Type II fatty acid synthesis enzymes in reverse β-oxidation
10450593 · 2019-10-22
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Inventors
Cpc classification
C12Y203/01009
CHEMISTRY; METALLURGY
C12N9/0071
CHEMISTRY; METALLURGY
C12N9/00
CHEMISTRY; METALLURGY
C12Y402/01059
CHEMISTRY; METALLURGY
C12P7/64
CHEMISTRY; METALLURGY
C10L1/02
CHEMISTRY; METALLURGY
C12N9/0008
CHEMISTRY; METALLURGY
C12Y206/00
CHEMISTRY; METALLURGY
C12Y103/01009
CHEMISTRY; METALLURGY
C12N9/1029
CHEMISTRY; METALLURGY
Y02E50/30
GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
C12Y114/00
CHEMISTRY; METALLURGY
C12Y101/011
CHEMISTRY; METALLURGY
International classification
C10L1/02
CHEMISTRY; METALLURGY
C12P7/64
CHEMISTRY; METALLURGY
C12N9/00
CHEMISTRY; METALLURGY
Abstract
This disclosure describes enzymes from the type II (a discrete set of enzymes) fatty acid synthesis (FAS) pathway that can be used in combination with thiolases to operate a functional reversal of the -oxidation cycle. A combination of thiolases with one or more of 3-oxoacyl-[acyl-carrier-protein] reductase (FabG, others), 3-hydroxyacyl-[acp] dehydratase (FabA, FabZ, others), and enoyl-[acyl-carrier-protein] reductase (FabI, FabK, FabL, FabV, others) yields a functional reversal of the -oxidation cycle. If only one or two enzymes are used, the remaining enzymes will be traditional beta oxidation enzymes. Once this cycle is coupled with the appropriate priming and termination pathways, the production of carboxylic acids, alcohols, hydrocarbons, amines and their -, -, and -functionalized derivatives from renewable carbon sources can be achieved.
Claims
1. A genetically engineered microorganism, said microorganism having a reverse beta oxidation (BOX-R) cycle that grows a primer by adding a 2-carbon donor thereto in each cycle, said BOX-R cycle comprising: a) an overexpressed thiolase that catalyzes the non-decarboxylative condensation of an acyl-CoA primer with a 2-carbon donor acetyl-CoA to produce a -ketoacyl-CoA; b) an overexpressed 3-oxoacyl-[acyl-carrier-protein] reductase or overexpressed 3-hydroxyacyl-CoA dehydrogenase that catalyzes the reduction of a -ketoacyl-CoA to a -hydroxyacyl-CoA; c) an overexpressed 3-hydroxyacyl-[acyl-carrier-protein] dehydratase or an overexpressed enoyl-CoA hydratase or 3-hydroxyacyl-CoA dehydratase that catalyzes the dehydration of a (3R)--hydroxyacyl-CoA to a transenoyl-CoA; d) an overexpressed enoyl-[acyl-carrier-protein] reductase or acyl-CoA dehydrogenase or trans-enoyl-CoA reductase that catalyzes the reduction of a transenoyl-CoA to an acyl-CoA that is two carbons longer than said acyl coA primer; i) wherein at least one of the enzymes from steps b-d is a fatty acid synthesis enzyme; and e) an overexpressed termination pathway that catalyzes the exit of an intermediate from said BOX-R cycle.
2. The microorganism of claim 1, wherein said termination pathway is selected from the group consisting of i) a thioesterase, ii) an acyl-CoA:acetyl-CoA transferase, and iii) a phosphotransacylase and a carboxylate kinase, and wherein said microorganism produces a product selected from the group consisting of carboxylic acids, (3R)--hydroxy carboxylic acids, -keto carboxylic acids, and ,-unsaturated carboxylic acids.
3. The microorganism of claim 1, wherein said termination pathway is selected from the group consisting of i) an alcohol-forming coenzyme-A thioester reductase, and ii) an aldehyde-forming CoA thioester reductase and an alcohol dehydrogenase, and wherein said microorganism produces a product selected from the group consisting of primary alcohols, 1,(3R)- diols, -keto primary alcohols, and ,-unsaturated primary alcohols.
4. The microorganism of claim 1, wherein said termination pathway consists of an aldehyde-forming CoA thioester reductase and an aldehyde decarbonylase, and wherein said microorganism produces a product selected from the group consisting of linear alkanes, linear alkan-3-ols, linear methyl-ketones, and 1-alkenes.
5. The microorganism of claim 1, wherein said termination pathway consists of an aldehyde-forming CoA thioester reductase and a transaminase, and wherein said microorganism produces a product selected from the group consisting of primary amines, 3-hydroxy-amines, 3-keto-amines, and ,-unsaturated primary amines.
6. The microorganism of claim 2, wherein said microorganism expresses a carboxylic acid omega hydroxylase and produces a product selected from the group consisting of -hydroxylated carboxylic acids, (3R)--, -dihydroxy carboxylic acids, -keto, -hydroxy carboxylic acids, and ,-unsaturated -hydroxylated carboxylic acids.
7. The microorganism of claim 3, wherein said microorganism expresses a carboxylic acid hydroxylase, an alcohol oxidase, and an aldehyde dehydrogenase, and produces a product selected from the group consisting of -hydroxylated carboxylic acids, (3R)--, -dihydroxy carboxylic acids, -keto, -hydroxy carboxylic acids, and ,-unsaturated omega-hydroxylated carboxylic acids.
8. The microorganism of claim 3, wherein said microorganism expresses a carboxylic acid hydroxylase, and produces a product selected from the group consisting of 1-,-diols, 1-,(3R)--, -triols, -keto, 1-,-diols, and ,-unsaturated 1-,-diols.
9. The microorganism of claim 2, wherein said microorganism expresses a carboxylic acid hydroxylase, an alcohol oxidase, and an aldehyde dehydrogenase, and produces a product selected from the group consisting of di-carboxylic acids, (3R)--hydroxy di-carboxylic acids, -keto di-carboxylic acids, and ,-unsaturated di-carboxylic acids.
10. The microorganism of claim 3, wherein said microorganism expresses a carboxylic acid hydroxylase, an alcohol oxidase, and a transaminase, and produces a product selected from the group consisting of primary alkanolamines (i.e. 1, -hydroxyamines), (3R)--hydroxy primary alkanolamines, -keto primary alkanolamines, and ,-unsaturated primary alkanolamines.
11. The microorganism of claim 5, wherein said microorganism expresses a carboxylic acid hydroxylase, and produces a product selected from the group consisting of primary alkanolamines (i.e. 1, -hydroxyamines), (3R)--hydroxy primary alkanolamines, -keto primary alkanolamines, and ,-unsaturated primary alkanolamines.
12. The microorganism of claim 5, wherein said microorganism expresses a carboxylic acid hydroxylase, an alcohol oxidase, and an aldehyde dehydrogenase, and produces a product selected from the group consisting of -amino acids, (3R)--hydroxy -amino acids, -keto -amino acids, and ,-unsaturated -amino acids.
13. The microorganism of claim 2, wherein said microorganism expresses a carboxylic acid alpha hydroxylase, and produces a product selected from the group alpha-hydroxy carboxylic acids, alpha-, (3R)--dihydroxy carboxylic acids, -hydroxy, -keto carboxylic acids, and ,-unsaturated -hydroxy carboxylic acids.
14. The microorganism of claim 3, wherein said microorganism expresses a carboxylic acid hydroxylase, and produces a product selected from the group consisting of 1,2-diols, 1,2,3-triols, -keto, 1,2-diols, and ,-unsaturated 1,2-diols.
15. The microorganism of claim 5, wherein said microorganism expresses a carboxylic acid hydroxylase, and produces a product selected from the group consisting of -hydroxylated primary amines, -, - dihydroxy primary amines, -hydroxy, -keto primary amines, and -hydroxy, ,-unsaturated primary amines.
16. The microorganisms of claim 1, further comprising reduced expression of fermentation enzymes leading to reduced production of lactate, acetate, ethanol and succinate.
17. The microorganism of claim 1, wherein said overexpressed thiolase is encoded by E. coli atoB (NP_416728.1), E. coli yqeF (NP_417321.2), E. coli fadA (YP_026272.1), E. coli fadI (NP_416844.1), Ralstonia eutropha bktB (AAC38322.1), Pseudomonas sp. Strain B13 catF (AAL02407.1), E coli paaJ (NP_415915.1), Pseudomonas putida pcaF (AAA85138.1), Rhodococcus opacus pcaF (YP_002778248.1), Streptomyces sp. pcaF (AAD22035.1), Ralstonia eutropha phaA (AEI80291.1), Clostridium acetobutylicum thlA (AAC26023.1), and Clostridium acetobutylicum thlB (AAC26026.1).
