PUFA polyketide synthase systems and uses thereof

• US 20020194641A1
• Filed: 04/16/2002
• Published: 12/19/2002
• Est. Priority Date: 01/14/1999
• Status: Active Grant

• Current Assignee: DSM IP Assets BV (DSM-Firmenich AG)
• Original Assignee: Martek Biosciences Corporation (DSM-Firmenich AG)
• Inventors: Barclay, William R., Metz, James G., Kuner, Jerry M., Flatt, James H.
• Granted Patent: US 7,247,461 B2
• Time in Patent Office: Days
• US Class Current: 800/281
• CPC Class Codes: C07K 14/28 from Vibrionaceae (F)
• CPC Class Codes: C07K 14/405 from algae
• CPC Class Codes: C12N 15/52 Genes encoding for enzymes or proenzymes
• CPC Class Codes: C12N 15/8247 involving modified lipid metabolism, e.g. seed oil composition
• CPC Class Codes: C12N 15/8273 for drought, cold, salt resistance
• CPC Class Codes: C12P 7/625 Polyesters of hydroxy carboxylic acids
• CPC Class Codes: C12P 7/6427 Polyunsaturated fatty acids [PUFA], i.e. having two or more double bonds in their backbone
• CPC Class Codes: C12P 7/6434 Docosahexenoic acids [DHA]
• CPC Class Codes: C12P 7/6472 containing polyunsaturated fatty acid [PUFA] residues, i.e. having two or more double bonds in their backbone

Abstract

The invention generally relates to polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) systems isolated from or derived from non-bacterial organisms, to homologues thereof, to isolated nucleic acid molecules and recombinant nucleic acid molecules encoding biologically active domains of such a PUFA PKS system, to genetically modified organisms comprising PUFA PKS systems, to methods of making and using such systems for the production of bioactive molecules of interest, and to novel methods for identifying new bacterial and non-bacterial microorganisms having such a PUFA PKS system.

Claims

1. An isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, and biologically active fragments thereof;

b. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32, and biologically active fragments thereof,

c. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to at least 500 consecutive amino acids of said amino acid sequence of (a), wherein said amino acid sequence has a biological activity of at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system;

d. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to said amino acid sequence of (b), wherein said amino acid sequence has a biological activity of at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system; and

e. a nucleic acid sequence that is fully complementary to the nucleic acid sequence of (a), (b), (c), or (d).

2. The isolated nucleic acid molecule of claim 1, wherein said nucleic sequence is selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence that is at least about 70% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. a nucleic acid sequence encoding an amino acid sequence that is at least about 70% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

3. The isolated nucleic acid molecule of claim 1, wherein said nucleic sequence is selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence that is at least about 80% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. a nucleic acid sequence encoding an amino acid sequence that is at least about 80% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

4. The isolated nucleic acid molecule of claim 1, wherein said nucleic sequence is selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence that is at least about 90% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. a nucleic acid sequence encoding an amino acid sequence that is at least about 90% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

5. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence encodes an amino acid sequence selected from the group consisting of:

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32 and biologically active fragments thereof.

6. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid molecule comprises a nucleic acid sequence selected from the group consisting of:

SEQ ID NO;

1, SEQ ID NO;

3, SEQ ID NO;

5, SEQ ID NO;

7, SEQ ID NO;

9, SEQ ID NO;

12, SEQ ID NO;

17, SEQ ID NO;

19, SEQ ID NO;

21, SEQ ID NO;

23, SEQ ID NO;

25, SEQ ID NO;

27, SEQ ID NO;

29, and SEQ ID NO;

31.

7. A recombinant nucleic acid molecule comprising the nucleic acid molecule of claim 1, operatively linked to at least one transcription control sequence.

8. A recombinant cell transfected with the recombinant nucleic acid molecule of claim 7.

70. The method of claim 55, wherein said microorganism selected in (a) contains greater than about 30% of its total fatty acids as C14:

0, C16;

0 and C16;

1 while also producing at least one long chain fatty acid with three or more unsaturated bonds.

115. The method of claim 114, wherein said endproduct is selected from the group consisting of a dietary supplement, a food product, a pharmaceutical formulation, a humanized animal milk, and an infant formula.

