Methods for biosynthesizing 1,3 butadiene

Abstract

This document describes biochemical pathways for producing butadiene by forming two vinyl groups in a butadiene synthesis substrate. These pathways described herein rely on enzymes such as mevalonate diphosphate decarboxylase, isoprene synthase, and dehydratases for the final enzymatic step.

1 . A method for the biosynthesis of butadiene, said method comprising forming two terminal vinyl groups in a butadiene synthesis substrate. 
     
     
         2 . The method of  claim 1 , wherein a first vinyl group is enzymatically formed in said butadiene synthesis substrate to produce a compound selected from the group consisting of 2-oxopent-4-enoate, propenyl-CoA, (R) 3-hydroxypent-4-enoate, 2,4-pentadienoyl-[acp], 2,4-pentadienoyl-CoA, crotonyl-CoA, and 3-buten-2-ol. 
     
     
         3 . The method of  claim 2 , wherein 2-oxopent-4-enoate is produced by forming a first vinyl group in (i) 4-oxalocrotonate using an 4-oxalocrotonate decarboxylase classified in EC 4.1.1.77, (ii) 2-hydroxymuconate semialdehyde using a 2-hydroxymuconate-semialdehyde hydrolase classified in EC 3.7.1.9, (iii) 2-hydroxy-6-oxonona-2,4-diene-1,9-dioate using a 2-hydroxy-6-oxonona-2,4-dienedioate hydrolase classified in EC 3.7.1.14 ,or (iv) by converting 2-hydroxymuconate semialdehyde to 2-hydroxymuconate using a 2 aminomuconate semialdehyde dehydrogenase classified under EC 1.2.1.32, converting 2-hydroxymuconate to 4-oxalocrotonate using a 2-hydroxymuconate tautomerase classified under EC 5.3.2.6, and converting 4-oxalocrotonate to 2-oxopent-4-enoate using a 4-oxalocrotonate decarboxylase classified under EC 4.1.1.77. 
     
     
         4 . (canceled) 
     
     
         5 . The method according to  claim 3 , wherein (i) 2-hydroxymuconate semialdehyde is produced by converting catechol to 2-hydroxymuconate semilaldehyde using a catechol 2,3-dioxygenase classified under EC 1.13.11.2, (ii) 2-hydroxymuconate semialdehyde is produced by converting 5-carboxy-2-hydroxymuconate-6-semiadehyde using a 5-carboxy-2-hydroxymuconate-6-semialdehyde decarboxylase or (iii) 2-hydroxy-6-oxonona-2,4-diene-1,9-dioate is produced by converting 2,3-dihydroxy phenylpropionate using a 3-carboxyethylcatechol 2,3-dioxygenase classified under EC 1.13.11.16. 
     
     
         6 . The method according to  claim 5 , wherein said catechol is produced by converting anthranilate using an anthranilate 1,2-dioxygenase classified under EC 1.14.12.1 or by converting protocatechuate using a protocatechuate decarboxylase classified under EC 4.1.1.63; said 5-carboxy-2-hydroxymuconate-6-semialdehyde decarboxylase is encoded by praH or produced by converting protocatechuate using a protocatechuate 2,3-dioxygenase, wherein said protocatechuate 2,3-dioxygenase is optionally encoded by praA; or said 2,3-dihydroxyphenylpropionate is produced by converting cis-3-(carboxy-ethyl)-3,5-cyclo-hexadiene-1,2-diol using a 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl) propanoate dehydrogenase classified under EC 1.3.1.87. 
     
     
         7 . The method of  claim 6 , wherein anthranilate is produced by converting chorismate using an anthranilate synthase classified under EC 4.1.3.27 or protocatechuate is produced by converting 3-dehydroshikimate using a 3-dehydroshikimate dehydratase classified under EC 4.2.1.118. 
     
