WO2012106516A1 - Microorganisms and methods for the biosynthesis of butadiene - Google Patents
Microorganisms and methods for the biosynthesis of butadiene Download PDFInfo
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- WO2012106516A1 WO2012106516A1 PCT/US2012/023632 US2012023632W WO2012106516A1 WO 2012106516 A1 WO2012106516 A1 WO 2012106516A1 US 2012023632 W US2012023632 W US 2012023632W WO 2012106516 A1 WO2012106516 A1 WO 2012106516A1
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Definitions
- the present invention relates generally to biosynthetic processes, and more specifically to organisms having butadiene biosynthetic capability.
- butadiene 1,3-butadiene, BD
- polymers such as synthetic rubbers and ABS resins, and chemicals such as hexamethylenediamine and 1,4-butanediol.
- Butadiene is typically produced as a by-product of the steam cracking process for conversion of petroleum feedstocks such as naphtha, liquefied petroleum gas, ethane or natural gas to ethylene and other olefins.
- petroleum feedstocks such as naphtha, liquefied petroleum gas, ethane or natural gas to ethylene and other olefins.
- the ability to manufacture butadiene from alternative and/or renewable feedstocks would represent a major advance in the quest for more sustainable chemical production processes
- butadiene renewably involves fermentation of sugars or other feedstocks to produce diols, such as 1,4-butanediol or 1,3-butanediol, which are separated, purified, and then dehydrated to butadiene in a second step involving metal-based catalysis.
- Direct fermentative production of butadiene from renewable feedstocks would obviate the need for dehydration steps and butadiene gas (bp -4.4°C) would be continuously emitted from the fermenter and readily condensed and collected.
- Developing a fermentative production process would eliminate the need for fossil-based butadiene and would allow substantial savings in cost, energy, and harmful waste and emissions relative to petrochemically-derived butadiene.
- Microbial organisms and methods for effectively producing butadiene from cheap renewable feedstocks such as molasses, sugar cane juice, and sugars derived from biomass sources, including agricultural and wood waste, as well as CI feedstocks such as syngas and carbon dioxide, are described herein and include related advantages.
- the invention provides non-naturally occurring microbial organisms containing butadiene pathways comprising at least one exogenous nucleic acid encoding a butadiene pathway enzyme expressed in a sufficient amount to produce butadiene.
- the invention additionally provides methods of using such microbial organisms to produce butadiene, by culturing a non-naturally occurring microbial organism containing butadiene pathways as described herein under conditions and for a sufficient period of time to produce butadiene.
- embodiments disclosed herein relate to a process for the production of butadiene that includes (a) culturing by fermentation in a sufficient amount of nutrients and media a non-naturally occurring microbial organism that produces crotyl alcohol; and (b) converting crotyl alcohol, produced by culturing the non-naturally occurring microbial organism, to butadiene.
- Figure 1 shows a natural pathway to isoprenoids and terpenes.
- Enzymes for transformation of the identified substrates to products include: A. acetyl-CoA:acetyl-CoA acyltransferase, B.
- Figure 2 shows exemplary pathways for production of butadiene from acetyl-CoA, glutaconyl- CoA, glutaryl-CoA, 3-aminobutyryl-CoA or 4-hydroxybutyryl-CoA via crotyl alcohol.
- Enzymes for transformation of the identified substrates to products include: A. acetyl-CoA:acetyl-CoA acyltransferase, B. acetoacetyl-CoA reductase, C. 3-hydroxybutyryl-CoA dehydratase, D.
- crotonyl-CoA reductase (aldehyde forming), E. crotonaldehyde reductase (alcohol forming), F. crotyl alcohol kinase, G. 2-butenyl-4-phosphate kinase, H. butadiene synthase, I. crotonyl-CoA hydrolase, synthetase, transferase, J. crotonate reductase, K. crotonyl-CoA reductase (alcohol forming), L. glutaconyl-CoA decarboxylase, M., glutaryl-CoA dehydrogenase, N.
- FIG. 3 shows exemplary pathways for production of butadiene from erythrose-4-phosphate.
- Enzymes for transformation of the identified substrates to products include: A. Erythrose-4- phosphate reductase, B. Erythritol-4-phospate cytidylyltransferase, C. 4-(cytidine 5'-diphospho)- erythritol kinase, D.
- Erythritol 2,4-cyclodiphosphate synthase E. l-Hydroxy-2-butenyl 4- diphosphate synthase, F. l-Hydroxy-2-butenyl 4-diphosphate reductase, G. Butenyl 4- diphosphate isomerase, H. Butadiene synthase I. Erythrose-4-phosphate kinase, J. Erythrose reductase, K. Erythritol kinase.
- Figure 4 shows an exemplary pathway for production of butadiene from malonyl-CoA plus acetyl-CoA.
- Enzymes for transformation of the identified substrates to products include: A. malonyl-CoA:acetyl-CoA acyltransferase, B. 3-oxoglutaryl-CoA reductase (ketone-reducing), C. 3-hydroxyglutaryl-CoA reductase (aldehyde forming), D. 3-hydroxy-5-oxopentanoate reductase, E. 3,5-dihydroxypentanoate kinase, F. 3H5PP kinase, G. 3H5PDP decarboxylase, H.
- butenyl 4- diphosphate isomerase I. butadiene synthase, J. 3-hydroxyglutaryl-CoA reductase (alcohol forming), K. 3-oxoglutaryl-CoA reductase (aldehyde forming), L. 3,5-dioxopentanoate reductase (ketone reducing), M. 3,5-dioxopentanoate reductase (aldehyde reducing), N. 5-hydroxy-3- oxopentanoate reductase, O. 3-oxo-glutaryl-CoA reductase (CoA reducing and alcohol forming).
- 3H5PP 3-Hydroxy-5-phosphonatooxypentanoate
- 3H5PDP 3-Hydroxy-5-[hydroxy(phosphonooxy)phosphoryl]oxy pentanoate.
- the present invention is directed to the design and production of cells and organisms having biosynthetic production capabilities for butadiene.
- the invention in particular, relates to the design of microbial organism capable of producing butadiene by introducing one or more nucleic acids encoding a butadiene pathway enzyme.
- the invention utilizes in silico stoichiometric models of Escherichia coli metabolism that identify metabolic designs for biosynthetic production of butadiene.
- the results described herein indicate that metabolic pathways can be designed and recombinantly engineered to achieve the biosynthesis of butadiene in Escherichia coli and other cells or organisms.
- Biosynthetic production of butadiene for example, for the in silico designs can be confirmed by construction of strains having the designed metabolic genotype.
- These metabolically engineered cells or organisms also can be subjected to adaptive evolution to further augment butadiene biosynthesis, including under conditions approaching theoretical maximum growth.
- the butadiene biosynthesis characteristics of the designed strains make them genetically stable and particularly useful in continuous bioprocesses.
- Separate strain design strategies were identified with incorporation of different non-native or heterologous reaction capabilities into E. coli or other host organisms leading to butadiene producing metabolic pathways from acetyl-CoA, glutaconyl-CoA, glutaryl-CoA, 3-aminobutyryl-CoA, 4- hydroxybutyryl-CoA, erythrose-4-phosphate or malonyl-CoA plus acetyl-CoA.
- silico metabolic designs were identified that resulted in the biosynthesis of butadiene in
- microorganisms from each of these substrates or metabolic intermediates.
- Strains identified via the computational component of the platform can be put into actual production by genetically engineering any of the predicted metabolic alterations, which lead to the biosynthetic production of butadiene or other intermediate and/or downstream products.
- strains exhibiting biosynthetic production of these compounds can be further subjected to adaptive evolution to further augment product biosynthesis.
- the levels of product biosynthesis yield following adaptive evolution also can be predicted by the
- non-naturally occurring when used in reference to a microbial organism or microorganism of the invention is intended to mean that the microbial organism has at least one genetic alteration not normally found in a naturally occurring strain of the referenced species, including wild-type strains of the referenced species.
- Genetic alterations include, for example, modifications introducing expressible nucleic acids encoding metabolic polypeptides, other nucleic acid additions, nucleic acid deletions and/or other functional disruption of the microbial organism's genetic material. Such modifications include, for example, coding regions and functional fragments thereof, for heterologous, homologous or both heterologous and homologous polypeptides for the referenced species. Additional modifications include, for example, non-coding regulatory regions in which the modifications alter expression of a gene or operon.
- Exemplary metabolic polypeptides include enzymes or proteins within a butadiene biosynthetic pathway.
- a metabolic modification refers to a biochemical reaction that is altered from its naturally occurring state. Therefore, non-naturally occurring microorganisms can have genetic modifications to nucleic acids encoding metabolic polypeptides, or functional fragments thereof. Exemplary metabolic modifications are disclosed herein.
- butadiene having the molecular formula C4H6 and a molecular mass of 54.09 g/mol (see Figures 2-4) (IUPAC name Buta-l,3-diene) is used interchangeably throughout with 1,3-butadiene, biethylene, erythrene, divinyl, vinylethylene.
- Butadiene is a colorless, non corrosive liquefied gas with a mild aromatic or gasoline-like odor.
- Butadiene is both explosive and flammable because of its low flash point.
- isolated when used in reference to a microbial organism is intended to mean an organism that is substantially free of at least one component as the referenced microbial organism is found in nature.
- the term includes a microbial organism that is removed from some or all components as it is found in its natural environment.
- the term also includes a microbial organism that is removed from some or all components as the microbial organism is found in non-naturally occurring environments. Therefore, an isolated microbial organism is partly or completely separated from other substances as it is found in nature or as it is grown, stored or subsisted in non-naturally occurring environments.
- Specific examples of isolated microbial organisms include partially pure microbes, substantially pure microbes and microbes cultured in a medium that is non-naturally occurring.
- microbial As used herein, the terms "microbial,” “microbial organism” or “microorganism” are intended to mean any organism that exists as a microscopic cell that is included within the domains of archaea, bacteria or eukarya. Therefore, the term is intended to encompass prokaryotic or eukaryotic cells or organisms having a microscopic size and includes bacteria, archaea and eubacteria of all species as well as eukaryotic microorganisms such as yeast and fungi. The term also includes cell cultures of any species that can be cultured for the production of a biochemical.
- CoA or "coenzyme A” is intended to mean an organic cofactor or prosthetic group (nonprotein portion of an enzyme) whose presence is required for the activity of many enzymes (the apoenzyme) to form an active enzyme system.
- Coenzyme A functions in certain condensing enzymes, acts in acetyl or other acyl group transfer and in fatty acid synthesis and oxidation, pyruvate oxidation and in other acetylation.
- substantially anaerobic when used in reference to a culture or growth condition is intended to mean that the amount of oxygen is less than about 10% of saturation for dissolved oxygen in liquid media.
- the term also is intended to include sealed chambers of liquid or solid medium maintained with an atmosphere of less than about 1% oxygen.
- Exogenous as it is used herein is intended to mean that the referenced molecule or the referenced activity is introduced into the host microbial organism.
- the molecule can be introduced, for example, by introduction of an encoding nucleic acid into the host genetic material such as by integration into a host chromosome or as non-chromosomal genetic material such as a plasmid. Therefore, the term as it is used in reference to expression of an encoding nucleic acid refers to introduction of the encoding nucleic acid in an expressible form into the microbial organism. When used in reference to a biosynthetic activity, the term refers to an activity that is introduced into the host reference organism.
- the source can be, for example, a homologous or heterologous encoding nucleic acid that expresses the referenced activity following introduction into the host microbial organism. Therefore, the term “endogenous” refers to a referenced molecule or activity that is present in the host. Similarly, the term when used in reference to expression of an encoding nucleic acid refers to expression of an encoding nucleic acid contained within the microbial organism. The term “heterologous” refers to a molecule or activity derived from a source other than the referenced species whereas
- homologous refers to a molecule or activity derived from the host microbial organism.
- exogenous expression of an encoding nucleic acid of the invention can utilize either or both a heterologous or homologous encoding nucleic acid.
- the more than one exogenous nucleic acids refers to the referenced encoding nucleic acid or biosynthetic activity, as discussed above. It is further understood, as disclosed herein, that such more than one exogenous nucleic acids can be introduced into the host microbial organism on separate nucleic acid molecules, on polycistronic nucleic acid molecules, or a combination thereof, and still be considered as more than one exogenous nucleic acid.
- a microbial organism can be engineered to express two or more exogenous nucleic acids encoding a desired pathway enzyme or protein.
- two exogenous nucleic acids encoding a desired activity are introduced into a host microbial organism
- the two exogenous nucleic acids can be introduced as a single nucleic acid, for example, on a single plasmid, on separate plasmids, can be integrated into the host chromosome at a single site or multiple sites, and still be considered as two exogenous nucleic acids.
- exogenous nucleic acids can be introduced into a host organism in any desired combination, for example, on a single plasmid, on separate plasmids, can be integrated into the host chromosome at a single site or multiple sites, and still be considered as two or more exogenous nucleic acids, for example three exogenous nucleic acids.
- the number of referenced exogenous nucleic acids or biosynthetic activities refers to the number of encoding nucleic acids or the number of biosynthetic activities, not the number of separate nucleic acids introduced into the host organism.
- the non-naturally occurring microbial organisms of the invention can contain stable genetic alterations, which refers to microorganisms that can be cultured for greater than five generations without loss of the alteration.
- stable genetic alterations include modifications that persist greater than 10 generations, particularly stable modifications will persist more than about 25 generations, and more particularly, stable genetic modifications will be greater than 50 generations, including indefinitely.
- E. coli metabolic modifications are described with reference to a suitable host organism such as E. coli and their corresponding metabolic reactions or a suitable source organism for desired genetic material such as genes for a desired metabolic pathway.
- a suitable host organism such as E. coli and their corresponding metabolic reactions or a suitable source organism for desired genetic material such as genes for a desired metabolic pathway.
- desired genetic material such as genes for a desired metabolic pathway.
- the E. coli metabolic alterations exemplified herein can readily be applied to other species by incorporating the same or analogous encoding nucleic acid from species other than the referenced species.
- Such genetic alterations include, for example, genetic alterations of species homologs, in general, and in particular, orthologs, paralogs or nonorthologous gene displacements.
- ortholog is a gene or genes that are related by vertical descent and are responsible for substantially the same or identical functions in different organisms.
- mouse epoxide hydrolase and human epoxide hydrolase can be considered orthologs for the biological function of hydrolysis of epoxides.
- Genes are related by vertical descent when, for example, they share sequence similarity of sufficient amount to indicate they are homologous, or related by evolution from a common ancestor.
- Genes can also be considered orthologs if they share three- dimensional structure but not necessarily sequence similarity, of a sufficient amount to indicate that they have evolved from a common ancestor to the extent that the primary sequence similarity is not identifiable.
- Genes that are orthologous can encode proteins with sequence similarity of about 25% to 100% amino acid sequence identity.
- Genes encoding proteins sharing an amino acid similarity less that 25% can also be considered to have arisen by vertical descent if their three-dimensional structure also shows similarities.
- Members of the serine protease family of enzymes, including tissue plasminogen activator and elastase, are considered to have arisen by vertical descent from a common ancestor.
- Orthologs include genes or their encoded gene products that through, for example, evolution, have diverged in structure or overall activity. For example, where one species encodes a gene product exhibiting two functions and where such functions have been separated into distinct genes in a second species, the three genes and their corresponding products are considered to be orthologs. For the production of a biochemical product, those skilled in the art will understand that the orthologous gene harboring the metabolic activity to be introduced or disrupted is to be chosen for construction of the non-naturally occurring microorganism.
- An example of orthologs exhibiting separable activities is where distinct activities have been separated into distinct gene products between two or more species or within a single species.
- a specific example is the separation of elastase proteolysis and plasminogen proteolysis, two types of serine protease activity, into distinct molecules as plasminogen activator and elastase.
- a second example is the separation of mycoplasma 5 '-3' exonuclease and Drosophila DNA polymerase III activity.
- the DNA polymerase from the first species can be considered an ortholog to either or both of the exonuclease or the polymerase from the second species and vice versa.
- paralogs are homologs related by, for example, duplication followed by evolutionary divergence and have similar or common, but not identical functions. Paralogs can originate or derive from, for example, the same species or from a different species.
- microsomal epoxide hydrolase epoxide hydrolase I
- soluble epoxide hydrolase epoxide hydrolase II
- paralogs are proteins from the same species with significant sequence similarity to each other suggesting that they are homologous, or related through co-evolution from a common ancestor.
- Groups of paralogous protein families include HipA homologs, luciferase genes, peptidases, and others.
- a nonorthologous gene displacement is a nonorthologous gene from one species that can substitute for a referenced gene function in a different species. Substitution includes, for example, being able to perform substantially the same or a similar function in the species of origin compared to the referenced function in the different species.
- a nonorthologous gene displacement will be identifiable as structurally related to a known gene encoding the referenced function, less structurally related but functionally similar genes and their corresponding gene products nevertheless will still fall within the meaning of the term as it is used herein.
- Functional similarity requires, for example, at least some structural similarity in the active site or binding region of a nonorthologous gene product compared to a gene encoding the function sought to be substituted. Therefore, a nonorthologous gene includes, for example, a paralog or an unrelated gene.
- Orthologs, paralogs and nonorthologous gene displacements can be determined by methods well known to those skilled in the art. For example, inspection of nucleic acid or amino acid sequences for two polypeptides will reveal sequence identity and similarities between the compared sequences. Based on such similarities, one skilled in the art can determine if the similarity is sufficiently high to indicate the proteins are related through evolution from a common ancestor. Algorithms well known to those skilled in the art, such as Align, BLAST, Clustal W and others compare and determine a raw sequence similarity or identity, and also determine the presence or significance of gaps in the sequence which can be assigned a weight or score. Such algorithms also are known in the art and are similarly applicable for determining nucleotide sequence similarity or identity.
- Parameters for sufficient similarity to determine relatedness are computed based on well known methods for calculating statistical similarity, or the chance of finding a similar match in a random polypeptide, and the significance of the match determined.
- a computer comparison of two or more sequences can, if desired, also be optimized visually by those skilled in the art.
- Related gene products or proteins can be expected to have a high similarity, for example, 25% to 100% sequence identity. Proteins that are unrelated can have an identity which is essentially the same as would be expected to occur by chance, if a database of sufficient size is scanned (about 5%). Sequences between 5% and 24% may or may not represent sufficient homology to conclude that the compared sequences are related.
- Exemplary parameters for determining relatedness of two or more sequences using the BLAST algorithm can be as set forth below.
- amino acid sequence alignments can be performed using BLASTP version 2.0.8 (Jan-05-1999) and the following parameters: Matrix: 0 BLOSUM62; gap open: 11; gap extension: 1; x dropoff: 50; expect: 10.0; wordsize: 3; filter: on.
- Nucleic acid sequence alignments can be performed using BLASTN version 2.0.6 (Sept- 16- 1998) and the following parameters: Match: 1; mismatch: -2; gap open: 5; gap extension: 2; x dropoff: 50; expect: 10.0; wordsize: 11; filter: off.
- Those skilled in the art will know what modifications can be made to the above parameters to either increase or decrease the stringency of the comparison, for example, and determine the relatedness of two or more sequences.