18. The microorganism of claim 1, wherein said overexpressed 3-oxoacyl-[acyl-carrier-protein] reductase is encoded by E. coli fabG (NP_415611.1).
19. The microorganism of claim 1, wherein said overexpressed 3-hydroxyacyl-[ acyl-carrier-protein] dehydratase is encoded by a gene selected from the group consisting of E. coli fabA (NP_415474.1), and E. coli fabZ (NP_414722.1).
20. The microorganism of claim 1, wherein said enoyl-[acyl-carrier-protein] reductase is encoded by a gene selected from the group consisting of E. coli fabI (NP_415804.1), Enterococcus faecalis fabK (NP_816503.1), Bacillus subtilis fabL (KFK80655.1), and Vibrio cholerae fabV (ABX38717.1).
21. The microorganism of claim 2, wherein said overexpressed thioesterase is encoded by a gene selected from the group consisting of E. coli tesA (NP_415027.1), E. coli tesB (NP_414986.1), E. coli yciA (NP_415769.1), E. coli fadM (NP_414977.1), E. coli ydil (NP_416201.1), E. coli ybgC (NP_415264.1), Alcanivorax borkumensis tesB2 (YP_692749.1) Fibrobacter succinogenes Fs2108 (YP_005822012.1), Prevotella ruminicola Pr655 (YP_003574018.1) and Prevotella ruminicola Pr1687 (YP_003574982.1).
22. The microorganism of claim 2, wherein said overexpressed acyl-CoA:acetyl-CoA transferase is encoded by a gene selected from the group consisting of E. coli atoD (NP_416725.1), Clostridium kluyveri cat2 (AAA92344.1), Clostridium acetobutylicum ctfAB (NP_149326.1, NP_149327.1) and E. coli ydiF (NP_416209.1).
23. The microorganism of claim 2, wherein said overexpressed phosphotransacylase is encoded by a gene selected from the group consisting of Clostridium acetobutylicum ptb (NP_349676.1), Enterococcus faecalis ptb (AAD55374.1), and Salmonella enterica pduL (AAD39011.1).
24. The microorganism of claim 2, wherein said overexpressed carboxylate kinase is encoded by a gene selected from the group consisting of Clostridium acetobutylicum buk (AAK81015.1), Enterococcus faecalis buk (AAD55375.1), and Salmonella enterica pduW (AAD39021.1).
25. The microorganism of claim 3, wherein said overexpressed alcohol-forming coenzyme-A thioester reductase is encoded by a gene selected from the group consisting of Clostridium acetobutylicum adhE2 (YP_009076789.1), Arabidopsis thaliana At3g11980 (AEE75132.1), Arabidopsis thaliana At3g44560 (AEE77915.1), Arabidopsis thaliana At3g56700 (AEE79553.1), Arabidopsis thaliana At5g22500 (AED93034.1), Arabidopsis thaliana CER4 (AEE86278.1), Marinobacter aquaeolei VT8 maqu_2220 (YP_959486.1), and Marinobacter aquaeolei VT8 maqu_2507 (YP_959769.1).
26. The microorganism of claim 3, wherein said overexpressed aldehyde-forming CoA thioester reductase is encoded by a gene selected from the group consisting of Acinetobacter calcoaceticus acr1 (AAC45217.1), Acinetobacter sp Strain M-1 acrM (BAB85476.1), Clostridium beijerinckii ald (AAT66436.1), E. coli eutE (NP_416950.1), Salmonella enterica eutE (AAA80209.1), and E. coli mhpF (NP_414885.1).
27. The microorganism of claim 3, wherein said overexpressed alcohol dehydrogenase is encoded by a gene selected from the group consisting of E. coli betA (NP_414845.1), E. coli dkgA (NP_417485.4), E. coli eutG (NP_416948.4), E. coli fucO (NP_417279.2), E. coli ucpA (NP_416921.4), E. coli yahK (NP_414859.1), E. coli ybbO (NP_415026.1), E. coli ybdH (NP_415132.1), E. coli yiaY (YP_026233.1), and E. coli yjgB (NP_418690.4).
28. The microorganism of claim 4, wherein said aldehyde decarbonylase overexpressed is encoded by a gene selected from the group consisting of Synechococcus elongatus PCC7942 orf1593 (Q54764.1), Nostoc punctiforme PCC73102 npun_R1711 (B2J1M1.1), and Prochlorococcus marinus MIT9313 pmt1231 (Q7V6D4.1).
29. The microorganism of claim 5, wherein said overexpressed transaminase is encoded by a gene selected from the group consisting of Arabidopsis thaliana At3g22200 (NP_001189947.1), Alcaligenes denitrificans AptA (AAP92672.1), Bordetella bronchiseptica BB0869 (WP_015041039.1), Bordetella parapertussis BPP0784 (WP_010927683.1), Brucella melitensis BAWG_0478 (EEW88370.1), Burkholderia pseudomallei BP1026B_10669 (AFI65333.1), Chromobacterium violaceum CV2025 (AAQ59697.1), Oceanicola granulosus OG2516_07293 (WP_007254984.1), Paracoccus denitrificans PD1222 Pden_3984 (ABL72050.1), Pseudogulbenkiania ferrooxidans -TA (WP_008952788.1), Pseudomonas putida-TA (P28269.1), Ralstonia solanacearum -TA (YP_002258353.1), Rhizobium meliloti SMc01534 (NP_386510.1), and Vibrio fluvialis -TA (AEA39183.1), Mus musculus abaT (AAH58521.1) and E. coli gabT (YP_490877.1).
30. The microorganism of claims 7, wherein said overexpressed carboxylic acid omega hydroxylase is encoded by a gene selected from the group consisting of Pseudomonas putida alkBGT (YP_009076004.1, Q9WWW4.1, Q9L4M8.1),Marinobacter aquaeolei CYP 153A (ABM17701.1),Mycobacterium marinum CYP 153A16 (YP_001851443.1), Polaromonas sp. CYP 153A (YP_548418.1), Nicotiana tabacum CYP94A5 (AAL54887.1), Vicia sativa CYP94Al (AAD10204.1), Vicia sativa CYP94A2 (AAG33645.1), Arabidopsis thaliana CYP94Bl (BAB08810.1), Arabidopsis thaliana CYP86A8 (CAC67445.1), Candida tropicalis CYP52Al (AAA63568.1, AAA34354.1, AAA34334.1), Candida tropicalis CYP52A2 (AAA34353.2, CAA35593.1), and Homo sapiens CYP4All (AAQ56847.1).
31. The microorganism of claim 7, wherein said overexpressed alcohol oxidase is encoded by a gene selected from the group consisting of Rhodococcus ruber SC1 cddC (AAL14237.1), Acinetobacter sp. SE19 chnD (AAG10028.1), E. coli yahK (NP_414859.1), and E. coli yjgB (NP_418690.4).
32. The microorganism of claim 7, wherein said overexpressed aldehyde dehydrogenase is encoded by a gene selected from the group consisting of Rhodococcus ruber SC1 cddD (AAL14238.1), and Acinetobacter sp. SE19 chnE (AAG10022.1).
33. The microorganism of claim 13, wherein said overexpressed fatty acid alpha hydroxylases is encoded by a gene selected from the group consisting of Myxococcus xanthus MXAN_0191 (YP_628473.1), and Stigmatella aurantiaca STIAU_3334 (YP_003957653.1).
34. The microorganism of claim 1, wherein said overexpressed thiolase is able to condense an omega-hydroxylated primer, an omega-carboxylated primer or a omega-aminated primer with acetyl-CoA and is encoded by a gene selected from the group consisting of E. coli atoB (NP_416728.1), E. coli yqeF (NP_417321.2), E. coli fadA (YP_026272.1), E. coli FadI (NP_416844.1), Ralstonia eutropha bktB (AAC38322.1), Pseudomonas sp. Strain B13 catF (AAL02407.1), E coli paaJ (NP_415915.1), Pseudomonas putida pcaF (AAA85138.1), Rhodococcus opacus pcaF (YP_002778248.1), Streptomyces sp. pcaF (AAD22035.1), Ralstonia eutropha phaA (AEI80291.1), Clostridium acetobutylicum thlA (AAC26023.1), and Clostridium acetobutylicum thlB (AAC26026.1).