     
         8 - 13 . (canceled) 
     
     
         14 . The method of  claim 6 , wherein 2,3-dihydroxyphenylpropionate is produced by converting cis-3-(carboxy-ethyl)-3,5-cyclo-hexadiene-1,2-diol using a 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl) propanoate dehydrogenase classified under EC 1.3.1.87; wherein cis-3-(carboxy-ethyl)-3,5-cyclo-hexadiene-1,2-diol is produced by converting 3-phenyl-propionate using a 3-phenylpropanoate dioxygenase classified under EC 1.14.12.19; wherein 3-phenyl-propionate is produced by converting E-cinnamate using a 2-enoate reductase classified under EC 1.3.1.31; and/or wherein E-cinnamate is produced by converting L-phenylalanine using a phenylalanine ammonia-lyase classified under EC 4.3.1.24. 
     
     
         15 - 17 . (canceled) 
     
     
         18 . The method according to  claim 1 , where said butadiene synthesis substrate is propanoyl-CoA. 
     
     
         19 . The method according to  claim 18 , where propenoyl-CoA is the compound that is produced by forming a first vinyl group in (i) propanoyl-CoA using a butyryl-CoA dehydrogenase classified under EC 1.3.8.1 or a medium-chain acyl-CoA dehydrogenase classified under EC 1.3.8.7, where propanoyl-CoA is optionally produced by converting (2S)-methylmalonyl-CoA using a methylmalonyl-CoA carboxytransferase classified under EC 2.1.3.1 or a methylmalonyl-CoA decarboxylase classified under EC 4.1.1.41; (ii) lactoyl-CoA using a lactoyl-CoA dehydratase classified under EC 4.2.1.54, where lactoyl-CoA is optionally produced by converting L-lactate using a proprionate CoA-transferase classified under EC 2.8.3.1, wherein produced by converting pyruvate using an L-lactate dehydrogenase classified under EC 1.1127 or (iii) 3-hydroxypropionyl-CoA using a 3-hydroxypropionyl-CoA dehydratase classified under EC 4.2.1.116, wherein 3-hydroxypropionyl-CoA is optionally produced by converting 3-hydroxypropionate using a 3-hydroxyisobutyryl-CoA hydrolase classified under EC 3.1.2.4 or by converting malonate semialdehyde using a 3-hydroxyprobionate dehydrogenase EC 1.1.1.59, wherein malonate semiladehyde is optionally produced by converting malonyl-CoA using a malonyl-CoA reductase classified under EC 1.2.1.75; by converting 2-oxo-butyrate using a 2-ketobutyrate formate-lyase classified under EC 2.3.1.-, wherein said 2-ketobutyrate formate-lyase is optionally encoded by tdcE or wherein 2-oxo-butryate is optionally produced by converting L-threonine using a threonine ammonia lyase classified under EC 4.3.1.19; by converting propanol using a propionaldehyde dehydrogenase wherein said propionaldehyde dehydrogenase is optionally encoded by pduP or wherein propanol is optionally produced by converting 1,2-propanediol using a propanediol dehydratase classified under EC 4.2.1.28; from levulinic acid by converting levulinyl-CoA using a transferase classified under EC 2.3.1.-, wherein levulinyl-CoA is optionally produced by converting levulinyl acid using an acyl-CoA synthetase or ligase classified under EC 6.2. 1.-; or by converting propenoyl-CoA using a butyryl-CoA dehydrogenase classified under EC 1.3.8.1 or a medium-chain acyl-CoA dehydrogenase classified under EC 1.3.8.7. 
     
     
         20 . (canceled) 
     
     
         21 . The method of  claim 19 , wherein (2S)-methylmalonyl-CoA is produced by converting (2R)-methylmalonyl-CoA using a methylmalonyl-CoA epimerase classified under EC 5.1.99.1; and/or wherein (2R)-methylmalonyl-CoA is produced by converting succinyl-CoA using a methylmalonyl-CoA mutase classified under EC 5.4.99.2. 
     
     
         22 - 36 . (canceled) 
     
     
         37 . The method of  claim 2 , where (R) 3-hydroxypent-4-enoate propenoyl-CoA is produced by forming a first vinyl in (R) 3-hydroxypentanoate using a desaturase/monooxygenas, wherein said desaturase is optionally a gene product of MdpJ e, or cytochrome P450, wherein said cytochrome P450 is optionally a gene product of the CYP4 family, wherein (R) 3-hydroxy-pentanoate is optionally produced by converting (R) 3-hydroxypentanoyl-CoA using a thioesterase classified under EC 3.1.2.-, wherein said thioesterase is optionally a gene product of tesB, wherein (R) 3-hydroxypentanoyl-CoA is optionally produced by converting 3-oxopentanoyl-CoA using an acetoacetyl-CoA reductase classified under EC 1.1.1.36, wherein said acetoacetyl-CoA reductase is optionally a gene product of phaB and/or wherein 3-oxopentanoyl-CoA is optionally produced by converting propanoyl-CoA u sing an acetyl-CoA C-acyltrans erase classified under EC 2.3.1.16. 
     
