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Ppor-L's Pports IPP DMAPP US 20120058535A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0058535 A1 Heaps et al. (43) Pub. Date: Mar. 8, 2012 (54) BIOFUEL PRODUCTION IN PROKARYOTES Publication Classification AND EUKARYOTES (51) Int. Cl. (75) Inventors: Nicole A. Heaps, San Diego, CA CI2N 9/00 (2006.01) (US); Craig A. Behnke, San Diego, CI2N I/2 (2006.01) CA (US); David Molina, San CI2N 15/63 (2006.01) Diego, CA (US) CI2N I/3 (2006.01) CI2N 5/10 (2006.01) (73) Assignee: SAPPHIRE ENERGY, INC., SAN C7H 2L/04 (2006.01) DIEGO, CA (US) CI2N I/19 (2006.01) (21) Appl. No.: 13/255,888 (52) U.S. Cl. ..................... 435/183: 536/23.1: 435/252.3: 435/254.2:435/257.2:435/419:435/320.1 (22) PCT Filed: Mar. 5, 2010 (86). PCT No.: PCT/US 10/26445 (57) ABSTRACT S371 (c)(1), Terpene synthases are enzymes that directly convert IPP & DMAPP to terpenes, such as fusicoccadiene. Described (2), (4) Date: Nov. 9, 2011 herein are methods and compositions for the production of (30) Foreign Application Priority Data terpenes and terpenoids for use as fuel molecules or other useful components. Genetically engineered enzymes capable Mar. 11, 2009 (US) .................................... 61159366 of producing terpenes and terpenoids are also described. ppor-l's pports IPP DMAPP IPP ppor--~s - Monoterpenes GPP PP Sterols --Squalene-PPO 2 2 1N -- Sesquiterpenes FPP PP PPO1 na 2 2 GGPP Terpenes (i.e. Fusicocca-2,10(14)-diene) Patent Application Publication Mar. 8, 2012 Sheet 1 of 32 US 2012/0058535 A1 ppor-l's pports IPP DMAPP PP ppor--~s Monoterpenes GPP IPP Sterols -HSqualene-HPPO 2 FSG 2 Sesquiterpenes PP PPO 12 12 1. 2 GGPP Terpenes (i.e. Fusicocca-2,10(14)-diene) FIG. 1 Patent Application Publication Mar. 8, 2012 Sheet 2 of 32 US 2012/0058535 A1 O O Por-sh -- 1 cooh CDP-ME OH DXP HN synthase 2 1s O O ~-S N-N-O-Ns N1O SR OH HO OH PorneOH synthaseCMEPP synthaseMEP NADPH Q p-4-O.HO9 O-F No OH OH HOs Por’sOH oH HDMAPP synthase CDP-ME 1 synthase O-P-O-P-O O O OH HOs H.N.'sn Q-i-o-H-or N.N., O O O OH OH O SR HDMAPP HO OH reductase FIG. 2 Patent Application Publication Mar. 8, 2012 Sheet 3 of 32 US 2012/0058535 A1 Pyruvate H Glyceraldehyde Acetyl-CoA 3-phosphate Deoxyxylulose-5 ! N / OPP t MeValonate / PP phosphate OPP N Monoterpenes G PP -r OPP Sesquiterpenes, N Triterpenes 2 PP |-r OP N Diterpenes, Tetraterpenes FIG. 3 Patent Application Publication Mar. 8, 2012 Sheet 4 of 32 US 2012/0058535 A1 (-)-Limonene (-)-a-Pinene Ö-Cadinene Vetispiradiene 5-epi-Aristolochene FPP -- loo CEO (E)-O-Bisabolene S-Selinene A.4, Abietadiene Taxa-4(5), 11(12)-diene GGPP -- r CO OPP (-)-Copalyl diphosphate ent-Kaurene FIG. 4 Patent Application Publication Mar. 8, 2012 Sheet 5 of 32 US 2012/0058535 A1 M Wetispiradiene Synthase III VIII XI XII XIII XIV A. thaliana 84.92 (putative protein) RK H H H DDXXD (607) M Casbene Synthase M III VIII XI XII XI XIV R. communis 86 91 125 73 47 83 96 C20 RP H H H DDXXD (601) 5-epi-Aristolochene III VIII XI XII XIII XIV A. thaliana 84.92 || 126 74 47 84 97 3 (putative protein) RK H H H DDXXD (604) 3 M 5-epi-Aristolochene III VIII XI XII XIII XIV N. tabacum 37.88 || 124 | 73 |46 82 98 g. C15 Rp H H H DDXXD (550) |2 Westispiradiene Synthase M III VIII XI XII XIII XIV H. muticus 13992. 126 73 147 82 98 C15 RP II H H DDXXD (555) E 8-Cadinene Synthase MMIII VIII XI XII XIII XIV 3. G. arboreum 4387 126 73 47 83 97 O C15 RP H H H DDXXD (556) 8-Cadinene Synthase III VIII XI XII XIII XIV A. thaliana 80 92 126 73 48 82 99 (putative protein) RK H H H DDXXD (600) M Limonene Synthase B III VIII XI XII XIII XIV A. thaliana 4994 124 73 47 80 98 (putative protein) RR H H H DDXXD (565) M Limonene Synthase Al III VIII XI XII XIII XIV A. thaliana 3989 (putative protein) TT H H H DDXXD (563) M Limonene Synthase A2 III VIII XI XII XI XIV A. thaliana 78 89 (putative protein) RR H H H DDXXD (602) M Limonene Synthase M II VIII XI XII XIII XIV M. spicata 81 92 C10 