35. The microorganism of claim 34, wherein said overexpressed 3-oxoacyl-[acyl-carrier-protein] reductase, overexpressed 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, and overexpressed enoyl-[acyl-carrier-protein] reductase are able to act on omega-hydroxylated, omega-carboxylated or omega-aminated substrates and encoded by genes selected from the group consisting of E. coli fabA, E. coli fabG, E. coli fabI, Enterococcus faecalis fabK, Bacillus subtilis fabL, Vibrio cholerae fabV and E. coli fabZ.
36. The microorganism of claim 35, wherein said overexpressed termination pathways are able to act on omega-hydroxylated, omega-carboxylated or omega-aminated substrates and encoded by genes selected from the group consisting of E. coli tesA, E. coli tesB, E. coli yciA, E. coli fadM, E. coli ydiI, E. coli ybgC, E. coli paal, E. coli ybdB, A. Borkumensis tesB, A. thaliana ACH2, M. musculus acot8, S. cerevisiae PTE1, E. coli atoD, Clostridium kluyveri cat2, Clostridium acetobutylicum ctfB, E. coli ydiF, Clostridium acetobutylicum ptb/buk, Enterococcus faecalis ptb/buk, Salmonella enterica pduL/pduW, Clostridium acetobutylicum adhE2, Arabidopsis thaliana At3g11980, Arabidopsis thaliana At3g44560, Arabidopsis thaliana At3g56700, Arabidopsis thaliana At5g22500, Arabidopsis thaliana CER4, Marinobacter aquaeolei VT8 maqu2507, Acinetobacter calcoaceticus acr 1, Acinetobacter sp Strain M-1 acrM, Clostridium beijerinckii ald, E. coli eutE, Salmonella enterica eutE, E. coli mhpF, E. coli betA, E. coli eutG, E. coli fucO, E. coli ucpA, E. coli ybbO, E. coli ybdH, E, coli Synechococcus elongatus PCC7942 orf1593, Nostoc punctiforme PCC73102 npun_R1711, Prochlorococcus marinus MIT9313 pmt1231, Mus musculus abaT and E. coli gabT.
37. The microorganism of claim 1, wherein said overexpressed thiolase is able to condense an omega-carboxylated primer (e.g. oxalyl-CoA, malonyl-CoA, succinyl-CoA) with acetyl-CoA and encoded by a gene selected from the group consisting of E. coli atoB (NP_416728.1), E. coli yqeF (NP_417321.2), E. coli fadA (YP_026272.1), E. coli FadI (NP_416844.1), Ralstonia eutropha bktB (AAC38322.1), Pseudomonas sp. Strain B13 catF (AAL02407.1), E coli paaj (NP_415915.1), Pseudomonas putida pcaF (AAA85138.1), Rhodococcus opacus pcaF (YP_002778248.1), Streptomyces sp. pcaF (AAD22035.1), Ralstonia eutropha phaA (AEI80291.1), Clostridium acetobutylicum thlA (AAC26023.1), and Clostridium acetobutylicum thlB (AAC26026.1).
38. The microorganism of claim 37, wherein said overexpressed 3-oxoacyl-[acyl-carrier-protein] reductase, overexpressed 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, and overexpressed enoyl-[acyl-carrier-protein] reductase are able to act on omega-carboxylated substrates and encoded by genes selected from the group consisting of E. coli fabA, E. coli fabG, E. coli fabI, Enterococcus faecalis fabK, Bacillus subtilis fabL, Vibrio cholerae fabV and E. coli fabZ.
39. The microorganism of claim 38, wherein said overexpressed termination pathways are able to act on omega-carboxylated substrates and encoded by genes selected from the group consisting of E. coli tesA, E. coli tesB, E. coli yciA, E. coli fadM, E. coli ydiI, E. coli ybgC, E. coli paal, E. coli ybdB, A. Borkumensis tesB, A. thaliana ACH2, M. musculus acot8, S. cerevisiae PTE1, E. coli atoD, Clostridium kluyveri cat2, Clostridium acetobutylicum ctfB, E. coli ydiF, Clostridium acetobutylicum ptb/buk, Enterococcus faecalis ptb/buk, Salmonella enterica pduL/pduW, Clostridium acetobutylicum adhE2, Arabidopsis thaliana At3g11980, Arabidopsis thaliana At3g44560, Arabidopsis thaliana At3g56700, Arabidopsis thaliana At5g22500, Arabidopsis thaliana CER4, Marinobacter aquaeolei VT8 maqu2507, Acinetobacter calcoaceticus acr 1, Acinetobacter sp Strain M-1 acrM, Clostridium beijerinckii ald, E. coli eutE, Salmonella enterica eutE, E. coli mhpF, E. coli betA, E. coli eutG, E. coli fucO, E. coli ucpA, E. coli ybbO, E. coli ybdH, E, coli yiaH, Synechococcus elongatus PCC7942 orf1593, Nostoc punctiforme PCC73102 npun_R1711, Prochlorococcus marinus MIT9313 pmt1231, Mus musculus abaT and E. coli gabT.
40. The microorganism of claim 1, wherein said overexpressed thiolase is able to condense an omega-aminated primer (e.g. 2-amino-acetyl-CoA, 3-amino-propionyl-CoA, 4-amino-butyryl-CoA) with acetyl-CoA and encoded by a gene selected from the group consisting of E. coli atoB (NP_416728.1), E. coli yqeF (NP_417321.2), E. coli fadA (YP_026272.1), E. coli fadI (NP_416844.1), Ralstonia eutropha bktB (AAC38322.1), Pseudomonas sp. Strain B13 catF (AAL02407.1), E coli paaj (NP_415915.1), Pseudomonas putida pcaF (AAA85138.1), Rhodococcus opacus pcaF (YP_002778248.1), Streptomyces sp. pcaF (AAD22035.1), Ralstonia eutropha phaA (AEI80291.1), Clostridium acetobutylicum thlA (AAC26023.1), and Clostridium acetobutylicum thlB (AAC26026.1).
41. The microorganism of claim 40, wherein said overexpressed 3-oxoacyl-[acyl-carrier-protein] reductase, overexpressed 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, and overexpressed enoyl-[acyl-carrier-protein] reductase are able to act on omega-aminated substrates and encoded by genes selected from the group consisting of E. coli fabA, E. coli fabG, E. coli fabI, Enterococcus faecalis fabK, Bacillus subtilis fabL, Vibrio cholerae fabV and E. coli fabZ.
42. The microorganism of claim 41, wherein said overexpressed termination pathways are able to act on omega-aminated substrates and encoded by genes selected from the group consisting of E. coli tesA, E. coli tesB, E. coli yciA, E. coli fadM, E. coli ydiI, E. coli ybgC, E. coli paal, E. coli ybdB, A. Borkumensis tesB, A. thaliana ACH2, M. musculus acot8 S. cerevisiae PTE1, E. coli atoD, Clostridium kluyveri cat2, Clostridium acetobutylicum ctfB, E. coli ydiF, Clostridium acetobutylicum ptb/buk, Enterococcus faecalis ptb/buk, Salmonella enterica pduL/pduW, Clostridium acetobutylicum adhE2, Arabidopsis thaliana At3g11980, Arabidopsis thaliana At3g44560, Arabidopsis thaliana At3g56700, Arabidopsis thaliana At5g22500, Arabidopsis thaliana CER4, Marinobacter aquaeolei VT8 maqu2507, Acinetobacter calcoaceticus acr 1, Acinetobacter sp Strain M-1 acrM, Clostridium beijerinckii ald, E. coli eutE, Salmonella enterica eutE, E. coli mhpF, E. coli betA, E. coli eutG, E. coli fucO, E. coli ucpA, E. coli ybbO, E. coli ybdH, E, coli yiaH, Synechococcus elongatus PCC7942 orf1593, Nostoc punctiforme PCC73102 npun_R1711, Prochlorococcus marinus MIT9313 pmt1231, Mus musculus abaT and E. coli gabT.
43. The microorganism of claim 16 wherein said reduced expression of fermentation enzymes are adhE, (pta or ackA or ackApta), poxB, ldhA, and frdA and less acetate, lactate, ethanol and succinate are thereby produced.
44. The microorganism of claim 1, comprising one or more termination enzymes from Table C.
45. A method of making a desired product, comprising growing the microorganism of claim 1 for a time sufficient to make a product by reverse beta oxidation, and then producing said product.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
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DETAILED DESCRIPTION
(18) The technology herein is based on developing an alternative strategy to the efficient production of -, -, and -functionalized carboxylic acids, alcohols, hydrocarbons, and amines that focuses on the use of type II fatty acid biosynthesis pathway genes/enzymes in E. coli and S. cerevisiae (as examples) to assemble a functional reversal of the -oxidation cycle by combining these type II fatty acid biosynthesis enzymes with the non-decarboxylating condensation reaction catalyzed by thiolases. However, these pathways are ubiquitous, and any type II FAS enzyme from any species can be used.
