
  • Another embodiment of the invention relates to a plant or part of a plant, wherein the plant has been genetically modified to express enzymes that produce at least one polyunsaturated fatty acid (PUFA) having at least twenty carbons and four or more carbon-carbon double bonds, wherein the total fatty acid profile in the plant or part of the plant comprises at least about 0.5% by weight of said at least one PUFA, and wherein the total fatty acids produced by said enzymes, other than said at least one PUFA, comprise less than about 10% of the total fatty acids produced by said plant.
  • the total fatty acids produced by said enzymes, other than said at least one PUFA comprise less than 5% by weight of the total fatty acids produced by said plant.
  • the fatty acids consisting of gamma-linolenic acid (GLA; 18:3, n-6), PUFAs having 18 carbons and four carbon-carbon double bonds, PUFAs having 20 carbons and three carbon-carbon double bonds, and PUFAs having 22 carbons and two or three carbon-carbon double bonds, comprise less than 5% by weight of the total fatty acids produced by said plant.
  • gamma-linolenic acid (GLA; 18:3, n-6) comprises less than 1% by weight of the total fatty acids produced by said plant.
  • the plant has not been genetically modified to express a desaturase or an elongase enzyme, and particularly, a desaturase or elongase enzyme that is used in a FAS-based, conventional, or standard pathway of PUFA production.
  • Another embodiment of the invention relates to a plant or part of a plant, wherein the plant has been genetically modified with a PUFA PKS system from a eukaryote that produces at least one polyunsaturated fatty acid (PUFA), and wherein the total fatty acid profile in the plant or part of the plant comprises a detectable amount of said at least one PUFA.
  • the total fatty acid profile in the plant or part of the plant comprises at least 0.5% by weight of said at least one PUFA.
  • the total fatty acids produced by said PUFA PKS system, other than said at least one PUFA comprises less than about 10% by weight of the total fatty acids produced by said plant.
  • the total fatty acids produced by said enzymes, other than said at least one PUFA comprises less than about 5% by weight of the total fatty acids produced by said plant.
  • the PUFA PKS system comprises: (a) at least one enoyl-ACP reductase (ER) domain; (b) at least four acyl carrier protein (ACP) domains; (c) at least two ⁇ -ketoacyl-ACP synthase (KS) domains; (d) at least one acyltransferase (AT) domain; (e) at least one ⁇ -ketoacyl-ACP reductase (KR) domain; (f) at least two FabA-like ⁇ -hydroxyacyl-ACP dehydrase (DH) domains; (g) at least one chain length factor (CLF) domain; and (h) at least one malonyl-CoA:ACP acyltransferase (MAT) domain.
  • ER enoyl-ACP reductase
  • ACP acyl carrier protein
  • KS ⁇ -ketoacyl-ACP synthase
  • AT acyltransferase
  • the PUFA PKS system comprises: (a) two enoyl ACP-reductase (ER) domains; (b) eight or nine acyl carrier protein (ACP) domains; (c) two ⁇ -keto acyl-ACP synthase (KS) domains; (d) one acyltransferase (AT) domain; (e) one ketoreductase (KR) domain; (f) two FabA-like ⁇ -hydroxy acyl-ACP dehydrase (DH) domains; (g) one chain length factor (CLF) domain; and (h) one malonyl-CoA:ACP acyltransferase (MAT) domain.
  • the above-described PUFA PKS system in one aspect, is from a Thraustochytriales microorganism.
  • the PUFA PKS system is from Schizochytrium .
  • the PUFA PKS system is from Thraustochytrium .
  • the PUFA PKS system is from a microorganism selected from: Schizochytrium sp. American Type Culture Collection (ATCC) No. 20888 ; Thraustochytrium 23B ATCC No. 20892, and a mutant of any of said microorganisms.
  • ATCC American Type Culture Collection
  • the nucleic acid sequences encoding the PUFA PKS system hybridize under stringent hybridization conditions to the genes encoding the PUFA PKS system from a microorganism selected from: Schizochytrium sp. American Type Culture Collection (ATCC) No. 20888; Thraustochytrium 23B ATCC No. 20892; and a mutant of any of said microorganisms.
  • the nucleic acid sequences encoding the PUFA PKS system hybridize under stringent hybridization conditions to the genes encoding the PUFA PKS system from Schizochytrium sp. American Type Culture Collection (ATCC) No. 20888 or a mutant thereof.
  • the PUFA PKS system comprises at least one domain from a PUFA PKS system from a Thraustochytriales microorganism.
  • the PUFA PKS system includes any one or more nucleic acid sequences or amino acid sequences selected from: SEQ ID NOs:1-32 or 38-68.
  • the PUFA PKS system further comprises a phosphopantetheinyl transferase (PPTase).
  • PPTase phosphopantetheinyl transferase
  • Yet another embodiment of the invention relates to a plant or part of a plant, wherein the plant has been genetically modified with a PUFA PKS system that produces at least one polyunsaturated fatty acid (PUFA), and wherein the total fatty acid profile in the plant or part of the plant comprises a detectable amount of said at least one PUFA, wherein the PUFA PKS system is a bacterial PUFA PKS system that produces PUFAs at temperatures of at least about 25° C., and wherein the bacterial PUFA PKS system comprises: (a) at least one enoyl ACP-reductase (ER) domain; (b) at least six acyl carrier protein (ACP) domains; (c) at least two ⁇ -keto acyl-ACP synthase (KS) domains; (d) at least one acyltransferase (AT) domain; (e) at least one ketoreductase (KR) domain; (f) at least two FabA-like
  • the PUFA PKS system is from a microorganism selected from: Shewanella olleyana Australian Collection of Antarctic Microorganisms (ACAM) strain number 644 ; Shewanella japonica ATCC strain number BAA-316, and a mutant of any of said microorganisms.
  • the nucleic acid sequences encoding the PUFA PKS system hybridize under stringent hybridization conditions to the genes encoding the PUFA PKS system from a microorganism selected from: Shewanella olleyana Australian Collection of Antarctic Microorganisms (ACAM) strain number 644; or Shewanella japonica ATCC strain number BAA-316, or a mutant of any of said microorganisms.
  • the PUFA PKS system includes any one or more nucleic acid sequences or amino acid sequence selected from: SEQ ID NOs:69-80.
  • Another embodiment of the invention relates to an oilseed plant, or part of the oilseed plant, that produces mature seeds in which the total seed fatty acid profile comprises at least 1.0% by weight of at least one polyunsaturated fatty acid having at least twenty carbon atoms and at least four carbon-carbon double bonds, and wherein the total fatty acid profile in the plant or part of the plant contains less than 5% in total of all of the following PUFAs: gamma-linolenic acid (GLA; 18:3, n-6), PUFAs having 18 carbons and four carbon-carbon double bonds, PUFAs having 20 carbons and three carbon-carbon double bonds, and PUFAs having 22 carbons and two or three carbon-carbon double bonds.
  • GLA gamma-linolenic acid
  • PUFAs having 18 carbons and four carbon-carbon double bonds PUFAs having 20 carbons and three carbon-carbon double bonds
  • PUFAs having 22 carbons and two or three carbon-carbon double bonds gamma-linolenic
  • Another embodiment of the invention relates to an oilseed plant, or part of the oilseed plant, that produces mature seeds in which the total seed fatty acid profile comprises at least 1.0% by weight of at least one polyunsaturated fatty acid having at least twenty carbon atoms and at least four carbon-carbon double bonds, and wherein the total fatty acid profile in the plant or part of the plant contains less than 1% of gamma-linolenic acid (GLA; 18:3, n-6).
  • GLA gamma-linolenic acid
  • the at least one PUFA has at least twenty carbons and five or more carbon-carbon double bonds.
  • the at least one PUFA is selected from: DHA (docosahexaenoic acid (C22:6, n-3)), ARA (eicosatetraenoic acid or arachidonic acid (C20:4, n-6)), DPA (docosapentaenoic acid (C22:5, n-6 or n-3)), and EPA (eicosapentaenoic acid (C20:5, n-3).
  • the at least one PUFA is selected from: DHA (docosahexaenoic acid (C22:6, n-3)), DPA (docosapentaenoic acid (C22:5, n-6 or n-3)), and EPA (eicosapentaenoic acid (C20:5, n-3).
  • the at least one PUFA is selected from: DHA (docosahexaenoic acid (C22:6, n-3)), ARA (eicosatetraenoic acid or arachidonic acid (C20:4, n-6)), DPA (docosapentaenoic acid (C22:5, n-6 or n-3)), EPA (eicosapentaenoic acid (C20:5, n-3), gamma-linolenic acid (GLA; 18:3, n-6); stearidonic acid (STA or SDA; 18:4, n-3); and dihomo-gamma-linolenic acid (DGLA or HGLA; 20:3, n-6).
  • DHA docosahexaenoic acid
  • ARA eicosatetraenoic acid or arachidonic acid
  • DPA docosapentaenoic acid (C22:5, n-6 or n-3)
  • EPA
  • the at least one PUFA is DHA. In another aspect, when the target PUFA is DHA, the ratio of EPA:DHA produced by the plant is less than 1:1. In another aspect, the at least one PUFA is EPA. In another aspect, the at least one PUFA is DHA and DPAn-6. In another aspect, the at least one PUFA is EPA and DHA. In another aspect, the at least one PUFA is ARA and DHA. In another aspect, the at least one PUFA is ARA and EPA.
  • the plant is an oilseed plant and wherein the part of the plant is a mature oilseed.
  • the plant is a crop plant.
  • the plant is a dicotyledonous plant.
  • the plant is a monocotyledonous plant.
  • the plant is selected from: canola, soybean, rapeseed, linseed, corn, safflower, sunflower and tobacco.
  • Yet another embodiment of the invention relates to plant or a part of the plant, wherein the total fatty acid profile in the plant or part of the plant comprises detectable amounts of DHA (docosahexaenoic acid (C22:6, n-3)), and DPA (docosapentaenoic acid (C22:5, n-6), wherein the ratio of DPAn-6 to DHA is 1:1 or greater than 1:1.
  • DHA docosahexaenoic acid
  • DPA docosapentaenoic acid
  • the total fatty acid profile in the plant or part of the plant contains less than 5% by weight in total of all of the following PUFAs: gamma-linolenic acid (GLA; 18:3, n-6), PUFAs having 18 carbons and four carbon-carbon double bonds, PUFAs having 20 carbons and three carbon-carbon double bonds, and PUFAs having 22 carbons and two or three carbon-carbon double bonds.
  • GLA gamma-linolenic acid
  • PUFAs having 18 carbons and four carbon-carbon double bonds PUFAs having 20 carbons and three carbon-carbon double bonds
  • PUFAs having 22 carbons and two or three carbon-carbon double bonds PUFAs having 22 carbons and two or three carbon-carbon double bonds.
  • Another embodiment of the invention relates to plant or part of a plant, wherein the plant has been genetically modified with a PUFA PKS system that produces at least one polyunsaturated fatty acid (PUFA), and wherein the total fatty acid profile in the plant or part of the plant comprises a detectable amount of said at least one PUFA, wherein the PUFA PKS system comprises: (a) two enoyl ACP-reductase (ER) domains; (b) eight or nine acyl carrier protein (ACP) domains; (c) two ⁇ -keto acyl-ACP synthase (KS) domains; (d) one acyltransferase (AT) domain; (e) one ketoreductase (KR) domain; (f) two FabA-like ⁇ -hydroxy acyl-ACP dehydrase (DH) domains; (g) one chain length factor (CLF) domain; (h) one malonyl-CoA:ACP acyltrans
  • Another embodiment of the invention relates to seeds obtained from any of the above-identified plants or part of plants. Yet another embodiment of the invention relates to a food product comprising such seeds.
  • Yet another embodiment of the invention relates to an oil obtained from seeds of any of the above-described plants.
  • Another embodiment of the invention includes an oil comprising the fatty acid profile shown in FIG. 2 or FIG. 3 .
  • Another embodiment of the invention includes an oil blend comprising any of the oils produced by the plants described herein and another oil.
  • the another oil is a microbial oil, and in another aspect, the another oil is a fish oil.
  • Yet another embodiment of the invention relates to an oil comprising the following fatty acids: DHA (C22:6n-3), DPAn-6 (C22:5n-6), oleic acid (C18:1), linolenic acid (C18:3), linoleic acid (C18:2), C16:0, C18.0, C20:0, C20:1n-9, C20:2n-6, C22:1n-9; wherein the oil comprises less than 0.5% of any of the following fatty acids: gamma-linolenic acid (GLA; 18:3, n-6), PUFAs having 18 carbons and four carbon-carbon double bonds, PUFAs having 20 carbons and three carbon-carbon double bonds, and PUFAs having 22 carbons and two or three carbon-carbon double bonds.
  • DHA C22:6n-3
  • DPAn-6 C22:5n-6
  • oleic acid C18:1
  • linolenic acid C18:3
  • Another embodiment of the invention relates to a plant oil comprising at least about 0.5% by weight of at least one polyunsaturated fatty acid (PUFA) having at least twenty carbons and four or more carbon-carbon double bonds, and wherein the total fatty acid profile oil contains less than 5% in total of all of the following PUFAs: gamma-linolenic acid (GLA; 18:3, n-6), PUFAs having 18 carbons and four carbon-carbon double bonds, PUFAs having 20 carbons and three carbon-carbon double bonds, and PUFAs having 22 carbons and two or three carbon-carbon double bonds.
  • PUFA polyunsaturated fatty acid
  • Another embodiment of the invention relates to a plant oil comprising detectable amounts of DHA (docosahexaenoic acid (C22:6, n-3)), and DPA (docosapentaenoic acid (C22:5, n-6), wherein the ratio of DPAn-6 to DHA is 1:1 or greater than 1:1.
  • DHA docosahexaenoic acid
  • DPA docosapentaenoic acid
  • Yet another embodiment of the invention relates to a food product that contains any of the above-described oils.
  • the food product further includes any of the seeds described above.
  • Another embodiment of the invention relates to a pharmaceutical product that contains any of the above-described oils.
  • Another embodiment of the invention relates to a method to produce an oil comprising at least one PUFA, comprising recovering an oil from any of the seeds described above.
  • Yet another embodiment of the invention relates to a method to produce an oil comprising at least one PUFA, comprising recovering an oil from any of the above-described plants or part of the plants.
  • Another embodiment of the invention relates to a method to provide a supplement or therapeutic product comprising at least one PUFA to an individual, comprising providing to the individual any of the above-described plants or part of plants, any of the above-described seeds, any of the above-described oils, any of the above-described food products, and/or any of the above-described pharmaceutical products.
  • FIG. 1 is a FAME profile of control yeast and yeast expressing Schizochytrium Orfs sA, sB, C and Het I.
  • FIG. 2 is the FAME profile for yeast from FIG. 1 , expanded to illustrate the production of target PUFAs.
  • FIG. 3 is the FAME profile of wild-type Arabidopsis and Arabidopsis Line 263 (Plastid targeted) expressing Schizochytrium Orfs A, B*, C and Het I.
  • the present invention generally relates to a method to produce PUFAs in an oil-seed plant that has been genetically modified to express a PUFA PKS system, and the oil seeds, oils, and products comprising such oils produced by this system.
  • the oils produced by the plant contain at least one PUFA produced by the PUFA PKS system and are free of the mixed shorter-chain and less unsaturated PUFAs that are fatty acid products produced by the modification of products of the FAS system.
  • PUFA synthase i.e., PUFA PKS system
  • PUFA synthase enzymes are capable of de novo synthesis of various PUFAs (e.g., EPA, DHA and DPA n-6) and that those products can accumulate in a host organism's phospholipids (PL) and in some cases, in the neutral lipids (e.g., triacylglycerols—TAG).
  • PUFA synthase systems to genetically modify host organisms, including plants, has been described.
  • Data provided herein show the production of PUFAs in a plant that has been genetically modified to express the genes encoding a PUFA PKS system from Schizochytrium and a PUFA PKS accessory enzyme, 4′-phosphopantetheinyl transferase (PPTase).
  • the oils produced by these plants contain significant quantities of both DHA (docosahexaenoic acid (C22:6, n-3)) and DPA (docosapentaenoic acid (C22:5, n-6), which are the predominant PUFAs (the primary PUFAs) produced by the Schizochytrium from which the PUFA PKS genes were derived.
  • oils from plants that produce PUFAs using the PUFA PKS pathway have a different fatty acid profile than plants that are genetically engineered to produce the same PUFAs by the “standard” pathway described above.
  • oils from plants that have been genetically engineered to produce specific PUFAs by the PUFA PKS pathway are substantially free of the various intermediate products and side products that accumulate in oils that are produced as a result of the use of the standard PUFA synthesis pathway. This characteristic is discussed in detail below.
  • the free fatty acid is exported from the plastid and converted to an acyl-CoA.
  • the 18:1 can be esterified to phosphatidylcholine (PC) and up to two more cis double bonds can be added.
  • the newly introduced elongases can utilize substrates in the acyl-CoA pool to add carbons in two-carbon increments.
  • Newly introduced desaturases can utilize either fatty acids esterified to PC, or those in the acyl-CoA pool, depending on the source of the enzyme.
  • One consequence of this scheme for long chain PUFA production is that intermediates or side products in the pathway accumulate, which often represent the majority of the novel fatty acids in the plant oil, rather than the target long chain PUFA.
  • the target PUFA product i.e., the PUFA product that one is targeting for production, trying to produce, or attempting to produce, by using the standard pathway
  • DHA or EPA e.g., produced using elongases and desaturases that will produce the DHA or EPA from the products of the FAS system
  • intermediate products and side products will be produced in addition to the DHA or EPA, and these intermediate or side products frequently represent the majority of the products produced by the pathway, or are at least present in significant amounts in the lipids of the production organism.
  • Such intermediate and side products include, but are not limited to, fatty acids having fewer carbons and/or fewer double bonds than the target, or primary PUFA, and can include unusual fatty acid side products that may have the same number of carbons as the target or primary PUFA, but which may have double bonds in unusual positions. This result is illustrated in an example of the production of EPA using the standard pathway (e.g., see U.S. Patent Application Publication 2004/0172682).
  • the oils produced by the system include a variety of intermediate and side products including: gamma-linolenic acid (GLA; 18:3, n-6); stearidonic acid (STA or SDA; 18:4, n-3); dihomo-gamma-linolenic acid (DGLA or HGLA; 20:3, n-6), arachidonic acid (ARA, C20:4, n-6); eicosatrienoic acid (ETA; 20:3, n-9) and various other intermediate or side products, such as 20:0; 20:1 ( ⁇ 5); 20:1 ( ⁇ 11); 20:2 ( ⁇ 8,11); 20:2 ( ⁇ 11,14); 20:3 ( ⁇ 5,11,14); 20:3 ( ⁇ 11,14,17); mead acid (20:3; ⁇ 5,8,11);
  • Intermediates of the system can also include long chain PUFAs that are not the target of the genetic modification (e.g., a standard pathway enzyme system for producing DHA can actually produce more EPA as an intermediate product than DHA, as illustrated, for example, in U.S. Patent Application Publication 2004/0172682, see additional discussion of this point below).
  • a standard pathway enzyme system for producing DHA can actually produce more EPA as an intermediate product than DHA, as illustrated, for example, in U.S. Patent Application Publication 2004/0172682, see additional discussion of this point below).
  • the PUFA PKS synthase of the present invention does not utilize the fatty acid products of FAS systems. Instead, it produces the final PUFA product (the primary PUFA product) from the same small precursor molecule that is utilized by FASs and elongases (malonyl-CoA). Therefore, intermediates in the synthesis cycle are not released in any significant amount, and the PUFA product (also referred to herein as the primary PUFA product) is efficiently transferred to phospholipids (PL) and triacylglycerol (TAG) fractions of the lipids.
  • PL phospholipids
  • TAG triacylglycerol
  • PUFA PKS genes are an excellent means of producing oils containing PUFAs, and particularly, long chain PUFAs (LCPUFAs) in a heterologous host, such as a plant, wherein the oils are substantially free (defined below) of the intermediates and side products that contaminate oils produced by the “standard” PUFA pathway (also defined below).
