Production of steviol glycoside in recombinant hosts

1. A recombinant host cell capable of producing a steviol glycoside, a glycosylated ent-kaurenol compound, and/or a glycosylated ent-kaurenoic acid compound in a cell culture, comprising a gene encoding a polypeptide capable of selectively converting rubusoside to stevioside and having 95% or greater sequence identity to the amino acid sequence set forth in SEQ ID NO:17 or 18 and a first gene encoding a first polypeptide capable of beta 1,2 glycosylation of the C2′ of the 13-O-glucose, 19-O-glucose, or both 13-O-glucose and 19-O-glucose of the steviol glycoside and having 95% or greater sequence identity to the amino acid sequence set forth in SEQ ID NO:16; wherein the recombinant host cell further comprises one or more of:

(a) a second gene encoding a second polypeptide capable of beta 1,2 glycosylation of the C2′ of the 13-O-glucose, 19-O-glucose, or both 13-O-glucose and 19-O-glucose of the steviol glycoside,

having 95% or greater sequence identity to the amino acid sequence set forth in SEQ ID NO:11;

(b) a gene encoding a polypeptide capable of glycosylating steviol or the steviol glycoside at its C-13 hydroxyl group

having 95% or greater sequence identity to the amino acid sequence set forth in SEQ ID NO:7; and

(c) a gene encoding a polypeptide capable of beta 1,3 glycosylation of the C3′ of the 13-O-glucose, 19-O-glucose, or both 13-O-glucose and 19-O-glucose of the steviol glycoside

having 95% or greater sequence identity to the amino acid sequence set forth in SEQ ID NO:9; or

(d) a gene encoding a polypeptide capable of glycosylating steviol or a steviol glycoside at its C-19 carboxyl group, wherein the polypeptide comprises a polypeptide having 95% or greater sequence identity to the amino acid sequence set forth in SEQ ID NO:4;

wherein at least one of the genes is a recombinant gene.

2. The recombinant host cell of claim 1 , wherein the second polypeptide capable of beta 1,2 glycosylation of the C2′ of the 13-O-glucose, 19-O-glucose, or both 13-O-glucose and 19-O-glucose of the steviol glycoside comprises a polypeptide having one or more amino acid substitutions of residues 93, 99, 114, 144, 148, 152, 195, 196, 199, 211, 213, 221, 286, 384, 426, 438, or 466 of SEQ ID NO:11 or at least one amino acid substitution of SEQ ID NO:11 that is P93V, S991, S114F, T144K, T144L, T144M, A148K, M152T, L195G, L195C, L195S, L195N, L195V, V196P, K199C, L211H, L211M, L211I, L211C, L211T, L213E, S221I, V286C, V286N, V286S, G384W, G384K, G384Y, E426G, E438H, E438M, or A466V.

3. The recombinant host cell of claim 1 , wherein the polypeptide capable of glycosylating steviol or the steviol glycoside at its C-13 hydroxyl group comprises a polypeptide having one or more amino acid substitutions of residues 21, 48, 49, 84, 86, 87, 91, 92, 95, 122, or 334 of SEQ ID NO:7 or at least one amino acid substitution of SEQ ID NO:7 that is Q21L, Q21T, Q21V, F48S, F48H, F48Y, F48R, F48Q, F48W, F48T, 149V, S84G, S84A, S84T, S84C, S84P, S84N, S84V, P86R, P86G, 187H, 187P, 187M, 187Y, L91K, L91R, L91T, L92F, L921, L92M, 195K, F122S, L334S, or L334M.

4. The recombinant host cell of claim 1 , wherein the polypeptide capable of beta 1,3 glycosylation of the C3′ of the 13-O-glucose, 19-O-glucose, or both 13-O-glucose and 19-O-glucose of the steviol glycoside comprises a polypeptide having one or more amino acid substitutions of residues 23, 26, 55, 146, 257, 283, and 337 of SEQ ID NO:9 or at least one amino acid substitution of SEQ ID NO:9 that is Q23H, I26W, T146G, H155L, L257G, S253W, T284G, S283N, K337P, or T55K.

5. The recombinant host cell of claim 1 , further comprising:

(a) a gene encoding a polypeptide capable of synthesizing geranylgeranyl pyrophosphate (GGPP) from farnesyl diphosphate (FPP) and isopentenyl diphosphate (IPP)

having 95% or greater sequence identity to the amino acid sequence set forth in any one of SEQ ID NOs:20, 22, 24, 26, 28, 30, 32, or 116;

(b) a gene encoding a polypeptide capable of synthesizing ent-copalyl diphosphate from GGPP,

having 95% or greater sequence identity to the amino acid sequence set forth in any one of SEQ ID NOs:34, 36, 38, 40, or 42;

(c) a gene encoding a polypeptide capable of synthesizing ent-kaurene from ent-copalyl diphosphate

having 95% or greater sequence identity to the amino acid sequence set forth in any one of SEQ ID NOs:44, 46, 48, 50, or 52;

(d) a gene encoding a polypeptide capable of synthesizing ent-kaurenoic acid from ent-kaurene

having 95% or greater sequence identity to the amino acid sequence set forth in any one of SEQ ID NOs:60, 62, 66, 68, 70, 72, 74, 76, or 117;

(e) a gene encoding a polypeptide capable of reducing cytochrome P450 complex

having 95% or greater sequence identity to the amino acid sequence set forth in any one of SEQ ID NOs:78, 80, 82, 84, 86, 88, 90, 92; and

(f) a gene encoding a polypeptide capable of synthesizing steviol from ent-kaurenoic acid

having 95% or greater sequence identity to the amino acid sequence set forth in any one of SEQ ID NOs:94, 97, 100-104, 106, 108, 110, 112, or 114;

wherein at least one of the genes is a recombinant gene.

