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Definitions

• This disclosure relates to recombinant production of steviol glycosides and stevioi glycoside precursors in recombinant hosts.
• this disclosure relates to production of steviol glycosides comprising steviol-13-O-glucoside (13-SMG), steviol-1 ,2-bioside, steviol-1 , 3- bioside, steviol-19-O-glucoside (19-SMG), stevioside, 1 ,3-stevioside, rubusoside, Rebaudioside A (RebA), Rebaudioside B (RebB), Rebaudioside C (RebC), Rebaudioside D (RebD), Rebaudioside E (RebE), Rebaudioside F (RebF), Rebaudioside M (RebM), Rebaudioside Q (RebQ), Rebaudioside I (Rebl), dulcoside A, or isomers thereof in recombinant hosts.
• Sweeteners are well known as ingredients used most commonly in the food, beverage, or confectionary industries.
• the sweetener can either be incorporated into a final food product during production or for stand-alone use, when appropriately diluted, as a tabletop sweetener or an at-home replacement for sugars in baking.
• Sweeteners include natural sweeteners such as sucrose, high fructose com syrup, molasses, maple syrup, and honey and artificial sweeteners such as aspartame, saccharine, and sucralose.
• Stevia extract is a natural sweetener that can be isolated and extracted from a perennial shrub, Stevia rebaudiana. Stevia is commonly grown in South America and Asia for commercial production of stevia extract. Stevia extract, purified to various degrees, is used commercially as a high intensity sweetener in foods and in blends or alone as a tabletop sweetener.
• Extracts of the Stevia plant generally comprise steviol glycosides that contribute to the sweet flavor, although the amount of each steviol glycoside often varies, inter alia, among different production batches.
• the recombinant host is capable of producing a steviol glycoside precursor.
• the invention also provides a recombinant host comprising:
• GGPPS geranylgeranyl diphosphate synthase
• CDPS ent-copalyl diphosphate synthase
• the recombinant host is capable of producing stevioi.
• the KO polypeptide comprises a KO polypeptide having at least 60% identity to an amino acid sequence set forth in SEQ ID NO:72 or SEQ ID NO:75; 65% identity to an amino acid sequence set forth in SEQ ID NO:54; at least 70% identity to an amino acid sequence set forth in SED ID NO: 70, SEQ ID NO:71 , or SEQ ID NO: 79; at least 40% identity to an amino acid sequence set forth in SEQ ID NO:77; or at least 50% identity to an amino acid sequence set forth in SEQ ID NO:78;
• the CPR polypeptide comprises a CPR polypeptide having at least 70% identity to an amino acid sequences set forth in SEQ ID NO:69, SEQ ID NO:74, SEQ ID N0.76, or SEQ ID NO:87; at least 80% identity to an amino acid sequence set forth in SEQ ID NO;73; at least 85% identity to an amino acid sequence set forth in SEQ ID NO:22; at least 65% identity to an amino acid sequence set forth in SEQ ID NO:28; or at least 50% identity to an amino acid sequence set forth in SEQ ID NO:98; and/or
• the KAH polypeptide comprises a KAH polypeptide having at least 40% identity to an amino acid sequence set forth in SEQ ID NO:82; at least 50% identity to an amino acid sequence set forth in SEQ ID NO:91 ; or at least 60% identity to an amino acid sequence set forth in SEQ ID NO:68.
• the invention further provides a recombinant host comprising one or more of:
• the recombinant host is capable of producing a steviol glycoside precursor.
• the invention further provides a recombinant host comprising one or more of:
• At least one of the genes is a recombinant gene; and wherein the recombinant host is capable of producing a steviol glycoside precursor.
• the host further comprises a gene encoding a KO polypeptide having at least 65% identity to an amino acid sequence set forth in SEQ ID NO:54.
• the recombinant host further comprises a gene encoding a KAH polypeptide having at least 60% identity to an amino acid sequence set forth in SEQ ID NO:68.
• the recombinant host further comprises a gene encoding a KO polypeptide having at least 70% identity to an amino acid sequence set forth in SEQ ID NO:79,
• the host further comprises one or more of:
• GGPPS geranylgeranyl diphosphate synthase
• CDPS ent-copalyl diphosphate synthase
• the recombinant host is capable of producing a steviol glycoside precursor.
• the GGPPS polypeptide comprises a polypeptide having at least 70% identity to an amino acid sequence set forth in SEQ ID NO:49;
• the CDPS polypeptide comprises a polypeptide having at least 70% identity to an amino acid sequence set forth in SEQ ID NO:37;
• the KS polypeptide comprises a polypeptide having at least 40% identity to an amino acid sequence set forth in SEQ ID NO:6.
• the recombinant host further comprises a gene encoding an endoplasmic reticulum membrane polypeptide.
• the endoplasmic reticulum membrane polypeptide comprises an Inheritance of cortical ER protein 2 (ICE2) polypeptide having at least 50% identity to the amino acid sequence set forth in SEQ ID NO:114.
• ICE2 cortical ER protein 2
• the KO polypeptide is a fusion construct.
• the fusion construct comprises a polypeptide having at least 60% identity to an amino acid sequence set forth in SEQ ID NO:118 or SEQ ID NO:120.
• the fusion construct has at least 50% identity to an amino acid sequence set forth in SEQ ID NO:100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NO:110, or SEQ ID NO:112.
• the host further comprises one or more of:
• the host is capable of producing a stevio! glycoside.
• the UGT85C2 polypeptide comprises a polypeptide having at least 55% identity to an amino acid sequence set forth in SEQ ID NO:30;
• the UGT76G1 polypeptide comprises a polypeptide having at least 50% identity to an amino acid sequence set forth in SEQ ID NO:83;
• the UGT74G1 polypeptide comprises a polypeptide having at least 55% identity to an amino acid sequence set forth in SEQ ID NO:29;
• the UGT91 D2 functional homolog polypeptide comprises a UGT91 D2 polypeptide having 90% or greater identity to the amino acid sequence set forth in SEQ ID NO:84 or a UGT91 D2e-b polypeptide having 90% or greater identity to the amino acid sequence set forth in SEQ ID NO:88; and/or (e) the EUGT11 polypeptide comprises a polypeptide having at least 65% identity to an amino acid sequence set forth in SEQ ID NO:86.
• the recombinant hosts disclosed herein comprise a plant cell, a mammalian cell, an insect cell, a fungal cell, or a bacterial cell.
• the bacterial cell comprises Escherichia bacteria cells, for example, Escherichia coli cells; Lactobacillus bacteria cells; Lactococcus bacteria cells; Cornebacterium bacteria cells; Acetobacter bacteria cells; Acinetobacter bacteria cells; or Pseudomonas bacterial cells.
• Escherichia bacteria cells for example, Escherichia coli cells; Lactobacillus bacteria cells; Lactococcus bacteria cells; Cornebacterium bacteria cells; Acetobacter bacteria cells; Acinetobacter bacteria cells; or Pseudomonas bacterial cells.
• the fungal cell comprises a yeast cell.
• the yeast cell is a cell from Saccharomyces cerevisiae, Schizosaccharomyces pombe, Yarrowia lipolytica, Candida glabrata, Ash by a gossypii, Cyberlindnera jadinii, Pichia pastoris, Kluyveromyces lactis, Hansenula polymorpha, Candida boidinii, Arxula adeninivorans, Xanthophyllomyces dendrorhous, or Candida albicans species.
• the yeast ceil is a Saccharomycete.
• the yeast cell is a cell from the Saccharomyces cerevisiae species.
• the invention further provides a method of producing a steviol glycoside or a steviol glycoside precursor, comprising:
• the steviol glycoside comprises steviol-13-O-glucoside (13-SMG), steviol-1 ,2-bioside, steviol-1 ,3-bioside, steviol-19-Oglucoside (19-SMG), stevioside, 1 ,3- stevioside, rubusoside, Rebaudioside A (RebA), Rebaudioside B (RebB), Rebaudioside C (RebC), Rebaudioside D (RebD), Rebaudioside E (RebE), Rebaudioside F (RebF), Rebaudioside M (RebM), Rebaudioside Q (RebQ), Rebaudioside I (Rebi), dulcoside A, di- glycosylated steviol, tri-glycosylated steviol, tetra-glycosylated steviol, penta-glycosylated steviol, hexa-glycosyiated steviol, hepta-glycosylated steviol, or iso
• the steviol glycoside or steviol glycoside precursor produced by the recombinant hosts or methods disclosed herein accumulates to a detectable concentration when cultured under said conditions.
• the steviol glycoside or steviol glycoside precursor produced by the recombinant hosts or methods disclosed herein has an undetectable concentration of stevia plant-derived contaminants.
• the steviol glycoside or steviol glycoside precursor produced by the recombinant hosts or methods disclosed herein has a steviol glycoside composition enriched for RebD or RebM relative to the steviol glycoside composition of a wild-type Stevia plant.
• Figure 1 shows a schematic of the engineered biosynthetic pathway for producing steviol in yeast from geranylgeranyl diphosphate using geranylgeranyl diphosphate synthase (GGPPS), ent-copalyl diphosphate synthase (CDPS), ent-kaurene synthase (KS), ent-kaurene oxidase (KO), and ent-kaurenoic acid hydroxylase (KAH) polypeptides.
• GGPPS geranylgeranyl diphosphate synthase
• CDPS ent-copalyl diphosphate synthase
• KS ent-kaurene synthase
• KO ent-kaurene oxidase
• KAH ent-kaurenoic acid hydroxylase
• Figure 2 shows representative steviol glycoside glycosylation reactions catalyzed by suitable uridine S'-diphospho (UDP) glycosyi transferases (UGT) enzymes and chemical structures for several steviol glycoside compounds.
• UDP uridine S'-diphospho
• UHT glycosyi transferases
• FIG. 3 shows Rebaudioside B (RebB) production in a steviol glycoside-producing S. cerevisiae strain individually expressing S. rebaudiana K01 (SrKOI ) encoded by the nucleotide sequence set forth in SEQ ID NO:59, the KO encoded by the codon-optimized nucleotide sequence set forth in SEQ ID NO:55, or the KO encoded by the nucleotide sequence set forth in SEQ ID NO:56.
• RebB production was measured by liquid chromatography-mass spectrometry (LC-MS) analysis as ⁇ /OD 600 of individual cultures. See Example 3.
• LC-MS liquid chromatography-mass spectrometry
• Figure 4 shows production of ent-kaurenoic acid in steviol glycoside-producing S. cerevisiae strains individually expressing SrKOI encoded by the nucleotide sequence set forth in SEQ ID NO:59, the KO encoded by the codon-optimized nucleotide sequence set forth in SEQ ID NO:55, or the KO encoded by the nucleotide sequence set forth in SEQ ID NO:56, as measured by LC-MS analysis of culture samples.
• Ent-kaurenoic acid levels were calculated as the Area under Curve (AUC) of LC-MS peaks corresponding to ent-kaurenoic acid. See Example 3.
• AUC Area under Curve
• Figure 5 shows production of total (extracellular plus intracellular) steviol glycosides in a steviol glycoside-producing S. cerevisiae strain overexpressing S. rebaudiana KAHel (SrKAHel ; encoded by the nucleotide sequence set forth in SEQ ID NO; 18) or in a steviol glycoside-producing S.
• SrKAHel cerevisiae stain co-expressing SrKAHel (encoded by the nucleotide sequence set forth in SEQ ID NO: 18) and a KO encoded by the nucleotide sequences set forth in any one of SEQ ID NOs: 55-60, compared to a control strain that does not overexpress SrKAHel or express a KO encoded by the nucleotide sequence set forth in any one of SEQ ID NOs: 55-60.
• Production of total steviol glycosides was quantified by comparision to a standard curve. Values plotted on the y-axis in ⁇ are an average of three biological replicates. See Example 4.
• FIG. 6 shows production of Rebaudioside A (RebA), Rebaudioside D (RebD), and Rebaudioside M (RebM) in a steviol glycoside-producing S. cerevisiae strain overexpressing SrKAHel (encoded by the nucleotide sequence set forth in SEQ ID NO:18) and further expressing either the KO encoded by the nucleotide sequence set forth in SEQ ID NO:56 or the KO encoded by the nucleotide sequence set forth in SEQ ID NO:65.
• Production of RebA + RebD + RebM was measured in ⁇ . See Example 4.
• Figure 7 shows production of glycosylated ent-kaurenoic acid in a steviol glycoside- producing S. cerevisiae strain overexpressing SrKAHel (encoded by the nucleotide sequence set forth in SEQ ID NO: 18) or in a steviol glycoside-producing strain coexpressing SrKAHel (encoded by the nucleotide sequence set forth in SEQ ID NO: 18) and a KO encoded by the nucleotide sequences set forth in any one of SEQ ID NOs: 55-60). Values were calculated as the AUC of LC-MS peaks corresponding to glycosylated ent-kaurenoic acid and as an average of three biological replicates. See Example 4.
• Figure 8 shows production of glycosylated ent-kaurenol in a steviol glycoside- producing S. cerevisiae strain overexpressing SrKAHel (encoded by the nucleotide sequence set forth in SEQ ID NO:18) or in a steviol glycoside-producing S. cerevisiae strain co-expressing SrKAHel (encoded by the nucleotide sequence set forth in SEQ ID NO:18) and a KO encoded by the nucleotide sequence set forth in SEQ ID NOs: 55-60).
• Values plotted on the y-axis were calculated as the AUC of LC-MS peaks corresponding to glycosylated ent-kaurenol. See Example 4.
• Figure 9 shows Rebaudioside IVf (RebM) production in a steviol glycoside-producing S. cerevisiae strain expressing CPR1 (encoded by the codon-optimized nucleotide sequence set forth in SEQ ID NO:61 ) or CPR7 (encoded by the nucleotide sequence set forth in SEQ ID NO:23). Values plotted on the y-axis were measured in ⁇ . See Example 5.
• FIG 10 shows Rebaudioside M (RebM) production in a steviol glycoside-producing S. cerevisiae strain overexpressing SrKAHel (encoded by the codon-optimized nucleotide sequence set forth in SEQ ID NO:18) and further expressing CPR4497 encoded by the nucleotide sequence set forth in SEQ ID NO;62. Values plotted on the y-axis indicate ⁇ concentration of RebM. See Example 5.
• Figure 11A shows an LC-MS chromatogram of a steviol-13-O-glucoside (13-SMG) standard.
