Production of carotenoids in oleaginous yeast and fungi

• US 7,851,199 B2
• Filed: 03/20/2006
• Issued: 12/14/2010
• Est. Priority Date: 03/18/2005
• Status: Active Grant

• Current Assignee: DSM IP Assets BV (DSM-Firmenich AG)
• Original Assignee: Microbia, Inc. (DSM-Firmenich AG)
• Inventors: Bailey, Richard, Trueheart, Joshua, Madden, Kevin T.
• Primary Examiner(s): Joike; Michele J
• Application Number:
  US11/385,580
• Publication Number:
  US 20070015237A1
• Time in Patent Office: 1,730 Days
• Field of Search: None
• US Class Current: 435/254.2
• CPC Class Codes: A23L 31/00 Edible extracts or preparations of fungi; Preparation or treatment thereof
• CPC Class Codes: A23L 31/10 Yeasts or derivatives thereof
• CPC Class Codes: A61P 1/16 for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
• CPC Class Codes: A61P 11/06 Antiasthmatics
• CPC Class Codes: A61P 13/12 of the kidneys
• CPC Class Codes: A61P 17/00 Drugs for dermatological disorders
• CPC Class Codes: A61P 27/02 Ophthalmic agents
• CPC Class Codes: A61P 29/00 Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
• CPC Class Codes: A61P 3/00 Drugs for disorders of the metabolism of the blood or the extracellular fluid A61P7/00
• CPC Class Codes: A61P 3/06 Antihyperlipidemics
• CPC Class Codes: A61P 3/10 for hyperglycaemia, e.g. antidiabetics
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 35/04 specific for metastasis
• CPC Class Codes: A61P 37/08 Antiallergic agents antiasthmatic agents A61P11/06; ophthalmic antiallergics A61P27/14
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: A61P 7/02 Antithrombotic agents; Anticoagulants; Platelet aggregation inhibitors
• CPC Class Codes: A61P 9/04 Inotropic agents, i.e. stimulants of cardiac contraction; Drugs for heart failure
• CPC Class Codes: A61P 9/10 for treating ischaemic or atherosclerotic diseases, e.g. antianginal drugs, coronary vasodilators, drugs for myocardial infarction, retinopathy, cerebrovascula insufficiency, renal arteriosclerosis
• CPC Class Codes: A61P 9/12 Antihypertensives
• CPC Class Codes: C12N 15/80 for fungi
• CPC Class Codes: C12P 23/00 : Preparation of compounds containing a cyclohexene ring having an unsaturated side chain containing at least ten carbon atoms bound by conjugated double bonds, e.g. carotenes containing heterorings C12P17/00

Abstract

The present invention provides systems for producing engineered oleaginous yeast or fungi that express carotenoids.

Claims

1. A genetically engineered Yarrowia fungus characterized by:

a. the fungus is oleaginous in that it can accumulate lipid to at least 20% of its dry cell weight; and

b. as a result of genetic engineering, the Yarrowia fungus produces at least one carotenoid, and can accumulate the produced carotenoid to at least 1% of its dry cell weight.

2. The Yarrowia fungus of claim 1 wherein the Yarrowia fungus is a strain of Yarrowia lipolytica.

3. The Yarrowia fungus of claim 1 wherein the fungus contains at least one oleaginic modification.

4. The Yarrowia fungus of claim 3 wherein the at least one oleaginic modification alters oleaginicity of the fungus.

5. The Yarrowia fungus of claim 3 wherein the fungus further comprises more than one carotenogenic modification.

6. The Yarrowia fungus of claim 3 wherein the at least one oleaginic modification increases expression or activity of at least one oleaginic polypeptide.

7. The Yarrowia fungus of claim 3, wherein the at least one oleaginic modification decreases expression or activity of at least one oleaginic polypeptide.

8. The Yarrowia fungus of claim 3, wherein the at least one oleaginic modification increases expression or activity of at least one oleaginic polypeptide and decreases expression or activity of at least one other oleaginic polypeptide.

9. The Yarrowia fungus of claim 6 or 7, wherein the at least one oleaginic polypeptide is selected from the group consisting of acetyl-CoA carboxylase polypeptide, pyruvate decarboxylase polypeptide, isocitrate dehydrogenase polypeptide, ATP-citrate lyase polypeptide, malic enzyme polypeptide, AMP deaminase polypeptide, and combinations thereof.

10. The Yarrowia fungus of claim 6 or 7 wherein the least one oleaginic polypeptide is at least one polypeptide selected from the group consisting of a polypeptide in any one of Tables 1 through 6.

11. The Yarrowia fungus of any one of claims 6-8, wherein the at least one oleaginic modification comprises expression of at least one heterologous oleaginic polypeptide in the fungus.