6. The recombinant host cell of claim 1 , wherein the cell culture comprises:

(a) the steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound produced by the recombinant host cell,

(b) glucose, fructose, sucrose, xylose, rhamnose, UDP-glucose, UDP-rhamnose, UDP-xylose, and/or N-acetyl-glucosamine; and

(c) supplemental nutrients comprising trace metals, vitamins, salts, yeast nitrogen base (YNB), and/or amino acids.

7. The recombinant host cell of claim 1 , wherein the recombinant host is a plant cell, a mammalian cell, an insect cell, a fungal cell, an algal cell, or a bacterial cell.

8. The recombinant host cell of claim 7 , wherein the bacterial cell is an Escherichia bacteria cell, a Lactobacillus bacteria cell, a Lactococcus bacteria cell, a Cornebacterium bacteria cell, an Acetobacter bacteria cell, an Acinetobacter bacteria cell, or a Pseudomonas bacterial cells.

9. The recombinant host cell of claim 7 , wherein the fungal cell comprises a yeast cell.

10. The recombinant host cell of claim 9 , wherein the yeast cell is a cell from Saccharomyces cerevisiae, Schizosaccharomyces pombe, Yarrowia lipolytica, Candida glabrata, Ashbya gossypii, Cyberlindnera jadinii, Pichia pastoris, Kluyveromyces lactis, Hansenula polymorpha, Candida boidinii, Arxula adeninivorans, Xanthophyllomyces dendrorhous , or Candida albicans species.

11. The recombinant host cell of claim 10 , wherein the yeast cell is a Saccharomycete.

12. The recombinant host cell of claim 11 , wherein the yeast cell is a cell from the Saccharomyces cerevisiae species.

13. A method of producing a steviol glycoside, a glycosylated ent-kaurenol compound, and/or a glycosylated ent-kaurenoic acid compound in a cell culture, comprising culturing the recombinant host cell of claim 1 in the cell culture, under conditions in which the genes are expressed; and

wherein the steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound is produced by the recombinant host cell.

14. The method of claim 13 , wherein the genes are constitutively expressed.

15. The method of claim 13 , wherein the recombinant host cell is grown in a fermentor at a temperature for a period of time, wherein the temperature and the period of time facilitate the production of the steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound.

16. The method of claim 13 , further comprising isolating the steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound, alone or in combination from the cell culture.

17. The method of claim 16 , wherein the isolating step comprises separating a liquid phase of the cell culture from a solid phase of the cell culture to obtain a supernatant comprising the produced steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound, and:

(a) contacting the supernatant with one or more adsorbent resins in order to obtain at least a portion of the produced steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound; or

(b) contacting the supernatant with one or more ion exchange or reversed-phase chromatography columns in order to obtain at least a portion of the produced steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound; or

(c) crystallizing or extracting the produced steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound;

thereby isolating the produced steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound.

18. The method of claim 13 , further comprising recovering the steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound alone or in combination from the cell culture.

19. The method of claim 18 , wherein the recovered steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound or a combination thereof is enriched for the steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound relative to a steviol glycoside composition of Stevia plant and has a reduced level of Stevia plant-derived components relative to a steviol glycoside composition obtained from a plant-derived Stevia extract.

20. The method of claim 13 , wherein the cell culture comprises:

(a) the steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound produced by the recombinant host cell,

(b) glucose, fructose, sucrose, xylose, rhamnose, UDP-glucose, UDP-rhamnose, UDP-xylose, and/or N-acetyl-glucosamine; and

(c) supplemental nutrients comprising trace metals, vitamins, salts, YNB, and/or amino acids.

21. The method of claim 13 , wherein the recombinant host cell is a plant cell, a mammalian cell, an insect cell, a fungal cell, an algal cell, or a bacterial cell.

22. The method of claim 21 , wherein the bacterial cell comprises Escherichia bacteria cells, Lactobacillus bacteria cells, Lactococcus bacteria cells, Cornebacterium bacteria cells, Acetobacter bacteria cells, Acinetobacter bacteria cells, or Pseudomonas bacterial cells.

23. The method of claim 21 , wherein the fungal cell comprises a yeast cell.

24. The method of claim 23 , wherein the yeast cell is a cell from Saccharomyces cerevisiae, Schizosaccharomyces pombe, Yarrowia lipolytica, Candida glabrata, Ashbya gossypii, Cyberlindnera jadinii, Pichia pastoris, Kluyveromyces lactis, Hansenula polymorpha, Candida boidinii, Arxula adeninivorans, Xanthophyllomyces dendrorhous , or Candida albicans species.