- the invention provides a non-naturally occurring microbial organism, including a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding a butadiene pathway enzyme expressed in a sufficient amount to produce butadiene, the butadiene pathway including an acetyl-CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2- butenyl-4-phosphate kinase, a butadiene synthase, a crotonyl-CoA hydrolase, synthetase, or transferase, a acetyl
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including an acetyl-CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl- CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase and a butadiene synthase (Figure 2, steps A-H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including an acetyl-CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotyl alcohol kinase, a 2- butenyl-4-phosphate kinase, a butadiene synthase and crotonyl-CoA reductase (alcohol forming) ( Figure 2, steps A-C, K, F, G, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including an acetyl-CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a butadiene synthase, a crotonyl-CoA reductase (alcohol forming) and a crotyl alcohol diphosphokinase (Figure 2, steps A-C, K, P, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including an acetyl-CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase, a crotonyl-CoA hydrolase, synthetase, or transferase and a crotonate reductase, ( Figure 2, steps A-C, I, J, E, F, G, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including an acetyl-CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3- hydroxybutyryl-CoA dehydratase, a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a crotonyl-CoA hydrolase, synthetase or transferase, a crotonate reductase and a crotyl alcohol diphosphokinase ( Figure 2, steps A-C, I, J, E, P, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including an acetyl-CoA:acetyl- CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a butadiene synthase and a crotyl alcohol diphosphokinase (Figure 2, steps A-E, P, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a glutaconyl-CoA decarboxylase, a crotonyl-CoA reductase (aldehyde forming), a
- crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase and a butadiene synthase ( Figure 2, steps L, D-H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a glutaconyl-CoA decarboxylase, a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase and crotonyl-CoA reductase (alcohol forming) (Figure 2, steps L, K, F, G, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a glutaconyl-CoA decarboxylase, a butadiene synthase, a crotonyl-CoA reductase (alcohol forming) and a crotyl alcohol diphosphokinase (Figure 2, steps L, K, P, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a glutaconyl-CoA decarboxylase, a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase, a crotonyl-CoA hydrolase, synthetase, or transferase and a crotonate reductase (Figure 2, steps L, I, J, E, F, G, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a glutaconyl-CoA decarboxylase, a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a crotonyl-CoA hydrolase, synthetase or transferase, a crotonate reductase and a crotyl alcohol diphosphokinase (Figure 2, steps L, I, J, E, P, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a 3-hydroxybutyryl- CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a butadiene a glutaconyl-CoA decarboxylase and a crotyl alcohol
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a glutaryl-CoA dehydrogenase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase and a butadiene synthase ( Figure 2, steps M, D-H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a glutaryl-CoA dehydrogenase, a crotyl alcohol kinase, a 2-butenyl-4- phosphate kinase, a butadiene synthase and crotonyl-CoA reductase (alcohol forming) ( Figure 2, steps M, K, F, G, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a glutaryl-CoA dehydrogenase, a butadiene synthase, a crotonyl- CoA reductase (alcohol forming) and a crotyl alcohol diphosphokinase (Figure 2, steps M, K, P, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a glutaryl-CoA dehydrogenase, a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase, a crotonyl-CoA hydrolase, synthetase, or transferase and a crotonate reductase (Figure 2, steps M, I, J, E, F, G, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a glutaryl-CoA dehydrogenase, a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a crotonyl-CoA hydrolase, synthetase or transferase, a crotonate reductase and a crotyl alcohol diphosphokinase (Figure 2, steps M, I, J, E, P, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a 3-hydroxybutyryl- CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a glutaryl-CoA dehydrogenase and a crotyl alcohol diphosphokinase (Figure 2, steps M, C, D, E, P, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a 3-aminobutyryl-CoA deaminase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase and a butadiene synthase (Figure 2, steps N, D-H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a 3-aminobutyryl-CoA deaminase, a crotyl alcohol kinase, a 2- butenyl-4-phosphate kinase, a butadiene synthase and crotonyl-CoA reductase (alcohol forming) ( Figure 2, steps N, K, F, G, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a 3-aminobutyryl-CoA deaminase, a butadiene synthase, a crotonyl-CoA reductase (alcohol forming) and a crotyl alcohol diphosphokinase (Figure 2, steps N, K, P, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a 3-aminobutyryl-CoA deaminase, a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase, a crotonyl-CoA hydrolase, synthetase, or transferase and a crotonate reductase (Figure 2, steps N, I, J, E, F, G, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a 3-aminobutyryl-CoA deaminase, a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a crotonyl-CoA hydrolase, synthetase or transferase, a crotonate reductase and a crotyl alcohol diphosphokmase (Figure 2, steps N, I, J, E, P, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a 3-aminobutyryl- CoA deaminase and a crotyl alcohol diphosphokmase (Figure 2, steps N, C, D, E, P, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a 4-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase and a butadiene synthase (Figure 2, steps O, D-H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a 4-hydroxybutyryl- CoA dehydratase, a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase and crotonyl-CoA reductase (alcohol forming) (Figure 2, steps O, K, F, G, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a 4-hydroxybutyryl-CoA dehydratase, a butadiene synthase, a crotonyl-CoA reductase (alcohol forming) and a crotyl alcohol diphosphokmase (Figure 2, steps O, K, P, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a 4- hydroxybutyryl-CoA dehydratase, a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase, a crotonyl-CoA hydrolase, synthetase, or transferase and a crotonate reductase (Figure 2, steps O, I, J, E, F, G, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a 4-hydroxybutyryl-CoA dehydratase, a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a crotonyl-CoA hydrolase, synthetase or transferase, a crotonate reductase and a crotyl alcohol diphosphokinase (Figure 2, steps O, I, J, E, P, H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a 3-hydroxybutyryl- CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a 4-hydroxybutyryl-CoA dehydratase and a crotyl alcohol diphosphokinase (Figure 2, steps L, C, D, E, P, H).
- the invention provides a non-naturally occurring microbial organism comprising a crotyl alcohol pathway.
- the crotyl alcohol pathway includes at least one exogenous nucleic acid encoding a crotyl alcohol pathway enzyme expressed in a sufficient amount to produce crotyl alcohol.
- the crotyl alcohol pathway includes an acetyl-CoA:acetyl- CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a crotonyl-CoA hydrolase, synthetase, or transferase, a crotonate reductase, a crotonyl-CoA reductase (alcohol forming), a glutaconyl-CoA decarboxylase, a glutaryl-CoA dehydrogenase, a 3-aminobutyryl-CoA deaminase, or a 4-hydroxybutyryl-CoA dehydratase.
- the microbial organism comprises two exogenous nucleic acids each encoding a crotyl alcohol pathway enzyme, in other embodiments, the microbial organism includes three exogenous nucleic acids each encoding a crotyl alcohol pathway enzyme, in still further embodiments the microbial organism includes four exogenous nucleic acids each encoding a crotyl alcohol pathway enzyme.
- the crotyl alcohol pathway includes an acetyl-CoA:acetyl-CoA
- the crotyl alcohol pathway includes an acetyl-CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, and a crotonaldehyde reductase (alcohol forming).
- the crotyl alcohol pathway includes an acetyl- CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotonaldehyde reductase (alcohol forming), a crotonyl-CoA hydrolase, synthetase or transferase and a crotonate reductase.
- the crotyl alcohol pathway includes a glutaconyl-CoA decarboxylase, a crotonyl-CoA reductase (aldehyde forming), and a crotonaldehyde reductase (alcohol forming). In some embodiments, the crotyl alcohol pathway includes a glutaconyl-CoA decarboxylase and crotonyl-CoA reductase (alcohol forming).
- the crotyl alcohol pathway includes a glutaconyl-CoA decarboxylase, a crotonaldehyde reductase (alcohol forming), a crotonyl-CoA hydrolase, synthetase, or transferase and a crotonate reductase.
- the crotyl alcohol pathway includes a glutaryl-CoA dehydrogenase, a crotonyl-CoA reductase (aldehyde forming), and a crotonaldehyde reductase (alcohol forming).
- the crotyl alcohol pathway includes a glutaryl-CoA dehydrogenase and crotonyl-CoA reductase (alcohol forming). In some embodiments, the crotyl alcohol pathway includes a glutaryl-CoA dehydrogenase, a crotonaldehyde reductase (alcohol forming), a crotonyl-CoA hydrolase, synthetase, or transferase and a crotonate reductase. In some embodiments, the crotyl alcohol pathway includes a 3- aminobutyryl-CoA deaminase, a crotonyl-CoA reductase (aldehyde forming), and a
- the crotyl alcohol pathway includes a 3-aminobutyryl-CoA deaminase and crotonyl-CoA reductase (alcohol forming). In some embodiments, the crotyl alcohol pathway includes a 3-aminobutyryl-CoA deaminase, a crotonaldehyde reductase (alcohol forming), a crotonyl-CoA hydrolase, synthetase or transferase and a crotonate reductase.
- the crotyl alcohol pathway includes a 4- hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), and a crotonaldehyde reductase (alcohol forming). In some embodiments, the crotyl alcohol pathway includes a 4-hydroxybutyryl-CoA dehydratase and crotonyl-CoA reductase (alcohol forming).
- the crotyl alcohol pathway includes a 4-hydroxybutyryl-CoA dehydratase, a crotonaldehyde reductase (alcohol forming), a crotonyl-CoA hydrolase, synthetase or transferase and a crotonate reductase.
- the non-naturally occurring microbial organism having a crotyl alcohol pathway has at least one exogenous nucleic acid that is a heterologous nucleic acid.
- the non-naturally occurring microbial organism having a crotyl alcohol pathway is in a substantially anaerobic culture medium.
- the invention provides a non-naturally occurring microbial organism, including a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding a butadiene pathway enzyme expressed in a sufficient amount to produce butadiene, the butadiene pathway including an erythrose-4-phosphate reductase, an erythritol-4- phospate cytidylyltransferase, a 4-(cytidine 5'-diphospho)-erythritol kinase, an erythritol 2,4- cyclodiphosphate synthase, a l-hydroxy-2-butenyl 4-diphosphate synthase, a l-hydroxy-2- butenyl 4-diphosphate reductase, a butenyl 4-diphosphate isomerase, a butadiene synthase, an erythrose-4-phosphate kin
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including an erythrose-4-phosphate reductase, an erythritol-4-phospate cytidylyltransferase, a 4-(cytidine 5'-diphospho)-erythritol kinase, an erythritol 2,4-cyclodiphosphate synthase, a l-hydroxy-2- butenyl 4-diphosphate synthase, a l-hydroxy-2 -butenyl 4-diphosphate reductase and a butadiene synthase ( Figure 3, steps A-F, and H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including an erythrose-4-phosphate reductase, an erythritol-4-phospate cytidylyltransferase, a 4-(cytidine 5'-diphospho)-erythritol kinase, an erythritol 2,4-cyclodiphosphate synthase, a l-hydroxy-2-butenyl 4-diphosphate synthase, a 1- hydroxy-2 -butenyl 4-diphosphate reductase, a butenyl 4-diphosphate isomerase and butadiene synthase ( Figure 3, steps A-H).
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including an erythritol-4-phospate cytidylyltransferase, a 4- (cytidine 5'-diphospho)-erythritol kinase, an erythritol 2,4-cyclodiphosphate synthase, a 1- hydroxy-2-butenyl 4-diphosphate synthase, a l-hydroxy-2-butenyl 4-diphosphate reductase, a butadiene synthase, an erythrose-4-phosphate kinase, an erythrose reductase and a erythritol kinase ( Figure 3, steps I, J, K, B
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including an erythritol-4-phospate
- cytidylyltransferase a 4-(cytidine 5'-diphospho)-erythritol kinase, an erythritol 2,4- cyclodiphosphate synthase, a l-hydroxy-2-butenyl 4-diphosphate synthase, a l-hydroxy-2- butenyl 4-diphosphate reductase, a butenyl 4-diphosphate isomerase, a butadiene synthase, an erythrose-4-phosphate kinase, an erythrose reductase and an erythritol kinase ( Figure 3, steps I, J, K, B-H).
- the invention provides a non-naturally occurring microbial organism, including a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding a butadiene pathway enzyme expressed in a sufficient amount to produce butadiene, the butadiene pathway including a malonyl-CoA:acetyl-CoA acyltransferase, a 3- oxoglutaryl-CoA reductase (ketone -reducing), a 3-hydroxyglutaryl-CoA reductase (aldehyde forming), a 3-hydroxy-5-oxopentanoate reductase, a 3,5-dihydroxypentanoate kinase, a 3- hydroxy-5-phosphonatooxypentanoate kinase, a 3-hydroxy-5-
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a malonyl-CoA:acetyl-CoA acyltransferase, a 3-oxoglutaryl-CoA reductase (ketone-reducing), a 3-hydroxyglutaryl-CoA reductase (aldehyde forming), a 3-hydroxy-5-oxopentanoate reductase, a 3,5-dihydroxypentanoate kinase, a 3-hydroxy-5-phosphonatooxypentanoate kinase, a 3-hydroxy- 5-[hydroxy(phosphonooxy)phosphoryl]oxy pentanoate decarboxylase, a butenyl 4-diphosphate isomerase and a butadiene synthas
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a malonyl-CoA:acetyl- CoA acyltransferase, a 3,5-dihydroxypentanoate kinase, a 3-hydroxy-5- phosphonatooxypentanoate kinase, a 3-hydroxy-5-[hydroxy(phosphonooxy)phosphoryl]oxy pentanoate decarboxylase, a butenyl 4-diphosphate isomerase, a butadiene synthase, a 3- oxoglutaryl-CoA reductase (aldehyde forming), a 3,5-dioxopentanoate reductase (aldehyde reducing) and a 5-hydroxy-3-ox
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a malonyl-CoA:acetyl-CoA acyltransferase, a 3-hydroxy-5-oxopentanoate reductase, a 3,5-dihydroxypentanoate kinase, a 3-Hydroxy-5-phosphonatooxypentanoate kinase, a 3- Hydroxy-5-[hydroxy(phosphonooxy)phosphoryl]oxy pentanoate decarboxylase, a butenyl 4- diphosphate isomerase, a butadiene synthase, a 3-oxoglutaryl-CoA reductase (al
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a malonyl-CoA:acetyl-CoA acyltransferase, a 3,5-dihydroxypentanoate kinase, a 3- hydroxy-5-phosphonatooxypentanoate kinase, a 3-hydroxy-5-
- the non-naturally occurring microbial organism includes a microbial organism having a butadiene pathway having at least one exogenous nucleic acid encoding butadiene pathway enzymes expressed in a sufficient amount to produce butadiene, the butadiene pathway including a malonyl-CoA:acetyl-CoA acyltransferase, a 3-oxoglutaryl-CoA reductase (ketone-reducing), a 3,5-dihydroxypentanoate kinase, a 3-hydroxy-5-phosphonatooxypentanoate kinase, a 3-hydroxy- 5-[hydroxy(phosphonooxy)phosphoryl]oxy pentanoate decarboxylase, a butenyl 4-diphosphate isomerase, a butadiene synthase and a 3-hydroxyglutaryl-CoA reductase (alcohol forming).
- the invention provides a non-naturally occurring microbial organism having a butadiene pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of acetyl-CoA to acetoacetyl-CoA, acetoacetyl-CoA to 3-hydroxybutyryl-CoA, 3-hydroxybutyryl-CoA to crotonyl-CoA, crotonyl- CoA to crotonaldehyde, crotonaldehyde to crotyl alcohol, crotyl alcohol to 2-betenyl-phosphate,
- the invention provides a non-naturally occurring microbial organism containing at least one exogenous nucleic acid encoding an enzyme or protein, where the enzyme or protein converts the substrates and products of a butadiene pathway, such as that shown in Figures 2-4.
- the invention additionally provides a non-naturally occurring microbial organism comprising at least one exogenous nucleic acid encoding a butadiene pathway enzyme expressed in a sufficient amount to produce an intermediate of a butadiene pathway.
- a butadiene pathway is exemplified in Figures 2-4.
- the invention additionally provides a non-naturally occurring microbial organism comprising at least one exogenous nucleic acid encoding a butadiene pathway enzyme, where the microbial organism produces a butadiene pathway intermediate, for example, acetoacetyl-CoA, 3-hydroxybutyryl- CoA, crotonyl-CoA, crotonaldehyde, crotyl alcohol, 2-betenyl-phosphate, 2-butenyl-4- diphosphate, erythritol-4-phosphate, 4-(cytidine 5'-diphospho)-erythritol, 2-phospho-4-(cytidine 5'-diphospho)-erythritol, erythritol-2,4-cyclodiphosphate, l-hydroxy-2-butenyl 4-diphosphate, butenyl 4-diphosphate, 2-buten
- any of the pathways disclosed herein, as described in the Examples and exemplified in the Figures, including the pathways of Figures 2-4, can be utilized to generate a non-naturally occurring microbial organism that produces any pathway intermediate or product, as desired.
- a microbial organism that produces an intermediate can be used in combination with another microbial organism expressing downstream pathway enzymes to produce a desired product.
- a non-naturally occurring microbial organism that produces a butadiene pathway intermediate can be utilized to produce the intermediate as a desired product.
- access to butadiene can be accomplished by biosynthetic production of crotyl alcohol and subsequent chemical dehydration to butadiene.
- the invention provides a process for the production of butadiene that includes (a) culturing by fermentation in a sufficient amount of nutrients and media a non-naturally occurring microbial organism that produces crotyl alcohol; and (b) converting crotyl alcohol produced by culturing the non-naturally occurring microbial organism to butadiene.
- a catalyzed thermal dehydration employs a metal oxide catalyst or silica.
- step (b) of the process is performed by chemical dehydration in the presence of a catalyst. For example, it has been indicated that crotyl alcohol can be dehydrated over bismuth molybdate (Adams, C.R. J. Catal. 10:355-361, 1968) to afford 1,3-butadiene.
- Dehydration can be achieved via activation of the alcohol group and subsequent elimination by standard elimination mechanisms such as El or E2 elimination. Activation can be achieved by way of conversion of the alcohol group to a halogen such as iodide, chloride, or bromide.
- a halogen such as iodide, chloride, or bromide.
- Activation can also be accomplished by way of a sulfonyl, phosphate or other activating functionality that convert the alcohol into a good leaving group.
- the activating group is a sulfate or sulfate ester selected from a tosylate, a mesylate, a nosylate, a brosylate, and a triflate.
- the leaving group is a phosphate or phosphate ester.
- the dehydrating agent is phosphorus pentoxide.
- processes of the invention that rely on bioproduction of crotyl alcohol utilize non-naturally occurring microbial organism that include a crotyl alcohol pathway having at least one exogenous nucleic acid encoding a crotyl alcohol pathway enzyme expressed in a sufficient amount to produce crotyl alcohol.
- the crotyl alcohol pathway includes an acetyl- CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a crotonyl-CoA hydrolase, synthetase, or transferase, a crotonate reductase, a crotonyl- CoA reductase (alcohol forming), a glutaconyl-CoA decarboxylase, a glutaryl-CoA
- dehydrogenase a 3-aminobutyryl-CoA deaminase, or a 4-hydroxybutyryl-CoA dehydratase.
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism that includes two exogenous nucleic acids each encoding a crotyl alcohol pathway enzyme. In some embodiments, processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism that includes three exogenous nucleic acids each encoding a crotyl alcohol pathway enzyme. In some embodiments, processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism that includes four exogenous nucleic acids each encoding a crotyl alcohol pathway enzyme.
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes an acetyl-CoA:acetyl- CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), and a crotonaldehyde reductase (alcohol forming).
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes an acetyl-CoA:acetyl- CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, and a crotonyl-CoA reductase (alcohol forming).
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes an acetyl-CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotonaldehyde reductase (alcohol forming), a crotonyl- CoA hydrolase, synthetase or transferase and a crotonate reductase.
- a crotyl alcohol pathway that includes an acetyl-CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotonaldehyde reductase (alcohol forming), a cro
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a glutaconyl-CoA decarboxylase, a crotonyl-CoA reductase (aldehyde forming), and a crotonaldehyde reductase (alcohol forming).
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a glutaconyl-CoA decarboxylase and crotonyl-CoA reductase (alcohol forming).
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a glutaconyl-CoA
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), and a glutaconyl- CoA decarboxylase.
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a glutaryl-CoA dehydrogenase, a crotonyl-CoA reductase (aldehyde forming), and a crotonaldehyde reductase (alcohol forming).
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a glutaryl-CoA dehydrogenase and crotonyl-CoA reductase (alcohol forming).
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a glutaryl-CoA dehydrogenase, a crotonaldehyde reductase (alcohol forming), a crotonyl-CoA hydrolase, synthetase, or transferase and a crotonate reductase.
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), and a glutaryl-CoA dehydrogenase.
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a 3-aminobutyryl- CoA deaminase, a crotonyl-CoA reductase (aldehyde forming), and a crotonaldehyde reductase (alcohol forming).
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a 3- aminobutyryl-CoA deaminase and crotonyl-CoA reductase (alcohol forming).
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a 3-aminobutyryl-CoA deaminase, a crotonaldehyde reductase (alcohol forming), a crotonyl-CoA hydrolase, synthetase or transferase and a crotonate reductase.
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), and a 3-aminobutyryl-CoA deaminase.
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a 4-hydroxybutyryl- CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), and a crotonaldehyde reductase (alcohol forming).
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a 4- hydroxybutyryl-CoA dehydratase and crotonyl-CoA reductase (alcohol forming).
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a 4-hydroxybutyryl-CoA dehydratase, a crotonaldehyde reductase (alcohol forming), a crotonyl-CoA hydrolase, synthetase or transferase and a crotonate reductase.
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having a crotyl alcohol pathway that includes a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), and a 4- hydroxybutyryl-CoA dehydratase.
- processes of the invention that rely on bioproduction of crotyl alcohol utilize a microbial organism having at least one exogenous nucleic acid is a heterologous nucleic acid. In some embodiments, processes of the invention that rely on bioproduction of crotyl alcohol utilize a non-naturally occurring microbial organism is in a substantially anaerobic culture medium.
- a process for the production of 1,3-butadiene includes a) culturing by fermentation in a sufficient amount of nutrients and media a non-naturally occurring microbial organism that produces crotonaldehyde; and (b) converting crotonaldehyde produced by culturing the non-naturally occurring microbial organism to butadiene.
- crotonaldehyde and ethanol can both be provided as fermentation products from a single non-naturally occurring organism, or from two separate organisms.
- the two fermentation products can be converted to 1,3-butadiene as described above using silica catalyst.
- the invention is described herein with general reference to the metabolic reaction, reactant or product thereof, or with specific reference to one or more nucleic acids or genes encoding an enzyme associated with or catalyzing, or a protein associated with, the referenced metabolic reaction, reactant or product. Unless otherwise expressly stated herein, those skilled in the art will understand that reference to a reaction also constitutes reference to the reactants and products of the reaction. Similarly, unless otherwise expressly stated herein, reference to a reactant or product also references the reaction, and reference to any of these metabolic constituents also references the gene or genes encoding the enzymes that catalyze or proteins involved in the referenced reaction, reactant or product.
- reference herein to a gene or encoding nucleic acid also constitutes a reference to the corresponding encoded enzyme and the reaction it catalyzes or a protein associated with the reaction as well as the reactants and products of the reaction.
- the intermediats crotanate; 3,5-dioxopentanoate, 5-hydroxy-3- oxopentanoate, 3-hydroxy-5-oxopentanoate, 3-oxoglutaryl-CoA and 3-hydroxyglutaryl-CoA, as well as other intermediates are carboxylic acids, which can occur in various ionized forms, including fully protonated, partially protonated, and fully deprotonated forms. Accordingly, the suffix "-ate,” or the acid form, can be used interchangeably to describe both the free acid form as well as any deprotonated form, in particular since the ionized form is known to depend on the pH in which the compound is found.
- carboxylate products or intermediates includes ester forms of carboxylate products or pathway intermediates, such as O-carboxylate and S-carboxylate esters.
- O- and S-carboxylates can include lower alkyl, that is CI to C6, branched or straight chain carboxylates.
- O- or S-carboxylates include, without limitation, methyl, ethyl, n-propyl, n-butyl, i-propyl, sec-butyl, and tert-butyl, pentyl, hexyl O- or S-carboxylates, any of which can further possess an unsaturation, providing for example, propenyl, butenyl, pentyl, and hexenyl O- or S-carboxylates.
- O-carboxylates can be the product of a biosynthetic pathway.