  • LCPUFAs long chain PUFAs
  • Examples of PUFAs that can be produced by the present invention include, but are not limited to, DHA (docosahexaenoic acid (C22:6, n-3)), ARA (eicosatetraenoic acid or arachidonic acid (C20:4, n-6)), DPA (docosapentaenoic acid (C22:5, n-6 or n-3)), and EPA (eicosapentaenoic acid (C20:5, n-3)).
  • DHA docosahexaenoic acid (C22:6, n-3)
  • ARA eicosatetraenoic acid or arachidonic acid
  • DPA docosapentaenoic acid (C22:5, n-6 or n-3)
  • EPA eicosapentaenoic acid
  • reference to a “primary PUFA”, “target PUFA”, “intended PUFA”, or “desired PUFA” refers to the particular PUFA or PUFAs that are the intended or targeted product of the enzyme pathway that is used to produce the PUFA(s).
  • a target or desired PUFA e.g., DHA or EPA.
  • target or desired PUFA produced by the standard pathway may not actually be a “primary” PUFA in terms of the amount of PUFA as a percentage of total fatty acids produced by the system, due to the formation of intermediates and side products that can actually represent the majority of products produced by the system.
  • primary PUFA even in that instance to refer to the target or intended PUFA product produced by the elongases or desaturases used in the system.
  • a given PUFA PKS system derived from a particular organism will produce particular PUFA(s), such that selection of a PUFA PKS system from a particular organism will result in the production of specified target or primary PUFAs.
  • PUFA PKS system from Schizochytrium will result in the production of DHA and DPAn-6 as the target or primary PUFAs.
  • Use of a PUFA PKS system from various Shewanella species, on the other hand, will result in the production of EPA as the target or primary PUFA.
  • the ratio of the primary or target PUFAs can differ depending on the selection of the particular PUFA PKS system and on how that system responds to the specific conditions in which it is expressed.
  • a PUFA PKS system from Thraustochytrium 23B ATCC No. 20892
  • DHA and DPAn-6 as the target or primary PUFAs
  • the ratio of DHA to DPAn-6 is about 10:1 (and can range from about 8:1 to about 40:1), whereas in Schizochytrium , the ratio is typically about 2.5:1.
  • Thraustochytrium PUFA PKS system or proteins or domains can alter the ratio of PUFAs produced by an organism as compared to Schizochytrium even though the target PUFAs are the same.
  • intermediate products or “side products” of an enzyme system that produces PUFAs refers to any products, and particularly, fatty acid products, that are produced by the enzyme system as a result of the production of the target or primary PUFA(s) of the system, but which are not the primary or target PUFA(s).
  • intermediate and side products may include non-target fatty acids that are naturally produced by the wild-type plant, or by the parent plant used as a recipient for the indicated genetic modification, but are now classified as intermediate or side products because they are produced in greater levels as a result of the genetic modification, as compared to the levels produced by the wild-type plant, or by the parent plant used as a recipient for the indicated genetic modification.
  • Intermediate and side products are particularly significant in the standard pathway for PUFA synthesis and are substantially less significant in the PUFA PKS pathway, as discussed above.
  • a primary or target PUFA of one enzyme system may be an intermediate of a different enzyme system where the primary or target product is a different PUFA, and this is particularly true of products of the standard pathway of PUFA production, since the PUFA PKS system substantially avoids the production of intermediates.
  • fatty acids such as GLA, DGLA and SDA are produced as intermediate products in significant quantities (e.g., U.S. Patent Application Publication 2004/0172682 illustrates this point).
  • U.S. Patent Application Publication 2004/0172682 illustrates this point.
  • Patent Application Publication 2004/0172682 when using the standard pathway to produce DHA, in addition to the fatty acids mentioned above, ETA and EPA (notably the target PUFA in the first example above) are produced in significant quantities and in fact, may be present in significantly greater quantities relative to the total fatty acid product than the target PUFA itself. This latter point is also shown in U.S. Patent Application Publication 2004/0172682, where a plant that was engineered to produce DHA by the standard pathway produces more EPA as a percentage of total fatty acids than the targeted DHA.
  • a PUFA PKS system (which may also be referred to as a PUFA synthase system or PUFA synthase) generally has the following identifying features: (1) it produces PUFAs, and particularly, long chain PUFAs, as a natural product of the system; and (2) it comprises several multifunctional proteins assembled into a complex that conducts both iterative processing of the fatty acid chain as well non-iterative processing, including trans-cis isomerization and enoyl reduction reactions in selected cycles.
  • the ACP domains present in the PUFA synthase enzymes require activation by attachment of a cofactor (4-phosphopantetheine).
  • PPTase phosphopantetheinyl transferases
  • PUFA PKS system produces polyunsaturated fatty acids (PUFAs) and particularly, long chain PUFAs (LCPUFAs), as products.
  • PUFAs are fatty acids with a carbon chain length of at least 16 carbons, and more preferably at least 18 carbons, and more preferably at least 20 carbons, and more preferably 22 or more carbons, with at least 3 or more double bonds, and preferably 4 or more, and more preferably 5 or more, and even more preferably 6 or more double bonds, wherein all double bonds are in the cis configuration.
  • LCPUFAs long chain polyunsaturated fatty acids
  • LCPUFAs of the omega-6 series include: gamma-linolenic acid (C18:3), di-homo-gamma-linolenic acid (C20:3n-6), arachidonic acid (C20:4n-6), adrenic acid (also called docosatetraenoic acid or DTA) (C22:4n-6), and docosapentaenoic acid (C22:5n-6).
  • the LCPUFAs of the omega-3 series include: alpha-linolenic acid (C18:3), eicosatrienoic acid (C20:3n-3), eicosatetraenoic acid (C20:4n-3), eicosapentaenoic acid (C20:5n-3), docosapentaenoic acid (C22:5n-3), and docosahexaenoic acid (C22:6n-3).
  • the LCPUFAs also include fatty acids with greater than 22 carbons and 4 or more double bonds including but not limited to C28:8(n-3).
  • a PUFA PKS system also comprises several multifunctional proteins (and can include single function proteins, particularly for PUFA PKS systems from marine bacteria) that are assembled into a complex that conducts both iterative processing of the fatty acid chain as well non-iterative processing, including trans-cis isomerization and enoyl reduction reactions in selected cycles.
  • These proteins can also be referred to herein as the core PUFA PKS enzyme complex or the core PUFA PKS system.
  • the general functions of the domains and motifs contained within these proteins are individually known in the art and have been described in detail with regard to various PUFA PKS systems from marine bacteria and eukaryotic organisms (see, e.g., U.S. Pat. No.
  • the domains may be found as a single protein (i.e., the domain and protein are synonymous) or as one of two or more (multiple) domains in a single protein, as mentioned above.
  • PUFA PKS systems and proteins or domains thereof that are useful in the present invention include both bacterial and non-bacterial PUFA PKS systems.
  • a non-bacterial PUFA PKS system is a PUFA PKS system that is from or derived from an organism that is not a bacterium, such as a eukaryote or an archaebacterium. Eukaryotes are separated from prokaryotes based on the degree of differentiation of the cells, with eukaryotes being more differentiated than prokaryotes.
  • prokaryotes do not possess a nuclear membrane, do not exhibit mitosis during cell division, have only one chromosome, contain 70S ribosomes in their cytoplasm, do not possess mitochondria, endoplasmic reticulum, chloroplasts, lysosomes or Golgi apparatus, and may have flagella, which if present, contain a single fibril.
  • eukaryotes have a nuclear membrane, exhibit mitosis during cell division, have many chromosomes, contain 80S ribosomes in their cytoplasm, possess mitochondria, endoplasmic reticulum, chloroplasts (in algae), lysosomes and Golgi apparatus, and may have flagella, which if present, contain many fibrils.
  • bacteria are prokaryotes, while algae, fungi, protist, protozoa and higher plants are eukaryotes.
  • genetically modified plants can be produced which incorporate non-bacterial PUFA PKS functional domains with bacterial PUFA PKS functional domains, as well as PKS functional domains or proteins from other PKS systems (Type I iterative or modular, Type II, or Type III) or FAS systems.
  • a PUFA PKS system of the present invention comprises at least the following biologically active domains that are typically contained on three or more proteins: (a) at least one enoyl-ACP reductase (ER) domain; (b) multiple acyl carrier protein (ACP) domain(s) (e.g., at least from one to four, and preferably at least five ACP domains, and in some embodiments up to six, seven, eight, nine, ten, or more than ten ACP domains); (c) at least two ⁇ -ketoacyl-ACP synthase (KS) domains; (d) at least one acyltransferase (AT) domain; (e) at least one ⁇ -ketoacyl-ACP reductase (KR) domain; (f) at least two FabA-like ⁇ -hydroxyacyl-ACP dehydrase (DH) domains; (g) at least one chain length factor (CLF) domain; (h) at least one malon
  • a PUFA PKS system comprises at least the following biologically active domains: (a) at least one enoyl-ACP reductase (ER) domain; (b) at least five acyl carrier protein (ACP) domains; (c) at least two ⁇ -ketoacyl-ACP synthase (KS) domains; (d) at least one acyltransferase (AT) domain; (e) at least one ⁇ -ketoacyl-ACP reductase (KR) domain; (f) at least two FabA-like ⁇ -hydroxyacyl-ACP dehydrase (DH) domains; (g) at least one chain length factor (CLF) domain; and (h) at least one malonyl-CoA:ACP acyltransferase (MAT) domain.
  • ER enoyl-ACP reductase
  • ACP acyl carrier protein
  • KS ⁇ -ketoacyl-ACP synthase
  • a PUFA PKS system also comprises at least one region or domain containing a dehydratase (DH) conserved active site motif that is not a part of a FabA-like DH domain.
  • DH dehydratase
  • a domain or protein having 3-keto acyl-ACP synthase (KS) biological activity (function) is characterized as the enzyme that carries out the initial step of the FAS (and PKS) elongation reaction cycle.
  • KS 3-keto acyl-ACP synthase
  • ⁇ -ketoacyl-ACP synthase can be used interchangeably with the terms “3-keto acyl-ACP synthase”, “ ⁇ -keto acyl-ACP synthase”, and “keto-acyl ACP synthase”, and similar derivatives.
  • the acyl group destined for elongation is linked to a cysteine residue at the active site of the enzyme by a thioester bond.
  • the acyl-enzyme undergoes condensation with malonyl-ACP to form -keto acyl-ACP, CO 2 and free enzyme.
  • the KS plays a key role in the elongation cycle and in many systems has been shown to possess greater substrate specificity than other enzymes of the reaction cycle.
  • E. coli has three distinct KS enzymes—each with its own particular role in the physiology of the organism (Magnuson et al., Microbiol. Rev. 57, 522 (1993)).
  • the two KS domains of the PUFA-PKS systems described in marine bacteria and the thraustochytrids described herein may have distinct roles in the PUFA biosynthetic reaction sequence.
  • KS's As a class of enzymes, KS's have been well characterized. The sequences of many verified KS genes are known, the active site motifs have been identified and the crystal structures of several have been determined. Proteins (or domains of proteins) can be readily identified as belonging to the KS family of enzymes by homology to known KS sequences.
  • a domain or protein having malonyl-CoA:ACP acyltransferase (MAT) biological activity is characterized as one that transfers the malonyl moiety from malonyl-CoA to ACP.
  • the term “malonyl-CoA:ACP acyltransferase” can be used interchangeably with “malonyl acyltransferase” and similar derivatives.
  • these enzymes possess an extended motif of R and Q amino acids in key positions that identifies them as MAT enzymes (e.g., in contrast to an AT domain described below).
  • MAT domains will preferentially load methyl- or ethyl-malonate on to the ACP group (from the corresponding CoA ester), thereby introducing branches into the linear carbon chain.
  • MAT domains can be recognized by their homology to known MAT sequences and by their extended motif structure.
  • a domain or protein having acyl carrier protein (ACP) biological activity is characterized as being small polypeptides (typically, 80 to 100 amino acids long), that function as carriers for growing fatty acyl chains via a thioester linkage to a covalently bound co-factor of the protein. They occur as separate units or as domains within larger proteins.
  • ACPs are converted from inactive apo-forms to functional holo-forms by transfer of the phosphopantetheinyl moiety of CoA to a highly conserved serine residue of the ACP.
  • Acyl groups are attached to ACP by a thioester linkage at the free terminus of the phosphopantetheinyl moiety.
  • ACPs can be identified by labeling with radioactive pantetheine and by sequence homology to known ACPs. The presence of variations of the above mentioned motif (LGIDS*) is also a signature of an ACP.
  • a domain or protein having ketoreductase activity also referred to as 3-ketoacyl-ACP reductase (KR) biological activity (function) is characterized as one that catalyzes the pyridine-nucleotide-dependent reduction of 3-keto acyl forms of ACP. It is the first reductive step in the de novo fatty acid biosynthesis elongation cycle and a reaction often performed in polyketide biosynthesis.
  • ⁇ -ketoacyl-ACP reductase can be used interchangeably with the terms “ketoreductase”, “3-ketoacyl-ACP reductase”, “keto-acyl ACP reductase” and similar derivatives of the term.
  • Significant sequence similarity is observed with one family of enoyl ACP reductases (ER), the other reductase of FAS (but not the ER family present in the PUFA PKS systems), and the short-chain alcohol dehydrogenase family.
  • Pfam analysis of the PUFA PKS region indicated above reveals the homology to the short-chain alcohol dehydrogenase family in the core region.
  • Blast analysis of the same region reveals matches in the core area to known KR enzymes as well as an extended region of homology to domains from the other characterized PUFA PKS systems.
  • a domain or protein is referred to as a chain length factor (CLF) based on the following rationale.
  • CLF was originally described as characteristic of Type II (dissociated enzymes) PKS systems and was hypothesized to play a role in determining the number of elongation cycles, and hence the chain length, of the end product.
  • CLF amino acid sequences show homology to KS domains (and are thought to form heterodimers with a KS protein), but they lack the active site cysteine. CLF's role in PKS systems has been controversial. New evidence (C.
  • acyltransferase refers to a general class of enzymes that can carry out a number of distinct acyl transfer reactions.
  • the term “acyltransferase” can be used interchangeably with the term “acyl transferase”.
  • the AT domains identified in the PUFA PKS systems described herein show good homology one another and to domains present in all of the other PUFA PKS systems currently examined and very weak homology to some acyltransferases whose specific functions have been identified (e.g. to malonyl-CoA:ACP acyltransferase, MAT).
  • the possible functions of the AT domain in a PUFA PKS system include, but are not limited to: transfer of the fatty acyl group from the ORFA ACP domain(s) to water (i.e. a thioesterase—releasing the fatty acyl group as a free fatty acid), transfer of a fatty acyl group to an acceptor such as CoA, transfer of the acyl group among the various ACP domains, or transfer of the fatty acyl group to a lipophilic acceptor molecule (e.g. to lysophosphadic acid).
  • this domain has enoyl reductase (ER) biological activity.
  • the ER enzyme reduces the trans-double bond (introduced by the DH activity) in the fatty acyl-ACP, resulting in fully saturating those carbons.
  • the ER domain in the PUFA-PKS shows homology to a newly characterized family of ER enzymes (Heath et al., Nature 406, 145 (2000)). Heath and Rock identified this new class of ER enzymes by cloning a gene of interest from Streptococcus pneumoniae , purifying a protein expressed from that gene, and showing that it had ER activity in an in vitro assay. All of the PUFA PKS systems currently examined contain at least one domain with very high sequence homology to the Schizochytrium ER domain, which shows homology to the S. pneumoniae ER protein.
  • a protein or domain having dehydrase or dehydratase (DH) activity catalyzes a dehydration reaction.
  • DH activity typically refers to FabA-like ⁇ -hydroxyacyl-ACP dehydrase (DH) biological activity.
  • FabA-like ⁇ -hydroxyacyl-ACP dehydrase (DH) biological activity removes HOH from a ⁇ -ketoacyl-ACP and initially produces a trans double bond in the carbon chain.
  • FabA-like ⁇ -hydroxyacyl-ACP dehydrase can be used interchangeably with the terms “FabA-like ⁇ -hydroxy acyl-ACP dehydrase”, “ ⁇ -hydroxyacyl-ACP dehydrase”, “dehydrase” and similar derivatives.
  • the DH domains of the PUFA PKS systems show homology to bacterial DH enzymes associated with their FAS systems (rather than to the DH domains of other PKS systems).
  • a subset of bacterial DH's, the FabA-like DH's possesses cis-trans isomerase activity (Heath et al., J. Biol. Chem., 271, 27795 (1996)). It is the homology to the FabA-like DH proteins that indicate that one or all of the DH domains described herein is responsible for insertion of the cis double bonds in the PUFA PKS products.
  • a PUFA PKS protein useful of the invention may also have dehydratase activity that is not characterized as FabA-like (e.g., the cis-trans activity described above is associated with FabA-like activity), generally referred to herein as non-FabA-like DH activity, or non-FabA-like ⁇ -hydroxyacyl-ACP dehydrase (DH) biological activity.
  • FabA-like e.g., the cis-trans activity described above is associated with FabA-like activity
  • DH non-FabA-like DH activity
  • DH non-FabA-like ⁇ -hydroxyacyl-ACP dehydrase
  • a conserved active site motif ⁇ 13 amino acids long: L*xxHxxxGxxxxP; e.g., illustrated by amino acids 2504-2516 of SEQ ID NO:70; *in the motif, L can also be I
  • L*xxHxxxGxxxxP e.g., illustrated by amino acids 2504-2516 of
  • DH dehydratase
  • a PUFA PKS system from Schizochytrium comprises at least the following biologically active domains: (a) two enoyl-ACP reductase (ER) domain; (b) between five and ten or more acyl carrier protein (ACP) domains, and in one aspect, nine ACP domains; (c) two ⁇ -ketoacyl-ACP synthase (KS) domains; (d) one acyltransferase (AT) domain; (e) one ⁇ -ketoacyl-ACP reductase (KR) domain; (f) two FabA-like ⁇ -hydroxyacyl-ACP dehydrase (DH) domains; (g) one chain length factor (CLF) domain; and (h) one malonyl-CoA:ACP acyltransferase (MAT) domain.
  • a Schizochytrium PUFA PKS system also comprises at least one region or domain containing a dehydratase (DH) conserved active site motif that is not a part of a FabA-like DH domain.
  • DH dehydratase
  • the structural and functional characteristics of these domains are generally individually known in the art (see, e.g., U.S. Pat. No. 6,566,583; Metz et al., Science 293:290-293 (2001); U.S. Patent Application Publication No. 20020194641; and PCT Publication No. WO 2006/135866).
  • each open reading frame There are three open reading frames that form the core Schizochytrium PUFA PKS system described previously.
  • the domain structure of each open reading frame is as follows.
  • OrfA is a 8730 nucleotide sequence (not including the stop codon) which encodes a 2910 amino acid sequence, represented herein as SEQ ID NO:2.
  • SEQ ID NO:2 The complete nucleotide sequence for OrfA is represented herein as SEQ ID NO:1.
  • OrfA is a 8730 nucleotide sequence (not including the stop codon) which encodes a 2910 amino acid sequence, represented herein as SEQ ID NO:2.
  • Within OrfA are twelve domains: (a) one ⁇ -keto acyl-ACP synthase (KS) domain; (b) one malonyl-CoA:ACP acyltransferase (MAT) domain; (c) nine acyl carrier protein (ACP) domains; and (d) one ketoreductase (KR) domain.
  • a genomic clone described herein as JK1126, isolated from Schizochytrium sp. ATCC 20888, comprises, to the best of the present inventors' knowledge, the nucleotide sequence spanning from position 1 to 8730 of SEQ ID NO:1, and encodes the corresponding amino acid sequence of SEQ ID NO:2.
  • Genomic clone pJK1126 (denoted pJK1126 OrfA genomic clone, in the form of an E. coli plasmid vector containing “OrfA” gene from Schizochytrium ATCC 20888) was deposited with the American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, Va. 20110-2209 USA on Jun. 8, 2006, and assigned ATCC Accession No. PTA-7648.
  • the nucleotide sequence of pJK1126 OrfA genomic clone, and the amino acid sequence encoded by this plasmid are encompassed by the present invention.
  • Genomic clone pJK306 OrfA genomic clone and pJK320 OrfA genomic clone, isolated from Schizochytrium sp. N230D, together (overlapping clones) comprise, to the best of the present inventors' knowledge, the nucleotide sequence of SEQ ID NO:1, and encode the amino acid sequence of SEQ ID NO:2.