• Figure 11 B shows production of 13-SMG by a steviol glycoside-producing S. cerevisiae strain expressing the KAH encoded by the nucleotide sequence set forth in SEQ ID NO:80 (amino acid sequence set forth in SEQ ID NO:82). See Example 7.
• Figure 12 shows steviol-13-O-glucoside (13-SMG) and Rebaudioside B (RebB) production in a steviol glycoside-producing S. cerevisiae strain co-expressing a KO and a CPR.
• the KO was selected from SrKOI (encoded by the codon-optimized nucleotide sequence set forth in SEQ ID NO:59), the KO encoded by the codon-optimized nucleotide sequence set forth in SEQ ID NO:63, or the KO encoded by the codon-optimized nucleotide sequence set forth in SEQ ID NO:64.
• the cytochrome P450 reductase (CPR) polypeptide was selected from the CPR encoded by the codon-optimized nucleotide sequence set forth in SEQ ID NO:66 or the CPR encoded by the codon-optimized nucleotide sequence set forth in SEQ ID NO:67. Values displayed on the y-axis are ⁇ concentrations of the indicated steviol glycosides. See Example 6.
• Figure 13 shows production of steviol-13-O-glucoside (13-SMG) and rubusoside in a steviol glycoside-producing S. cerevisiae strain expressing SrKAHel (encoded by the nucleotide sequence set forth in SEQ ID NO: 18), the KAH encoded by the nucleotide sequence set forth in SEQ ID NO:80, or the KAH encoded by the codon-optimized nucleotide sequence set forth in SEQ ID NO:81.
• Values displayed in the y-axis are ⁇ concentrations of 13-SMG and rubusoside, averaged over eight biological replicates and normalized to OD 600 measured using a plate reader. Error bars are ⁇ the respective standard deviation. See Example 7.
• Figure 14 shows cytochrome P450 reductase (CPR) polypeptide activity on cytochrome c upon incubation with microsomal protein prepared from S. cerevisiae strains expressing SrKAHel (encoded by the nucleotide sequence set forth in SEQ ID NO:18) alone or in combination with CPR1 (encoded by the nucleotide sequence set forth in SEQ ID NO:61 ) or CPR12 (encoded by the nucleotide sequence set forth in SEQ ID NO:97). Results are shown in U/mg as an average of two biological replicates. See Example 9.
• CPR cytochrome P450 reductase
• Figure 15A shows steviol accumulation upon 30 min incubation of ent-kaurenoic acid with microsomal protein prepared from S. cerevisiae strains expressing SrKAHel (encoded by the nucleotide sequence set forth in SEQ ID NO: 18) alone or in combination with CPR1 (encoded by the nucleotide sequence set forth in SEQ ID NO:61 ) or CPR12 (encoded by the nucleotide sequence set forth in SEQ ID NO:97). Results are shown in AUC as an average of three biological replicates. Control reactions comprised the microsomal protein described above, but these were not incubated for 30 min prior to measurement of steviol accumulation.
• Figure 15B shows levels of ent-kaurenoic acid following 30 min incubation of ent-kaurenoic acid with microsomal protein prepared from S. cerevisiae strains expressing SrKAHel (encoded by the nucleotide sequence set forth in SEQ ID NO:18) alone or in combination with CPR1 (encoded by the nucleotide sequence set forth in SEQ ID NO:61 ) or CPR12 (encoded by the nucleotide sequence set forth in SEQ ID NO:97). Results are shown in ⁇ as an average of three biological replicates. Control reactions comprised the microsomal protein described above but were not incubated for 30 min prior to measurement of ent-kaurenoic acid levels. See Example 9.
• Figure 16 shows steviol-13-O-glucoside (13-SMG), 1 ,2-bioside, Rebaudioside B (RebB), ent-kaurenoic acid, and ent-kaurene levels accumulated by a steviol glycoside- producing S.
• FIG. 16A shows levels of 13-SMG, 1 ,2-bioside, and RebB measured by LC-MS for a steviol glycoside-producing S.
• SrKOI cerevisiae strain expressing SrKOI (SEQ ID NO:59, SEQ ID NO:79), a fusion construct of SrKOI and BMR (SEQ ID NO:99, SEQ ID NO:100), a fusion construct of SrKOI and BMR W 1046 A (SEQ ID NO:101 , SEQ ID NO:102), a fusion construct of truncated SrKOI and BMR (SEQ ID NO: 103, SEQ ID NO:104), a fusion construct of truncated SrKOI and BMR W1046A (SEQ ID ⁇ . ⁇ 05, SEQ ID NO:106), or a control plasmid.
• SrKOI cerevisiae strain expressing SrKOI (SEQ ID NO:59, SEQ ID NO:79), a fusion construct of SrKOI and BMR (SEQ ID NO:99, SEQ ID NO:100), a fusion construct of SrKOI and BMR W 1046 A (S
• Figure 16B shows levels of ent-kaurenoic acid and ent-kaurene measured by LC-UV for a steviol glycoside- producing S. cerevisiae strain expressing SrKOI (SEQ ID NO:59, SEQ ID NO:79), a fusion construct of SrKOI and BMR (SEQ ID NO:99, SEQ ID NO: 100), a fusion construct of SrKOI and BMR W 1046 A (SEQ ID NO:101 , SEQ ID NO:102), a fusion construct of truncated SrKOI and BMR (SEQ ID NO:103, SEQ ID NO:104), a fusion construct of truncated SrKOI and BMR W1046A (SEQ ID NO:105, SEQ ID NO:106), or a control plasmid.
• SrKOI SEQ ID NO:59, SEQ ID NO:79
• SrKOI and BMR SEQ ID NO:99, SEQ ID NO: 100
• Figure 16C shows levels of 13-SMG, 1 ,2-bioside, and RebB measured by LC-MS for a steviol glycoside-producing S. cerevisiae strain expressing the KO encoded by the nucleotide sequence set forth in SEQ ID NO:65, a fusion construct of the KO encoded by the nucleotide sequence set forth in SEQ ID NO:65 and BMR (SEQ ID NO:107, SEQ ID NO:108), a fusion construct of the KO encoded by the nucleotide sequence set forth in SEQ ID NO:65 and BMR W1046A (SEQ ID NO: 109, SEQ ID NO:110), a fusion construct of a truncated KO encoded by the nucleotide sequence set forth in SEQ ID NO:65 and BMR W1046A (SEQ ID NO:111 , SEQ ID NO:112), or a plasmid control.
• Figure 16D shows levels of ent-kaurenoic acid or ent-kaurene accumulated by a steviol glycoside-producing S, cerevisiae strain expressing the KO encoded by the nucleotide sequence set forth in SEQ ID NO:65, a fusion construct of the KO encoded by the nucleotide sequence set forth in SEQ ID NO:65 and BMR (SEQ ID NO:107, SEQ ID NO:108), a fusion construct of the KO encoded by the nucleotide sequence set forth in SEQ ID NO:65 and BMR W 1046 A (SEQ ID NO:109, SEQ ID NO:110), a fusion construct of a truncated KO encoded by the nucleotide sequence set forth in SEQ ID NO:65 and BMR W1046A (SEQ ID NO:11 1 , SEQ ID NO:112), or a plasmid control. See Example 10.
• nucleic acid means one or more nucleic acids.
• terms like "preferably,” “commonly,” and “typically” are not utilized herein to limit the scope of the claimed invention or to imply that certain features are critical, essential, or even important to the structure or function of the claimed invention. Rather, these terms are merely intended to highlight alternative or additional features that can or cannot be utilized in a particular embodiment of the present invention.
• Methods well known to those skilled in the art can be used to construct genetic expression constructs and recombinant cells according to this invention. These methods include in vitro recombinant DNA techniques, synthetic techniques, in vivo recombination techniques, and polymerase chain reaction (PGR) techniques.
• PGR polymerase chain reaction
• nucleic acid can be used interchangeably to refer to nucleic acid comprising DNA, RNA, derivatives thereof, or combinations thereof.
• the terms "microorganism,” “microorganism host,” “microorganism host cell,” “recombinant host,” and “recombinant host cell” can be used interchangeably.
• the term “recombinant host” is intended to refer to a host, the genome of which has been augmented by at ieast one DNA sequence. Such DNA sequences include but are not limited to genes that are not naturally present, DNA sequences that are not normally transcribed into RNA or translated into a protein (“expressed"), and other genes or DNA sequences which one desires to introduce into a host. It will be appreciated that typically the genome of a recombinant host described herein is augmented through stable introduction of one or more recombinant genes.
• introduced DNA is not originally resident in the host that is the recipient of the DNA, but it is within the scope of this disclosure to isolate a DNA segment from a given host, and to subsequently introduce one or more additional copies of that DNA into the same host, e.g., to enhance production of the product of a gene or alter the expression pattern of a gene, in some instances, the introduced DNA will modify or even replace an endogenous gene or DNA sequence by, e.g., homologous recombination or site-directed mutagenesis.
• Suitable recombinant hosts include microorganisms.
• recombinant gene refers to a gene or DNA sequence that is introduced into a recipient host, regardless of whether the same or a similar gene or DNA sequence may already be present in such a host. "Introduced,” or “augmented” in this context, is known in the art to mean introduced or augmented by the hand of man.
• a recombinant gene can be a DNA sequence from another species or can be a DNA sequence that originated from or is present in the same species but has been incorporated into a host by recombinant methods to form a recombinant host.
• a recombinant gene that is introduced into a host can be identical to a DNA sequence that is normally present in the host being transformed, and is introduced to provide one or more additional copies of the DNA to thereby permit overexpression or modified expression of the gene product of that DNA.
• said recombinant genes are encoded by cDNA.
• recombinant genes are synthetic and/or codon-optimized for expression in S. cerevisiae.
• engineered biosynthetic pathway refers to a biosynthetic pathway that occurs in a recombinant host, as described herein. In some aspects, one or more steps of the biosynthetic pathway do not naturally occur in an unmodified host. In some embodiments, a heterologous version of a gene is introduced into a host that comprises an endogenous version of the gene.
• the term "endogenous" gene refers to a gene that originates from and is produced or synthesized within a particular organism, tissue, or cell.
• the endogenous gene is a yeast gene.
• the gene is endogenous to S. cerevisiae, including, but not limited to S. cerevisiae strain S288C.
• an endogenous yeast gene is overexpressed.
• the term “overexpress” is used to refer to the expression of a gene in an organism at levels higher than the level of gene expression in a wild type organism. See, e.g., Prelich, 2012, Genetics 190:841-54.
• an endogenous yeast gene is deleted. See, e.g., Giaever & Nislow, 2014, Genetics 197(2):451-65.
• the terms “deletion,” “deleted,” “knockout,” and “knocked out” can be used interchangabley to refer to an endogenous gene that has been manipulated to no longer be expressed in an organism, including, but not limited to, S. cerevisiae.
• heterologous sequence and “heterologous coding sequence” are used to describe a sequence derived from a species other than the recombinant host, in some embodiments, the recombinant host is an S. cerevisiae cell, and a heterologous sequence is derived from an organism other than S. cerevisiae.
• a heterologous coding sequence for example, can be from a prokaryotic microorganism, a eukaryotic microorganism, a plant, an animal, an insect, or a fungus different than the recombinant host expressing the heterologous sequence.
• a coding sequence is a sequence that is native to the host.
• a "selectable marker” can be one of any number of genes that complement host cell auxotrophy, provide antibiotic resistance, or result in a color change.
• Linearized DNA fragments of the gene replacement vector then are introduced into the cells using methods well known in the art (see below). Integration of the linear fragments into the genome and the disruption of the gene can be determined based on the selection marker and can be verified by, for example, PGR or Southern blot analysis. Subsequent to its use in selection, a selectable marker can be removed from the genome of the host cell by, e.g., Cre-LoxP systems (see, e.g., Gossen et a/., 2002, Ann. Rev. Genetics 36:153-173 and U.S.
• a gene replacement vector can be constructed in such a way as to include a portion of the gene to be disrupted, where the portion is devoid of any endogenous gene promoter sequence and encodes none, or an inactive fragment of, the coding sequence of the gene.
• variant and mutant are used to describe a protein sequence that has been modified at one or more amino acids, compared to the wild-type sequence of a particular protein.
• the term "inactive fragment” is a fragment of the gene that encodes a protein having, e.g., less than about 10% (e.g., less than about 9%, less than about 8%, less than about 7%, less than about 6%, less than about 5%, less than about 4%, less than about 3%, less than about 2%, less than about 1 %, or 0%) of the activity of the protein produced from the full-length coding sequence of the gene.
• Such a portion of a gene is inserted in a vector in such a way that no known promoter sequence is operably linked to the gene sequence, but that a stop codon and a transcription termination sequence are operably linked to the portion of the gene sequence.
• This vector can be subsequently linearized in the portion of the gene sequence and transformed into a cell. By way of single homologous recombination, this linearized vector is then integrated in the endogenous counterpart of the gene with inactivation thereof.
• the term "stevio! glycoside” refers to Rebaudioside A (RebA) (CAS # 58543-16-1 ), Rebaudioside B (RebB) (CAS # 58543-17-2), Rebaudioside C (RebC) (CAS # 63550-99-2), Rebaudioside D (RebD) (CAS # 63279-13-0), Rebaudioside E (RebE) (CAS # 63279-14-1 ), Rebaudioside F (RebF) (CAS # 438045-89-7), Rebaudioside M (RebM) (CAS # 1220616-44-3), Rubusoside (CAS # 63849-39-4), Dulcoside A (CAS # 64432-06-0), Rebaudioside I (Rebl) (MassBank Record: FU000332), Rebaudioside Q (RebQ), 1 ,2-Stevioside (CAS # 57817-89-7), 1 ,3-Stevioside (RebG), 1 ,2-bioside (MassBank Record: FU000
• steviol glycoside precursor and “steviol glycoside precursor compound” are used to refer to intermediate compounds in the steviol glycoside biosynthetic pathway.
• Steviol glycoside precursors include, but are not limited to, geranylgeranyl diphosphate (GGPP), ent-copalyl -diphosphate, ent-kaurene, ent-kaurenol, ent- kaurenai, ent-kaurenoic acid, and steviol. See Figure 1.
• steviol glycoside precursors are themselves steviol glycoside compounds.
• 19-SMG, rubusoside, stevioside, and RebE are steviol glycoside precursors of RebM. See Figure 2.