     
         38 - 40 . (canceled) 
     
     
         41 . The method of  claim 2 , wherein 2,4-pentadienoyl-[acp] is produced by forming a first vinyl group in pent-2-enoyl-acp using an acyl-[acp] dehydrogenase, wherein pent-2-enoyl-[acp] is optionally produced by converting (R) 3-hydroxypentanoyl-[acp] using a 3-Hydroxyacyl-[acp] dehydratase classified under EC 4.2.1.59 or by converting pent-2-enoyl-CoA using an acyl transferase, wherein (R) 3-hydroxypentanoyl-[acp] is optionally produced by converting 3-oxopentanoyl-[acp] using a 3-oxoacyl-[acp] reductase classified under EC 1.1.1.100, and/or wherein 3-oxopentanoyl-[acp] is optionally produced by converting propanoyl-CoA using as beta-ketoacyl-[acp] synthase I classified under EC 2.3.1.41, wherein said beta-ketoacyl-[acp]synthase I is optionally a gene product of tcsB, and an acyl-transferase such as tcsA; or wherein pent-2-enoyl-CoA is optionally produced by converting (R) 3-hydroxypentanoyl-CoA using an enoyl-CoA hydratase classified under EC 4.2.1.119, wherein said enoyl-CoA hydratase is optionally a gene product of phaJ, wherein (R) 3-hydroxypentanoyl-CoA is optionally produced by converting 3-oxopentanoyl-CoA using an acetoacetyl-CoA reductase classified under EC 1.1.1.36, wherein said acetoacetyl-CoA reductase is optionally a gene product of phaB, and/or wherein 3-oxopentanoyl-CoA is optionally produced by converting propanoyl-CoA using an acetyl-CoA C-acyltransferase classified under EC 2.3.1.16. 
     
     
         42 . The method of  claim 2 , wherein 2,4-pentadienoyl-CoA is produced by forming a first vinyl group in
 (i) 5-hydroxypentanoyl-CoA using a 5-hydroxyvaleryl-CoA dehydratase classified under EC 4.2.1.-, wherein said 5-hydroxyvaleryl-CoA dehydratase optionally originates from  Clostridium viride  and/or wherein 5-hydroxypentanoyl-CoA is optionally produced by converting either 5-hydroxypentanoate using 5-hydroxypentanoate CoA-transferase classified under EC 2.8.3.14or pentanoyl-CoA using a cytochrome P450 wherein said cytochrome P450 is optionally a gene product of CYP153A6,   wherein 5-hydroxypentanoate is optionally produced by converting 5-oxopentanoate using a 5-hydroxyvalerate dehydrogenase or by converting 5-aminovalerate using a 5-aminovalerate transaminase classified under EC 2.6.1.48, wherein 5-hydroxyvalerate dehydrogenase is optionally a gene product of cpnD or a dehydrogenase from  Clostridium viride,  wherein 5-aminovalerate is optionally produced by converting D-proline using a D-proline reductase classified under EC 1.21.4.1, wherein D-proline is optionally produced by converting L-proline using a proline racemase classified under EC 5.1.1.4, wherein L-proline is optionally produced by converting (S)-1-Pyrroline-5-carboxlate using a pyrroline-5-carboxlate reductase classified under EC 1.5.1.2, wherein (S)-1-Pyrroline-5-carboxylate is optionally produced by spontaneous conversion of L-glutamate 5-semialdehyde, wherein L-glutamate 5-semialdehyde is optionally produced by converting L-glutamyl-5-phosphate using a glutamate-5-semialdehyde dehydrogenase classified under EC 1.2.1.41, and/or wherein L-glutamyl-5-phosphate is optionally produced by converting L-glutamate using glutamate 5-kinase classified under EC 2.7.2.11,   or wherein pentanoyl-CoA is optionally produced by converting pent-2-enoyl-CoA using a trans-2-enoyl-CoA reductase classified under EC 1.3.1.38; or   (ii) pent-3-enoyl-CoA using a 2,4-dienoyl coenzyme A reductase classified under EC 1.3.1.34, wherein pent-3-enoyl-CoA is optionally produced by converting pent-2-enoyl-CoA using an isomerase classified under EC 5.3.3.8.   
     
