Patent Grant
11365432
The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Sep. 17, 2019, is named 12956-485-999_Sequence_Listing.txt and is 500,400 bytes in size.
The present invention relates to a method for preparing an adipate ester or thioester. The invention further relates to a method for preparing adipic acid from said ester or thioester. Further the invention provides a number of methods for preparing an intermediate for said ester or thioester. Further the invention relates to a method for preparing 6-amino caproic acid (6-ACA), a method for preparing 5-formyl valeric acid (5-FVA), and a method for preparing caprolactam. Further, the invention relates to a host cell for use in a method according to the invention.
Adipic acid (hexanedioic acid) is inter alia used for the production of polyamide. Further, esters of adipic acid may be used in plasticisers, lubricants, solvent and in a variety of polyurethane resins. Other uses of adipic acid are as food acidulans, applications in adhesives, insecticides, tanning and dyeing. Known preparation methods include the oxidation of cyclohexanol or cyclohexanone or a mixture thereof (KA oil) with nitric acid.
Caprolactam is a lactam which may also be used for the production of polyamide, for instance nylon-6 or caprolactam-laurolactam copolymers (nylon-6,12). Various manners of preparing caprolactam from bulk chemicals are known in the art and include the preparation of caprolactam from cyclohexanone, toluene, phenol, cyclohexanol, benzene or cyclohexane.
The intermediate compounds, such as cyclohexanol, cyclohexanone or phenol, for preparing adipic acid or caprolactam are generally obtained from mineral oil. In view of a growing desire to prepare materials using more sustainable technology it would be desirable to provide a method wherein adipic acid or caprolactam is prepared from an intermediate compound that can be obtained from a biologically renewable source or at least from an intermediate compound that is converted into adipic acid or caprolactam using a biochemical method.
In U.S. Pat. No. 5,487,987, a method is described for the production of adipic acid, wherein use is made of a bacterial cell, wherein a carbon source is converted into 3-dehydroshikimate by the enzymes in the common pathway or aromatic amino acid biosynthesis of the bacterial cell, to produce cis, cis muconic acid, by the biocatalytic conversion of 3-dehydroshikimate. The cis, cis muconic acid is thereafter chemically reduced (using a platinum catalyst) to produce adipic acid. Thus, the final step requires chemical catalysis. It is further envisaged by the present inventors that the aromatic intermediates formed in the bacterial cell, may be toxic to the cell, likely requiring their concentration to be low in vivo as well as in the cell culture.
It is known to prepare caprolactam from 6-aminocaproic acid (6-ACA), e.g. as described in U.S. Pat. No. 6,194,572. As disclosed in WO 2005/068643, 6-ACA may be prepared biochemically by converting 6-aminohex-2-enoic acid (6-AHEA) in the presence of an enzyme having α,β-enoate reductase activity. The 6-AHEA may be prepared from lysine, e.g. biochemically or by pure chemical synthesis. Although 6-ACA can be prepared via the reduction of 6-AHEA by the methods disclosed in WO 2005/068643, the inventors have found that—under the reduction reaction conditions—6-AHEA may spontaneously and substantially irreversible cyclise to form an undesired side-product, notably β-homoproline. This cyclisation may be a bottleneck in the production of 6-ACA, and lead to a considerable loss in yield.
It is an object of the invention to provide a novel method for preparing adipic acid or caprolactam—which may, inter alia, be used for the preparation of polyamide—or an intermediate compound for adipic acid or caprolactam, that can serve as an alternative to known methods.
It is a further object to provide a novel method that would overcome one or more of the drawbacks mentioned above.
One or more further objects which may be solved in accordance with the invention will follow from the description, below.
