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(12) Patent Application Publication (10) Pub. No.: US 2010/0028966 A1 Blanchard Et Al

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(12) Patent Application Publication (10) Pub. No.: US 2010/0028966 A1 Blanchard Et Al US 20100028966A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2010/0028966 A1 Blanchard et al. (43) Pub. Date: Feb. 4, 2010 (54) METHODS AND COMPOSITIONS FOR Related U.S. Application Data IMPROVING THE PRODUCTION OF (60) Provisional application No. 61/228,922, filed on Jul. PRODUCTS IN MICROORGANISMS 27, 2009, provisional application No. 61/084.233, filed on Jul. 28, 2008. (76) Inventors: Jeffrey Blanchard, Leverett, MA Publication Classification (US); Elsa Petit, Northampton, MA (US); John Fabel, Amherst, MA (51) Int. C. CI2P 7/10 (2006.01) (US); Susan Leschine, Leverett, CI2N IS/II (2006.01) MA (US) CI2N IS/00 (2006.01) CI2P 7/06 (2006.01) Correspondence Address: (52) U.S. Cl. ..................... 435/165:536/23.2:435/252.3: FSH & RICHARDSON PC 435/161 P.O. BOX 1022 ABSTRACT MINNEAPOLIS, MN 55440-1022 (US) (57) Methods and compositions are provided for improving the production of products. Such as fuel products like ethanol, in (21) Appl. No.: 12/510,952 microorganisms. In particular, methods and compositions are described for improving ethanol production utilizing genes (22) Filed: Jul. 28, 2009 identified in Clostridium phytofermentans. EXTRACELLULARHYDROLASES MEMBRANE-BOUNDHYDROLASES CPHYDRAFT O995. CELLULASE • CPHYDRAFT 1067 END0-{EXO-GLUCANASE CPHYDRAFT 1068.EXOGLUCANASE - CELLULASEGHS) - - GH9 - CBM3 - DUF291-DUF291 CBM3 - . GH48 DUF291 CBM3 - CPHYDRAF 1460. CELLULASE ; : CPHYDRAFT 2095. MANNANENDO-1,4- MANNOSIDASE CELLULASEGHS) DUF294 CBD GH28 ; : CPHYDRAFT 3365: ENDO. NACETYLGLUCOSAMINIDASE D CPHYDRAFT 2150. CELLULASE PKD CELLULASEGH5) • CPHYDRAF 0433. CPHYDRAFT 0434: CPHYDRAFT 0435: GLYCOSDEHYDROLASE ENDO-14. XYLOSIDASE • CPHYDRAFT 0560. MANNANENDO-14. MANNOSIDASE XYANASE CBM6 GH26 CBM3 - - - - - GH3 - GH3C -- - - - - - -XYNA (GH10)- CPHYDRAFT 1793: ENDO-1,4-XYLANASE • CPHYDRAF 3622. MANNAN ENDO-1,4- -A1ANNOSIDASE XYNA (GH10) - GH26 -DUF291-DUF291 CBM3 - - CPHYDRAFT3641: ENDO-1,4-XYLANASE CARBOHYDRATE BINDING DOMAIN G-IKE DOMAN CPHYDRAFT 2095. MANNAN ENDO-1,4- MANNOSIDASE XYNA GHO). CBM49 CATALYTC DOMAINDEGRADING CELLULOSE GH26 CPHYDRAF 3644: ENDO-1,4- XYLANASE CATALYTC DOMAINDEGRADING XYLAN GH1 CPHYDRAFT 2913. ENDO-1,4- XYLANASE CATALYTC DOMAINDEGRADING MANNAN XYNA (GHG) XYNA (GH10) E. CPHYDRAFT 1850. PUTATIVE PECTINASE CATALYTIC DOMAINDEGRADING PECTIN GH28 OHER CATALYTIC DOMAINDEGRADING PLANT CPHYDRAF 1307. ENDOGLUCANASE . CPHYDRAFT 0239. PUTATIVE PECTINASE CELL WALL COMPONENTS GH12 - - GH28 - SINGLEPEPTIDECLEANAGE CPHYDRAFT 11.10: ENDO-13(4)--GLUCANASE CPHYDRAFT 1555. GLYCOSIDE HYDROLASE GH16 -CBM49-CBM49-CBM49-CBM49-CBM49- BIG2 - - GH3 - GH3C - : (ABOUT50 DVERSEANDNUMEROUSSUGARABCTYPETRANSPORTERSSYSTEMS l Patent Application Publication Feb. 4, 2010 Sheet 1 of 17 US 2010/0028966 A1 Possible gene combinations S I R R FIG. 1 Patent Application Publication Feb. 4, 2010 Sheet 2 of 17 US 2010/0028966 A1 Specific examples in Cphy related to cellulose and Xylan FIG. 2 Patent Application Publication Feb. 4, 2010 Sheet 3 of 17 US 2010/0028966 A1 co ; : 15 CD E| ||O CD - : Patent Application Publication Feb. 4, 2010 Sheet 4 of 17 US 2010/0028966 A1 47000014800001100001 460000 00001 450000 300001 4400001 "too 4300001 - 4200001 w (g O 400001 y 00 4000001 