     
         43 . (canceled) 
     
     
         44 . The method of  claim 2 , where crotonyl-CoA is produced by forming a first vinyl group in
 (i) glutaconyl-CoA using a glutaconyl-CoA decarboxylase classified under EC 4.1.1.70, wherein glutaconyl-CoA is optionally produced by converting 2-hydroxyglutaryl-CoA using a dehydratase classified under glutaconate-CoA is optionally produced by converting 2-hydroxyglutarate using a glutaconate CoA-transferase classified under EC 2.8.3.12 and/or wherein 2-hydroxyglutarate is optionally produced by converting 2-oxoglutarate using a 2-hydroxyglutarate dehydrogenase classified under EC 1.1.99.2;   (ii) 4-hydroxybutyryl-CoA using a 4-hydroxybutanoyl-CoA dehydratase classified under EC 4.2.1.120 and a vinylacetyl-CoA isomerase classified under EC 5.3.3.3, wherein 4-hydroxybutyryl-CoA is optionally produced by converting 4-hydroxybutyrate using a CoA-transferase, wherein said CoA-transferase is optionally a gene product of Ck-cat2, wherein 4-hydroxybutyrate is optionally produced by converting succinate semialdehyde using a 4-hydroxybutyrate dehydrogenase classified under EC 1.1.1.61, and/or wherein succinate semialdehyde is optionally produced by converting succinyl-CoA using a succinate-semialdehyde dehydrogenase classified under EC 1.2176; or   iii) (R) 3-hydroxybutanoyl-CoA using an enoyl-CoA hydratase classified under EC 4.2.1.119, wherein enoyl-CoA hydratase is optionally a gene product of phaJ, wherein 3-hydroxybutanoyl-CoA is optionally produced by converting acetoacetyl-CoA using 3-hydroxybutyryl-CoA dehydrogenase classified under EC 1.1.1.36, wherein acetoacetyl-CoA is optionally produced by converting acetyl-CoA using acetyl-CoA C-acetyltransferase classified under EC 2.3.1.9, and/or wherein acetyl-CoA C-acyltransferase is optionally a gene product of BktB.   
     
     
         45 . (canceled) 
     
