WO 2017/050853 Al 30 March 2017 (30.03.2017) P O P C T
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(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2017/050853 Al 30 March 2017 (30.03.2017) P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12P 19/44 (2006.01) C12N 15/52 (2006.01) kind of national protection available): AE, AG, AL, AM, C12P 17/06 (2006.01) AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (21) Number: International Application DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, PCT/EP20 16/072474 HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (22) International Filing Date: KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, 2 1 September 2016 (21 .09.201 6) MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (25) Filing Language: English SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, (26) Publication Language: English TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: 62/222,919 24 September 2015 (24.09.2015) US (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (71) Applicant: EVOLVA SA [CH/CH]; Duggingerstrasse 23, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, 4153 Reinach (CH). TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, (72) Inventors: NAESBY, Michael; 2, rue de l'hotel de ville, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, 68330 Huningue (FR). ZOKOURI, Zina; Schreinerstrasse LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, 43, 8004 Zurich (CH). FISCHER, David; Gotthelfweg 5, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, 4144 Arlesheim (CH). EICHENBERGER, Michael; Gil- GW, KM, ML, MR, NE, SN, TD, TG). genbergerstrasse 23, 4053 Basel (CH). HANSSON, An¬ ders; Riehentorstrasse 33, 4058 Basel (CH). Published: (74) Agent: SMAGGASGALE, Gillian Helen; 138 Fetter — with international search report (Art. 21(3)) Lane, London EC4A 1BT (GB). — with sequence listing part of description (Rule 5.2(a)) (54) Title: PRODUCTION OF ANTHOCYANIN FROM SIMPLE SUGARS b) ∞ o o FIG. 1 (57) Abstract: Methods for producing anthocyanin by expression in a microorganism are disclosed including culturing of the mi o croorganism under anthocyanin producing conditions, wherein the microorgamsm has an operative metabolic pathway including at least one heterologous enzyme activity, the pathway producing anthocyanin from simple sugars or other simple carbon sources. PRODUCTION OF ANTHOCYANIN FROM SIMPLE SUGARS BACKGROUND OF THE INVENTION Field of the Invention [0001] Provided are methods for producing anthocyanins in recombinant host cells. Description of Related Art [0002] Over the last decade there have been several reports of heterologous production of flavonoids, including anthocyanins, using unicellular hosts, particularly in the prokaryote, Escherichia coli, and the eukaryote, Saccharomyces cerevisiae. Especially in E. coli there has been some success, predominantly after feeding intermediates of the flavonoid pathway to the bacteria. This has allowed several flavanones, flavones, and flavonols to be produced from phenyl propanoid precursors (see e.g., Yan 2005; Jiang 2005; Leonard 2007, respectively). In addition, several other flavonoids were made by intermediate feeding, such as isoflavonoids from liquiritigenin; flavan-3-ols and flavan-4-ols from flavanones; and anthocyanins from either flavanones or from (+)-catechin. However, there are no reports of anthocyanins being produced from basal medium components such as sugar or from the natural precursors phenylalanine or tyrosine. [0003] The anthocyanin biosynthetic pathway is shown n FIG. As shown, in this pathway the flavonoid intermediate coumaroyl-CoA is produced via the plant phenylpropanoid pathway. Phenylalanine is deaminated by the action of phenylalanine ammonia lyase (PAL), an enzyme of the ammonia lyase family, to form cinnamic acid. Cinnamic acid is then hydroxylated to p-coumaric acid (also called 4-coumaric acid) by cinnamate 4-hydroxylase (C4H), a CYP450 enzyme. Alternatively, p-coumaric acid is formed directly from tyrosine by the action of tyrosine ammonia lyase (TAL). Some enzymes have both PAL and TAL activity. The enzyme 4-coumarate-CoA-ligase (4CL) activates p-coumaric acid to p-coumaroyl CoA by attachment of a CoA group. [0004] Chalcone synthase (CHS), a polyketide synthase, is the first committed enzyme in the flavonoid pathway, and catalyzes synthesis of naringenin chalcone from one molecule of p-coumaroyl CoA and three molecules of malonyl CoA . Naringenin chalcone is rapidly and stereospecifically isomerized to the colorless (2S)-naringenin by chalcone isomerase (CHI). (2S)-Naringenin is hydroxylated at the 3-position by flavanone 3-hydroxylase (F3H) to yield (2R,3R)-dihydrokaempferol, a dihydroflavonol. F3H belongs to the 2-oxoglutarate-dependent dioxygenase (20DD) family. Flavonoid 3'-hydroxylase (F3'H) and flavonoid 3',5'-hydroxylase (F3'5'H), which are P450 enzymes, catalyze hydroxylation