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Pro- Pro IP P DMAPP IPP PP, { GPP Synthase

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Pro- Pro IP P DMAPP IPP PP, { GPP Synthase US 2012O064629A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0064629 A1 Mendez et al. (43) Pub. Date: Mar. 15, 2012 (54) VARIANT ISOPRENOID PRODUCING Publication Classification ENZYMES AND USES THEREOF (51) Int. Cl. CI2N 5/10 (2006.01) (75) Inventors: Michael Mendez, San Diego, CA CI2N 15/63 (2006.01) (US); Craig A. Behnke, San Diego, CI2N I/19 (2006.01) CA (US); Nicole A. Heaps, San CI2N I/3 (2006.01) Diego, CA (US) C7H 2L/00 (2006.01) CI2N I/2 (2006.01) (73) Assignee: Shapphire Energy, Inc., San (52) U.S. Cl. ..................... 435/419,536/23.2:435/252.3: Diego, CA (US) 435/254.2:435/257.2:435/320.1 (57) ABSTRACT (21) Appl. No.: 13/260,696 This disclosure provides methods of designing and generat ing polypeptide variants that have altered properties com (22) PCT Filed: Mar. 29, 2010 pared to a parent polypeptide. The present disclosure pro vides methods of generating polypeptide variants, for (86). PCT No.: PCT/US 10/29071 example, variant isoprenoid synthases and/or variant prenyl transferases that have at least one desired property not present S371 (c)(1), in the parent polypeptide. The present disclosure further pro (2), (4) Date: Dec. 5, 2011 vides polypeptides and polynucleotides encoding variant polypeptides, as well as vectors and host cells comprising the Related U.S. Application Data polynucleotides that encode the variant polypeptides. In other embodiments, the present disclosure provides methods of (60) Provisional application No. 61/164.369, filed on Mar. using the variant polypeptides to generate useful products, 27, 2009. Such as isoprenoid compounds and/or isoprenoid products. pro- pro IP P DMAPP IPP PP, { GPP Synthase PPO a 2 - Monoterpenes GPP IPP PP, (FPP Synthase Sterols--Squalene --PPO 2 2 4N -- Sesquiterpenes FPP IPP PP, { GGPP Synthase PPO 2 2 2 GGPP Terpenes (i.e. Fusicocca-2,10(14)-diene) Patent Application Publication Mar. 15, 2012 Sheet 1 of 14 US 2012/0064629 A1 pports pports IPP DMAPP PP PP, { GPP Synthase PPO 2 4N - - Monoterpenes GPP PP PP, (FPP Synthase Sterols --Squalene --PPO 1 1 21N - Sesquiterpenes FPP IPP PP, { GGPP Synthase PPO 1 1 1 2 GGPP Terpenes (i.e. Fusicocca-2,10(14)-diene) Figure 1 Patent Application Publication Mar. 15, 2012 Sheet 2 of 14 US 2012/0064629 A1 CDP-ME kinase O O POs DXP synthase HN2 Ys O-P-O-O O D O or NN, O s O O OH OH YO SR HO OH CMEPP synthase MFP NADPH HO 2 synthase O O-P-O, O1"Y no OH OH HOS Por’s HDMAPP OH OH synthase COP-ME synthase O-P-O--O 2 O O OH HOS H.N.'sn O O ~-> N.N. Os OH OH O HDMAPP HO OH reductase Patent Application Publication Mar. 15, 2012 Sheet 3 of 14 US 2012/0064629 A1 Pyruvate H Glyceraldehyde Acetyl-CoA Cytosol and Plastid sopo ! OPP >r. Deoxyxylulose-5 Mevalonate IPP phosphate --- O PP N Monoterpenes GPPP PP O PP Sesquiterpenes, N Triterpenes 21 FP P PP O P N Diterpenes, Tetraterpenes Patent Application Publication Mar. 15, 2012 Sheet 4 of 14 US 2012/0064629 A1 (-)-Limonene (+)-Linalool (-)-a-Pinene 5-Cadinene Vetispiradiene 5-epi-Aristolochene FPP-> loo Co (E)-a-Bisabolene 8-Selinene Abietadiene Taxa-4(5), 11(12)-diene GGPP-p- (-)-Copalyldiphosphate ent-Kaurene Figure 4 Patent Application Publication Mar. 15, 2012 Sheet 5 of 14 US 2012/0064629 A1 M Wetispiradiene Synthase III VIII XI XII XIII XTW A. thaliana 84 92 126 74 48 83 100 (putative protein) RK H H H DDXXD (607) M Casbene Synthase M III VIII XI XII XIII XIW 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 18492. 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 137188|| 124 | 73 146 82 | 98. C15 R H H H DDXXD (550) |2 Westispiradiene Synthase M II VIII XI XII XIII XTW E. H. muticus 13992, 126 73 147 82 98 C15 RP H H H DDXXD (555) E 8-Cadinene Synthase MMI WI XI XII XIII XIW E. G. arboreum 4387 126 73 47 83 97 O C15 RP H H H DDXXD (556) 8-Cadinene Synthase I VIII XI XII XIII XIW A. thaliana 80 92 126 73 48 82 99 (putative protein) RK H H H DDXXD (600) M Limonene Synthase B I VIII XI XII XIII XTW A. thaliana 4994 124 73 47 80 98 (putative protein) RR H H H DDXXD (565) M Limonene Synthase Al I WI XI XII XIII XIW A. thaliana 3989 132 73 47 83 100 (putative protein) TT H H H DDXXD (563) M Limonene Synthase A2 I WII XI XII XI XIW A. thaliana 78 89 132 73 47 83 100 (putative protein) RR H H H DDXXD (602) M Limonene Synthase M III VIII XI XII XIII XIW M. spicata 81 92 126 73 47 83 97 C10 RR H H H DDXXD (599) Limonene Synthase MM III VIII XI XII XII XIV Pfutescens 84 87 132 73 47 83 97 C10 RR H H H DDXXD (603) Figure 5A Patent Application Publication Mar. 15, 2012 Sheet 6 of 14 US 2012/0064629 A1 (-) Limonene Synthase MM III WTIVIII IX X XI XII XIII XIV A. grandis 93 6639 71 3433 72 47 83 99 C10 RR H H H DDXXD (637) M 3 (-) Pinene Synthase M M III WIWII IX X XI XII XIII XIW D A. grandis 87.6738 713133 72 47 83 99 : C10 RR H H H DDXXD (628) M 8-Selinene Synthase 2 III WIVIII DXXI XII XIII XIW 3. A. grandis 34.6239 79 10 71 47 83 100 C15 RR H H H DDXXD DDXXD (525) a c M O 8-Selinene Synthase 1 I WIWII IX X X XII XIII XIW A. grandis 34.6439 79 3232 72 47 83 100 C15 RR H H H ED DDXXD (581) Figure 5B Patent Application Publication Mar. 15, 2012 Sheet 7 of 14 US 2012/0064629 A1 Seued eseupuAS euede-LI SSeo Patent Application Publication Mar. 15, 2012 Sheet 8 of 14 US 2012/0064629 A1 Figure 6 Chrysanthern in Synthase ----------------------------------------- MASFISLSS IS-45 FPPS/GPPS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - art.CmiSia FPPS -------------------------------------------------- COrn GGPPS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - KluyverOrry CeS FPPS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - SaCCharOrryCeS FPPS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - IS-9 FPPS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MHKFTGVNAKFC BOS FPPS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - EYPSNNLDLC MyZUS FPPS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MNKMLTFTRA MyZUS bifunctional ------------------------------------------- AnthonOnLS FPPS MFSWKLCRNRSCRELIKNIRRGITKTSTDSNSDAISRAODHNOMNNFNLE