     
         46 . The method of  claim 1 , where the second vinyl group is enzymatically formed in (R) 3-hydroxypent-4-enoate by
 a mevalonate diphosphate decarboxylase (MDD), wherein said mevalonate diphosphate decarboxylase is optionally classified under EC 4.1.1.33 and its amino acid sequence comprises a minimum number of four serine residues within five residues either side of the catalytic arginine residue of the catalytic cleft, wherein said mevalonate diphosphate decarboxylase optionally originates from the genus  Streptococcus  or  Staphylococcus,  wherein (R) 3-hydroxypent-4-enoate is optionally produced by converting 3-hydroxypent-4-enoyl-CoA using a thioesterase classified under EC 3.1.2.- or by converting (R) 3-hydroxypent-4-enoyl-CoA using a thioesterase classified under EC 3.1.2.- and/or wherein said thioesterase is the gene product of tesB,   wherein 3-hydroxypent-4-enoyl-CoA is optionally produced by converting 2,4-pentadienoyl-CoA using an enoyl-CoA dehydratase 2 classified under EC 4.2.1, wherein 2,4-pentadienoyl-CoA is optionally produced by converting 2-hydroxypent-4-enoyl-CoA using a 2-Hydroxyisocaproyl-CoA dehydratase, wherein said 2-Hydroxyisocaproyl-CoA dehydratase is optionally a gene product of the initiator HadI and HadBC, wherein 2-hydroxypent-4-enoyl-CoA is produced by converting 2-hydroxypent-4-enoate using a CoA-transferase, wherein said CoA-transferase is optionally a gene product of GctAB, wherein 2-hydroxypent-4-enoate is optionally produced by converting 2-oxopent-4-enoate using a (R)-2-hydroxyisocaproate dehydrogenase, and/or wherein said (R)-2-hydroxyisocaproate dehydrogenase is optionally a gene product of LdhA from  Clostridium difficile,  or   wherein (R) 3-hydroxypent-4-enoyl-CoA is optionally produced by   converting 3-oxopent-4-enoyl-CoA using an acetoacetyl-CoA reductase classified under EC 1.1.1.36, wherein said acetoacetyl-CoA reductase is optionally a gene product of phaB wherein 3-oxopent-4-enoyl-CoA is optionally produced by converting propenoyl-CoA using a β-ketothiolase classified under EC 2.3.1.16,   by converting (R)-3-hydroxypen-4-enoyl-[acp] using a (R)-3-hydroxyacyl-ACP:CoA transacylase, wherein said (R)-3-hydroxyacyl-ACP:CoA transacylase is optionally a gene product of phaG, and/or wherein (R)-3-hydroxypen-4-enoyl-[acp] is optionally produced by converting 2,4 pentadienoyl-[acp] using a 3-hydroxyacyl-[acyl-carrier-protein] dehydratase classified under EC 4.2.1.59, or   by converting 2,4-pentadienoyl-CoA using an enoyl-CoA dehydratase 2 classified under EC 4.2.1.119; or   by enzymatic formation in either 2-buten-1-ol diphosphate or 3-buten-2-ol diphosphate by an isoprene synthase (ISPS),   wherein 2-buten-1-ol diphosphate is optionally produced by converting 2-buten-1-ol phosphate using a phosphomevalonate kinase classified under EC 2.7.4.2 or using a diphosphokinase classified under EC 2.7.6.- or by converting 2-buten-1-ol using a mevalonate kinase classified under EC 2.7.1.36, wherein 2-buten-1-ol is optionally produced by converting 2-buten-1-al using an allyl-alcohol dehydrogenase classified under EC 1.1.1.54, wherein 2-buten-1-al is optionally produced by converting crotonic acid using a long-chain-aldehyde dehydrogenase classified under EC 1.2.1.48, and/or wherein crotonic acid is optionally produced by converting crotonyl-CoA using a succinate-CoA ligase classified under EC 6.2.1.5; or   3-buten-2-ol diphosphate is optionally produced by converting 3-buten-2-ol using a diphosphokinase classified under EC 2.7.6.-, where said diphosphokinase is optionally a thiamine diphosphokinase classified under EC 2.7.6.2, or 3-buten-2-ol phosphate using a phosphomevalonate kinase classified under EC 2.7.4.2, wherein 3-buten-2-ol phosphate is optionally produced by converting 3-buten-2-ol using mevalonate kinase classified under EC 2.7.1.36.   
     
     
         47 - 108 . (canceled) 
     
     
         109 . The method of  claim 1 , wherein said method is performed using isolated enzymes, cell lysates comprising enzymes or in a recombinant host. 
     
     
         110 - 112 . (canceled) 
     
     
         113 . The method according to  claim 109 , where said recombinant host cells are retained in ceramic hollow fibre membranes to maintain a high cell density during fermentation. 
     
     
         114 . The method of  claim 109 , wherein the principal carbon source fed to the fermentation derives from biological or non-biological feedstocks. 
     
     
         115 . The method of  claim 114 , where the biological feedstock is or derives from monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin such as levulinic acid and furfural, lignin, triglycerides such as glycerol and fatty acids, agricultural waste or municipal waste or the non-biological feedstock is or derives from either natural gas, syngas, carbon monoxide CO 2 /H 2 , methanol, ethanol, or waste stream from a chemical or petrochemical industry. 
     