of dihydrokaempferol (DHK) to form (2R.3R)- dihydroquercetin and dihydromyricetin, respectively. F3'H and F3'5'H determine the hydroxylation pattern of the B-ring of flavonoids and anthocyanins and are necessary for cyanidin and delphinidin production, respectively. They are the key enzymes that determine the structures of anthocyanins and thus their color. Dihydroflavonols are reduced to corresponding 3,4-cis leucoanthocyanidins by the action of dihydroflavonol 4-reductase (DFR). Anthocyanidin synthase (ANS, also called leucoanthocyanidin dioxygenase or LDOX), which belongs to the 20DD family, catalyzes synthesis of corresponding colored anthocyanidins. In contrast to the well-conserved main pathway of flavonoid biosynthesis described above, modification of anthocyanidins is family- or species-dependent and can be very diverse. Additionally, in order to form more stable anthocyanins, anthocyanidins can be 3-glucosylated by the action of UDP- glucose:flavonoid (or anthocyanidin) 3GT. [0005] In yeast {e.g., S. cerevisiae), some of the same molecules (flavanones, flavones, and flavonols) have been made from phenyl propanoids. In addition, a few examples have been reported of production of flavonoids from sugar, e.g., naringenin (Koopman et al. 2012) and various flavanones and flavonols (Naesby 2009). However, production of anthocyanins has never been reported. [0006] Therefore, new approaches are required for producing anthocyanins via heterologous biosynthetic pathways in microbes. SUMMARY OF THE INVENTION [0007] It is against the above background that the present invention provides certain advantages and advancements over the prior art. Set forth herein are methods developed by selection of highly active heterologous genes, and by balancing the expression thereof, that produce anthocyanins from glucose in a microorganism host cell. Specifically provided herein are operative metabolic pathways for producing anthocyanins from glucose or other simple sugars. [0008] In a first aspect, the invention provides a microorganism including an operative metabolic pathway capable of producing an anthocyanin from glucose. The operative metabolic pathway includes at least a 4-coumaric acid-CoA ligase (4CL), a chalcone synthase (CHS), a flavanone 3-hydroxylase (F3H), a dihydroflavonol-4- reductase (DFR), an anthocyanidin synthase (ANS), an anthocyanidin 3-0- glycosyltransferase (A3GT), a chalcone isomerase (CHI), and at least one of a) a tyrosine ammonia lyase; or b) a phenylalanine ammonia lyase (PAL) and a trans- cinnamate 4-monooxygenase (C4H). At least one enzyme of the operative metabolic pathway is encoded by a gene heterologous to the microorganism is encoded by a gene heterologous to the microorganism. In particular embodiments, the anthocyanin is produced in a ratio of at least 1:1 to its anthocyanidin precursor by the operative metabolic pathway. [0009] In a second aspect, the invention provides a fermentation vessel including a microorganism having an operative metabolic pathway producing an anthocyanin from glucose. The operative metabolic pathway includes a 4-coumaric acid-CoA ligase (4CL), a chalcone synthase (CHS), a flavanone 3-hydroxylase (F3H), a dihydroflavonol- 4-reductase (DFR), an anthocyanidin synthase (ANS), an anthocyanidin 3-0- glycosyltransferase (A3GT), a chalcone isomerase (CHI), and a tyrosine ammonia lyase or a phenylalanine ammonia lyase (PAL) and a trans-cinnamate 4-monooxygenase (C4H), wherein at least one enzyme of the operative metabolic pathway is encoded by a gene heterologous to the microorganism. [0010] In a third aspect, the invention provides a microorganism including an operative metabolic pathway producing an anthocyanin from glucose. The operative metabolic pathway includes a 4-coumaric acid-CoA ligase (4CL) encoded by the nucleic acid sequence set forth in SEQ ID NO: , a chalcone synthase (CHS) encoded by the nucleic acid sequence set forth in SEQ ID NO: 2 1, a flavanone 3-hydroxylase (F3H) encoded by the nucleic acid sequence set forth in SEQ ID NO: 3, a dihydroflavonol-4- reductase (DFR) encoded by the nucleic acid sequence set forth in SEQ D NO: 5 or SEQ D NO: 7 , an anthocyanidin synthase (ANS) encoded by the nucleic acid sequence set forth in SEQ ID NO: 9, an anthocyanidin 3-O-glycosyltransferase (A3GT) encoded by the nucleic acid sequence set forth in SEQ ID NO: 11, a chalcone isomerase (CHI) encoded by the nucleic acid sequence set forth n SEQ ID NO: 13, and at least one of a) a tyrosine ammonia lyase (TAL) encoded by the nucleic acid sequence set forth in SEQ ID NO: 15 or b) a phenylalanine ammonia lyase (PAL) encoded by the nucleic acid sequence set forth in SEQ ID NO: 17 and a trans-cinnamate 4-monooxygenase (C4H) encoded by the nucleic acid sequence set forth in SEQ D NO: 19. [0011] In a fourth aspect, a microorganism includes an operative metabolic pathway capable of producing an anthocyanin from a simple sugar.