The inventors have realised that adipate (or a ester or thioester thereof) can be produced from succinate (or a ester or thioester thereof). In particular, the inventors concluded that an adipate (thio)ester may be prepared from succinate (thio)ester and acetate (thio)ester via a sequence of specific reactions, e. g. similar to reverse beta-oxidation and fatty acid biosynthesis in living cells, as shown in
Thus, the inventors came to the conclusion that it should be possible to biocatalytically prepare adipic acid (or a ester or thioester thereof) via a cascade of reactions from succinate (or a ester or thioester thereof) and acetate (or a ester or thioester thereof). Further, they realised that adipic acid may be converted biocatalytically into 5-formylpentanoic acid (‘5-FVA’, 5-formylvaleric acid), which is an intermediate for the preparation of 6-ACA, and that for this conversion a specific biocatalyst may be used.
Accordingly, the present invention relates to a method for preparing an adipate ester or thioester from a succinate ester or thioester, via a plurality of reactions, wherein at least one of the reactions is catalysed by a biocatalyst.
In particular, the invention relates to a method for preparing an adipate ester or adipate thioester, comprising converting a 2,3-dehydroadipate (IUPAC name: 5-carboxy-2-pentanoate) ester or 2,3-dehydroadipate thioester into the adipate ester or thioester in the presence of a biocatalyst.
When referred herein to carboxylic acids or carboxylates, e.g. 6-ACA, another amino acid, 5-FVA, adipic acid/adipate, succinic acid/succinate, acetic acid/acetate, these terms are meant to include the protonated carboxylic acid (free acid), the corresponding carboxylate (its conjugated base) as well as a salt thereof, unless specified otherwise. When referring herein to amino acids, e.g. 6-ACA, this term is meant to include amino acids in their zwitterionic form (in which the amino group is in the protonated and the carboxylate group is in the deprotonated form), the amino acid in which the amino group is protonated and the carboxylic group is in its neutral form, and the amino acid in which the amino group is in its neutral form and the carboxylate group is in the deprotonated form, as well as salts thereof.
When referred to ester or thioester of a carboxylic acid, e. g. adipate ester or thioester, acetate ester of thioester, succinate ester or thioester, these terms are meant to include any activating group, in particular any biological activating group, including coenzyme A (also referred to as CoA), phospho-pantetheine, which may be bound to an acyl or peptidyl carrier protein (ACP or PCP, respectively), N-acetyl-cysteamine, methyl-thio-glycolate, methyl-mercapto-propionate, ethyl-mercapto-propionate, methyl-mercapto-butyrate, methyl-mercapto-butyrate, mercaptopropionate and other esters or thioesters providing the same or a similar function. In case living cells are used as a biocatalyst, the ester or thioester, in particular CoA, may be produced by the used biocatalyst or originate from an organism also capable of producing a suitable enzyme for catalysing the reaction. CoA-ligase and CoA-transferases have been identified in many organisms and may provide the desired activated esters or thioesters.
The preparation of the adipate ester or thioester from the succinate ester or thioester may in particular comprise the following reaction steps (numbers between parentheses also correspond to
(1) providing a succinate ester or thioester and reacting said ester or thioester with an acetate ester or thioester, thereby forming a 3-oxoadipate ester or thioester;
(2) hydrogenating the 3-oxo group of the 3-oxoadipate ester or thioester thereby forming a 3-hydroxyadipate ester or thioester;
(3) dehydrating the 3-hydroxyadipate ester or thioester thereby forming a 2,3-dehydroadipate ester or thioester; and
(4) hydrogenating of the C═C double bond of the 2,3-dehydroadipate ester or thioester, thereby forming an adipate ester or thioester.
The invention also relates to a method for preparing an intermediate compound, suitable for use in a method for preparing adipic acid, comprising carrying out one or more of said reactions steps 1-4, in the presence of a biocatalyst catalyzing such reaction step.
In an embodiment, the adipate ester or thioester is converted into 5-FVA (5).