• Steviol glycosides and/or steviol glycoside precursors can be produced in vivo (i.e., in a recombinant host), in vitro (i.e., enzymatically), or by whole cell byconversion.
• produce and “accumulate” can be used interchangeably to describe synthesis of steviol glycosides and steviol glycoside precursors in vivo, in vitro, or by whole cell bioconversion.
• di-glycosylated steviol can be used to refer to a steviol molecule comprising two sugar moieties, such as glucose or N-acetylglucosamine (GicNAc).
• Di-glycosylated steviol molecules include steviol-1 ,3-bioside, steviol- 1 ,2-bioside, rubusoside, a steviol molecule comprising two glucose moieties, a steviol molecule comprising one glucose moiety and one GicNAc moiety, and isomers thereof.
• tri-glycosylated steviol can be used to refer to a steviol molecule comprising three sugar moieties, such as glucose or GicNAc.
• sugar moieties such as glucose or GicNAc.
• tri-glycosylated steviol molecules include RebB, RebG, stevioside, a steviol molecule comprising two glucose moieties and one GlcNAc moiety, and isomers thereof.
• tetra-glycosylated steviol can be used to refer to a steviol molecuie comprising four sugar moieties, such as glucose or GlcNAc.
• Non-limiting examples of tetra-glycosylated steviol molecules include RebA, RebE, RebQ, a steviol molecule comprising four glucose moieties, a steviol molecule comprising three glucose moieties and one GlcNAc moiety, and isomers thereof.
• penta-glycosylated steviol can be used to refer to a steviol molecule comprising five sugar moieties, such as glucose or GlcNAc.
• penta-glycosylated steviol molecules include RebD, a steviol molecule comprising five glucose moieties, a steviol molecule comprising four glucose moieties and one GlcNAc moiety, and isomers thereof.
• hexa-glycosyiated steviol can be used to refer to a steviol molecule comprising six sugar moieties, such as glucose or GlcNAc.
• Non-limiting examples of hexa-glycosylated steviol molecules include RebM, a steviol molecule comprising six glucose moieties, a steviol molecule comprising five glucose moieties and one GlcNAc moiety, and isomers thereof.
• hepta-glycosylated steviol can be used to refer to a steviol molecule comprising seven sugar moieties, such as glucose or GlcNAc.
• hepta-glycosylated steviol molecules include a steviol molecule comprising seven glucose moieties and isomers thereof.
• glycosylated ent-kaurenoic acid can be used to refer to an ent-kaurenoic acid molecule comprising sugar moieties, such as glucose or GlcNAc.
• Non- limiting examples of glycosylated ent-kaurenoic acid molecules include ent-kaurenoic acid molecule comprising two glucose moieties and one GlcNAc moiety, an ent-kaurenoic acid molecule comprising three glucose moieties, an ent-kaurenoic acid molecule comprising one glucose moiety and one GlcNAc moiety, an ent-kaurenoic acid molecule comprising two glucose moieties, and isomers thereof.
• glycosylated ent-kaurenol can be used to refer to an ent- kaurenol molecule comprising sugar moieties, such as glucose or GlcNAc.
• Non-limiting examples of glycosylated ent-kaurenol molecules include an ent-kaurenol molecule comprising three glucose moieties, an ent-kaurenol molecule comprising one glucose moiety and one GlcNAc moiety, an ent-kaureno! molecule comprising two glucose moieties, and isomers thereof.
• Recombinant steviol glycoside-producing Saccharomyces cerevisiae (S. cerevisiae) strains are described in WO 201 1/153378, WO 2013/022989, WO 2014/122227, and WO 2014/122328.
• Methods of producing steviol glycosides in recombinant hosts, by whole cell bio- conversion, and in vitro are also described in WO 2011/153378, WO 2013/022989, WO 2014/122227, and WO 2014/122328.
• steviol glycosides and/or steviol glycoside precursors are produced in vivo through expression of one or more enzymes involved in the steviol glycoside biosynthetic pathway in a recombinant host.
• a steviol-producing recombinant host expressing one or more of a gene encoding a GGPPS polypeptide, a gene encoding a CDPS polypeptide, a gene encoding a KS polypeptide, a gene encoding a KO polypeptide, a gene encoding a KAH polypeptide, a gene encoding a CPR polypeptide, and a gene encoding a UGT polypeptide can produce a steviol glycoside and/or steviol glycoside precursors in vivo.
• a recombinant host expressing a gene encoding a GGPPS polypeptide, a gene encoding a CDPS polypeptide, a gene encoding a KS polypeptide, a gene encoding a KO polypeptide, a gene encoding a KAH polypeptide, and a gene encoding a CPR polypeptide can produce steviol in vivo. See, e.g., Figures 1.
• one or more of these genes can be endogenous to the host provided that at least one (and in some embodiments, all) of these genes is a recombinant gene introduced into the recombinant host.
• a steviol-producing recombinant host expressing a gene encoding a GGPPS polypeptide, a gene encoding a CDPS polypeptide, a gene encoding a KS polypeptide, a gene encoding a KO polypeptide, a gene encoding a KAH polypeptide, a gene encoding a CPR polypeptide, and one or more of a gene encoding a UGT polypeptide can produce a steviol glycoside in vivo. See, e.g., Figures 1 and 2.
• Non-limiting examples of KS polypeptides are set forth in SEQ ID NOs:1-4 and SEQ ID NO:6.
• Non-limiting examples of KO polypeptides are set forth in SEQ ID NOs:7-10, 54, 70- 72, 75, and 77-79.
• Non-limiting examples of KAH polypeptides are set forth in SEQ ID NOs:13- 17, 68, 82, and 91.
• Non-limiting examples of CPR polypeptides are set forth in SEQ ID NOs:20- 22, 28, 69, 73, 74, 76, 87, and 98.
• Non-limiting examples of CDPS polypeptides are set forth in SEQ ID NOs:33-39.
• Non-limiting examples of CDPS-KS polypeptides are set forth in SEQ ID NOs:40-42.
• Non-limiting examples of GGPPS polypeptides are set forth in SEQ ID NOs:43-50.
• a recombinant host comprises a nucleic acid encoding a UGT85C2 polypeptide (SEQ ID NO:32), a nucleic acid encoding a UGT76G1 polypeptide (SEQ ID NO:83), a nucleic acid encoding a UGT74G1 polypeptide (SEQ ID NO:29), a nucleic acid encoding a UGT91 D2 polypeptide, and/or a nucleic acid encoding a EUGT11 polypeptide (SEQ ID NO:86).
• the UGT91 D2 polypeptide can be a UGT91 D2e polypeptide (SEQ ID NO:84) or a UGT91 D2e-b polypeptide (SEQ ID NO:88).
• SEQ ID NO:84 UGT91 D2e polypeptide
• UGT91 D2e-b polypeptide SEQ ID NO:88
• expression of these genes may be necessary to produce a particular steviol glycoside but that one or more of these genes can be endogenous to the host provided that at least one (and in some embodiments, all) of these genes is a recombinant gene introduced into the recombinant host.
• a steviol-producing recombinant microorganism comprises exogenous nucleic acids encoding UGT85C2, UGT76G1 , or UGT91 D2 polypeptides.
• a steviol-producing recombinant microorganism comprises exogenous nucleic acids encoding UGT85C2, UGT76G1 , UGT74G1 , and UGT91 D2 polypeptides.
• a steviol-producing recombinant microorganism comprises exogenous nucleic acids encoding UGT85C2, UGT76G1 , UGT74G1 , and EUGT11 polypeptides.
• a steviol-producing recombinant microorganism comprises the exogenous nucleic acids encoding UGT85C2, UGT76G1 , UGT74G1 , UGT91 D2 (including inter alia 91 D2e, 91 D2m, 91 D2e-b, and functional homologs thereof), and EUGT11 polypeptides.
• the steviol glycoside is RebA, RebB, RebD, and/or RebM.
• RebA can be synthesized in a steviol-producing recombinant microorganism expressing UGT85C2, UGT76G1 , UGT74G1 , and UGT91 D2.
• RebB can be synthesized in a steviol- producing recombinant microorganism expressing UGT85C2, UGT76G1 , and UGT91 D2.
• RebD can be synthesized in a steviol-producing recombinant microorganism expressing UGT85C2, UGT76G1 UGT74G1 , and UGT91 D2 and/or EUGT1 1.
• RebM can be synthesized in a steviol- producing recombinant microorganism expressing UGT85C2, UGT76G1 , UGT74G1 , and UGT91 D2 and/or EUGT11 (see Figure 2).
• steviol glycosides and/or steviol glycoside precursors are produced through contact of a steviol glycoside precursor with one or more enzymes involved in the steviol glycoside pathway in vitro.
• contacting steviol with a UGT polypeptide can result in production of a steviol glycoside in vitro.
• a steviol glycoside precursor is produced through contact of an upstream steviol glycoside precursor with one or more enzymes involved in the steviol glycoside pathway in vitro.
• contacting ent- kaurenoic acid with a KAH enzyme can result in production of steviol in vitro.
• a steviol glycoside or steviol glycoside precursor is produced by whole cell bioconversion.
• a host cell expressing one or more enzymes involved in the steviol glycoside pathway takes up and modifies a stevioi glycoside precursor in the cell; following modification in vivo, a steviol glycoside remains in the cell and/or is excreted into the culture medium.
• a host cell expressing a gene encoding a UGT polypeptide can take up steviol and glycosylate steviol in the cell; following glycosylation in vivo, a steviol glycoside can be excreted into the culture medium.
• the cell is permeabilized to take up a substrate to be modified or to excrete a modified product.
• stevioi, one or more steviol glycoside precursors, and/or one or more steviol glycosides are produced by co-culturing of two or more hosts.
• a host comprising a GGPPS, a CDPS, a KO, a KS, a KAH, and/or a CPR and a host comprising one or more UGTs produce one or more stevioi glycosides.
• a steviol glycoside or steviol glycoside precursor composition produced in vivo, in vitro, or by whole cell bioconversion comprises less contaminants than a stevia extract from, inter alia, a stevia plant.
• Contaminants include plant-derived compounds that contribute to off-flavors.
• Potential contaminants include pigments, lipids, proteins, phenolics, saccharides, spathulenol and other sesquiterpenes, labdane diterpenes, monoterpenes, decanoic acid, 8,1 1 ,14-eicosatrienoic acid, 2-methy!octadecane, pentacosane, octacosane, tetracosane, octadecanol, stigmasterol, ⁇ -sitosterol, a-amyrin, ⁇ -amyrin, lupeol, ⁇ - amryin acetate, pentacyclic triterpenes, centauredin, quercitin, epi-alpha-cadinoi, carophyllenes and derivatives, beta-pinene, beta-sitosterol, and gibberellin.
• the terms “detectable amount,” “detectable concentration,” “measurable amount,” and “measurable concentration” refer to a level of steviol glycosides measured in AUC, ⁇ /OD 600 , mg/L, ⁇ , or mM.
• Steviol glycoside production i.e., total, supernatant, and/or intracellular steviol glycoside levels
• LC-MS liquid chromatography-mass spectrometry
• TLC thin layer chromatography
• HPLC high- performance liquid chromatography
• UV-Vis ultraviolet-visible spectroscopy/ spectrophotometry
• MS mass spectrometry
• NMR nuclear magnetic resonance spectroscopy
• the term "undetectable concentration” refers to a level of a compound that is too low to be measured and/or analyzed by techniques such as TLC, HPLC, UV-Vis, MS, or NMR. In some embodiments, a compound of an "undetectable concentration" is not present in a steviol glycoside or steviol glycoside precursor composition.
• x, y, and/or z can refer to “x” alone, “y” alone, “z” alone, “x, y, and z,” “(x and y) or z,” “x or (y and z),” or “x or y or z.”
• "and/or” is used to refer to the exogenous nucleic acids that a recombinant cell comprises, wherein a recombinant cell comprises one or more exogenous nucleic acids selected from a group.
• "and/or” is used to refer to production of steviol glycosides and/or steviol glycoside precursors. In some embodiments, “and/or” is used to refer to production of steviol glycosides, wherein one or more steviol glycosides are produced. In some embodiments, “and/or” is used to refer to production of steviol glycosides, wherein one or more steviol glycosides are produced through one or more of the following steps: culturing a recombinant microorganism, synthesizing one or more steviol glycosides in a recombinant microorganism, and/or isolating one or more steviol glycosides.
• nucleotide sequence of a nucleic acid encoding a KO polypeptide is set forth in SEQ ID NO: 55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, or SEQ ID NO:60, SEQ ID NO:63, SEQ ID NO:64, or SEQ ID NO:65.
• the nucleic acid encoding the KO polypeptide has at least 70% identity to the nucleotide sequence set forth in SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59 or SEQ ID NO:60, at least 80% identity to the nucleotide sequence set forth in SEQ ID NO:56 or SEQ ID NO:58, at least 95% identity to the nucleotide sequence set forth in SEQ ID NO:63, or at least 75% identity to the nucleotide sequence set forth in SEQ ID NO:64 or SEQ ID NO:65.
• the amino acid sequence of a KO enzyme is set forth in SEQ ID NO:54, SEQ ID NO.70, SEQ ID NO:71 , SEQ ID NO:72, SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:78, OR SEQ ID NO:79.
• a host ceil comprises one or more copies of one or more nucleic acids encoding a KO polypeptide.
• expression of a KO gene set forth in SEQ ID NO:55 or SEQ ID NO:56 in a RebB-producing S. cerevisiae strain results in higher production of RebB compared to expression of SrKOI (SEQ ID NO:59, SEQ ID NO:79) in a RebB-producing S. cerevisiae strain. See Example 3.
• expression of a KO gene set forth in SEQ ID NO:55, SEQ ID NO:56, or SEQ ID NO:57 in an S, cerevisiae strain capable of producing RebB with a functional KO results in production of ent-kaurenoic acid. See Example 3.
• the terms "ent-kaurenoic acid hydroxylase” and “steviol synthase” can be used interchangeably and be abbreviated "KAH.”
• the nucleotide sequence of a nucleic acid encoding a KAH enzyme is set forth in SEQ ID NO:18, SEQ ID NO:80, SEQ ID NO:81 , SEQ ID NO:90, or SEQ ID NO:96.
• the nucleic acid encoding the KAH polypeptide has at least 75% identity to a nucleotide sequence set forth in SEQ ID NO:80; or at least 70% identity to a nucleotide sequence set forth in SEQ ID NO:18, SEQ ID NO:81 , SEQ ID NO:90, or SEQ ID NO:96.