  • Genomic clone pJK306 (denoted pJK306 OrfA genomic clone, in the form of an E. coli plasmid containing 5′ portion of OrfA gene from Schizochytrium sp.
  • N230D (2.2 kB overlap with pJK320) was deposited with the American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, Va. 20110-2209 USA on Jun. 8, 2006, and assigned ATCC Accession No. PTA-7641.
  • ATCC American Type Culture Collection
  • the nucleotide sequence of pJK306 OrfA genomic clone, and the amino acid sequence encoded by this plasmid are encompassed by the present invention.
  • Genomic clone pJK320 (denoted pJK320 OrfA genomic clone, in the form of an E. coli plasmid containing 3′ portion of OrfA gene from Schizochytrium sp.
  • N230D (2.2 kB overlap with pJK306) was deposited with the American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, Va. 20110-2209 USA on Jun. 8, 2006, and assigned ATCC Accession No. PTA-7644.
  • ATCC American Type Culture Collection
  • the nucleotide sequence of pJK320 OrfA genomic clone, and the amino acid sequence encoded by this plasmid are encompassed by the present invention.
  • the first domain in OrfA is a KS domain, also referred to herein as ORFA-KS, and the nucleotide sequence containing the sequence encoding the ORFA-KS domain is represented herein as SEQ ID NO:7 (positions 1-1500 of SEQ ID NO:1).
  • the amino acid sequence containing the ORFA-KS domain is represented herein as SEQ ID NO:8 (positions 1-500 of SEQ ID NO:2).
  • the ORFA-KS domain contains an active site motif: DXAC* (*acyl binding site C 215 ).
  • DXAC* *acyl binding site C 215
  • GFGG a characteristic motif at the end of the Schizochytrium KS region
  • the second domain in OrfA is a MAT domain, also referred to herein as ORFA-MAT, and the nucleotide sequence containing the sequence encoding the ORFA-MAT domain is represented herein as SEQ ID NO:9 (positions 1723-3000 of SEQ ID NO:1).
  • the amino acid sequence containing the ORFA-MAT domain is represented herein as SEQ ID NO:10 (positions 575-1000 of SEQ ID NO:2).
  • the MAT domain comprises an aspartate at position 93 and a histidine at position 94 (corresponding to positions 667 and 668, respectively, of SEQ ID NO:2).
  • the ORFA-MAT domain contains an active site motif: GHS*XG (*acyl binding site S 706 ), represented herein as SEQ ID NO:11.
  • Domains 3-11 of OrfA are nine tandem ACP domains, also referred to herein as ORFA-ACP (the first domain in the sequence is ORFA-ACP1, the second domain is ORFA-ACP2, the third domain is ORFA-ACP3, etc.).
  • the first ACP domain, ORFA-ACP1 is contained within the nucleotide sequence spanning from about position 3343 to about position 3600 of SEQ ID NO:1 (OrfA).
  • the nucleotide sequence containing the sequence encoding the ORFA-ACP1 domain is represented herein as SEQ ID NO:12 (positions 3343-3600 of SEQ ID NO:1).
  • the amino acid sequence containing the first ACP domain spans from about position 1115 to about position 1200 of SEQ ID NO:2.
  • the amino acid sequence containing the ORFA-ACP1 domain is represented herein as SEQ ID NO:13 (positions 1115-1200 of SEQ ID NO:2). It is noted that the ORFA-ACP1 domain contains an active site motif: LGIDS* (*pantetheine binding motif S 1157 ), represented herein by SEQ ID NO:14.
  • nucleotide and amino acid sequences of all nine ACP domains are highly conserved and therefore, the sequence for each domain is not represented herein by an individual sequence identifier. However, based on the information disclosed herein, one of skill in the art can readily determine the sequence containing each of the other eight ACP domains. All nine ACP domains together span a region of OrfA of from about position 3283 to about position 6288 of SEQ ID NO:1, which corresponds to amino acid positions of from about 1095 to about 2096 of SEQ ID NO:2.
  • the nucleotide sequence for the entire ACP region containing all nine domains is represented herein as SEQ ID NO:16.
  • the region represented by SEQ ID NO:16 includes the linker segments between individual ACP domains.
  • the repeat interval for the nine domains is approximately every 330 nucleotides of SEQ ID NO:16 (the actual number of amino acids measured between adjacent active site serines ranges from 104 to 116 amino acids).
  • Each of the nine ACP domains contains a pantetheine binding motif LGIDS* (represented herein by SEQ ID NO:14), wherein S* is the pantetheine binding site serine (S).
  • S* is the pantetheine binding site serine
  • S The pantetheine binding site serine
  • S is located near the center of each ACP domain sequence.
  • At each end of the ACP domain region and between each ACP domain is a region that is highly enriched for proline (P) and alanine (A), which is believed to be a linker region.
  • ACP domains 1 and 2 are the sequence: APAPVKAAAPAAPVASAPAPA, represented herein as SEQ ID NO:15.
  • an ACP domain is about 85 amino acids, excluding the linker, and about 110 amino acids including the linker, with the active site serine being approximately in the center of the domain, one of skill in the art can readily determine the positions of each of the nine ACP domains in OrfA.
  • Domain 12 in OrfA is a KR domain, also referred to herein as ORFA-KR, and the nucleotide sequence containing the sequence encoding the ORFA-KR domain is represented herein as SEQ ID NO:17 (positions 6598-8730 of SEQ ID NO:1).
  • the amino acid sequence containing the ORFA-KR domain is represented herein as SEQ ID NO:18 (positions 2200-2910 of SEQ ID NO:2).
  • Within the KR domain is a core region with homology to short chain aldehyde-dehydrogenases (KR is a member of this family). This core region spans from about position 7198 to about position 7500 of SEQ ID NO:1, which corresponds to amino acid positions 2400-2500 of SEQ ID NO:2.
  • OrfB is a 6177 nucleotide sequence (not including the stop codon) which encodes a 2059 amino acid sequence, represented herein as SEQ ID NO:4.
  • SEQ ID NO:4 Within OrfB are four domains: (a) one -keto acyl-ACP synthase (KS) domain; (b) one chain length factor (CLF) domain; (c) one acyl transferase (AT) domain; and, (d) one enoyl ACP-reductase (ER) domain.
  • KS -keto acyl-ACP synthase
  • CLF chain length factor
  • AT acyl transferase
  • ER enoyl ACP-reductase
  • a genomic clone described herein as pJK1129, isolated from Schizochytrium sp. ATCC 20888, comprises, to the best of the present inventors' knowledge, the nucleotide sequence of SEQ ID NO:3, and encodes the amino acid sequence of SEQ ID NO:4.
  • Genomic clone pJK1129 (denoted pJK1129 OrfB genomic clone, in the form of an E. coli plasmid vector containing “OrfB” gene from Schizochytrium ATCC 20888) was deposited with the American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, Va. 20110-2209 USA on Jun. 8, 2006, and assigned ATCC Accession No. PTA-7649.
  • the nucleotide sequence of pJK1126 OrfB genomic clone, and the amino acid sequence encoded by this plasmid are encompassed by the present invention.
  • a genomic clone described herein as pJK324 OrfB genomic clone, isolated from Schizochytrium sp. N230D, comprises, to the best of the present inventors' knowledge, the nucleotide sequence of SEQ ID NO:3, and encodes the amino acid sequence of SEQ ID NO:4.
  • Genomic clone pJK324 (denoted pJK324 OrfB genomic clone, in the form of an E. coli plasmid containing the OrfB gene sequence from Schizochytrium sp. N230D) was deposited with the American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, Va. 20110-2209 USA on Jun. 8, 2006, and assigned ATCC Accession No. PTA-7643.
  • ATCC American Type Culture Collection
  • the nucleotide sequence of pJK324 OrfB genomic clone, and the amino acid sequence encoded by this plasmid are encompassed by the
  • the first domain in OrfB is a KS domain, also referred to herein as ORFB-KS, and the nucleotide sequence containing the sequence encoding the ORFB-KS domain is represented herein as SEQ ID NO:19 (positions 1-1350 of SEQ ID NO:3).
  • the amino acid sequence containing the ORFB-KS domain is represented herein as SEQ ID NO:20 (positions 1-450 of SEQ ID NO:4).
  • This KS domain comprises a valine at position 371 of SEQ ID NO:20 (also position 371 of SEQ ID NO:20).
  • the ORFB-KS domain contains an active site motif: DXAC* (*acyl binding site C 196 ).
  • DXAC* *acyl binding site C 196
  • GFGG a characteristic motif at the end of this KS region, is present in this domain in SEQ ID NO:4 and accordingly, in SEQ ID NO:20.
  • the second domain in OrfB is a CLF domain, also referred to herein as ORFB-CLF, and the nucleotide sequence containing the sequence encoding the ORFB-CLF domain is represented herein as SEQ ID NO:21 (positions 1378-2700 of SEQ ID NO:3).
  • the amino acid sequence containing the ORFB-CLF domain is represented herein as SEQ ID NO:22 (positions 460-900 of SEQ ID NO:4). It is noted that the ORFB-CLF domain contains a KS active site motif without the acyl-binding cysteine.
  • the third domain in OrfB is an AT domain, also referred to herein as ORFB-AT, and the nucleotide sequence containing the sequence encoding the ORFB-AT domain is represented herein as SEQ ID NO:23 (positions 2701-4200 of SEQ ID NO:3).
  • the amino acid sequence containing the ORFB-AT domain is represented herein as SEQ ID NO:24 (positions 901-1400 of SEQ ID NO:4).
  • the ORFB-AT domain contains an active site motif of GxS*xG (*acyl binding site S 1140 ) that is characteristic of acyltransferse (AT) proteins.
  • the fourth domain in OrfB is an ER domain, also referred to herein as ORFB-ER, and the nucleotide sequence containing the sequence encoding the ORFB-ER domain is represented herein as SEQ ID NO:25 (positions 4648-6177 of SEQ ID NO:3).
  • the amino acid sequence containing the ORFB-ER domain is represented herein as SEQ ID NO:26 (positions 1550-2059 of SEQ ID NO:4).
  • OrfC The complete nucleotide sequence for OrfC is represented herein as SEQ ID NO:5.
  • OrfC is a 4506 nucleotide sequence (not including the stop codon) which encodes a 1502 amino acid sequence, represented herein as SEQ ID NO:6.
  • Within OrfC are three domains:
  • Genomic DNA clones encoding OrfC from both Schizochytrium sp. ATCC 20888 and a daughter strain of ATCC 20888, denoted Schizochytrium sp., strain N230D, have been isolated and sequenced.
  • a genomic clone described herein as pJK1131, isolated from Schizochytrium sp. ATCC 20888, comprises, to the best of the present inventors' knowledge, the nucleotide sequence of SEQ ID NO:5, and encodes the amino acid sequence of SEQ ID NO:6.
  • Genomic clone pJK1131 (denoted pJK1131 OrfC genomic clone, in the form of an E. coli plasmid vector containing “OrfC” gene from Schizochytrium ATCC 20888) was deposited with the American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, Va. 20110-2209 USA on Jun. 8, 2006, and assigned ATCC Accession No. PTA-7650.
  • the nucleotide sequence of pJK1131 OrfC genomic clone, and the amino acid sequence encoded by this plasmid are encompassed by the present invention.
  • a genomic clone described herein as pBR002 OrfC genomic clone, isolated from Schizochytrium sp. N230D, comprises, to the best of the present inventors' knowledge, the nucleotide sequence of SEQ ID NO:5, and encodes the amino acid sequence of SEQ ID NO:6.
  • Genomic clone pBR002 (denoted pBR002 OrfC genomic clone, in the form of an E. coli plasmid vector containing the OrfC gene sequence from Schizochytrium sp. N230D) was deposited with the American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, Va. 20110-2209 USA on Jun. 8, 2006, and assigned ATCC Accession No. PTA-7642.
  • ATCC American Type Culture Collection
  • the nucleotide sequence of pBR002 OrfC genomic clone, and the amino acid sequence encoded by this plasmid are encompassed by the present invention
  • the first domain in OrfC is a DH domain, also referred to herein as ORFC-DH1.
  • This is one of two DH domains in OrfC, and therefore is designated DH1.
  • the nucleotide sequence containing the sequence encoding the ORFC-DH1 domain is represented herein as SEQ ID NO:27 (positions 1-1350 of SEQ ID NO:5).
  • the amino acid sequence containing the ORFC-DH1 domain is represented herein as SEQ ID NO:28 (positions 1-450 of SEQ ID NO:6).
  • the second domain in OrfC is a DH domain, also referred to herein as ORFC-DH2.
  • This is the second of two DH domains in OrfC, and therefore is designated DH2.
  • the nucleotide sequence containing the sequence encoding the ORFC-DH2 domain is represented herein as SEQ ID NO:29 (positions 1351-2847 of SEQ ID NO:5).
  • the amino acid sequence containing the ORFC-DH2 domain is represented herein as SEQ ID NO:30 (positions 451-949 of SEQ ID NO:6).
  • This DH domain comprises the amino acids H-G-I-A-N-P-T-F-V-H-A-P-G-K-I (positions 876-890 of SEQ ID NO:6) at positions 426-440 of SEQ ID NO:30.
  • the third domain in OrfC is an ER domain, also referred to herein as ORFC-ER, and the nucleotide sequence containing the sequence encoding the ORFC-ER domain is represented herein as SEQ ID NO:31 (positions 2995-4506 of SEQ ID NO:5).
  • the amino acid sequence containing the ORFC-ER domain is represented herein as SEQ ID NO:32 (positions 999-1502 of SEQ ID NO:6).
  • a Thraustochytrium PUFA PKS system comprises at least the following biologically active domains: (a) two enoyl-ACP reductase (ER) domain; (b) between five and ten or more acyl carrier protein (ACP) domains, and in one aspect, eight ACP domains; (c) two ⁇ -ketoacyl-ACP synthase (KS) domains; (d) one acyltransferase (AT) domain; (e) one ⁇ -ketoacyl-ACP reductase (KR) domain; (f) two FabA-like ⁇ -hydroxyacyl-ACP dehydrase (DH) domains; (g) one chain length factor (CLF) domain; and (h) one malonyl-CoA:ACP acyltransferase (MAT) domain.
  • a Thraustochytrium PUFA PKS system also comprises at least one region or domain containing a dehydratase (DH) conserved active site motif that is not a part of a FabA-like DH domain.
  • DH dehydratase
  • the structural and functional characteristics of these domains are generally individually known in the art (see, e.g., U.S. Patent Publication No. 2004035127, supra).
  • each open reading frame There are three open reading frames that form the core Thraustochytrium 23B PUFA PKS system described previously.
  • the domain structure of each open reading frame is as follows.
  • Th. 23B OrfA is a 8433 nucleotide sequence (not including the stop codon) which encodes a 2811 amino acid sequence, represented herein as SEQ ID NO:39.
  • SEQ ID NO:38 encodes the following domains in Th. 23B OrfA: (a) one ⁇ -ketoacyl-ACP synthase (KS) domain; (b) one malonyl-CoA:ACP acyltransferase (MAT) domain; (c) eight acyl carrier protein (ACP) domains; and (d) one ⁇ -ketoacyl-ACP reductase (KR) domain.
  • KS ⁇ -ketoacyl-ACP synthase
  • MAT malonyl-CoA:ACP acyltransferase
  • ACP eight acyl carrier protein
  • KR ⁇ -ketoacyl-ACP reductase
  • Th23BOrfA_pBR812.1 and Th23BOrfA_pBR811 Two genomic clone described herein as Th23BOrfA_pBR812.1 and Th23BOrfA_pBR811 (OrfA genomic clones), isolated from Thraustochytrium 23B, together (overlapping clones) comprise, to the best of the present inventors' knowledge, the nucleotide sequence of SEQ ID NO:38, and encodes the amino acid sequence of SEQ ID NO:39.
  • Genomic clone Th23BOrfA_pBR812.1 dedenoted Th23BOrfA_pBR812.1 genomic clone, in the form of an E.
  • coli plasmid vector containing the OrfA gene sequence from Thraustochytrium 23B was deposited with the American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, Va. 20110-2209 USA on Mar. 1, 2007, and assigned ATCC Accession No. ______.
  • ATCC American Type Culture Collection
  • the nucleotide sequence of Th23BOrfA_pBR812.1, an OrfA genomic clone, and the amino acid sequence encoded by this plasmid are encompassed by the present invention.
  • Genomic clone Th23BOrfA_pBR811 (denoted Th23BOrfA_pBR811 genomic clone, in the form of an E.
  • coli plasmid vector containing the OrfA gene sequence from Thraustochytrium 23B was deposited with the American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, Va. 20110-2209 USA on Mar. 1, 2007, and assigned ATCC Accession No. ______.
  • ATCC American Type Culture Collection
  • the nucleotide sequence of Th23BOrfA_pBR811, an OrfA genomic clone, and the amino acid sequence encoded by this plasmid are encompassed by the present invention.
  • the first domain in Th. 23B OrfA is a KS domain, also referred to herein as Th. 23B OrfA-KS, and is contained within the nucleotide sequence spanning from about position 1 to about position 1500 of SEQ ID NO:38, represented herein as SEQ ID NO:40.
  • the amino acid sequence containing the Th. 23B K domain is a region of SEQ ID NO:39 spanning from about position 1 to about position 500 of SEQ ID NO:39, represented herein as SEQ ID NO:41.
  • This region of SEQ ID NO:39 has a Pfam match to FabB ( ⁇ -ketoacyl-ACP synthase) spanning from position 1 to about position 450 of SEQ ID NO:39 (also positions 1 to about 450 of SEQ ID NO:41). It is noted that the Th. 23B OrfA-KS domain contains an active site motif: DXAC* (*acyl binding site C 207 ). Also, a characteristic motif at the end of the Th. 23B K region, GFGG, is present in positions 453-456 of SEQ ID NO:39 (also positions 453-456 of SEQ ID NO:41).
  • Th. 23B OrfA is a MAT domain, also referred to herein as Th. 23B OrfA-MAT, and is contained within the nucleotide sequence spanning from between about position 1503 and about position 3000 of SEQ ID NO:38, represented herein as SEQ ID NO:42.
  • the amino acid sequence containing the Th. 23B MAT domain is a region of SEQ ID NO:39 spanning from about position 501 to about position 1000, represented herein by SEQ ID NO:43.
  • This region of SEQ ID NO:39 has a Pfam match to FabD (malonyl-CoA:ACP acyltransferase) spanning from about position 580 to about position 900 of SEQ ID NO:39 (positions 80-400 of SEQ ID NO:43). It is noted that the Th. 23B OrfA-MAT domain contains an active site motif: GHS*XG (*acyl binding site S 697 ), represented by positions 695-699 of SEQ ID NO:39.
  • Th. 23B OrfA are eight tandem ACP domains, also referred to herein as Th. 23B OrfA-ACP (the first domain in the sequence is OrfA-ACP1, the second domain is OrfA-ACP2, the third domain is OrfA-ACP3, etc.).
  • the first Th. 23B ACP domain, Th. 23B OrfA-ACP1 is contained within the nucleotide sequence spanning from about position 3205 to about position 3555 of SEQ ID NO:38 (OrfA), represented herein as SEQ ID NO:44.
  • the amino acid sequence containing the first Th. 23B ACP domain is a region of SEQ ID NO:39 spanning from about position 1069 to about position 1185 of SEQ ID NO:39, represented herein by SEQ ID NO:45.
  • the eight ACP domains in Th. 23B OrfA are adjacent to one another and can be identified by the presence of the phosphopantetheine binding site motif, LGXDS* (represented by SEQ ID NO:46), wherein the S* is the phosphopantetheine attachment site.
  • LGXDS* represented by SEQ ID NO:46
  • the amino acid position of each of the eight S* sites are 1128 (ACP1), 1244 (ACP2), 1360 (ACP3), 1476 (ACP4), 1592 (ACP5), 1708 (ACP6), 1824 (ACP7) and 1940 (ACP8).
  • the nucleotide and amino acid sequences of all eight Th are 1128 (ACP1), 1244 (ACP2), 1360 (ACP3), 1476 (ACP4), 1592 (ACP5), 1708 (ACP6), 1824 (ACP7) and 1940 (ACP8).