- Exemplary O-carboxylates accessed via biosynthetic pathways can include, without limitation: methyl crotanate; methy-3,5-dioxopentanoate; methyl-5-hydroxy-3- oxopentanoate; methyl-3-hydroxy-5-oxopentanoate; 3-oxoglutaryl-CoA, methyl ester; 3- hydroxyglutaryl-CoA, methyl ester; ethyl crotanate; ethyl-3,5-dioxopentanoate; ethyl-5 -hydroxy- 3-xopentanoate; ethyl-3-hydroxy-5-oxopentanoate; 3-oxoglutaryl-CoA, ethyl ester; 3- hydroxyglutaryl-CoA, ethyl ester; n-propyl crotanate; n-propyl-3,5-dioxopentanoate; n-propyl-5-
- O- carboxylates can include medium to long chain groups, that is C7-C22, O-carboxylate esters derived from fatty alcohols, such heptyl, octyl, nonyl, decyl, undecyl, lauryl, tridecyl, myristyl, pentadecyl, cetyl, palmitolyl, heptadecyl, stearyl, nonadecyl, arachidyl, heneicosyl, and behenyl alcohols, any one of which can be optionally branched and/or contain unsaturations.
- O-carboxylate esters derived from fatty alcohols, such heptyl, octyl, nonyl, decyl, undecyl, lauryl, tridecyl, myristyl, pentadecyl, cetyl, palmitolyl, heptadecyl, stearyl
- O- carboxylate esters can also be accessed via a biochemical or chemical process, such as esterification of a free carboxylic acid product or transesterification of an O- or S-carboxylate.
- S-carboxylates are exemplified by CoA S-esters, cysteinyl S-esters, alkylthioesters, and various aryl and heteroaryl thioesters.
- non-naturally occurring microbial organisms of the invention can be produced by
- nucleic acids encoding one or more of the enzymes or proteins participating in one or more butadiene biosynthetic pathways.
- nucleic acids for some or all of a particular butadiene biosynthetic pathway can be expressed. For example, if a chosen host is deficient in one or more enzymes or proteins for a desired biosynthetic pathway, then expressible nucleic acids for the deficient enzyme(s) or protein(s) are introduced into the host for subsequent exogenous expression.
- a non-naturally occurring microbial organism of the invention can be produced by introducing exogenous enzyme or protein activities to obtain a desired biosynthetic pathway or a desired biosynthetic pathway can be obtained by introducing one or more exogenous enzyme or protein activities that, together with one or more endogenous enzymes or proteins, produces a desired product such as butadiene.
- Host microbial organisms can be selected from, and the non-naturally occurring microbial organisms generated in, for example, bacteria, yeast, fungus or any of a variety of other microorganisms applicable to fermentation processes.
- Exemplary bacteria include species selected from Escherichia coli, Klebsiella oxytoca, Anaerobio spirillum succiniciproducens, Actinobacillus succinogenes, Mannheimia succiniciproducens, Rhizobium etli, Bacillus subtilis, Corynebacterium glutamicum, Gluconobacter oxydans, Zymomonas mobilis, Lactococcus lactis, Lactobacillus plantarum, Streptomyces coelicolor, Clostridium acetobutylicum, Pseudomonas fluorescens, and Pseudomonas putida.
- Exemplary yeasts or fungi include species selected from Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis, Kluyveromyces marxianus, Aspergillus terreus, Aspergillus niger, Pichia pastoris, Rhizopus arrhizus, Rhizobus oryzae, Yarrowia lipolytica, and the like.
- E. coli is a particularly useful host organism since it is a well characterized microbial organism suitable for genetic engineering.
- Other particularly useful host organisms include yeast such as Saccharomyces cerevisiae. It is understood that any suitable microbial host organism can be used to introduce metabolic and/or genetic modifications to produce a desired product.
- the non-naturally occurring microbial organisms of the invention will include at least one exogenously expressed butadiene pathway-encoding nucleic acid and up to all encoding nucleic acids for one or more butadiene biosynthetic pathways.
- butadiene biosynthesis can be established in a host deficient in a pathway enzyme or protein through exogenous expression of the corresponding encoding nucleic acid.
- exogenous expression of all enzyme or proteins in the pathway can be included, although it is understood that all enzymes or proteins of a pathway can be expressed even if the host contains at least one of the pathway enzymes or proteins.
- exogenous expression of all enzymes or proteins in a pathway for production of butadiene can be included, such as an acetyl-CoA:acetyl-CoA acyltransferase, an acetoacetyl- CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4- phosphate kinase and a butadiene synthase (Figure 2, steps A-H).
- an acetyl-CoA:acetyl-CoA acyltransferase an acetoacetyl- CoA reductase, a 3-hydroxybutyryl-CoA dehydratase
- a non-naturally occurring microbial organism of the invention can have one, two, three, four, five, six, seven, eight, nine or ten, up to all nucleic acids encoding the enzymes or proteins constituting a butadiene biosynthetic pathway disclosed herein.
- the non-naturally occurring microbial organisms also can include other genetic modifications that facilitate or optimize butadiene biosynthesis or that confer other useful functions onto the host microbial organism.
- One such other functionality can include, for example, augmentation of the synthesis of one or more of the butadiene pathway precursors such as acetyl-CoA, glutaconyl-CoA, glutaryl-CoA, 3-aminobutyryl-CoA, 4-hydroxybutyryl-CoA, erythrose-4-phosphate or malonyl- CoA.
- the butadiene pathway precursors such as acetyl-CoA, glutaconyl-CoA, glutaryl-CoA, 3-aminobutyryl-CoA, 4-hydroxybutyryl-CoA, erythrose-4-phosphate or malonyl- CoA.
- a host microbial organism is selected such that it produces the precursor of a butadiene pathway, either as a naturally produced molecule or as an engineered product that either provides de novo production of a desired precursor or increased production of a precursor naturally produced by the host microbial organism.
- acetyl-CoA, glutaconyl-CoA, glutaryl-CoA, 3-aminobutyryl-CoA, 4-hydroxybutyryl-CoA, erythrose-4-phosphate or malonyl- CoA are produced naturally in a host organism such as E. coli.
- a host organism can be engineered to increase production of a precursor, as disclosed herein.
- a microbial organism that has been engineered to produce a desired precursor can be used as a host organism and further engineered to express enzymes or proteins of a butadiene pathway.
- a non-naturally occurring microbial organism of the invention is generated from a host that contains the enzymatic capability to synthesize butadiene.
- it can be useful to increase the synthesis or accumulation of a butadiene pathway product to, for example, drive butadiene pathway reactions toward butadiene production.
- Increased synthesis or accumulation can be accomplished by, for example, overexpression of nucleic acids encoding one or more of the above-described butadiene pathway enzymes or proteins.
- Over expression the enzyme or enzymes and/or protein or proteins of the butadiene pathway can occur, for example, through exogenous expression of the endogenous gene or genes, or through exogenous expression of the heterologous gene or genes.
- naturally occurring organisms can be readily generated to be non-naturally occurring microbial organisms of the invention, for example, producing butadiene, through overexpression of one, two, three, four, five, six, seven, eight, nine, or ten, that is, up to all nucleic acids encoding butadiene biosynthetic pathway enzymes or proteins.
- a non-naturally occurring organism can be generated by mutagenesis of an endogenous gene that results in an increase in activity of an enzyme in the butadiene biosynthetic pathway.
- exogenous expression of the encoding nucleic acids is employed.
- Exogenous expression confers the ability to custom tailor the expression and/or regulatory elements to the host and application to achieve a desired expression level that is controlled by the user.
- endogenous expression also can be utilized in other embodiments such as by removing a negative regulatory effector or induction of the gene's promoter when linked to an inducible promoter or other regulatory element.
- an endogenous gene having a naturally occurring inducible promoter can be up-regulated by providing the appropriate inducing agent, or the regulatory region of an endogenous gene can be engineered to incorporate an inducible regulatory element, thereby allowing the regulation of increased expression of an endogenous gene at a desired time.
- an inducible promoter can be included as a regulatory element for an exogenous gene introduced into a non-naturally occurring microbial organism.
- any of the one or more exogenous nucleic acids can be introduced into a microbial organism to produce a non-naturally occurring microbial organism of the invention.
- the nucleic acids can be introduced so as to confer, for example, a butadiene biosynthetic pathway onto the microbial organism.
- encoding nucleic acids can be introduced to produce an intermediate microbial organism having the biosynthetic capability to catalyze some of the required reactions to confer butadiene biosynthetic capability.
- a non-naturally occurring microbial organism having a butadiene biosynthetic pathway can comprise at least two exogenous nucleic acids encoding desired enzymes or proteins, such as the combination of a crotyl alcohol kinase and a butadiene synthase, or alternatively a 4-(cytidine 5'-diphospho)-erythritol kinase and butadiene synthase , or
- a l-hydroxy-2-butenyl 4-diphosphate synthase and a butadiene synthase or alternatively a 3-hydroxy-5-phosphonatooxypentanoate kinase and a butadiene synthase, or alternatively a crotonyl-CoA hydrolase and a crotyl alcohol diphosphokinase, or alternatively a an erythrose reductase and butadiene synthase or alternatively a 3-oxo-glutaryl-CoA reductase (Co A reducing and alcohol forming) and 3-Hydroxy-5-[hydroxy(phosphonooxy)phosphoryl]oxy pentanoate decarboxylase, and the like.
- any combination of two or more enzymes or proteins of a biosynthetic pathway can be included in a non-naturally occurring microbial organism of the invention.
- any combination of three or more enzymes or proteins of a biosynthetic pathway can be included in a non-naturally occurring microbial organism of the invention, for example, a crotyl alcohol kinase, a 2-butenyl-4- phosphate kinase and a butadiene synthase, or alternatively a l-hydroxy-2-butenyl 4-diphosphate synthase, a l-hydroxy-2-butenyl 4-diphosphate reductase, and butadiene synthase, or
- a 3-oxoglutaryl-CoA reductase, a 3-hydroxy-5-oxopentanoate reductase, and a butadiene synthase or alternatively an acetyl-CoA:acetyl-CoA acyltransferase, a crotyl alcohol kinase and a butadiene synthase, or alternatively a glutaconyl-CoA decarboxylase, a crotonyl- CoA reductase (alcohol forming), and a crotyl alcohol diphosphokinase, or alternatively a an erythrose-4-phosphate kinase, a 4-(cytidine 5'-diphospho)-erythritol kinase and a l-hydroxy-2- butenyl 4-diphosphate synthase, or alternatively a 3,5-dioxopentanoate reductase (
- any combination of four such as a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4- phosphate kinase and a butadiene synthase, or alternatively a l-hydroxy-2-butenyl 4-diphosphate synthase, a l-hydroxy-2-butenyl 4-diphosphate reductase, a butenyl 4-diphosphate isomerase and butadiene synthase, or alternatively a 3-hydroxy-5-phosphonatooxypentanoate kinase, a 3- hydroxy-5-[hydroxy(phosphonooxy)phosphoryl]oxy pentanoate kinase, a butenyl 4-diphosphate isomerase and a butadiene synthase, or alternatively an erythrose-4-phosphate reductase, an erythritol-4
- the non-naturally occurring microbial organisms and methods of the invention also can be utilized in various combinations with each other and with other microbial organisms and methods well known in the art to achieve product biosynthesis by other routes.
- one alternative to produce butadiene other than use of the butadiene producers is through addition of another microbial organism capable of converting a butadiene pathway intermediate to butadiene.
- One such procedure includes, for example, the fermentation of a microbial organism that produces a butadiene pathway intermediate.
- the butadiene pathway intermediate can then be used as a substrate for a second microbial organism that converts the butadiene pathway intermediate to butadiene.
- the butadiene pathway intermediate can be added directly to another culture of the second organism or the original culture of the butadiene pathway intermediate producers can be depleted of these microbial organisms by, for example, cell separation, and then subsequent addition of the second organism to the fermentation broth can be utilized to produce the final product without intermediate purification steps.
- the non-naturally occurring microbial organisms and methods of the invention can be assembled in a wide variety of subpathways to achieve biosynthesis of, for example, butadiene.
- biosynthetic pathways for a desired product of the invention can be segregated into different microbial organisms, and the different microbial organisms can be co-cultured to produce the final product.
- the product of one microbial organism is the substrate for a second microbial organism until the final product is synthesized.
- the biosynthesis of butadiene can be accomplished by constructing a microbial organism that contains biosynthetic pathways for conversion of one pathway intermediate to another pathway intermediate or the product.
- butadiene also can be biosynthetically produced from microbial organisms through co-culture or co- fermentation using two organisms in the same vessel, where the first microbial organism produces a butadiene intermediate and the second microbial organism converts the intermediate to butadiene.
- Sources of encoding nucleic acids for a butadiene pathway enzyme or protein can include, for example, any species where the encoded gene product is capable of catalyzing the referenced reaction.
- species include both prokaryotic and eukaryotic organisms including, but not limited to, bacteria, including archaea and eubacteria, and eukaryotes, including yeast, plant, insect, animal, and mammal, including human.
- Exemplary species for such sources include, for example, Escherichia coli, Acidaminococcus fermentans, Acinetobacter baylyi, Acinetobacter calcoaceticus, Acinetobacter sp. ADP1, Acinetobacter sp. Strain M-l, Aquifex aeolicus,
- Arabidopsis thaliana Arabidopsis thaliana, Arabidopsis thaliana col, Arabidopsis thaliana col, Archaeoglobus fulgidus DSM 4304, Azoarcus sp. CIB, Bacillus cereus, Bacillus subtilis, Bos Taurus, Brucella melitensis, Burkholderia ambifaria AMMD, Burkholderia phymatum, Campylobacter jejuni, Candida albicans, Candida magnoliae, Chloroflexus aurantiacus, Citrobacter youngae ATCC 29220, Clostridium acetobutylicum, Clostridium aminobutyricum, Clostridium beijerinckii, Clostridium beijerinckii NCIMB 8052, Clostridium beijerinckii NRRL B593, Clostridium botulinum C str.
- thermoglucosidasius Haematococcus pluvialis, Haemophilus influenzae, Haloarcula
- HTCC2080 Metallosphaera sedula, Methanocaldococcus jannaschii, Mus musculus,
- Mycobacterium marinum M Mycobacterium smegmatis MC2 155, Mycobacterium tuberculosis, Mycoplasma pneumoniae Ml 29, Nocardia farcinica IFM 10152, Nocardia iowensis (sp.
- NRRL 5646 Oryctolagus cuniculus, Paracoccus denitrificans, Penicillium chrysogenum, Populus alba, Populus tremula x Populus alba, Porphyromonas gingivalis, Porphyromonas gingivalis W83, Pseudomonas aeruginosa, Pseudomonas aeruginosa PAOl, Pseudomonas fluorescens, Pseudomonas fluorescens Pf-5, Pseudomonas knackmussii (B13), Pseudomonas putida,
- Saccharomyces cerevisiae Saccharopolyspora rythraea NRRL 2338, Salmonella enterica subsp. arizonae serovar, Salmonella typhimurium, Schizosaccharomyces pombe, Simmondsia chinensis, Sinorhizobium meliloti, Staphylococcus , ureus, Streptococcus pneumoniae, Streptomyces coelicolor, Streptomyces griseus subsp. griseus , BRC 13350, Streptomyces sp. ACT-1,
- coli can be readily applied to other microorganisms, including prokaryotic and eukaryotic organisms alike. Given the teachings and guidance provided herein, those skilled in the art will know that a metabolic alteration exemplified in one organism can be applied equally to other organisms.
- butadiene biosynthesis can be conferred onto the host species by, for example, exogenous expression of a paralog or paralogs from the unrelated species that catalyzes a similar, yet non-identical metabolic reaction to replace the referenced reaction. Because certain differences among metabolic networks exist between different organisms, those skilled in the art will understand that the actual gene usage between different organisms may differ.
- teachings and methods of the invention can be applied to all microbial organisms using the cognate metabolic alterations to those exemplified herein to construct a microbial organism in a species of interest that will synthesize butadiene.
- Methods for constructing and testing the expression levels of a non-naturally occurring butadiene-producing host can be performed, for example, by recombinant and detection methods well known in the art. Such methods can be found described in, for example, Sambrook et al, Molecular Cloning: A Laboratory Manual, Third Ed., Cold Spring Harbor Laboratory, New York (2001); and Ausubel et al, Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, MD (1999).
- Exogenous nucleic acid sequences involved in a pathway for production of butadiene can be introduced stably or transiently into a host cell using techniques well known in the art including, but not limited to, conjugation, electroporation, chemical transformation, transduction, transfection, and ultrasound transformation.
- nucleic acid sequences in the genes or cDNAs of eukaryotic nucleic acids can encode targeting signals such as an N-terminal mitochondrial or other targeting signal, which can be removed before transformation into prokaryotic host cells, if desired.
- targeting signals such as an N-terminal mitochondrial or other targeting signal, which can be removed before transformation into prokaryotic host cells, if desired.
- removal of a mitochondrial leader sequence led to increased expression in E. coli (Hoffmeister et al, J. Biol. Chem. 280:4329-4338 (2005)).
- genes can be expressed in the cytosol without the addition of leader sequence, or can be targeted to mitochondrion or other organelles, or targeted for secretion, by the addition of a suitable targeting sequence such as a mitochondrial targeting or secretion signal suitable for the host cells.
- a suitable targeting sequence such as a mitochondrial targeting or secretion signal suitable for the host cells.
- An expression vector or vectors can be constructed to include one or more butadiene biosynthetic pathway encoding nucleic acids as exemplified herein operably linked to expression control sequences functional in the host organism.
- Expression vectors applicable for use in the microbial host organisms of the invention include, for example, plasmids, phage vectors, viral vectors, episomes and artificial chromosomes, including vectors and selection sequences or markers operable for stable integration into a host chromosome.
- the expression vectors can include one or more selectable marker genes and appropriate expression control sequences. Selectable marker genes also can be included that, for example, provide resistance to antibiotics or toxins, complement auxotrophic deficiencies, or supply critical nutrients not in the culture media.
- Expression control sequences can include constitutive and inducible promoters, transcription enhancers, transcription terminators, and the like which are well known in the art.
- both nucleic acids can be inserted, for example, into a single expression vector or in separate expression vectors.
- the encoding nucleic acids can be operationally linked to one common expression control sequence or linked to different expression control sequences, such as one inducible promoter and one constitutive promoter.
- the transformation of exogenous nucleic acid sequences involved in a metabolic or synthetic pathway can be confirmed using methods well known in the art. Such methods include, for example, nucleic acid analysis such as
- the invention provides a method for producing butadiene that includes culturing a non-naturally occurring microbial organism, including a microbial organism having a butadiene pathway, the butadiene pathway including at least one exogenous nucleic acid encoding a butadiene pathway enzyme expressed in a sufficient amount to produce butadiene, the butadiene pathway including an acetyl-CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase, a crotonyl
- acyltransferase an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotonyl- CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase and a butadiene synthase ( Figure 2, steps A-H).
- the method includes a microbial organism having a butadiene pathway including an acetyl-CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl- CoA dehydratase, a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase and crotonyl-CoA reductase (alcohol forming) ( Figure 2, steps A-C, K, F, G, H).
- the method includes a microbial organism having a butadiene pathway including an acetyl- CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a butadiene synthase, a crotonyl-CoA reductase (alcohol forming) and a crotyl alcohol diphosphokinase ( Figure 2, steps A-C, K, P, H).
- the method includes a microbial organism having a butadiene pathway including an acetyl-CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase, a crotonyl-CoA hydrolase, synthetase, or transferase and a crotonate reductase, ( Figure 2, steps A-C, I, J, E, F, G, H).
- the method includes a microbial organism having a butadiene pathway including an acetyl-CoA:acetyl-CoA
- acyltransferase an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a crotonyl-CoA hydrolase, synthetase or transferase, a crotonate reductase and a crotyl alcohol diphosphokinase ( Figure 2, steps A-C, I, J, E, P, H).
- the method includes a microbial organism having a butadiene pathway including an acetyl-CoA:acetyl-CoA acyltransferase, an acetoacetyl-CoA reductase, a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a butadiene synthase and a crotyl alcohol diphosphokinase ( Figure 2, steps A-E, P, H).
- the method includes a microbial organism having a butadiene pathway including a glutaconyl-CoA decarboxylase, a crotonyl- CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a crot
- the method includes a microbial organism having a butadiene pathway including a glutaconyl-CoA decarboxylase, a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase and crotonyl-CoA reductase (alcohol forming) ( Figure 2, steps L, K, F, G, H).
- the method includes a microbial organism having a butadiene pathway including a glutaconyl-CoA decarboxylase, a butadiene synthase, a crotonyl-CoA reductase (alcohol forming) and a crotyl alcohol diphosphokinase (Figure 2, steps L, K, P, H).
- the method includes a microbial organism having a butadiene pathway including a glutaconyl-CoA decarboxylase, a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase, a crotonyl-CoA hydrolase, synthetase, or transferase and a crotonate reductase (Figure 2, steps L, I, J, E, F, G, H).
- the method includes a microbial organism having a butadiene pathway including a glutaconyl-CoA decarboxylase, a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a crotonyl-CoA hydrolase, synthetase or transferase, a crotonate reductase and a crotyl alcohol diphosphokinase ( Figure 2, steps L, I, J, E, P, H).
- the method includes a microbial organism having a butadiene pathway including a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a butadiene a glutaconyl-CoA decarboxylase and a crotyl alcohol diphosphokinase (Figure 2, steps L, C, D, E, P, H).
- the method includes a microbial organism having a butadiene pathway including a glutaryl-CoA dehydrogenase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase and a butadiene synthase ( Figure 2, steps M, D-H).
- the method includes a microbial organism having a butadiene pathway including a glutaryl-CoA dehydrogenase, a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase and crotonyl-CoA reductase (alcohol forming) ( Figure 2, steps M, K, F, G, H).
- the method includes a microbial organism having a butadiene pathway including a glutaryl-CoA dehydrogenase, a butadiene synthase, a crotonyl-CoA reductase (alcohol forming) and a crotyl alcohol
- the method includes a microbial organism having a butadiene pathway including a glutaryl-CoA dehydrogenase, a
- crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase, a crotonyl-CoA hydrolase, synthetase, or transferase and a crotonate reductase (Figure 2, steps M, I, J, E, F, G, H).