• the amino acid sequence of a KAH enzyme is set forth in SEQ ID NO:68, SEQ ID NO:82, or SEQ ID NO:91.
• a host cell comprises one or more copies of one or more nucleic acids encoding a KAH enzyme.
• one or more copies of SrKAHel are expressed in an S, cerevisiae strain.
• two copies of SrKAHel are expressed in an S. cerevisiae strain.
• the nucleotide sequence of a nucleic acid encoding a KAH enzyme is set forth in SEQ ID NO:80.
• the nucleic acid of SEQ ID NO:80 encodes a KAH with an amino acid sequence set forth in SEQ ID NO:82.
• a version of SEQ ID NO:80 codon- optimized for expression in S, cerevisiae is set forth in SEQ ID NO:81.
• a host cell comprises one or more copies of one or more nucleic acids encoding a KAH enzyme. See Example 7.
• SrKAHel SEQ ID NO:18, SEQ ID NO:68
• KAH KAH encoded by the nucleotide sequence set forth in SEQ ID NO:80
• KAH encoded by the codon-optimized nucleotide sequence set forth in SEQ ID NO:81 are co-expressed in a steviol glycoside-producing S. cerevisiae strain.
• co-expression of SrKAHel results in higher production of steviol glycosides compared to a control steviol glycoside-producing strain or a steviol glycoside producing strain overexpressing SrKAHel . See Example 7 and Table 6.
• overexpressing SrKAHel results in production of 85.5 ⁇ 13-SMG
• expression of SrKAHel and the KAH encoded by the nucleotide set forth in SEQ ID NO:80 results in production of 153.8 ⁇ 13-SMG
• expression of SrKAHel and the KAH encoded by the nucleotide set forth in SEQ ID NO:81 results in production of 130.5 ⁇ 13-SMG.
• a KO gene is expressed in a steviol glycoside-producing S. cerevisiae strain that further overexpresses SrKAHel (SEQ ID NO:18, SEQ ID NO:68).
• SrKAHel cerevisiae strain overexpressing SrKAHel results in higher expression of steviol glycosides compared to a control steviol-glycoside producing strain or a steviol glycoside- producing strain overexpressing SrKAHel (SEQ ID NO:18, SEQ ID NO:68). See Example 4.
• expression of a KO gene of SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, or SEQ ID NO:60 in a steviol glycoside-producing S. cerevisiae strain overexpressing SrKAHel results in higher levels of glycosylated ent-kaurenoic acid compared to a control S. cerevisiae strain. See Example 4.
• expression of a KO gene of SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:59, or SEQ ID NO:60 in a steviol glycoside-producing S. cerevisiae strain overexpressing SrKAHel results in improved metabolic conversion of a glycosylated ent-kaurenol intermediate compound relative to a control S. cerevisiae strain or a steviol glycoside-producing S. cerevisiae strain overexpressing SrKAHel (SEQ ID NO:18, SEQ ID NO:68). See Example 4.
• a KAH is a Prunus KAH, such as a Prunus avium, Prunus mume, or Prunus persica KAH.
• a KAH is a KAH of the CYP72A219 or CYP71A219-like family.
• the nucleotide sequence of a nucleic acid encoding a KAH enzyme is set forth in SEQ ID NO:90 or SEQ ID NO:96.
• the nucleic acids of SEQ ID NO:90 and SEQ ID NO:96 encode a KAH from Prunus avium with an amino acid sequence set forth in SEQ ID NO:91.
• a KAH polypeptide is a polypeptide with an amino acid sequence set forth in SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, or SEQ ID NO:95. In some embodiments, a KAH polypeptide is a KAH polypeptide with at least 50% sequence identity to an amino acid sequence set forth in SEQ ID NO:91 , SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, or SEQ ID NO:95.
• expression of a gene encoding a polypeptide having at least 50% sequence identity to an amino acid sequence set forth in SEQ ID NO:91 , SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:94, or SEQ ID NO:95 in a recombinant host results in production of a steviol glycoside or steviol glycoside precursor, such as 13-SMG and/or rubusoside. See Example 8.
• the nucleotide sequence of the nucleic acid encoding a CPR enzyme is set forth in SEQ ID NO:23, SEQ ID NO:51 , SEQ ID NO:61 , SEQ ID NO:62, SEQ ID NO:66, SEQ ID NO:67, or SEQ ID NO:97.
• the nucleic acid encoding the CPR polypeptide has at least 75% identity to the nucleotide sequence set forth in SEQ ID NO:23, SEQ ID NO:61 , or SEQ ID NO:62, or at least 70% identity to the nucleotide sequence set forth in SEQ ID NO:24, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:51 , or SEQ ID NO:97.
• the amino acid sequence of the CPR enzyme is set forth in SEQ ID NO:22, SEQ ID NO:28, SEQ ID NO:69, SEQ ID NO:73, SEQ ID NO:74, or SEQ ID NO:76, SEQ ID NO:87, or SEQ ID NO:98.
• a host cell comprises one or more copies of one or more nucleic acids encoding a CPR enzyme.
• SrKAHel is activated by the S. cerevisiae CPR encoded by gene NCP1 (YHR042W).
• Enhanced activation of the KAH encoded by SrKAHel is observed when the Arabidopsis thaliana CPR encoded by the gene ATR2 (SEQ ID NO:51 ) or the S. rebaudiana CPR encoded by the genes CPR7 (SEQ ID NO:23) or CPR8 (SEQ ID NO:24, SEQ ID NO:28) are co-expressed in a recombinant cell.
• Amino acid sequences of the A are known as amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino
• thaliana polypeptides ATR1 and ATR2 are set forth in SEQ ID NO:25 and SEQ ID NO:26, respectively.
• the S. rebaudiana polypeptides CPR7 and CPR8 are set forth in SEQ ID NO:27 and SEQ ID NO:28, respectively.
• expression of CPR1 (SEQ ID NO:61 , SEQ ID NO:76) or of CPR7 in the steviol glycoside-producing S. cerevisiae strain co-expressing S. rebaudiana CPR8 (SEQ ID NO:24, SEQ ID NO:28) and A. thaliana ATR2 (SEQ ID NO:51 ) results in higher levels of RebM compared to a control steviol glycoside-producing S. cerevisiae strain expressing S. rebaudiana CPR8 (SEQ ID NO:24, SEQ ID NO:28) and A. thaliana ATR2 (SEQ ID N0:51 ).
• expression of the CPR set forth in SEQ ID NO:62 in a steviol glycoside- producing S. cerevisiae strain overexpressing SrKAHel results in higher levels of RebM compared to a steviol glycoside-producing S. cerevisiae strain that does not express the nucleic acid set forth in SEQ ID NO:62 or overexpress SrKAHel . See Example 5.
• co-expression of SrKOI (SEQ ID NO:59, SEQ ID NO:79) and a CPR gene of SEQ ID NO:66 or SEQ ID NO:77 in a RebB-producing strain results in higher production of 13-SMG and RebB than co-expression of a KO gene of SEQ ID NO:63 or SEQ ID NO:64 and a CPR gene of SEQ ID NO:66 or SEQ ID NO:77. See Example 6.
• CPR1 (SEQ ID NO:61 , SEQ ID NO:76) or CPR12 (SEQ ID NO:97, SEQ ID NO:98) activates cytochrome c.
• CPR1 (SEQ ID NO:61 , SEQ ID NO:76) or CPR12 (SEQ ID NO:97, SEQ ID NO:98) in the presence of SrKAHel (SEQ ID NO:18, SEQ ID NO:68) activate cytochrome c.
• CPR1 (SEQ ID NO:61 , SEQ ID NO:76) or CPR12 (SEQ ID NO:97, SEQ ID NO:98) regulate conversion of ent- kaurenoic acid to steviol.
• CPR1 (SEQ ID NO:61 , SEQ ID NO:76) or CPR12 (SEQ ID NO:97, SEQ ID NO:98) in combination with SrKAHel (SEQ ID NO: 18, SEQ ID NO:68) convert ent-kaurenoic acid to steviol.
• steviol production is detected upon incubation of ent-kaurenoic acid with microsomal protein prepared from S. cerevisiae strains expressing CPR1 (SEQ ID NO:61 , SEQ ID NO:76) or CPR12 (SEQ ID NO:97, SEQ ID NO:98) in combination with SrKAHel (SEQ ID NO:18, SEQ ID NO:68).
• expression of CPR1 (SEQ ID NO:61 , SEQ ID NO:76) or CPR12 (SEQ ID NO:97, SEQ ID NO:98) in a recombinant host results in production of a steviol glycoside or steviol glycoside precursor. See Example 9.
• a steviol glycoside-producing strain expresses a fusion construct comprising a KO and the NADPH-dependent P450 oxidoreductase domain of CYP102A1 , referred to herein as "BMR.”
• BMR The codon-optimized nucleotide sequence encoding the BMR polypeptide is set forth in SEQ ID NO:117; the BMR amino acid sequence is set forth in SEQ ID NO: 118.
• BMR is a mutant BMR, including, but not limited to a BMR W 1046 A mutant (SEQ ID NO:119, SEQ ID NO:120). The BMR mutant can be specific for NADH.
• the KO-BMR fusion construct comprises a linker (SEQ ID NO:121 , SEQ ID NO:122).
• the KO of the fusion construct is SrKOI (SEQ ID NO:59, SEQ ID NO:79) or the KO encoded by the nucleotide sequence set forth in SEQ ID NO:65 (corresponding to the amino acid sequence set forth in SEQ ID N0.75).
• the KO of the fusion construct is a truncated KO.
• Exemplary KO-BMR fusion constructs are set forth in SEQ ID NOs:99-112. See Example 10.
• expression of SrK01-BMR fusion constructs (SEQ ID NOs:99-106) in a steviol glycoside-producing strain results in an increase in ent-kaurenoic acid, 13-SMG, and RebB levels, compared to expression of SrKOI (SEQ ID NO:59, SEQ ID NO:79) in a steviol glycoside-producing strain.
• expression of a fusion construct (SEQ ID NO:107, SEQ ID NO:108) in a steviol glycoside-producing strain results in greater conversion of ent-kaurene to ent-kaurenoic acid and greater conversion of ent-kaurenoic acid to 13-SMG, compared to expression of the KO encoded by the nucleotide sequence set forth in SEQ ID NO:65 in a steviol glycoside-producing strain.
• expression of a fusion construct comprising the KO encoded by the nucleotide sequence set forth in SEQ ID NO:65 and the W1046A mutant BMR results in incrased ent- kaurenoic acid levels. See Figure 16 (B and D) and Example 10.
• a steviol glycoside-producing strain comprises inheritance of cortical ER protein 2 (ICE2; SEQ ID NO:113, SEQ ID NO:114).
• ICE2 is also referred to as YIL090W.
• ICE2 is overexpressed.
• ICE2 can be expressed in a strain comprising CPR1 (SEQ ID NO:61 , SEQ ID NO:76) and/or CPR12 (SEQ ID NO:97, SEQ ID NO:98).
• a steviol glycoside-producing strain comprises two copies of ICE2.
• expression of ICE2 increases ent-kaurene metabolism (resulting in decreased accumulation of ent-kaurene, ent-kaurenol, ent-kaurenal, and ent-kaurenol glycosides), resulting in increased accumulation of steviol glycosides, compared to a control strain. See Table 10 and Example 11.
• expression of the KO encoded by nucleotide sequence set forth in SEQ ID NO:56 in a steviol glycoside-producing strain cultivated by fermentation results in a lower accumulation of ent-kaurene compounds, compared to a control steviol glycoside- producing strain.
• higher levels of ent-kaurenoic acid and steviol glycosides result, as compared to a control strain.
• expression of the KAH encoded by nucleotide sequence set forth in SEQ ID NO:80, the KO encoded by nucleotide sequence set forth in SEQ ID NO:56, and the KO encoded by nucleotide sequence set forth in SEQ ID NO:65 in a steviol glycoside-producing strain cultivated by fermentation results in decreased accumulation of ent-kaurene, ent-kaurenol, ent-kaurenal, ent-kaurenol glycosides, ent-kaurenoic acid, and ent-kaurenoic acid glycosides and increased production of steviol glycosides, as compared to a control strain.
• expression of CPR12 (SEQ ID NO:97, SEQ ID NO:98), the KAH encoded by nucleotide sequence set forth in SEQ ID NO:80, and the KO encoded by nucleotide sequence set forth in SEQ ID NO;56 cultivated by fermentation results in decreased ent-kaurene, ent-kaurenol, ent-kaurenal, ent-kaurenol glycosides, ent- kaurenoic acid, and ent-kaurenoic acid glycosides accumulation and higher levels of steviol glycosides, as compared to a control strain. See Table 12 and Example 12.
• a functional homolog is a polypeptide that has sequence similarity to a reference polypeptide, and that carries out one or more of the biochemical or physiological function(s) of the reference polypeptide.
• a functional homolog and the reference polypeptide can be a natural occurring polypeptide, and the sequence similarity can be due to convergent or divergent evolutionary events. As such, functional homologs are sometimes designated in the literature as homologs, or orthologs, or paralogs.
• Variants of a naturally occurring functional homolog can themselves be functional homologs.
• Functional homologs can also be created via site-directed mutagenesis of the coding sequence for a polypeptide, or by combining domains from the coding sequences for different naturally-occurring polypeptides ("domain swapping").
• Techniques for modifying genes encoding functional polypeptides described herein are known and include, inter alia, directed evolution techniques, site-directed mutagenesis techniques and random mutagenesis techniques, and can be useful to increase specific activity of a polypeptide, alter substrate specificity, alter expression levels, alter subcellular location, or modify polypeptide-polypeptide interactions in a desired manner. Such modified polypeptides are considered functional homologs.
• the term "functional homolog” is sometimes applied to the nucleic acid that encodes a functionally homologous polypeptide.
• Functional homologs can be identified by analysis of nucleotide and polypeptide sequence alignments. For example, performing a query on a database of nucleotide or polypeptide sequences can identify homologs of steviol glycoside biosynthesis polypeptides. Sequence analysis can involve BLAST, Reciprocal BLAST, or PSI-BLAST analysis of non- redundant databases using a KO, KAH, or CPR amino acid sequence as the reference sequence. Amino acid sequence is, in some instances, deduced from the nucleotide sequence. Those polypeptides in the database that have greater than 40% sequence identity are candidates for further evaluation for suitability as a steviol glycoside biosynthesis polypeptide.