  • the nucleotide and amino acid sequences of all eight Th are 1128 (ACP1), 1244 (A
  • ACP domains are highly conserved and therefore, the sequence for each domain is not represented herein by an individual sequence identifier. However, based on the information disclosed herein, one of skill in the art can readily determine the sequence containing each of the other seven ACP domains in SEQ ID NO:38 and SEQ ID NO:39.
  • Th. 23B ACP domains together span a region of Th. 23B OrfA of from about position 3205 to about position 5994 of SEQ ID NO:38, which corresponds to amino acid positions of from about 1069 to about 1998 of SEQ ID NO:39.
  • the nucleotide sequence for the entire ACP region containing all eight domains is represented herein as SEQ ID NO:47.
  • SEQ ID NO:47 encodes an amino acid sequence represented herein by SEQ ID NO:48.
  • SEQ ID NO:48 includes the linker segments between individual ACP domains. The repeat interval for the eight domains is approximately every 116 amino acids of SEQ ID NO:48, and each domain can be considered to consist of about 116 amino acids centered on the active site motif (described above).
  • Th. 23B OrfA The last domain in Th. 23B OrfA is a KR domain, also referred to herein as Th. 23B OrfA-KR, which is contained within the nucleotide sequence spanning from between about position 6001 to about position 8433 of SEQ ID NO:38, represented herein by SEQ ID NO:49.
  • the amino acid sequence containing the Th. 23B K domain is a region of SEQ ID NO:39 spanning from about position 2001 to about position 2811 of SEQ ID NO:39, represented herein by SEQ ID NO:50.
  • This region of SEQ ID NO:39 has a Pfam match to FabG ( ⁇ -ketoacyl-ACP reductase) spanning from about position 2300 to about 2550 of SEQ ID NO:39 (positions 300-550 of SEQ ID NO:50).
  • SEQ ID NO:51 The complete nucleotide sequence for Th. 23B OrfB is represented herein as SEQ ID NO:51, which is a 5805 nucleotide sequence (not including the stop codon) that encodes a 1935 amino acid sequence, represented herein as SEQ ID NO:52.
  • SEQ ID NO:51 encodes the following domains in Th. 23B OrfB: (a) one ⁇ -ketoacyl-ACP synthase (KS) domain; (b) one chain length factor (CLF) domain; (c) one acyltransferase (AT) domain; and, (d) one enoyl-ACP reductase (ER) domain.
  • Th23BOrfB_pBR800 OrfB genomic clone
  • Th23BOrfB_pBR800 genomic clone
  • genomic clone Th23BOrfB_pBR800 denoted Th23BOrfB_pBR800 genomic clone, in the form of an E. coli plasmid vector containing the OrfB gene sequence from Thraustochytrium 23B
  • ATCC American Type Culture Collection
  • the first domain in the Th. 23B OrfB is a KS domain, also referred to herein as Th. 23B OrfB-KS, which is contained within the nucleotide sequence spanning from between about position 1 and about position 1500 of SEQ ID NO:51 (Th. 23B OrfB), represented herein as SEQ ID NO:53.
  • the amino acid sequence containing the Th. 23B K domain is a region of SEQ ID NO: 52 spanning from about position 1 to about position 500 of SEQ ID NO:52, represented herein as SEQ ID NO:54.
  • This region of SEQ ID NO:52 has a Pfam match to FabB ( ⁇ -ketoacyl-ACP synthase) spanning from about position 1 to about position 450 (positions 1-450 of SEQ ID NO:54). It is noted that the Th. 23B OrfB-KS domain contains an active site motif: DXAC*, where C* is the site of acyl group attachment and wherein the C* is at position 201 of SEQ ID NO:52. Also, a characteristic motif at the end of the KS region, GFGG is present in amino acid positions 434-437 of SEQ ID NO:52.
  • the second domain in Th. 23B OrfB is a CLF domain, also referred to herein as Th. 23B OrfB-CLF, which is contained within the nucleotide sequence spanning from between about position 1501 and about position 3000 of SEQ ID NO:51 (OrfB), represented herein as SEQ ID NO:55.
  • the amino acid sequence containing the CLF domain is a region of SEQ ID NO: 52 spanning from about position 501 to about position 1000 of SEQ ID NO:52, represented herein as SEQ ID NO:56.
  • SEQ ID NO:52 has a Pfam match to FabB ( ⁇ -ketoacyl-ACP synthase) spanning from about position 550 to about position 910 (positions 50-410 of SEQ ID NO:56).
  • CLF has homology to KS proteins, it lacks an active site cysteine to which the acyl group is attached in KS proteins.
  • Th. 23B OrfB The third domain in Th. 23B OrfB is an AT domain, also referred to herein as Th. 23B OrfB-AT, which is contained within the nucleotide sequence spanning from between about position 3001 and about position 4500 of SEQ ID NO:51 (Th. 23B OrfB), represented herein as SEQ ID NO:58.
  • the amino acid sequence containing the Th. 23B A domain is a region of SEQ ID NO: 52 spanning from about position 1001 to about position 1500 of SEQ ID NO:52, represented herein as SEQ ID NO:58.
  • This region of SEQ ID NO:52 has a Pfam match to FabD (malonyl-CoA:ACP acyltransferase) spanning from about position 1100 to about position 1375 (positions 100-375 of SEQ ID NO:58).
  • FabD malonyl-CoA:ACP acyltransferase
  • This AT domain of the PUFA synthases has homology to MAT proteins, it lacks the extended motif of the MAT (key arginine and glutamine residues) and it is not thought to be involved in malonyl-CoA transfers.
  • the GXS*XG motif of acyltransferases is present, with the S* being the site of acyl attachment and located at position 1123 with respect to SEQ ID NO:52.
  • Th. 23B OrfB The fourth domain in Th. 23B OrfB is an ER domain, also referred to herein as Th. 23B OrfB-ER, which is contained within the nucleotide sequence spanning from between about position 4501 and about position 5805 of SEQ ID NO:51 (OrfB), represented herein as SEQ ID NO:59.
  • the amino acid sequence containing the Th. 23B E domain is a region of SEQ ID NO: 52 spanning from about position 1501 to about position 1935 of SEQ ID NO:52, represented herein as SEQ ID NO:60.
  • This region of SEQ ID NO:52 has a Pfam match to a family of dioxygenases related to 2-nitropropane dioxygenases spanning from about position 1501 to about position 1810 (positions 1-310 of SEQ ID NO:60). That this domain functions as an ER can be further predicted due to homology to a newly characterized ER enzyme from Streptococcus pneumoniae.
  • SEQ ID NO:61 The complete nucleotide sequence for Th. 23B OrfC is represented herein as SEQ ID NO:61, which is a 4410 nucleotide sequence (not including the stop codon) that encodes a 1470 amino acid sequence, represented herein as SEQ ID NO:62.
  • SEQ ID NO:61 encodes the following domains in Th.
  • OrfC (a) two FabA-like ⁇ -hydroxyacyl-ACP dehydrase (DH) domains, both with homology to the FabA protein (an enzyme that catalyzes the synthesis of trans-2-decenoyl-ACP and the reversible isomerization of this product to cis-3-decenoyl-ACP); and (b) one enoyl-ACP reductase (ER) domain with high homology to the ER domain of Schizochytrium OrfB.
  • DH ⁇ -hydroxyacyl-ACP dehydrase
  • Th23BOrfC_pBR709A OrfC genomic clone
  • isolated from Thraustochytrium 23B comprises, to the best of the present inventors' knowledge, the nucleotide sequence of SEQ ID NO:61, and encodes the amino acid sequence of SEQ ID NO:62.
  • Genomic clone Th23BOrfC_pBR709A denoted Th23BOrfC_pBR709A genomic clone, in the form of an E. coli plasmid vector containing the OrfC gene sequence from Thraustochytrium 23B was deposited with the American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, Va.
  • ATCC American Type Culture Collection
  • the first domain in Th. 23B OrfC is a DH domain, also referred to herein as Th. 23B OrfC-DH1, which is contained within the nucleotide sequence spanning from between about position 1 to about position 1500 of SEQ ID NO:61 (OrfC), represented herein as SEQ ID NO:63.
  • the amino acid sequence containing the Th. 23B D1 domain is a region of SEQ ID NO: 62 spanning from about position 1 to about position 500 of SEQ ID NO:62, represented herein as SEQ ID NO:64. This region of SEQ ID NO:62 has a Pfam match to FabA, as mentioned above, spanning from about position 275 to about position 400 (positions 275-400 of SEQ ID NO:64).
  • Th. 23B OrfC is also a DH domain, also referred to herein as Th. 23B OrfC-DH2, which is contained within the nucleotide sequence spanning from between about position 1501 to about 3000 of SEQ ID NO:61 (OrfC), represented herein as SEQ ID NO:65.
  • the amino acid sequence containing the Th. 23B D2 domain is a region of SEQ ID NO: 62 spanning from about position 501 to about position 1000 of SEQ ID NO:62, represented herein as SEQ ID NO:66. This region of SEQ ID NO:62 has a Pfam match to FabA, as mentioned above, spanning from about position 800 to about position 925 (positions 300-425 of SEQ ID NO:66).
  • Th. 23B OrfC The third domain in Th. 23B OrfC is an ER domain, also referred to herein as Th. 23B OrfC-ER, which is contained within the nucleotide sequence spanning from between about position 3001 to about position 4410 of SEQ ID NO:61 (OrfC), represented herein as SEQ ID NO:67.
  • the amino acid sequence containing the Th. 23B E domain is a region of SEQ ID NO: 62 spanning from about position 1001 to about position 1470 of SEQ ID NO:62, represented herein as SEQ ID NO:68.
  • This region of SEQ ID NO:62 has a Pfam match to the dioxygenases related to 2-nitropropane dioxygenases, as mentioned above, spanning from about position 1025 to about position 1320 (positions 25-320 of SEQ ID NO:68).
  • This domain function as an ER can also be predicted due to homology to a newly characterized ER enzyme from Streptococcus pneumoniae.
  • each open reading frame There are five open reading frames that form the Shewanella japonica core PUFA PKS system and its PPTase described previously.
  • the domain structure of each open reading frame is as follows.
  • SEQ ID NO:69 is the nucleotide sequence for Shewanella japonica cosmid 3F3 and is found to contain 15 ORFs.
  • the ORFs related to the PUFA PKS system in this microorganism are characterized as follows.
  • pfaA encodes PFAS A (SEQ ID NO:70), a PUFA PKS protein harboring the following domains: ⁇ -ketoacyl-synthase (KS) (nucleotides 10575-12029 of SEQ ID NO:69, amino acids 29-513 of SEQ ID NO:70); malonyl-CoA: ACP acyltransferase (MAT) (nucleotides 12366-13319 of SEQ ID NO:69, amino acids 625-943 of SEQ ID NO:70); six tandem acyl-carrier proteins (ACP) domains (nucleotides 14280-16157 of SEQ ID NO:69, amino acids 1264-1889 of SEQ ID NO:70); ⁇ -ketoacyl-ACP reductase (KR) (nucleotides 17280-17684 of SEQ ID NO:69, amino acids 2264-
  • KR ⁇ -ketoacyl-ACP reductase
  • KS active site DXAC* is located at amino acids 226-229 of SEQ ID NO:70 with the C* being the site of the acyl attachment.
  • a MAT active site, GHS*XG is located at amino acids 721-725 of SEQ ID NO:70, with the S* being the acyl binding site.
  • ACP active sites of LGXDS* are located at the following positions: amino acids 1296-1300, amino acids 1402-1406, amino acids 1513-1517, amino acids 1614-1618, amino acids 1728-1732, and amino acids 1843-1847 in SEQ ID NO:70, with the S* being the phosphopantetheine attachment site.
  • the PFAS A also contains the dehydratase (DH) conserved active site motif LxxHxxxGxxxxP (amino acids 2504-2516 of SEQ ID NO:70) referenced above.
  • DH dehydratase
  • pfaB encodes PFAS B (SEQ ID NO:71), a PUFA PKS protein harboring the following domain: acyltransferase (AT) (nucleotides 19982-20902 of SEQ ID NO:69, amino acids 378-684 of SEQ ID NO:71).
  • an active site GXS*XG motif is located at amino acids 463-467 of SEQ ID NO:71, with the S* being the site of acyl-attachment.
  • pfaC encodes PFAS C (SEQ ID NO:72), a PUFA PKS protein harboring the following domains: KS (nucleotides 21139-22575 of SEQ ID NO:69, amino acids 5-483 of SEQ ID NO:72); chain length factor (CLF) (nucleotides 22591-23439 of SEQ ID NO:69, amino acids 489-771 of SEQ ID NO:72); and two FabA 3-hydroxyacyl-ACP dehydratases, referred to as DH1 (nucleotides 25408-25836 of SEQ ID NO:69, amino acids 1428-1570 of SEQ ID NO:72) and DH2 (nucleotides 26767-27183 of SEQ ID NO:69, amino acids 1881-2019 of SEQ ID NO:72).
  • KS active site DXAC* is located at amino acids 211-214 of SEQ ID NO:72 with the C* being the site of the acyl attachment.
  • pfaD encodes the PFAS D (SEQ ID NO:73), a PUFA PKS protein harboring the following domain: an enoyl reductase (ER) (nucleotides 27446-28687 of SEQ ID NO:69, amino acids 84-497 of SEQ ID NO:73).
  • ER enoyl reductase
  • pfaE (nucleotides 6150-7061 of SEQ ID NO:69 on the reverse complementary strand) encodes PFAS E (SEQ ID NO:74), a 4′-phosphopantetheinyl transferase (PPTase) with the identified domain (nucleotides 6504-6944 of SEQ ID NO:69, amino acids 40-186 of SEQ ID NO:74).
  • each open reading frame There are five open reading frames that form the Shewanella olleyana core PUFA PKS system and its PPTase described previously.
  • the domain structure of each open reading frame is as follows.
  • SEQ ID NO:75 is the nucleotide sequence for Shewanella olleyana cosmid 9A10 and was found to contain 17 ORFs.
  • the ORFs related to the PUFA PKS system in this microorganism are characterized as follows.
  • pfaA encodes PFAS A (SEQ ID NO:76), a PUFA PKS protein harboring the following domains: ⁇ -ketoacyl-synthase (KS) (nucleotides 17521-18975 of SEQ ID NO:75, amino acids 29-513 of SEQ ID NO:76); malonyl-CoA: ACP acyltransferase (MAT) (nucleotides 19309-20265 of SEQ ID NO:75, amino acids 625-943 of SEQ ID NO:76); six tandem acyl-carrier proteins (ACP) domains (nucleotides 21259-23052 of SEQ ID NO:75, amino acids 1275-1872 of SEQ ID NO:76); ⁇ -ketoacyl-ACP reductase (KR) (nucleotides 24154-24558 of SEQ ID NO:75, amino acids 2240
  • a KS active site DXAC* is located at AA 226-229 of SEQ ID NO:76 with the C* being the site of the acyl attachment.
  • a MAT active site, GHS*XG is located at amino acids 721-725 of SEQ ID NO:76 with the S* being the acyl binding site.
  • ACP active sites of LGXDS* are located at: amino acids 1307-1311, amino acids 1408-1412, amino acids 1509-1513, amino acids 1617-1621, amino acids 1721-1725, and amino acids 1826-1830 in SEQ ID NO:76, with the S* being the phosphopantetheine attachment site.
  • the PFAS A also contains the dehydratase (DH) conserved active site motif LxxHxxxGxxxxP (amino acids 2480-2492 of SEQ ID NO:76) referenced above.
  • DH dehydratase
  • pfaB encodes PFAS B (SEQ ID NO:77), a PUFA PKS protein harboring the following domain: acyltransferase (AT) (nucleotides 26837-27848 of SEQ ID NO:75, amino acids 366-703 of SEQ ID NO:77).
  • an active site GXS*XG motif is located at amino acids 451-455 of SEQ ID NO:77 with the S* being the site of acyl-attachment.
  • pfaC encodes PFAS C (SEQ ID NO:78), a PUFA PKS protein harboring the following domains: KS (nucleotides 27995-29431 SEQ ID NO:75, amino acids 10-488 SEQ ID NO:78); chain length factor (CLF) (nucleotides 29471-30217 SEQ ID NO:75, amino acids 502-750 SEQ ID NO:78); and two FabA 3-hydroxyacyl-ACP dehydratases, referred to as DH1 (nucleotides 32258-32686 SEQ ID NO:75, amino acids 1431-1573 SEQ ID NO:78), and DH2 (nucleotides 33611-34027 of SEQ ID NO:75, amino acids 1882-2020 of SEQ ID NO:78).
  • KS active site DXAC* is located at amino acids 216-219 of SEQ ID NO:78 with the C* being the site of the acyl attachment.
  • pfaD encodes the PFAS D (SEQ ID NO:79), a PUFA PKS protein harboring the following domain: an enoyl reductase (ER) (nucleotides 34290-35531 of SEQ ID NO:75, amino acids 84-497 of SEQ ID NO:79).
  • ER enoyl reductase
  • pfaE (nucleotides 13027-13899 of SEQ ID NO:75 on the reverse complementary strand) encodes PFAS E (SEQ ID NO:80), a 4′-phosphopantetheinyl transferase (PPTase) with the identified domain (nucleotides 13369-13815 of SEQ ID NO:75, amino acid 29-177 of SEQ ID NO:80).
  • SEQ ID NO:35 denoted sOrfA, represents the nucleic acid sequence encoding OrfA from Schizochytrium (SEQ ID NO:1) that has been resynthesized for optimized codon usage in yeast.
  • SEQ ID NO:1 and SEQ ID NO:35 each encode SEQ ID NO:2.
  • SEQ ID NO:36 denoted sOrfB, represents the nucleic acid sequence encoding OrfB from Schizochytrium (SEQ ID NO:3) that has been resynthesized for optimized codon usage in yeast.
  • SEQ ID NO:3 and SEQ ID NO:36 each encode SEQ ID NO:4.
  • SEQ ID NO:37 represents a nucleic acid sequence encoding OrfB from Schizochytrium (SEQ ID NO:3) that has been resynthesized within a portion of SEQ ID NO:3 for use in plant cells, and that was derived from a very similar sequence initially developed for optimized codon usage in E. coli , also referred to as OrfB*.
  • OrfB* in both forms is identical to SEQ ID NO:3 with the exception of a resynthesized BspHI (nucleotide 4415 of SEQ ID NO:3) to a SacII fragment (unique site in SEQ ID NO:3).
  • a PUFA PKS system can additionally include one or more accessory proteins, which are defined herein as proteins that are not considered to be part of the core PUFA PKS system as described above (i.e., not part of the PUFA synthase enzyme complex itself), but which may be, or are, necessary for PUFA production or at least for efficient PUFA production using the core PUFA synthase enzyme complex of the present invention.
  • accessory proteins which are defined herein as proteins that are not considered to be part of the core PUFA PKS system as described above (i.e., not part of the PUFA synthase enzyme complex itself), but which may be, or are, necessary for PUFA production or at least for efficient PUFA production using the core PUFA synthase enzyme complex of the present invention.
  • a PUFA PKS system in order to produce PUFAs, a PUFA PKS system must work with an accessory protein that transfers a 4′-phosphopantetheinyl moiety from coenzyme A to the acyl
  • a PUFA PKS system can be considered to include at least one 4′-phosphopantetheinyl transferase (PPTase) domain, or such a domain can be considered to be an accessory domain or protein to the PUFA PKS system.
  • PPTase 4′-phosphopantetheinyl transferase
  • a domain or protein having 4′-phosphopantetheinyl transferase (PPTase) biological activity is characterized as the enzyme that transfers a 4′-phosphopantetheinyl moiety from Coenzyme A to the acyl carrier protein (ACP).
  • ACP acyl carrier protein
  • This transfer to an invariant serine reside of the ACP activates the inactive apo-form to the holo-form.
  • the phosphopantetheine group forms thioesters with the growing acyl chains.
  • the PPTases are a family of enzymes that have been well characterized in fatty acid synthesis, polyketide synthesis, and non-ribosomal peptide synthesis.
