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Aroa 5-O-(1-Carboxyvinyl)-3-Phosphoshikimate Aroc Chorismate Patent Application Publication Dec US 20160348O87A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2016/0348087 A1 Behrendorff et al. (43) Pub. Date: Dec. 1, 2016 (54) GENETICALLY ENGINEERED Publication Classification MCROORGANISMS FOR THE PRODUCTION OF CHORISMATE-DERVED (51) Int. Cl. PRODUCTS CI2N 9/88 (2006.01) CI2P 7/62 (2006.01) (71) Applicant: LanzaTech New Zealand Limited, (52) U.S. Cl. Skokie, IL (US) CPC. CI2N 9/88 (2013.01); CI2P 7/62 (2013.01); CI2Y 401/0304 (2013.01) (72) Inventors: James Bruce Yarnton Haycock Behrendorff, Skokie, IL (US); Michael (57) ABSTRACT Koepke, Skokie, IL (US); Loan Phuong Tran, Skokie, IL (US); Wyatt The invention provides genetically engineered microorgan Eric Allen, Skokie, IL (US) isms and methods for producing chorismate-derived prod ucts, such as para-hydroxybenzoic acid, salicylate, 2-amin (21) Appl. No.: 15/166,224 obenzoate, 2,3-dihydroxybenzoate, and 4-hydroxycyclohexane carboxylic acid. Typically, the (22) Filed: May 26, 2016 microorganism comprises at least one of (a) an exogenous chorismate pyruvate lyase, (b) an exogenous isochorismate Related U.S. Application Data synthase, (c) an exogenous isochorismate pyruvate lyase, (60) Provisional application No. 62/167,101, filed on May and (d) a prephenate synthase comprising a disruptive 27, 2015. mutation. erythrose-4-phosphate + phosphoenolpyruvate aroG* arOG DAHP arokB 3-dehydroquinate aOD 3-dehydroshikimate aroE shikimate arOKB shikimate 3-phosphate . arOA 5-O-(1-carboxyvinyl)-3-phosphoshikimate arOC chorismate Patent Application Publication Dec. 1, 2016 Sheet 1 of 32 US 2016/0348087 A1 erythrose-4-phosphate + phosphoenolpyruvate aroG aroG DAHP arOKB 3-dehydroquinate aroD 3-dehydroshikimate arOE shikimate aro KB shikimate 3-phosphate arOA 5-O-(1-carboxyvinyl)-3-phosphoshikimate aroC chorismate Fig. 1 Patent Application Publication Dec. 1, 2016 Sheet 2 of 32 US 2016/0348087 A1 - erythrose-4-phosphate 38: ghosphoenogy wate , &* Siikiate pathway k. - Acetyl-CoA Pyravate sixxi-ji:gdahi* -- / Tryptoghai <-- *r Charisiiate' - beai 4 p-8A gathway - & ephenate8.- : as Y: Top-ABA CO, CC is /x \;Y. s: Foite ity site heyaarine Fig. 2 erythross-4-phosphate we -----------: 3 phospice soigyravate f ; Shikimate gathway ', f -- Acetyl-CoA rivate oxi-jurgda: / ryptoghat: K-K-- Ctoristiate peria.A. sociatistate pct: saidylate pathway y - ’8. / Prephenate s p-ABA CR. O. his « ». *. w *. cate tyrosia Pterytsiarie Fig. 3 Patent Application Publication Dec. 1, 2016 Sheet 3 of 32 US 2016/0348087 A1 - erythrose-4-phosphate --> A phosphoeoisy rivate : : f Shikimate pathway * f yl - Acetyl-CoA fisci-3 agaiahi tryptophan K-x *r horismate patiway & Xphea x 8.& Pr:gh state {{, , i. & X, '. Foiate al Tytosine Pierryiaiaire 8 & 2-airobenzoate i 2,3-dihydroxybenzoate :3-hyxi oxycyclishexae carboxylicacic Fig. 4 gi:8A staircia's carya Patent Application Publication Dec. 1, 2016 Sheet 4 of 32 US 2016/0348087 A1 &cc::::::: 488 s: 33-33- - :::: s :33x :& 33: 333.38 38:33.