• nucleic acids and polypeptides are identified from transcriptome data based on expression levels rather than by using BLAST analysis.
• conserveed regions can be identified by locating a region within the primary amino acid sequence of a steviol glycoside biosynthesis polypeptide that is a repeated sequence, forms some secondary structure (e.g., helices and beta sheets), establishes positively or negatively charged domains, or represents a protein motif or domain. See, e.g., the Pfam web site describing consensus sequences for a variety of protein motifs and domains on the World Wide Web at sanger.ac.uk/Software/Pfam/ and pfam.janelia.org/. The information included at the Pfam database is described in Sonnhammer et al., Nucl.
• conserveed regions also can be determined by aligning sequences of the same or related polypeptides from closely related species. Closely related species preferably are from the same family. In some embodiments, alignment of sequences from two different species is adequate to identify such homologs.
• polypeptides that exhibit at least about 40% amino acid sequence identity are useful to identify conserved regions.
• conserved regions of related polypeptides exhibit at least 45% amino acid sequence identity (e.g., at least 50%, at least 60%, at least 70%, at least 80%, or at least 90% amino acid sequence identity).
• a conserved region exhibits at least 92%, 94%, 96%, 98%, or 99% amino acid sequence identity.
• polypeptides suitable for producing steviol in a recombinant host include functional homologs of KO, KAH, and CPR.
• a candidate sequence typically has a length that is from 80% to 200% of the length of the reference sequence, e.g., 82, 85, 87, 89, 90, 93, 95, 97, 99, 100, 105, 110, 115, 120, 130, 140, 150, 160, 170, 180, 190, or 200% of the length of the reference sequence.
• a functional homolog polypeptide typically has a length that is from 95% to 105% of the length of the reference sequence, e.g., 90, 93, 95, 97, 99, 100, 105, 110, 115, or 120% of the length of the reference sequence, or any range between.
• A% identity for any candidate nucleic acid or polypeptide relative to a reference nucleic acid or polypeptide can be determined as follows.
• a reference sequence e.g., a nucleic acid sequence or an amino acid sequence described herein
• Clusta!W ⁇ version 1.83, default parameters which allows alignments of nucleic acid or polypeptide sequences to be carried out across their entire length (global alignment). Chenna et a/., 2003, Nucleic Acids Res. 31(13):3497-500.
• CiustalW calculates the best match between a reference and one or more candidate sequences, and aligns them so that identities, similarities and differences can be determined. Gaps of one or more residues can be inserted into a reference sequence, a candidate sequence, or both, to maximize sequence alignments.
• word size 2; window size: 4; scoring method: % age; number of top diagonals: 4; and gap penalty: 5.
• gap opening penalty 10.0; gap extension penalty: 5.0; and weight transitions: yes.
• the CiustalW output is a sequence alignment that reflects the relationship between sequences.
• CiustalW can be run, for example, at the Baylor College of Medicine Search Launcher site on the World Wide Web (searchlauncher.bcm.tmc.edu/multi-align/multi-align.html) and at the European Bioinformatics Institute site on the World Wide Web (ebi.ac.uk/clustalw).
• % identity of a candidate nucleic acid or amino acid sequence to a reference sequence the sequences are aligned using CiustalW, the number of identical matches in the alignment is divided by the length of the reference sequence, and the result is multiplied by 100. It is noted that the % identity value can be rounded to the nearest tenth. For example, 78.1 1 , 78.12, 78.13, and 78.14 are rounded down to 78.1 , while 78.15, 78.16, 78.17, 78.18, and 78.19 are rounded up to 78.2.
• KO, KAH, or CPR proteins can include additional amino acids that are not involved in the enzymatic activities carried out by the enzymes.
• KO, KAH, or CPR proteins are fusion proteins.
• the terms “chimera,” “fusion polypeptide,” “fusion protein,” “fusion enzyme,” “fusion construct,” “chimeric protein,” “chimeric polypeptide,” “chimeric construct,” and “chimeric enzyme” can be used interchangeably herein to refer to proteins engineered through the joining of two or more genes that code for different proteins.
• a nucleic acid sequence encoding a KO, KAH, or CPR polypeptide can include a tag sequence that encodes a "tag" designed to facilitate subsequent manipulation (e.g., to facilitate purification or detection), secretion, or localization of the encoded polypeptide.
• Tag sequences can be inserted in the nucleic acid sequence encoding the polypeptide such that the encoded tag is located at either the carboxyl or amino terminus of the polypeptide.
• Non-limiting examples of encoded tags include green fluorescent protein (GFP), human influenza hemagglutinin (HA), glutathione S transferase (GST), polyhistidine-tag (HIS tag), and FlagTM tag (Kodak, New Haven, CT).
• Other examples of tags include a chloroplast transit peptide, a mitochondrial transit peptide, an amyloplast peptide, signal peptide, or a secretion tag.
• a fusion protein is a protein altered by domain swapping.
• domain swapping is used to describe the process of replacing a domain of a first protein with a domain of a second protein.
• the domain of the first protein and the domain of the second protein are functionally identical or functionally similar.
• the structure and/or sequence of the domain of the second protein differs from the structure and/or sequence of the domain of the first protein.
• a KO polypeptide is altered by domain swapping. See Example 10.
• a recombinant gene encoding a polypeptide described herein comprises the coding sequence for that polypeptide, operably linked in sense orientation to one or more regulatory regions suitable for expressing the polypeptide. Because many microorganisms are capable of expressing multiple gene products from a polycistronic mRNA, multiple polypeptides can be expressed under the control of a single regulatory region for those microorganisms, if desired.
• a coding sequence and a regulatory region are considered to be operably linked when the regulatory region and coding sequence are positioned so that the regulatory region is effective for regulating transcription or translation of the sequence.
• the translation initiation site of the translational reading frame of the coding sequence is positioned between one and about fifty nucleotides downstream of the regulatory region for a monocistronic gene.
• the coding sequence for a polypeptide described herein is identified in a species other than the recombinant host, i.e., is a heterologous nucleic acid.
• the coding sequence can be from other prokaryotic or eukaryotic microorganisms, from plants or from animals. In some case, however, the coding sequence is a sequence that is native to the host and is being reintroduced into that organism.
• a native sequence can often be distinguished from the naturally occurring sequence by the presence of non-natural sequences linked to the exogenous nucleic acid, e.g., non-native regulatory sequences flanking a native sequence in a recombinant nucleic acid construct.
• stably transformed exogenous nucleic acids typically are integrated at positions other than the position where the native sequence is found.
• "Regulatory region” refers to a nucleic acid having nucleotide sequences that influence transcription or translation initiation and rate, and stability and/or mobility of a transcription or translation product.
• Regulatory regions include, without limitation, promoter sequences, enhancer sequences, response elements, protein recognition sites, inducible elements, protein binding sequences, 5 ' and 3 ' untranslated regions (UTRs), transcriptional start sites, termination sequences, polyadenylation sequences, introns, and combinations thereof.
• a regulatory region typically comprises at least a core (basal) promoter.
• a regulatory region also may include at least one control element, such as an enhancer sequence, an upstream element or an upstream activation region (UAR).
• a regulatory region is operably linked to a coding sequence by positioning the regulatory region and the coding sequence so that the regulatory region is effective for regulating transcription or translation of the sequence.
• the translation initiation site of the translational reading frame of the coding sequence is typically positioned between one and about fifty nucleotides downstream of the promoter.
• a regulatory region can, however, be positioned as much as about 5,000 nucleotides upstream of the translation initiation site, or about 2,000 nucleotides upstream of the transcription start site.
• regulatory regions The choice of regulatory regions to be included depends upon several factors, including, but not limited to, efficiency, selectability, inducibility, desired expression level, and preferential expression during certain culture stages. It is a routine matter for one of skill in the art to modulate the expression of a coding sequence by appropriately selecting and positioning regulatory regions relative to the coding sequence. It will be understood that more than one regulatory region may be present, e.g., introns, enhancers, upstream activation regions, transcription terminators, and inducible elements.
• One or more genes can be combined in a recombinant nucleic acid construct in "modules" useful for a discrete aspect of steviol and/or steviol glycoside production.
• Combining a plurality of genes in a module, particularly a polycistronic module facilitates the use of the module in a variety of species.
• a steviol biosynthesis gene cluster, or a UGT gene cluster can be combined in a polycistronic module such that, after insertion of a suitable regulatory region, the module can be introduced into a wide variety of species.
• a UGT gene cluster can be combined such that each UGT coding sequence is operably linked to a separate regulatory region, to form a UGT module.
• a module can be used in those species for which monocistronic expression is necessary or desirable.
• a recombinant construct typically also contains an origin of replication, and one or more selectable markers for maintenance of the construct in appropriate species.
• nucleic acids can encode a particular polypeptide; i.e., for many amino acids, there is more than one nucleotide triplet that serves as the codon for the amino add.
• codons in the coding sequence for a given polypeptide can be modified such that optimal expression in a particular host is obtained, using appropriate codon bias tables for that host (e.g., microorganism).
• these modified sequences can exist as purified molecules and can be incorporated into a vector or a virus for use in constructing modules for recombinant nucleic acid constructs.
• an endogenous polypeptide in order to divert metabolic intermediates towards steviol or steviol glycoside biosynthesis.
• a nucleic acid that overexpresses the polypeptide or gene product may be included in a recombinant construct that is transformed into the strain.
• mutagenesis can be used to generate mutants in genes for which it is desired to increase or enhance function.
• Recombinant hosts can be used to express polypeptides for the producing steviol glycosides, including mammalian, insect, plant, and algal cells.
• a number of prokaryotes and eukaryotes are also suitable for use in constructing the recombinant microorganisms described herein, e.g., gram-negative bacteria, yeast, and fungi.
• a species and strain selected for use as a steviol glycoside production strain is first analyzed to determine which production genes are endogenous to the strain and which genes are not present. Genes for which an endogenous counterpart is not present in the strain are advantageously assembled in one or more recombinant constructs, which are then transformed into the strain in order to supply the missing function(s).
• the recombinant microorganism is grown in a fermenter at a defined temperature(s) for a desired period of time.
• the constructed and genetically engineered microorganisms provided by the invention can be cultivated using conventional fermentation processes, including, inter alia, chemostat, batch, fed-batch cultivations, semi-continuous fermentations such as draw and fill, continuous perfusion fermentation, and continuous perfusion cell culture.
• other recombinant genes such as isopentenyl biosynthesis genes and terpene synthase and cyclase genes may also be present and expressed.
• Levels of substrates and intermediates e.g., isopentenyl diphosphate, dimethylailyl diphosphate, GGPP, ent-kaurene and ent-kaurenoic acid, can be determined by extracting samples from culture media for analysis according to published methods.
• Carbon sources of use in the instant method include any molecule that can be metabolized by the recombinant host cell to facilitate growth and/or production of the steviol glycosides.
• suitable carbon sources include, but are not limited to, sucrose (e.g., as found in molasses), fructose, xylose, ethanol, glycerol, glucose, cellulose, starch, cellobiose or other glucose-comprising polymer.
• sucrose e.g., as found in molasses
• fructose xylose
• ethanol glycerol
• glucose e.glycerol
• glucose e.glycerol
• the carbon source can be provided to the host organism throughout the cultivation period or alternatively, the organism can be grown for a period of time in the presence of another energy source, e.g., protein, and then provided with a source of carbon only during the fed-batch phase.
• steviol and/or one or more steviol glycosides can then be recovered from the culture using various techniques known in the art.
• a permeabilizing agent can be added to aid the feedstock entering into the host and product getting out.
• a crude iysate of the cultured microorganism can be centrifuged to obtain a supernatant.
• the resulting supernatant can then be applied to a chromatography column, e.g., a C-18 column, and washed with water to remove hydrophilic compounds, followed by elution of the compound(s) of interest with a solvent such as methanol.
• the compound(s) can then be further purified by preparative HPLC. See also, WO 2009/140394.
• genes and modules discussed herein can be present in two or more recombinant hosts rather than a single host. When a plurality of recombinant hosts is used, they can be grown in a mixed culture to accumulate steviol and/or steviol glycosides.
• the two or more hosts each can be grown in a separate culture medium and the product of the first culture medium, e.g., steviol, can be introduced into second culture medium to be converted into a subsequent intermediate, or into an end product such as, for example, RebA.
• the product produced by the second, or final host is then recovered.
• a recombinant host is grown using nutrient sources other than a culture medium and utilizing a system other than a fermenter.
• prokaryotic and eukaryotic species are described in more detail below. However, it will be appreciated that other species can be suitable.
• suitable species can be in a genus such as Agaricus, Aspergillus, Bacillus, Candida, Corynebacteriurn, Eremothecium, Escherichia, Fusarium/Cibberella, Kluyveromyces, Laetiporus, Lentinus, Phaffia, Phanerochaete, Pichia, Physcomitrella, Rhodoturu!a, Saccharomyces, Schizosaccharomyces, Sphaceloma, Xanthophyllomyces or Yarrowia.
• Exemplary species from such genera include Lentinus tigrinus, Laetiporus sulphureus, Phanerochaete chrysosporium, Pichia pastoris, Cyberlindnera jadinii, Physcomitrella patens, Rhodoturula glutinis, Rhodoturula mucilaginosa, Phaffia rhodozyma, Xanthophyllomyces dendrorhous, Fusarium fujikuroi/Gibberella fujikuroi, Candida utilis, Candida glabrata, Candida albicans, and Yarrowia lipolytica.
• a microorganism can be a prokaryote such as Escherichia bacteria cells, for example, Escherichia coli cells; Lactobacillus bacteria cells; Lactococcus bacteria cells; Cornebacterium bacteria cells; Acetobacter bacteria cells; Acinetobacter bacteria cells; or Pseudomonas bacterial cells.
• a microorganism can be an Ascomycete such as Gibberella fujikuroi, Kluyveromyces lactis, Schizosaccharomyces pombe, Aspergillus niger, Yarrowia lipolytica, Ashbya gossypii, or S. cerevisiae.
• a microorganism can be an algal cell such as Blakeslea trispora, Dunaliella salina, Haematococcus pluvialis, Chlorella sp., Undaria pinnatifida, Sargassum, Laminaria japonica, Scenedesmus almeriensis species.
• a microorganism can be a cyanobacterial cell such as Blakeslea trispora, Dunaliella salina, Haematococcus pluvialis, Chlorella sp., Undaria pinnatifida, Sargassum, Laminaria japonica, Scenedesmus almeriensis.