  • crystal structures have been determined (e.g., Reuter K, Mofid M R, Marahiel M A, Ficner R. “Crystal structure of the surfactin synthetase-activating enzyme sfp: a prototype of the 4′-phosphopantetheinyl transferase superfamily” EMBO J. 1999 Dec. 1;18(23):6823-31) as well as mutational analysis of amino acid residues important for activity (Mofid M R, Finking R, Essen LO, Marahiel M A.
  • Het I protein of Nostoc sp. PCC 7120 (formerly called Anabaena sp. PCC 7120). Het I is present in a cluster of genes in Nostoc known to be responsible for the synthesis of long chain hydroxy-fatty acids that are a component of a glyco-lipid layer present in heterocysts of that organism (Black and Wolk, 1994 , J. Bacteriol. 176, 2282-2292; Campbell et al., 1997 , Arch. Microbiol. 167, 251-258).
  • Het I is likely to activate the ACP domains of a protein, Hgl E, present in that cluster.
  • the two ACP domains of Hgl E have a high degree of sequence homology to the ACP domains found in Schizochytrium Orf A.
  • SEQ ID NO:34 represents the amino acid sequence of the Nostoc Het I protein, and is a functional PPTase that can be used with a PUFA PKS system described herein, including the PUFA PKS systems from Schizochytrium and Thraustochytrium .
  • SEQ ID NO:34 is encoded by SEQ ID NO:33. The endogenous start codon of Het I has not been identified (there is no methionine present in the putative protein).
  • sfp derived from Bacillus subtilis .
  • Sfp has been well characterized, and is widely used due to its ability to recognize a broad range of substrates. Based on published sequence information (Nakana, et al., 1992 , Molecular and General Genetics 232: 313-321), an expression vector was previously produced for sfp by cloning the coding region, along with defined up- and downstream flanking DNA sequences, into a pACYC-184 cloning vector.
  • This construct encodes a functional PPTase as demonstrated by its ability to be co-expressed with Schizochytrium Orfs A, B*, and C in E. coli which, under appropriate conditions, resulted in the accumulation of DHA in those cells (see U.S. Patent Application Publication No. 20040235127).
  • some host organisms may endogenously express accessory proteins that are needed to work with the PUFA PKS to produce PUFAs (e.g., PPTases).
  • some organisms may be transformed with nucleic acid molecules encoding one or more accessory proteins described herein to enable and/or to enhance production of PUFAs by the organism, even if the organism endogenously produces a homologous accessory protein (i.e., some heterologous accessory proteins may operate more effectively or efficiently with the transformed PUFA synthase proteins than the host cells' endogenous accessory protein).
  • the present invention provides an example of yeast and plants that have been genetically modified with the PUFA PKS system of the present invention that includes the accessory PPTase. Structural and functional characteristics of PPTases have been described in detail, for example, in U.S. Patent Application Publication No. 20020194641; U.S. Patent Application Publication No. 20040235127; and U.S. Patent Application Publication No. 20050100995.
  • a “standard” or “classical” pathway for the production of PUFAs refers to the fatty acid synthesis pathway where medium chain-length saturated fatty acids (products of a fatty acid synthase (FAS) system) are modified by a series of elongation and desaturation reactions.
  • the substrates for the elongation reaction are fatty acyl-CoA (the fatty acid chain to be elongated) and malonyl-CoA (the source of the 2 carbons added during each elongation reaction).
  • the product of the elongase reaction is a fatty acyl-CoA that has two additional carbons in the linear chain.
  • the desaturases create cis double bonds in the preexisting fatty acid chain by extraction of 2 hydrogens in an oxygen-dependant reaction.
  • Such pathways and the genes involved in such pathways are well-known in the literature as discussed above.
  • lipid includes phospholipids (PL); free fatty acids; esters of fatty acids; triacylglycerols (TAG); diacylglycerides; monoacylglycerides; phosphatides; waxes (esters of alcohols and fatty acids); sterols and sterol esters; carotenoids; xanthophylls (e.g., oxycarotenoids); hydrocarbons; and other lipids known to one of ordinary skill in the art.
  • TAG triacylglycerols
  • PUFA include not only the free fatty acid form, but other forms as well, such as the TAG form and the PL form.
  • a plant can be genetically modified to introduce a PUFA PKS system into the plant.
  • Plants are not known to endogenously contain a PUFA PKS system, and therefore, the PUFA PKS systems of the present invention represent an opportunity to produce plants with unique fatty acid production capabilities.
  • the present invention offers the ability to create any one of a number of “designer oils” in various ratios and forms.
  • the disclosure of the PUFA PKS genes from the particular marine organisms described herein offer the opportunity to more readily extend the range of PUFA production and successfully produce such PUFAs within temperature ranges used to grow most crop plants.
  • one embodiment of the present invention relates to a genetically modified plant or part of a plant (e.g., wherein the plant has been genetically modified to express a PUFA PKS system described herein), which includes at least the core PUFA PKS enzyme complex and, in one embodiment, at least one PUFA PKS accessory protein, (e.g., a PPTase), so that the plant produces PUFAs.
  • the plant is an oil seed plant, wherein the oil seeds, and/or the oil in the oil seeds, contain PUFAs produced by the PUFA PKS system.
  • oils contain a detectable amount of at least one target or primary PUFA that is the product of the PUFA PKS system.
  • oils are substantially free of intermediate or side products that are not the target or primary PUFA products and that are not naturally produced by the endogenous FAS system in the wild-type plants (i.e., wild-type plants produce some shorter or medium chain PUFAs, such as 18 carbon PUFAs, via the FAS system, but there will be new, or additional, fatty acids produced in the plant as a result of genetic modification with a PUFA PKS system).
  • the majority of additional fatty acids (new fatty acids or increased fatty acids resulting from the genetic modification) in the profile of total fatty acids produced by plants that have been genetically modified with a PUFA PKS system comprise the target or intended PUFA products of the PUFA PKS system (i.e., the majority of additional, or new, fatty acids in the total fatty acids that are produced by the genetically modified plant are the target PUFA(s)).
  • intermediate products and side products that are not present in substantial amounts in the total lipids of plants genetically modified with such PUFA PKS can include, but are not limited to: gamma-linolenic acid (GLA; 18:3, n-6); stearidonic acid (STA or SDA; 18:4, n-3); dihomo-gamma-linolenic acid (DGLA or HGLA; 20:3, n-6), arachidonic acid (ARA, C20:4, n-6); eicosatrienoic acid (ETA; 20:3, n-9) and various other intermediate or side products, such as 20:0; 20:1 ( ⁇ 5); 20:1 ( ⁇ 11); 20:2 ( ⁇ 8,11); 20:2 ( ⁇ 11,14); 20:3 ( ⁇ 5,11,14); 20:3 ( ⁇ 11,14,17); mead
  • the target product is a particular PUFA, such as DHA
  • the intermediate products and side products that are not present in substantial amounts in the total lipids of the genetically modified plants also include other PUFAs, including other PUFAs that are a natural product of a different PUFA PKS system, such as EPA in this example.
  • the PUFA PKS system of the present invention can also be used, if desired, to produce as a target PUFA a PUFA that can include GLA, SDA or DGLA.
  • the present inventors Using the knowledge of the genetic basis and domain structure of PUFA PKS systems as described herein, the present inventors have designed and produced constructs encoding such a PUFA PKS system and have successfully produced transgenic plants expressing the PUFA PKS system.
  • the transgenic plants produce oils containing PUFAs, and the oils are substantially free of intermediate products that accumulate in a standard PUFA pathway.
  • the present inventors have also demonstrated the use of the constructs to produce PUFAs in another eukaryote, yeast, as a proof-of-concept experiment prior to the production of the transgenic plants.
  • the genetically modified plant useful in the present invention has been genetically modified to express a PUFA PKS system.
  • the PUFA PKS system can include any PUFA PKS system, such as any PUFA PKS system described in, for example, U.S. Pat. No. 6,566,583; U.S. Patent Application Publication No. 20020194641; U.S. Patent Application Publication No. 20040235127; U.S. Patent Application Publication No. 20050100995; and PCT Publication No. WO 2006/135866.
  • the PUFA PKS system can be chosen from, but is not limited to, any of the specific PUFA PKS systems identified and characterized in these patents and patent publications, such as the PUFA PKS systems from Schizochytrium sp. American Type Culture Collection (ATCC) No. 20888, and mutant strains derived therefrom (e.g., strain N230D); Thraustochytrium 23B ATCC No. 20892, and mutant strains derived therefrom; Shewanella olleyana Australian Collection of Antarctic Microorganisms (ACAM) strain number 644, and mutant strains derived therefrom; or Shewanella japonica ATCC strain number BAA-316, and mutant strains derived therefrom.
  • ATCC American Type Culture Collection
  • ACAM Alpha-1
  • the PUFA PKS system comprises domains selected from any of the above PUFA PKS systems, wherein the domains are combined (mixed and matched) to form a complete PUFA PKS system meeting the minimum requirements as discussed above.
  • the plant can also be further modified with at least one domain or biologically active fragment thereof of another PKS system, including, but not limited to, Type I PKS systems (iterative or modular), Type II PKS systems, and/or Type III PKS systems, which may substitute for a domain in a PUFA PKS system.
  • any of the domains of a PUFA PKS system can be modified from their natural structure to modify or enhance the function of that domain in the PUFA PKS system (e.g., to modify the PUFA types or ratios thereof produced by the system).
  • Such mixing of domains to produce chimeric PUFA PKS proteins is described in the patents and patent publications referenced above.
  • the genetic modification of the plant can include the introduction of one or more accessory proteins that will work with the core PUFA PKS enzyme complex to enable, facilitate, or enhance production of PUFAs by the plant.
  • the present invention includes the transformation of the plant with nucleic acid molecules encoding both a PUFA PKS enzyme complex and a PPTase that will operate with the PUFA PKS complex.
  • Other accessory molecules may also be used to transform the plant, such as any molecules that facilitate the transfer to and accumulation of the PUFAs in the TAG and PL fractions within the plant.
  • a genetically modified plant can include any genetically modified plant including higher plants and particularly, any consumable plants or plants useful for producing a desired PUFA of the present invention.
  • Plant parts include any parts of a plant, including, but not limited to, seeds (immature or mature), oils, pollen, embryos, flowers, fruits, shoots, leaves, roots, stems, explants, etc.
  • a genetically modified plant has a genome that is modified (i.e., mutated or changed) or contains modified or exogenously introduced nucleic acids, as compared to its normal (i.e., wild-type or naturally occurring) form such that the desired result is achieved (i.e., PUFA PKS activity and production of PUFAs).
  • Genetic modification of a plant can be accomplished using classical strain development and/or molecular genetic techniques. Methods for producing a transgenic plant, wherein a recombinant nucleic acid molecule encoding a desired amino acid sequence is incorporated into the genome of the plant, are known in the art.
  • a preferred plant to genetically modify according to the present invention is preferably a plant suitable for consumption by animals, including humans.
  • Preferred plants to genetically modify according to the present invention include, but are not limited to any higher plants, including both dicotyledonous and monocotyledonous plants, and particularly consumable plants, including crop plants and especially plants used for their oils.
  • Such plants can include, for example: canola, soybeans, rapeseed, linseed, corn, safflowers, sunflowers and tobacco.
  • Other preferred plants include those plants that are known to produce compounds used as pharmaceutical agents, flavoring agents, nutraceutical agents, functional food ingredients or cosmetically active agents or plants that are genetically engineered to produce these compounds/agents.
  • a genetically modified plant includes a plant that has been modified using recombinant technology, which may be combined with classical mutagenesis and screening techniques.
  • genetic modifications that result in a decrease in gene expression, in the function of the gene, or in the function of the gene product (i.e., the protein encoded by the gene) can be referred to as inactivation (complete or partial), deletion, interruption, blockage or down-regulation of a gene.
  • a genetic modification in a gene which results in a decrease in the function of the protein encoded by such gene can be the result of a complete deletion of the gene (i.e., the gene does not exist, and therefore the protein does not exist), a mutation in the gene which results in incomplete or no translation of the protein (e.g., the protein is not expressed), or a mutation in the gene which decreases or abolishes the natural function of the protein (e.g., a protein is expressed which has decreased or no enzymatic activity or action).
  • Genetic modifications that result in an increase in gene expression or function can be referred to as amplification, overproduction, overexpression, activation, enhancement, addition, or up-regulation of a gene.
  • the genetic modification of a plant according to the present invention results in the production of one or more PUFAs by the plant.
  • the PUFA profile and the ratio of the PUFAs produced by the plant is not necessarily the same as the PUFA profile or ratio of PUFAs produced by the organism from which the PUFA PKS system was derived.
  • A. tumefaciens and A. rhizogenes are plant pathogenic soil bacteria which genetically transform plant cells.
  • the Ti and R1 plasmids of A. tumefaciens and A. rhizogenes carry genes responsible for genetic transformation of the plant. See, for example, Kado, C. I., Crit. Rev. Plant. Sci. 10:1 (1991).
  • Agrobacterium vector systems and methods for Agrobacterium -mediated gene transfer are provided by numerous references, including Gruber et al., supra, Miki et al., supra, Moloney et al., Plant Cell Reports 8:238 (1989), and U.S. Pat. Nos. 4,940,838 and 5,464,763.
  • microprojectile-mediated transformation wherein DNA is carried on the surface of microprojectiles.
  • the expression vector is introduced into plant tissues with a biolistic device that accelerates the microprojectiles to speeds sufficient to penetrate plant cell walls and membranes.
  • the targeting of gene products to the plastid or chloroplast is controlled by a signal sequence found at the amino terminal end of various proteins and which is cleaved during import yielding the mature protein (e.g. with regard to chloroplast targeting, see, e.g., Comai et al., J. Biol. Chem. 263: 15104-15109 (1988)).
  • These signal sequences can be fused to heterologous gene products to effect the import of heterologous products into the chloroplast (van den Broeck et al. Nature 313: 358-363 (1985)).
  • DNA encoding for appropriate signal sequences can be isolated from the cDNAs encoding the RUBISCO protein, the CAB protein, the EPSP synthase enzyme, the GS2 protein and many other proteins which are known to be chloroplast localized.
  • chloroplast targeted proteins synthesized as larger precursor proteins containing an amino-terminal chloroplast targeting peptide directing the precursor to the chloroplast import machinery, are well known in the art.
  • Chloroplast targeting peptides are generally cleaved by specific endoproteases located within the chloroplast organelle, thus releasing the targeted mature and preferably active enzyme from the precursor into the chloroplast milieu.
  • sequences encoding peptides which are suitable for directing the targeting of the gene or gene product to the chloroplast or plastid of the plant cell include the petunia EPSPS CTP, the Arabidopsis EPSPS CTP2 and intron, and others known to those skilled in the art.
  • chloroplast targeting peptides include the Arabidopsis thaliana ribulose bisphosphate carboxylase small subunit ats1A transit peptide, an Arabidopsis thaliana EPSPS transit peptide, and a Zea maize ribulose bisphosphate carboxylase small subunit transit peptide.
  • Transit peptide An optimized transit peptide is described, for example, by Van den Broeck et al., “Targeting of a foreign protein to chloroplasts by fusion to the transit peptide from the small subunit of ribulose 1,5-biphosphate carboxylase”, Nature, 313:358-363 (1985). Prokaryotic and eukaryotic signal sequences are disclosed, for example, by Michaelis et al. (1982) Ann. Rev. Microbiol. 36, 425. Additional examples of transit peptides that may be used in the invention include the chloroplast transit peptides such as those described in Von Heijne et al., Plant Mol. Biol. Rep. 9:104-126 (1991); Mazur et al., Plant Physiol.
  • CTP that has functioned herein to localize heterologous proteins to the chloroplast was derived from Brassica napus acyl-ACP thioesterase (e.g., for sequence of Brassica napus acyl-ACP thioesterase, see Loader et al., 1993 , Plant Mol. Biol. 23: 769-778; Loader et al., 1995 , Plant Physiol. 110:336-336).
  • An alternative means for localizing genes to chloroplast or plastid includes chloroplast or plastid transformation.
  • Recombinant plants can be produced in which only the chloroplast DNA has been altered to incorporate the molecules envisioned in this application. Promoters which function in chloroplasts have been known in the art (Hanley-Bowden et al., Trends in Biochemical Sciences 12:67-70, 1987). Methods and compositions for obtaining cells containing chloroplasts into which heterologous DNA has been inserted have been described, for example by Daniell et al. (U.S. Pat. No. 5,693,507; 1997) and Maliga et al. (U.S. Pat. No. 5,451,513; 1995).
  • encompassed by the present invention are methods to genetically modify plant cells by making use of genes from certain marine bacterial and any thraustochytrid or other eukaryotic PUFA PKS systems, and further can utilize gene mixing to extend and/or alter the range of PUFA products to include EPA, DHA, DPA (n-3 or n-6), ARA, GLA, SDA and others.
  • the method to obtain these altered PUFA production profiles includes not only the mixing of genes from various organisms into the thraustochytrid PUFA PKS genes, but also various methods of genetically modifying the endogenous thraustochytrid PUFA PKS genes disclosed herein.
  • Novel PUFA PKS constructs prepared in microorganisms such as a thraustochytrid or in E. coli can be isolated and used to transform plants to impart similar PUFA production properties onto the plants.
  • Detailed discussions of particular modifications of PUFA PKS systems that are encompassed by the present invention are set forth, for example, in U.S. Patent Application Publication No. 20020194641; U.S. Patent Application Publication No. 20040235127; and U.S. Patent Application Publication No. 20050100995).
  • a genetically modified plant is preferably cultured in a fermentation medium or grown in a suitable medium such as soil.
  • a suitable growth medium for higher plants includes any growth medium for plants, including, but not limited to, soil, sand, any other particulate media that support root growth (e.g. vermiculite, perlite, etc.) or hydroponic culture, as well as suitable light, water and nutritional supplements which optimize the growth of the higher plant.
  • the genetically modified plants of the present invention are engineered to produce PUFAs through the activity of the PUFA PKS system.
  • the PUFAs can be recovered through purification processes which extract the compounds from the plant.
  • the PUFAs are recovered by harvesting the plant.
  • the PUFAs are recovered by harvesting the oil from the plant (e.g., from the oil seeds).
  • the plant can also be consumed in its natural state or further processed into consumable products.
  • a genetically modified plant of the invention produces one or more polyunsaturated fatty acids including, but not limited to, EPA (C20:5, n-3), DHA (C22:6, n-3), DPA (C22:5, n-6 or n-3), ARA (C20:4, n-6), GLA (C18:3, n-6), ALA (C18:3, n-3), and/or SDA (C18:4, n-3)), and more preferably, one or more long chain fatty acids (LCPUFAs), including, but not limited to, EPA (C20:5, n-3), DHA (C22:6, n-3), DPA (C22:5, n-6 or n-3), or DTA (C22:4, n-6).
  • EPA C20:5, n-3
  • DHA C22:6, n-3
  • DPA C22:5, n-6 or n-3
  • ARA C20:4, n-6
  • GLA C18:3, n-6
  • ALA C18:
  • a genetically modified plant of the invention produces one or more polyunsaturated fatty acids including, but not limited to, EPA (C20:5, n-3), DHA (C22:6, n-3), and/or DPA (C22:5, n-6 or n-3).
  • one embodiment of the present invention relates to a plant, and preferably an oil seed plant, wherein the plant produces (e.g., in its mature seeds, if an oil seed plant, or in the oil of the seeds of an oil seed plant) at least one PUFA (the target PUFA), and wherein the total fatty acid profile in the plant, or the part of the plant that accumulates PUFAs (e.g., mature seeds, if the plant is an oil seed plant or the oil of the seeds of an oil seed plant), comprises a detectable amount of this PUFA or PUFAs.
  • the plant produces (e.g., in its mature seeds, if an oil seed plant, or in the oil of the seeds of an oil seed plant) at least one PUFA (the target PUFA), and wherein the total fatty acid profile in the plant, or the part of the plant that accumulates PUFAs (e.g., mature seeds, if the plant is an oil seed plant or the oil of the seeds of an oil seed plant), comprises a detectable amount
  • the target PUFA is at least a 20 carbon PUFA and comprises at least 3 double bonds, and more preferably at least 4 double bonds, and even more preferably, at least 5 double bonds.