(19) Technologies developed prior to this are based on the native version of the FAS pathway, which uses a decarboxylative condensation step catalyzed by keto-acyl-ACP/CoA synthases. However, the operation of this pathway is less efficient because it consumes ATP in the synthesis of malonyl-ACP, which is the donor of two-carbon units for chain elongation/decarboxylating condensation reaction. As a consequence, the ATP yield associated with the production of products through the FAS pathway is very low. This, in turn, greatly limits cell growth and production of products.
(20) In more detail, the recombinant engineering to make the BOX-R is:
(21) 1) Express the Enzymes Required for a Functional -Oxidation Cycle Reversal Using Enzymes of the Type II Fatty Acid Biosynthesis Pathway. Previously, expression of the -oxidation cycle was accomplished through an approach in which, first 1) mutations fadR and atoC(c) enable expression of the genes encoding beta oxidation enzymes in the absence of fatty acids; 2) an arcA knockout (arcA) enabled the expression of genes encoding beta oxidation cycle enzymes/proteins under anaerobic/microaerobic conditions (microaerobic/anaerobic conditions are used in the production of fuels and chemicals but lead to repression of beta oxidation genes by ArcA); and 3) replacement of native cyclic AMP receptor protein (crp) with a cAMP-independent mutant (crp*) enabled the expression of genes encoding beta oxidation cycle enzymes/proteins in the presence of a catabolite-repressing carbon source such as glucose (glucose is the most widely used carbon source in fermentation processes and represses the beta oxidation genes).
(22) However, the cycle can also be made to run in reverse by individually overexpressing the rate limiting enzymes as opposed to this regulatory approach. Furthermore, the active enzymes can be purified and combined in vitro and made to run the BOX-R pathway in a test tube or flask, or resting cells could be used as a bioreactor for same.
(23) The overall idea in this disclosure, however is to replace some or all genes (other than the thiolase) with type II FAS enzymes (i.e. 3-oxoacyl-[acyl-carrier-protein] (FabG, others), 3-hydroxyacyl-[acyl-carrier-protein] dehydratase (FabA, FabZ, others), and enoyl-[acyl-carrier-protein] reductase (FabI, FabK, FabL, FabV)).
(24) Thus, for a functional reversal of the BOX-R using type II FAS enzymes, 1) non-decarboxylative thiolase(s) are expressed in combination with 2) 3-oxoacyl-[acyl-carrier-protein]/p-ketoacyl-[ACP] reductase (FabG, others), 3) 3-hydroxyacyl-[acp] dehydratase (FabA, FabZ, others), and 4) enoyl-[acyl-carrierprotein] reductase/enoyl-ACP reductase (FabI, FabK, FabL, FabV) to enable the generation of a diverse set of CoA thioester intermediates (
(25) 2) Driving the Beta Oxidation Cycle in the Reverse/Biosynthetic Direction (as Opposed to its Natural Catabolic/Degradative Direction). In addition to functionally expressing the -oxidation cycle with non-decarboxylative thiolase(s) and type II fatty acid biosynthesis enzymes, we propose the following modifications to improve yields on the reverse operation of this pathway: 1) the use of microaerobic/anaerobic conditions prevents/minimizes the metabolism of acetyl-CoA through the tricarboxylic acids (TCA) cycle and makes acetyl-CoA available to drive the beta oxidation cycle in the reverse/biosynthetic direction; 2) pta (or ackA or both), poxB, adhE, yqhD, and eutE knockouts block/reduce the synthesis of acetate (pta or ackA and poxB) and ethanol (adhE, yqhD, and eutE) from acetyl-CoA and therefore make acetyl-CoA available to drive the beta oxidation cycle in the reverse/biosynthetic direction; 3) ldhA, mgsA, and frdA knockouts block/reduce the synthesis of lactate (ldhA and mgsA) and succinate (frdA) from pyruvate and phosphoenolpyruvate, respectively, making more phosphoenolpyruvate and pyruvate available for the synthesis acetyl-CoA and therefore making acetyl-CoA available to drive the beta oxidation cycle in the reverse/biosynthetic direction.
(26) 3) Conversion of CoA thioester intermediates to the desired end products. Generally speaking, there are several termination enzymes that will pull reaction intermediates out the reverse -oxidation cycle and produce the desired end product (
(27) One or more of these termination enzymes can be overexpressed, as needed depending on the desired end product. The termination enzymes can be native or non-native as desired for particular products, but it may be preferred that the reverse beta oxidation cycle use native genes.
(28) 4. Regulation of Product Chain Length. The chain length of thioester intermediates determines the length of end products, and can be controlled by using appropriate termination enzymes with the desired chain-length specificity. Additionally, chain elongation can be inhibited or promoted by reducing or increasing the activity of thiolases with the desired chain-length specificity. These two methods can be used together or independently. For example:
(29) 1) knockout of fadA, fadI, and paaJ to avoid chain elongation beyond 1-to-2 turns of the cycle (generates 4- & 6-carbon intermediates and products, or 5- & 7-carbon intermediates and products, depending on the use of acetyl-CoA or propionyl-CoA as primer/starter molecule) and overexpression of the short-chain thiolases yqeF or atoB and short chains alcohol dehydrogenases such as fucO or yqhD for alcohol production for example.
(30) 2) overexpression of thiolase(s) of appropriate substrate length specificity (such as E. coli atoB, E. coli yqeF, E. coli fadA, E. coli fadI, Ralstonia eutropha bktB, Pseudomonas sp. Strain B13 catF, E coli paaJ, Pseudomonas putida pcaF Rhodococcus opacus pcaF, Streptomyces sp. pcaF, Ralstonia eutropha phaA, Clostridium acetobutylicum thlA, or Clostridium acetobutylicum thlB) to promote chain elongation and overexpression of specific chain length termination pathways such as long-chain thioesterases (such as E. coli tesA, tesB, fadM, ybgC or yciA, among others) or long chain alcohol dehydrogenases (such as ucpA, ybbO, yiaY, betA, ybdH or eutG) for carboxylic acid or alcohol production, respectively. The term appropriate is used herein to refer to an enzyme with the required specificity toward a given intermediate (i.e. acyl-CoA, enoyl-CoA, hydroxyacyl-CoA, and ketoacyl-CoA) of a specific chain length.
(31) Clomburg et al (2012) focused on bottom-up/synthetic approach to reconstruct a beta-oxidation pathway in reverse (BOX-R) and hence address short-coming of an early system-level approach that focused on the use of global regulators. Clomburg et al (2012) was successful on identifying and exploiting native enzymes for 3 of the four steps of the BOX-R: thiolase (e.g. AtoB, FadA), 3-hydroxyacyl-CoA dehydrogenase (FadB) and enoyl-CoA dehydratase (fadB). While both of our previous reports (Dellomonaco et al. 2011 and Clomburg et al. 2012) indicate that there is a native E. coli enzyme that catalyzes the last step of the BOX-R (trans-enoyl-CoAs to acyl-CoAs), the identity of this enzyme remained elusive.
(32) In this study, we identified fabI-encoded enoyl-CoA reductase as the activity responsible for this conversion and demonstrated that enoyl-ACP reductases of different families can support the efficient operation of an engineered functional reversal of the -oxidation cycle.
(33) Since acetyl-coA dehydrogenases (ACDH) utilize a bound FAD cofactor to reduce the 2,3 enoyl-CoA bonds, they often require additional enzymes such as flavoproteins and ferrodoxins in order to function, although the initial reducing equivalents may be sourced to NAD(P)H. Because these enzymes utilize FAD molecules, the chemical reduction/dehydrogenation can be considered reversible, though that might not be the practical result in vivo and they are generally considered to be slow enzymes. In contrast to ACDHs, trans-enoyl-CoA reductase (TER) enzymes that directly utilize NAD(P)H molecules to reduce enoyl bonds are considered irreversible reactions as exampled by their inability to oxidize butyryl-CoA substrates (Tucci & Martin, 2007) and do not require electron transfer proteins to function.
(34) This effectively irreversible activity for reduction of crotonyl-CoA by TER-like enzymes has previously been identified as a beneficial property in improving butanol titers (Atsumi et al., 2008; Bond-Watts, Bellerose, & Chang, 2011b; Shen et al., 2011). In addition, modeling studies have shown that E. coli engineered for butyrate production by the reversal of -oxidation cycle would benefit from crotonyl-CoA reduction by enzymes that utilize NADH, given the stoichiometric constraints imposed by the use of ferrodoxins (Cintolesi et al., 2014).