• Saccharomyces is a widely used chassis organism in synthetic biology, and can be used as the recombinant microorganism platform. For example, there are libraries of mutants, plasmids, detailed computer models of metabolism and other information available for S. cerevisiae, allowing for rational design of various modules to enhance product yield. Methods are known for making recombinant microorganisms.
• Aspergillus species such as A. oryzae, A. niger and A. sojae are widely used microorganisms in food production and can also be used as the recombinant microorganism platform.
• Nucleotide sequences are available for genomes of A. nidulans, A. fumigatus, A. oryzae, A. clavatus, A. flavus, A. niger, and A. terreus, allowing rational design and modification of endogenous pathways to enhance flux and increase product yield.
• Metabolic models have been developed for Aspergillus, as well as transcriptomtc studies and proteomics studies.
• A. niger is cultured for the industrial production of a number of food ingredients such as citric acid and gluconic acid, and thus species such as A. niger are generally suitable for producing steviol glycosides.
• E. coli another widely used platform organism in synthetic biology, can also be used as the recombinant microorganism platform. Similar to Saccharomyces, there are libraries of mutants, plasmids, detailed computer models of metabolism and other information available for E. coli, allowing for rational design of various modules to enhance product yield. Methods similar to those described above for Saccharomyces can be used to make recombinant E. coli microorganisms.
• Agaricus, Gibberella, and Phanerochaete spp. can be useful because they are known to produce large amounts of isoprenoids in culture.
• the terpene precursors for producing large amounts of steviol glycosides are already produced by endogenous genes.
• modules comprising recombinant genes for steviol glycoside biosynthesis polypeptides can be introduced into species from such genera without the necessity of introducing mevalonate or MEP pathway genes.
• Arxuia adeninivorans (Blastobotrys adeninivorans)
• Arxuia adeninivorans is dimorphic yeast (it grows as budding yeast like the baker's yeast up to a temperature of 42°C, above this threshold it grows in a filamentous form) with unusual biochemical characteristics. It can grow on a wide range of substrates and can assimilate nitrate. It has successfully been applied to the generation of strains that can produce natural plastics or the development of a biosensor for estrogens in environmental samples.
• Yarrowia lipolytica is dimorphic yeast (see Arxuia adeninivorans) and belongs to the family Hemiascomycetes. The entire genome of Yarrowia lipolytica is known. Yarrowia species is aerobic and considered to be non-pathogenic. Yarrowia is efficient in using hydrophobic substrates (e.g. aikanes, fatty acids, oils) and can grow on sugars. It has a high potential for industrial applications and is an oleaginous microorgamism. Yarrowia lipolyptica can accumulate lipid content to approximately 40% of its dry cell weight and is a model organism for lipid accumulation and remobilization.
• hydrophobic substrates e.g. aikanes, fatty acids, oils
• Rhodotorula is unicellular, pigmented yeast.
• the oleaginous red yeast, Rhodotorula glutinis has been shown to produce lipids and carotenoids from crude glycerol (Saenge et al., 2011 , Process Biochemistry 46(1 ):210-8).
• Rhodotorula toruloides strains have been shown to be an efficient fed-batch fermentation system for improved biomass and lipid productivity (Li et al., 2007, Enzyme and Microbial Technology 41 :312-7).
• Rhodosporidium toruioides Rhodosporidium toruioides
• Rhodosporidium toruioides is oleaginous yeast and useful for engineering iipid- production pathways (See e.g. Zhu et al., 2013, Nature Commun. 3:1112; Ageitos et al., 2011 , Applied Microbiology and Biotechnology 90(4): 1219-27).
• Candida boidinii is methylotrophic yeast (it can grow on methanol). Like other methylotrophic species such as Hansenula polymorpha and Pichia pastoris, it provides an excellent platform for producing heterologous proteins. Yields in a multigram range of a secreted foreign protein have been reported.
• a computational method, IPRO recently predicted mutations that experimentally switched the cofactor specificity of Candida boidinii xylose reductase from NADPH to NADH. See, e.g., Mattanovich et al., 2012, Methods Mol Biol. 824:329-58; Khoury et al., 2009, Protein Sci. 18(10):2125-38.
• Hansenula polymorpha is methylotrophic yeast (see Candida boidinii). It can furthermore grow on a wide range of other substrates; it is therm o-tolerant and can assimilate nitrate (see also Kluyveromyces lactis). It has been applied to producing hepatitis B vaccines, insulin and interferon alpha-2a for the treatment of hepatitis C, furthermore to a range of technical enzymes. See, e.g., Xu et al., 2014, Virol Sin. 29(6):403-9.
• Kluyveromyces lactis is yeast regularly applied to the production of kefir. It can grow on several sugars, most importantly on lactose which is present in milk and whey. It has successfully been applied among others for producing chymosin (an enzyme that is usually present in the stomach of calves) for producing cheese. Production takes place in fermenters on a 40,000 L scale. See, e.g., van Ooyen et al., 2006, FEMS Yeast Res. 6(3):381-92.
• Pichia pastoris is methylotrophic yeast (see Candida boidinii and Hansenula polymorpha). It provides an efficient platform for producing foreign proteins. Platform elements are available as a kit and it is worldwide used in academia for producing proteins. Strains have been engineered that can produce complex human N-glycan (yeast glycans are similar but not identical to those found in humans). See, e.g., Piirainen et al., 2014, N Biotechnol. 31 (6):532-7.
• Physcomitrella spp. when grown in suspension culture, have characteristics similar to yeast or other fungal cultures. This genera can be used for producing plant secondary metabolites, which can be difficult to produce in other types of cells.
• Steviol glycosides do not necessarily have equivalent performance in different food systems. It is therefore desirable to have the ability to direct the synthesis to steviol glycoside compositions of choice.
• Recombinant hosts described herein can produce compositions that are selectively enriched for specific steviol glycosides (e.g., RebD or Reb ) and have a consistent taste profile.
• enriched is used to describe a steviol glycoside composition with an increased proportion of a particular steviol glycoside, compared to a steviol glycoside composition (extract) from a stevia plant.
• the recombinant hosts described herein can facilitate the production of compositions that are tailored to meet the sweetening profile desired for a given food product and that have a proportion of each steviol glycoside that is consistent from batch to batch.
• hosts described herein do not produce or produce a reduced amount of undesired plant by-products found in Stevia extracts.
• steviol glycoside compositions produced by the recombinant hosts described herein are distinguishable from compositions derived from Stevia plants.
• the amount of an individual steviol glycoside (e.g., RebA, RebB, RebD, or RebM) accumulated can be from about 1 to about 7,000 mg/L, e.g., about 1 to about 10 mg/L, about 3 to about 10 mg/L, about 5 to about 20 mg/L, about 10 to about 50 mg/L, about 10 to about 100 mg/L, about 25 to about 500 mg/L, about 100 to about 1 ,500 mg/L, or about 200 to about 1 ,000 mg/L, at least about 1 ,000 mg/L, at least about 1 ,200 mg/L, at least about at least 1 ,400 mg/L, at least about 1 ,600 mg/L, at least about 1 ,800 mg/L, at least about 2,800 mg/L, or at least about 7,000 mg/L.
• an individual steviol glycoside e.g., RebA, RebB, RebD, or RebM
• the amount of an individual steviol glycoside can exceed 7,000 mg/L.
• the amount of a combination of steviol glycosides (e.g., RebA, RebB, RebD, or RebM) accumulated can be from about 1 mg/L to about 7,000 mg/L, e.g., about 200 to about 1 ,500, at least about 2,000 mg/L, at least about 3,000 mg/L, at least about 4,000 mg/L, at least about 5,000 mg/L, at least about 6,000 mg/L, or at least about 7,000 mg/L.
• the amount of a combination of steviol glycosides can exceed 7,000 mg/L. In general, longer culture times will lead to greater amounts of product.
• the recombinant microorganism can be cultured for from 1 day to 7 days, from 1 day to 5 days, from 3 days to 5 days, about 3 days, about 4 days, or about 5 days.
• the various genes and modules discussed herein can be present in two or more recombinant microorganisms rather than a single microorganism.
• they can be grown in a mixed culture to produce steviol and/or steviol glycosides.
• a first microorganism can comprise one or more biosynthesis genes for producing a steviol glycoside precursor, while a second microorganism comprises steviol glycoside biosynthesis genes.
• a recombinant microorganism is grown using nutrient sources other than a culture medium and utilizing a system other than a fermenter.
• the two or more microorganisms each can be grown in a separate culture medium and the product of the first culture medium, e.g., steviol, can be introduced into second culture medium to be converted into a subsequent intermediate, or into an end product such as RebA. The product produced by the second, or final microorganism is then recovered.
• a recombinant microorganism is grown using nutrient sources other than a culture medium and utilizing a system other than a fermenter.
• Steviol glycosides and compositions obtained by the methods disclosed herein can be used to make food products, dietary supplements and sweetener compositions. See, e.g., WO 2011/153378, WO 2013/022989, WO 2014/122227, and WO 2014/122328.
• substantially pure steviol or steviol glycoside such as RebM or RebD can be included in food products such as ice cream, carbonated beverages, fruit juices, yogurts, baked goods, chewing gums, hard and soft candies, and sauces.
• substantially pure steviol or steviol glycoside can also be included in non-food products such as pharmaceutical products, medicinal products, dietary supplements and nutritional supplements.
• substantially pure steviol or steviol glycosides may also be included in animal feed products for both the agriculture industry and the companion animal industry.
• a mixture of steviol and/or steviol glycosides can be made by culturing recombinant microorganisms separately, each producing a specific steviol or steviol glycoside, recovering the steviol or steviol glycoside in substantially pure form from each microorganism and then combining the compounds to obtain a mixture comprising each compound in the desired proportion.
• the recombinant microorganisms described herein permit more precise and consistent mixtures to be obtained compared to current Stevia products.
• a substantially pure steviol or steviol glycoside can be incorporated into a food product along with other sweeteners, e.g.
• the steviol or steviol glycoside may be provided with a flavor (e.g., citrus) as a flavor modulator.
• compositions produced by a recombinant microorganism described herein can be incorporated into food products.
• a steviol glycoside composition produced by a recombinant microorganism can be incorporated into a food product in an amount ranging from about 20 mg steviol glycoside/kg food product to about 1800 mg steviol glycoside/kg food product on a dry weight basis, depending on the type of steviol glycoside and food product.
• a steviol glycoside composition produced by a recombinant microorganism can be incorporated into a dessert, cold confectionary (e.g., ice cream), dairy product (e.g., yogurt), or beverage (e.g., a carbonated beverage) such that the food product has a maximum of 500 mg steviol glycoside/kg food on a dry weight basis.
• a steviol glycoside composition produced by a recombinant microorganism can be incorporated into a baked good (e.g., a biscuit) such that the food product has a maximum of 300 mg steviol glycoside/kg food on a dry weight basis.
• a steviol glycoside composition produced by a recombinant microorganism can be incorporated into a sauce (e.g., chocolate syrup) or vegetable product (e.g., pickles) such that the food product has a maximum of 1000 mg steviol glycoside/kg food on a dry weight basis.
• a steviol glycoside composition produced by a recombinant microorganism can be incorporated into a bread such that the food product has a maximum of 160 mg steviol glycoside/kg food on a dry weight basis.
• a steviol glycoside composition produced by a recombinant microorganism, plant, or plant cell can be incorporated into a hard or soft candy such that the food product has a maximum of 1600 mg steviol glycoside/kg food on a dry weight basis.
• a steviol glycoside composition produced by a recombinant microorganism, plant, or plant cell can be incorporated into a processed fruit product (e.g., fruit juices, fruit filling, jams, and jellies) such that the food product has a maximum of 1000 mg steviol glycoside/kg food on a dry weight basis.
• a steviol glycoside composition produced herein is a component of a pharmaceutical composition.
• such a steviol glycoside composition can have from 90-99 weight % RebA and an undetectable amount of stevia plant-derived contaminants, and be incorporated into a food product at from 25-1600 mg/kg, e.g., 100-500 mg/kg, 25-100 mg/kg, 250-1000 mg/kg, 50-500 mg/kg or 500-1000 mg/kg on a dry weight basis.
• Such a steviol glycoside composition can be a RebB-enriched composition having greater than 3 weight % RebB and be incorporated into the food product such that the amount of RebB in the product is from 25-1600 mg/kg, e.g., 100-500 mg/kg, 25-100 mg/kg, 250-1000 mg/kg, 50-500 mg/kg or 500-1000 mg/kg on a dry weight basis.
• the RebB-enriched composition has an undetectable amount of stevia plant-derived contaminants.
• Such a steviol glycoside composition can be a RebD-enriched composition having greater than 3 weight % RebD and be incorporated into the food product such that the amount of RebD in the product is from 25-1600 mg/kg, e.g., 100-500 mg/kg, 25-100 mg/kg, 250-1000 mg/kg, 50-500 mg/kg or 500-1000 mg/kg on a dry weight basis.
• the RebD-enriched composition has an undetectable amount of stevia plant-derived contaminants.
• Such a steviol glycoside composition can be a RebE-enriched composition having greater than 3 weight % RebE and be incorporated into the food product such that the amount of RebE in the product is from 25-1600 mg/kg, e.g., 100-500 mg/kg, 25-100 mg/kg, 250-1000 mg/kg, 50-500 mg/kg or 500-1000 mg/kg on a dry weight basis.
• the RebE-enriched composition has an undetectable amount of stevia plant-derived contaminants.
• Such a steviol glycoside composition can be a RebM-enriched composition having greater than 3 weight % RebM and be incorporated into the food product such that the amount of RebM in the product is from 25-1600 mg/kg, e.g., 100-500 mg/kg, 25-100 mg/kg, 250-1000 mg/kg, 50-500 mg/kg or 500-1000 mg/kg on a dry weight basis.
• the RebM-enriched composition has an undetectable amount of stevia plant-derived contaminants.
• a substantially pure steviol or steviol glycoside is incorporated into a tabletop sweetener or "cup-for-cup" product.
• Such products typically are diluted to the appropriate sweetness level with one or more bulking agents, e.g., maltodextrins, known to those skilled in the art.
• Steviol glycoside compositions enriched for RebA, RebB, RebD, RebE, or RebM can be package in a sachet, for example, at from 10,000 to 30,000 mg steviol glycoside/kg product on a dry weight basis, for tabletop use.