- the method includes a microbial organism having a butadiene pathway including a glutaryl-CoA dehydrogenase, a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a crotonyl-CoA hydrolase, synthetase or transferase, a crotonate reductase and a crotyl alcohol diphosphokinase ( Figure 2, steps M, I, J, E, P, H).
- the method includes a microbial organism having a butadiene pathway including a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a glutaryl-CoA dehydrogenase and a crotyl alcohol diphosphokinase ( Figure 2, steps M, C, D, E, P, H).
- the method includes a microbial organism having a butadiene pathway including a 3-aminobutyryl-CoA deaminase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase and a butadiene synthase ( Figure 2, steps N, D-H).
- the method includes a microbial organism having a butadiene pathway including a 3-aminobutyryl-CoA deaminase, a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase and crotonyl-CoA reductase (alcohol forming) ( Figure 2, steps N, K, F, G, H).
- the method includes a microbial organism having a butadiene pathway including a 3-aminobutyryl-CoA deaminase, a butadiene synthase, a crotonyl-CoA reductase (alcohol forming) and a crotyl alcohol diphosphokmase ( Figure 2, steps N, K, P, H).
- the method includes a microbial organism having a butadiene pathway including a 3-aminobutyryl-CoA deaminase, a
- crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase, a crotonyl-CoA hydrolase, synthetase, or transferase and a crotonate reductase (Figure 2, steps N, I, J, E, F, G, H).
- the method includes a microbial organism having a butadiene pathway including a 3-aminobutyryl-CoA deaminase, a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a crotonyl-CoA hydrolase, synthetase or transferase, a crotonate reductase and a crotyl alcohol diphosphokmase (Figure 2, steps N, I, J, E, P, H).
- the method includes a microbial organism having a butadiene pathway including a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a 3- aminobutyryl-CoA deaminase and a crotyl alcohol diphosphokmase ( Figure 2, steps N, C, D, E, P, H).
- the method includes a microbial organism having a butadiene pathway including a 4-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kina
- the method includes a microbial organism having a butadiene pathway including a 4-hydroxybutyryl-CoA dehydratase, a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase and crotonyl-CoA reductase (alcohol forming) ( Figure 2, steps O, K, F, G, H).
- the method includes a microbial organism having a butadiene pathway including a 4-hydroxybutyryl-CoA
- the method includes a microbial organism having a butadiene pathway including a 4-hydroxybutyryl-CoA dehydratase, a crotonaldehyde reductase (alcohol forming), a crotyl alcohol kinase, a 2-butenyl-4-phosphate kinase, a butadiene synthase, a crotonyl-CoA hydrolase, synthetase, or transferase and a crotonate reductase (Figure 2, steps O, I, J, E, F, G, H).
- the method includes a microbial organism having a butadiene pathway including a 4-hydroxybutyryl-CoA dehydratase, a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a crotonyl-CoA hydrolase, synthetase or transferase, a crotonate reductase and a crotyl alcohol diphosphokmase ( Figure 2, steps O, I, J, E, P, H).
- the method includes a microbial organism having a butadiene pathway including a 3-hydroxybutyryl-CoA dehydratase, a crotonyl-CoA reductase (aldehyde forming), a crotonaldehyde reductase (alcohol forming), a butadiene synthase, a 4- hydroxybutyryl-CoA dehydratase and a crotyl alcohol diphosphokinase ( Figure 2, steps O, C, D, E, P, H).
- the invention provides a method for producing butadiene that includes culturing a non-naturally occurring microbial organism, including a microbial organism having a butadiene pathway, the butadiene pathway including at least one exogenous nucleic acid encoding a butadiene pathway enzyme expressed in a sufficient amount to produce butadiene, the butadiene pathway including an erythrose-4-phosphate reductase, an erythritol-4-phospate cytidylyltransferase, a 4-(cytidine 5'-diphospho)-erythritol kinase, an erythritol 2,4- cyclodiphosphate synthase, a l-hydroxy-2-butenyl 4-diphosphate synthase, a l-hydroxy-2- butenyl 4-diphosphate reductase, a butenyl 4-diphosphate isomerase,
- the method includes a microbial organism having a butadiene pathway including an erythrose-4-phosphate reductase, an erythritol-4-phospate cytidylyltransferase, a 4-(cytidine 5'- diphospho)-erythritol kinase, an erythritol 2,4-cyclodiphosphate synthase, a l-hydroxy-2-butenyl 4-diphosphate synthase, a l-hydroxy-2-butenyl 4-diphosphate reductase and a butadiene synthase ( Figure 3, steps A-F, and H).
- a microbial organism having a butadiene pathway including an erythrose-4-phosphate reductase, an erythritol-4-phospate cytidylyltransferase, a 4-(cytidine 5'- diphospho)-ery
- the method includes a microbial organism having a butadiene pathway including an erythrose-4-phosphate reductase, an erythritol-4- phospate cytidylyltransferase, a 4-(cytidine 5'-diphospho)-erythritol kinase, an erythritol 2,4- cyclodiphosphate synthase, a l-hydroxy-2-butenyl 4-diphosphate synthase, a l-hydroxy-2- butenyl 4-diphosphate reductase, a butenyl 4-diphosphate isomerase and butadiene synthase ( Figure 3, steps A-H).
- the method includes a microbial organism having a butadiene pathway including an erythritol-4-phospate cytidylyltransferase, a 4-(cytidine 5'- diphospho)-erythritol kinase, an erythritol 2,4-cyclodiphosphate synthase, a l-hydroxy-2-butenyl 4-diphosphate synthase, a l-hydroxy-2-butenyl 4-diphosphate reductase, a butadiene synthase, an erythrose-4-phosphate kinase, an erythrose reductase and a erythritol kinase ( Figure 3, steps I, J, K, B-F, H).
- the method includes a microbial organism having a butadiene pathway including an erythritol-4-phospate cytidylyltransferase, a 4-(cytidine 5'-diphospho)- erythritol kinase, an erythritol 2,4-cyclodiphosphate synthase, a l-hydroxy-2-butenyl 4- diphosphate synthase, a l-hydroxy-2-butenyl 4-diphosphate reductase, a butenyl 4-diphosphate isomerase, a butadiene synthase, an erythrose-4-phosphate kinase, an erythrose reductase and an erythritol kinase ( Figure 3, steps I, J, K, B-H).
- the invention provides a method for producing butadiene that includes culturing a non-naturally occurring microbial organism, including a microbial organism having a butadiene pathway, the butadiene pathway including at least one exogenous nucleic acid encoding a butadiene pathway enzyme expressed in a sufficient amount to produce butadiene, the butadiene pathway including a malonyl-CoA:acetyl-CoA acyltransferase, a 3-oxoglutaryl- CoA reductase (ketone-reducing), a 3-hydroxyglutaryl-CoA reductase (aldehyde forming), a 3- hydroxy-5 -oxopentanoate reductase, a 3,5-dihydroxypentanoate kinase, a 3 -hydroxy-5 - phosphonatooxypentanoate kinase, a 3-hydroxy-5-[hydroxy(phosphonooxy)phosphoryl]oxy
- the method includes a microbial organism having a butadiene pathway including a malonyl-CoA:acetyl-CoA acyltransferase, a 3- oxoglutaryl-CoA reductase (ketone-reducing), a 3-hydroxyglutaryl-CoA reductase (aldehyde forming), a 3 -hydroxy-5 -oxopentanoate reductase, a 3,5-dihydroxypentanoate kinase, a 3- hydroxy-5-phosphonatooxypentanoate kinase, a 3 -hydroxy-5 -
- the method includes a microbial organism having a butadiene pathway including a malonyl-CoA:acetyl-CoA acyltransferase, a 3,5-dihydroxypentanoate kinase, a 3 -hydroxy-5 -phosphonatooxypentanoate kinase, a 3-hydroxy-5-[hydroxy(phosphonooxy)phosphoryl]oxy pentanoate decarboxylase, a butenyl 4-diphosphate isomerase, a butadiene synthase, a 3-oxoglutaryl-CoA reductase
- the method includes a microbial organism having a butadiene pathway including a malonyl-CoA:acetyl-CoA acyltransferase, a 3 -hydroxy-5 -oxopentanoate reductase, a 3,5-dihydroxypentanoate kinase, a 3- Hydroxy-5 -phosphonatooxypentanoate kinase, a 3 -Hydroxy-5 -
- the method includes a microbial organism having a butadiene pathway including a malonyl-CoA:acetyl-CoA acyltransferase, a 3,5-dihydroxypentanoate kinase, a 3-hydroxy-5- phosphonatooxypentanoate kinase, a 3-hydroxy-5-[hydroxy(phosphonooxy)phosphoryl]oxy pentanoate decarboxylase, a butenyl 4-diphosphate isomerase, a butadiene synthase, a 5- hydroxy-3-oxopentanoate reductase and a 3-oxo-glutaryl-CoA reductase (Co A reducing and alcohol forming). ( Figure 4, steps A, O, N, E, F, G, H, I).
- the method includes a microbial organism having a butadiene pathway including a malonyl-CoA:acetyl-CoA
- acyltransferase a 3-oxoglutaryl-CoA reductase (ketone-reducing), a 3,5-dihydroxypentanoate kinase, a 3-hydroxy-5-phosphonatooxypentanoate kinase, a 3-hydroxy-5- [hydroxy(phosphonooxy)phosphoryl]oxy pentanoate decarboxylase, a butenyl 4-diphosphate isomerase, a butadiene synthase and a 3-hydroxyglutaryl-CoA reductase (alcohol forming).
- Figure 4 steps A, B, J, E, F, G, H, I).
- Suitable purification and/or assays to test for the production of butadiene can be performed using well known methods. Suitable replicates such as triplicate cultures can be grown for each engineered strain to be tested. For example, product and byproduct formation in the engineered production host can be monitored. The final product and intermediates, and other organic compounds, can be analyzed by methods such as HPLC (High Performance Liquid
- the butadiene can be separated from other components in the culture using a variety of methods well known in the art.
- separation methods include, for example, extraction procedures as well as methods that include continuous liquid-liquid extraction, pervaporation, membrane filtration, membrane separation, reverse osmosis, electrodialysis, distillation, crystallization, centrifugation, extractive filtration, ion exchange chromatography, size exclusion chromatography, adsorption chromatography, and ultrafiltration. All of the above methods are well known in the art.
- any of the non-naturally occurring microbial organisms described herein can be cultured to produce and/or secrete the biosynthetic products of the invention.
- the butadiene producers can be cultured for the biosynthetic production of butadiene.
- the recombinant strains are cultured in a medium with carbon source and other essential nutrients. It is sometimes desirable and can be highly desirable to maintain anaerobic conditions in the fermenter to reduce the cost of the overall process. Such conditions can be obtained, for example, by first sparging the medium with nitrogen and then sealing the flasks with a septum and crimp-cap. For strains where growth is not observed anaerobically, microaerobic or substantially anaerobic conditions can be applied by perforating the septum with a small hole for limited aeration. Exemplary anaerobic conditions have been described previously and are well-known in the art. Exemplary aerobic and anaerobic conditions are described, for example, in United State publication 2009/0047719, filed August 10, 2007. Fermentations can be performed in a batch, fed-batch or continuous manner, as disclosed herein.
- the pH of the medium can be maintained at a desired pH, in particular neutral pH, such as a pH of around 7 by addition of a base, such as NaOH or other bases, or acid, as needed to maintain the culture medium at a desirable pH.
- the growth rate can be determined by measuring optical density using a spectrophotometer (600 nm), and the glucose uptake rate by monitoring carbon source depletion over time.
- the growth medium can include, for example, any carbohydrate source which can supply a source of carbon to the non-naturally occurring microorganism.
- Such sources include, for example, sugars such as glucose, xylose, arabinose, galactose, mannose, fructose, sucrose and starch.
- Other sources of carbohydrate include, for example, renewable feedstocks and biomass.
- Exemplary types of biomasses that can be used as feedstocks in the methods of the invention include cellulosic biomass, hemicellulosic biomass and lignin feedstocks or portions of feedstocks.
- Such biomass feedstocks contain, for example, carbohydrate substrates useful as carbon sources such as glucose, xylose, arabinose, galactose, mannose, fructose and starch.
- carbohydrate substrates useful as carbon sources such as glucose, xylose, arabinose, galactose, mannose, fructose and starch.
- the butadiene microbial organisms of the invention also can be modified for growth on syngas as its source of carbon.
- one or more proteins or enzymes are expressed in the butadiene producing organisms to provide a metabolic pathway for utilization of syngas or other gaseous carbon source.
- Synthesis gas also known as syngas or producer gas
- syngas is the major product of gasification of coal and of carbonaceous materials such as biomass materials, including agricultural crops and residues.
- Syngas is a mixture primarily of H 2 and CO and can be obtained from the gasification of any organic feedstock, including but not limited to coal, coal oil, natural gas, biomass, and waste organic matter. Gasification is generally carried out under a high fuel to oxygen ratio. Although largely H 2 and CO, syngas can also include C0 2 and other gases in smaller quantities.
- synthesis gas provides a cost effective source of gaseous carbon such as CO and, additionally, C0 2 .
- the Wood-Ljungdahl pathway catalyzes the conversion of CO and H 2 to acetyl-CoA and other products such as acetate.
- Organisms capable of utilizing CO and syngas also generally have the capability of utilizing C0 2 and C0 2 /H 2 mixtures through the same basic set of enzymes and transformations encompassed by the Wood-Ljungdahl pathway.
- H 2 -dependent conversion of C0 2 to acetate by microorganisms was recognized long before it was revealed that CO also could be used by the same organisms and that the same pathways were involved.
- non-naturally occurring microorganisms possessing the Wood-Ljungdahl pathway can utilize C0 2 and H 2 mixtures as well for the production of acetyl-CoA and other desired products.
- the Wood-Ljungdahl pathway is well known in the art and consists of 12 reactions which can be separated into two branches: (1) methyl branch and (2) carbonyl branch.
- the methyl branch converts syngas to methyl-tetrahydrofolate (methyl-THF) whereas the carbonyl branch converts methyl-THF to acetyl-CoA.
- the reactions in the methyl branch are catalyzed in order by the following enzymes or proteins: ferredoxin oxidoreductase, formate dehydrogenase,
- methyltetrahydrofolatexorrinoid protein methyltransferase for example, AcsE
- corrinoid iron- sulfur protein for example, nickel-protein assembly protein
- nickel-protein assembly protein for example, AcsF
- ferredoxin for example, ferredoxin
- acetyl-CoA synthase carbon monoxide dehydrogenase and nickel-protein assembly protein (for example, CooC).
- the reductive (reverse) tricarboxylic acid cycle coupled with carbon monoxide dehydrogenase and/or hydrogenase activities can also be used for the conversion of CO, C0 2 and/or H 2 to acetyl-CoA and other products such as acetate.
- Organisms capable of fixing carbon via the reductive TCA pathway can utilize one or more of the following enzymes: ATP citrate - lyase, citrate lyase, aconitase, isocitrate dehydrogenase, alpha-ketoglutarate: ferredoxin oxidoreductase, succinyl-CoA synthetase, succinyl-CoA transferase, fumarate reductase, fumarase, malate dehydrogenase, NAD(P)H: ferredoxin oxidoreductase, carbon monoxide dehydrogenase, and hydrogenase.
- ATP citrate - lyase citrate lyase
- citrate lyase citrate lyase
- aconitase isocitrate dehydrogenase
- alpha-ketoglutarate ferredoxin oxidoreductase
- the reducing equivalents extracted from CO and/or H 2 by carbon monoxide dehydrogenase and hydrogenase are utilized to fix C0 2 via the reductive TCA cycle into acetyl-CoA or acetate.
- Acetate can be converted to acetyl-CoA by enzymes such as acetyl-CoA transferase, acetate kinase/phosphotransacetylase, and acetyl-CoA synthetase.
- Acetyl-CoA can be converted to the butadiene, glyceraldehyde-3 -phosphate, phosphoenolpyruvate, and pyruvate, by pyruvate: ferredoxin oxidoreductase and the enzymes of gluconeo genesis.
- pyruvate ferredoxin oxidoreductase and the enzymes of gluconeo genesis.
- a non-naturally occurring microbial organism can be produced that secretes the biosynthesized compounds of the invention when grown on a carbon source such as a carbohydrate.
- Such compounds include, for example, butadiene and any of the intermediate metabolites in the butadiene pathway. All that is required is to engineer in one or more of the required enzyme or protein activities to achieve biosynthesis of the desired compound or intermediate including, for example, inclusion of some or all of the butadiene biosynthetic pathways.
- the invention provides a non-naturally occurring microbial organism that produces and/or secretes butadiene when grown on a carbohydrate or other carbon source and produces and/or secretes any of the intermediate metabolites shown in the butadiene pathway when grown on a carbohydrate or other carbon source.
- the butadiene producing microbial organisms of the invention can initiate synthesis from an intermediate, for example, acetoacetyl-CoA, 3-hydroxybutyryl-CoA, crotonyl-CoA, crotonaldehyde, crotyl alcohol, 2- betenyl-phosphate, 2-butenyl-4-diphosphate, erythritol-4-phosphate, 4-(cytidine 5'-diphospho)- erythritol, 2-phospho-4-(cytidine 5'-diphospho)-erythritol, erythritol-2,4-cyclodiphosphate, 1- hydroxy-2-butenyl 4-diphosphate, butenyl 4-diphosphate, 2-butenyl 4-diphosphate, 3- oxoglutaryl-CoA, 3-hydroxyglutaryl-CoA, 3-hydroxy-5-oxopentanoate, 3,5-dihydroxy pentanoate, 3-hydroxy-5-phosphon
- the non-naturally occurring microbial organisms of the invention are constructed using methods well known in the art as exemplified herein to exogenously express at least one nucleic acid encoding a butadiene pathway enzyme or protein in sufficient amounts to produce butadiene. It is understood that the microbial organisms of the invention are cultured under conditions sufficient to produce butadiene. Following the teachings and guidance provided herein, the non- naturally occurring microbial organisms of the invention can achieve biosynthesis of butadiene resulting in intracellular concentrations between about 0.001-2000 mM or more.
- the intracellular concentration of butadiene is between about 3-1500 mM, particularly between about 5-1250 mM and more particularly between about 8-1000 mM, including about 10 mM, 100 mM, 200 mM, 500 mM, 800 mM, or more. Intracellular concentrations between and above each of these exemplary ranges also can be achieved from the non-naturally occurring microbial organisms of the invention.
- culture conditions include anaerobic or substantially anaerobic growth or maintenance conditions.
- Exemplary anaerobic conditions have been described previously and are well known in the art.
- Exemplary anaerobic conditions for fermentation processes are described herein and are described, for example, in U.S. publication 2009/0047719, filed August 10, 2007. Any of these conditions can be employed with the non-naturally occurring microbial organisms as well as other anaerobic conditions well known in the art.
- the butadiene producers can synthesize butadiene at intracellular concentrations of 5-10 mM or more as well as all other concentrations exemplified herein. It is understood that, even though the above description refers to intracellular
- butadiene producing microbial organisms can produce butadiene intracellularly and/or secrete the product into the culture medium.
- the carbon feedstock and other cellular uptake sources such as phosphate, ammonia, sulfate, chloride and other halogens can be chosen to alter the isotopic distribution of the atoms present in butadiene or any butadiene pathway intermediate.
- uptake sources can provide isotopic enrichment for any atom present in the product butadiene or butadiene pathway intermediate including any butadiene impurities generated in diverging away from the pathway at any point. Isotopic enrichment can be achieved for any target atom including, for example, carbon, hydrogen, oxygen, nitrogen, sulfur, phosphorus, chloride or other halogens.
- the uptake sources can be selected to alter the carbon- 12, carbon- 13, and carbon- 14 ratios. In some embodiments, the uptake sources can be selected to alter the oxygen- 16, oxygen- 17, and oxygen- 18 ratios. In some embodiments, the uptake sources can be selected to alter the hydrogen, deuterium, and tritium ratios. In some embodiments, the uptake sources can be selected to alter the nitrogen- 14 and nitrogen- 15 ratios. In some embodiments, the uptake sources can be selected to alter the sulfur-32, sulfur-33, sulfur-34, and sulfur-35 ratios. In some embodiments, the uptake sources can be selected to alter the phosphorus-31 , phosphorus-32, and phosphorus-33 ratios. In some embodiments, the uptake sources can be selected to alter the chlorine-35, chlorine-36, and chlorine-37 ratios.
- a target isotopic ratio of an uptake source can be obtained via synthetic chemical enrichment of the uptake source.
- Such isotopically enriched uptake sources can be purchased commercially or prepared in the laboratory.
- a target isotopic ratio of an uptake source can be obtained by choice of origin of the uptake source in nature.
- a source of carbon for example, can be selected from a fossil fuel- derived carbon source, which can be relatively depleted of carbon- 14, or an environmental carbon source, such as C0 2 , which can possess a larger amount of carbon- 14 than its petroleum- derived counterpart.
- the unstable carbon isotope carbon-14 or radiocarbon makes up for roughly 1 in 10 12 carbon atoms in earth's atmosphere. Carbon-14 has a half-life of about 5700 years. The stock is replenished in the upper atmosphere by a nuclear reaction involving cosmic rays and ordinary nitrogen ( 14 N). Fossil fuels contain no carbon-14, as it decayed long ago. Burning fossil fuels should lower the atmospheric carbon-14 fraction (the " Suess effect'). Indeed, atmospheric carbon-14, measured on tree rings, dropped by 2 to 2.5 % from about 1850 to 1954, when nuclear bomb tests started to inject carbon-14 into the atmosphere.