If desired, the adipate ester or thioester can be converted into adipic acid. This may be accomplished by hydrolysing the ester bond or thioester bond (7), thereby forming adipic acid or by a transfer reaction, wherein ‘the alcohol’ or ‘thiol’ moiety (such as CoA) is transferred from the adipate ester or thioester to an acid different from adipic acid, thereby forming adipic acid and a (thio)ester of the acid different from adipic acid (7). If succinic acid or acetate is used as the different acid, this reaction may be advantageous in that the alcohol or thiol moiety, such as CoA may be recycled. E.g. adipyl-CoA+succinate or acetate may be converted (usually in the presence of a CoA transferase) to form succinyl-CoA or acetyl-CoA+adipic acid. The succinyl-CoA or acetyl-CoA may then be used as a starting compound in a method of the invention.
Adipic acid (or a ester or thioester thereof) may, e.g., be converted into 5-FVA (8).
In an embodiment, 5-FVA, obtained in a method of the invention is converted into 6-ACA (6). Thereafter, 6-ACA may be converted into caprolactam, e.g. in a manner known in the art per se.
In a further embodiment, adipic acid or caprolactam obtained in a method according to the invention is used for the preparation of polyamide.
The term “a” or “an” as used herein is defined as “at least one” unless specified otherwise.
When referring to a noun (e.g. a compound, an additive etc.) in the singular, the plural is meant to be included.
When referring to a compound of which several isomers exist (e.g. a cis and a trans isomer, an R and an S enantiomer), the compound in principle includes all enantiomers, diastereomers and cis/trans isomers of that compound that may be used in the particular method of the invention.
When an enzyme is mentioned with reference to an enzyme class (EC) between brackets, the enzyme class is a class wherein the enzyme is classified or may be classified, on the basis of the Enzyme Nomenclature provided by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), which nomenclature may be found at URL: chem-dot-qmul-dot-ac-dot-uk-forward slash-iubmb-forward slash-enzyme-forward slash. Other suitable enzymes that have not (yet) been classified in a specified class but may be classified as such, are meant to be included.
When referred herein to a protein by reference to a accession number, this number in particular is used to refer to a protein having a sequence as found in Uniprot on 11 Mar. 2008, unless specified otherwise.
The term “homologue” is used herein in particular for polynucleotides or polypeptides having a sequence identity of at least 30%, preferably at least 40%, more preferably at least 60%, more preferably at least 65%, more preferably at least 70%, more preferably at least 75%, more preferably at least 80%, in particular at least 85%, more in particular at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%. The term homologue is also meant to include nucleic acid sequences (polynucleotide sequences) which differ from another nucleic acid sequence due to the degeneracy of the genetic code and encode the same polypeptide sequence.
Sequence identity or similarity is herein defined as a relationship between two or more polypeptide sequences or two or more nucleic acid sequences, as determined by comparing the sequences. Usually, sequence identities or similarities are compared over the whole length of the sequences, but may however also be compared only for a part of the sequences aligning with each other. In the art, “identity” or “similarity” also means the degree of sequence relatedness between polypeptide sequences or nucleic acid sequences, as the case may be, as determined by the match between such sequences. Preferred methods to determine identity or similarity are designed to give the largest match between the sequences tested. In context of this invention a preferred computer program method to determine identity and similarity between two sequences includes BLASTP and BLASTN (Altschul, S. F. et al., J. Mol. Biol. 1990, 215, 403-410, publicly available from NCBI and other sources (BLAST Manual, Altschul, S., et al., NCBI NLM NIH Bethesda, Md. 20894). Preferred parameters for polypeptide sequence comparison using BLASTP are gap open 10.0, gap extend 0.5, Blosum 62 matrix. Preferred parameters for nucleic acid sequence comparison using BLASTN are gap open 10.0, gap extend 0.5, DNA full matrix (DNA identity matrix).