12. The Yarrowia fungus of claim 11, wherein the at least one oleaginic modification comprises expression of at least one heterologous gene encoding the at least one heterologous oleaginic polypeptide.

13. The Yarrowia fungus of claim 11, wherein the at least one heterologous oleaginic polypeptide comprises an animal polypeptide, a mammalian polypeptide, an insect polypeptide, a plant polypeptide, a fungal polypeptide, a yeast polypeptide, an algal polypeptide, a bacterial polypeptide, a cyanobacterial polypeptide, an archaebacterial polypeptide, or a protozoal polypeptide.

14. The Yarrowia fungus of claim 11, wherein the at least one heterologous oleaginic polypeptide comprises at least two heterologous oleaginic polypeptides.

15. The Yarrowia fungus of claim 14, wherein the at least two heterologous oleaginic polypeptides are from a single source organism.

16. The Yarrowia fungus of claim 14, wherein the at least two heterologous oleaginic polypeptides are from at least two different source organisms.

17. The Yarrowia fungus of claim 1 wherein the fungus contains more than one carotenogenic modification.

18. The Yarrowia fungus of claim 17 wherein the carotenogenic modifications confers to the fungus the ability to produce the at least one carotenoid to a level at least 1% of its dry cell weight.

19. The Yarrowia fungus of claim 17 wherein the carotenogenic modifications confers to the fungus the ability to produce at least one carotenoid which the fungus does not naturally produce.

20. The Yarrowia fungus of claim 17 wherein the fungus further comprises at least one oleaginic modification wherein the oleaginic modification alters oleaginicity of the fungus.

21. The Yarrowia fungus of claim 17, wherein the carotenogenic modifications confer the ability to the fungus to produce the at least one carotenoid to a level selected from the group consisting of at least 2%, at least 3%, at least 5%, and at least 10% of the fungus'"'"' dry cell weight.

22. The Yarrowia fungus of claim 17, wherein the carotenoids are selected from the group consisting of astaxanthin, β

-carotene, canthaxanthin, zeaxanthin, lutein, lycopene, and combinations thereof.

23. The Yarrowia fungus of claim 17 wherein the predominant type of carotenoid is astaxanthin.

24. The Yarrowia fungus of claim 17, wherein at least one of the carotenogenic modifications increases expression or activity of a carotenogenic polypeptide.

25. The Yarrowia fungus of claim 17, wherein at least one of the carotenogenic modifications decreases expression or activity of a carotenogenic polypeptide.

26. The Yarrowia fungus of claim 17, wherein at least one of the carotenogenic modifications increases expression or activity of at least one carotenogenic polypeptide and decreases expression or activity of at least one other carotenogenic polypeptide.

27. The Yarrowia fungus of any one of claims 24-26, wherein the carotenogenic modifications comprises expression of at least one heterologous carotenogenic polypeptide.

28. The Yarrowia fungus of claim 27 wherein the carotenogenic modifications comprises expression of at least one heterologous gene encoding the at least one heterologous carotenogenic polypeptide.

29. The Yarrowia fungus of claim 24 or 25, wherein the carotenogenic polypeptide is selected from the group consisting of:

isoprenoid biosynthesis polypeptides, carotenoid biosynthesis polypeptides, isoprenoid biosynthesis competitor polypeptides, and combinations thereof.

30. The Yarrowia fungus of claim 29 wherein the isoprenoid biosynthesis polypeptides are selected from the group consisting of:

acetoacetyl-CoA thiolase polypeptide, HMG-CoA synthase polypeptide, HMG-CoA reductase polypeptide, mevalonate kinase polypeptide, phosphomevalonate kinase polypeptide, mevalonate pyrophosphate decarboxylase polypeptide, IPP isomerase polypeptide, FPP synthase polypeptide, and GGPP synthase polypeptide.

31. The Yarrowia fungus of claim 29, wherein the carotenoid biosynthesis polypeptides are selected from the group consisting of:

phytoene synthase polypeptide, phytoene dehydrogenase polypeptide, lycopene cyclase polypeptide, carotenoid ketolase polypeptide, carotenoid hydroxylase polypeptide, astaxanthin synthase polypeptide, carotenoid epsilon hydroxylase polypeptide, carotenoid glucosyltransferase polypeptide, lycopene cyclase (beta and epsilon subunits) polypeptides, and acyl CoA;

diacyglycerol acyltransferase polypeptide.

32. The Yarrowia fungus of claim 29, wherein the isoprenoid biosynthesis competitor polypeptides are selected from the group consisting of squalene synthase polypeptide, prenyldiphosphate synthase and PHB polyprenyltransferase.