- ASTM D6866 was developed in the United States as a standardized analytical method for determining the biobased content of solid, liquid, and gaseous samples using radiocarbon dating. Specifically, ASTM D6866 was developed at the request of the United States Department of Agriculture to satisfy legislation requiring federal agencies to give preference in procurement to manufacturers using the greatest amount of biomass in their products (per the Farm Security and Rural Investment Act of 2002). It was quickly established that radiocarbon dating was the only viable and accurate technique to use for the determination of a product's biobased content. A working standard of radiocarbon dating for industrial use was completed in 2004 and is now cited in US Federal Law (7 CFR part 2902). ASTM D6866 was first published in 2004. There have been several versions released since then. The current active version of the standard is ASTM D6866-11 effective April 1, 2011.
- Isotopic enrichment is readily assessed by mass spectrometry using techniques known in the art such as Stable Isotope Ratio Mass Spectrometry (SIRMS) and Site-Specific Natural Isotopic Fractionation by Nuclear Magnetic Resonance (SNIF-NMR).
- SIRMS Stable Isotope Ratio Mass Spectrometry
- SNIF-NMR Site-Specific Natural Isotopic Fractionation by Nuclear Magnetic Resonance
- mass spectral techniques can be integrated with separation techniques such as liquid chromatography (LC) and/or high performance liquid chromatography (HPLC).
- the biobased content of monomers is estimated by the ratio of carbon-14 ( 14 C) to carbon-12 ( 12 C) measured by accelerator mass spectrometry (AMS).
- An oxalic acid standard (SRM 4990b or HOx 1) was made from a crop of 1955 sugar beet.
- Oxalic Acid II was prepared when stocks of SRM 4990b began to dwindle.
- the Oxalic Acid II standard (HOx 2; N.I.S.T designation SRM 4990 C) was made from a crop of 1977 French beet molasses. In the early 1980's, a group of 12 laboratories measured the ratios of the two standards. The ratio of the activity of Oxalic acid II to 1 is 1.2933 ⁇ 0.001 (the weighted mean). Mann, Radiocarbon, 25(2):519-527 (1983). The isotopic ratio of HOx II is -17.8 per mille.
- ASTM D6866-11 suggests use of SRM 4990 C for the modern standard.
- a Fm 0% represents the entire lack of carbon-14 atoms in a material thus indicating a fossil (for example, petroleum based) carbon source.
- a Fm 100%, after correction for the post-1950 bomb injection of carbon-14 into the atmosphere, likewise indicates an entirely modern carbon source.
- the percent modern carbon can be greater than 100% because of the continuing but diminishing effects of the 1950s nuclear testing programs, which resulted in a considerable enrichment of carbon-14 in the atmosphere as described in ASTM D6866-1 1. Because all sample carbon-14 activities are referenced to a "pre-bomb" standard, and because nearly all new biobased products are produced in a post-bomb environment, all pMC values (after correction for isotopic fraction) must be multiplied by 0.95 (as of 2010) to better reflect the true biobased content of the sample. A biobased content that is greater than 103% suggests that either an analytical error has occurred, or that the source of biobased carbon is more than several years old.
- ASTM D6866 quantifies the biobased content relative to the material's total organic content and does not consider the inorganic carbon and other non-carbon containing substances present. To illustrate, below are some exemplary formulations and their corresponding ASTM D6866 results:
- Product 3 solid that is 50%> glass and 50%> polyethylene from petroleum.
- Biobased Content 0%> (product 3 has 50%> organic carbon but from fossil sources; glass is not carbon-containing);
- Biobased Content 62.5% (product 5 has 80% organic carbon but only 50% of it is renewable).
- Applications of carbon- 14 dating techniques to quantify bio-based content of renewable materials are known in the art. Currie et al., Nuclear Instruments and Methods in Physics Research B, 172:281-287 (2000). For example, carbon-14 dating has been used to quantify bio- based content in terephthalate-containing materials. Colonna et al., Green Chemistry, 13:2543- 2548 (2011).
- polypropylene terephthalate (PPT) polymers derived from renewable 1,3- propanediol and petroleum-derived terephthalic acid resulted in Fm values near 30% (i.e., since 3/11 of the polymeric carbon derives from renewable 1,3-propanediol and 8/11 from the fossil end member terephthalic acid).
- PPT polypropylene terephthalate
- polybutylene terephthalate polymer derived from both renewable 1 ,4-butanediol and renewable terephthalic acid resulted in bio-based content exceeding 90%. Colonna et al, supra.
- the present invention provides butadiene or a butadiene intermediate that has a carbon- 12, carbon- 13, and carbon-14 ratio that reflects an atmospheric carbon uptake source.
- the butadiene or a butadiene intermediate can have an Fm value of at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%o, at least 90%>, at least 95%>, at least 98 or at much as 100%).
- the uptake source is C0 2 .
- the present invention provides butadiene or a butadiene intermediate that has a carbon- 12, carbon- 13, and carbon-14 ratio that reflects petroleum-based carbon uptake source.
- the butadiene or a butadiene intermediate can have an Fm value of less than 10%, less than 5%, less than 2% or less than 1%.
- the present invention provides butadiene or a butadiene intermediate that has a carbon- 12, carbon-13, and carbon-14 ratio that is obtained by a combination of an atmospheric carbon uptake source with a petroleum-based uptake source.
- Such combination of uptake sources is one means by which the carbon- 12, carbon-13, and carbon-14 ratio can be varied.
- growth condition for achieving biosynthesis of butadiene can include the addition of an osmoprotectant to the culturing conditions.
- the non-naturally occurring microbial organisms of the invention can be sustained, cultured or fermented as described herein in the presence of an osmoprotectant.
- an osmoprotectant refers to a compound that acts as an osmolyte and helps a microbial organism as described herein survive osmotic stress.
- Osmoprotectants include, but are not limited to, betaines, amino acids, and the sugar trehalose.
- Non-limiting examples of such are glycine betaine, praline betaine, dimethylthetin, dimethylslfonioproprionate, 3- dimethylsulfonio-2-methylproprionate, pipecolic acid, dimethylsulfonioacetate, choline, L- carnitine and ectoine.
- the osmoprotectant is glycine betaine. It is understood to one of ordinary skill in the art that the amount and type of osmoprotectant suitable for protecting a microbial organism described herein from osmotic stress will depend on the microbial organism used.
- the amount of osmoprotectant in the culturing conditions can be, for example, no more than about 0.1 mM, no more than about 0.5 mM, no more than about 1.0 mM, no more than about 1.5 mM, no more than about 2.0 mM, no more than about 2.5 mM, no more than about 3.0 mM, no more than about 5.0 mM, no more than about 7.0 mM, no more than about 10 mM, no more than about 50 mM, no more than about 100 mM or no more than about 500 mM.
- the culture conditions can include, for example, liquid culture procedures as well as
- biosynthetic products of the invention can be obtained under anaerobic or substantially anaerobic culture conditions.
- one exemplary growth condition for achieving biosynthesis of butadiene includes anaerobic culture or fermentation conditions.
- the non-naturally occurring microbial organisms of the invention can be sustained, cultured or fermented under anaerobic or substantially anaerobic conditions.
- anaerobic conditions refers to an environment devoid of oxygen.
- substantially anaerobic conditions include, for example, a culture, batch fermentation or continuous fermentation such that the dissolved oxygen concentration in the medium remains between 0 and 10% of saturation.
- Substantially anaerobic conditions also includes growing or resting cells in liquid medium or on solid agar inside a sealed chamber maintained with an atmosphere of less than 1% oxygen. The percent of oxygen can be maintained by, for example, sparging the culture with an N 2 /C0 2 mixture or other suitable non-oxygen gas or gases.
- the culture conditions described herein can be scaled up and grown continuously for
- Exemplary growth procedures include, for example, fed-batch fermentation and batch separation; fed-batch fermentation and continuous separation, or continuous fermentation and continuous separation. All of these processes are well known in the art. Fermentation procedures are particularly useful for the biosynthetic production of commercial quantities of butadiene.
- the continuous and/or near-continuous production of butadiene will include culturing a non- naturally occurring butadiene producing organism of the invention in sufficient nutrients and medium to sustain and/or nearly sustain growth in an exponential phase. Continuous culture under such conditions can be include, for example, growth for 1 day, 2, 3, 4, 5, 6 or 7 days or more.
- continuous culture can include longer time periods of 1 week, 2, 3, 4 or 5 or more weeks and up to several months.
- organisms of the invention can be cultured for hours, if suitable for a particular application. It is to be understood that the continuous and/or near-continuous culture conditions also can include all time intervals in between these exemplary periods. It is further understood that the time of culturing the microbial organism of the invention is for a sufficient period of time to produce a sufficient amount of product for a desired purpose.
- Fermentation procedures are well known in the art. Briefly, fermentation for the biosynthetic production of butadiene can be utilized in, for example, fed-batch fermentation and batch separation; fed-batch fermentation and continuous separation, or continuous fermentation and continuous separation. Examples of batch and continuous fermentation procedures are well known in the art.
- the butadiene producers also can be, for example, simultaneously subjected to chemical synthesis procedures to convert the product to other compounds or the product can be separated from the fermentation culture and sequentially subjected to chemical or enzymatic conversion to convert the product to other compounds, if desired.
- Modeling can be utilized to optimize growth conditions. Modeling can also be used to design gene knockouts that additionally optimize utilization of the pathway (see, for example, U.S. patent publications US 2002/0012939, US 2003/0224363, US 2004/0029149, US 2004/0072723, US 2003/0059792, US 2002/0168654 and US 2004/0009466, and U.S. Patent No. 7,127,379). Modeling analysis allows reliable predictions of the effects on cell growth of shifting the metabolism towards more efficient production of butadiene.
- One computational method for identifying and designing metabolic alterations favoring biosynthesis of a desired product is the OptKnock computational framework (Burgard et al., Biotechnol. Bioeng.
- OptKnock is a metabolic modeling and simulation program that suggests gene deletion or disruption strategies that result in genetically stable microorganisms which overproduce the target product.
- the framework examines the complete metabolic and/or biochemical network of a microorganism in order to suggest genetic manipulations that force the desired biochemical to become an obligatory byproduct of cell growth.
- OptKnock is a term used herein to refer to a computational method and system for modeling cellular metabolism.
- the OptKnock program relates to a framework of models and methods that incorporate particular constraints into flux balance analysis (FBA) models. These constraints include, for example, qualitative kinetic information, qualitative regulatory information, and/or DNA microarray experimental data.
- OptKnock also computes solutions to various metabolic problems by, for example, tightening the flux boundaries derived through flux balance models and subsequently probing the performance limits of metabolic networks in the presence of gene additions or deletions.
- OptKnock computational framework allows the construction of model formulations that allow an effective query of the performance limits of metabolic networks and provides methods for solving the resulting mixed-integer linear programming problems.
- SimPheny® is a computational system that can be used to produce a network model in silico and to simulate the flux of mass, energy or charge through the chemical reactions of a biological system to define a solution space that contains any and all possible functionalities of the chemical reactions in the system, thereby determining a range of allowed activities for the biological system.
- This approach is referred to as constraints-based modeling because the solution space is defined by constraints such as the known stoichiometry of the included reactions as well as reaction thermodynamic and capacity constraints associated with maximum fluxes through reactions. The space defined by these constraints can be interrogated to determine the phenotypic capabilities and behavior of the biological system or of its biochemical components.
- metabolic modeling and simulation methods include, for example, the computational systems exemplified above as SimPheny® and OptKnock.
- SimPheny® and OptKnock For illustration of the invention, some methods are described herein with reference to the OptKnock computation framework for modeling and simulation.
- OptKnock computation framework for modeling and simulation.
- Those skilled in the art will know how to apply the identification, design and implementation of the metabolic alterations using OptKnock to any of such other metabolic modeling and simulation computational frameworks and methods well known in the art. The methods described above will provide one set of metabolic reactions to disrupt.
- Identification of a set of reactions and their corresponding genes encoding the enzymes participating in each reaction is generally an automated process, accomplished through correlation of the reactions with a reaction database having a relationship between enzymes and encoding genes.
- the set of reactions that are to be disrupted in order to achieve production of a desired product are implemented in the target cell or organism by functional disruption of at least one gene encoding each metabolic reaction within the set.
- One particularly useful means to achieve functional disruption of the reaction set is by deletion of each encoding gene.
- These latter aberrations, resulting in less than total deletion of the gene set can be useful, for example, when rapid assessments of the coupling of a product are desired or when genetic reversion is less likely to occur.
- an optimization method termed integer cuts. This method proceeds by iteratively solving the OptKnock problem exemplified above with the incorporation of an additional constraint referred to as an integer cut at each iteration. Integer cut constraints effectively prevent the solution procedure from choosing the exact same set of reactions identified in any previous iteration that obligatorily couples product biosynthesis to growth. For example, if a previously identified growth-coupled metabolic modification specifies reactions 1, 2, and 3 for disruption, then the following constraint prevents the same reactions from being simultaneously considered in subsequent solutions.
- the integer cut method is well known in the art and can be found described in, for example, Burgard et al, Biotechnol. Prog. 17:791-797 (2001). As with all methods described herein with reference to their use in combination with the OptKnock computational framework for metabolic modeling and simulation, the integer cut method of reducing redundancy in iterative computational analysis also can be applied with other computational frameworks well known in the art including, for example, SimPheny®.
- the set of metabolic modifications can include, for example, addition of one or more biosynthetic pathway enzymes and/or functional disruption of one or more metabolic reactions including, for example, disruption by gene deletion.
- the OptKnock methodology was developed on the premise that mutant microbial networks can be evolved towards their computationally predicted maximum-growth phenotypes when subjected to long periods of growth selection. In other words, the approach leverages an organism's ability to self-optimize under selective pressures.
- the OptKnock framework allows for the exhaustive enumeration of gene deletion combinations that force a coupling between biochemical production and cell growth based on network stoichiometry.
- the identification of optimal gene/reaction knockouts requires the solution of a bilevel optimization problem that chooses the set of active reactions such that an optimal growth solution for the resulting network overproduces the biochemical of interest (Burgard et al, Biotechnol. Bioeng. 84:647-657 (2003)).
- An in silico stoichiometric model of E. coli metabolism can be employed to identify essential genes for metabolic pathways as exemplified previously and described in, for example, U.S. patent publications US 2002/0012939, US 2003/0224363, US 2004/0029149, US 2004/0072723, US 2003/0059792, US 2002/0168654 and US 2004/0009466, and in U.S. Patent No. 7,127,379.
- the OptKnock mathematical framework can be applied to pinpoint gene deletions leading to the growth-coupled production of a desired product. Further, the solution of the bilevel OptKnock problem provides only one set of deletions.
- integer cuts an optimization technique, termed integer cuts. This entails iteratively solving the OptKnock problem with the incorporation of an additional constraint referred to as an integer cut at each iteration, as discussed above.
- a nucleic acid encoding a desired activity of a butadiene pathway can be introduced into a host organism.
- it can be desirable to modify an activity of a butadiene pathway enzyme or protein to increase production of butadiene.
- known mutations that increase the activity of a protein or enzyme can be introduced into an encoding nucleic acid molecule.
- optimization methods can be applied to increase the activity of an enzyme or protein and/or decrease an inhibitory activity, for example, decrease the activity of a negative regulator.
- Directed evolution is a powerful approach that involves the introduction of mutations targeted to a specific gene in order to improve and/or alter the properties of an enzyme. Improved and/or altered enzymes can be identified through the development and implementation of sensitive high-throughput screening assays that allow the automated screening of many enzyme variants (for example, >10 4 ). Iterative rounds of mutagenesis and screening typically are performed to afford an enzyme with optimized properties. Computational algorithms that can help to identify areas of the gene for mutagenesis also have been developed and can significantly reduce the number of enzyme variants that need to be generated and screened. Numerous directed evolution technologies have been developed (for reviews, see Hibbert et al, Biomol.Eng 22: 11-19 (2005); Huisman and Lalonde, In
- Enzyme characteristics that have been improved and/or altered by directed evolution technologies include, for example: selectivity/specificity, for conversion of non-natural substrates; temperature stability, for robust high temperature processing; pH stability, for bioprocessing under lower or higher pH conditions; substrate or product tolerance, so that high product titers can be achieved; binding (K m ), including broadening substrate binding to include non-natural substrates; inhibition (3 ⁇ 4), to remove inhibition by products, substrates, or key intermediates; activity (kcat), to increases enzymatic reaction rates to achieve desired flux; expression levels, to increase protein yields and overall pathway flux; oxygen stability, for operation of air sensitive enzymes under aerobic conditions; and anaerobic activity, for operation of an aerobic enzyme in the absence of oxygen.
- Described below in more detail are exemplary methods that have been developed for the mutagenesis and diversification of genes to target desired properties of specific enzymes. Such methods are well known to those skilled in the art. Any of these can be used to alter and/or optimize the activity of a butadiene pathway enzyme or protein.
- EpPCR (Pritchard et al., J Theor.Biol. 234:497-509 (2005)) introduces random point mutations by reducing the fidelity of DNA polymerase in PCR reactions by the addition of Mn 2+ ions, by biasing dNTP concentrations, or by other conditional variations.
- the five step cloning process to confine the mutagenesis to the target gene of interest involves: 1) error-prone PCR amplification of the gene of interest; 2) restriction enzyme digestion; 3) gel purification of the desired DNA fragment; 4) ligation into a vector; 5) transformation of the gene variants into a suitable host and screening of the library for improved performance.
- This method can generate multiple mutations in a single gene simultaneously, which can be useful to screen a larger number of potential variants having a desired activity.
- a high number of mutants can be generated by EpPCR, so a high-throughput screening assay or a selection method, for example, using robotics, is useful to identify those with desirable characteristics.
- Error-prone Rolling Circle Amplification (epRCA) (Fujii et al., Nucleic Acids Res. 32:el45 (2004); and Fujii et al, Nat. Protoc. 1 :2493-2497 (2006)) has many of the same elements as epPCR except a whole circular plasmid is used as the template and random 6-mers with exonuclease resistant thiophosphate linkages on the last 2 nucleotides are used to amplify the plasmid followed by transformation into cells in which the plasmid is re-circularized at tandem repeats. Adjusting the Mn 2+ concentration can vary the mutation rate somewhat.
- This technique uses a simple error-prone, single-step method to create a full copy of the plasmid with 3 - 4 mutations/kbp. No restriction enzyme digestion or specific primers are required. Additionally, this method is typically available as a commercially available kit.
- DNA or Family Shuffling typically involves digestion of two or more variant genes with nucleases such as Dnase I or EndoV to generate a pool of random fragments that are reassembled by cycles of annealing and extension in the presence of DNA polymerase to create a library of chimeric genes. Fragments prime each other and recombination occurs when one copy primes another copy (template switch).
- This method can be used with >lkbp DNA sequences.
- this method introduces point mutations in the extension steps at a rate similar to error-prone PCR. The method can be used to remove deleterious, random and neutral mutations.
- Staggered Extension (StEP) (Zhao et al, Nat. Biotechnol. 16:258-261 (1998)) entails template priming followed by repeated cycles of 2 step PCR with denaturation and very short duration of annealing/extension (as short as 5 sec). Growing fragments anneal to different templates and extend further, which is repeated until full-length sequences are made. Template switching means most resulting fragments have multiple parents. Combinations of low- fidelity
- Random Priming Recombination random sequence primers are used to generate many short DNA fragments complementary to different segments of the template (Shao et al., Nucleic Acids Res 26:681-683 (1998)). Base misincorporation and mispriming via epPCR give point mutations. Short DNA fragments prime one another based on homology and are recombined and reassembled into full-length by repeated thermocycling. Removal of templates prior to this step assures low parental recombinants. This method, like most others, can be performed over multiple iterations to evolve distinct properties. This technology avoids sequence bias, is independent of gene length, and requires very little parent DNA for the application.
- Random Chimeragenesis on Transient Templates (RACHITT) (Coco et al., Nat. Biotechnol. 19:354-359 (2001)) employs Dnase I fragmentation and size fractionation of single stranded DNA (ssDNA). Homologous fragments are hybridized in the absence of polymerase to a complementary ssDNA scaffold. Any overlapping unhybridized fragment ends are trimmed down by an exonuclease. Gaps between fragments are filled in and then ligated to give a pool of full-length diverse strands hybridized to the scaffold, which contains U to preclude amplification. The scaffold then is destroyed and is replaced by a new strand complementary to the diverse strand by PCR amplification.
- the method involves one strand (scaffold) that is from only one parent while the priming fragments derive from other genes, and the parent scaffold is selected against. Thus, no reannealing with parental fragments occurs. Overlapping fragments are trimmed with an exonuclease. Otherwise, this is conceptually similar to DNA shuffling and StEP. Therefore, there should be no siblings, few inactives, and no unshuffled parentals. This technique has advantages in that few or no parental genes are created and many more crossovers can result relative to standard DNA shuffling.
- Incremental Truncation for the Creation of Hybrid Enzymes creates a combinatorial library with 1 base pair deletions of a gene or gene fragment of interest (Ostermeier et al., Proc. Natl. Acad. Sci. USA 96:3562-3567 (1999); and Ostermeier et al, Nat. Biotechnol. 17: 1205- 1209 (1999)). Truncations are introduced in opposite direction on pieces of 2 different genes. These are ligated together and the fusions are cloned.
- THIO-ITCHY Thio-Incremental Truncation for the Creation of Hybrid Enzymes
- ITCHY Thio-Incremental Truncation for the Creation of Hybrid Enzymes
- SCRATCHY combines two methods for recombining genes, ITCHY and DNA shuffling (Lutz et al, Proc. Natl. Acad. Sci. USA 98: 11248-11253 (2001)). SCRATCHY combines the best features of ITCHY and DNA shuffling. First, ITCHY is used to create a comprehensive set of fusions between fragments of genes in a DNA homology-independent fashion. This artificial family is then subjected to a DNA-shuffling step to augment the number of crossovers.