9. A genetically modified microorganism, wherein said microorganism expresses a PKS system comprising at least one biologically active domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system, wherein said at least one domain of said PUFA PKS system is encoded by a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system from a Thraustochytrid microorganism;

b. a nucleic acid sequence encoding at least one domain of a PUFA PKS system from a microorganism identified by the following method;

(i) selecting a microorganism that produces at least one PUFA; and

,

(ii) identifying a microorganism from (i) that has an ability to produce increased PUFAs under dissolved oxygen conditions of less than about 5% of saturation in the fermentation medium, as compared to production of PUFAs by said microorganism under dissolved oxygen conditions of greater than about 5% of saturation in the fermentation medium;

c. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, and biologically active fragments thereof;

d. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ

ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32, and biologically active fragments thereof;

e. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

f. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system;

wherein said microorganism is genetically modified to affect the activity of said PKS system.

10. The genetically modified microorganism of claim 9, wherein said microorganism endogenously expresses a PKS system comprising said at least one domain of said PUFA PKS system, and wherein said genetic modification is in a nucleic acid sequence encoding said at least one domain of said PUFA PKS system.

11. The genetically modified microorganism of claim 10, wherein said genetic modification is in a nucleic acid sequence that encodes a domain having a biological activity of at least one of the following proteins:

malonyl-CoA;

ACP acyltransferase (MAT), β

-keto acyl-ACP synthase (KS), ketoreductase (KR), acyltransferase (AT), FabA-like β

-hydroxy acyl-ACP dehydrase (DH), phosphopantetheine transferase, chain length factor (CLF), acyl carrier protein (ACP), enoyl ACP-reductase (ER), an enzyme that catalyzes the synthesis of trans-2-decenoyl-ACP, an enzyme that catalyzes the reversible isomerization of trans-2-deconoyl-ACP to cis-3-decenoyl-ACP, and an enzyme that catalyzes the elongation of cis-3-decenoyl-ACP to cis-vaccenic acid.

12. The genetically modified microorganism of claim 10, wherein said genetic modification is in a nucleic acid sequence that encodes an amino acid sequence selected from the group consisting of:

a. an amino acid sequence that is at least about 70% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. an amino acid sequence that is at least about 70% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

13. The genetically modified microorganism of claim 10, wherein said genetic modification is in a nucleic acid sequence that encodes an amino acid sequence selected from the group consisting of:

a. an amino acid sequence that is at least about 80% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. an amino acid sequence that is at least about 80% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

14. The genetically modified microorganism of claim 10, wherein said genetic modification is in a nucleic acid sequence that encodes an amino acid sequence selected from the group consisting of:

a. an amino acid sequence that is at least about 90% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. an amino acid sequence that is at least about 90% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

15. The genetically modified microorganism of claim 10, wherein said genetic modification is in a nucleic acid sequence that encodes an amino acid sequence selected from the group consisting of:

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32 and biologically active fragments thereof.

16. The genetically modified microorganism of claim 10, wherein said microorganism is a Thraustochytrid.

17. The genetically modified microorganism of claim 16, wherein said Thraustochytrid is from a genus selected from the group consisting of Schizochytrium and Thraustochytrium.

18. The genetically modified microorganism of claim 10, wherein said microorganism has been further genetically modified to recombinantly express at least one nucleic acid molecule encoding at least one biologically active domain from a bacterial PUFA PKS system.

19. The genetically modified microorganism of claim 10, wherein said microorganism has been further genetically modified to recombinantly express at least one biologically active domain of a PKS system from a Type I PKS system.

20. The genetically modified microorganism of claim 10, wherein said microorganism has been further genetically modified to recombinantly express at least one biologically active domain of a PKS system from a Type II PKS system.

21. The genetically modified microorganism of claim 10, wherein said microorganism has been further genetically modified to recombinantly express at least one biologically active domain of a PKS system from a modular PKS system.

22. The genetically modified microorganism of claim 9, wherein said microorganism endogenously expresses a PUFA PKS system comprising said at least one biologically active domain of a PUFA PKS system, and wherein said genetic modification comprises expression of a recombinant nucleic acid molecule selected from the group consisting of a recombinant nucleic acid molecule encoding at least one biologically active domain from a second PKS system and a recombinant nucleic acid molecule encoding a protein that affects the activity of said PUFA PKS system.

