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WO 2014/207087 Al 31 December 2014 (31.12.2014) P O P C T

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WO 2014/207087 Al 31 December 2014 (31.12.2014) P O P C T (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 2014/207087 Al 31 December 2014 (31.12.2014) P O P C T (51) International Patent Classification: Seville (ES). GUTIERREZ GOMEZ, Pablo; Campus C12N 9/00 (2006.01) C12N 9/90 (2006.01) Palmas Altas, Calle Energia Solar 1, E-41014 Seville (ES). C12N 9/02 (2006.01) C12P 5/02 (2006.01) (74) Agent: NEDERLANDSCH OCTROOIBUREAU; J.W. C12N 9/10 (2006.01) C12P 7/76 (2006.01) Frisolaan 13, NL-2517 JS The Hague (NL). C12N 9/12 (2006.01) C12P 7/64 (2006.01) C12N 9/88 (2006.01) C12N 1/1 9 (2006.01) (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, (21) International Application Number: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, PCT/EP2014/063484 BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (22) International Filing Date: DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, 26 June 2014 (26.06.2014) HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, (25) Filing Language: English MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, (26) Publication Language: English OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, (30) Priority Data: TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, 13382241 .1 26 June 2013 (26.06.2013) EP ZW. (71) Applicant: ABENGOA BIOENERGIA NUEVAS (84) Designated States (unless otherwise indicated, for every TECNOLOGIAS S.A. [ES/ES]; Campus Palmas Altas, kind of regional protection available): ARIPO (BW, GH, Calle Energia Solar no 1, E-41014 Seville (ES). GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, (72) Inventors: DE ΒΟΝΤ,, Johannes Adrianus Maria; UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, Lawickse Allee 68, NL-6707 AK Wageningen (NL). TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, RAAB, Andreas; Ilsenburger Str. 13, 10589 Berlin (DE). EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, SCHILLING, Michael; Schonensche Str. 6, 10439 Berlin (DE). TAMAME GONZALEZ, Maria Mercedes; Calle TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Zacarias Gonzalez 2, E-37007 Salamanca (ES). DE LOS ANGELES SANTOS GARCIA, Maria; Edificio De- Published: partamental, Campus Unamuno, E-37007 Salamanca (ES). — with international search report (Art. 21(3)) MARTINS DOS SANTOS, Vitor; Harzstrasse 27, 38300 Wolfenbuettel (DE). ARJONA ANTOLIN, Ricardo; — with sequence listing part of description (Rule 5.2(a)) Campus Palmas Altas, Calle Energia Solar 1, E-41014 (54) Title: PRODUCTION OF ADVANCED FUELS AND OF CHEMICALS BY YEASTS ON THE BASIS OF SECOND GEN ERATION FEEDSTOCKS 00 o (57) Abstract: The present invention relates to modified eukaryotic microbial cells that have been engineered for producing ferment ation products such as fatty acids, 1-alcohols, β- keto-acids and -alcohols, β-hydroxyacids, 1,3-diols, trans-A -fatty acids, alkenes, al- o kanes and derivatives thereof, from second generation feedstocks, including at least pentoses. To this end the eukaryotic microbial cells have been modified to express enzymes of the fatty acid β-oxidation cycle in the cytosol of the cell in the absence of fatty acids and in the presence of a carbon source containing pentoses. The cells are further modified to express enzymes for metabolizing o pentose like xylose and arabinose, as well as to express a metabolic route for producing under oxic conditions, acetyl-CoA from the non- fatty acid carbon source to feed into and drive the β-oxidation cycle in the bio synthetic direction and, to express termination enzymes for conversion of reaction β-oxidation cycle intermediates into the desired fermentation product. The invention further o relates to oxic processes wherein the cells are used to produce fermentation products such as fatty acids, 1-alcohols, β-keto-acids and -alcohols, β- hydroxyacids, 1,3-diols, trans-A -fatty acids, alkenes, alkanes or derivatives thereof. Production of advanced fuels and of chemicals by yeasts on the basis of second generation feedstocks Field of the invention The present invention relates to the utilization of second generation feedstocks in the microbial production of advanced fuels and chemicals. The invention is based on metabolic engineering of and fermentation by yeasts such as Saccharomyces cerevisiae. In particular, the invention relates to S. cerevisiae strains that have been engineered to express in the absence of fatty acids several of the enzymes that are required in the degradation of such acids along with certain other enzymes. The expression of some of the native yeast enzymes has been prevented in order to avoid the formation of undesired by-products. By varying the expression of the various enzymes in yeast, it