33. The Yarrowia fungus of claim 29, wherein the carotenogenic polypeptide is selected from the group consisting of any of the polypeptides of any one of Tables 7-25, Table 29, and Table 30, and combinations thereof.

34. The Yarrowia fungus of any one of claims 24-26, wherein the carotenogenic modifications comprises an animal polypeptide, a mammalian polypeptide, an insect polypeptide, a plant polypeptide, a fungal polypeptide, a yeast polypeptide, an algal polypeptide, a bacterial polypeptide, cyanobacterial polypeptide, an archaebacterial polypeptide, or a protozoal polypeptide.

35. TheYarrowia fungus of any one of claims 24-26, wherein the carotenogenic modifications comprises at least two heterologous carotenogenic polypeptides.

36. The Yarrowia fungus of claim 35, wherein the at least two heterologous carotenogenic polypeptides are from a single source organism.

37. The Yarrowia fungus of claim 35, wherein the at least two heterologous carotenogenic polypeptides are from at least two different source organisms.

38. A Yarrowia fungus according to claim 1 wherein the Yarrowia fungus accumulates the produced at least one carotenoid to a level selected from the group consisting of:

above 1%, above 2%, above 3%, above 5%, and above 10% of the fungus'"'"' dry cell weight.

39. A Yarrowia fungus according to claim 1 characterized in that the Yarrowia fungus accumulates lipid in the form of cytoplasmic bodies.

40. The Yarowia fungus of claim 39 wherein the at least one carotenoid accumulates in the cytoplasmic oil bodies.

48. A method of producing a carotenoid, the method comprising steps of:

a. cultivating the fungus of claim 1 under conditions that allow production of the carotenoid;

b. and isolating the produced carotenoid.

49. The method of claim 48, wherein the step of isolating comprises fractionating the cultivation medium to obtain at least one carotenoid-enriched fraction.

50. The method of claim 48, wherein:

the step of cultivating comprises cultivating the fungus under conditions that allow accumulation of the carotenoid in cytoplasmic oil bodies; and

the step of isolating comprises isolating oil derived from the cytoplasmic oil bodies.

51. The method of claim 48, wherein the carotenoid is selected from the group consisting of astaxanthin, β

-carotene, canthaxanthin, zeaxanthin, lutein, lycopene, and combinations thereof.

52. The method of claim 48, wherein the carotenoid comprises astaxanthin.

53. A method of preparing a food or feed additive containing a carotenoid, the method comprising steps of:

a. cultivating the fungus of claim 1 under conditions that allow production of the carotenoid;

b. isolating the carotenoid; and

c. combining the isolated carotenoid with one or more other food or feed additive components.

41. A strain of Yarrowia lipolytica comprising one or more modifications selected from the group consisting of an oleaginic modification, a carotenogenic modification, and combinations thereof, such that the strain accumulates from 1% to 10% of its dry cell weight as at least one carotenoid.

42. The strain of claim 41 further characterized in that it accumulates from 20% to 50% of its dry cell weight as lipid.

43. The strain of claim 42, wherein the strain accumulates from 20% to 50% of its dry cell weight as lipid in the form of cytoplasmic oil bodies.

44. The strain of claim 41, wherein the strain comprises a carotenogenic modification selected from the group consisting of:

a. expression of a polypeptide selected from a group consisting of a truncated endogenous HMG CoA reductase polypeptide that lacks the N-terminal membrane spanning domain, acetoacetyl-CoA thiolase, HMG-CoA synthase, FPP synthase, and GGPP synthase;

b. expression of a heterologous polypeptide selected from the group consisting of phytoene synthase, phytoene desaturase, lycopene cyclase, carotenoid ketolase, carotenoid hydroxylase, and combinations thereof.

45. The strain of any one of claims 41-44, wherein the strain accumulates 1-10% of its dry cell weight as β

-carotene.

46. The strain of claim 41, wherein the strain comprises a carotenogenic modification selected from the group consisting of:

a. expression of a polypeptide selected from a group consisting of a truncated endogenous HMG CoA reductase polypeptide that lacks the N-terminal membrane spanning domain, acetoacetyl-CoA thiolase, HMG-CoA synthase, FPP synthase, and GGPP synthase;

b. expression of a heterologous polypeptide selected from the group consisting of phytoene synthase, phytoene desaturase, lycopene cyclase, carotenoid ketolase, carotenoid hydroxylase, astaxanthin synthase, carotenoid epsilon hydroxylase, lycopene cyclase (beta and epsilon subunits), carotenoid glucosyltransferase, acyl CoA;

diacyglycerol acyltransferase, and combinations thereof.

47. The strain of any one of claim 41-43 or 46, wherein the strain accumulates 1-10% of its dry cell weight as astaxanthin or lutein.