In a method of the invention, a biocatalyst is used, i.e. at least one reaction step in the method is catalysed by a biological material or moiety derived from a biological source, for instance an organism or a biomolecule derived there from. The biocatalyst may in particular comprise one or more enzymes. The biocatalyst may be used in any form. In an embodiment, one or more enzymes are used isolated from the natural environment (isolated from the organism it has been produced in), for instance as a solution, an emulsion, a dispersion, (a suspension of) freeze-dried cells, a lysate, or immobilised on a support. The use of an enzyme isolated from the organism it originates from may in particular be useful in view of an increased flexibility in adjusting the reaction conditions such that the reaction equilibrium is shifted to the desired side.
In an embodiment, one or more enzymes form part of a living organism (such as living whole cells). The enzymes may perform a catalytic function inside the cell. It is also possible that the enzyme may be secreted into a medium, wherein the cells are present.
Living cells may be growing cells, resting or dormant cells (e.g. spores) or cells in a stationary phase. It is also possible to use an enzyme forming part of a permeabilised cell (i.e. made permeable to a substrate for the enzyme or a precursor for a substrate for the enzyme or enzymes).
A biocatalyst used in a method of the invention may in principle be any organism, or be obtained or derived from any organism. The organism may be an eukaryote, a bacterium or an archea. In particular the organism may be selected from animals (including humans), plants, bacteria, archaea, yeasts and fungi.
Suitable bacteria may in particular be selected amongst the group of Absidia, Achromobacter, Acinetobacter, Agrobacterium, Aeromonas, Alcaligenes, Arthrobacter, Arzoarcus, Azomonas, Azospirillum, Azotobacter, Bacillus, Beijerinckia, Bradyrhizobium, Burkholderia, Byssochlamys, Citrobacter, Clostridium, Comamonas, Corynebacterium, Deinococcus, Escherichia, Enterobacter, Flavobacterium, Fusobacterium, Gossypium, Klebsiella, Lactobacillus, Listeria, Megasphaera, Micrococcus, Mycobacterium, Norcadia, Porphyromonas, propionibacterium, Pseudomonas, Ralstonia, Rhizobium, Rhodopseudomonas, Rhodospirillum, Rodococcus, Roseburia, Shewanella, Streptomycetes, Xanthomonas, Xylella, Yersinia, Treponema, Vibrio, Streptococcus, Lactococcus, Zymomonas, Staphylococcus, Salmonella, Brucella, Microscilla.
Suitable eukaryotes can be selected in particular from the group of fungi; metazoan; Viridiplantae (in particular Arabidopsis and Chlamydomonadales); Diplomonads (in particular Giardiinae); Entamoebidae (in particular Entaboeba); Euglenozoa (in particular Euglena); Pelobiontida (in particular Mastigamoeba); and Alveolata (in particular Cryptosporidium).
Suitable fungi in particular include fungi and yeasts selected amongst the group of Rhizopus, Neurospora, Penicillium, Aspergillus, Piromyces, Trichosporon, Candida, Hansenula, Kluyveromyces, Saccharomyces, Rhodotorula, Schizosaccharomyces, Yarrowia (such as Yarrowia lypolytica).
Suitable metazoan in particular include metazoan selected amongst the group of mammals (including human), more in particular selected from the group of Leporidae, Muridae, Suidae, Bovidae, hominidae. A biocatalyst can originate from any part of a metazoan, e.g. liver, pancreas, brain, kidney, heart or other organ. Suitable metazoan may also include in particular Caenorhabditis and Drosophila.
Organisms which in particular may provide a suitable biocatalyst for a specific reaction step are mentioned below, when describing specific reaction steps of a method of the invention.