has been possible to obtain a range of metabolically-engineered yeasts that each produce a particular valuable compound from sugars such as hexoses and/or pentoses. The invention further relates to the processes wherein the engineered strains of the invention produce compounds from sugars. Background of the invention The production of ethanol from first generation feedstocks such as corn, wheat and sugarcane has been optimized and it currently is applied world-wide. The process, however, has generic drawbacks at two levels. Firstly, ethanol is not an optimal fuel compound in view of its chemical structure and the associated physical properties. Secondly, first generation feedstocks are under pressure both reasons of economics and of sustainability. These two drawbacks call for a radical change in the bioproduction of fuels. Novel ways should be explored to arrive at production processes for advanced fuels that are more suitable than ethanol. And such compounds should be produced from second rather from first generation feedstocks. In developing processes for advanced fuels it is possible to develop hand in hand production processes for chemicals. Second generation feedstocks are lignocellulosic materials. They may be derived from stalks, cobs, etc. from plants that now are used as first generation feedstocks. In other words bagasse, wheat straw, corn stover, etc. Such materials also can be obtained by growing dedicated energy crops on marginal lands thus not competing directly with food crops. Waste streams may be used as ell such as solid municipal wastes. Lignocellulosic materials are cheaper than first generation sugar streams, but they require specific treatments. Harvesting may be an issue and the feedstocks require costly pretreatment and enzymatic treatments for liberating sugars. An important aspect is that lignocellulosics contain not only C6 sugars (glucose, fructose) but also C5 sugars (xylose, arabinose). For a profitable process, it consequently is required that also the C5 sugars are converted into the desired product along with the C6 sugars. Another issue with lignocellulosics as feedstocks is that pretreatment results often in compounds that are toxic to microbes such as acetic acid, furfural and hydroxymethylfurfural . Zhang et al (Current Opinion in Biotechnology 201 1, 22:775-783) disclose that production of biofuels from renewable resources provides a source of liquid transportation fuel to replace petroleum-based fuels. This endeavor requires the conversion of cellulosic biomass into simple sugars, and the transformation of simple sugars into biofuels. Recently, microorganisms have been engineered to convert simple sugars into several types of biofuels, such as alcohols, fatty acid alkyl esters, alkanes, and terpenes, with high titers and yields. Several engineered metabolic pathways for the production of advanced biofuels were reported. Peralta-Yahya et al (2012, Nature, 488(741 1):320-8) disclose that advanced biofuels produced by microorganisms have similar properties to petroleum-based fuels, and can 'drop in' to the existing transportation infrastructure. However, producing these biofuels in yields high enough to be useful requires the engineering of the microorganism's metabolism. Pathways for fatty-acid-derived fuels were quoted from published data. Clomburg and Gonzalez (2010, Biotechnol Bioeng. 108(4):867-79) disclose biofuel production in E. coli with an emphasis on metabolic engineering and synthetic biology. Dellomonaco et al. (201 1, Nature, 476:355-361; WO 2012/109176) disclose the engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals in E. coli. They produced long-chain products via elongation of short-chain metabolites. They applied a reversal of the β-oxidation cycle as based on CoA-thioester intermediates that directly uses acetyl-CoA for acyl-chain elongation. Gulevich et al. (2012, Biotechnol Lett. 34(3):463-9) disclose metabolic engineering of E. coli for 1-butanol synthesis through the inverted aerobic fatty acid β- oxidation pathway. Zheng et al. (2012, Microbial Cell Factories 11:65) disclose that they have studied the bioproduction of C12/C14 and C16/18 alcohols in E. coli. They improved the fatty alcohol production by systematically optimizing the fatty alcohol biosynthesis pathway, mainly by targeting three key steps from fatty acyl-acyl carrier proteins (ACPs) to fatty alcohols, which are sequentially catalyzed by thioesterase, acyl- coenzyme A (CoA) synthase and fatty acyl-CoA reductase. Bernard et al. (2012, Plant Cell. 24(7):3106-18) disclose that reconstitution of plant alkane biosynthesis is possible in yeast. The specific approaches in producing biofuels compounds as quoted above depend on the enzyme machinery for either fatty acid oxidation (e.g. Dellamonaco et al.
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