800001 90000 390000 1000001 380000 1100001 370000 20000 360000 1300001 350000 140000 3400001 1500001 3300001 160000 3200001 X 1700001 300001 3000001 180000 1900001 290000 2000001 280000 21 OOOO 'S6000 2300002200001 2500001 2400001 FIG. 5 Patent Application Publication Feb. 4, 2010 Sheet 5 of 17 US 2010/0028966 A1 . Position in Genome (Mb) FIG. 6 Patent Application Publication Feb. 4, 2010 Sheet 6 of 17 US 2010/0028966 A1 Patent Application Publication Feb. 4, 2010 Sheet 7 of 17 US 2010/0028966 A1 Lactobacillales 1% Bacillales 6% \ ACtinomycetales 1% Other O Unique to C. Clostridiales 4% Other 6% Phytofermentans 15% Cluster VIII Custer V 196 Cluster X Cluster v Cluster1% XI S 1% Cluster III Cluster XIVa 38% Cluster I FG. 8 Patent Application Publication Feb. 4, 2010 Sheet 8 of 17 US 2010/0028966 A1 GH Cluster XIVa Other 30% 14% Cluster I 11% Cluster III 17% Bacili 18% Cluster X - E - 5% Other strida Cluster V O 1% All Genes Other Clostridia ... Other 6% 4% Bacili Unique to C. Cluster V phytotonians 1% Cluster X 1% Cluster IV Cluster XIVa 1% 38% Cluster XI 4% Cluster III 7% Cluster I FIG. 9B 13% Patent Application Publication Feb. 4, 2010 Sheet 9 of 17 US 2010/0028966 A1 Patent Application Publication Feb. 4, 2010 Sheet 11 of 17 US 2010/0028966 A1 as Se SEs ess s 8 s s: 3. s Patent Application Publication Feb. 4, 2010 Sheet 12 of 17 US 2010/0028966 A1 BSWT/ITTEO9660TIHWHOMHd0 –(GHQ)JSWINTEO ESWINTEOOG??TI-VACAHd0 (GHQ)ESWINTEO |ZH?HET Patent Application Publication Feb. 4, 2010 Sheet 13 of 17 US 2010/0028966 A1 ABC transporter Cphy 1219 Xylose isomerase Kinase F.G. 13 Patent Application Publication Feb. 4, 2010 Sheet 14 of 17 US 2010/0028966 A1 -F COSE Cpy 2010-2 L-FUCOSE Cphy 3153 y -FUCOSE Cphy 355 Ap ADP -FCJOSE Cphy 3154 -UCJOSE - P-OSP-AE Cphy 177 EMP 4-w OAP ACALE-Y). Pathway NA) Cphy 185 NA) 12-PROPANEDO Cphy 174-5 t PROPONADEYE NAD NAD Cyphy 78 NAD Cphypity 9 PROPONY-COA ROPANO Chy 83 AOP py A PROPONYP-OSP-AEy PROPONAE FIG. 14 Patent Application Publication Feb. 4, 2010 Sheet 15 of 17 US 2010/0028966A1 R-AMNOSE Cpy 0580-3 -R-AMNOSE Cphy 149 -R-AMNOSE Cphy 147 Ap AP -R-AMNUOSE Cphy 146 y -R-AMNOSE - P-OSP-AE Cphy 77 -- DHAP + L-LACTALDEHYDE Pathway NA) Cphy it 85 Sa NAO 12-PROPANEDO Cphy 1174-5 t PROPONADE-Y) NAD NAD Cphyphy 78 NAO- Cphypity 9 PROPONYCOA PROPANO Chy 83 /* A) pay As PROPONY-P-OSP-AEy ROPONAE FIG. 15 Patent Application Publication Feb. 4, 2010 Sheet 16 of 17 US 2010/0028966 A1 CO V CD -OEDITO Patent Application Publication Feb. 4, 2010 Sheet 17 of 17 US 2010/0028966 A1 C-3 3. Cphy 2-6-6 ABC transporter CHESH - N Cphy (430 Y Nice obiose phosphoryliase A A. C.S.- {COS 8-3- FIG. 17 US 2010/0028966 A1 Feb. 4, 2010 METHODS AND COMPOSITIONS FOR tans In further embodiments, the polynucleotide can contain IMPROVING THE PRODUCTION OF a regulatory sequence operably linked to the isolated nucleic PRODUCTS IN MICROORGANISMS acid encoding the hydrolase. 0007 Some embodiments include polynucleotides con CLAIM OF PRIORITY taining an isolated nucleic acid encoding at least one ATP 0001. This application claims the benefit of priority from binding cassette (ABC)-transporter identified in C. phytofer U.S. Provisional Patent Application Ser. No. 61/084.233, mentans. In Such embodiments, the isolated nucleic acid can filed on Jul. 28, 2008, and U.S. Provisional Patent Application be selected from Table 7. In particular embodiments, the Ser. No. 61/228,922, filed on Jul.27, 2009, the entire contents ABC-transporter is selected from the group