23. The genetically modified microorganism of claim 22, wherein said recombinant nucleic acid molecule comprises a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system from a Thraustochytrid microorganism;

b. a nucleic acid sequence encoding at least one domain of a PUFA PKS system from a microorganism identified by the following method;

(i) selecting a microorganism that produces at least one PUFA; and

,

(ii) identifying a microorganism from (i) that has an ability to produce increased PUFAs under dissolved oxygen conditions of less than about 5% of saturation in the fermentation medium, as compared to production of PUFAs by said microorganism under dissolved oxygen conditions of greater than about 5% of saturation in the fermentation medium;

c. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, and biologically active fragments thereof;

d. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32, and biologically active fragments thereof ,

e. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to at least 500 consecutive amino acids of said amino acid sequence of (a), wherein said amino acid sequence has a biological activity of at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system; and

f. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to said amino acid sequence of (b), wherein said amino acid sequence has a biological activity of at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system.

24. The genetically modified microorganism of claim 23, wherein said Thraustochytrid microorganism of (a) is from a genus selected from the group consisting of Schizochytrium and Thraustochytrium.

25. The genetically modified microorganism of claim 23, wherein said recombinant nucleic acid molecule comprises a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence that is at least about 70% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. a nucleic acid sequence encoding an amino acid sequence that is at least about 70% identical to an amino acid sequence selected from the group consisting of;

SEQ IDNO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

26. The genetically modified microorganism of claim 23, wherein said recombinant nucleic acid molecule comprises a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence that is at least about 80% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. a nucleic acid sequence encoding an amino acid sequence that is at least about 80% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

27. The genetically modified microorganism of claim 23, wherein said recombinant nucleic acid molecule comprises a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence that is at least about 90% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. a nucleic acid sequence encoding an amino acid sequence that is at least about 90% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

28. The genetically modified microorganism of claim 23, wherein said recombinant nucleic acid molecule comprises a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of:

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32 and biologically active fragments thereof.

29. The genetically modified microorganism of claim 22, wherein said recombinant nucleic acid molecule encodes a phosphopantetheine transferase.

30. The genetically modified microorganism of claim 22, wherein said recombinant nucleic acid molecule comprises a nucleic acid sequence encoding at least one biologically active domain from a bacterial PUFA PKS system.

31. The genetically modified microorganism of claim 22, wherein said recombinant nucleic acid molecule comprises a nucleic acid sequence encoding at least one biologically active domain from a type I PKS system.

32. The genetically modified microorganism of claim 22, wherein said recombinant nucleic acid molecule comprises a nucleic acid sequence encoding at least one biologically active domain from a type II PKS system.

33. The genetically modified microorganism of claim 22, wherein said recombinant nucleic acid molecule comprises a nucleic acid sequence encoding at least one biologically active domain from a modular PKS system.

34. The genetically modified microorganism of claim 9, wherein said microorganism is genetically modified by transfection with a recombinant nucleic acid molecule encoding said at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system.

35. The genetically modified microorganism of claim 34, wherein said recombinant nucleic acid molecule comprises a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system from a Thraustochytrid microorganism;

b. a nucleic acid sequence encoding at least one domain of a PUFA PKS system from a microorganism identified by the following method;

(i) selecting a microorganism that produces at least one PUFA; and

,

(ii) identifying a microorganism from (i) that has an ability to produce increased PUFAs under dissolved oxygen conditions of less than about 5% of saturation in the fermentation medium, as compared to production of PUFAs by said microorganism under dissolved oxygen conditions of greater than about 5% of saturation in the fermentation medium;

c. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, and biologically active fragments thereof;

d. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32, and biologically active fragments thereof;

e. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to at least 500 consecutive amino acids of said amino acid sequence of (a), wherein said amino acid sequence has a biological activity of at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system; and

f. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to said amino acid sequence of (b), wherein said amino acid sequence has a biological activity of at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system.

36. The genetically modified microorganism of claim 35, wherein said Thraustochytrid of (a) is from a genus selected from the group consisting of Schizochytrium and Thraustochytrium.

37. The genetically modified microorganism of claim 35, wherein said recombinant nucleic acid molecule comprises a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence that is at least about 70% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. a nucleic acid sequence encoding an amino acid sequence that is at least about 70% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

38. The genetically modified microorganism of claim 35, wherein said recombinant nucleic acid molecule comprises a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence that is at least about 80% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. a nucleic acid sequence encoding an amino acid sequence that is at least about 80% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

39. The genetically modified microorganism of claim 35, wherein said recombinant nucleic acid molecule comprises a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence that is at least about 90% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. a nucleic acid sequence encoding an amino acid sequence that is at least about 90% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

40. The genetically modified microorganism of claim 35, wherein said recombinant nucleic acid molecule comprises a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of:

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32 and biologically active fragments thereof.