RR H H H DDXXD (599) Limonene Synthase MM III VIII XI XII XIII XIV P. frutescens 84 87 132 73 47 83 97 C10 RR H H H DDXXD (603) FIG. 5A Patent Application Publication Mar. 8, 2012 Sheet 6 of 32 US 2012/0058535 A1 M (-) Limonene Synthase M M III VII VIII IX X XI XII XIII XIV A. grandis 93 6639 71 3433 72 47 83 C10 RR H H H DDXXD (637) 2 M (3 (-) Pinene Synthase M M III VII VIII IX X XI XII XIII XIV X A. grandis 87.6738 713133 72 47 83 99 3 C10 RR. H. H. H DDXXD (628) 5, M M 8-Selinene Synthase 2 III VII VIII IX XI XII XIII XIV É. A. grandis 34.6239 79 10 71 47 83 100 9 C15 RR H H H DDXXD DDXXD (525) M O 8-Selinene Synthase 1 III WIWII IX X XI XII XIII XIV A. grandis 34.6439 79 3232 72 47 83 C15 RR H H H ED DDXXD (581) FIG. 5B Patent Application Publication Mar. 8, 2012 Sheet 8 of 32 US 2012/0058535 A1 OZZ00Z08|,09|07|| 08 I'SS 09 07 0008 0009 0007 000Z Patent Application Publication Mar. 8, 2012 Sheet 9 of 32 US 2012/0058535 A1 ZZLZ 082 OZZ00Z08|,09|07|| I’IZI 08 09 07 0008 0009 0007 000Z Patent Application Publication Mar. 8, 2012 Sheet 10 of 32 US 2012/0058535 A1 „O9’5).I.H. Z’ZZI I'S6I'SS ZLOI000Z ['6L0009 0009 Patent Application Publication Mar. 8, 2012 Sheet 11 of 32 US 2012/0058535 A1 00|| 08 09 0000?7|| 0000Z? 00000|| 00009 00009 00007 0000Z Patent Application Publication Mar. 8, 2012 Sheet 12 of 32 US 2012/0058535 A1 009 ?Ouepunq\/ 0000?7|| 0000Z). 00000|| 00008 00009 00007 Patent Application Publication Mar. 8, 2012 Sheet 13 of 32 US 2012/0058535 A1 |OZ'5).I.H. 00|| 08 09 ?Ouepunq\/ 00007|| 0000Z|. 00000|| 00008 00009 00007 0000Z Patent Application Publication Mar. 8, 2012 Sheet 14 of 32 US 2012/0058535 A1 Fusicoccadiene Carotenoids IS87 IS88 IS89 FIG. B. Patent Application Publication Mar. 8, 2012 Sheet 15 of 32 US 2012/0058535 A1 1 2 3 4 5 6 WT WT WT -- - - FIG. 9 Patent Application Publication US 2012/0058535 A1 VOI"50IH Patent Application Publication Mar. 8, 2012 Sheet 18 of 32 US 2012/0058535 A1 FIG. 11 Patent Application Publication Mar. 8, 2012 Sheet 20 of 32 US 2012/0058535 A1 Abund. Ion 272.00 (271.70 to 272.30):0036-IS88-1.D\datams 1550 1500 1450 1400 1350 1300 1250 1200 1150 1100 1050 1000 950 900 850 800 750 700 650 600 550 500 450 400 350 300 250 200 150 100 50 Times" boso 600 700 800 900 1000 1100 1200 13.OO 1400 1500 1600 1700 1800 1900 2000 2100 22.00 FIG. 13A Patent Application Publication Mar. 8, 2012 Sheet 21 of 32 US 2012/0058535 A1 Abundance Scan 1291 (12,489 min):0036-IS88-1D\datams (-1303 (-) 1400 95.0 1350 1300 1250 1200 135.1 1150 1100 1050 1000 950 701 900 850 800 83.0 750 148.9 700 650 600 229.4 550 500 450 53.1 2721 400 402 116.9 350 1632 243.4 300 193.1 250 1801 200 150 100 50 m/z.--> O 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 25026O 270 280 FIG. 13B Patent Application Publication Mar. 8, 2012 Sheet 22 of 32 US 2012/0058535 A1 Abundance Ion 272.00 (271.70 to 272,30).0036-BD11.D\datams 320 300 280 260 240 220 200 180 160 140 120 100 80 60 40 20 Tim-" 400 S.OO 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000 21.00 22.00 FIG. 1 BC Patent Application Publication Mar. 8, 2012 Sheet 23 of 32 US 2012/0058535 A1 Abundance Ion 272.00 (271.70 to 272,30): IS1181.D.data.ms 125000 120000 115000 110000 105000 100000 95000 90000 85000 80000 75000 70000 65000 60000 55000 50000 45000 40000 35000 30000 25000 20000 15000 10000 5000 Time' 4OO 450 SOO 5.5O 600 650 TOO 7SO 800 8.5O 900 950 1000 FIG. 14A Patent Application Publication Mar. 8, 2012 Sheet 24 of 32 US 2012/0058535 A1 Abundance 250000 257.1 240000 Scan 322 (8.365min): IS1181.D\datams (-331)(-) 230000 910 220000 210000 200000 190000 180000 170000 690 105.0 160000 229.1 150000 140000 55.0 1230 130000 2721 120000 1470 110000 213.1 100000 90000 80000 70000 1871 60000 16.1 115 50000 40000 BDO 14C 201.1 30000 20000 10000 243.1 2949 m/z->' 50 60 TO 80 90 100 110 120 130 140 150 16O 170 180 190 200 210 220 230 240 25026027O 280 290 300 FIG.
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