consisting of of both of which are incorporated by reference herein. Cphy3854, Cphy3855, Cphy3857, Cphy3858, Cphy3859, Cphy3860, Cphy3861, and Cphy3862. In further embodi FIELD OF THE INVENTION ments, the polynucleotide can contain a regulatory sequence 0002 The present invention relates to the field of micro operably linked to the isolated nucleic acid encoding the biology, molecular biology and biotechnology. More specifi ABC-transporter. cally, the present invention relates to methods and composi 0008. Some embodiments include polynucleotides con tions for improving the production of products, such as taining an isolated nucleic acid encoding at least one tran ethanol and hydrogen, in microorganisms. Scriptional regulator identified in C. phytofermentans. In Such embodiments, the isolated nucleic acid can be selected from BACKGROUND Table 8. In further embodiments, the polynucleotide can con tain a regulatory sequence operably linked to the isolated 0003. There is an interest in developing methods and com nucleic acid encoding the transcriptional regulator. positions for producing usable energy from renewable and 0009. Some embodiments include polynucleotide cas Sustainable biomass resources. Energy in the form of carbo settes containing any combination of the nucleic acids encod hydrates can be found in waste biomass, and in dedicated ing hydrolases, ABC-transporters, and transcriptional regu energy crops, for example, grains, such as corn or wheat, or lators described herein. In one embodiment, a polynucleotide grasses, such as Switchgrass. cassette can contain an isolated nucleic acid encoding at least 0004. A current challenge is to develop viable and eco one hydrolase, and an isolated nucleic acid encoding at least nomical strategies for the conversion of carbohydrates into one ABC-transporter. In another embodiment, a polynucle usable energy forms. Strategies for deriving useful energy otide cassette can contain an isolated nucleic acid encoding at from carbohydrates include the production of ethanol and least one hydrolase, and an isolated nucleic acid encoding at other alcohols, conversion of carbohydrates into hydrogen, least one transcriptional regulator. In another embodiment, a and direct conversion of carbohydrates into electrical energy polynucleotide cassette can contain an isolated nucleic acid through fuel cells. Examples of strategies to derive ethanol encoding at least one ABC-transporter, and an isolated form biomass are described by DiPardo, Journal of Outlook nucleic acid encoding at least one transcriptional regulator. In for Biomass Ethanol Production and Demand (EIA Fore yet another embodiment, a polynucleotide cassette can con casts), 2002; Sheehan, Biotechnology Progress, 15:8,179, tain an isolated nucleic acid encoding at least one hydrolase, 1999; Martin, Enzyme Microbes Technology, 31:274, 2002: and an isolated nucleic acid encoding at least one ABC Greer, BioCycle, 61-65, April 2005; Lynd, Microbiology and transporter, and an isolated nucleic acid encoding at least one Molecular Biology Reviews, 66:3, 506-577, 2002; and Lynd transcriptional regulator. et al. in “Consolidated Bioprocessing of Cellulosic Biomass: 0010 Some embodiments include expression cassettes An Update. Current Opinion in Biotechnology, 16:577-583, containing any polynucleotide described herein and a regu 2005. latory sequence operably linked to the polynucleotide cas SUMMARY Sette.
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