41. The genetically modified microorganism of claim 34, wherein said microorganism has been further genetically modified to recombinantly express at least one nucleic acid molecule encoding at least one biologically active domain from a bacterial PUFA PKS system.

42. The genetically modified microorganism of claim 34, wherein said microorganism has been further genetically modified to recombinantly express at least one biologically active domain of a PKS system from a Type I PKS system.

43. The genetically modified microorganism of claim 34, wherein said microorganism has been further genetically modified to recombinantly express at least one biologically active domain of a PKS system from a Type II PKS system.

44. The genetically modified microorganism of claim 34, wherein said microorganism has been further genetically modified to recombinantly express at least one biologically active domain of a PKS system from a modular PKS system.

46. The genetically modified plant of claim 45, wherein said nucleic acid sequence is selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence that is at least about 70% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. a nucleic acid sequence encoding an amino acid sequence that is at least about 70% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

47. The genetically modified plant of claim 45, wherein said nucleic acid sequence is selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence that is at least about 80% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. a nucleic acid sequence encoding an amino acid sequence that is at least about 80% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

48. The genetically modified plant of claim 45, wherein said nucleic acid sequence is selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence that is at least about 90% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. a nucleic acid sequence encoding an amino acid sequence that is at least about 90% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

49. The genetically modified plant of claim 45, wherein said nucleic acid sequence encodes an amino acid sequence selected from the group consisting of:

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32 and biologically active fragments thereof.

50. The genetically modified plant of claim 45, wherein said Thraustochytrid of (a) is from a genus selected from the group consisting of Schizochytrium and Thraustochytrium.

51. The genetically modified plant of claim 45, wherein said plant has been further genetically modified to recombinantly express at least one nucleic acid molecule encoding at least one biologically active domain from a bacterial PUFA PKS system.

52. The genetically modified plant of claim 45, wherein said plant has been further genetically modified to recombinantly express at least one biologically active domain of a PKS system from a Type I PKS system.

53. The genetically modified plant of claim 45, wherein said plant has been further genetically modified to recombinantly express at least one biologically active domain of a PKS system from a Type II PKS system.

54. The genetically modified plant of claim 45, wherein said plant has been further genetically modified to recombinantly express at least one biologically active domain of a PKS system from a modular PKS system.

45. A genetically modified plant, wherein said plant has been genetically modified to recombinantly express a PKS system comprising at least one biologically active domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system, wherein said domain is encoded by a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system from a Thraustochytrid microorganism;

b. a nucleic acid sequence encoding at least one domain of a PUFA PKS system from a microorganism identified by the following method;

(i) selecting a microorganism that produces at least one PUFA; and

,

(ii) identifying a microorganism from (i) that has an ability to produce increased PUFAs under dissolved oxygen conditions of less than about 5% of saturation in the fermentation medium, as compared to production of PUFAs by said microorganism under dissolved oxygen conditions of greater than about 5% of saturation in the fermentation medium;

c. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, and biologically active fragments thereof;

d. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32, and biologically active fragments thereof;

e. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

f. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

55. A method to identify a microorganism that has a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system, comprising:

a. selecting a microorganism that produces at least one PUFA; and

,

b. identifying a microorganism from (a) that has an ability to produce increased PUFAs under dissolved oxygen conditions of less than about 5% of saturation in the fermentation medium, as compared to production of PUFAs by said microorganism under dissolved oxygen conditions of greater than about 5% of saturation in the fermentation medium;

wherein a microorganism that produces at least one PUFA and has an ability to produce increased PUFAs under dissolved oxygen conditions of less than about 5% of saturation is identified as a candidate for containing a PUFA PKS system.

56. The method of claim 55, wherein step (b) comprises identifying a microorganism from (a) that has an ability to produce increased PUFAs under dissolved oxygen conditions of less than about 2% of saturation.

57. The method of claim 55, wherein step (b) comprises identifying a microorganism from (a) that has an ability to produce increased PUFAs under dissolved oxygen conditions of less than about 1% of saturation.

58. The method of claim 55, wherein step (b) comprises identifying a microorganism from (a) that has an ability to produce increased PUFAs under dissolved oxygen conditions of about 0% of saturation.