     
         116 - 119 . (canceled) 
     
     
         120 . The method of  claim 109 , wherein the recombinant host is a prokaryote either from the genus  Escherichia  such as  Escherichia coli;  from the genus  Clostridia  such as  Clostridium ljungdahlii, Clostridium autoethanogenum  or  Clostridium kluyveri;  from the genus  Corynebacteria  such as  Corynebacterium glutamicum;  from the genus  Cupriavidus  such as  Cupriavidus necator  or  Cupriavidus metallidurans;  from the genus  Pseudomonas  such as  Pseudomonas fluorescens, Pseudomonas putida  or  Pseudomonas oleavorans;  from the genus  Delftia  such as  Delftia acidovorans;  from the genus  Bacillus  such as  Bacillus subtillis;  from the genus  Lactobacillus  such as  Lactobacillus delbrueckii;  or from the genus  Lactococcus  such as  Lactococcus lactis  or a eukaryote either from the genus  Aspergillus  such as  Aspergillus niger;  from the genus  Saccharomyces  such as  Saccharomyces cerevisiae;  from the genus  Pichia  such as  Pichia pastoris;  from the genus  Yarrowia  such as  Yarrowia lipolytica;  from the genus  Issatchenkia  such as  Issathenkia orientalist  from the genus  Debaryomyces  such as  Debaryomyces hansenii;  from the genus  Arxula  such as  Arxula adenoinivorans;  or from the genus  Kluyveromyces  such as  Kluyveromyces lactis.    
     
     
         121 . (canceled) 
     
     
         122 . The method of  claim 109 , wherein in the recombinant host:
 enzymes catalyzing the hydrolysis of propionyl-CoA and acetyl-CoA are attenuated;   enzymes consuming propanoyl-CoA via the methyl-citrate cycle are attenuated;   enzymes consuming propanoyl-CoA to pyruvate are attenuated;   enzymes consuming propanoyl-CoA to malonyl-CoA are attenuated;   a feedback-resistant threonine deaminase is genetically engineered;   β-ketothiolases catalysing the condensation of acetyl-CoA to acetoacetyl-CoA such as the gene products of A to B or phaA are attenuated;   polymer synthase enzymes in a host strain that naturally accumulates polyhydroxyalkanoates are attenuated;   a gene encoding a phosphotransacetylase, such as pta, is attenuated;   a gene encoding an acetate kinase degrading propanoate, such as ack, is attenuated;   a gene encoding the degradation of pyruvate to lactate is attenuated;   a gene encoding the degradation of phophoenolpyruvate to succinate such as frdBC is attenuated;   a gene encoding the degradation of acetyl-CoA to ethanol such as adhE is attenuated;   enzymes catalysing anaplerotic reactions supplementing the citric acid cycle intermediates are amplified;   a puridine nucleotide transhydrogenase gene such as UdhA is overexpressed;   a glyceraldehyde-3P-dehydrogenase gene such as GapN is overexpressed;   a malic enzyme gene such as maeA or maeB is overexpressed;   a glucose-6-phosphate dehydrogenase gene such as zwf is overexpressed;   afructose 1,6 diphosphatase gene such as fbp is overexpressed;   efflux of butadiene across the cell membrane to the extracellular media is enhanced or amplified by genetically engineering structural modifications to the cell membrane;   efflux of butadiene across the cell membrane to the extracellular media is enhanced or amplified by genetically engineering an increase to any associated transporter activity for butadiene; or   oxygenases degrading butadiene to toxic intermediates such as 1,2-epoxy-3-butene and 1,2:3,4-diepoxybutane are attenuated in the host organism.   
     
     
         123 - 151 . (canceled) 
     
     
         152 . A recombinant host for the biosynthesis of butadiene, said recombinant host being capable of forming two terminal vinyl groups in a butadiene synthesis substrate in accordance with the method of  claim 1 . 
     
     
         153 . The recombinant host of  claim 152 , wherein a first vinyl group is enzymatically formed in said butadiene synthesis substrate to produce a compound selected from the group consisting of 2-oxopent-4-enoate, propenyl-CoA, (R) 3-hydroxypent-4-enoate, 2,4-pentadienoyl-[acp], 2,4-pentadienoyl-CoA, crotonyl-CoA, and 3-buten-2-ol. 
     