- Random Drift Mutagenesis mutations are made via epPCR followed by
- RNDM is usable in high throughput assays when screening is capable of detecting activity above background. RNDM has been used as a front end to DOGS in generating diversity. The technique imposes a requirement for activity prior to shuffling or other subsequent steps; neutral drift libraries are indicated to result in higher/quicker improvements in activity from smaller libraries. Though published using epPCR, this could be applied to other large-scale mutagenesis methods.
- Sequence Saturation Mutagenesis is a random mutagenesis method that: 1) generates a pool of random length fragments using random incorporation of a phosphothioate nucleotide and cleavage; this pool is used as a template to 2) extend in the presence of "universal" bases such as inosine; 3) replication of an inosine-containing complement gives random base incorporation and, consequently, mutagenesis (Wong et al, Biotechnol. J. 3:74-82 (2008); Wong et al, Nucleic Acids Res. 32:e26 (2004); and Wong et al, Anal. Biochem. 341 : 187-189 (2005)).
- overlapping oligonucleotides are designed to encode "all genetic diversity in targets" and allow a very high diversity for the shuffled progeny (Ness et al., Nat. Biotechnol. 20: 1251-1255 (2002)).
- this technique one can design the fragments to be shuffled. This aids in increasing the resulting diversity of the progeny.
- sequence/codon biases to make more distantly related sequences recombine at rates approaching those observed with more closely related sequences. Additionally, the technique does not require physically possessing the template genes.
- Nucleotide Exchange and Excision Technology NexT exploits a combination of dUTP incorporation followed by treatment with uracil DNA glycosylase and then piperidine to perform endpoint DNA fragmentation (Muller et al., Nucleic Acids Res. 33:el 17 (2005)).
- the gene is reassembled using internal PCR primer extension with proofreading polymerase.
- the sizes for shuffling are directly controllable using varying dUPT::dTTP ratios. This is an end point reaction using simple methods for uracil incorporation and cleavage.
- Other nucleotide analogs, such as 8-oxo-guanine can be used with this method. Additionally, the technique works well with very short fragments (86 bp) and has a low error rate. The chemical cleavage of DNA used in this technique results in very few unshuffled clones.
- SHIPREC Sequence Homology-Independent Protein Recombination
- GSSMTM Gene Site Saturation Mutagenesis
- the starting materials are a supercoiled dsDNA plasmid containing an insert and two primers which are degenerate at the desired site of mutations (Kretz et al., Methods Enzymol. 388:3-11 (2004)).
- Primers carrying the mutation of interest, anneal to the same sequence on opposite strands of DNA.
- the mutation is typically in the middle of the primer and flanked on each side by approximately 20 nucleotides of correct sequence.
- Dpnl is used to digest dam-methylated DNA to eliminate the wild-type template.
- This technique explores all possible amino acid substitutions at a given locus (that is, one codon).
- the technique facilitates the generation of all possible replacements at a single-site with no nonsense codons and results in equal to near-equal representation of most possible alleles.
- This technique does not require prior knowledge of the structure, mechanism, or domains of the target enzyme. If followed by shuffling or Gene Reassembly, this technology creates a diverse library of recombinants containing all possible combinations of single-site up-mutations. The usefulness of this technology combination has been demonstrated for the successful evolution of over 50 different enzymes, and also for more than one property in a given enzyme.
- Combinatorial Cassette Mutagenesis involves the use of short oligonucleotide cassettes to replace limited regions with a large number of possible amino acid sequence alterations (Reidhaar-Olson et al. Methods Enzymol. 208:564-586 (1991); and Reidhaar-Olson et al.
- CMCM Combinatorial Multiple Cassette Mutagenesis
- this method can test virtually all possible alterations over a target region. If used along with methods to create random mutations and shuffled genes, it provides an excellent means of generating diverse, shuffled proteins. This approach was successful in increasing, by 51 -fold, the enantioselectivity of an enzyme.
- conditional ts mutator plasmids allow increases of 20 to 4000- X in random and natural mutation frequency during selection and block accumulation of deleterious mutations when selection is not required (Selifonova et al., Appl. Environ. Microbiol. 67:3645-3649 (2001)).
- This technology is based on a plasmid-derived mutD5 gene, which encodes a mutant subunit of DNA polymerase III. This subunit binds to endogenous DNA polymerase III and compromises the proofreading ability of polymerase III in any strain that harbors the plasmid. A broad- spectrum of base substitutions and frameshift mutations occur.
- the mutator plasmid should be removed once the desired phenotype is achieved; this is accomplished through a temperature sensitive (ts) origin of replication, which allows for plasmid curing at 41oC.
- ts temperature sensitive origin of replication
- mutator strains have been explored for quite some time (see Low et al, J. Mol. Biol. 260:359-3680 (1996)). In this technique, very high spontaneous mutation rates are observed. The conditional property minimizes non-desired background mutations. This technology could be combined with adaptive evolution to enhance mutagenesis rates and more rapidly achieve desired phenotypes.
- LTM Look-Through Mutagenesis
- Gene Reassembly is a DNA shuffling method that can be applied to multiple genes at one time or to create a large library of chimeras (multiple mutations) of a single gene (Tunable
- TGRTM GeneReassemblyTM
- Verenium Corporation assemblyTM Technology supplied by Verenium Corporation.
- this technology is used in combination with ultra-high-throughput screening to query the represented sequence space for desired improvements.
- This technique allows multiple gene recombination independent of homology. The exact number and position of cross-over events can be predetermined using fragments designed via bioinformatic analysis. This technology leads to a very high level of diversity with virtually no parental gene reformation and a low level of inactive genes.
- GSSMTM a large range of mutations can be tested for improved activity.
- the method allows "blending" and "fine tuning" of DNA shuffling, for example, codon usage can be optimized.
- PDA Silico Protein Design Automation
- This technology uses in silico structure-based entropy predictions in order to search for structural tolerance toward protein amino acid variations.
- Statistical mechanics is applied to calculate coupling interactions at each position. Structural tolerance toward amino acid substitution is a measure of coupling.
- this technology is designed to yield desired modifications of protein properties while maintaining the integrity of structural characteristics.
- the method computationally assesses and allows filtering of a very large number of possible sequence variants (1050).
- the choice of sequence variants to test is related to predictions based on the most favorable thermodynamics. Ostensibly only stability or properties that are linked to stability can be effectively addressed with this technology.
- the method has been successfully used in some therapeutic proteins, especially in engineering immunoglobulins. In silico predictions avoid testing extraordinarily large numbers of potential variants. Predictions based on existing three-dimensional structures are more likely to succeed than predictions based on hypothetical structures. This technology can readily predict and allow targeted screening of multiple simultaneous mutations, something not possible with purely experimental technologies due to exponential increases in numbers.
- ISM Iterative Saturation Mutagenesis involves: 1) using knowledge of structure/function to choose a likely site for enzyme improvement; 2) performing saturation mutagenesis at chosen site using a mutagenesis method such as Stratagene QuikChange (Stratagene; San Diego CA); 3) screening/selecting for desired properties; and 4) using improved clone(s), start over at another site and continue repeating until a desired activity is achieved (Reetz et al., Nat. Protoc. 2:891- 903 (2007); and Reetz et al, Angew. Chem. Int. Ed Engl. 45:7745-7751 (2006)). This is a proven methodology, which assures all possible replacements at a given position are made for screening/selection.
- any of the aforementioned methods for mutagenesis can be used alone or in any combination. Additionally, any one or combination of the directed evolution methods can be used in conjunction with adaptive evolution techniques, as described herein.
- novel processes for the direct production of butadiene or crotyl alcohol using engineered non-natural microorganisms that possess the enzymes necessary for conversion of common metabolites into the four carbon diene, 1,3-butadiene or crotyl alcohol One novel route to direct production of butadiene entails reduction of the known butanol pathway metabolite crotonyl-CoA to crotyl alcohol via reduction with aldehyde and alcohol
- FIG. 3 Another route ( Figure 3) is a variant of the well-characterized DXP pathway for isoprenoid biosynthesis.
- the substrate lacks a 2-methyl group and provides butadiene rather than isoprene via a butadiene synthase.
- Such a butadiene synthase can be derived from a isoprene synthase using methods, such as directed evolution, as described herein.
- Figure 4 shows a pathway to butadiene involving the substrate 3-hydroxyglutaryl-CoA, which serves as a surrogate for the natural mevalonate pathway substrate 3-hydroxy-3-methyl-glutaryl-CoA (shown in Figure 1). Enzyme candidates for steps A-P of Figure 2, steps A-K of Figure 3 and steps A-0 of Figure 4 are provided below.
- Acetoacetyl-CoA thiolase converts two molecules of acetyl-CoA into one molecule each of acetoacetyl-CoA and CoA.
- Exemplary acetoacetyl-CoA thiolase enzymes include the gene products of atoB from E. coli (Martin et al, Nat.Biotechnol 21 :796-802 (2003)), thlA and MB from C. acetobutylicum (Hanai et al, Appl Environ Microbiol 73:7814-7818 (2007); Winzer et al, J. Mol.Microbiol Biotechnol 2:531-541 (2000)), and ERG10 from S. cerevisiae (Hiser et al, J.Biol.Chem. 269:31383-31389 (1994)).
- Acetoacetyl-CoA reductase catalyzing the reduction of acetoacetyl-CoA to 3-hydroxybutyryl- CoA participates in the acetyl-CoA fermentation pathway to butyrate in several species of Clostridia and has been studied in detail (Jones et al, Microbiol Rev. 50:484-524 (1986)).
- the enzyme from Clostridium acetobutylicum, encoded by hbd has been cloned and functionally expressed in E. coli (Youngleson et al, J Bacteriol. 171 :6800-6807 (1989)). Additionally, subunits of two fatty acid oxidation complexes in E.
- coli encoded by fadB and fadJ, function as 3-hydroxyacyl-CoA dehydrogenases (Binstock et al, Methods Enzymol. 71 Pt C:403-411 (1981)).
- Yet other gene candidates demonstrated to reduce acetoacetyl-CoA to 3- hydroxybutyryl-CoA are phbB from Zoogloea ramigera (Ploux et al, Eur.J Biochem. 174: 177- 182 (1988)) and phaB from Rhodobacter sphaeroides (Alber et al, Mol.Microbiol 61 :297-309 (2006)).
- the former gene candidate is NADPH-dependent, its nucleotide sequence has been determined (Peoples et al, Mol.Microbiol 3:349-357 (1989)) and the gene has been expressed in E. coli. Substrate specificity studies on the gene led to the conclusion that it could accept 3- oxopropionyl-CoA as a substrate besides acetoacetyl-CoA (Ploux et al, supra, (1988)).
- Hbdl C-terminal domain
- Hbd2 N-terminal domain
- HSD17B10 Bos taurus
- 3-Hydroxybutyryl-CoA dehydratase (EC 4.2.1.55), also called crotonase, is an enoyl-CoA hydratase that reversibly dehydrates 3-hydroxybutyryl-CoA to form crotonyl-CoA.
- Crotonase enzymes are required for n-butanol formation in some organisms, particularly Clostridial species, and also comprise one step of the 3-hydroxypropionate/4-hydroxybutyrate cycle in thermoacidophilic Archaea of the genera Sulfolobus, Acidianus, and Metallosphaera. Exemplary genes encoding crotonase enzymes can be found in C.
- Escherichia coli genes have been shown to demonstrate enoyl-CoA hydratase functionality including maoC (Park et al, J Bacteriol. 185:5391-5397 (2003)), paaF (Ismail et al, Eur. J Biochem. 270:3047-3054 (2003); Park et al, Appl.Biochem.Biotechnol 113-116:335-346 (2004); Park et al, Biotechnol Bioeng 86:681-686 (2004)) and paaG (Ismail et al, supra, (2003); Park and Lee, supra, (2004); Park and Yup, supra, (2004)). These proteins are identified below.
- acyl-CoA dehydrogenases are capable of reducing an acyl-CoA to its corresponding aldehyde. Thus they can naturally reduce crotonyl-CoA to crotonaldehyde or can be engineered to do so.
- Exemplary genes that encode such enzymes include the Acinetobacter calcoaceticus acrl encoding a fatty acyl-CoA reductase (Reiser et al, J. Bacteriol. 179:2969-2975 (1997)), the Acinetobacter sp. M-l fatty acyl-CoA reductase (Ishige et al, Appl. Environ. Microbiol.
- acylating acetaldehyde dehydrogenase in Pseudomonas sp, encoded by bphG is yet another capable enzyme as it has been demonstrated to oxidize and acylate acetaldehyde, propionaldehyde, butyraldehyde, isobutyraldehyde and formaldehyde (Powlowski et al, J. Bacteriol. 175:377-385 (1993)).
- malonyl-CoA reductase which transforms malonyl-CoA to malonic semialdehyde.
- Malonyl-CoA reductase is a key enzyme in autotrophic carbon fixation via the 3-hydroxypropionate cycle in thermoacidophilic archael bacteria (Berg et al., Science 318: 1782-1786 (2007b); Thauer, 318: 1732-1733 (2007)).
- the enzyme utilizes NADPH as a cofactor and has been characterized in Metallosphaera and Sulfolobus spp (Alber et al, J. Bacteriol. 188:8551-8559 (2006); Hugler et al, J. Bacteriol. 184:2404-2410 (2002)).
- the enzyme is encoded by Msed_0709 in
- malonyl-CoA reductase enzyme candidates have high sequence similarity to aspartate-semialdehyde dehydrogenase, an enzyme catalyzing the reduction and concurrent dephosphorylation of aspartyl-4-phosphate to aspartate semialdehyde. Additional gene candidates can be found by sequence homology to proteins in other organisms including Sulfolobus solfataricus and Sulfolobus acidocaldarius . Yet another candidate for CoA-acylating aldehyde dehydrogenase is the aid gene from Clostridium beijerinckii (Toth, Appl. Environ. Microbiol. 65:4973-4980 (1999).
- This enzyme has been reported to reduce acetyl-CoA and butyryl-CoA to their corresponding aldehydes.
- This gene is very similar to eutE that encodes acetaldehyde dehydrogenase of Salmonella typhimurium and E. coli (Toth, Appl. Environ.
- Enzymes exhibiting crotonaldehyde reductase (alcohol forming) activity are capable of forming crotyl alcohol from crotonaldehyde.
- the following enzymes can naturally possess this activity or can be engineered to exhibit this activity.
- Exemplary genes encoding enzymes that catalyze the conversion of an aldehyde to alcohol include air A encoding a medium-chain alcohol dehydrogenase for C2-C14 (Tani et al., Appl. Environ.Microbiol.
- ADH1 from Zymomonas mobilis has been demonstrated to have activity on a number of aldehydes including formaldehyde, acetaldehyde, propionaldehyde, butyraldehyde, and acrolein (Kinoshita, Appl. Microbiol. Biotechnol. 22:249-254 (1985)).
- Cbei_2181 from Clostridium beijerinckii NCIMB 8052 encodes yet another useful alcohol dehydrogenase capable of converting crotonaldehyde to crotyl alcohol.
- Protein ( ,cn Bank ID GI Number Organism
- Enzymes exhibiting 4-hydroxybutyrate dehydrogenase activity also fall into this category. Such enzymes have been characterized in Ralstonia eutropha (Bravo et al, J. Forensic Sci. 49:379-387 (2004)), Clostridium kluyveri (Wolff et al, Protein Expr. Purif. 6:206-212 (1995)) and Arabidopsis thaliana (Breit Regen et al, J.Biol.Chem. 278:41552-41556 (2003)).
- Crotyl alcohol kinase enzymes catalyze the transfer of a phosphate group to the hydroxyl group of crotyl alcohol.
- the enzymes described below naturally possess such activity or can be engineered to exhibit this activity.
- Kinases that catalyze transfer of a phosphate group to an alcohol group are members of the EC 2.7.1 enzyme class.
- the table below lists several useful kinase enzymes in the EC 2.7.1 enzyme class.
- mevalonate kinase (EC 2.7.1.36) that phosphorylates the terminal hydroxyl group of the methyl analog, mevalonate, of 3,5-dihydroxypentanote.
- Some gene candidates for this step are erg 12 from S. cerevisiae, mvk from Methanocaldococcus jannaschi, MVK from Homo sapeins, and mvk from Arabidopsis thaliana col.
- Glycerol kinase also phosphorylates the terminal hydroxyl group in glycerol to form glycerol-3- phosphate. This reaction occurs in several species, including Escherichia coli, Saccharomyces cerevisiae, and Thermotoga maritima.
- the E. coli glycerol kinase has been shown to accept alternate substrates such as dihydroxyacetone and glyceraldehyde (Hayashi et al, J Biol.Chem. 242: 1030-1035 (1967)).
- T maritime has two glycerol kinases (Nelson et al, Nature 399:323-329 (1999)). Glycerol kinases have been shown to have a wide range of substrate specificity. Crans and Whiteside studied glycerol kinases from four different organisms ⁇ Escherichia coli, S.
- Homoserine kinase is another possible candidate that can lead to the phosphorylation of 3,5 - dihydroxypentanoate.
- This enzyme is also present in a number of organisms including E. coli, Streptomyces sp, and S. cerevisiae.
- Homoserine kinase from E. coli has been shown to have activity on numerous substrates, including, L-2-amino,l ,4- butanediol, aspartate semialdehyde, and 2-amino-5-hydroxyvalerate (Huo et al, Biochemistry 35 : 16180-16185 (1996); Huo et al, Arch.Biochem.Biophys. 330:373-379 (1996)).
- This enzyme can act on substrates where the carboxyl group at the alpha position has been replaced by an ester or by a hydroxymethyl group.
- the gene candidates are:
- 2-Butenyl-4-phosphate kinase enzymes catalyze the transfer of a phosphate group to the phosphate group of 2-butenyl-4-phosphate.
- the enzymes described below naturally possess such activity or can be engineered to exhibit this activity.
- Kinases that catalyze transfer of a phosphate group to another phosphate group are members of the EC 2.7.4 enzyme class.
- the table below lists several useful kinase enzymes in the EC 2.7.4 enzyme class.
- Phosphomevalonate kinase enzymes are of particular interest.
- Phosphomevalonate kinase (EC 2.7.4.2) catalyzes the analogous transformation to 2-butenyl-4-phosphate kinase.
- This enzyme is encoded by erg8 in Saccharomyces cerevisiae (Tsay et al, Mol.Cell Biol. 11 :620-631 (1991)) and mvaK2 in Streptococcus pneumoniae, Staphylococcus aureus and Enterococcus faecalis (Doun et al, Protein Sci. 14: 1134-1139 (2005); Wilding et al, J ' Bacterial. 182:4319-4327 (2000)).
- Streptococcus pneumoniae and Enterococcus faecalis enzymes were cloned and characterized in E. coli (Pilloff et al., J Biol.Chem. 278:4510-4515 (2003); Doun et al., Protein Sci. 14: 1134-1139 (2005)).
- Butadiene synthase catalyzes the conversion of 2-butenyl-4-diphosphate to 1,3-butadiene.
- the enzymes described below naturally possess such activity or can be engineered to exhibit this activity.
- Isoprene synthase naturally catalyzes the conversion of dimethylallyl diphosphate to isoprene, but can also catalyze the synthesis of 1,3-butadiene from 2-butenyl-4-diphosphate.
- Isoprene synthases can be found in several organisms including Populus alba (Sasaki et al, FEBS Letters, 2005, 579 (11), 2514-2518), Pueraria montana (Lindberg et al, Metabolic Eng, 2010, 12 (1), 70-79; Sharkey et al, Plant Physiol, 2005, 137 (2), 700-712), and Populus tremula x Populus alba (Miller et al, Planta, 2001, 213 (3), 483-487).
- isoprene synthase enzymes are described in (Chotani et al, WO/2010/031079, Systems Using Cell Culture for Production of Isoprene; Cervin et al, US Patent Application 20100003716, Isoprene Synthase Variants for Improved Microbial Production of Isoprene).
- Crotonyl-CoA hydrolase synthetase, transferase ( Figure 2, Step I)
- Crotonyl-CoA hydrolase catalyzes the conversion of crotonyl-CoA to crotonate.
- the enzymes described below naturally possess such activity or can be engineered to exhibit this activity.
- 3- Hydroxyisobutyryl-CoA hydrolase efficiently catalyzes the conversion of 3-hydroxyisobutyryl- CoA to 3-hydroxyisobutyrate during valine degradation (Shimomura et al, J Biol Chem.
- mitochondrion of the pea leaf also has a broad substrate specificity, with demonstrated activity on acetyl-CoA, propionyl-CoA, butyryl-CoA, palmitoyl-CoA, oleoyl-CoA, succinyl-CoA, and crotonyl-CoA (Zeiher et al, Plant. Physiol. 94:20-27 (1990)).
- the acetyl-CoA hydrolase, ACH1 represents another candidate hydrolase (Buu et al, J. Biol. Chem. 278: 17203-17209 (2003)) .
- Another candidate hydrolase is the human dicarboxylic acid thioesterase, acotS, which exhibits activity on glutaryl-CoA, adipyl-CoA, suberyl-CoA, sebacyl-CoA, and dodecanedioyl-CoA (Westin et al, J Biol. Chem. 280:38125-38132 (2005)) and the closest E. coli homolog, tesB, which can also hydrolyze a broad range of CoA thioesters (Naggert et al., J Biol. Chem.
- E. coli thioester hydrolases include the gene products of tesA (Bonner et al, Chem. 247:3123-3133 (1972)), ybgC (Kuznetsova et al, FEMS Microbiol Rev 29:263-279 (2005); and (Zhuang et al, FEBS Lett. 516: 161-163 (2002)), paal (Song et al, J Biol. Chem. 281 : 11028-11038 (2006)), and ybdB (Leduc et al, J Bacteriol. 189:7112-7126 (2007)). These proteins are identified below.
- Crotonyl-CoA synthetase catalyzes the conversion of crotonyl-CoA to crotonate.
- the enzymes described below naturally possess such activity or can be engineered to exhibit this activity.
