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(12) Patent Application Publication (10) Pub. No.: US 2002/0194641 A1 Metz Et Al US 2002O194641A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2002/0194641 A1 Metz et al. (43) Pub. Date: Dec. 19, 2002 (54) PUFA POLYKETIDE SYNTHASE SYSTEMS Publication Classification AND USES THEREOF (76) Inventors: James G. Metz, Longmont, CO (US); (51) Int. Cl." ............................ A01H 5700; CO7H 21/04; James H. Flatt, Longmont, CO (US); C12P 19/62; C12N 9/10; C12P 21/02; Jerry M. Kuner, Longmont, CO (US); C12N 5/04; C12N 1/21 William R. Barclay, Boulder, CO (US) (52) U.S. Cl. ...................... 800/281; 435/193; 435/252.3; Correspondence Address: 435/69.1; 435/320.1; 536/23.2; Angela K. Dallas 435/76 SHERIDAN ROSS PC. Suite 1200 1560 Broadway (57) ABSTRACT Denver, CO 80202-5141 (US) (21) Appl. No.: 10/124,800 The invention generally relates to polyunsaturated fatty acid (22) Filed: Apr. 16, 2002 (PUFA) polyketide synthase (PKS) systems isolated from or derived from non-bacterial organisms, to homologues Related U.S. Application Data thereof, to isolated nucleic acid molecules and recombinant nucleic acid molecules encoding biologically active (63) Continuation-in-part of application No. 09/231,899, domains of such a PUFA PKS system, to genetically modi filed on Jan. 14, 1999. fied organisms comprising PUFA PKS systems, to methods (60) Provisional application No. 60/284.066, filed on Apr. of making and using Such Systems for the production of 16, 2001. Provisional application No. 60/298,796, bioactive molecules of interest, and to novel methods for filed on Jun. 15, 2001. Provisional application No. identifying new bacterial and non-bacterial microorganisms 60/323,269, filed on Sep. 18, 2001. having such a PUFA PKS system. Patent Application Publication Dec. 19, 2002 Sheet 1 of 3 US 2002/0194641 A1 É N O er i t g s 2 2 Patent Application Publication Dec. 19, 2002 Sheet 2 of 3 US 2002/0194641 A1 HTIOSX! Z*OIH J.JO9JJO/ :Su?eUIOp/SJIOSYIAHJOUOS?.IeduI0O p113upº?tat/SSAunt/1/(?OOz??OS Patent Application Publication Dec. 19, 2002 Sheet 3 of 3 US 2002/0194641 A1 US 2002/0194641 A1 Dec. 19, 2002 PUFA POLYKETIDE SYNTHASE SYSTEMS AND production of the end product. The domains are found in USES THEREOF very large proteins and the product of each reaction is passed on to another domain in the PKS protein. Additionally, in all CROSS-REFERENCE TO RELATED of the PKS systems described above, if a carbon-carbon APPLICATIONS double bond is incorporated into the end product, it is always 0001. This application claims the benefit of priority under in the trans configuration. 35 U.S.C. S 119(e) to: U.S. Provisional Application Serial 0006. In the Type I and Type II PKS systems described No. 60/284,066, filed Apr. 16, 2001, entitled “A Polyketide above, the same Set of reactions is carried out in each cycle Synthase System and Uses Thereof; U.S. Provisional until the end product is obtained. There is no allowance for Application Serial No. 60/298,796, filed Jun. 15, 2001, the introduction of unique reactions during the biosynthetic entitled “A Polyketide Synthase System and Uses Thereof; procedure. The modular PKS Systems require huge proteins and U.S. Provisional Application Serial No. 60/323,269, that do not utilize the economy of iterative reactions (i.e., a filed Sep. 18, 2001, entitled “Thraustochytrium PUFA PKS distinct domain is required for each reaction). Additionally, System and Uses Thereof'. This application is also a con as Stated above, carbon-carbon double bonds are intro tinuation-in-part of copending U.S. application Ser. No.09/ duced in the trans configuration in all of the previously 231,899, filed Jan. 14, 1999, entitled “Schizochytrium PKS described PKS systems. Genes”. Each of the above-identified patent applications is incorporated herein by reference in its entirety. 0007 Polyunsaturated fatty acids (PUFAs) are critical components of membrane lipids in most eukaryotes (Lau 0002 This application does not claim the benefit of ritzen et al., Prog. Lipid Res. 401 (2001); McConn et al., priority from U.S. application Ser. No. 09/090,793, filed Jun. Plant J. 15, 25 521 (1998)) and are precursors of certain 4, 1998, now U.S. Pat. No. 6,140,486, although U.S. appli hormones and signaling molecules (Heller et al., Drugs 55, cation Ser. No. 09/090,793 is incorporated herein by refer 487 (1998); Creelman et al., Annu. Rev. Plant Physiol. Plant ence in its entirety. Mol. Biol. 48, 355 (1997)). Known pathways of PUFA synthesis involve the processing of Saturated 16:0 or 18:0 FIELD OF THE INVENTION fatty acids (the abbreviation X:Y indicates an acyl group 0003. This invention relates to polyunsaturated fatty acid containing X carbon atoms and Y cis double bonds; double (PUFA) polyketide synthase (PKS) systems from microor bond positions of PUFAs are indicated relative to the methyl ganisms, including eukaryotic organisms, Such as ThrauS carbon of the fatty acid chain (c)3 or (O6) with systematic tochytrid microorganisms. More particularly, this invention