  • the target PUFA is preferably a PUFA that is not naturally produced by the plant (i.e., the wild-type plant in the absence of genetic modification or the parent plant used as a recipient for the indicated genetic modification).
  • the total fatty acid profile in the plant or in the part of the plant that accumulates PUFAs comprises at least 0.1% of the target PUFA(s) by weight of the total fatty acids, and more preferably at least about 0.2%, and more preferably at least about 0.3%, and more preferably at least about 0.4%, and more preferably at least about 0.5%, and more preferably at least about 1%, and more preferably at least about 1.5%, and more preferably at least about 2%, and more preferably at least about 2.5%, and more preferably at least about 3%, and more preferably at least about 3.5%, and more preferably at least about 4%, and more preferably at least about 4.5%, and more preferably at least about 5%, and more preferably at least about 5.5%, and more preferably at least about 10%, and more preferably at least about 15%, and more preferably at least about 20%, and more preferably at least about 25%, and more preferably at least about 30%, and more preferably at least about 35%, and
  • total fatty acids produced by a plant are presented as a weight percent as determined by gas chromatography (GC) analysis of a fatty acid methyl ester (FAME) preparation, although determination of total fatty acids is not limited to this method.
  • GC gas chromatography
  • FAME fatty acid methyl ester
  • these total fatty acids produced by the plant comprise less than (or do not contain any more than) about 10% by weight of any fatty acids, other than the target PUFA(s) that are produced by the enzyme complex that produces the target PUFA(s).
  • any fatty acids that are produced by the enzyme complex that produces the target PUFA(s) are present at less than about 9%, and more preferably less than about 8%, and more preferably less than about 7%, and more preferably less than about 6%, and more preferably less than about 5%, and more preferably less than about 4%, and more preferably less than about 3%, and more preferably less than about 2%, and more preferably less than about 1% by weight of the total fatty acids produced by the plant.
  • any fatty acids that are produced by the enzyme complex that produces the target PUFA(s) other than the target PUFA(s) are present at less than (or do not contain any more than) about 10% by weight of the total fatty acids that are produced by the enzyme complex that produces the target PUFA(s) in the plant (i.e., this measurement is limited to those total fatty acids that are produced by the enzyme complex that produces the target PUFAs), and more preferably less than about 9%, and more preferably less than about 8%, and more preferably less than about 7%, and more preferably less than about 6%, and more preferably less than about 5%, and more preferably less than about 4%, and more preferably less than about 3%, and more preferably less than about 2%, and more preferably less than about 1% by weight of the total fatty acids, and more preferably less than about 0.5% by weight of the total fatty acids that are produced by the enzyme complex that produces the target PUFA(s) in the plant.
  • the total fatty acids produced by the plant contain less than (or do not contain any more than) 10% PUFAs having 18 or more carbons by weight of the total fatty acids produced by the plant, other than the target PUFA(s) or the PUFAs that are present in the wild-type plant (not genetically modified) or in the parent plant used as a recipient for the indicated genetic modification.
  • the total fatty acids produced by the plant (and/or parts of plants or seed oil fraction) contain less than 9% PUFAs having 18 or more carbons, or less than 8% PUFAs having 18 or more carbons, or less than 7% PUFAs having 18 or more carbons, or less than 6% PUFAs having 18 or more carbons, or less than 5% PUFAs having 18 or more carbons, or less than 4% PUFAs having 18 or more carbons, or less than 3% PUFAs having 18 or more carbons, or less than 2% PUFAs having 18 or more carbons, or less than 1% PUFAs having 18 or more carbons by weight of the total fatty acids produced by the plant, other than the target PUFA(s) or the PUFAs that are present in the wild-type plant (not genetically modified) or the parent plant used as a recipient for the indicated genetic modification.
  • the total fatty acids produced by the plant contain less than (or do not contain any more than) 10% PUFAs having 20 or more carbons by weight of the total fatty acids produced by the plant, other than the target PUFA(s) or the PUFAs that are present in the wild-type plant (not genetically modified) or the parent plant used as a recipient for the indicated genetic modification.
  • the total fatty acids produced by the plant (and/or parts of plants or seed oil fraction) contain less than 9% PUFAs having 20 or more carbons, or less than 8% PUFAs having 20 or more carbons, or less than 7% PUFAs having 20 or more carbons, or less than 6% PUFAs having 20 or more carbons, or less than 5% PUFAs having 20 or more carbons, or less than 4% PUFAs having 20 or more carbons, or less than 3% PUFAs having 20 or more carbons, or less than 2% PUFAs having 20 or more carbons, or less than 1% PUFAs having 20 or more carbons by weight of the total fatty acids produced by the plant, other than the target PUFA(s) or the PUFAs that are present in the wild-type plant (not genetically modified) or the parent plant used as a recipient for the indicated genetic modification.
  • the total fatty acids in the plant contain less than about 10% by weight of the total fatty acids produced by the plant, and more preferably less than about 9%, and more preferably less than about 8%, and more preferably less than about 7%, and more preferably less than about 6%, and more preferably less than about 5%, and more preferably less than about 4%, and more preferably less than about 3%, and more preferably less than about 2%, and more preferably less than about 1% of a fatty acid selected from any one or more of: gamma-linolenic acid (GLA; 18:3, n-6); stearidonic acid (STA or SDA; 18:4, n-3); dihomo-gamma-linolenic acid (DGLA or HGLA; 20:3, n-6), arachidonic acid (ARA, C20:4, n-6); eicosatrienoic acid (ETA; 20:3, n-9) and various other gamma-linolenic acid (GLA; 18
  • the fatty acids that are produced by the enzyme system that produces the long chain PUFAs in the plant contain less than about 10% by weight of a fatty acid selected from: gamma-linolenic acid (GLA; 18:3, n-6); stearidonic acid (STA or SDA; 18:4, n-3); dihomo-gamma-linolenic acid (DGLA or HGLA; 20:3, n-6), arachidonic acid (ARA, C20:4, n-6); eicosatrienoic acid (ETA; 20:3, n-9) and various other fatty acids, such as 20:0; 20:1 ( ⁇ 5); 20:1 ( ⁇ 11); 20:2 ( ⁇ 8,11); 20:2 ( ⁇ 11,14); 20:3 ( ⁇ 5,11,14); 20:3 ( ⁇ 11,14,17); mead acid (20:3; ⁇ 5,8,11); or 20:4 ( ⁇ 5,1,14,17), as a percentage of the total fatty acids produced by the plant,
  • the fatty acids that are produced by the enzyme system that produces the long chain PUFAs in the plant contain less than about 10% by weight of all of the following PUFAs: gamma-linolenic acid (GLA; 18:3, n-6), PUFAs having 18 carbons and four carbon-carbon double bonds, PUFAs having 20 carbons and three carbon-carbon double bonds, and PUFAs having 22 carbons and two or three carbon-carbon double bonds, as a percentage of the total fatty acids produced by the plant, and more preferably less than about 9%, and more preferably less than about 8%, and more preferably less than about 7%, and more preferably less than about 6%, and more preferably less than about 5%, and more preferably less than about 4%, and more preferably less than about 3%, and more preferably less than about 2%, and more preferably less than about 1% of all of the following PUFAs: gamma-linolenic acid (GLA; 18:3, n-6), PUFAs having
  • the fatty acids that are produced by the enzyme system that produces the long chain PUFAs in the plant contain less than about 10% by weight of each of the following PUFAs: gamma-linolenic acid (GLA; 18:3, n-6), PUFAs having 18 carbons and four carbon-carbon double bonds, PUFAs having 20 carbons and three carbon-carbon double bonds, and PUFAs having 22 carbons and two or three carbon-carbon double bonds, as a percentage of the total fatty acids produced by the plant, and more preferably less than about 9%, and more preferably less than about 8%, and more preferably less than about 7%, and more preferably less than about 6%, and more preferably less than about 5%, and more preferably less than about 4%, and more preferably less than about 3%, and more preferably less than about 2%, and more preferably less than about 1% of each of the following PUFAs: gamma-linolenic acid (GLA; 18:3, n-6), PUFAs having
  • the fatty acids that are produced by the enzyme system that produces the long chain PUFAs in the plant contain less than about 10% by weight of any one or more of the following PUFAs: gamma-linolenic acid (GLA; 18:3, n-6), PUFAs having 18 carbons and four carbon-carbon double bonds, PUFAs having 20 carbons and three carbon-carbon double bonds, and PUFAs having 22 carbons and two or three carbon-carbon double bonds, as a percentage of the total fatty acids produced by the plant, and more preferably less than about 9%, and more preferably less than about 8%, and more preferably less than about 7%, and more preferably less than about 6%, and more preferably less than about 5%, and more preferably less than about 4%, and more preferably less than about 3%, and more preferably less than about 2%, and more preferably less than about 1% of any one or more of the following PUFAs: gamma-linolenic acid (GLA; 18:3,
  • the plant produces at least two target PUFAs, and the total fatty acid profile in the plant, or the part of the plant that accumulates PUFAs (including oils from the oil seeds), comprises a detectable amount of these PUFAs.
  • the PUFAs are preferably each at least a 20 carbon PUFA and comprise at least 3 double bonds, and more preferably at least 4 double bonds, and even more preferably, at least 5 double bonds.
  • Such PUFAs are most preferably chosen from DHA, DPAn-6 and EPA.
  • the plant produces DHA and DPAn-6, and the ratio of DHA to DPAn-6 is from about 1:10 to about 10:1, including any ratio in between. In a one embodiment, the ratio of DHA to DPA is from about 1:1 to about 3:1, and in another embodiment, about 2.5:1.
  • the plant produces DHA and EPA.
  • the plant produces the total fatty acid profile represented by FIG. 3 .
  • the invention further includes any seeds produced by the plants described herein, as well as any oils produced by the plants or seeds described herein.
  • the invention also includes any products produced using the plants, seed or oils described herein.
  • a plant having any of the above-identified characteristics is a plant that has been genetically modified to express a PUFA PKS system (PUFA synthase) as described in detail herein (i.e., the PUFA PKS system is the enzyme system that produces the target PUFA(s) in the plant).
  • the plant has been genetically modified to express a PUFA PKS system comprised of PUFA PKS proteins/domains from a thraustochytrid, including, but not limited to, Schizochytrium, Thraustochytrium, Ulkenia, Japonochytrium, Aplanochytrium, Althornia , or Elina .
  • the plant has been genetically modified to express a PUFA PKS system comprised of PUFA PKS proteins/domains from a labrynthulid. In another embodiment, the plant has been genetically modified to express a PUFA PKS system comprised of PUFA PKS proteins/domains from a marine bacterium, including, but not limited to, Shewanella japonica or Shewanella olleyana .
  • the plant has been genetically modified to express a PUFA PKS system comprised of Schizochytrium OrfsA, B and C (including homologues or synthetic versions thereof), and a PPTase (e.g., HetI) as described above (e.g., see SEQ ID NOs:1-32 and SEQ ID NO:33, and discussion of Schizochytrium PUFA PKS system above).
  • a PUFA PKS system comprised of Schizochytrium OrfsA, B and C (including homologues or synthetic versions thereof), and a PPTase (e.g., HetI) as described above (e.g., see SEQ ID NOs:1-32 and SEQ ID NO:33, and discussion of Schizochytrium PUFA PKS system above).
  • the plant has been genetically modified to express a PUFA PKS system comprised of Thraustochytrium OrfsA, B and C (including homologues or synthetic versions thereof), and a PPTase (e.g., HetI) as described above (e.g., see SEQ ID NOs:38-68 and SEQ ID NO:33, and discussion of Thraustochytrium PUFA PKS system above; see also U.S. Patent Application Publication No. 20050014231).
  • a PUFA PKS system comprised of Thraustochytrium OrfsA, B and C (including homologues or synthetic versions thereof), and a PPTase (e.g., HetI) as described above (e.g., see SEQ ID NOs:38-68 and SEQ ID NO:33, and discussion of Thraustochytrium PUFA PKS system above; see also U.S. Patent Application Publication No. 20050014231).
  • the plant has been genetically modified to express a PUFA PKS system comprised of other thraustochytrid OrfsA, B and C (including homologues or synthetic versions thereof), and a PPTase (e.g., HetI) (e.g., see PCT Patent Publication No. WO 05/097982).
  • a PUFA PKS system comprised of other thraustochytrid OrfsA, B and C (including homologues or synthetic versions thereof), and a PPTase (e.g., HetI) (e.g., see PCT Patent Publication No. WO 05/097982).
  • the plant has been genetically modified to express a PUFA PKS system comprised of PUFA PKS Orfs from marine bacteria such as Shewanella (including homologues or synthetic versions thereof), and a PPTase (e.g., the endogenous Shewanella PPTase) as described above (e.g., see SEQ ID NOs:1-6 for Shewanella japonica , SEQ ID NOs: 7-12 for Shewanella olleyana ).
  • the plant has been genetically modified to express any combinations of domains and proteins from such PUFA PKS systems (e.g., a chimeric PUFA PKS system).
  • the invention further includes any seeds produced by the plants described herein, as well as any oils produced by the plants or seeds described herein.
  • the invention also includes any products produced using the plants, seed or oils described herein.
  • One embodiment of the present invention relates to a method to modify a product containing at least one fatty acid, comprising adding to the product a plant, a plant part, a seed or an oil produced by a genetically modified plant according to the invention and as described herein (e.g., a plant that has been genetically modified with a PUFA PKS system and has the fatty acid profile described herein).
  • a genetically modified plant e.g., a plant that has been genetically modified with a PUFA PKS system and has the fatty acid profile described herein.
  • the product is selected from the group consisting of a food, a dietary supplement, a pharmaceutical formulation, a humanized animal milk, and an infant formula.
  • suitable pharmaceutical formulations include, but are not limited to, an anti-inflammatory formulation, a chemotherapeutic agent, an active excipient, an osteoporosis drug, an anti-depressant, an anti-convulsant, an anti- Heliobactor pylori drug, a drug for treatment of neurodegenerative disease, a drug for treatment of degenerative liver disease, an antibiotic, and a cholesterol lowering formulation.
  • the product is used to treat a condition selected from the group consisting of: chronic inflammation, acute inflammation, gastrointestinal disorder, cancer, cachexia, cardiac restenosis, neurodegenerative disorder, degenerative disorder of the liver, blood lipid disorder, osteoporosis, osteoarthritis, autoimmune disease, preeclampsia, preterm birth, age related maculopathy, pulmonary disorder, and peroxisomal disorder.
  • a condition selected from the group consisting of: chronic inflammation, acute inflammation, gastrointestinal disorder, cancer, cachexia, cardiac restenosis, neurodegenerative disorder, degenerative disorder of the liver, blood lipid disorder, osteoporosis, osteoarthritis, autoimmune disease, preeclampsia, preterm birth, age related maculopathy, pulmonary disorder, and peroxisomal disorder.
  • Suitable food products include, but are not limited to, fine bakery wares, bread and rolls, breakfast cereals, processed and unprocessed cheese, condiments (ketchup, mayonnaise, etc.), dairy products (milk, yogurt), puddings and gelatine desserts, carbonated drinks, teas, powdered beverage mixes, processed fish products, fruit-based drinks, chewing gum, hard confectionery, frozen dairy products, processed meat products, nut and nut-based spreads, pasta, processed poultry products, gravies and sauces, potato chips and other chips or crisps, chocolate and other confectionery, soups and soup mixes, soya based products (milks, drinks, creams, whiteners), vegetable oil-based spreads, and vegetable-based drinks.
  • thraustochytrid refers to any members of the order Thraustochytriales, which includes the family Thraustochytriaceae
  • labyrinthulid refers to any member of the order Labyrinthulales, which includes the family Labyrinthulaceae.
  • Labyrinthulaceae were at one time considered to be members of the order Thraustochytriales, but in more recent revisions of the taxonomy of such organisms, the family is now considered to be a member of the order Labyrinthulales, and both Labyrinthulales and Thraustochytriales are considered to be members of the phylum Labyrinthulomycota. Developments have resulted in frequent revision of the taxonomy of the thraustochytrids and labyrinthulids. However, taxonomic theorists now generally place both of these groups of microorganisms with the algae or algae-like protists within the Stramenopile lineage. The current taxonomic placement of the thraustochytrids and labyrinthulids can be summarized as follows:
  • thraustochytrids include the following organisms: Order: Thraustochytriales; Family: Thraustochytriaceae; Genera: Thraustochytrium (Species: sp., arudimentale, aureum, benthicola, globosum, kinnei, motivum, multirudimentale, pachydermum, proliferum, roseum, striatum ), Ulkenia (Species: sp., amoeboidea, kerguelensis, minuta, profunda, radiata, sailens, sarkariana, schizochytrops, visurgensis, yorkensis ), Schizochytrium (Species: sp., aggregatum, limnaceum, mangrovei, minutum, octosporum ), Japonochytrium (Species: sp., arudimentale, aureum, benthicola, globosum, kinnei, motivum
  • Labyrinthulids include the following organisms: Order: Labyrinthulales, Family: Labyrinthulaceae, Genera: Labyrinthula (Species: sp., algeriensis, coenocystis, chattonii, macrocystis, macrocystis atlantica, macrocystis macrocystis, marina, minuta, roscoffensis, valkanovii, vitellina, vitellina pacifica, vitellina vitellina, zopfii ), Labyrinthuloides (Species: sp., haliotidis, yorkensis ), Labyrinthomyxa (Species: sp., marina ), Diplophrys (Species: sp., archeri ), Pyrrhosorus (Species: sp., marinus ), Sorodiplophrys
  • an isolated protein or peptide such as a protein or peptide from a PUFA PKS system
  • a protein or a fragment thereof including a polypeptide or peptide
  • isolated does not reflect the extent to which the protein has been purified.
  • an isolated protein of the present invention is produced recombinantly.
  • An isolated peptide can be produced synthetically (e.g., chemically, such as by peptide synthesis) or recombinantly.
  • modification and “mutation” can be used interchangeably, particularly with regard to the modifications/mutations to the primary amino acid sequences of a protein or peptide (or nucleic acid sequences) described herein.
  • modification can also be used to describe post-translational modifications to a protein or peptide including, but not limited to, methylation, farnesylation, carboxymethylation, geranyl geranylation, glycosylation, phosphorylation, acetylation, myristoylation, prenylation, palmitation, and/or amidation.
  • Modifications can also include, for example, complexing a protein or peptide with another compound. Such modifications can be considered to be mutations, for example, if the modification is different than the post-translational modification that occurs in the natural, wild-type protein or peptide.
  • homologue is used to refer to a protein or peptide which differs from a naturally occurring protein or peptide (i.e., the “prototype” or “wild-type” protein) by one or more minor modifications or mutations to the naturally occurring protein or peptide, but which maintains the overall basic protein and side chain structure of the naturally occurring form (i.e., such that the homologue is identifiable as being related to the wild-type protein).
  • Such changes include, but are not limited to: changes in one or a few amino acid side chains; changes one or a few amino acids, including deletions (e.g., a truncated version of the protein or peptide) insertions and/or substitutions; changes in stereochemistry of one or a few atoms; and/or minor derivatizations, including but not limited to: methylation, farnesylation, geranyl geranylation, glycosylation, carboxymethylation, phosphorylation, acetylation, myristoylation, prenylation, palmitation, and/or amidation.
  • a homologue can have either enhanced, decreased, or substantially similar properties as compared to the naturally occurring protein or peptide.
  • homologues of a PUFA PKS protein or domain are described in detail below. It is noted that homologues can include synthetically produced homologues, naturally occurring allelic variants of a given protein or domain, or homologous sequences from organisms other than the organism from which the reference sequence was derived.
  • Conservative substitutions typically include substitutions within the following groups: glycine and alanine; valine, isoleucine and leucine; aspartic acid, glutamic acid, asparagine, and glutamine; serine and threonine; lysine and arginine; and phenylalanine and tyrosine. Substitutions may also be made on the basis of conserved hydrophobicity or hydrophilicity (Kyte and Doolittle, J. Mol. Biol. 157:105 (1982)), or on the basis of the ability to assume similar polypeptide secondary structure (Chou and Fasman, Adv. Enzymol. 47: 45 (1978)).
  • allelic variants can be the result of natural allelic variation or natural mutation.