• a stevio! glycoside produced in vitro, in vivo, or by whole cell byconversion
• Elution was carried out using a mobile phase of eluent B (MeCN with 0.1 % formic acid) and eluent A (water with 0.1% formic acid) by increasing the gradient from 25% to 47% B from min 0.0 to 4.0, increasing 47% to 100% B from min 4.0 to 5.0, and holding 100% B from min 5.0 to 6.5.
• the flow rate was 0.4 mL/min and the column temperature 35°C.
• Steviol glycosides were detected using SIM (Single Ion Monitoring) with the following m/z-traces.
• Table 1A LC-MS analytical information for Steviol Glycosides.
• Table 1B MS analytical information for Steviol Glycosides.
• LC-MS analyses were performed on Waters ACQUITY UPLC (Waters Corporation, Milford, MA) using a Waters Acquity UPLC® BEH C18 column (2.1 x 50 mm, 1.7 pm particles, 130 A) coupled to a Waters single quadropole mass spectrometer (SQD), equipped with an ESI and operated in negative mode.
• Compound separation was achieved by a gradient of the two mobile phases: A (water with 0.1% formic acid) and B (acetonitrile with 0.1 % formic acid) by increasing from 60% to 100% B between 0.3 to 2.5 min, holding 100% B for 0.1 min, and re-equilibrating for 0.2 min.
• the flow rate was 0.6 mL/min, and the column temperature was set at 55°C.
• Steviol or ent-kaurenoic acid was monitored using SIM (Single Ion Monitoring) and quantified by comparing with authentic standards.
• Table 1C MS analytical information for steviol and ent-kaurenoic acid.
• Steviol glycoside-producing S. cerevisiae strains were constructed as described in WO 2011/153378, WO 2013/022989, WO 2014/122227, and WO 2014/122328.
• a yeast strain comprising a recombinant gene encoding a Synechococcus sp. GGPPS (SEQ ID NO:49) polypeptide, a recombinant gene encoding a truncated Zea mays CDPS (SEQ ID NO:37) polypeptide, a recombinant gene encoding an A. thaliana KS (SEQ ID NO:6) polypeptide, a recombinant gene encoding an S.
• rebaudiana KO (SEQ ID NO:59, SEQ ID NO:79) polypeptide, a recombinant gene encoding an A. thaliana ATR2 (SEQ ID NO:51 , SEQ ID NO:87) polypeptide, a recombinant gene encoding an O. sativa EUGT11 (SEQ ID NO:86) polypeptide, a recombinant gene encoding an SrKAHel (SEQ ID NO:18, SEQ ID NO:68) polypeptide, a recombinant gene encoding an S. rebaudiana CPR8 (SEQ ID NO:24, SEQ ID NO:28) polypeptide, a recombinant gene encoding an S.
• rebaudiana UGT85C2 (SEQ ID NO:30) polypeptide, a recombinant gene encoding an S. rebaudiana UGT74G1 (SEQ ID NO:29) polypeptide, a recombinant gene encoding an S, rebaudiana UGT76G1 (SEQ ID NO:2) polypeptide, and a recombinant gene encoding an S. rebaudiana UGT91 D2 variant, UGT91 D2e-b (SEQ ID NO:88), polypeptide accumulated steviol glycosides.
• the UGT91 D2e-b variant of UGT91 D2 (SEQ ID NO:5 from PCT/US2012/050021 ) includes a substitution of a methionine for leucine at position 211 and a substitution of an alanine for valine at position 286. Additional variants can include variants (except T144S, M152L, L213F, S364P, and G384C variants) described in Table 14 and Example 11 of the PCT/US2012/050021. GeneArt codon-optimized sequence encoding a S.
• a separate S. cerevisiae strain was constructed to accumulate RebB.
• This strain comprised a recombinant gene encoding a Synechococcus sp. GGPPS (SEQ ID NO:49) polypeptide, a recombinant gene encoding a truncated Z. mays CDPS (SEQ ID NO:37) polypeptide, a recombinant gene encoding an A. thaliana KS (SEQ ID NO:6) polypeptide, a recombinant gene encoding an S. rebaudiana KO (SEQ ID NO:59, SEQ ID NO:79) polypeptide, a recombinant gene encoding an A.
• thaliana ATR2 (SEQ ID NO:51 , SEQ ID NO:87) polypeptide, a recombinant gene encoding an O. sativa EUGT11 (SEQ ID NO:86) polypeptide, a recombinant gene encoding an SrKAHei (SEQ ID NO: 18, SEQ ID NO:68) polypeptide, a recombinant gene encoding an S. rebaudiana CPR8 (SEQ ID NO:24, SEQ ID NO:28) polypeptide, a recombinant gene encoding an S. rebaudiana UGT85C2 (SEQ ID NO:30) polypeptide, a recombinant gene encoding an S.
• KO genes were analyzed. Putative KO genes were identified using the NCBi Basic Local Alignment Sequence Search Tool (BLAST). Genes encoding KO polypeptides were cloned and expressed the RebB-producing S. cerevisiae strain described in Example 2, which was modified to lack KO genes. Thus, RebB was only accumulated upon expression of a functional KO.
• BLAST Basic Local Alignment Sequence Search Tool
• the KO polypeptides encoded by nucleotide sequences set forth in SEQ ID NOs: 55-57 more efficiently converted ent-kaurene, ent-kaurenol, and/or ent-kaurenal to ent-kaurenoic acid in S. cerevisiae, as compared to the SrKOI polypeptide encoded by nucleotide sequence set forth in SEQ ID NO:59.
• S. cerevisiae strains co-expressing any of the heterologous nucleic acids encoding a KO enzyme of Table 2 and further overexprssing SrKAHel (SEQ ID NO:18, SEQ ID NO:68) accumulated higher levels of steviol glycosides than the control S. cerevisiae strain (not expressing a KO of Table 2) or a steviol glycoside-producing S. cerevisiae strain only overexpressing SrKAHel , as shown in Figure 5.
• S. cerevisiae strain expressing a codon-optimized version of SEQ ID NO:56, identified herein as SEQ ID NO:65, and overexpressing SrKAHel accumulated higher levels of steviol glycosides (RebA, RebD, and RebM) than the steviol glycoside-producing S. cerevisiae strain co-expressing the nucleic acid set forth in SEQ ID NO:56 and SrKAHel ( Figure 6).
• S, cerevisiae strains co-expressing a nucleic acid set forth in SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, or SEQ ID NO:60 and further overexpressing SrKAHel accumulated higher levels of glycosylated ent-kaurenoic acid than the control S. cerevisiae strain not expressing a KO of Table 2 ( Figure 7).
• S. cerevisiae strains co-expressing a nucleic acid set forth in SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:59, or SEQ ID NO:60 and further overexpressing SrKAHel demonstrated improved metabolic conversion of intermediate compound, ent-kaurenol, which, in turn, resulted in reduced accumulation of glycosylated ent- kaurenol, relative to the control S. cerevisiae strain not expressing a KO of Table 2 or the steviol glycoside-producing S. cerevisiae strain only overexpressing SrKAHel , as shown in Figure 8.
• cerevisiae strain only overexpressing SrKAHel each accumulated higher leveis of glycosylated ent-kaurenol than did S. cerevisiae strains expressing a nucleic acid set forth in SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:59, or SEQ ID NO:60 and further overexpressing SrKAHel .
• CPR genes were individually expressed in a steviol glycoside-producing S. cerevisiae strain.
• S. rebaudiana CPR8 SEQ ID NO:24, SEQ ID NO:28
• A. thaliana ATR2 SEQ ID NO:51
• cerevisiae strain expressing the nucleic acid set forth in SEQ ID NO:62 and overexpressing SrKAHel (SEQ ID NO:18, SEQ ID NO:68) accumulated higher levels of RebM than those accumulated by the control steviol glycoside-producing S. cerevisiae strain that only overexpressed SrKAHel ( Figure 10).
• Candidate KAH enzymes were cloned and expressed in an S. cerevisiae strain engineered to accumulate 13-SMG.
• the 13-SMG-producing S. cerevisiae strain comprised a recombinant gene encoding a Synechococcus sp. GGPPS7 polypeptide (SEQ ID NO:49), a recombinant gene encoding a truncated Z. mays CDPS polypeptide (SEQ ID NO:37), a recombinant gene encoding an A.
• thaliana KS polypeptide SEQ ID NO:6
• SrKOI SEQ ID NO:59, SEQ ID NO:79
• CPR8 SEQ ID NO:24, SEQ ID NO:28
• the KO encoded by the nucleotide sequence set forth in SEQ ID NO:56 amino acid sequence set forth in SEQ ID NO:75
• UGT85C2 SEQ ID NO:30
• the KAH encoded by the nucleotide sequence set forth in SEQ ID NO:80 was codon-optimized for expression in yeast (SEQ ID NO:81 ) and expressed in the above-described 13-SMG-producing S. cerevisiae strain. Similar to expression of SrKAHel (SEQ ID NO:18) or the KAH encoded by the nucleotide sequence set forth in SEQ ID NO:80, expression of the codon-optimized nucleotide sequence set forth in SEQ ID NO:81 resulted in production of 13- SMG plus rubusoside ( Figure 13).
• KAHs encoded by the nucleotide sequence set forth in SEQ ID NO:80 and the codon-optimized nucleotide sequence set forth in SEQ ID NO:81 were also individually expressed in a steviol glycoside-producing strain, as described in Example 2, which expresses SrKAHel .
• SrKAHel SEQ ID NO: 18
• the KAH encoded by the nucleotide sequence set forth in SEQ ID NO:80 or of the KAH encoded by the codon-optimized nucleotide sequence set forth in SEQ ID NO:81
• a control strain not expressing the KAH encoded by the nucleotide sequence set forth in SEQ ID NO:80, the KAH encoded by the codon-optimized nucleotide sequence set forth in SEQ ID NO:81 or overexpressing SrKAHel . See Table 6.
• a nucleic acid of SEQ ID NO:90 which was codon-optimized for expression in S. cerevisiae and encodes the polypeptide of SEQ ID NO:91 , was cloned and expressed in an S. cerevisiae strain described in Example 7, which was engineered to accumulate 13-SMG.
• the 13-SMG-producing S. cerevisiae strain comprised a recombinant gene encoding a Synechococcus sp.
• GGPPS7 polypeptide SEQ ID NO:49
• a recombinant gene encoding a truncated Z. mays CDPS polypeptide (SEQ ID NO:37), a recombinant gene encoding an A.
• thaliana KS polypeptide SEQ ID NO:6
• SrKOI SEQ ID NO:59, SEQ ID NO:79
• CPR8 SEQ ID NO:24, SEQ ID NO:28
• the KO encoded by the nucleotide sequence set forth in SEQ ID NO:56 amino acid sequence set forth in SEQ ID NO:75
• UGT85C2 SEQ ID NO:30
• the protein encoded by the nucleic acid sequence of SEQ ID NO:90, set forth in SEQ ID NO:91 is a KAH.
• Table 7 Quantification of Steviol Glycosides Accumulated by Yeast Expressing the KAH encoded by the Nucleotide Sequence Set Forth in SEQ ID NO:90 (Amino Acid
• CPR1 and CPR12 were measured using an in vitro microsomal assay.
• Microsomes were prepared by a modified version of the method taught by Pompon et a/., "Yeast expression of animal and plant P450s in optimized redox environments," Methods Enzymol. 272:51-64 (1996).
• S. cerevisiae cells were sedimented for 10 min at 4°C.
• the pellets were washed with 10 mL TEK buffer (50 mM Tris-HCI (pH 7.5), 1 mM EDTA, 100 mM KCI.) The cells were sedimented again for 10 min at 4°C, and the pellets were resuspended in 1-3 mL of TES2 buffer (50 mM Tri-HCI (pH 7.5) 1 mM EDTA, 600 mM sorbitol). Glass beads (425-600 microns) were added to the samples, and the cells were broken vigorously by shaking and vortexing for 5 min at 4°C. The supernatant was collected, and the beads were washed several times with TES2 buffer.
• TES2 buffer 50 mM Tris-HCI (pH 7.5), 1 mM EDTA, 100 mM KCI.
• the washes were combined with the supernatant, and the samples were centrifuged for 15 min at 4°C to remove unbroken cells and glass beads. Samples were then ultracentrifuged for 1 h at 4°C. The pellets were washed twice with TES buffer (50 mM Tris-HCI (pH 7.5), 1 mM EDTA, 600 mM sorbitol, 1 % (w/V) BSA, 5 mM DTT), and once with TEG buffer (50 mM Tris-HCI (pH 7.5), 1 mM EDTA, 30% (V/V) glycerol). The samples were resuspended in 1-3 mL TEG, and the pellets were homogenized.
• TES buffer 50 mM Tris-HCI (pH 7.5), 1 mM EDTA, 600 mM sorbitol, 1 % (w/V) BSA, 5 mM DTT
• TEG buffer 50 mM
• Wild-type control microsomal protein was prepared as described above from wild- type S. cerevisiae cells that did not comprise a heterologous KAH or CPR.
• Microsomal protein was also prepared from S. cerevisiae cells expressing i) SrKAHel (SEQ ID NO:18, SEQ ID NO:68), ii) SrKAHel (SEQ ID NO:18, SEQ ID NO:68) and CPR1 (SEQ ID NO:61 , SEQ ID NO:76), or iii) SrKAHel (SEQ ID NO:18, SEQ ID NO:68) and CPR12 (SEQ ID NO:97, SEQ ID NO:98) from a genetic construct integrated at the chromosome level.
• Microsomal protein from a steviol glycoside-producing strain was prepared from S. cerevisiae cells expressing the genes described in Example 2 and additionally comprising codon-optimized CPR1 from S. rebaudiana (SEQ ID NO:61 corresponding to amino acid sequence SEQ ID NO:76) as well as the KO encoded by SEQ ID NO:75).
• CPR1 and CPR12 activities were first determined using a cytochrome C reductase assay kit (Sigma-Aldrich; CY0100-1 KT) to measure the ability of CPR1 or CPR12 to reduce cytochrome C in the presence of NADPH in vitro. Reduction of cytochrome C resulted in an increase in absorbance at 550 nm, which could quantified spectrophotometrically.
• Working solution was prepared by adding 9 mg cytochrome C to 20 mt_ assay buffer, and solution was stored at 25°C until use. NADPH was diluted in H 2 0 to a concentration of 0.85 mg/mL.