59. The method of claim 55, wherein said microorganism selected in (a) has an ability to consume bacteria by phagocytosis.

60. The method of claim 55, wherein said microorganism selected in (a) has a simple fatty acid profile.

61. The method of claim 55, wherein said microorganism selected in (a) is a non-bacterial microorganism.

62. The method of claim 55, wherein said microorganism selected in (a) is a eukaryote.

63. The method of claim 55, wherein said microorganism selected in (a) is a member of the order Thraustochytriales.

64. The method of claim 55, wherein said microorganism selected in (a) has an ability to produce PUFAs at a temperature greater than about 15°

C.

65. The method of claim 55, wherein said microorganism selected in (a) has an ability to produce PUFAs at a temperature of greater than about 20°

C.

66. The method of claim 55, wherein said microorganism selected in (a) has an ability to produce PUFAs at a temperature of greater than about 25°

C.

67. The method of claim 55, wherein said microorganism selected in (a) has an ability to produce PUFAs at a temperature of greater than about 30°

C.

68. The method of claim 55, wherein said microorganism selected in (a) has an ability to produce bioactive compounds of interest at greater than about 5% of the dry weight of the organism.

69. The method of claim 55, wherein said microorganism selected in (a) has an ability to produce bioactive compounds of interest at greater than about 10% of the dry weight of the organism.

71. The method of claim 55, wherein said microorganism selected in (a) contains greater than about 40% of its total fatty acids as C14:

0, C16;

0 and C16;

1 while also producing at least one long chain fatty acid with three or more unsaturated bonds.

72. The method of claim 55, wherein said microorganism selected in (a) contains greater than about 30% of its total fatty acids as C14:

0, C16;

0 and C16;

1 while also producing at least one long chain fatty acid with four or more unsaturated bonds.

73. The method of claim 55, wherein said microorganism selected in (a) contains greater than about 30% of its total fatty acids as C14:

0, C16;

0 and C16;

1 while also producing at least one long chain fatty acid with five or more unsaturated bonds.

74. The method of claim 55, further comprising:

a. detecting whether said organism comprises a PUFA PKS system.

75. The method of claim 74, wherein said step of detecting comprises detecting a nucleic acid sequence in said microorganism that hybridizes under stringent conditions with a nucleic acid sequence encoding an amino acid sequence from a Thraustochytrid PUFA PKS system.

76. The method of claim 74, wherein said step of detecting comprises detecting a nucleic acid sequence in said organism that is amplified by oligonucleotide primers from a nucleic acid sequence from a Thraustochytrid PUFA PKS system.

77. A microorganism identified by the method of claim 55 and being genetically modified to regulate the production of molecules by said PUFA PKS system.

79. The method of claim 78, wherein said Thraustochytrid of (a) is from a genus selected from the group consisting of Thraustochytrium and Schizochytrium.

80. The method of claim 78, wherein said Thraustochytrid of (a) is Thraustochytrium sp. 23B (ATCC 20892).

81. The method of claim 78, wherein said Thraustochytrid of (a) is Schizochytrium sp. SR21.

82. The method of claim 78, wherein said Thraustochytrid of (a) is Schizochytrium strain ATCC 20888.

83. The method of claim 78, wherein said Thraustochytrid of (a) is Schizochytrium limacium (IFO 32693).

84. The method of claim 78, wherein said Thraustochytrid of(a) is Ulkenia (BP-5601).

85. The method of claim 78, wherein said nucleic acid sequence is selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence that is at least about 70% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. a nucleic acid sequence encoding an amino acid sequence that is at least about 70% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

86. The method of claim 78, wherein said nucleic acid sequence is selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence that is at least about 80% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. a nucleic acid sequence encoding an amino acid sequence that is at least about 80% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

87. The method of claim 78, wherein said nucleic acid sequence is selected from the group consisting of:

a. a nucleic acid sequence encoding an amino acid sequence that is at least about 90% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

b. a nucleic acid sequence encoding an amino acid sequence that is at least about 90% identical to an amino acid sequence selected from the group consisting of . SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

88. The method of claim 78, wherein said nucleic acid sequence encodes an amino acid sequence selected from the group consisting of:

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, SEQ ID NO;

8, SEQ ID NO;

I0, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32 and biologically active fragments thereof.

89. The method of claim 78, wherein said organism endogenously expresses a PKS system comprising said at least one domain of said PUFA PKS system, and wherein said genetic modification is in a nucleic acid sequence encoding said at least one domain of said PUFA PKS system.