It will be clear to the person skilled in the art that use can be made of a naturally occurring biocatalyst (wild type) or a mutant of a naturally occurring biocatalyst with suitable activity in a method according to the invention. Properties of a naturally occurring biocatalyst may be improved by biological techniques known to the skilled person in the art, such as e.g. molecular evolution or rational design. Mutants of wild-type biocatalysts can for example be made by modifying the encoding DNA of an organism capable of acting as a biocatalyst or capable of producing a biocatalytic moiety (such as an enzyme) using mutagenesis techniques known to the person skilled in the art (random mutagenesis, site-directed mutagenesis, directed evolution, gene recombination, etc.). In particular the DNA may be modified such that it encodes an enzyme that differs by at least one amino acid from the wild-type enzyme, so that it encodes an enzyme that comprises one or more amino acid substitutions, deletions and/or insertions compared to the wild-type, or such that the mutants combine sequences of two or more parent enzymes or by effecting the expression of the thus modified DNA in a suitable (host) cell. The latter may be achieved by methods known to the skilled person in the art such as codon optimisation or codon pair optimisation, e.g. based on a method as described in WO 2008/000632.
A mutant biocatalyst may have improved properties, for instance with respect to one or more of the following aspects: selectivity towards the substrate, activity, stability, solvent tolerance, pH profile, temperature profile, substrate profile, susceptibility to inhibition, cofactor utilisation and substrate-affinity. Mutants with improved properties can be identified by applying e.g. suitable high through-put screening or selection methods based on such methods known to the skilled person in the art.
The substrate specificity of enzymes acting on alkyl or alkyl esters or thioesters can be modified. Molecular evolution to create diversity followed by screening for desired mutants and/or rational engineering of substrate binding pockets may be utilised. Techniques to modify the substrate specificity of an enzyme used in a method of the invention may be based on those described in the art. For instance, rational engineering employing structural and sequence information to design specific mutations has been utilised to modify the substrate specificity of the acyl transferase domain 4 from the erythromycin polyketide synthase to accept alternative acyl donors. It has been shown that modifying the proposed substrate binding site resulted in a modified binding pocket able to accommodate alternative substrates resulting in a different product ratio (Reeves, C. D.; Murli, S.; Ashley, G. W.; Piagentini, M.; Hutchinson, C. R.; McDaniel, R. Biochemistry 2001, 40(51), 15464-15470). Both rational design and molecular evolution approaches have been used to alter the substrate specificity of the biocatalyst BM3 resulting in a large number of mutants capable of oxidizing a large variety of different alkenes, cycloalkenes, arenes and heteroarenes instead or in addition to the natural substrate of medium chain fatty acids (e.g. myristic acid) (Peters, M. W.; Meinhold, P.; Glieder, A.; Arnold, F. H. Journal of the American Chemical Society 2003, 125(44), 13442-13450; Appel, D.; Lutz-Wahl, S.; Fischer, P.; Schwaneberg, U.; Schmid, R. D. Journal of Biotechnology 2001, 88(2), 167-171 and references therein).
When referred to a biocatalyst, in particular an enzyme, from a particular source, recombinant biocatalysts, in particular enzymes, originating from a first organism, but actually produced in a (genetically modified) second organism, are specifically meant to be included as biocatalysts, in particular enzymes, from that first organism.
The Preparation of 3-Oxoadipate (Ester or Thioester) (‘Reaction 1’)
In an embodiment of the invention, 3-oxoadipate (ester or thioester) is prepared from succinate and acetate, which succinate and/or acetate which are usually provided with an activating group, in particular to yield an ester or a thioester, facilitating the reaction.
The 3-oxoadipate (ester of thioester) may be accomplished biocatalytically or chemically, in particular by a ‘Claisen condensation’, wherein an acetate ester or thioester and a succinate ester or thioester are coupled
In a preferred method of the invention, the preparation comprises a biocatalytic reaction in the presence of a biocatalyst capable of catalysing an acyl-group transfer. An enzyme having such catalytic activity may therefore be referred to as an acyltransferase.
In a preferred method an acyl transfer takes place between two acyl thioesters or acyl esters. Preferred acyl thioesters are acetyl-CoA and succinyl-CoA. Preferably, the said biocatalyst is selective towards the said acyl thioesters.