  • a naturally occurring allelic variant of a nucleic acid encoding a protein is a gene that occurs at essentially the same locus (or loci) in the genome as the gene which encodes such protein, but which, due to natural variations caused by, for example, mutation or recombination, has a similar but not identical sequence.
  • Allelic variants typically encode proteins having similar activity to that of the protein encoded by the gene to which they are being compared.
  • One class of allelic variants can encode the same protein but have different nucleic acid sequences due to the degeneracy of the genetic code.
  • Allelic variants can also comprise alterations in the 5′ or 3′ untranslated regions of the gene (e.g., in regulatory control regions). Allelic variants are well known to those skilled in the art.
  • Homologues can be produced using techniques known in the art for the production of proteins including, but not limited to, direct modifications to the isolated, naturally occurring protein, direct protein synthesis, or modifications to the nucleic acid sequence encoding the protein using, for example, classic or recombinant DNA techniques to effect random or targeted mutagenesis.
  • Modifications or mutations in protein homologues as compared to the wild-type protein, either increase, decrease, or do not substantially change, the basic biological activity of the homologue as compared to the naturally occurring (wild-type) protein.
  • the biological activity or biological action of a protein refers to any function(s) exhibited or performed by the protein that is ascribed to the naturally occurring form of the protein as measured or observed in vivo (i.e., in the natural physiological environment of the protein) or in vitro (i.e., under laboratory conditions).
  • Biological activities of PUFA PKS systems and the individual proteins/domains that make up a PUFA PKS system have been described in detail elsewhere herein and in the referenced patents and applications.
  • Modifications of a protein may result in proteins having the same biological activity as the naturally occurring protein, or in proteins having decreased or increased biological activity as compared to the naturally occurring protein. Modifications which result in a decrease in protein expression or a decrease in the activity of the protein, can be referred to as inactivation (complete or partial), down-regulation, or decreased action (or activity) of a protein. Similarly, modifications which result in an increase in protein expression or an increase in the activity of the protein, can be referred to as amplification, overproduction, activation, enhancement, up-regulation or increased action (or activity) of a protein.
  • a functional domain of a PUFA PKS system is a domain (i.e., a domain can be a portion of a protein) that is capable of performing a biological function (i.e., has biological activity).
  • Methods of detecting and measuring PUFA PKS protein or domain biological activity include, but are not limited to, measurement of transcription of a PUFA PKS gene, measurement of translation of a PUFA PKS protein or domain, measurement of posttranslational modification of a PUFA PKS protein or domain, measurement of enzymatic activity of a PUFA PKS protein or domain, and/or measurement production of one or more products of a PUFA PKS system (e.g., PUFA production).
  • an isolated protein of the present invention (including a homologue) is not necessarily required to have the biological activity of the wild-type protein.
  • a PUFA PKS protein or domain can be a truncated, mutated or inactive protein, for example. Such proteins are useful in screening assays, for example, or for other purposes such as antibody production.
  • the isolated proteins of the present invention have a biological activity that is similar to that of the wild-type protein (although not necessarily equivalent, as discussed above).
  • Methods to measure protein expression levels generally include, but are not limited to: Western blot, immunoblot, enzyme-linked immunosorbant assay (ELISA), radioimmunoassay (RIA), immunoprecipitation, surface plasmon resonance, chemiluminescence, fluorescent polarization, phosphorescence, immunohistochemical analysis, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, microcytometry, microarray, microscopy, fluorescence activated cell sorting (FACS), and flow cytometry, as well as assays based on a property of the protein including but not limited to enzymatic activity or interaction with other protein partners. Binding assays are also well known in the art.
  • a BIAcore machine can be used to determine the binding constant of a complex between two proteins.
  • the dissociation constant for the complex can be determined by monitoring changes in the refractive index with respect to time as buffer is passed over the chip (O'Shannessy et al. Anal. Biochem. 212:457 (1993); Schuster et al., Nature 365:343 (1993)).
  • suitable assays for measuring the binding of one protein to another include, for example, immunoassays such as enzyme linked immunoabsorbent assays (ELISA) and radioimmunoassays (RIA); or determination of binding by monitoring the change in the spectroscopic or optical properties of the proteins through fluorescence, UV absorption, circular dichroism, or nuclear magnetic resonance (NMR).
  • immunoassays such as enzyme linked immunoabsorbent assays (ELISA) and radioimmunoassays (RIA); or determination of binding by monitoring the change in the spectroscopic or optical properties of the proteins through fluorescence, UV absorption, circular dichroism, or nuclear magnetic resonance (NMR).
  • the term “contiguous” or “consecutive”, with regard to nucleic acid or amino acid sequences described herein, means to be connected in an unbroken sequence.
  • a first sequence to comprise 30 contiguous (or consecutive) amino acids of a second sequence means that the first sequence includes an unbroken sequence of 30 amino acid residues that is 100% identical to an unbroken sequence of 30 amino acid residues in the second sequence.
  • a first sequence to have “100% identity” with a second sequence means that the first sequence exactly matches the second sequence with no gaps between nucleotides or amino acids.
  • a homologue of a reference protein has an amino acid sequence that is at least about 50% identical, and more preferably at least about 55% identical, and more preferably at least about 60% identical, and more preferably at least about 65% identical, and more preferably at least about 70% identical, and more preferably at least about 75% identical, and more preferably at least about 80% identical, and more preferably at least about 85% identical, and more preferably at least about 90% identical, and more preferably at least about 95% identical, and more preferably at least about 96% identical, and more preferably at least about 97% identical, and more preferably at least about 98% identical, and more preferably at least about 99% identical (or any percentage between 60% and 99%, in whole single percentage increments) to the amino acid sequence of the reference protein (e.g., to a protein that is a part of a PUFA PKS system, or to a domain contained within such protein).
  • the homologue preferably has a biological activity of the protein or domain from which it is derived or related (i.e., the
  • reference to a percent (%) identity refers to an evaluation of homology which is performed using: (1) a BLAST 2.0 Basic BLAST homology search using blastp for amino acid searches, blastn for nucleic acid searches, and blastX for nucleic acid searches and searches of translated amino acids in all 6 open reading frames, all with standard default parameters, wherein the query sequence is filtered for low complexity regions by default (described in Altschul, S. F., Madden, T. L., Schaaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.” Nucleic Acids Res.
  • PSI-BLAST provides an automated, easy-to-use version of a “profile” search, which is a sensitive way to look for sequence homologues.
  • the program first performs a gapped BLAST database search.
  • the PSI-BLAST program uses the information from any significant alignments returned to construct a position-specific score matrix, which replaces the query sequence for the next round of database searching. Therefore, it is to be understood that percent identity can be determined by using any one of these programs.
  • BLAST 2 sequence alignment is performed in blastp or blastn using the BLAST 2.0 algorithm to perform a Gapped BLAST search (BLAST 2.0) between the two sequences allowing for the introduction of gaps (deletions and insertions) in the resulting alignment.
  • BLAST 2.0 Gapped BLAST search
  • a BLAST 2 sequence alignment is performed using the standard default parameters as follows.
  • an amino acid sequence that has a biological activity of at least one domain of a PUFA PKS system is an amino acid sequence that has the biological activity of at least one domain of the PUFA PKS system described in detail herein (e.g., a KS domain, an AT domain, a CLF domain, etc.). Therefore, an isolated protein useful in the present invention can include: the translation product of any PUFA PKS open reading frame, any PUFA PKS domain, any biologically active fragment of such a translation product or domain, or any homologue of a naturally occurring PUFA PKS open reading frame product or domain which has biological activity.
  • a PUFA PKS protein or domain encompassed by the present invention comprises an amino acid sequence that includes at least about 100 consecutive amino acids of the amino acid sequence from the reference PUFA PKS protein, wherein the amino acid sequence of the homologue has a biological activity of at least one domain or protein as described herein.
  • the amino acid sequence of the protein is comprises at least about 200 consecutive amino acids, and more preferably at least about 300 consecutive amino acids, and more preferably at least about 400 consecutive amino acids, and more preferably at least about 500 consecutive amino acids, and more preferably at least about 600 consecutive amino acids, and more preferably at least about 700 consecutive amino acids, and more preferably at least about 800 consecutive amino acids, and more preferably at least about 900 consecutive amino acids, and more preferably at least about 1000 consecutive amino acids of any of the amino acid sequence of the reference protein.
  • an isolated protein or domain of the present invention comprises, consists essentially of, or consists of, any of the amino acid sequences described in any of U.S. Pat. No. 6,566,583; Metz et al., Science 293:290-293 (2001); U.S. Patent Application Publication No. 20020194641; U.S. Patent Application Publication No. 20040235127; and U.S. Patent Application Publication No. 20050100995, PCT Publication No. WO 2006/135866, or any biologically active homologues, fragments or domains thereof.
  • an amino acid sequence having the biological activity of at least one domain of a PUFA PKS system of the present invention includes an amino acid sequence that is sufficiently similar to a naturally occurring PUFA PKS protein or polypeptide that is specifically described herein that a nucleic acid sequence encoding the amino acid sequence is capable of hybridizing under moderate, high, or very high stringency conditions (described below) to (i.e., with) a nucleic acid molecule encoding the naturally occurring PUFA PKS protein or polypeptide (i.e., to the complement of the nucleic acid strand encoding the naturally occurring PUFA PKS protein or polypeptide).
  • an amino acid sequence having the biological activity of at least one domain of a PUFA PKS system of the present invention is encoded by a nucleic acid sequence that hybridizes under moderate, high or very high stringency conditions to the complement of a nucleic acid sequence that encodes any of the above-described amino acid sequences for a PUFA PKS protein or domain.
  • Methods to deduce a complementary sequence are known to those skilled in the art. It should be noted that since amino acid sequencing and nucleic acid sequencing technologies are not entirely error-free, the sequences presented herein, at best, represent apparent sequences of PUFA PKS domains and proteins of the present invention.
  • hybridization conditions refer to standard hybridization conditions under which nucleic acid molecules are used to identify similar nucleic acid molecules. Such standard conditions are disclosed, for example, in Sambrook et al., Molecular Cloning: A Laboratoy Manual , Cold Spring Harbor Labs Press (1989). Sambrook et al., ibid., is incorporated by reference herein in its entirety (see specifically, pages 9.31-9.62). In addition, formulae to calculate the appropriate hybridization and wash conditions to achieve hybridization permitting varying degrees of mismatch of nucleotides are disclosed, for example, in Meinkoth et al., Anal. Biochem. 138, 267 (1984); Meinkoth et al., ibid., is incorporated by reference herein in its entirety.
  • moderate stringency hybridization and washing conditions refer to conditions which permit isolation of nucleic acid molecules having at least about 70% nucleic acid sequence identity with the nucleic acid molecule being used to probe in the hybridization reaction (i.e., conditions permitting about 30% or less mismatch of nucleotides).
  • High stringency hybridization and washing conditions refer to conditions which permit isolation of nucleic acid molecules having at least about 80% nucleic acid sequence identity with the nucleic acid molecule being used to probe in the hybridization reaction (i.e., conditions permitting about 20% or less mismatch of nucleotides).
  • Very high stringency hybridization and washing conditions refer to conditions which permit isolation of nucleic acid molecules having at least about 90% nucleic acid sequence identity with the nucleic acid molecule being used to probe in the hybridization reaction (i.e., conditions permitting about 10% or less mismatch of nucleotides).
  • conditions permitting about 10% or less mismatch of nucleotides i.e., one of skill in the art can use the formulae in Meinkoth et al., ibid. to calculate the appropriate hybridization and wash conditions to achieve these particular levels of nucleotide mismatch. Such conditions will vary, depending on whether DNA:RNA or DNA:DNA hybrids are being formed. Calculated melting temperatures for DNA:DNA hybrids are 10° C. less than for DNA:RNA hybrids.
  • stringent hybridization conditions for DNA:DNA hybrids include hybridization at an ionic strength of 6 ⁇ SSC (0.9 M Na + ) at a temperature of between about 20° C. and about 35° C. (lower stringency), more preferably, between about 28° C. and about 40° C. (more stringent), and even more preferably, between about 35° C. and about 45° C. (even more stringent), with appropriate wash conditions.
  • stringent hybridization conditions for DNA:RNA hybrids include hybridization at an ionic strength of 6 ⁇ SSC (0.9 M Na + ) at a temperature of between about 30° C. and about 45° C., more preferably, between about 38° C.
  • wash conditions should be as stringent as possible, and should be appropriate for the chosen hybridization conditions.
  • hybridization conditions can include a combination of salt and temperature conditions that are approximately 20-25° C. below the calculated T m of a particular hybrid, and wash conditions typically include a combination of salt and temperature conditions that are approximately 12-20° C.
  • hybridization conditions suitable for use with DNA:DNA hybrids includes a 2-24 hour hybridization in 6 ⁇ SSC (50% formamide) at about 42° C., followed by washing steps that include one or more washes at room temperature in about 2 ⁇ SSC, followed by additional washes at higher temperatures and lower ionic strength (e.g., at least one wash as about 37° C. in about 0.1 ⁇ 0.5 ⁇ SSC, followed by at least one wash at about 68° C. in about 0.1 ⁇ 0.5 ⁇ SSC).
  • the present invention also includes a fusion protein that includes any PUFA PKS protein or domain or any homologue or fragment thereof attached to one or more fusion segments.
  • Suitable fusion segments for use with the present invention include, but are not limited to, segments that can: enhance a protein's stability; provide other desirable biological activity; and/or assist with the purification of the protein (e.g., by affinity chromatography).
  • a suitable fusion segment can be a domain of any size that has the desired function (e.g., imparts increased stability, solubility, biological activity; and/or simplifies purification of a protein). Fusion segments can be joined to amino and/or carboxyl termini of the protein and can be susceptible to cleavage in order to enable straight-forward recovery of the desired protein.
  • Fusion proteins are preferably produced by culturing a recombinant cell transfected with a fusion nucleic acid molecule that encodes a protein including the fusion segment attached to either the carboxyl and/or amino terminal end of the protein of the invention as discussed above.
  • any of the above-described PUFA PKS amino acid sequences, as well as homologues of such sequences can be produced with from at least one, and up to about 20, additional heterologous amino acids flanking each of the C- and/or N-terminal end of the given amino acid sequence.
  • the resulting protein or polypeptide can be referred to as “consisting essentially of” a given amino acid sequence.
  • the heterologous amino acids are a sequence of amino acids that are not naturally found (i.e., not found in nature, in vivo) flanking the given amino acid sequence or which would not be encoded by the nucleotides that flank the naturally occurring nucleic acid sequence encoding the given amino acid sequence as it occurs in the gene, if such nucleotides in the naturally occurring sequence were translated using standard codon usage for the organism from which the given amino acid sequence is derived.
  • the phrase “consisting essentially of”, when used with reference to a nucleic acid sequence herein, refers to a nucleic acid sequence encoding a given amino acid sequence that can be flanked by from at least one, and up to as many as about 60, additional heterologous nucleotides at each of the 5′ and/or the 3′ end of the nucleic acid sequence encoding the given amino acid sequence.
  • the heterologous nucleotides are not naturally found (i.e., not found in nature, in vivo) flanking the nucleic acid sequence encoding the given amino acid sequence as it occurs in the natural gene.
  • the minimum size of a protein or domain and/or a homologue or fragment thereof of the present invention is, in one aspect, a size sufficient to have the requisite biological activity, or sufficient to serve as an antigen for the generation of an antibody or as a target in an in vitro assay.
  • a protein of the present invention is at least about 8 amino acids in length (e.g., suitable for an antibody epitope or as a detectable peptide in an assay), or at least about 25 amino acids in length, or at least about 50 amino acids in length, or at least about 100 amino acids in length, or at least about 150 amino acids in length, or at least about 200 amino acids in length, or at least about 250 amino acids in length, or at least about 300 amino acids in length, or at least about 350 amino acids in length, or at least about 400 amino acids in length, or at least about 450 amino acids in length, or at least about 500 amino acids in length, and so on, in any length between 8 amino acids and up to the full length of a protein or domain of the invention or longer, in whole integers (e.g., 8, 9, 10, .
  • the protein can include a portion of a PUFA PKS protein, domain, or biologically active or useful fragment thereof, or a full-length PUFA PKS protein or domain, plus additional sequence (e.g., a fusion protein sequence), if desired.
  • an isolated nucleic acid molecule comprising, consisting essentially of, or consisting of nucleic acid sequences that encode any of the PUFA PKS proteins or domains described herein, including a homologue or fragment of any of such proteins or domains, as well as nucleic acid sequences that are fully complementary thereto.
  • an isolated nucleic acid molecule is a nucleic acid molecule that has been removed from its natural milieu (i.e., that has been subject to human manipulation), its natural milieu being the genome or chromosome in which the nucleic acid molecule is found in nature.
  • isolated does not necessarily reflect the extent to which the nucleic acid molecule has been purified, but indicates that the molecule does not include an entire genome or an entire chromosome in which the nucleic acid molecule is found in nature.
  • An isolated nucleic acid molecule can include a gene.
  • An isolated nucleic acid molecule that includes a gene is not a fragment of a chromosome that includes such gene, but rather includes the coding region and regulatory regions associated with the gene, but no additional genes that are naturally found on the same chromosome, with the exception of other genes that encode other proteins of the PUFA PKS system as described herein.
  • An isolated nucleic acid molecule can also include a specified nucleic acid sequence flanked by (i.e., at the 5′ and/or the 3′ end of the sequence) additional nucleic acids that do not normally flank the specified nucleic acid sequence in nature (i.e., heterologous sequences).
  • Isolated nucleic acid molecule can include DNA, RNA (e.g., mRNA), or derivatives of either DNA or RNA (e.g., cDNA).
  • nucleic acid molecule primarily refers to the physical nucleic acid molecule and the phrase “nucleic acid sequence” primarily refers to the sequence of nucleotides on the nucleic acid molecule, the two phrases can be used interchangeably, especially with respect to a nucleic acid molecule, or a nucleic acid sequence, being capable of encoding a protein or domain of a protein.
  • an isolated nucleic acid molecule of the present invention is produced using recombinant DNA technology (e.g., polymerase chain reaction (PCR) amplification, cloning) or chemical synthesis.
  • Isolated nucleic acid molecules include natural nucleic acid molecules and homologues thereof, including, but not limited to, natural allelic variants and modified nucleic acid molecules in which nucleotides have been inserted, deleted, substituted, and/or inverted in such a manner that such modifications provide the desired effect on PUFA PKS system biological activity as described herein.
  • Protein homologues e.g., proteins encoded by nucleic acid homologues
  • a nucleic acid molecule homologue can be produced using a number of methods known to those skilled in the art (see, for example, Sambrook et al., Molecular Cloning: A Laboratoy Manuals , Cold Spring Harbor Labs Press (1989)).
  • nucleic acid molecules can be modified using a variety of techniques including, but not limited to, classic mutagenesis techniques and recombinant DNA techniques, such as site-directed mutagenesis, chemical treatment of a nucleic acid molecule to induce mutations, restriction enzyme cleavage of a nucleic acid fragment, ligation of nucleic acid fragments, PCR amplification and/or mutagenesis of selected regions of a nucleic acid sequence, synthesis of oligonucleotide mixtures and ligation of mixture groups to “build” a mixture of nucleic acid molecules and combinations thereof.
  • Nucleic acid molecule homologues can be selected from a mixture of modified nucleic acids by screening for the function of the protein encoded by the nucleic acid and/or by hybridization with a wild-type gene.
  • the minimum size of a nucleic acid molecule of the present invention is a size sufficient to form a probe or oligonucleotide primer that is capable of forming a stable hybrid (e.g., under moderate, high or very high stringency conditions) with the complementary sequence of a nucleic acid molecule of the present invention, or of a size sufficient to encode an amino acid sequence having a biological activity of at least one domain of a PUFA PKS system according to the present invention.
  • the size of the nucleic acid molecule encoding such a protein can be dependent on nucleic acid composition and percent homology or identity between the nucleic acid molecule and complementary sequence as well as upon hybridization conditions per se (e.g., temperature, salt concentration, and formamide concentration).
  • the minimal size of a nucleic acid molecule that is used as an oligonucleotide primer or as a probe is typically at least about 12 to about 15 nucleotides in length if the nucleic acid molecules are GC-rich and at least about 15 to about 18 bases in length if they are AT-rich.