- One candidate enzyme, ADP-forming acetyl-CoA synthetase (ACD, EC 6.2.1.13) couples the conversion of acyl-CoA esters to their corresponding acids with the concurrent synthesis of ATP.
- ACD ADP-forming acetyl-CoA synthetase
- Haloarcula marismortui annotated as a succinyl-CoA synthetase accepts propionate, butyrate, and branched-chain acids (isovalerate and isobutyrate) as substrates, and was shown to operate in the forward and reverse directions (Brasen et al, Arch Microbiol 182:277-287 (2004)).
- the ACD encoded by PAE3250 from hyperthermophilic crenarchaeon Pyrobaculum aerophilum showed the broadest substrate range of all characterized ACDs, reacting with acetyl-CoA, isobutyryl-CoA (preferred substrate) and phenylacetyl-CoA (Brasen et al, supra).
- the enzymes from A. fulgidus, H. marismortui and P. aerophilum have all been cloned, functionally expressed, and characterized in E. coli
- Another candidate CoA synthetase is succinyl-CoA synthetase.
- the sucCD genes of E. coli form a succinyl-CoA synthetase complex which naturally catalyzes the formation of succinyl-CoA from succinate with the concaminant consumption of one ATP, a reaction which is reversible in vivo (Buck et al, Biochem. 24:6245-6252 (1985)).
- Additional exemplary CoA-ligases include the rat dicarboxylate-CoA ligase for which the sequence is yet uncharacterized (Vamecq et al, BiochemicalJournal 230:683-693 (1985)), either of the two characterized phenylacetate-CoA ligases from P. chrysogenum (Lamas-Maceiras et al, Biochem. J. 395: 147-155 (2005); Wang et al, Biochem Biophy Res Commun 360(2):453-458 (2007)), the phenylacetate-CoA ligase from Pseudomonas putida (Martinez-Bianco et al., J. Biol. Chem.
- Crotonyl-CoA transferase catalyzes the conversion of crotonyl-CoA to crotonate.
- the enzymes described below naturally possess such activity or can be engineered to exhibit this activity.
- Many transferases have broad specificity and thus can utilize CoA acceptors as diverse as acetate, succinate, propionate, butyrate, 2-methylacetoacetate, 3-ketohexanoate, 3- ketopentanoate, valerate, crotonate, 3-mercaptopropionate, propionate, vinylacetate, butyrate, among others.
- an enzyme from Roseburia sp an enzyme from Roseburia sp.
- A2-183 was shown to have butyryl- CoA:acetate:CoA transferase and propionyl-CoA:acetate:CoA transferase activity (Charrier et al, Microbiology 152, 179-185 (2006)). Close homologs can be found in, for example, Roseburia intestinalis LI -82, Roseburia inulinivorans DSM 16841, Eubacterium rectale ATCC 33656. Another enzyme with propionyl-CoA transferase activity can be found in Clostridium propionicum (Selmer et al, Eur J Biochem 269, 372-380 (2002)).
- This enzyme can use acetate, (R)-lactate, (S)-lactate, acrylate, and butyrate as the CoA acceptor (Selmer et al., Eur J Biochem 269, 372-380 (2002); Schweiger and Buckel, FEBS Letters, 171(1) 79-84 (1984)). Close homologs can be found in, for example, Clostridium novyi NT, Clostridium beijerinckii NCIMB 8052, and Clostridium botulinum C str. Eklund. YgfH encodes a propionyl CoA:succinate CoA transferase in E. coli (Haller et al., Biochemistry, 39(16) 4622-4629). Close homologs can be found in, for example, Citrobacter youngae ATCC 29220, Salmonella enterica subsp. arizonae serovar, and Yersinia intermedia ATCC 29909. These proteins are identified below
- An additional candidate enzyme is the two-unit enzyme encoded by peal and pcaJ in
- a CoA transferase that can utilize acetate as the CoA acceptor is acetoacetyl-CoA transferase, encoded by the E. coli atoA (alpha subunit) and atoD (beta subunit) genes (Vanderwinkel et al, Biochem.Biophys.Res Commun. 33:902-908 (1968); Korolev et al., Acta Crystallogr.D Biol Crystallogr. 58:2116-2121 (2002)).
- This enzyme has also been shown to transfer the CoA moiety to acetate from a variety of branched and linear acyl-CoA substrates, including isobutyrate (Matthies et al, Appl Environ Microbiol 58: 1435-1439 (1992)), valerate
- the above enzymes can also exhibit the desired activities on crotonyl-CoA.
- Additional exemplary transferase candidates are catalyzed by the gene products of catl, cat2, and cat3 of Clostridium kluyveri which have been shown to exhibit succinyl-CoA, 4-hydroxybutyryl-CoA, and butyryl-CoA transferase activity, respectively (Seedorf et al, supra; Sohling et al, Eur.J Biochem. 212: 121-127 (1993); Sohling et al, J Bacteriol. 178:871-880 (1996)).
- Acidaminococcus fermentans reacts with diacid glutaconyl-CoA and 3-butenoyl-CoA (Mack et al, FEBS Lett. 405:209-212 (1997)).
- the genes encoding this enzyme are gctA and gctB.
- This enzyme has reduced but detectable activity with other CoA derivatives including glutaryl-CoA, 2-hydroxyglutaryl-CoA, adipyl-CoA and acrylyl-CoA (Buckel et al., Eur. J. Biochem. 118:315- 321 (1981)).
- the enzyme has been cloned and expressed in E. coli (Mack et al., Eur. J. Biochem. 226:41-51 (1994)). These proteins are identified below. Protein ( ,cn Bank ID GI Number Organism
- Crotonate reductase enzymes are capable of catalyzing the conversion of crotonate to crotonaldehyde.
- the enzymes described below naturally possess such activity or can be engineered to exhibit this activity.
- Carboxylic acid reductase catalyzes the magnesium, ATP and NADPH-dependent reduction of carboxylic acids to their corresponding aldehydes
- Additional car and npt genes can be identified based on sequence homology.
- alpha-aminoadipate reductase (AAR, EC 1.2.1.31), participates in lysine biosynthesis pathways in some fungal species. This enzyme naturally reduces alpha-aminoadipate to alpha-aminoadipate semialdehyde. The carboxyl group is first activated through the ATP-dependent formation of an adenylate that is then reduced by
- NAD(P)H to yield the aldehyde and AMP.
- this enzyme utilizes magnesium and requires activation by a PPTase.
- Enzyme candidates for AAR and its corresponding PPTase are found in Saccharomyces cerevisiae (Morris et al., Gene 98:141-145 (1991)), Candida albicans (Guo et al., Mol. Genet. Genomics 269:271-279 (2003)), and Schizosaccharomyces pombe (Ford et al., Curr. Genet. 28: 131-137 (1995)).
- the AAR from S. pombe exhibited significant activity when expressed in E.
- Penicillium chrysogenum accepts S-carboxymethyl-L-cysteine as an alternate substrate, but did not react with adipate, L-glutamate or diaminopimelate (Hijarrubia et al., J. Biol. Chem. 278:8250-8256 (2003)).
- the gene encoding the P. chrysogenum PPTase has not been identified to date.
- Crotonaldehyde reductase (alcohol forming) enzymes catalyze the 2 reduction steps required to form crotyl alcohol from crotonyl-CoA.
- Exemplary 2-step oxidoreductases that convert an acyl- CoA to an alcohol are provided below.
- Such enzymes can naturally convert crotonyl-CoA to crotyl alcohol or can be engineered to do so.
- These enzymes include those that transform substrates such as acetyl-CoA to ethanol (e.g., adhE from E. coli (Kessler et al, FEBS.Lett. 281 :59-63 (1991))) and butyryl-CoA to butanol (e.g.
- adhE2 from C. acetobutylicum (Fontaine et al, J.Bacteriol. 184:821-830 (2002))).
- the adhE2 enzyme from C. acetobutylicum was specifically shown in ref. (Burk et al, supra, (2008)) to produce BDO from 4-hydroxybutyryl- CoA.
- the enzyme encoded by adhE in addition to reducing acetyl-CoA to ethanol, the enzyme encoded by adhE in
- Leuconostoc mesenteroides has been shown to oxide the branched chain compound
- Another exemplary enzyme can convert malonyl-CoA to 3 -HP.
- An NADPH-dependent enzyme with this activity has characterized in Chloroflexus aurantiacus where it participates in the 3- hydroxypropionate cycle (Hugler et al, supra, (2002); Strauss et al, 215:633-643 (1993)).
- This enzyme with a mass of 300 kDa, is highly substrate-specific and shows little sequence similarity to other known oxidoreductases (Hugler et al, supra, (2002)). No enzymes in other organisms have been shown to catalyze this specific reaction; however there is bioinformatic evidence that other organisms can have similar pathways (Klatt et al., Environ Microbiol. 9:2067-2078 (2007)).
- Enzyme candidates in other organisms including Roseiflexus castenholzii, Erythrobacter sp. NAP1 and marine gamma proteobacterium HTCC2080 can be inferred by sequence
- Glutaconyl-CoA decarboxylase enzymes characterized in glutamate-fermenting anaerobic bacteria, are sodium-ion translocating decarboxylases that utilize biotin as a cofactor and are composed of four subunits (alpha, beta, gamma, and delta) (Boiangiu et al, J Mol. Microbiol Biotechnol 10: 105-119 (2005); Buckel, Biochim Biophys Acta. 1505: 15-27 (2001)). Such enzymes have been characterized in Fusobacterium nucleatum (Beatrix et al., Arch Microbiol.
- Glutaryl-CoA dehydrogenase (GCD, EC 1.3.99.7 and EC 4.1.1.70) is a bifunctional enzyme that catalyzes the oxidative decarboxylation of glutaryl-CoA to crotonyl-CoA ( Figure 3, step 3).
- Bifunctional GCD enzymes are homotetramers that utilize electron transfer flavoprotein as an electron acceptor (Hartel et al., Arch Microbiol. 159: 174-181 (1993)). Such enzymes were first characterized in cell extracts of Pseudomonas strains KB740 and K172 during growth on aromatic compounds (Hartel et al, supra, (1993)), but the associated genes in these organisms is unknown.
- gcdH glutaryl-CoA dehydrogenase
- gcdR cognate transcriptional regulator
- a GCD in Syntrophus aciditrophicus operates in the C0 2 -assimilating direction during growth on crotonate (Mouttaki et al., Appl Environ Microbiol. 73:930-938 (2007))).
- Two GCD genes in S. aciditrophicus were identified by protein sequence homology to the Azoarcus GcdH: syn_00480 (31%) and syn_01146 (31%). No significant homology was found to the Azoarcus GcdR regulatory protein.
- 3 ⁇ ammob ' utyryI ⁇ CoA is an intermediate in lysine fermentation, It also can be formed from acetoacetyl-CoA via a transaminase or an animating dehydrogenase.
- 3-aminobutyryl-CoA deaminase (or 3-ammobutyryi ⁇ CoA ammonia lyase) catalyzes the deammation of 3 ⁇
- Crotyl alcohol diphosphokinase enzymes catalyze the transfer of a diphosphate group to the hydroxyl group of crotyl alcohol.
- the enzymes described below naturally possess such activity or can be engineered to exhibit this activity.
- Kinases that catalyze transfer of a diphosphate group are members of the EC 2.7.6 enzyme class.
- the table below lists several useful kinase enzymes in the EC 2.7.6 enzyme class.
- ribose-phosphate diphosphokinase enzymes which have been identified in Escherichia coli (Hove-Jenson et al, J Biol Chem, 1986, 261(15);6765-71) and Mycoplasma pneumoniae M129 (McElwain et al, International Journal of Systematic Bacteriology, 1988, 38:417-423) as well as thiamine diphosphokinase enzymes.
- diphosphokinase enzymes are found in Arabidopsis thaliana (Ajjawi, Plant Mol Biol, 2007, 65(l-2);151-62).
- Step A of the pathway erythrose-4-phosphate is converted to erythritol-4-phosphate by the erythrose-4-phosphate reductase or erythritol-4-phosphate dehydrogenase.
- the reduction of erythrose-4-phosphate was observed in Leuconostoc oenos during the production of erythritol (Veiga-da-Cunha et al, J Bacteriol. 175:3941-3948 (1993)).
- NADPH was identified as the cofactor (Veiga-da-Cunha et al, supra, (1993)).
- gene for erythrose-4-phosphate was not identified.
- erythrose-4-phosphate reductase gene from Leuconostoc oenos and apply to this step.
- enzymes catalyzing similar reactions can be utilized for this step.
- An example of these enzymes is l-deoxy-D-xylulose-5 -phosphate reductoisomerase (EC 1.1.1.267) catalyzing the conversion of 1-deoxy-D-xylylose 5-phosphate to 2-C-methyl-D-erythritol-4-phosphate, which has one additional methyl group comparing to Step A.
- the dxr or ispC genes encode the l-deoxy-D-xylulose-5 -phosphate reductoisomerase have been well studied: the Dxr proteins from Escherichia coli and Mycobacterium tuberculosis were purified and their crystal structures were determined (Yajima et al, Acta
- Escherichia coli catalyzes the conversion between glyceraldehyde 3-phosphate and glycerol-3- phosphate (Desai et al, Biochemistry 47:7983-7985 (2008)) can also be applied to this step.
- the following genes can be used for Step A conversion:
- Step B of the pathway erythritol-4-phosphate is converted to 4-(cytidine 5'-diphospho)- erythritol by the erythritol-4-phospate cytidylyltransferase or 4-(cytidine 5'-diphospho)-erythritol synthase.
- the exact enzyme for this step has not been identified. However, enzymes catalyzing similar reactions can be applied to this step.
- the 2-C-methyl-D-erythritol 4-phospate cytidylyltransferase is in the
- methylerythritol phosphate pathway for the isoprenoid biosynthesis catalyzes the conversion between 2-C-methyl-D-erythritol 4-phospate and 4-(cytidine 5'-diphospho)-2-C-methyl-D- erythritol, with an extra methyl group comparing to Step B conversion.
- the 2-C-methyl-D- erythritol 4-phosphate cytidylyltransferase is encoded by ispD gene and the crystal structure of Escherichia coli IspD was determined (Kemp et al, Acta Cry stallogr. D.Biol. Cry stallogr.
- the ispD gene from Mycobacterium tuberculosis H37Rv was cloned and expressed in Escherichia coli, and the recombinant proteins were purified with N-terminal His-tag (Shi et al, J Biochem.Mol.Biol. 40:911-920 (2007)). Additionally, the Streptomyces coelicolor ispD gene was cloned and expressed in E. coli, and the recombinant proteins were characterized physically and kinetically (Cane et al., Bioorg.Med.Chem. 9: 1467-1477 (2001)). The following genes can be used for Step B conversion:
- Step C of the pathway 4-(cytidine 5'-diphospho)-erythritol is converted to 2-phospho-4- (cytidine 5'-diphospho)-erythritol by the 4-(cytidine 5'-diphospho)-erythritol kinase.
- the exact enzyme for this step has not been identified. However, enzymes catalyzing similar reactions can be applied to this step.
- An example is the 4-diphosphocytidyl-2-C-methylerythritol kinase (EC 2.7.1.148).
- the 4-diphosphocytidyl-2-C-methylerythritol kinase is also in the methylerythritol phosphate pathway for the isoprenoid biosynthesis and catalyzes the conversion between 4- (cytidine 5'-diphospho)-2-C-methyl-D-erythritol and 2-phospho-4-(cytidine 5'-diphospho)-2-C- methyl-D-erythritol, with an extra methyl group comparing to Step C conversion.
- the 4- diphosphocytidyl-2-C-methylerythritol kinase is encoded by ispE gene and the crystal structures of Escherichia coli, Thermus thermophilus HB8, and Aquifex aeolicus IspE were determined (Sgraja et al, FEBS J 275 :2779-2794 (2008); Miallau et al, Proc.Natl.Acad.Sci. U.S.A 100:9173- 9178 (2003); Wada et al, J Biol.Chem. 278:30022-30027 (2003)).
- the ispE genes from above organism were cloned and expressed, and the recombinant proteins were purified for
- Step D of the pathway 2-phospho-4-(cytidine 5'-diphospho)-erythritol is converted to erythritol-2,4-cyclodiphosphate by the Erythritol 2,4-cyclodiphosphate synthase.
- the exact enzyme for this step has not been identified. However, enzymes catalyzing similar reactions can be applied to this step.
- An example is the 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12).
- the 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase is also in the methylerythritol phosphate pathway for the isoprenoid biosynthesis and catalyzes the conversion between 2-phospho-4-(cytidine 5'diphospho)-2-C-methyl-D-erythritol and 2-C-methyl-D- erythritol-2,4-cyclodiphosphate, with an extra methyl group comparing to step D conversion.
- the 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase is encoded by ispF gene and the crystal structures of Escherichia coli, Thermus thermophilus, Haemophilus influenzae, and Campylobacter jejuni IspF were determined (Richard et al, J Biol.Chem. 277:8667-8672 (2002); Steinbacher et al, JMol.Biol. 316:79-88 (2002); Lehmann et al, Proteins 49: 135-138 (2002); Kishida et al, Acta Crystallogr.D.Biol.Crystallogr. 59:23-31 (2003); Gabrielsen et al, J
- Step E of Figure 3 entails conversion of erythritol-2,4-cyclodiphosphate to l-hydroxy-2-butenyl 4-diphosphate by l-hydroxy-2-butenyl 4-diphosphate synthase.
- An enzyme with this activity has not been characterized to date.
- This transformation is analogous to the reduction of 2-C-methyl- D-erythritol-2,4-cyclodiphosphate to l-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate by (E)-4- hydroxy-3-methylbut-2-enyl-diphosphate synthase (EC 1.17.7.1).
- This enzyme is an iron- sulfur protein that participates in the non-mevalonate pathway for isoprenoid biosynthesis found in bacteria and plants.
- thermophilic cyanobacterium An analogous enzyme from the thermophilic cyanobacterium
- Butenyl 4-diphosphate isomerase catalyzes the reversible interconversion of 2-butenyl-4- diphosphate and butenyl-4-diphosphate.
- the following enzymes can naturally possess this activity or can be engineered to exhibit this activity.
- Useful genes include those that encode enzymes that interconvert isopenenyl diphosphate and dimethylallyl diphosphate.
- Butadiene synthase catalyzes the conversion of 2-butenyl-4-diphosphate to 1,3-butadiene.
- the enzymes described below naturally possess such activity or can be engineered to exhibit this activity.
- Isoprene synthase naturally catalyzes the conversion of dimethylallyl diphosphate to isoprene, but can also catalyze the synthesis of 1,3-butadiene from 2-butenyl-4-diphosphate.
- Isoprene synthases can be found in several organisms including Populus alba (Sasaki et al, FEBS Letters, 579 (11), 2514-2518 (2005)), Pueraria montana (Lindberg et al, Metabolic Eng, , 12(l):70-79 (2010); Sharkey et al, Plant Physiol, 137(2):700-712 (2005)), and Populus tremula x Populus alba (Miller et al, Planta, 213(3):483-487 (2001)).
- isoprene synthase enzymes are described in (Chotani et al, WO/2010/031079, Systems Using Cell Culture for Production of Isoprene; Cervin et al, US Patent Application 20100003716, Isoprene Synthase Variants for Improved Microbial Production of Isoprene).
- Step I of the pathway erythrose-4-phosphate is converted to erythrose by the erythrose-4- phosphate kinase.
- glucose was converted to erythrose-4-phosphate through the pentose phosphate pathway and erythrose-4- phosphate was dephosphorylated and reduced to produce erythritol (Moon et al, Appl.Microbioi Biotechnol 86: 1017-1025 (2010)).
- erythrose-4-phosphate kinase is present in many of these erythritol-producing yeasts, including Trichosporonoides megacMUensis SN-G42(Sawada et al, J Biosci.Bioeng. 108:385-390 (2009)), Candida magnolia (Kohl et al, Biotechnol. Lett. 25:2103-2105 (2003)), and Torula sp. (HAJNY et al, Appl.Microbioi 12:240-246 (1964); Oh et al., J Ind.Microbiol Biotechnol. 26:248-252 (2001)).
- the erythrose-4-phosphate kinase genes were not identified yet. There are many poiyoi phosphotransferases with wide substrate range that can be applied to this step.
- An example is the triose kinase (EC 2.7.1.28) catalyzing the reversible conversion between glyceraldehydes and glyceraldehydes-3 -phosphate, which are one carbon shorter comparing to Step I.
- Other examples include the xylulokinase (EC 2.7.1.17) or arabinokinase (EC 2.7.1.54) that catalyzes phosphorylation of 5C polyol aldehyde.
- the following genes can be used for Step I conversion:
- Step J of the pathway erythrose is converted to erythritol by the erythrose reductase.
- glucose was converted to erythrose-4- phosphate through the pentose phosphate pathway and erythrose-4-phosphate was
- erythrose reductase is present in many of these erythritol-producing yeasts, including Trichosporonoides megachiliensis SN-G42 (Sawada et al., supra, (2009)), Candida magnolia (Kohl et al., supra, (2003)), and Torula sp. (HAJNY et al, supra, (1964); Oh et al, supra, (2001)). Erythrose reductase was characterized and purified from Torula corallina (Lee et al, Biotechnol.Prog.
- Step K of the pathway erythritol is converted to erythritol-4-phosphate by the erythritol kinase.
- Erythritol kinase (EC 2.7.1.27) catalyzes the phosphorylation of erythritol.
- Erythritol kinase was characterized in erythritol utilizing bacteria such as Brucella abortus (Sperry et al., J Bacteriol. 121 :619-630 (1975)).
- the eryA gene of Brucella abortus has been functionally expressed in Escherichia coli and the resultant EryA was shown to catalyze the ATP-dependent conversion of erythritol to erythritol-4-phosphate (Lillo et al., Bioorg.Med.Chem.Lett. 13 :737- 739 (2003)).