** 1s: : 8 : 8 8 Patent Application Publication Dec. 1, 2016 Sheet 5 of 32 US 2016/0348087 A1 -- 8: - 38 S- 3.. (i) 3. s 3. s: s (w) ---------------------------------------------------------xx-xx-as-s-s-------------- Fig. 6b Patent Application Publication Dec. 1, 2016 Sheet 6 of 32 US 2016/0348087 A1 Fig. 7 Patent Application Publication Dec. 1, 2016 Sheet 7 of 32 US 2016/0348087 A1 Patent Application Publication Dec. 1, 2016 Sheet 8 of 32 US 2016/0348087 A1 Oasis & i. i. Agai:3.33 Patent Application Publication Dec. 1, 2016 Sheet 9 of 32 US 2016/0348087 A1 2::::::::::::::::: 3:38 3.3-8:hy8roxybenzoic 3c: : Fig. 10 Patent Application Publication Dec. 1, 2016 Sheet 10 of 32 US 2016/0348087 A1 ::::::::::::::::::: aki: 3:2:3:23 *::::::::ce: 33 3:3:g: {3} ::::: ii: :::: Fig. 1 a *:::::::::::::c :: :E: :::::::::::::::: 3.3 ::::::::::::33 a ::::::::::::3: 8. Patent Application Publication Dec. 1, 2016 Sheet 11 of 32 US 2016/0348087 A1 20 -: 1,000 : ...'...'...', * Siomass : 8 cis-a-hydroxy cyclohexanecarboxylic acid - 900 6 a 2-aminobenzoic acid 800 S. w8x3,4-dihydroxybenzoic acid E. 14 700 U 12 600 3. CO TO -: - 500 9 : W & s 8 : 400 6 -: 's 300 4 -: 2 -: 100 O ---------------------------------C8---------- O O 2 3 4 6 7 8 9 O Patent Application Publication Dec. 1, 2016 Sheet 12 of 32 US 2016/0348087 A1 Genbank Microorganism Accession Microorganism Genbank Accession Proteobacteria WP 0013266441 Bartonea carridgeiae WP 01354.4696.1 Escherichia Co WP 032343343.1 Providencia acaifaciens WP 036955412.1 Enterobacteriaceae WP 001295693.1 Providencia rustigianii WP OO6816067.1 Shigella flexneri WP 005071384.1 8artonella rattimassiliensis WP 0.0734.7862.1 Shigella sp. SF-2015 WP OO5002785.1 Edwardsiella anguiarum WP 034163029.1 Escherichia WP 000019214.1 Edwardsiella WP 045427790.1 Shigella sonnel WP 05299.0089.1 Phaseolibacter flectens WP 028684858.1 Escherichia alberti WP 000019228.1 Providencia Stuartii WP 004925912.1 Citrobacter youngae WP OO6688307.1 *dwardsiella ictauri WP 015869674.1 Citrobacter freundii WP 054527959.1 Edwardsiella piscicida WP 015460726.1 Citrobacter WP 043213934.1 Sodalis praecaptivus WP 0514401951 Citrobacter pasteurii WP 0.05132668.1 Sodalis gossinidius WP 011411956.1 Citrobacter freundii complex WPO3294.2095.1 Edwardsiella tarda WP 035597793.1 Enterobacter cloacae WP 063411731.1 Providencia Sneebia WP 008916956.1 Providencia Citrobacter amatonaticus WP 061075585.1 burhodogranariea WP_008913736.1 Gammaproteobacteria WP 042999.031.1 Edwardsiela hoshinae WP 024524687.1 Candidatus Sodalis Enterobacter WP 014882105.1 pierantonius WP 025246620.1 Enterobacter cloacae Complex WP 045355219.1 Photobacterium aquae WP 047877737.1 Enterobacter sp. BEDMC 29 WP 041911565.1 Photobacterium marinum WP 007469524.1 Photobacterium Enterobacter sp., 35730 WP 045268808.1 Sanguinicanci WP 062688249.1 Enterobacter sp. T1-1 WP O29882656.1 Photobacterium Swingsii WP 048893785.1 Enterobacter cloacae Complex 'Hoffmann cluster IV WP 008500083.1 Photobacterium damseiae WP 044173922.1 Enterobacter asburiae WP 023617246.1 Photobacterium sanctipauli WP 036818650,1 Enterobacter sp. BEDMC92 WP 047957525.1 AgarivoranS albus WPO16399749.1 Enterobacter sp. 638 WP 011915505.1 Photobacterium profundum WP 0.06233275.1 Citrobacter farmer WP 042321063.1 Vibrio maritimus WP 042478790.1 Citrobacter koser WP 012134646.1 Vibrio metoecus WP O55052109.1 Enterobacter hormaechei WP 023299.087.1 