Strains, Plasmids, and Methods
(35) Genomic DNAs from E. faecalis V583 (ATCC 700802), B. subtilis (Ehrenberg) Cohn (ATCC 23857), and V. cholerea N16961 (ATCC 39315), as well as, the M. elsdenii Rogosa strain were acquired from ATCC (Manassas, Va.). E. coli genomic DNA from MG1655 (Kang et al., 2004) and M. elsdenii Rogosa were purified using the Wizard Genomic DNA Purification Kit (PROMEGA, Madison, Wis.). E. gracilis TER was amplified from a plasmid harboring a codon-optimized egTER synthesized by GENSCRIPT (Piscataway, N.J.).
(36) All restriction enzymes were purchased from NEW ENGLAND BIOLABS (Ipswich, Mass.). Plates were prepared using LB medium containing 1.5% agar, and antibiotics were included at the following concentrations when appropriate: ampicillin (100 g/mL), kanamycin (50 g/mL), spectinomycin (50 g/mL), chloramphenicol (12.5 g/mL chromosomal/34 g/mL plasmids) and zeocin (25-50 g/mL).
(37) Gene overexpression was achieved by cloning the desired gene(s) into either pETDuet-1 (pET) or pCDFDuet-1 (pCDF) (NOVAGEN, Darmstadt, Germany) digested with NcoI and EcoRI restriction enzymes utilizing In-Fusion PCR cloning technology (CLONTECH LABORATORIES, Mountain View, Calif.). These vectors have 2 promotors that genes can be cloned behind, referred to herein as P1 and P2.
(38) Cloning inserts were created via PCR of ORFs of interest from their respective genomic or codon-optomized DNA with Phusion DNA polymerase (THERMO SCIENTIFIC, Waltham, Mass.). The resulting In-Fusion products were used to transform E. coli Stellar cells (CLONTECH LABORATORIES) and PCR identified clones were confirmed by DNA sequencing.
(39) Strain JC01 (MG1655 ldhA poxB pta adhE frdA) (Clomburg, Vick, Blankschien, Rodriguez-moya, & Gonzalez, 2012), a derivative of wild-type K12 E. coli strain MG1655 (Kang et al., 2004), was used as the host for all genetic modifications. JC01 (DE3) was constructed from JC01 using a DE3 Lysogenization Kit (NOVAGEN) to allow the expression of genes under the T7lac promoter.
(40) Gene knockouts were introduced in JC01 (DE3) and its derivatives by P1 phage transduction (Miller, 1972; Shams Yazdani & Gonzalez, 2008). Single gene knockout mutants from the National BioResource Project (NIG, Japan) (Baba et al., 2006) were used as donors of specific mutations. All mutations were confirmed by polymerase chain reaction and the disruption of multiple genes in a common host was achieved as previously described (Shams Yazdani & Gonzalez, 2008).
(41) Strain JC01 (DE3) was further modified to allow for cumate inducible control (Choi et al., 2010) from the genome. To enable this, first the construction of pUCBB-p.sup.CT5-ntH6-eGFP based on previous BioBrick vector designs (Vick et al., 2011).
(42) E. coli atoB and fadB genes were PCR amplified and digested with BglII and NotI and ligated by T4 ligase (Invitrogen, Carlsbad, Calif.) into pUCBB-P.sup.CT5-ntH6-eGFP that was previously digested with BglII and NotI to produce pUCBB-P.sup.CT5-atoB and pUCBB-P.sup.CT5-fadB. The resulting ligation products were used to transform E. coli DH5 (INVITROGEN, Carlsbad, Calif.) and positive clones identified by PCR were confirmed by DNA sequencing.
(43) To integrate the cumate-controlled atoB and fadB constructs onto the chromosome, first the cumate repressor (cymR), promoter/operator regions (P.sup.CT5), and respective ORFs were PCR amplified, as well as, kanamycin or chloramphenicol drug constructs (respectively via pKD4 and pKD3 (Datsenko & Wanner, 2000). These respective products were linked together via overlap extension PCR to create a final chromosomal targeting construct. Integration of the cumate-controlled constructs was achieved via standard recombineering protocols using strain HME45 and selecting on respective LB drug plates (Thomason et al., 2007).
(44) The gene fadA was separately deleted via recombineering in the HME45 derivative harboring the cumate-controlled fadBA contract by replacement of the fadA ORF with a zeocin-resistance marker amplified from pKDzeo (Magner et al., 2007). All constructs were verified via PCR and sequencing.
(45) All chemicals were obtained from FISHER SCIENTIFIC (Pittsburgh, Pa.) and SIGMA-ALDRICH (St. Louis, Mo.). Fermentations were conducted as previously described using the identical medium formulation (Clomburg et al., 2012) with the exception of 5.0 M Isopropyl -D-1-thiogalactopyranoside (Vector-based expression) and 0.1 mM cumate (chromosomal-based expression) included for induction when appropriate.
(46) Measurement of cell growth, quantification of glycerol and metabolic products by high-performance liquid chromatography (HPLC), quantification of fatty acids (C4-C6) by HPLC, and quantification of fatty acids (C7-C14,C16,C18) by Gas ChromatographyFlame Ionization Detection (GC-FID) were performed as previously described (Clomburg et al., 2012).
(47) For quantification purposes of odd-chain fatty acids, samples were run with and without the C13 fatty acid internal standard, verifying that C13 was not produced. Propionic (C.sub.3:0), Valeric (C.sub.5:0), Enanthic (C.sub.7:0), Pelargonic (C.sub.9:0) and Undecyclic (C.sub.11:0) acid (SIGMA-ALDRICH CO.) standards were used to calibrate HPLC and GC-FID analysis.
(48) For measurement of enzymatic activities from fermentation samples, cells were disrupted as previously reported (Dellomonaco, Clomburg, Miller, & Gonzalez, 2011). The HIS Tagged FabI protein was expressed from pCA24N-FabI from the ASKA collection (Kitagawa et al., 2005) in BL21(DE3) cells (NEW ENGLAND BIOLABS) induced at OD.sub.6000.4 with 0.1 mM IPTG and shaken O/N at Room Temperature. FabI protein was harvested and purified as previously reported using Talon Metal Affinity Resin (CLONTECH LABORATORIES) (Clomburg et al., 2012).
(49) Thiolase activity (Wiesenborn, Rudolph, & Papoutsakis, 1988) and -hydroxybutyryl-CoA dehydrogenase activity (Bond-Watts, Bellerose, & Chang, 2011a) were monitored accordingly as previously described (Clomburg et al., 2012). Trans-enoyl-CoA reductase activity for egTER, FabI, bsFabL, efFabK and vcFabV were monitored by loss of NADH (Bond-Watts et al., 2011a; Clomburg et al., 2012). Acyl-CoA dehydrogenase activity was monitored by measuring the reduction of Methyl-Thiazolyl Blue (MTT) coupled to the oxidation of butyryl-CoA (O'Brien & Frerman, 1977) in cellular extracts disrupted as above with the addition of 5 M flavin adenine dinucleotide (FAD).
(50) Reactions conditions were as follows: 25 mM Tris pH 7.5, 240 M MTT, 1.7 mM phanazine methosulfate (PMS), 15 mM sodium cyanide, and 250 M butyryl-CoA in a final volume of 200 L at 30 C. All substrates and chemicals for enzyme assays were obtained from FISHER SCIENTIFIC and SIGMA-ALDRICH.
(51) High performance liquid chromatography-mass spectrometry (HPLC-MS) was performed on a BRUKER MicroTOP ESI (Fremont, Calif.) with an AGILENT 1200 HPLC System (Santa Clara, Calif.). Enzymatic reactions were quenched with 10% of IN HCl and diluted 10 fold with dH.sub.2O, 2 L of which was used for injection. HPLC-MS assays were performed using a SHIMADZU Shim-pack XR-ODS II column (2.0 mm I,d.75 mm) (Tokyo, Japan) at a flow rate of 0.15 mL/min with a maximum pressure of 380 bar at room temperature. Liquid chromatography was performed with 40 mM ammonium acetate (Buffer A) and methanol (Buffer B). The time course was as follows: 0 min-2.5% methanol, linear gradient to 70% methanol at 7 min, hold at 70% methanol to 12 min, linear gradient to 2.5% methanol at 12.1 min, hold at 2.5% methanol to 24 min.