     
         154 . The recombinant host of  claim 152 , wherein the second vinyl group is enzymatically formed in either (R) 3-hydroxypent-4-enoate by a mevalonate diphosphate decarboxylase (MDD),2-buten-1-ol diphosphate or 3-buten-2-ol diphosphate by an isoprene synthase (ISPS) or 3-buten-2-ol or 2-buten-1-ol by a dehydratase in enzyme class EC 4.2.1. 
     
     
         155 . A bio-derived, bio-based or fermentation-derived product, wherein said product comprises:
 i. a composition comprising at least one bio-derived, bio-based or fermentation-derived compound according to  claim 1  or any combination thereof,   ii. a bio-derived, bio-based or fermentation-derived polymer comprising the bio-derived, bio-based or fermentation-derived composition or compound of i., or any combination thereof,   iii. a bio-derived, bio-based or fermentation-derived resin comprising the bio-derived, bio-based or fermentation-derived compound or bio-derived, bio-based or fermentation-derived composition of i. or any combination thereof or the bio-derived, bio-based or fermentation-derived polymer of ii. or any combination thereof,   iv. a molded substance obtained by molding the bio-derived, bio-based or fermentation-derived polymer of ii. or the bio-derived, bio-based or fermentation-derived resin of iii., or any combination thereof,   v. a bio-derived, bio-based or fermentation-derived formulation comprising the bio-derived, bio-based or fermentation-derived composition of i., bio-derived, bio-based or fermentation-derived compound of i., bio-derived, bio-based or fermentation-derived polymer of ii., bio-derived, bio-based or fermentation-derived resin of iii., or bio-derived, bio-based or fermentation-derived molded substance of iv, or any combination thereof, or   vi. a bio-derived, bio-based or fermentation-derived semi-solid or a non-semi-solid stream, comprising the bio-derived, bio-based or fermentation-derived composition of i., bio-derived, bio-based or fermentation-derived compound of i., bio-derived, bio-based or fermentation-derived polymer of ii., bio-derived, bio-based or fermentation-derived resin of iii., bio-derived, bio-based or fermentation-derived formulation of v., or bio-derived, bio-based or fermentation-derived molded substance of iv., or any combination thereof.   
     
     
         156 . A non-naturally occurring biochemical network comprising at least one substrate of  FIG. 1 ,  FIG. 2 ,  FIG. 3 ,  FIG. 4 ,  FIG. 5 ,  FIG. 6 ,  FIG. 7 ,  FIG. 8 ,  FIG. 9 ,  FIG. 10  or  FIG. 11 , at least one exogenous nucleic acid encoding a polypeptide having the activity of at least one enzyme of  FIG. 1 ,  FIG. 2 ,  FIG. 3 ,  FIG. 4 ,  FIG. 5 ,  FIG. 6 ,  FIG. 7 ,  FIG. 8 ,  FIG. 9 ,  FIG. 10  or  FIG. 11  and at least one product of  FIG. 1 ,  FIG. 2 ,  FIG. 3 ,  FIG. 4 ,  FIG. 5 ,  FIG. 6 ,  FIG. 7 ,  FIG. 8 ,  FIG. 9 ,  FIG. 10  or  FIG. 11 . 
     
     
         157 . A non-naturally occurring composition, comprising at least one substrate of  FIG. 1 ,  FIG. 2 ,  FIG. 3 ,  FIG. 4 ,  FIG. 5 ,  FIG. 6 ,  FIG. 7 ,  FIG. 8 ,  FIG. 9 ,  FIG. 10  or  FIG. 11 , wherein said substrate is optionally bio-based, bio-derived or fermentation derived; at least one exogenous nucleic acid encoding a polypeptide having the activity of at least one enzyme of  FIG. 1 ,  FIG. 2 ,  FIG. 3 ,  FIG. 4 ,  FIG. 5 ,  FIG. 6 ,  FIG. 7 ,  FIG. 8 ,  FIG. 9 ,  FIG. 10  or  FIG. 11 ; and at least one bio-based, bio-derived or fermentation derived product of  FIG. 1 ,  FIG. 2 ,  FIG. 3 ,  FIG. 4 ,  FIG. 5 ,  FIG. 6 ,  FIG. 7 ,  FIG. 8 ,  FIG. 9 ,  FIG. 10  or  FIG. 11 .