Grimonitia celer WP 062666858.1 Escherichia fergusonii WP 000019211.1 Viorio WP 001072883.1 Enterobacter cancerogenus WP 042321179.1 Agarivoransgivus WP 055733842.1 Enterobacter sp. GNO24.54 WP 047742368.1 Vibrio aginolyticus WP 053311436.1 Salmonella enterica WP 000019223.1 Grimonitia indica WP 0025354O7.1 Leliottia amnigena WP 059179835.1 Photobacterium ganghwense WP 047887262.1 Enterobacter sp. Bisph1 WP 039055748.1 Grimontia sp. AD028 WP 0463.03386.1 Salmonella bongori WP 020845807.1 Vibrio neptunius WP 045975676.1 Fig. 13 Patent Application Publication Dec. 1, 2016 Sheet 13 of 32 US 2016/0348087 A1 Genbank Microorganism Accession Microorganism Genbank Accession Enterobacter sp. FY-07 WP 061.498857.1 Vibrio Corailiilyticus WP 0430.06692.1 Escherichia vulneris WP O42388891.1 Photobacterium aphoticum WP 047873744.1 Yokeneia regensburgei WP 04O902665,1. Photobacterium leiognathi WP O53987423.1 Trabusiella odontotermitis WP 054179777.1 Plesiomonas WP 010862816.1 Trabulsiella guamensis WP 038158396.1 Vibrio Xui WP 053441,696.1 Enterobacter sp. MT20 WP 061706855.1 Vibrio sp. VPAP30 WP O49845305. Kosakonia radicincitans WP 043955.711.1 Vibrio tubiashii WP 038.197373.1 Kluyvera intermedia WP 047372194.1 Sainvibrio Socompensis WP O256.73764.1 Enterobacter sp. Bisph2 WP 039077918.1 Grinnota marina WP 062709804.1 Kiebsiella oxytoca WP 004109561.1 Vibrio galatheae WP 045956983.1 Enterobacter xiangfangensis WP O58715018.1 Grimontia hoisae WP O055O1667.1 Leclercia adecarboxylata WPO39031929.1 Photobacterium sp. SKA34 WPOO6647642.1 Enterobacter aerogenes WP 045362420.1 Vibrio cholerae WP 032480537.1 Kebsiela WP 01422.7537.1 Vibrio Caribbeanicus WP 0096.02602.1 Vibrionales bacterium SWAT Enterobacter massiiensis WP 044180994.1 3 WP O08224249.1 Citrobacter rodentium WP 012907701.1 Enterovibrio Caviensis WP 017016798.1 Raouitella terrigena WP045853463.1 Vibrio bivavicida WP 054963396.1 Klebsiella sp. OBRC7 WP 009654674.1 Vibrio Orientalis WP 004.409565.1 Klebsiella sp. RT-P-d WP 049838501.1 Vibrio sp. HOOD65 WPO63524665.1 Raouitella ornithinolytica WP 041143590.1 Wibrio ordaii WP 038198194.1 Klebsiella pneumoniae WP 023342419.1 Vibrio splendidus WP 032554291. Kebsiella sp. 10982 WP O25713803.1 Vibrio nigripulchritudo WP 045967092.1 Enterobacteriaceae bacterium Photobacterium strain FG 57 WP 015966334.1 phosphoreum WP 045031601.1 Pluralibacter gergoviae WP 04828491.1 Saliniwibrio sp. KP-1 WP 046074636.1 Kluyvera cryocrescens WP 061283371.1 Photobacterium gaetbulicola WP 044622288.1 Franconibacter helveticus WP 024553577.1 Photobacterium WP 045083799.1 Kluyvera aScorbata WP 035896877.1 Enterovibrio norvegicus WP 01696.1855.1 Franconibacter pulveris WP O29593165.1 Photobacterium angustum WP 005372020.1 Shimweia battae WP 002445222.1 Wibrio brasiliensis WP 040895.525.1 Enterobacteriaceae bacterium LSCA WP 017373629.1 Aiivibrio fischer WP 012534390.1 Cronobacter WP 007796820.1 Vibrio pacinii WP 038175692.1 Erwinia sp. SCU-B244 WP 058912420.1 Vibrio titoralis WP 051241116.1 Cronobacter sakazaki WP 054624,115.1 Vibrio sp. hENC-03 WP O09705152.1 Cronobacter turicensis WP 007764634.1 Vibrio genomosp, F6 WP 017051810.1 Cronobacter maionaticus WP 032994815.1 Photobacterium
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