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WO 2012/109274 Al 16 August 2012 (16.08.2012) P O P C T

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WO 2012/109274 Al 16 August 2012 (16.08.2012) 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 2012/109274 Al 16 August 2012 (16.08.2012) P O P C T (51) International Patent Classification: (72) Inventors; and CUP 7/08 (2006.01) (75) Inventors/Applicants (for US only): DOUDNA CATE, James, H. [US/US]; 164 Vicente Rd., Berkeley, CA 94705 (21) International Application Number: (US). JIN, Yong-Su [KR/US]; 3005 Sandhill Ln, Cham PCT/US20 12/024 186 paign, IL 61822 (US). GALAZKA, Jonathan, M. (22) International Filing Date: [US/US]; 3018 Deakin St. Apt. A, Berkeley, CA 94705 7 February 2012 (07.02.2012) (US). HA, Suk-Jin [KR/US]; 208 Paddock Dr. E., Savoy, IL 61874 (US). (25) Filing Language: English (74) Agents: WARD, Michael, R. et al; Morrison & Foerster (26) Publication Language: English LLP, 425 Market Street, San Francisco, CA 94105-2482 (30) Priority Data: (US). 61/440,305 7 February 201 1 (07.02.201 1) US (81) Designated States (unless otherwise indicated, for every 61/566,548 2 December 201 1 (02. 12.201 1) US kind of national protection available): AE, AG, AL, AM, (71) Applicants (for all designated States except US): THE AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, REGENTS OF THE UNIVERSITY OF CALIFORNIA CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, [US/US]; 1111 Frankllin Street, 12th Floor, Oakland, CA DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, 94607-5200 (US). THE BOARD OF TRUSTEES OF HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, THE UNIVERSITY OF ILLINOIS [US/US]; 352 Henry KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, Administration Building, 506 South Wright Street, Urbana, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, IL 61801 (US). OM, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. [Continued on nextpage] (54) Title: ENHANCED CELLODEXTRIN METABOLISM (57) Abstract: The present disclosure relates to host cells containing two or more of a recombinant cellodextrin trans porter, a recombinant cellodextrin phosphorylase, a recom binant β-glucosidase, a recombinant phosphoglucomutase, or a recombinant hexokinase; and to methods of using such cells for degrading cellodextrin, for producing hydrocarbons or hydrocarbon derivatives from cellodextrin, and for redu cing ATP consumption during glucose utilization. I © FIG. 1 o o w o 2012/109274 Al HI II III 111 II I 11II 1111II 11111II III (84) Designated States (unless otherwise indicated, for every Published: Mnd of regional protection available): ARIPO (BW, GH, — with international search report (Art. 21(3)) GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, — before the expiration of the time limit for amending the RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, claims and to be republished in the event of receipt of DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, amendments (Rule 48.2(h)) LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, — with sequence listing part of description (Rule 5.2(a)) SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, ML, MR, NE, SN, TD, TG). ENHANCED CELLODEXTRIN METABOLISM CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application claims the benefit of U.S. Provisional Application No. 61/440,305, filed February 7, 2011, and U.S. Provisional Application No. 61/566,548, filed December 2, 201 1, both of which are hereby incorporated by reference in their entirety. SUBMISSION OF SEQUENCE LISTING AS ASCII TEXT FILE [0002] The content of the following submission on ASCII text file is incorporated herein by reference in its entirety: a computer readable form (CRF) of the Sequence Listing (file name: 677792001340SeqList.txt, date recorded: February 6, 2012, size: 1209 KB). FIELD [0003] The present disclosure relates to methods and compositions for degrading cellodextrin and for producing hydrocarbons and hydrocarbon derivatives. BACKGROUND [0004] Biofuels are under intensive investigation due to increasing concerns about energy security, sustainability, and global climate change (Lynd et al., Science, 1991). Bioconversion of plant-derived lignocellulosic materials into biofuels has been regarded as an attractive alternative to chemical production of fossil fuels (Lynd et al., Nat Biotech, 2008; Hahn-Hagerdal et al., Biotechnol Biofuels, 2006). The engineering of microorganisms to perform the conversion of lignocellulosic biomass to ethanol efficiently remains a major goal of the biofuels field. Much research has been focused on genetically manipulating microorganisms that naturally ferment simple sugars to alcohol to express cellulases and other enzymes that would allow