  • nucleic acid molecule of the present invention can include a sequence sufficient to encode a biologically active fragment of a domain of a PUFA PKS system, an entire domain of a PUFA PKS system, several domains within an open reading frame (Orf) of a PUFA PKS system, an entire single- or multi-domain protein of a PUFA PKS system, or more than one protein of a PUFA PKS system.
  • a recombinant nucleic acid molecule comprising a recombinant vector and a nucleic acid sequence encoding protein or peptide having a biological activity of at least one domain (or homologue or fragment thereof) of a PUFA PKS protein as described herein.
  • a recombinant vector is an engineered (i.e., artificially produced) nucleic acid molecule that is used as a tool for manipulating a nucleic acid sequence of choice and for introducing such a nucleic acid sequence into a host cell.
  • the recombinant vector is therefore suitable for use in cloning, sequencing, and/or otherwise manipulating the nucleic acid sequence of choice, such as by expressing and/or delivering the nucleic acid sequence of choice into a host cell to form a recombinant cell.
  • a vector typically contains heterologous nucleic acid sequences, that is nucleic acid sequences that are not naturally found adjacent to nucleic acid sequence to be cloned or delivered, although the vector can also contain regulatory nucleic acid sequences (e.g., promoters, untranslated regions) which are naturally found adjacent to nucleic acid molecules of the present invention or which are useful for expression of the nucleic acid molecules of the present invention (discussed in detail below).
  • the vector can be either RNA or DNA, either prokaryotic or eukaryotic, and typically is a plasmid.
  • the vector can be maintained as an extrachromosomal element (e.g., a plasmid) or it can be integrated into the chromosome of a recombinant organism (e.g., a microbe or a plant).
  • the entire vector can remain in place within a host cell, or under certain conditions, the plasmid DNA can be deleted, leaving behind the nucleic acid molecule of the present invention.
  • the integrated nucleic acid molecule can be under chromosomal promoter control, under native or plasmid promoter control, or under a combination of several promoter controls. Single or multiple copies of the nucleic acid molecule can be integrated into the chromosome.
  • a recombinant vector of the present invention can contain at least one selectable marker.
  • a recombinant vector used in a recombinant nucleic acid molecule of the present invention is an expression vector.
  • expression vector is used to refer to a vector that is suitable for production of an encoded product (e.g., a protein of interest).
  • a nucleic acid sequence encoding the product to be produced e.g., a PUFA PKS domain or protein is inserted into the recombinant vector to produce a recombinant nucleic acid molecule.
  • the nucleic acid sequence encoding the protein to be produced is inserted into the vector in a manner that operatively links the nucleic acid sequence to regulatory sequences in the vector that enable the transcription and translation of the nucleic acid sequence within the recombinant host cell.
  • a recombinant vector used in a recombinant nucleic acid molecule of the present invention is a targeting vector.
  • targeting vector is used to refer to a vector that is used to deliver a particular nucleic acid molecule into a recombinant host cell, wherein the nucleic acid molecule is used to delete, inactivate, or replace an endogenous gene or portion of a gene within the host cell or microorganism (i.e., used for targeted gene disruption or knock-out technology).
  • Such a vector may also be known in the art as a “knock-out” vector.
  • a portion of the vector but more typically, the nucleic acid molecule inserted into the vector (i.e., the insert), has a nucleic acid sequence that is homologous to a nucleic acid sequence of a target gene in the host cell (i.e., a gene which is targeted to be deleted or inactivated).
  • the nucleic acid sequence of the vector insert is designed to associate with the target gene such that the target gene and the insert may undergo homologous recombination, whereby the endogenous target gene is deleted, inactivated, attenuated (i.e., by at least a portion of the endogenous target gene being mutated or deleted), or replaced.
  • a recombinant nucleic acid molecule includes at least one nucleic acid molecule of the present invention operatively linked to one or more expression control sequences.
  • the phrase “recombinant molecule” or “recombinant nucleic acid molecule” primarily refers to a nucleic acid molecule or nucleic acid sequence operatively linked to a expression control sequence, but can be used interchangeably with the phrase “nucleic acid molecule”, when such nucleic acid molecule is a recombinant molecule as discussed herein.
  • the phrase “operatively linked” refers to linking a nucleic acid molecule to an expression control sequence (e.g., a transcription control sequence and/or a translation control sequence) in a manner such that the molecule can be expressed when transfected (i.e., transformed, transduced, transfected, conjugated or conducted) into a host cell.
  • Transcription control sequences are sequences that control the initiation, elongation, or termination of transcription. Particularly important transcription control sequences are those that control transcription initiation, such as promoter, enhancer, operator and repressor sequences.
  • Suitable transcription control sequences include any transcription control sequence that can function in a host cell or organism into which the recombinant nucleic acid molecule is to be introduced.
  • Recombinant nucleic acid molecules of the present invention can also contain additional regulatory sequences, such as translation regulatory sequences, origins of replication, and other regulatory sequences that are compatible with the recombinant cell.
  • a recombinant molecule of the present invention including those that are integrated into the host cell chromosome, also contains secretory signals (i.e., signal segment nucleic acid sequences) to enable an expressed protein to be secreted from the cell that produces the protein.
  • Suitable signal segments include a signal segment that is naturally associated with the protein to be expressed or any heterologous signal segment capable of directing the secretion of the protein according to the present invention.
  • a recombinant molecule of the present invention comprises a leader sequence to enable an expressed protein to be delivered to and inserted into the membrane of a host cell.
  • Suitable leader sequences include a leader sequence that is naturally associated with the protein, or any heterologous leader sequence capable of directing the delivery and insertion of the protein to the membrane of a cell.
  • One or more recombinant molecules of the present invention can be used to produce an encoded product (e.g., a PUFA PKS domain, protein, or system) of the present invention.
  • an encoded product is produced by expressing a nucleic acid molecule as described herein under conditions effective to produce the protein.
  • a preferred method to produce an encoded protein is by transfecting a host cell with one or more recombinant molecules to form a recombinant cell. Suitable host cells to transfect include, but are not limited to, any bacterial, fungal (e.g., yeast), insect, plant or animal cell that can be transfected.
  • a preferred host cell is a plant host cell. Host cells can be either untransfected cells or cells that are already transfected with at least one other recombinant nucleic acid molecule.
  • the term “transfection” is used to refer to any method by which an exogenous nucleic acid molecule (i.e., a recombinant nucleic acid molecule) can be inserted into a cell.
  • the term “transformation” can be used interchangeably with the term “transfection” when such term is used to refer to the introduction of nucleic acid molecules into microbial cells, such as algae, bacteria and yeast, or into plant cells.
  • transfection is used to describe an inherited change due to the acquisition of exogenous nucleic acids by the microorganism or plant and is essentially synonymous with the term “transfection.”
  • transformation has acquired a second meaning which can refer to changes in the growth properties of cells in culture after they become cancerous, for example. Therefore, to avoid confusion, the term “transfection” is preferably used with regard to the introduction of exogenous nucleic acids into animal cells, and the term “transfection” will be used herein to generally encompass transfection of animal cells, and transformation of microbial cells or plant cells, to the extent that the terms pertain to the introduction of exogenous nucleic acids into a cell. Therefore, transfection techniques include, but are not limited to, transformation, particle bombardment, diffusion, active transport, bath sonication, electroporation, microinjection, lipofection, adsorption, infection and protoplast fusion.
  • recombinant DNA technologies can improve control of expression of transfected nucleic acid molecules by manipulating, for example, the number of copies of the nucleic acid molecules within the host cell, the efficiency with which those nucleic acid molecules are transcribed, the efficiency with which the resultant transcripts are translated, and the efficiency of post-translational modifications.
  • the promoter sequence might be genetically engineered to improve the level of expression as compared to the native promoter.
  • Recombinant techniques useful for controlling the expression of nucleic acid molecules include, but are not limited to, integration of the nucleic acid molecules into one or more host cell chromosomes, addition of vector stability sequences to plasmids, substitutions or modifications of transcription control signals (e.g., promoters, operators, enhancers), substitutions or modifications of translational control signals (e.g., ribosome binding sites, Shine-Dalgamo sequences), modification of nucleic acid molecules to correspond to the codon usage of the host cell, and deletion of sequences that destabilize transcripts.
  • transcription control signals e.g., promoters, operators, enhancers
  • substitutions or modifications of translational control signals e.g., ribosome binding sites, Shine-Dalgamo sequences
  • PUFA profile PUFA expression profile
  • PUFA production profile can be used interchangeably and describe the overall profile of PUFAs expressed/produced by a organism.
  • the PUFA expression profile can include the types of PUFAs expressed by the organism, as well as the absolute and/or relative amounts of the PUFAs produced.
  • a PUFA profile can be described in terms of the ratios of PUFAs to one another as produced by the organism, in terms of the types of PUFAs produced by the organism, and/or in terms of the types and absolute and/or relative amounts of PUFAs produced by the organism.
  • the present inventor shows examples in which the PUFA synthase derived from Schizochytrium , along with a PPTase from Nostoc (HetI), are expressed in yeast and in Arabidopsis .
  • the biochemical characteristics of the Schizochytrium PUFA synthase combined with a general knowledge of yeast and higher plant biochemistry suggested that expression of this system in the cytoplasm of yeast or plant cells as well as in plastids of plants should result in PUFA accumulation, and that is indeed what has been observed.
  • the work shown here shows that when the Schizochytrium PUFA synthase is expressed in yeast or in the cytoplasm or plastids of plant cells, detection of DHA and DPAn-6 in those hosts is dependant on the co-expression of HetI (or any appropriate PPTase).
  • Orfs were resynthesized for better expression in yeast.
  • the resynthesized Orfs are designated sOrfA (SEQ ID NO:35) and sOrfB (SEQ ID NO:36).
  • the proteins encoded by sOrfA and sOrf B have the same amino acid sequences as those encoded by the native Orf A (SEQ ID NO:2) and Orf B (SEQ ID NO:4), respectively. Similar strategies can be used to optimize codon usage for expression of the constructs in other heterologous organisms.
  • the following example shows the expression of genes encoding the Schizochytrium PUFA synthase (sOrf A, sOrfB and native Orf C) along with Het I in baker's yeast ( Saccharomyces cerevisiae ).
  • the Schizochytrium PUFA synthase genes and Het I were expressed in yeast using materials obtained from Invitrogen.
  • the INVscl strain of Saccharomyces cerevisiae was used along with the following transformation vectors: pYESLeu (sOrfA, SEQ ID NO:35)), pYES3/CT (sOrfB, SEQ ID NO:36)), pYES2/CT (OrfC, SEQ ID NO:5) and pYESHis (HetI, SEQ ID NO:33).
  • Some of the vectors were modified to accommodate specific cloning requirements. Appropriate selection media were used, depending on the particular experiment.
  • the genes were cloned, in each case, behind a GAL1 promoter and expression was induced by re-suspension of washed cells in media containing galactose according to guidelines provide by Invitrogen. Cells were grown at 30° C. and harvested (by centrifugation) at the indicated times after being transferred to the induction medium. The cell pellets were freeze dried and FAMEs were prepared using acidic methanol, extracted into hexane and analyzed by GC.
  • FIG. 1 shows a comparison of the fatty acid profile from yeast cells expressing the Schizochytrium PUFA synthase system (sOrf A, sOrf B, Orf C and Het I) and one obtained from control cells (lacking the sOrf A gene). Cells were collected ⁇ 20 hrs after induction. It can be seen that two novel FAME peaks have appeared it the profile of the strain expressing the complete PUFA synthase system. These two peaks were identified as DPA n-6 and DHA by comparison of the elution time with authentic standards and subsequently by MS analyses. As predicted from our characterization of the Schizochytrium PUFA synthase, aside from DHA and DPA n-6, no other novel peaks are evident in the profile.
  • FIG. 2 shows the region of the GC chromatogram of FIG. 1 which contains the PUFA FAMEs.
  • Both the control cells and the cell expressing the PUFA synthase contain a peak that elutes near the DHA FAME. This has been identified as C26:0 FAME and (based on literature references) is derived from sphingolipids. Although it elutes close to the DHA peak the resolution is sufficient so that it does not interfere with the quantitation of DHA.
  • the DPA n-6 peak is well separated from other endogenous yeast lipids in the FAME profile.
  • the cells expressing the Schizochytrium PUFA synthase system accumulated 2.4% DHA and 2.0% DPA n-6 (as a percentage of the total FAMEs).
  • the sum of DHA and DPA n-6 4.4% of the measured fatty acids in the cells.
  • the ratio of DHA to DPAn-6 observed in the cells was ⁇ 1.2:1.
  • the Schizochytrium OrfA (nucleotide sequence represented by SEQ ID NO:1), OrfB* (nucleotide sequence represented by SEQ ID NO:37) and OrfC (nucleotide sequence represented by SEQ ID NO:5) along with Het I (nucleotide sequence represented by SEQ ID NO:33) were cloned (separately or in various combinations including all 4 genes on one superconstruct) into the appropriate binary vectors for introduction of the genes into plants. Examples of such constructs and vectors are described below (three expression constructs) and also in Example 13 (one “superconstruct” for 4127).
  • the Orf B* (SEQ ID NO:37, encoding SEQ ID NO:4), was restriction cloned into an expression cassette under the control of the flax linin promoter/terminator (U.S. Pat. No. 6,777,591).
  • the linin promoter controls the specific-temporal and tissue-specific expression of the transgene(s) during seed development.
  • Directly upstream and in-frame of the Schizochytrium Orf B* was the plastid targeting sequence derived from Brassica napus acyl-ACP thioesterase (PT-signal peptide), to target Orf B* to the plastid.
  • the plant binary vector also contained an existing E.
  • the Schizochytrium Orf C (nucleotide sequence represented by SEQ ID NO:5, encoding SEQ ID NO:6) along with HetI (nucleotide sequence represented by SEQ ID NO:33, encoding SEQ ID NO:34) were cloned into expression cassettes under the control of a flax linin promoter/terminator (U.S. Pat. No. 6,777,591).
  • the linin promoter controls the specific-temporal and tissue-specific expression of the transgene(s) during seed development.
  • the Schizochytrium Orf A (nucleotide sequence represented by SEQ ID NO:1, encoding SEQ ID NO:2) was cloned into expression cassettes under the control of a flax linin promoter/terminator (U.S. Pat. No. 6,777,591).
  • the linin promoter controls the specific-temporal and tissue-specific expression of the transgene(s) during seed development.
  • Directly upstream and in-frame of the Schizochytrium Orf A was the plastid targeting sequence derived from Brassica napus acyl-ACP thioesterase (PT-signal peptide), to target the PUFA synthase and PPTase to the plastid.
  • the expression cassette was contained within a plant binary vector containing a nptII gene conferring host plant kanamycin resistance driven by the MAS promoter/terminator between the left and right border sequences.
  • transgenes were cloned into three separate expression cassettes: a construct denoted 5720 (containing OrfB*, encoding SEQ ID NO:4), a construct denoted 4107 (containing OrfC, encoding SEQ ID NO:6 and HetI, encoding SEQ ID NO:34) and a construct denoted 4757 (containing OrfA, containing SEQ ID NO:2), as described above.
  • the gene was cloned.
  • additional 5′ sequences encoding a plastid targeting sequence derived from a Brassica napus acyl-ACP thioesterase were located directly upstream of Orfs A, B*, C and HetI.
  • the nucleotide sequences encoding this peptide were placed in-frame with the start methionine codons of each PUFA synthase Orf, as well as the engineered start codon (ATG) of Het I.
  • ATG engineered start codon
  • Standard methods were used for introduction of the genes into Arabidopsis (floral dipping into suspension of Agrobacterium strains containing the appropriate vectors, substantially as described in Clough et al., 1998 , Plant J. 16: 735-743). Briefly, the integrity of all plant binary vectors were confirmed by diagnostic restriction digests and sequence analysis. Isolated plasmids were then used to transform competent Agrobacterium strain EH101 (Hood et al., 1986, J. Bacteriol. 144: 732-743) by electroporation (25 ⁇ F, 2.5 kV, 200 ⁇ ).
  • Recombinant Agrobacterium were plated on AB-spectinomycin/kanamycin (20 ⁇ AB salts, 2 M glucose, 0.25 mg/ml FeSO 4 7H 2 O, 1 M MgSO 4 , 1 M CaCl 2 ) and a single colony was used to inoculate 5 ml of AB-spectinomycin/kanamycin broth. These cultures were grown overnight at 28° C.
  • the recombinant Agrobacteria containing the plasmids were then used to transform wild type C24 Arabidopsis thaliana plants by the flower dipping method (Clough et al., 1998 , Plant J. 16: 735-743).
  • Seeds obtained from these plants were plated on selective medium. Positively identified seedlings were transferred to soil and taken to maturity, after which the seeds were analyzed for PUFA content. Based on PUFA content, some of those seeds were taken forward to the next generation. Pooled seeds obtained from those plants were analyzed for their fatty acid content.
  • the target PUFAs expected from these transgenic plants were docosahexaenoic acid (DHA) and docosapentaenoic acid (DPAn-6), which are the primary PUFAs produced by the Schizochytrium PUFA PKS system from which the genes used to transform the plants were derived.
  • DHA docosahexaenoic acid
  • DPAn-6 docosapentaenoic acid
  • Results from one exemplary fatty acid analysis in one of the exemplary transgenic plant lines is shown in FIG. 3 .
  • the top panel of FIG. 3 shows the typical fatty acid profile of wild type Arabidopsis seeds as represented by GC separation and FID detection of FAMEs prepared from a pooled seed sample.
  • the predominant fatty acids are: 16:0, 18:0, 16:1, 18:1, 20:1, 20:2 and 22:1.
  • No DHA or DPA n-6 are present in the samples from wild type seed.
  • the lower panel of FIG. 3 shows the fatty acid profile of a pooled seed sample from one of the exemplary transgenic Arabidopsis lines (line 263) expressing the Schizochytrium PUFA synthase genes and the Het I gene, introduced from three separate expression cassettes (5720, 4107 and 4757) all targeted to the plastid, as described above.
  • line 263 expressing the Schizochytrium PUFA synthase genes and the Het I gene, introduced from three separate expression cassettes (5720, 4107 and 4757) all targeted to the plastid, as described above.
  • two FAME peaks are present in the profile from the transgenic plant seeds that are not present in the profile from wild type seeds.
  • the elution pattern of these two peaks exactly corresponds to the elution of authentic DHA and DPAn-6 (using FAMEs prepared from Schizochytrium oil as standards, as well as a commercially purchased DHA standard from NuCheck Prep).
  • the DHA peak represents 0.8% of total calculated FAMEs while the DPA n-6 peak represents 1.7%.
  • the sum of novel PUFAs is 2.5% of total FAMEs.
  • transgenic line 269 which was transformed with the same constructs and in the same manner as the 263 line, produced approximately 0.75% DHA or total calculated FAMEs, and 1.41% DPAn-6 of total calculated FAMEs) (data not shown).
  • transgenic Arabidopsis plants produced using the same nucleic acid molecules described above also produced the target PUFAs, regardless of whether they were produced using constructs providing the PUFA PKS genes and the HetI PPTase on separate constructs, combination constructs, or a single superconstruct.
  • transgenic plants targeting the PUFA PKS genes to the cytosol all expressed the target PUFAs (data not shown in detail).
  • a plant line expressing the Schizochytrium PUFA PKS plus HetI in the cytosol introduced on three separate expression cassettes as described above (without the plastid targeting sequence) produced approximately 0.45% DHA and approximately 0.8% DPA as a percentage of total FAME.
  • a plant line expressing the Schizochytrium PUFA PKS plus HetI in the cytosol introduced on a single superconstruct produced approximately 0.2-0.3% DHA and approximately 0.5% DPA as a percentage of total FAME.
  • DHA and DPAn-6 in the seed fatty acid profile shown in FIG. 3 (and in the other similar transgenic plant seeds) demonstrates that introduced Schizochytrium PUFA synthase system functions when expressed in the plant cell and that the proteins can be targeted to the plastid or to the cytosol.
  • the only novel fatty acids detected in the profile of the seed from the transgenic plants are DHA and DPA n-6, further illustrating the advantages of the PUFA PKS system over the standard pathway enzymes for the production of PUFAs in a plant.

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