• the enzymatic reactions were initiated by addition of NADPH, the samples were thoroughly mixed by pipetting, and absorbance was measured at 550 nm for 70 s with 10 s intervals between reads. Two independent rate measurements were taken for each microsomal preparation, and rates were averaged for calculation of specific activity. After the reactions were completed, results were normalized to protein concentration, which was measured using a standard BCA assay (Thermo Scientific).
• Units/mL was calculated using the following equation, where ⁇ A 550 /min represents the change in absorbance at 550 nm during the absorbance reading period, 1.1 represents the reaction volume in mL, and 21.1 represents the extinction coefficient for reduced cytochrome c:
• Units/mL ( ⁇ A 550 /min x dilution factor x 1.1 ) / (21.1 x enzyme volume)
• FIG. 14 shows the activity measurements of the i) SrKAHel (SEQ ID NO:18, SEQ ID NO:68), ii) SrKAHel (SEQ ID NO:18, SEQ ID NO:68) and CPR1 (SEQ ID NO:61 , SEQ ID NO:76), and iii) SrKAHel (SEQ ID NO: 18, SEQ ID NO:68) and CPR12 (SEQ ID NO:97, SEQ ID NO:98) microsomal samples.
• microsomal preparation from the wild-type control showed only minimal CPR activity, reflecting the low activity of native NCP1 (YHR042W).
• the microsomal preparation from a yeast strain overexpressing KAHel did not demonstrate an increase in CPR activity.
• microsomal preparation from strains expressing SrKAHel (SEQ ID NO:18, SEQ ID NO:68) and CPR1 (SEQ ID NO:61 , SEQ ID NO:76) or SrKAHel (SEQ ID NO:18, SEQ ID NO:68) and CPR12 (SEQ ID NO:97, SEQ ID NO:98) demonstrated high CPR activity, with 7- and 14-fold higher activity, respectively, compared to the negative control ( Figure 14).
• microsomal reactions were extracted with DMSO (1 :1 ) at 80°C for 10 min and submitted for LC-MS analysis after centrifugation.
• DMSO dimethyl methoxysulfoxide
• ent-kaurenoic acid quantification the microsomes reactions were extracted with acetonitrile 1 :4 (20% microsomal reaction and 80% acetonitrile) at 80°C for 10 min and after centrifugation submitted for LC-MS analysis.
• the AUC values obtained for the ent- kaurenoic acid measurements were converted to concentrations using a standard curve.
• microsomal protein prepared from an S. cerevisiae strain expressing SrKAHel (SEQ ID NO: 18, SEQ ID NO:68) and either CPR1 (SEQ ID NO:61 , SEQ ID NO:76) or CPR12 (SEQ ID NO:97, SEQ ID NO:98) converted ent-kaurenoic acid to steviol during the 30 minute incubation period.
• the steviol level shown in Figure 15A for the steviol- glycoside-producing strain control (extracted immediately with no 30 min incubation period) corresponds to steviol that was accumulated by the strain prior to microsomal preparation and that had co-purified with the microsomes.
• ent-kaurenoic acid Ievels decreased upon incubation with microsomal protein prepared from S. cerevisiae strains expressing SrKAHel (SEQ ID NO:18, SEQ ID NO:68) alone or in combination with CPR1 (SEQ ID NO:61 , SEQ ID NO:76) or CPR12 (SEQ ID NO:97, SEQ ID NO:98).
• the increased ent- kaurenoic acid Ievels shown in Figure 15B for the steviol glycoside-producing strain microsomal sample incubated for 30 min corresponds to ent-kaurenoic acid that was accumulated by the strain prior to microsomal preparation and to ent-kaurenoic acid accumulated from ent-kaurene that had co-purified with the microsomes.
• the levels of ent-kaurenoic acid shown in Figure 15B were corrected for the dilution factor used.
• CYP102A1 (also referred to as P450 BM3 ; SEQ ID NO:1 15, SEQ ID NO:116) is a catalytically self-sufficient soluble enzyme from Bacillus megatarium. See, e.g., Whitehouse et ai, 2012, Chem Soc Rev. 41 (3): 1218-60. Two domains are present in the CYP102A1 polypeptide chain: a P450 heme domain (BMP) and an NADPH-dependent P450 oxidoreductase domain (BMR). CYP102A1 utilizes nearly 100% of the reducing power of NADPH to produce a monooxygenated product. See, e.g., Yuan et ai, 2009, Biochemistry 48(38):9140-6.
• BMR BMR domain of CYP102A1
• SrKOi SEQ ID NO:59, SEQ ID NO:79
• a linker SEQ ID NO:121 , SEQ ID NO:122
• SrKOi SEQ ID NO:59, SEQ ID NO:79
• the KO encoded by the nucleotide sequence set forth in SEQ ID NO:65 were also truncated prior to fusion with the BMR domain of CYP102A1 ; these truncations were predicted by bioinformatics to result in loss of membrane anchors of the KO genes and in cytosolic versions of the KO-BMR fusion constructs.
• the KO-BMR fusion constructs analyzed are shown in Table 8.
• Table 8 KO-BMR fusion constructs and sequences.
• KO-BMR fusion constructs were cloned and transformed in the RebB-producing strain described in Example 2, which was modified to not comprise any additional KO genes.
• steviol glycosides including 13-SMG, 1 ,2-bioside, and RebB, were only accumulated upon expression of a functional KO.
• Three scrapes (1 ⁇ L. loop of cells) from each transformation plate were resuspended in 200 ⁇ nanopure H 2 O. 70 were ⁇ L then transferred to 1 mL SC-URA in a 96 deep well plate and incubated at 30°C for 5 days at 400 rpm.
• Biological triplicates were analyzed by LC-MS (method 2 of Example 1 ) to measure 13-SMG, 1 ,2-bioside, and RebB levels, and single samples were analyzed by LC-UV to measure ent-kaurene and ent-kaurenoic acid levels.
• LC-MS For LC-MS, 50 ⁇ L samples were mixed with 50 ⁇ L 100% DMSO and heated to 80°C for 10 min. Subsequently, the samples were spun down at 4000 RCF for 10 min, and 85 ⁇ L. of the resulting supernatant was transferred to an LC-MS plate. The LC-MS results were normalized by OD 600 of individual cultures, which was measured by a Wallac, 2104 EnVision (Perkin Elmer) plate reader.
• LC-UV was conducted with an Agilent 1290 instrument comprising a variable wavelength detector (VWD), a thermostatted column compartment (TCC), an autosampler, an autosampler cooling unit, and a binary pump and using SB-C18 rapid resolution high definition (RRHD) 2.1 mm x 300 mm, 1.8 pm analytical columns (two 150 mm columns in series; column temperature of 65°C).
• RRHD rapid resolution high definition
• Steviol glycosides and steviol glycoside precursors were separated by a reversed phase C18 column followed by detection by UV absorbance at 210 mm. Quantification of steviol glycosides was done by comparing the peak area of each analyte to standards of RebA and applying a correction factor for species with differing molar absorptivities.
• steviol glycoside precursors such as kaurenoic acid, kaurenal, kaurenol, ent-kaurene, and geranylgeraniol
• steviol glycoside precursors such as kaurenoic acid, kaurenal, kaurenol, ent-kaurene, and geranylgeraniol
• ICE2 is an endoplasmic reticulum (ER) membrane protein involved in mechanisms such as ER zinc homeostasis and cytochrome P450 stability and/or activity. See, e.g., Estrada de Martin et al., 2005, J Cell Sci. 118(Pt 1 ):65-77 and Emmerstorfer et al., 2015, Biotechnol J. 10(4):623-35.
• ICE2 SEQ ID NO:113, SEQ ID NO:114
• GGPPS polypeptide (SEQ ID NO:49), a recombinant gene encoding a truncated Z. mays CD PS polypeptide (SEQ ID NO:37), a recombinant gene encoding an A. thaliana KS polypeptide (SEQ ID NO:6), a recombinant gene encoding a recombinant S. rebaudiana KO polypeptide (SEQ ID NO:59, SEQ ID NO:79), a recombinant gene encoding an A.
• thaliana ATR2 polypeptide (SEQ ID NO:51 , SEQ ID NO:87), a recombinant gene encoding an SrKAHel (SEQ ID NO:18, SEQ ID NO:68) polypeptide, a recombinant gene encoding an S.
• rebaudiana CPR8 polypeptide (SEQ ID NO:24, SEQ ID NO:28), a recombinant KAH gene encoded by the nucleotide sequence set forth in SEQ ID NO:81 (corresponding to the amino acid sequence set forth in SEQ ID NO:82), a recombinant KO gene encoded by the nucleotide sequence set forth in SEQ ID NO:56 (corresponding to the amino acid sequence set forth in SEQ ID NO:75), a recombinant KO gene encoded by the nucleotide sequence set forth in SEQ ID NO:65 (corresponding to the amino acid sequence set forth in SEQ ID NO:75), a recombinant gene encoding a UGT76G1 (SEQ ID NO:83) polypeptide, a recombinant gene encoding an S, rebaudiana UGT85C2 polypeptide (SEQ ID NO:30), a recombinant gene encoding an S.
• Table 9 shows additional recombinant genes (ICE2 and/or CPR12) expressed in the above-described strain.
• the control strain did not comprise recombinant genes encoding ICE2 (SEQ ID NO:113, SEQ ID NO: 114) or CPR12 (SEQ ID NO:97, SEQ ID NO:98) polypeptides.
• Table 9 ICE2 steviol glycoside-producing strains.
• Fed-batch fermentation was carried out aerobically in 2 L fermenters at 30°C with an approximate 16 h growth phase in minimal medium comprising glucose, ammonium sulfate, trace metals, vitamins, salts, and buffer followed by an approximate 110 h feeding phase with a glucose-comprising defined feed medium.
• a pH near 6.0 and glucose-limiting conditions were maintained.
• Whole culture samples (without cell removal) were analysed by the LC-UV method of Example 10 to determine levels of steviol glycosides and steviol pathway intermediates.
• Total Flux was calculated as a sum (in g/L RebD equivalents) of measured RebA, RebB, RebD, RebE, RebM, 13-SMG, rubusoside, steviol-1 ,2- bioside, di-glycosylated steviol, tri-glycosylated steviol, tetra-glycosylated steviol, penta- glycosytated steviol, hexa-glycosylated steviol, hepta-glycosylated steviol, copalol, ent- kaurenoic acid, glycosylated ent-kaurenoic acid, glycosylated ent-kaurenol, ent-kaurena!, geranylgeraniol, ent-kaurenal, and ent-kaurene levels.
• Pre-steviol glycoside/flux was calculated as (("total flux” - (geranylgeraniol + copalol + ent-kaurene + glycosylated ent- kaurenol + ent-kaurenol + ent-kaurenal + ent-kaurenoic acid + glycosylated ent-kaurenoic acid) / "total flux”).
• KAH step/flux was calculated as ((ent-kaurenoic acid + glycosylated ent- kaurenoic acid) / "total flux”).
• “KO step/flux” was calculated as ((ent-kaurene + glycosylated ent- kaurenol + ent-kaurenol + ent-kaurenal) / "total flux”).
• the pre-steviol glycoside/flux, KO step/flux, and KAH step/flux values are shown in Table 10 below. Decreased amounts of ent-kaurene, ent-kaurenol, ent-kaurenal, glycosylated ent-kaurenol and increased amounts of ent-kaurenoic acid and glycosylated ent-kaurenoic acid were observed in the strains comprising ICE2, as compared to the control steviol glycoside- producing strain. These effects were stronger in the presence of CPR1 and/or CPR12 (Table 10).
• ICE2 strain B Overexpression of two copies of ICE2 (ICE2 strain B) resulted decreased ent-kaurene, ent- kaurenol, ent-kaurenal, and ent-kaurenol glycoside levels and increased steviol glycoside levels, compared to the control strain, ICE2 strain A, or ICE2 strain C (Table 10). Steviol glycoside levels increased most in the steviol glycoside-producing strain comprising two copies of ICE2. Thus, ICE2 was found to improve cytochrome P450 function.
• Table 10 Pre-steviol glycoside/flux, KO step/flux, and KAH step/flux values for steviol glycoside-producing strains comprising ICE2.
• Steviol glycoside-producing S, cerevisiae strains comprising a recombinant gene encoding a Synechococcus sp. GGPPS polypeptide (SEQ ID NO:49), a recombinant gene encoding a truncated Z. mays CDPS polypeptide (SEQ ID NO:37), a recombinant gene encoding an A. thaliana KS polypeptide (SEQ ID NO:6), a recombinant gene encoding a recombinant S. rebaudiana KO polypeptide (SEQ ID NO:59, SEQ ID NO:79), a recombinant gene encoding an A.
• thaliana ATR2 polypeptide (SEQ ID NO:51 , SEQ ID NO:87), a recombinant gene encoding an SrKAHei (SEQ ID NO:18, SEQ ID NO:68) polypeptide, a recombinant gene encoding an S.
• pre-steviol glycoside/flux, KO step/flux, and KAH step/flux values are shown in Table 12 below.
• strain A the KO encoded by nucleotide sequence set forth in SEQ ID NO:56
• strain A lower accumulation of ent-kaurene, ent-kaurenol, ent-kaurnal, and ent-kaurenol glycosides resulted.
• Higher levels of ent-kaurenoic acid and steviol glycosides were also measured, as compared to the control strain.
• strain B In the strain comprising the KAH encoded by nucleotide sequence set forth in SEQ ID NO:80, the KO encoded by nucleotide sequence set forth in SEQ ID NO:56 (corresponding to amino acid sequence set forth in SEQ ID NO:75), and the KO encoded by nucleotide sequence set forth in SEQ ID NO:65 (strain B), ent- kaurene, ent-kaurenol, ent-kaurenal, ent-kaurenol glycosides, and ent-kaurenoic acid accumulation decreased and accumulation of steviol glycosides increased, as compared to the control strain.
• CPR12 SEQ ID NO:97, SEQ ID NO:98
• the KAH encoded by nucleotide sequence set forth in SEQ ID NO:80 and the KO encoded by nucleotide sequence set forth in SEQ ID NO:56
• ent-kaurenol, ent-kaurenal, ent-kaurenol glycosides, and ent-kaurenoic acid accumulation decreased and accumulation of steviol glycosides increased, as compared to the control. See Table 12.
• CPR12 was found to be a reductase protein that improves KAH and/or KO activity.

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