Chromosomal Expression
(52) Previously, an engineered reversal of BOX-R was constructed in E. coli by utilizing strain JC01, a fermentation-deficient derivative of E. coli K12 strain MG1655 (MG1655 ldhA poxB pta adhE frdA), with the vector level expression of native thiolase (AtoB), 3-hydroxyacyl-CoA dehydrogenase (FadB), and enoyl-CoA hydratase (FadB), as well as the foreign trans-enoyl-CoA reductase from Euglena gracilis (egTER) (Clomburg et al., 2012).
(53) An interesting result of this work was the ability to produce small amounts of butyrate in the absence of an overexpressed acyl-CoA dehydrogenase (ACDH) or trans-enoyl-CoA reductase (TER). Using strain JC01 with the pTH.atoB.fadB vector, the two main products from the reversal of the -oxidation cycle were 3-hydroxybutyrate (3-HB) (2.5 g/L) and butyrate (0.2 g/L). When E. gracilis trans-enoyl-CoA reductase (egTER) is overexpressed via pTH.atoB.fadB.egTER, a 17-fold increase in butyrate production is observed (3.4 g/L) while virtually eliminating production of the 3-hydroxybutyrate (Clomburg et al., 2012).
(54) The product profile can then be altered to longer-chain carboxylic acids (up to C12) with the inclusion of a longer chain specific thiolase (FadA). This work clearly established thiolases (AtoB, FadA), 3-hydroxyacyl-Coa dehydrogenase (FadB), and enoyl-CoA dehydratase (FadB) as key native enzymes necessary to facilitate the functional reversal of -oxidation (
(55) In order to establish a clean, vector-free platform to identify the unknown native ACDH or TER-like enzymes that catalyze the final step of the -oxidation reversal, we constructed a strain with tunable chromosomal expression of AtoB and FadB by engineering their native chromosomal loci. Using an in-house developed expression system based on a cumate-inducible promoter (Choi et al., 2010) adapted into a BioBrick vector system (Vick et al., 2011), atoB and fadB genomic level expression was altered to be controlled by cumate while the fadA gene was knocked out.
(56) For atoB and fadB, the native promoter was replaced by both the T5 promoter controlled by the CymR operator (CT5) as well as an upstream constitutive expression system for CymR. By removing FadA expression, butyrate production can be utilized as proxy for flux through a single turn of the reversal of -oxidation cycle, thus facilitating the identification of native enzyme(s) responsible for the reduction of crotonyl-CoA.
(57) Prior to the aforementioned modifications, strain JC01 was modified to include the DE3 cassette to allow the use of Novagen's Duet vector system for the expression of hypothesized ACDHs and TER-like enzymes. The resulting strain will be referred to throughout the manuscript as JC01(DE3) atoB.sup.CT5fadB.sup.CT5 fadA.
(58) Enzyme activities and fermentation profiles of JC01(DE3) atoB.sup.CT5 fadB.sup.CT5 fadA were compared to those of the vector-based expression system in strain JC01(DE3) [pETDuet-atoB pCDFDuet-fadB]. The chromosomal expression strain produced more butyrate (0.630.01 g/L) and 3-hydroxybutyrate (4.330.04 g/L) than the vector based system (butyrate=0.420.03 g/L, 3-hydroxybutyrate=3.230.07 g/L) (data not shown). The chromosomal strain had similar 3-hydroxybutyryl-CoA dehydrogenase activity (2.20.7 mol/mg/min) to that of pCDFDuet-fadB (1.70.7 mol/mg/min) while thiolase activity was greater from pETDuet-atoB (25.03.2 mol/mg/min) in comparison to atoB expression from the chromosome (3.80.3 mol/mg/min). The higher product yield from JC01(DE3) atoB.sup.CT5 fadB.sup.CT5 fadA indicates that adequate amounts of thiolase and 3-hydroxybutryl-CoA dehydrogenase activities are produced by chromosomal expression.
Identification of Native Enzyme(s)
(59) Multiple enzymes in E. coli have the potential to reduce a 2,3-trans enoyl-CoA (e.g. crotonyl-CoA) to the corresponding acyl-CoA (e.g. butyryl-CoA). E. coli has two reported ACDHs as part of -oxidation pathways. FadE is the reported aerobic ACDH (Campbell & Jr, 2002; O'Brien & Frerman, 1977) while YdiO is a member of a butyryl-CoA dehydrogenase (BCD) electron transfer protein (Etf) complex (BCD/EtfBA) necessary for growth on fatty acids under anaerobic conditions (Campbell 2003). Two additional ACDH enzymes are present that could potentially reduce crotonyl-CoA as a promiscuous substrate; the crotonobetaine reductase complex CaiAB (Elssner 1999) and AidB, the isovaleryl-CoA dehydrogenase (Landini 1994; Rohankhedkar 2006), although AidB is reported to not work on butyryl-CoA. In an attempt to identify the native enzyme reducing crotonyl-CoA, the genes encoding these ACDH enzymes were knocked out and their effect on butyrate production in JC01(DE3) atoB.sup.ct5 fadB.sup.ct5 fadA was assessed. Interestingly, the individual deletion of these enzymes had little impact on either butyrate or 3-HB production levels (
(60) The genes encoding the aforementioned ACDHs were deleted and overexpressed in strain JC01(DE3) atoB.sup.CT5 fadB.sup.CT5 fadA and their effect on butyrate production assessed. The deletions had little impact on either butyrate or 3-hydroxybutyrate production levels and did not impair growth (
(61) Given the advantageous nature of TER enzymes and the fact that none of the investigated ACDH enzymes significantly altered butyrate production, another potential native enzyme that can catalyze the NAD(P)H-dependent conversion of crotonyl-CoA to butyryl-CoA is FabI, an essential enzyme from the fatty acid biosynthesis pathway (Heath & Rock, 1995). Although the fatty acid biosynthesis pathway utilizes Acyl Carrier Proteins (ACP) as substrates, FabI has been demonstrated to reduce crotonyl-CoA to butyryl-CoA (Helmut Bergler, 1996; Weeks & Wakil, 1968).
(62) Despite the potential for the native enzyme, when crude extracts from JC01(DE3) atoB.sup.ct5 fadB.sup.ct5 fadA were assayed for NAD(P)H dependent reduction of crotonyl-CoA no detectable activity was observed (Table 1). However, this is not necessarily an unexpected result, as FabI only reduces crotonyl-CoA as a promiscuous substrate with a K.sub.M (2.7 mM) (Helmet Bergler 1994) that is roughly 30-fold higher than the concentration of crotonyl-CoA (80 M) used in the standard assay of trans-enoyl-CoA reductases (80 M crotonyl-CoA) (Bond-Watts 2011a).
(63) To better assess the potential involvement of FabI, the trans-enoyl-CoA reductase assay was performed using 1 mM crotonyl-CoA, a concentration that is similar to the reported K.sub.M of 2.7 mM. Utilizing this substrate concentration, NADH-dependent crotonyl-CoA reduction activities of 0.1000.001 mol/mg/min and 0.0800.007 mol/mg/min were observed in crude cell extracts from fermentation samples of JC01(DE3) atoB.sup.ct5 fadB.sup.ct5 fadA harvested at 8 hrs and 48 hrs, respectively (Table 1). These results revealed the potential involvement of FabI in butyrate production from a one-turn reversal of the -oxidation cycle.
(64) To further investigate the potential role of FabI, vectors containing fabI or egTER were constructed and transformed into JC01(DE3) atoB.sup.cT5 fadB.sup.cT5 fadA to assess butyrate production from a one-turn BOX-R. In
(65) In order to provide further evidence that promiscuous crotonyl-CoA reduction by FabI is involved in native BOX cycle, fabI deletion is required. Given the essential nature of FabI (this is the only ENR in E. coli), construction of a fabI strain requires complementation with another trans-enoyl-ACP activity. Moreover, to verify the hypothesis that FabI indeed functions as the enoyl-CoA reductase of the BOX-R, the complementing enoyl-ACP reductase should not promiscuously reduce crotonyl-CoA as well. Since no enoyl-ACP reductase has been reported with these explicit characteristics, we investigated the following representative members of bacterial ENR families for their lack of crotonyl-CoA reductase activity: Bacillus subtilis FabL (bsFabL) (Heath 2000), Enterococcus faecalis FabK (efFabK) (Bi 2014, Zhu 2013), and Vibrio cholerae FabV (vcFabV) (Massengo-Tiasse 2008).