them to degrade lignocellulosic biomass polymers and generate ethanol within one cell, a process known as consolidated bioprocessing (CBP). [0005] Saccharomyces cerevisiae, also known as baker's yeast, has been used for bioconversion of simple hexose sugars into ethanol for thousands of years. It is also the most widely used microorganism for large scale industrial fermentation of D-glucose into ethanol. S. cerevisiae is a very suitable candidate for bioconversion of lignocellulosic biomass into biofuels (van Maris et al., Antonie Van Leeuwenhoek, 2006). It has a well-studied genetic and physiological background, ample genetic tools, and high tolerance to high ethanol concentration and inhibitors present in lignocellulosic hydrolysates (Jeffries, Curr Opin Biotechnol, 2006). The low fermentation pH of S. cerevisiae can also prevent bacterial contamination during fermentation. [0006] S. cerevisiae, however, does not naturally degrade and ferment the more complex biomass polymers, such as cellulose, that are present in plant cell walls. Enzymes useful for the degradation of biomass polymers have been sought after in those organisms that naturally degrade biomass, such as Neurospora crassa and Trichoderma reesei. A recent study of plant wall degradation in N. crassa showed that in addition to the expression of various cellulases, N. crassa expresses cellodextrin transporters and an intracellular β-glucosidase in response to cellulose (Tian et al., PNAS USA 106, 22157, 2009; Galazka et al., Science 330, 84, 2010). Cellodextrins are β (1— 4 ) linked oligosaccharides of glucose and are the product of cellulose depolymerization by fungal cellulases (Zhang and Lynd, Biotechnol Bioeng 88, 797, 2004). β-glucosidase hydrolyzes cellodextrins to glucose. [0007] S. cerevisiae engineered to express a cellodextrin transporter and an intracellular β-glucosidase are able to grow with cellodextrins as the sole carbon source and ferment cellobiose to ethanol efficiently (Galazka et al., Science 330, 84, 2010). However using a β-glucosidase to hydrolyze cellodextrins to glucose requires that all produced glucose be phosphorylated to glucose-6-phosphate in a reaction that consumes 1 ATP per glucose before further processing can occur. This is problematic when ATP is in short supply. [0008] In addition, transport of cellodextrins followed by intracellular hydrolysis facilitates the co-fermentation of cellulose-derived glucose and hemicellulose-derived xylose, which S. cerevisiae is normally unable to do. However, these engineered strains may not ferment glucose with optimal metabolism because their endogenous system for detecting and responding to the presence of glucose is dependent on the extracellular level of glucose. In the engineered strains, the extracellular level of glucose is no longer tied to the level of glucose available to the cell since glucose is generated intracellularly by transporting cellodextrins into the cell and intracellularly degrading the cellodextrins to glucose. [0009] Accordingly, a need exists for improved engineered yeast strains that can perform consolidated bioprocessing of biomass polymers to biofuels and other useful chemicals, and that consume less ATP wehn phosphorylating the glucose produced from the cleavage of cellodextrins. BRIEF SUMMARY [0010] In order to meet the above needs, the present disclosure provides host cells containing two or more of a recombinant cellodextrin transporter, a recombinant cellodextrin phosphorylase, a recombinant β-glucosidase, a recombinant phosphoglucomutase, or a recombinant hexokinase; and methods of using such cells for degrading cellodextrin, for producing hydrocarbons or hydrocarbon derivatives from cellodextrin, and for reducing ATP consumption during cellodextrin utilization. Moreover, the present disclosure is based at least in part on the novel discovery that yeast strains engineered to express an intracellular cellodextrin phosphorylase rather than a β-glucosidase consumed less ATP in the utilization of cellodextrins and produced nearly equivalent amounts of ethanol as compared to a yeast strain that expresses a β-glucosidase. Advantageously, cellodextrin phosphorylases utilize inorganic phosphate to cleave the β-glucosidic linkage between glucose moieties in cellodextrins. The phosphorolysis reaction saves 1 ATP equivalent per cleavage reaction and results in the release of glucose- 1- phosphate (Fig. 1). The resulting glucose- 1-phosphate can then be converted to glucose-6- phosphate by phosphoglucomutases (Fig. 1). Moreover, the yeast can directly utilize the resulting glucose-6-phosphate for growth and fermentation. [0011] Accordingly, certain aspects of the present disclosure relate to a method for
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