25. The method of claim 23 , wherein the yeast cell is a Saccharomycete.

26. The method of claim 25 , wherein the yeast cell is a cell from the Saccharomyces cerevisiae species.

27. The recombinant host cell of claim 1 , wherein:

(a) the steviol glycoside comprises steviol-13-O-glucoside (13-SMG), steviol-19-O-glucoside (19-SMG), steviol-1,2-bioside, steviol-1,3-bioside, 1,2-stevioside, 1,3-stevioside, rubusoside, Rebaudioside A (RebA), Rebaudioside B (RebB), Rebaudioside D (RebD), Rebaudioside E (RebE), Rebaudioside M (RebM), a di-glycosylated steviol, a tri-glycosylated steviol, a tetra-glycosylated steviol, a penta-glycosylated steviol, a hexa-glycosylated steviol, a hepta-glycosylated steviol, and/or isomers thereof;

(b) the glycosylated ent-kaurenol compound comprises di-glycosylated ent-kaurenol, tri-glycosylated ent-kaurenol, and/or isomers thereof; and

(c) the glycosylated ent-kaurenoic acid compound comprises di-glycosylated ent-kaurenoic acid, tri-glycosylated ent-kaurenoic acid, and/or isomers thereof.

28. The recombinant host cell of claim 27 , wherein:

(a) the di-glycosylated steviol comprises compound 2.23 of Table 1;

(b) the tri-glycosylated steviol comprises compound 3.1 and/or compound 3.34 of Table 1;

(c) the tetra-glycosylated steviol comprises compound 4.26 and/or compound 4.33 of Table 1;

(d) the penta-glycosylated steviol comprises compound 5.22, compound 5.24, and/or compound 5.25 of Table 1;

(e) the hexa-glycosylated steviol comprises compound 6.1 and/or compound 6.23 of Table 1;

(f) the hepta-glycosylated steviol comprises compound 7.2, compound 7.5, and/or compound 7.13 of Table 1;

(g) the glycosylated ent-kaurenoic acid compound comprises compound KA3.1, compound KA3.2, and/or compound KA2.7 of Table 1; and

(h) the glycosylated ent-kaurenol compound comprises compound KL2.8 and/or compound KL3.1 co-eluted with compound KL3.6 of Table 1.

29. The recombinant host cell of claim 28 , wherein:

(a) compound 4.26 has the structure:

(b) compound 5.22 has the structure:

(c) compound 6.1 has the structure:

(d) compound 7.2 has the structure:

(e) compound 7.5 has the structure:

(f) compound KA3.1 has the structure:

(g) compound KA3.2 has the structure:

and

(h) compound KL3.1 has the structure:

30. A cell culture, comprising the recombinant host cell of claim 1 , the cell culture further comprising:

(a) the steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound produced by the recombinant host cell;

(b) glucose, fructose, sucrose, xylose, rhamnose, UDP-glucose, UDP-rhamnose, UDP-xylose, and/or N-acetyl-glucosamine; and

(c) supplemental nutrients comprising trace metals, vitamins, salts, YNB, and/or amino acids;

wherein the steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound are present at a concentration of at least 1 mg/liter of the cell culture;

wherein the cell culture is enriched for the steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound relative to a steviol glycoside composition from a Stevia plant and has a reduced level of Stevia plant-derived components relative to a plant-derived Stevia extract.

31. A cell lysate from the recombinant host cell of claim 1 grown in the cell culture, comprising:

(a) the steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound produced by the recombinant host cell;

(b) glucose, fructose, sucrose, xylose, rhamnose, UDP-glucose, UDP-rhamnose, UDP-xylose, and/or N-acetyl-glucosamine; and

(c) supplemental nutrients comprising trace metals, vitamins, salts, yeast nitrogen base, YNB, and/or amino acids;

wherein the steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound produced by the recombinant host cell is present at a concentration of at least 1 mg/liter of the cell culture.

32. The recombinant host cell of claim 1 , wherein the recombinant host cell is a Yarrowia lipolytica cell.

33. The method of claim 13 , wherein the expression of the genes is induced.

34. The recombinant host cell of claim 1 , wherein the total amount of the steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid compound produced by the recombinant host cell is by at least about 5%, at least about 10%, at least about 25%, at least about 50%, at least about 75%, or at least about 100% relative to a corresponding host lacking the one or more recombinant genes.

35. The recombinant host cell of claim 1 , wherein expression of the one or more recombinant genes increases the amount of the steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid, accumulated by the cell by at least about 5%, at least about 10%, at least about 25%, at least about 50%, at least about 75%, or at least about 100% relative to a corresponding host lacking the one or more recombinant genes.

36. The recombinant host cell of claim 1 , wherein expression of the one or more recombinant genes decreases the amount of the steviol glycoside, the glycosylated ent-kaurenol compound, and/or the glycosylated ent-kaurenoic acid, accumulated by the cell by at least about 5%, at least about 10%, at least about 25%, at least about 50%, at least about 75%, or at least about 100% relative to a corresponding host lacking the one or more recombinant genes.