90. The method of claim 89, wherein said genetic modification changes at least one product produced by said endogenous PKS system, as compared to a wild-type organism.

91. The method of claim 78, wherein said organism endogenously expresses a PKS system comprising said at least one biologically active domain of said PUFA PKS system, and wherein said genetic modification comprises transfection of said organism with a recombinant nucleic acid molecule selected from the group consisting of:

a recombinant nucleic acid molecule encoding at least one biologically active domain from a second PKS system and a recombinant nucleic acid molecule encoding a protein that affects the activity of said PUFA PKS system.

92. The method of claim 91, wherein said genetic modification changes at least one product produced by said endogenous PKS system, as compared to a wild-type organism.

93. The method of claim 78, wherein said organism is genetically modified by transfection with a recombinant nucleic acid molecule encoding said at least one domain of said polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system.

94. The method of claim 78, wherein the organism produces a polyunsaturated fatty acid (PUFA) profile that differs from the naturally occurring organism without a genetic modification.

95. The method of claim 78, wherein said organism endogenously expresses a non-bacterial PUFA PKS system, and wherein said genetic modification comprises substitution of a domain from a different PKS system for a nucleic acid sequence encoding at least one domain of said non-bacterial PUFA PKS system.

96. The method of claim 78, wherein said organism endogenously expresses a non-bacterial PUFA PKS system that has been modified by transfecting said organism with a recombinant nucleic acid molecule encoding a protein that regulates the chain length of fatty acids produced by said PUFA PKS system.

97. The method of claim 96, wherein said recombinant nucleic acid molecule encoding a protein that regulates the chain length of fatty acids replaces a nucleic acid sequence encoding a chain length factor in said non-bacterial PUFA PKS system.

98. The method of claim 96, wherein said protein that regulates the chain length of fatty acids produced by said PUFA PKS system is a chain length factor.

99. The method of claim 96, wherein said protein that regulates the chain length of fatty acids produced by said PUFA PKS system is a chain length factor that directs the synthesis of C20 units.

100. The method of claim 96, wherein said organism expresses a non-bacterial PUFA PKS system comprising a genetic modification in a domain selected from the group consisting of a domain encoding FabA-like β

-hydroxy acyl-ACP dehydrase (DH) domain and a domain encoding β

-ketoacyl-ACP synthase (KS), wherein said modification alters the ratio of long chain fatty acids produced by said PUFA PKS system as compared to in the absence of said modification.

101. The method of claim 100, wherein said modification comprises substituting a DH domain that does not possess isomerization activity for a FabA-like β

-hydroxy acyl-ACP dehydrase (DH) in said non-bacterial PUFA PKS system.

102. The method of claim 100, wherein said modification is selected from the group consisting of a deletion of all or a part of said domain, a substitution of a homologous domain from a different organism for said domain, and a mutation of said domain.

103. The method of claim 96, wherein said organism expresses a non-PUFA PKS system and wherein said genetic modification comprises substituting a FabA-like β

-hydroxy acyl-ACP dehydrase (DH) domain from a PUFA PKS system for a DH domain that does not posses isomerization activity.

104. The method of claim 78, wherein said organism expresses a non-bacterial PUFA PKS system comprising a modification in an enoyl-ACP reductase (ER) domain, wherein said modification results in the production of a different compound as compared to in the absence of said modification.

105. The method of claim 104, wherein said modification is selected from the group consisting of a deletion of all or a part of said ER domain, a substitution of an ER domain from a different organism for said ER domain, and a mutation of said ER domain.

106. The method of claim 78, wherein said bioactive molecule is selected from the group consisting of:

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.

107. The method of claim 78, wherein said bioactive molecule is an antibiotic.

108. The method of claim 78, wherein said bioactive molecule is a polyunsaturated fatty acid (PUFA).

109. The method of claim 78, wherein said bioactive molecule is a molecule including carbon—

carbon double bonds in the cis configuration.

110. The method of claim 78, wherein said bioactive molecule is a molecule including a double bond at every third carbon.

111. The method of claim 78, wherein said organism is a microorganism.

112. The method of claim 78, wherein said organism is a plant.

116. The method of claim 115, wherein said pharmaceutical formulation is selected from the group consisting of 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.