(66) Genes encoding each of the aforementioned ENRs were cloned into pETDuet and the resulting vectors transformed into JC01(DE3) atoB.sup.CT5 fadB.sup.CT5 fadA, and the resulting strains assayed for crotonyl-CoA reductase activity using 80 M crotonyl-CoA. While detectable activity was measured for cells with efFabK or vcFabV, no activity was detected for the cells overexpressing bsFabL (Table 1). Even when assayed with 1 mM crotonyl-CoA, the levels of crotonyl-CoA reductase activity shown by cell extracts of JC01(DE3) atoB.sup.CT5 fadB.sup.CT5 fadA fabI [pETDuet-bsfabL] are similar to the background levels measured for JC01(DE3) atoB.sup.CT5 fadB.sup.CT5 fadA [pETDuet], making bsfabL an ideal candidate to complement a fabI deletion without also providing the ability to promiscuously reduce crotonyl-CoA. As such, JC01(DE3) atoB.sup.CT5fadB.sup.CT5 fadA fabI strains were constructed in the presence of either pETDuet fabI or pETDuet-bsfabL. These vectors complemented the fabI deletion equally well, as evidenced by the isolation of viable transductions as well as the similar growth of both strains during fermentations (
(67) When assayed with NADPH, FabI is able to reduce enoyl-ACPs at an optimum of pH 6.5 on chain lengths of C4 to C10, while not able to reduce enoyl-CoAs. With NADH, FabI has a broader pH range for enoyl-ACP reduction that is optimal at pH 7.5 and is active over a chain length from C4 to C16. NADH is also necessary for FabI to reduce CoA substrates, though the reported catalytic efficiency with crotonyl-CoA (k.sub.cat/K.sub.M=8.5210.sup.1 M.sup.1 sec.sup.1) is several orders of magnitude lower than that reported with crotonyl-ACP (k.sub.cat/K.sub.M=1.9110.sup.6M.sup.1 sec.sup.1) at pH 7.5.
(68) The low catalytic efficiency reported for FabI with crotonyl-CoA contrasts with our observation that this enzyme supports butyrate synthesis fluxes as high as those supported by egTER, an enzyme with a very high catalytic efficiency with crotonyl-CoA (k.sub.cat/K.sub.M=1.20.1 M.sup.1 sec.sup.1) (Clomburg et al., 2012). A comparison of crotonyl-CoA reduction activity observed in our cultures to the expected activity based on reported kinetic parameters (Helmet Bergler et al., 1994) revealed an interesting picture. After 8 hours of cultivation, strain JC01(DE3) atoB.sup.ct5 fadB.sup.ct5 fadA exhibited an NADH-dependent crotonyl-CoA reduction activity of 0.1000.001 mol/mg/min, which corresponds to an observed rate of 4.8810.sup.8 M s.sup.1. The total protein concentration of the same culture was 2.94 mg/mL, from which the concentration of FabI is estimated to be between 6.8310.sup.8 M and 6.8310.sup.12M (Ishihama et al., 2008). Considering this concentration of FabI in the culture, the reported kcat (0.23 s.sup.1) and Km (2.7 mM) (Helmet Bergler et al., 1994), and a 1 mM crotonyl-CoA concentration, the expected rate of crotonyl-CoA reduction by FabI was calculated to be between 7.8610.sup.13M s.sup.1 and 7.8610.sup.9M s.sup.1. These calculations indicate that the expected rate calculated from reported kinetic parameters is only a small fraction of the rate observed in our cultures, which warrants re-evaluation of the kinetic parameters of FabI using crotonyl-CoA as the substrate.
(69) N-terminal His-tagged FabI was purified from an ASKA collection vector (Kitagawa et al., 2005) expressed in the strain BL21(DE3). The purified enzyme had a K.sub.M (4.60.6 mM) quite similar to the reported K.sub.M of 2.7 mM (Helmet Bergler et al., 1994), but our measurement of k.sub.cat was 5.30.6 s.sup.1 in comparison to 0.23 s.sup.1 that was previously reported, resulting in a 13-fold improvement of catalytic efficiency (k.sub.cat/K.sub.M) from 8.5210.sup.1 M.sup.1 sec.sup.1 to 1.1510.sup.3. This change in k.sub.cat increases the expected rate of crotonyl-CoA reduction by FabI to a value between 1.0210.sup.7M s.sup.1 and 7.8610.sup.11 M s.sup.1, which is in agreement with the rate observed in our cultures. To verify that FabI is utilizing NADH to convert crotonyl-CoA to butyryl-CoA, the reaction was monitored via HPLC-MS, which confirmed that FabI converts crotonyl-CoA almost completely to butyryl-CoA (
(70) Factors such as the presence of Mg.sup.2+ during our purification as well as Trisma-HCl vs. phosphate based buffer systems had marginal effect on activity levels (data not shown), and the most likely cause for this discrepancy is that previous studies used a maximum of approximately 1.25 mM crotonyl-CoA, which is less than their reported K.sub.M indicating that there was an inaccurate estimation of V.sub.max.
(71) As an essential gene for FAS, FabI is inhibited when large amounts of palmitic acid (C16) is present, and has been demonstrated to have a K.sub.i of 5.4 M towards palmitoyl-ACP and 20 M towards palmitoyl-CoA, but this inhibition is quickly lost for shorter fatty acids as the K.sub.i for decaonyl-CoA is approx 900 M (Helmut Bergler 1996).
(72) To understand the potential of utilizing FabI for BOX-R, we examined the effect of key CoA thioester intermediates of the BOX-R as well as a broad range of acyl-CoAs on FabI activity (
(73) The pH profile for FabI was also examined for comparison to the reported profile for crotonyl-ACP (Weeks & Wakil, 1968) (
FABI Supports Synthesis of C>4 Carboxylic Acids
(74) Employing AtoB as the thiolase limits the operation of the BOX-R pathway to one cycle and product synthesis to C4 molecules. FadA, which has longer chain length specificity, produces longer chain products. When fabI is overexpressed from pETDuet in JC01(DE3) atoB.sup.CT5 fadBA.sup.CT5, the production of extracellular longer chain length carboxylic acids is observed (
(75) The deletion of fadD has been utilized in numerous studies to facilitate the accumulation of longer chain carboxylic acids by preventing the uptake of free fatty acids from the media (Lennen 2012). Under these conditions, the deletion of fadD in JC01(DE3) atoB.sup.CT5fadBA.sup.CT5 with pETDuet-fabI resulted in the extracellular production of 19.40.1 mg/L tetradecanoic acid (C14) and a slight increase in dodecanoic acid (C12), with minimal impact on the levels of C4-C10 carboxylic acids produced (
Production of Odd Chain Carboxylic Acids
(76) In order to investigate the potential for FabI to be used in the production odd-chain carboxylic acids, strain JC01(DE3) atoB.sup.CT5 fadBA.sup.CT5 fadD yciA was further complemented with the propionate CoA transferase (PCT) from M. elsdenii (Taguchi et al., 2008), which has been used to successfully produce a variety of C5 fatty acid molecules (Tseng & Prather, 2012). mePCT was cloned into the pCDFDuet vector to facilitate co-expression with pETDuet-fabI. The two vectors were co-transformed into JC01 (DE3) atoB.sup.CT5 fadBA.sup.CT5 fadD yciA to determine odd chain carboxylic acid production in the presence of 15 mM propionate. This strain produced odd chain carboxylic acids ranging from 1874 mg/L of valerate (C5) to a maximum chain length of C11 at 30.90.6 mg/L (
FABI Supports Product Synthesis
(77) One concern when utilizing FabI as a trans-enoyl-CoA reductase is that product synthesis (e.g. butyrate and other products) could actually be proceeding through the type II FAS pathway, instead of the BOX-R. Fortunately, the condensation reactions responsible for carbon chain elongation in these two pathways are very different, providing an opportunity to clearly distinguish them. The BOX-R, which employ acetyl-CoA as the extender unit and a non-decarboxylating condensation mechanism (Binstock 1981, Jenkins 1987). The fatty acid biosynthesis pathway uses keto-acyl-ACP synthases, which employ a decarboxylating condensation mechanism and malonyl-ACP as the extender unit (White 2005).