Chrysanthomin SynthasC KSASWNASSCPHPSVOPFWTRKNWRYHKPTSSEPSYSPLTTTLSSNLNS IS-45 FPPS/GPPS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TLSSNLNS artemisia FPPS ------------------------------------------ MSSTDLKS COrn. GGPPS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MAAGGNGAGGDTRA KluyverOrryCeS FPPS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MSDN----RA SaCCharOrry CeS FPPS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MASEKEIRRE IS-9 FPPS OPALRN- - - - - - - - - - - - - - - - - - - - LSPWWWE - - - - - - - - - - - - - RERE BOS FPPS -PASRNRA - - - - - - - - - - - - - - - - - FYSSLRVNGDOKLDA----YAOERO Myzus FPPS SRRSAFLLCDS----AVWRNN\FRAMSTWRAPPVPPWITGTAWSKDETR Myzus bifunctional . STWRAPPVPPVITGTAVSKDETR AnthonOnLS FPPS GPSSOYHTNVNNKRWHKOMOFNNLRALSTOOTIPKPSHSSTLVSKEOSR Chrysanther? in Synthase CFMOVYETLKSELIHDPL-FEFDDDSROWERMIDYTVPGGKMVRGYSWV IS-45 FPPS/GPPS OFMOVYETLKSELIHDPL-FEFDDDSROWVERMIDYTVPGGKMVRGYSVV artemisia FPPS KFLKWYDTLKSEL INDPA-FEFDDDSROWIEKMLDYNVPGGKLNRG SVV Corn GGPPS AFARIYKTLKEELLTDPA-FEFTEESROWIDRMVDYNVLCCKCNRG SVN Kluyveromyces FPPS CFLEVFPSLVOELRDILAGYGMPEEAIEWYEKSLNYNTPGGKLNRGLSVN SaccharOryces FPPS RFLNWFPKL WEELNASLLAYGMPKEACDWYAHSLNYNTPGGKLNRGLSWW IS-9 FPPS EFVGFFPOIVRDLTEDGIGHPEVGDAVARLKEWLOYNAPGGKCNRGLTVW BOS FPPS DFIOHFSOIWKVLTEEDIGHPEIGDAITRLKEWLEYNAIGGKYNRGLTWV MyZUS FPPS DFMAWFPDWVRDLTDTGR-NLDV PDWTKWLAKLLOYNWPGGKKNRGLALV Myzus bifunctional DFMAWFPDNVRDLTDTGR-NLDV PDWTKWAKLLOYNWPGGKKNRGALV AnthonOnLS FPPS DFMALFPDLVRELTELGR-NPEPDVMRRVARVLOYNVPNGKKNRGLILI k k . kik k Chrysanthem in Synthase DSYOLLK---GEE-LTEEEAFLACALGWCTEWFOAFILLHDDMMDGSHTR IS-45 FPPS/GPPS DSYOLLK---GEE-LTEEEAFLACALGWCTEWFOAFILLHDDMMDGSHTR artemisia FPPS DSYOLLK---GGE-LSDDEIFLSSALGWCIEWLOAYFLVLDDIMDESHTR COrr, GGPPS DSYKLLK---GADALGEEETFLACTLGWCIEWLOAFFLVLDDIMDDSHTR Kluyveromyces FPPS DTYALLKGYKSVSELSAEEYKKVAILGWCIELLOAYFLVADDMMDOSITR Saccharomyces (PPS DTYAILS-KKTVEOLGQEEYEKVAILGWCIELLOAYLVADDMMDKSITR IS-9 FPPS AAYRELS---GPGOKDAESLRCALAWGWCIELFOAFFLWADDIMDOSLTR BOS FPPS ITFRELV---EPGKODPDSLORALTYGWCVELLOAFFLVSDDIMDSSLTR MyZUS FPPS LSYKMLS---SPSDOTDENLKLSYILGWCWEILOAYOLVLDDIMDNAITR Myzus bifunctional LSYKMLS---SPSDOTDENLKLSYILGWCWEILOAYOLVLDDIMDNAITR AnthonOnLS FPPS SAYKMLE---DPKNLTPENIKLASWLGWCLEMIHSCFLWLDDIMDNSETR k ... k.kk k . k. k.k. k.k. k. k Patent Application Publication Mar. 15, 2012 Sheet 10 of 14 US 2012/0064629 A1 Figure 6 (CONTD) IS-45 FPPS/GPPS AWFEDYEATSYKKLITSIENHP-SKAVOA-VLKSFLGKIYKROKG artemisia FPPS AWFEDYEATSYKKLITSIENHP-SKAVOA-VLKSFLGKIYKROK COrn (GGPPS AVFOEYENESYKKLIADIEAOP-SIAWOK-VLKSFLHKIYKROK Kluyveromyces FPPS DIYHKYEEETASNLREKIANIDESRGFKAEWLTL FLNKIYHRKK SaCCharomyces FPPS OLYHEYEESIAKDLKAKISOWDESRGFKADVLTAFLNKWYKRSK IS-9 FPPS AAFOOYEESSYRRLOELIEKHS--NRLPKEIFLGLAOKIYKROK BOS FPPS AVYMOYEEDSYNHIMGLIEOYA--APLPPAIFLGLAOKIYKRKK MyZUS FPPS DTFHLYEEESYKLICTHIOOLS--RGLSODMFFKFLEKIYKRTL Myzus bifunctional DTFHFYEEESYKLICTHIOOLS--RGLSODMFFKFLEKIYKRTL Anthononus FPPS NTYAIYEEESYNIIKTHIOOIS--KGLRHDLFFSIMEKLYKREC k k k. k. Patent Application Publication Mar. 15, 2012
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