117. The method of claim 114, wherein said endproduct 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.

121. The recombinant host cell of claim 120, wherein said PUFA PKS system is a eukaryotic PUFA PKS system.

122. The recombinant host cell of claim 120, wherein said PUFA PKS system is an algal PUFA PKS system.

123. The recombinant host cell of claim 120, wherein said PUFA PKS system is a Thraustochytriales PUFA PKS system.

124. The recombinant host cell of claim 120, wherein said PUFA PKS system is a Schizochytrium PUFA PKS system.

125. The recombinant host cell of claim 120, wherein said PUFA PKS system is a Thraustochytrium PUFA PKS system.

126. The recombinant host cell of claim 120, wherein said PUFA PKS system can be expressed in a prokaryotic host cell.

127. The recombinant host cell of claim 120, wherein said PUFA PKS system can be expressed in a eukaryotic host cell.

128. The recombinant host cell of claim 120, wherein said host cell is a plant cell.

129. A method to produce a product containing at least one PUFA, comprising growing a plant comprising the plant cell of claim 128 under conditions effective to produce said product.

130. The recombinant host cell of claim 120, wherein said host cell is a microbial cell.

131. A method to produce a product containing at least one PUFA, comprising culturing a culture containing said microbial cell of claim 130 under conditions effective to produce said product.

132. The recombinant host cell of claim 120, wherein said PKS system catalyzes the direct production of triglycerides.

134. The genetically modified microorganism of claim 133, wherein said microorganism is a eukaryotic microorganism.

78. A method to produce a bioactive molecule that is produced by a polyketide synthase system, comprising culturing under conditions effective to produce said bioactive molecule a genetically modified organism that expresses a PKS system comprising at least one biologically active domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system, wherein said at least one domain of said PUFA PKS system is encoded by a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system from a Thraustochytrid microorganism;

b. a nucleic acid sequence encoding at least one domain of a PUFA PKS system from a microorganism identified by the following method;

(i) selecting a microorganism that produces at least one PUFA; and

,

(ii) identifying a microorganism from (i) that has an ability to produce increased PUFAs under dissolved oxygen conditions of less than about 5% of saturation in the fermentation medium, as compared to production of PUFAs by said microorganism under dissolved oxygen conditions of greater than about 5% of saturation in the fermentation medium;

c. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, and biologically active fragments thereof;

d. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32, and biologically active fragments thereof;

e. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

f. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system;

wherein said organism is genetically modified to affect the activity of said PKS system.

113. A method to produce a plant that has a polyunsaturated fatty acid (PUFA) profile that differs from the naturally occurring plant, comprising genetically modifying cells of said plant to express a PKS system comprising at least one recombinant nucleic acid molecule comprising a nucleic acid sequence encoding at least one biologically active domain of a PUFA PKS system, wherein said at least one domain of said PUFA PKS system is encoded by a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system from a Thraustochytrid microorganism;

b. a nucleic acid sequence encoding at least one domain of a PUFA PKS system from a microorganism identified by the following method;

(i) selecting a microorganism that produces at least one PUFA; and

,

(ii) identifying a microorganism from (i) that has an ability to produce increased PUFAs under dissolved oxygen conditions of less than about 5% of saturation in the fermentation medium, as compared to production of PUFAs by said microorganism under dissolved oxygen conditions of greater than about 5% of saturation in the fermentation medium;

c. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, and biologically active fragments thereof;

d. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32, and biologically active fragments thereof;

e. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

f. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

114. A method to modify an endproduct containing at least one fatty acid, comprising adding to said endproduct an oil produced by a recombinant host cell that expresses at least one recombinant nucleic acid molecule comprising a nucleic acid sequence encoding at least one biologically active domain of a PUFA PKS system, wherein said at least one domain of a PUFA PKS system is encoded by a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system from a Thraustochytrid microorganism;

b. a nucleic acid sequence encoding at least one domain of a PUFA PKS system from a microorganism identified by the following method;

(i) selecting a microorganism that produces at least one PUFA; and

,

(ii) identifying a microorganism from (i) that has an ability to produce increased PUFAs under dissolved oxygen conditions of less than about 5% of saturation in the fermentation medium, as compared to production of PUFAs by said microorganism under dissolved oxygen conditions of greater than about 5% of saturation in the fermentation medium;

c. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, and biologically active fragments thereof;

d. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32, and biologically active fragments thereof;

e. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

f. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

118. A method to produce a humanized animal milk, comprising genetically modifying milk-producing cells of a milk-producing animal with at least one recombinant nucleic acid molecule comprising a nucleic acid sequence encoding at least one biologically active domain of a PUFA PKS system, wherein said at least one domain of said PUFA PKS system is encoded by a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system from a Thraustochytrid microorganism;

b. a nucleic acid sequence encoding at least one domain of a PUFA PKS system from a microorganism identified by the following method;