methylene interruption of the double bonds) derived from relates to nucleic acids encoding non-bacterial PUFA PKS fatty acid Synthase (FAS) by elongation and aerobic desatu systems, to non-bacterial PUFAPKS systems, to genetically ration reactions (Sprecher, Curr. Opin. Clin. Nutr. Metab. modified organisms comprising non-bacterial PUFA PKS Care 2, 135 (1999); Parker-Barnes et al., Proc. Natl. Acad. Systems, and to methods of making and using the non Sci. USA97, 8284 (2000); Shanklin et al., Annu. Rev. Plant bacterial PUFA PKS systems disclosed herein. This inven Physiol. Plant Mol. Biol. 49, 611 (1998)). Starting from tion also relates to a method to identify bacterial and acetyl-CoA, the Synthesis of DHA requires approximately non-bacterial microorganisms comprising PUFA PKS sys 30 distinct enzyme activities and nearly 70 reactions includ temS. ing the four repetitive Steps of the fatty acid Synthesis cycle. Polyketide synthases (PKSs) carry out some of the same BACKGROUND OF THE INVENTION reactions as FAS (Hopwood et al., Annu. Rev. Genet. 24, 37 0004 Polyketide synthase (PKS) systems are generally (1990); Bentley et al., Annu. Rev. Microbial 53,411 (1999)) known in the art as enzyme complexes derived from fatty and use the same Small protein (or domain), acyl carrier acid synthase (FAS) systems, but which are often highly protein (ACP), as a covalent attachment site for the growing modified to produce Specialized products that typically Show carbon chain. However, in these enzyme Systems, the com little resemblance to fatty acids. Researchers have attempted plete cycle of reduction, dehydration and reduction Seen in to exploit polyketide synthase (PKS) systems that have been FAS is often abbreviated so that a highly derivatized carbon described in the literature as falling into one of three basic chain is produced, typically containing many keto- and types, typically referred to as: Type II, Type I and modular. hydroxy-groupS as well as carbon-carbon double bonds in The Type II System is characterized by Separable proteins, the trans configuration. The linear products of PKSs are each of which carries out a distinct enzymatic reaction. The often cyclized to form complex biochemicals that include enzymes work in concert to produce the end product and antibiotics and many other Secondary products (Hopwood et each individual enzyme of the System typically participates al., (1990) Supra; Bentley et al., (1999), Supra; Keating et al., Several times in the production of the end product. This type Curr. Opin. Chem. Biol. 3,598 (1999)). of System operates in a manner analogous to the fatty acid 0008 Very long chain PUFAs such as docosahexaenoic Synthase (FAS) Systems found in plants and bacteria. Type acid (DHA; 22:603) and eicosapentaenoic acid (EPA; I PKS systems are similar to the Type II system in that the 20:5c)3) have been reported from several species of marine enzymes are used in an iterative fashion to produce the end bacteria, including Shewanella sp (Nichols et al., Curr. Op. product. The Type I differs from Type II in that enzymatic Biotechnol. 10, 240 (1999); Yazawa, Lipids 31, S (1996); activities, instead of being associated with Separable pro DeLong et al., Appl. Environ. Microbiol. 51, 730 (1986)). teins, occur as domains of larger proteins. This System is Analysis of a genomic fragment (cloned as plasmid pEPA) analogous to the Type I FAS Systems found in animals and from Shewanella sp. strain SCRC2738 led to the identifi fungi. cation of five open reading frames (Orfs), totaling 20 Kb, 0005. In contrast to the Type I and II systems, in modular that are necessary and sufficient for EPA production in E. PKS Systems, each enzyme domain is used only once in the coli (Yazawa, (1996), Supra). Several of the predicted pro US 2002/0194641 A1 Dec. 19, 2002 least for EPA and DHA. Additionally, for production of about 60% identical to the amino acid sequence of (b), uSeable quantities of Such PUFAS, additional engineering wherein the amino acid Sequence has a biological activity of efforts may be required, for instance the down regulation of at least one domain of a polyunsaturated fatty acid (PUFA) enzymes competing for Substrate, engineering of higher polyketide synthase (PKS) system; and (e) a nucleic acid enzyme activities Such as by mutagenesis or targeting of Sequence that is fully complementary to the nucleic acid enzymes to plastid organelles. Therefore it is of interest to Sequence of (a), (b), (c), or (d). In alternate aspects, the obtain genetic material involved in PUFA biosynthesis from nucleic acid Sequence encodes an amino acid Sequence that Species that naturally produce these fatty acids and to is at least about 70% identical, or at least about 80% express the isolated material alone or in combination in a identical, or at least about 90% identical, or is identical to: heterologous System which can be manipulated to allow (1) at least 500 consecutive amino acids of an amino acid production of commercial quantities of PUFAs.
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