- the following genes can be used for Step K conversion:
- Step A of the pathway described in Figure 4 malonyl-CoA and acetyl-CoA are condensed to form 3-oxoglutaryl-CoA by malonyl-CoA:acetyl-CoA acyl transferase, a beta-keothiolase.
- beta-ketoadipyl-CoA thiolase (EC 2.3.1.174), also called 3-oxoadipyl- CoA thiolase that converts beta-ketoadipyl-CoA to succinyl-CoA and acetyl-CoA, and is a key enzyme of the beta-ketoadipate pathway for aromatic compound degradation.
- the enzyme is widespread in soil bacteria and fungi including Pseudomonas putida (Harwood et al, J
- coli (Nogales et al, Microbiology, 153 :357-365 (2007)) also catalyze this transformation.
- beta-ketothiolases exhibit significant and selective activities in the oxoadipyl-CoA forming direction including bkt from Pseudomonas putida, pcaF and bkt from Pseudomonas aeruginosa PAOl, bkt from Burkholderia ambifaria AMMD, paaJ from E. coli, and phaD from P. putida.
- These enzymes can also be employed for the synthesis of 3-oxoglutaryl-CoA, a compound structurally similar to 3-oxoadipyl-CoA.
- oxopimeloyl-CoA glutaryl-CoA acyltransferase (EC 2.3.1.16) that combines glutaryl-CoA and acetyl-CoA to form 3-oxopimeloyl-CoA.
- An enzyme catalyzing this transformation is found in Ralstonia eutropha (formerly known as Alcaligenes eutrophus), encoded by genes bktB and bktC (Slater et al, J.Bacteriol. 180: 1979-1987 (1998); Haywood et al, F EMS Microbiology Letters 52:91-96 (1988)).
- the sequence of the BktB protein is known; however, the sequence of the BktC protein has not been reported.
- the pirn operon of Rhodopseudomonas palustris also encodes a beta-ketothiolase, encoded by pimB, predicted to catalyze this transformation in the degradative direction during benzoyl-CoA degradation (Harrison et al., Microbiology 151 :727-736 (2005)).
- Beta-ketothiolase enzymes catalyzing the formation of beta-ketovaleryl-CoA from acetyl-CoA and propionyl-CoA can also be able to catalyze the formation of 3-oxoglutaryl-CoA.
- Zoogloea ramigera possesses two ketothiolases that can form ⁇ -ketovaleryl-CoA from propionyl-CoA and acetyl-CoA and R.
- eutropha has a ⁇ -oxidation ketothiolase that is also capable of catalyzing this transformation (Slater et al, J. Bacteriol, 180: 1979-1987 (1998)).
- the sequences of these genes or their translated proteins have not been reported, but several candidates in R. eutropha, Z. ramigera, or other organisms can be identified based on sequence homology to bktB from R. eutropha. These include:
- Additional candidates include beta-ketothiolases that are known to convert two molecules of acetyl-CoA into acetoacetyl-CoA (EC 2.1.3.9).
- Exemplary acetoacetyl-CoA thiolase enzymes include the gene products of atoB from E. coli (Martin et al, supra, (2003)), thlA and MB from C acetobutylicum (Hanai et al, supra, (2007); Winzer et al, supra, (2000)), and ERG10 from S. cerevisiae (Hiser et al, supra, (1994)).
- This enzyme catalyzes the reduction of the 3-oxo group in 3-oxoglutaryl-CoA to the 3 -hydroxy group in Step B of the pathway shown in Figure 4.
- 3-Oxoacyl-CoA dehydrogenase enzymes convert 3-oxoacyl-CoA molecules into 3 -hydroxy acyl- CoA molecules and are often involved in fatty acid beta-oxidation or phenylacetate catabolism.
- subunits of two fatty acid oxidation complexes in E. coli, encoded by fadB and fadJ function as 3-hydroxyacyl-CoA dehydrogenases (Binstock et al, Methods Enzymol. 71 Pt C:403-411 (1981)).
- 3-Hydroxybutyryl-CoA dehydrogenase also called acetoacetyl-CoA reductase, catalyzes the reversible NAD(P)H-dependent conversion of acetoacetyl-CoA to 3-hydroxybutyryl-CoA.
- This enzyme participates in the acetyl-CoA fermentation pathway to butyrate in several species of Clostridia and has been studied in detail (Jones and Woods, supra, (1986)).
- Enzyme candidates include hbd from C. acetobutylicum (Boynton et al, J. Bacteriol. 178:3015-3024 (1996)), hbd from C.
- genes demonstrated to reduce acetoacetyl-CoA to 3-hydroxybutyryl-CoA are phbB from Zoogloea ramigera (Ploux et al, supra, (1988)) and phaB from Rhodobacter sphaeroides (Alber et al, supra, (2006)).
- the former gene is NADPH- dependent, its nucleotide sequence has been determined (Peoples and Sinskey, supra, (1989)) and the gene has been expressed in E. coli.
- Additional genes include hbdl (C-terminal domain) and hbd2 (N-terminal domain) in Clostridium kluyveri (Hillmer and Gottschalk, Biochim.
- Rhodobacter sphaeroides 353825.1 77464321 Rhodobacter sphaeroides
- 3-hydroxyglutaryl-CoA reductase reduces 3-hydroxyglutaryl-CoA to 3-hydroxy-5- oxopentanoate.
- acyl-CoA dehydrogenases reduce an acyl-CoA to its corresponding aldehyde (EC 1.2.1).
- Exemplary genes that encode such enzymes include the Acinetobacter calcoaceticus acrl encoding a fatty acyl-CoA reductase (Reiser and Somerville, supra, (1997)), the Acinetobacter sp. M-l fatty acyl-CoA reductase (Ishige et al, supra, (2002)), and a CoA- and NADP- dependent succinate semialdehyde dehydrogenase encoded by the sucD gene in
- Leuconostoc mesenteroides has been shown to oxidize the branched chain compound
- Butyraldehyde dehydrogenase catalyzes a similar reaction, conversion of butyryl-CoA to butyraldehyde, in solventogenic organisms such as Clostridium saccharoperbutylacetonicum (Kosaka et al, Biosci. Biotechnol Biochem. 71 :58-68 (2007)).
- acrl YP 047869.1 50086359 Acinetobacter calcoaceticus acrl AAC45217 1684886 Acinetobacter baylyi acrl BAB85476.1 18857901 Acinetobacter sp.
- malonyl-CoA reductase which transforms malonyl-CoA to malonic semialdehyde.
- Malonyl-CoA reductase is a key enzyme in autotrophic carbon fixation via the 3-hydroxypropionate cycle in thermoacidophilic archael bacteria (Berg et al, supra, (2007b); Thauer, supra, (2007)).
- the enzyme utilizes NADPH as a cofactor and has been characterized in Metallosphaera and Sulfolobus spp (Alber et al, supra, (2006); Hugler et al, supra, (2002)).
- the enzyme is encoded by Msed_0709 in Metallosphaera sedula (Alber et al., supra, (2006); Berg et al., supra,
- aldehyde forming candidate is the aid gene from Clostridium beijerinckii (Toth et al, Appl Environ.Microbiol 65:4973-4980 (1999)). This enzyme has been reported to reduce acetyl-CoA and butyryl-CoA to their corresponding aldehydes. This gene is very similar to eutE that encodes acetaldehyde dehydrogenase of Salmonella typhimurium and E. coli (Toth et al, supra, (1999)).
- This enzyme reduces the terminal aldehyde group in 3-hydroxy-5-oxopentanote to the alcohol group.
- exemplary genes encoding enzymes that catalyze the conversion of an aldehyde to alcohol include air A encoding a medium-chain alcohol dehydrogenase for C2-C14 (Tani et al, supra, (2000)), ADH2 from Saccharomyces cerevisiae (Atsumi et al., supra, (2008)), yqhD from E.
- the adhA gene product from Zymomonas mobilis has been demonstrated to have activity on a number of aldehydes including formaldehyde, acetaldehyde, propionaldehyde, butyraldehyde, and acrolein (Kinoshita et al, Appl Microbiol Biotechnol 22:249-254 (1985)).
- Enzymes exhibiting 4-hydroxybutyrate dehydrogenase activity also fall into this category. Such enzymes have been characterized in Ralstonia eutropha (Bravo et al, supra, (2004)), Clostridium kluyveri (Wolff and Kenealy, supra, (1995)) and Arabidopsis thaliana (Breitnch et al., supra, (2003)). The A. thaliana enzyme was cloned and characterized in yeast [12882961]. Yet another gene is the alcohol dehydrogenase adhl from Geobacillus
- thermoglucosidasius (Jeon et al., J Biotechnol 135: 127-133 (2008)).
- Another exemplary enzyme is 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) which catalyzes the reversible oxidation of 3-hydroxyisobutyrate to methylmalonate semialdehyde.
- This enzyme participates in valine, leucine and isoleucine degradation and has been identified in bacteria, eukaryotes, and mammals.
- thermophilus HB8 has been structurally characterized (Lokanath et al., J Mol Biol 352:905-17 (2005)). The reversibility of the huma 3-hydroxyisobutyrate dehydrogenase was demonstrated using isotopically-labeled substrate (Manning et al, Biochem J 231 :481-4 (1985)). Additional genes encoding this enzyme include 3hidh in Homo sapiens (Hawes et al, Methods Enzymol 324:218-228 (2000)) and Oryctolagus cuniculus (Hawes et al, supra, (2000); Chowdhury et al, Biosci.Biotechnol Biochem.
- malonic semialdehyde to 3 -HP can also be accomplished by two other enzymes: NADH-dependent 3-hydroxypropionate dehydrogenase and NADPH-dependent malonate semialdehyde reductase.
- An NADH-dependent 3-hydroxypropionate dehydrogenase is thought to participate in beta-alanine biosynthesis pathways from propionate in bacteria and plants (Rathinasabapathi B., Journal of Plant Pathology 159:671-674 (2002); Stadtman, J.Am.Chem.Soc. 77:5765-5766 (1955)). This enzyme has not been associated with a gene in any organism to date.
- NADPH-dependent malonate semialdehyde reductase catalyzes the reverse reaction in autotrophic C02-fixing bacteria. Although the enzyme activity has been detected in Metallosphaera sedula, the identity of the gene is not known (Alber et al, supra, (2006)).
- mevalonate kinase (EC 2.7.1.36) that phosphorylates the terminal hydroxyl group of the methyl analog, mevalonate, of 3,5-dihydroxypentanote.
- Some gene candidates for this step are erg 12 from S. cerevisiae, mvk from Methanocaldococcus jannaschi, MVK from Homo sapeins, and mvk from Arabidopsis thaliana col.
- Glycerol kinase also phosphorylates the terminal hydroxyl group in glycerol to form glycerol-3- phosphate. This reaction occurs in several species, including Escherichia coli, Saccharomyces cerevisiae, and Thermotoga maritima.
- the E. coli glycerol kinase has been shown to accept alternate substrates such as dihydroxyacetone and glyceraldehyde (Hayashi and Lin, supra, (1967)).
- T maritime has two glycerol kinases (Nelson et al, supra, (1999)). Glycerol kinases have been shown to have a wide range of substrate specificity.
- Homoserine kinase is another possible candidate that can lead to the phosphorylation of 3,5- dihydroxypentanoate.
- This enzyme is also present in a number of organisms including E. coli, Streptomyces sp, and S. cerevisiae.
- Homoserine kinase from E. coli has been shown to have activity on numerous substrates, including, L-2-amino,l,4- butanediol, aspartate semialdehyde, and 2-amino-5-hydroxyvalerate (Huo and Viola, supra, (1996); Huo and Viola, supra, (1996)).
- This enzyme can act on substrates where the carboxyl group at the alpha position has been replaced by an ester or by a hydroxymethyl group.
- the gene candidates are:
- Phosphomevalonate kinase (EC 2.7.4.2) catalyzes the analogous transformation in the mevalonate pathway.
- This enzyme is encoded by erg8 in Saccharomyces cerevisiae (Tsay et al, Mol. Cell Biol. 11 :620-631 (1991)) and mvaK2 in Streptococcus pneumoniae, Staphylococcus aureus and Enterococcus faecalis (Doun et al, Protein Sci. 14: 1134-1139 (2005); Wilding et al, J Bacteriol. 182:4319-4327 (2000)).
- Streptococcus pneumoniae and Enterococcus faecalis enzymes were cloned and characterized in E. coli (Pilloff et al., J Biol.Chem. 278:4510-4515 (2003); Doun et al, Protein Sci. 14: 1134-1139 (2005)).
- Butenyl 4-diphosphate is formed from the ATP-dependent decarboxylation of 3H5PDP by 3H5PDP decarboxylase ( Figure 4, Step G).
- mevalonate diphosphate decarboxylase EC 4.1.1.33
- This reaction is catalyzed by MVD1 in Saccharomyces cerevisiae, MVD in Homo sapiens and MDD in Staphylococcus aureus and Trypsonoma brucei (Toth et al., J Biol.Chem. 271 :7895- 7898 (1996); Byres et al, JMol.Biol. 371 :540-553 (2007)).
- Butenyl 4-diphosphate isomerase catalyzes the reversible interconversion of 2-butenyl-4- diphosphate and butenyl-4-diphosphate.
- the following enzymes can naturally possess this activity or can be engineered to exhibit this activity.
- Useful genes include those that encode enzymes that interconvert isopenenyl diphosphate and dimethylallyl diphosphate.
- Butadiene synthase catalyzes the conversion of 2-butenyl-4-diphosphate to 1,3-butadiene.
- the enzymes described below naturally possess such activity or can be engineered to exhibit this activity.
- Isoprene synthase naturally catalyzes the conversion of dimethylallyl diphosphate to isoprene, but can also catalyze the synthesis of 1,3-butadiene from 2-butenyl-4-diphosphate.
- Isoprene synthases can be found in several organisms including Populus alba (Sasaki et al, FEBS Letters, 2005, 579 (11), 2514-2518), Pueraria montana (Lindberg et al, Metabolic Eng, 12(l):70-79 (2010); Sharkey et al, Plant Physiol, 137(2):700-712 (2005)), and Populus tremula x Populus alba (Miller et al, Planta, 213(3):483-487 (2001)).
- isoprene synthase enzymes are described in (Chotani et al, WO/2010/031079, Systems Using Cell Culture for Production of Isoprene; Cervin et al, US Patent Application 20100003716, Isoprene Synthase Variants for Improved Microbial Production of Isoprene).
- This step catalyzes the reduction of the acyl-CoA group in 3-hydroxyglutaryl-CoA to the alcohol group.
- exemplary bifunctional oxidoreductases that convert an acyl-CoA to alcohol include those that transform substrates such as acetyl-CoA to ethanol (e.g., adhE from E. coli (Kessler et al, supra, (1991)) and butyryl-CoA to butanol (e.g. adhE2 from C. acetobutylicum (Fontaine et al, supra, (2002)).
- Another exemplary enzyme can convert malonyl-CoA to 3 -HP.
- An NADPH-dependent enzyme with this activity has characterized in Chloroflexus aurantiacus where it participates in the 3- hydroxypropionate cycle (Hugler et al, supra, (2002); Strauss and Fuchs, supra, (1993)).
- This enzyme with a mass of 300 kDa, is highly substrate-specific and shows little sequence similarity to other known oxidoreductases (Hugler et al, supra, (2002)). No enzymes in other organisms have been shown to catalyze this specific reaction; however there is bioinformatic evidence that other organisms can have similar pathways (Klatt et al., supra, (2007)).
- Enzyme candidates in other organisms including Roseiflexus castenholzii, Erythrobacter sp. NAP1 and marine gamma proteobacterium HTCC2080 can be inferred by sequence similarity.
- Longer chain acyl-CoA molecules can be reduced to their corresponding alcohols by enzymes such as the jojoba (Simmondsia chinensis) FAR which encodes an alcohol-forming fatty acyl- CoA reductase. Its overexpression in E. coli resulted in FAR activity and the accumulation of fatty alcohol (Metz et al, Plant Physiology 122:635-644 (2000)).
- jojoba Simmondsia chinensis
- Another candidate for catalyzing this step is 3-hydroxy-3-methylglutaryl-CoA reductase (or HMG-CoA reductase). This enzyme reduces the CoA group in 3-hydroxy-3-methylglutaryl-CoA to an alcohol forming mevalonate.
- Gene candidates for this step include:
- the hmgA gene of Sulfolobus solfataricus, encoding 3-hydroxy-3-methylglutaryl-CoA reductase, has been cloned, sequenced, and expressed in E. coli (Bochar et al, J Bacteriol. 179:3632-3638 (1997)).
- S. cerevisiae also has two HMG-CoA reductases in it (Basson et al, Proc.Natl.Acad.Sci. U.S.A 83:5563-5567 (1986)).
- the gene has also been isolated from Arabidopsis thaliana and has been shown to complement the HMG-COA reductase activity in S. cerevisiae (Learned et al, Proc.Natl.Acad.Sci. U.S.A 86:2779-2783 (1989)).
- acyl-CoA dehydrogenases are capable of reducing an acyl-CoA to its corresponding aldehyde. Thus they can naturally reduce 3-oxoglutaryl-CoA to 3,5-dioxopentanoate or can be engineered to do so. Exemplary genes that encode such enzymes were discussed in Figure 4, Step C.
- alcohol dehydrogenases that convert a ketone to a hydroxyl functional group.
- Two such enzymes from E. coli are encoded by malate dehydrogenase (mdh) and lactate dehydrogenase (IdhA).
- mdh malate dehydrogenase
- IdhA lactate dehydrogenase
- lactate dehydrogenase from Ralstonia eutropha has been shown to demonstrate high activities on 2-ketoacids of various chain lengths including lactate, 2-oxobutyrate, 2-oxopentanoate and 2-oxoglutarate (Steinbuchel et al., Eur.J.Biochem. 130:329-334 (1983)).
- alpha-ketoadipate Conversion of alpha-ketoadipate into alpha-hydroxyadipate can be catalyzed by 2-ketoadipate reductase, an enzyme reported to be found in rat and in human placenta (Suda et al, Arch.Biochem.Biophys. 176:610-620 (1976); Suda et al,
- Methyl ethyl ketone reductase catalyzes the reduction of MEK to form 2-butanol.
- Exemplary enzymes can be found in Rhodococcus ruber (Kosjek et al, Biotechnol Bioeng. 86:55-62 (2004)) and Pyrococcus furiosus (van der et al, Eur.J.Biochem. 268:3062-3068 (2001)).
- Protein ,cn Bank ID GI Number Organism
- a number of organisms can catalyze the reduction of 4-hydroxy-2-butanone to 1,3-butanediol, including those belonging to the genus Bacillus, Brevibacterium, Candida, and Klebsiella among others, as described by Matsuyama et al. US Patent 5,413,922.
- a mutated Rhodococcus phenylacetaldehyde reductase (Sar268) and a Leifonia alcohol dehydrogenase have also been shown to catalyze this transformation at high yields (Itoh et al, Appl. Microbiol. Biotechnol. 75(6): 1249-1256).
- Homoserine dehydrogenase (EC 1.1.1.13) catalyzes the NAD(P)H-dependent reduction of aspartate semialdehyde to homoserine.
- homoserine dehydrogenase is a bifunctional enzyme that also catalyzes the ATP-dependent conversion of aspartate to aspartyl-4-phosphate (Starnes et al, Biochemistry 11 :677-687 (1972)).
- the functional domains are catalytically independent and connected by a linker region (Sibilli et al., J Biol Chem 256: 10228-10230 (1981)) and both domains are subject to allosteric inhibition by threonine.
- aldehyde reducing reductases are capable of reducing an aldehyde to its corresponding alcohol. Thus they can naturally reduce 3,5-dioxopentanoate to 5-hydroxy-3-oxopentanoate or can be engineered to do so. Exemplary genes that encode such enzymes were discussed in Figure 4, Step D.
- ketone reducing reductases are capable of reducing a ketone to its corresponding hydroxyl group. Thus they can naturally reduce 5-hydroxy-3-oxopentanoate to 3,5- dihydroxypentanoate or can be engineered to do so. Exemplary genes that encode such enzymes were discussed in Figure 4, Step L.
- 3-oxo-glutaryl-CoA reductase (CoA reducing and alcohol forming) enzymes catalyze the 2 reduction steps required to form 5-hydroxy-3-oxopentanoate from 3-oxo-glutaryl-CoA.
- Typical catalysts can include bismuth molybdate, phosphate-phosphoric acid, cerium oxide, kaolin-iron oxide, kaolin-phosphoric acid, silica-alumina, and alumina.
- Typical process throughputs are in the range of 0.1-20,000 kg/h.
- Typical solvents are toluene, heptane, octane, ethylbenzene, and xylene.
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Also Published As
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CN103459602B (en) | 2016-08-10 |
MY162964A (en) | 2017-07-31 |
CN106191132A (en) | 2016-12-07 |
AU2012212118B2 (en) | 2015-11-12 |
JP2014504508A (en) | 2014-02-24 |
KR20140145935A (en) | 2014-12-24 |
JP5960729B2 (en) | 2016-08-02 |
CA2826293A1 (en) | 2012-08-09 |
BR112013019811A2 (en) | 2017-02-21 |
US9321701B2 (en) | 2016-04-26 |
EP2670852A1 (en) | 2013-12-11 |
MY179664A (en) | 2020-11-11 |
JP2016192974A (en) | 2016-11-17 |
US20190048366A1 (en) | 2019-02-14 |
MX348334B (en) | 2017-06-07 |
MX2013008988A (en) | 2014-03-21 |
US20210147881A1 (en) | 2021-05-20 |
AU2012212118A1 (en) | 2013-05-02 |
US20120225466A1 (en) | 2012-09-06 |
EP2670852A4 (en) | 2017-04-26 |
SG192614A1 (en) | 2013-09-30 |
CN103459602A (en) | 2013-12-18 |
JP2018166514A (en) | 2018-11-01 |
US20170044572A1 (en) | 2017-02-16 |
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