(i) selecting a microorganism that produces at least one PUFA; and

,

(ii) identifying a microorganism from (i) that has an ability to produce increased PUFAs under dissolved oxygen conditions of less than about 5% of saturation in the fermentation medium, as compared to production of PUFAs by said microorganism under dissolved oxygen conditions of greater than about 5% of saturation in the fermentation medium;

c. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, and biologically active fragments thereof;

d. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32, and biologically active fragments thereof;

e. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

f. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

119. A method to produce a recombinant microbe, comprising genetically modifying microbial cells to express at least one recombinant nucleic acid molecule comprising a comprising a nucleic acid sequence encoding at least one biologically active domain of a PUFA PKS system, wherein said at least one domain of said PUFA PKS system is encoded by a nucleic acid sequence selected from the group consisting of:

a. a nucleic acid sequence encoding at least one domain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system from a Thraustochytrid microorganism;

b. a nucleic acid sequence encoding at least one domain of a PUFA PKS system from a microorganism identified by the following method;

(i) selecting a microorganism that produces at least one PUFA; and

,

(ii) identifying a microorganism from (i) that has an ability to produce increased PUFAs under dissolved oxygen conditions of less than about 5% of saturation in the fermentation medium, as compared to production of PUFAs by said microorganism under dissolved oxygen conditions of greater than about 5% of saturation in the fermentation medium;

c. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, SEQ ID NO;

6, and biologically active fragments thereof;

d. a nucleic acid sequence encoding an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, SEQ ID NO;

32, and biologically active fragments thereof;

e. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to at least 500 consecutive amino acids of an amino acid sequence selected from the group consisting of;

SEQ ID NO;

2, SEQ ID NO;

4, and SEQ ID NO;

6;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system; and

,

f. a nucleic acid sequence encoding an amino acid sequence that is at least about 60% identical to an amino acid sequence selected from the group consisting of;

SEQ ID NO;

8, SEQ ID NO;

10, SEQ ID NO;

13, SEQ ID NO;

18, SEQ ID NO;

20, SEQ ID NO;

22, SEQ ID NO;

24, SEQ ID NO;

26, SEQ ID NO;

28, SEQ ID NO;

30, and SEQ ID NO;

32;

wherein said amino acid sequence has a biological activity of at least one domain of a PUFA PKS system.

120. A recombinant host cell which has been modified to express a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system, wherein said PKS catalyzes both iterative and non-iterative enzymatic reactions, and wherein said PUFA PKS system comprises:

a. at least two enoyl ACP-reductase (ER) domains;

b. at least six acyl carrier protein (ACP) domains;

c. at least two β

-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 β

-hydroxy acyl-ACP dehydrase (DH) domains;

g. at least one chain length factor (CLF) domain; and

h. at least one malonyl-CoA;

ACP acyltransferase (MAT) domain.

133. A genetically modified microorganism comprising a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system, wherein said PKS catalyzes both iterative and non-iterative enzymatic reactions, and wherein said PUFA PKS system comprises:

a. at least two enoyl ACP-reductase (ER) domains;

b. at least six acyl carrier protein (ACP) domains;

c. at least two β

-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 β

-hydroxy acyl-ACP dehydrase (DH) domains;

g. at least one chain length factor (CLF) domain; and

h. at least one malonyl-CoA;

ACP acyltransferase (MAT) domain;

wherein the genetic modification affects the activity of said PUFA PKS system.

135. A recombinant host cell which has been modified to express a non-bacterial polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system, wherein said non-bacterial PUFA PKS catalyzes both iterative and non-iterative enzymatic reactions, and wherein said non-bacterial PUFA PKS system comprises:

a. at least one enoyl ACP-reductase (ER) domain;

b. multiple acyl carrier protein (ACP) domains;

c. at least two β

-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 β

-hydroxy acyl-ACP dehydrase (DH) domains;

g. at least one chain length factor (CLF) domain; and

h. at least one malonyl-CoA;

ACP acyltransferase (MAT) domain.