(78) Overexpression of FabI in strain JC01(DE3) resulted predominantly in the production of acetate, a fermentation profile essentially undistinguishable from that of JC01(DE3) carrying the empty pETDuet vector (
Other Enoyl-ACP Reductases
(79) The identification of FabI as an enzyme that enables efficient operation of the -oxidation reversal prompted us to investigate whether other ENRs from the type II fatty acid biosynthesis pathway can play a similar role. While bsFabL was found to complement a fabI deletion without promiscuous activity on CoA substrates, measurement of crotonyl-CoA reduction activity with strains expressing effabK and vcfabV indicated their potential to support a -oxidation reversal (Table 1). When overexpressed in JC01(DE3) atoB.sup.CT5 fadB.sup.CT5 fadA, both efFabK and vcFabV resulted in a marked increase in butyrate production, similar to that fabI overexpression (
Other Type II Fatty Acid Synthesis Enzymes
(80) In addition to the use of FabI or other enoyl-[acyl-carrier-protein] reductases from the type II fatty acid biosynthesis pathway, the 3-oxoacyl-[acyl-carrier-protein]/-ketoacyl-[ACP] reductase (FabG, others) and 3-hydroxyacyl-[ACP] dehydratase (FabA, FabZ, others) enzymes of the type II FAS pathway can be utilized during BOX-R in place of BOX enzyme(s) (FadB). In order to establish the potential of these enzymes for product formation when expressed with non-decarboxylative thiolase(s), enoyl-[acyl-carrier-protein] reductases, and appropriate termination pathways, product formation was first investigated from a one-turn BOX-R with the overexpression of various combinations of FabG, FabZ, and FabI.
(81) For this purpose, pETDuet vectors containing FabG (pET-P1-P2-fabG), FabG and FabZ (pET-P1-P2-fabG-fabZ), and all of FabG, FabZ, and FabI (pET-P1-fabI-P2-fabG-fabZ) were utilized for the overexpression of these enzymes in both JC01(DE3) and a JC01(DE3) variant containing the cumate-controlled atoB expression construct. This latter strain also included deletions to fadB and fabJ to ensure any product formation was not a result of endogenous -oxidation enzymes (JC01(DE3) atoB.sup.CT5 fadB fadJ). As seen in
(82) The ability for BOX-R with the use of type II FAS pathway to support longer chain product synthesis was investigated through the replacement of AtoB with the longer chain specific thiolase BktB from Ralstonia eutropha (Kim 2014). With this thiolase was utilized with FabG, FabZ, and FabI expression in the JC01(DE3) derivative lacking key -oxidation enzymes (JC01(DE3) btkB.sup.CT5 fadB fadJ) the synthesis of extracellular longer chain carboxylic acids up to ten carbons in length was observed (
Other Primary Termination Pathways
(83) The establishment of the ability for three E. coli type II FAS pathway enzymes to support one- and multiple-turn BOX-R cycles when overexpressed with a non-decarboxylative thiolase utilized endogenous termination pathways for the direct conversion of pathway intermediates to carboxylic acids. However, further product diversification can be achieved through the use of additional primary termination pathways for the synthesis of varying product families from -oxidation reversal intermediates.
(84) To demonstrate this potential, the overexpression of a primary termination pathway for alcohol production was investigated in strains shown to produce one-turn and multiple-turn BOX-R products (i.e. JC01(DE3) atoB.sup.CT5 fadB fadJ or JC01(DE3) btkB.sup.CT5 fadB fadJ containing pET-P1-fabI-P2-fabG-fabZ). For this purpose, the combination of the Clostridium beijerinckii aldehyde-forming acyl-CoA reductase ALD (cbjALD) (Yan 1990) and E. coli alcohol dehydrogenase FucO (Dellomonaco 2011) were cloned into pCDFDuet to provide the ability to co-express all FAS enzymes along with this alcohol producing termination pathway.
(85) As seen in
Production of Odd Chain Products
(86) The ability for type II FAS enzymes to support odd-chain product synthesis through a BOX-R was investigated through the use of propionyl-CoA as the initial primer. This was accomplished through the overexpression of the propionate CoA transferase (PCT) from M. elsdenii (Taguchi et al., 2008) for the activation of propionate to propionyl-CoA. When this enzyme was overexpressed from a pCDF vector in strain JC01(DE3) btkB.sup.CT5 fadB fadJ (pET-P1-fabI-P2-fabG-fabZ) in the presence of propionate, the synthesis of C5, C7, and C9 carboxylic acids was observed through endogenous termination pathways (
(87) Thus, in addition to demonstrating the ability for odd-chain product synthesis through a full BOX-R with enzymes from the type II FAS pathway, the production of alcohols with Maqu2507 represents the use of an additional primary termination pathway. As opposed to alcohol production with the combination of an aldehyde-forming acyl-CoA reductase and an alcohol dehydrogenase, the production of primary alcohols in this case makes use of a bi-functional enzyme for the 2-step reduction of an acyl-CoA to an alcohol.
Secondary Termination Pathways
(88) Another route to additional product diversification is the use of secondary termination pathways to add additional functional groups to the above mentioned products of primary termination pathways (
(89) In order to demonstrate the potential for the use of secondary termination to provide increased product functionality and diversity, the alkBGT genes from P. putida were cloned into pCDF to allow for co-expression with all other enzymes required to generate carboxylic acids from a BOX-R with type II FAS enzymes. When AlkBGT was overexpressed in strain JC01(DE3) btkB.sup.CT5 fadB fadJ (pET-P1-fabI-P2-fabG-fabZ), the synthesis of 6-hydroxyhexanoic, 8-hydroxyoctanoic, and 10-hydrodecanoic acids was observed from the omega oxidation of carboxylic acids generated from primary termination pathways (
(90) For example, the synthesis of dicarboxylic acids can be achieved through the further oxidation of omega-hydroxyacids, through the use of an alcohol and aldehyde dehydrogenase (Cheng 2000), while omega amino acids such as 6-aminocaproic acid can be synthesized from omega-hydroxyacids through the overexpression of an alcohol dehydrogenase and a transaminase (Schrewe 2013). These product classes represent just a small sample of the potential products that can be generated through a -oxidation reversal with the use of type II fatty acid biosynthesis enzymes (
Product Diversity Through Functionalized Primers
(91) An additional route to generating further product diversity is the introduction of functional groups at the initial priming step of the BOX-R. For example, the use of a priming molecule such as succinyl-CoA or glycolyl-CoA for initial condensation with acetyl-CoA can introduce -carboxyl or -hydroxyl groups, respectively, with subsequent -oxidation cycle turns and primary termination leading to various product classes (
(92) Several thiolases have been identified with the potential to condense functionalized acyl-CoA molecules such as succinyl-CoA and glycolyl-CoA with acetyl-CoA, including Ralstonia eutropha bktB (Martin 2013), E coli paaJ (Ismail 2010), and Pseudomonas putida pcaF (Harwood 1994) among others. Genetic constructs for the overexpression of these enzymes have been assembled and are currently being investigated along with enzymes for the activation of potential acid primer molecules to their CoA derivatives (such as mePCT and Clostridium kluyveri Cat1) to determine their potential for this route to product synthesis (
(93) TABLE-US-00007 Enzyme activity (mol/mg protein/min).sup.a NADH-Dependent Trans-enoyl-CoA reductase Acyl-CoA Crotonyl-CoA concentration.sup.b Strain Vector dehydrogenase 80 M 1 mM JC01(DE3) atoB.sup.CT5 fadB.sup.CT5 fadA pETDuet (8 hours) 0.0034 .0001 n.d..sup.c 0.10 .001 pETDuet (48 hours) 0.0020 .0002 n.d..sup.c 0.080 .007 JC01(DE3) atoB.sup.CT5 fadB.sup.CT5 fadA pETDuet 0.0016 .00002 fadE JC01(DE3) atoB.sup.CT5 fadB.sup.CT5 fadA pETDuet 0.0018 .0001 ydiO JC01(DE3) atoB.sup.CT5 fadB.sup.CT5 fadA pETDuet 0.0011 .0001 cai4 JC01(DE3) atoB.sup.CT5 fadB.sup.CT5 fadA pETDuet 0.0026 .00003 aidB JC01(DE3) atoB.sup.CT5 fadB.sup.CT5 fadA pETDuet-fadE 0.019 .002 pETDuet-ydiO 0.0031 .0003 pETDuet-caiA 0.0014 .0002 pETDuet-egTER 3.1 0.4 pETDuet-fabI 0.5 0.05 3.4 .27 pETDuet-effabK 0.05 .010 0.14 .01 pETDuet-bsfabL n.d..sup.c 0.019 .006 pETDuet-vcfabV 0.053 .010 4.3 1.6 JC01(DE3) atoB.sup.CT5 fadB.sup.CT5 fadA pETDuet-fabI 0.0010 .0032 0.14 .006 1.8 .10 fabI pETDuet-bsfabL 0.0020 .0002 n.d. n.d.
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