The biocatalyst may in particular comprise an enzyme capable of acyl-group transfer selected from the group of acyltransferases (E.C. 2.3.1), preferably from the group of acetyl-CoA:acetyl-CoA C-acetyltransferases (EC 2.3.1.9), acyl-CoA:acetyl-CoA C-acyltransferases (EC 2.3.1.16) and succinyl-CoA:acetyl-CoA C-succinyltransferases (EC 2.3.1.174, also known as beta-ketoadipyl-CoA thiolases). Acyltransferase activity has for instance been described in beta-oxidation, fatty acid biosynthesis, polyketide biosynthesis, or butanoate metabolism in the KEGG (Kyoto Encyclopedia of Genes and Genomes) database.
An acyltransferase may in particular be an acyltransferase of an organism selected from the group of archae, bacteria and eukaryota.
In particular, the enzyme may originate from a microorganism that is able to degrade organic compounds comprising an aromatic or alicyclic ring structure, in particular a 5, 6 or 7 membered ring structure. The organic compound may optionally comprise one or more heteroatoms in the ring or as a substituent or a part of a substituent. For instance, the organic moiety may be an aromatic compound, in particular an aromatic comprising a six-membered ring. In particular the aromatic compound may be selected from the group of phenylacetate, benzoate, catechol, protocatechuate and gentisate. The organic compound may be a alicyclic compound, in particular a cyclic alcohol, such as cyclohexanol, a cyclic ketone, such as cyclohexanone, or a cycloalkane, such as cyclohexane. The organic compound may be a lactam, such as caprolactam. In an embodiment the enzyme originates from an organism capable of degrading a dicarboxylic acid (usually C6-C10), in particular a straight-chain saturated dicarboxylic acid, such as adipic acid.
In a further embodiment, the enzyme originates from an organism capable of synthesizing 3-keto-adipate e.g. as part of a secondary metabolite (e.g. malonomycin) are preferred, for instance, from Streptomycetes (in particular Streptomyces rimosus), from Actinomycres, from other Actinobacteria or other known secondary metabolite producers.
Preferred microorganism for providing a biocatalyst capable of catalysing the preparation of 3-oxoadipate (ester or thioester) further include Acinetobacter (in particular Acinetobacter sp. Strain ADP1 and A. calcoaceticus), Agrobacterium (in particular A. tumefaciens), Alicaligenes (in particular Alicaligenes strains D2 and A. eutrophus), Arthrobacter, Arzoarcus (in particular A. evansii), Azomonas, Azotobacter, Bacillus (in particular B. halodurans), Beijerinckia, Bradyrhizobium, Burkholderia, Clostridia (in particular C. kluyveri, C. acetobutylicum, C. beijerinckii), Comamonas, Corynebacterium (in particular C. glutamicum and C. aurantiacum), E. coli, Enterobacter, Flavobacterium, Megasphera (in particular M. elsdenii), Norcadia, Pseudomonas (in particular P. putida, P. aeruginosa and Pseudomonas sp. strain B13), Ralstonia (in particular R. eutropha), Rhizobium, Rhodopseudomonas (in particular R. palustris), Rodococcus (in particular R. erythropolis, R. opacus, and Rodococcus sp strain RHA1), Aspergillus (in particular A. niger), Euglenozoa (in particular Euglena gracilis), Neurospora (in particular N. crassa), Penicillium (in particular P. chrysogenum), Rhodotorula, Saccharomyces, Trichosporon (in particular T. cutaneum).
In a specific embodiment, the biocatalyst comprises an enzyme comprising an amino acid sequence as identified in any of the SEQUENCE ID's 1-13 or a homologue thereof.
The Preparation of 3-Hydroxyadipate (Ester or Thioester) (‘Reaction 2’)
In an embodiment, 3-hydroxyadipate (ester or thioester) is prepared from 3-oxoadipate (ester or thioester). Usually, the 3-oxoadipate is provided with an activating group, as indicated above.
In principle, the 3-hydroxyadipate (ester or thioester) may be prepared chemically, e.g. by selective hydrogenation of the 3-oxo group in 3-oxo-adipate (ester or thioester).
This reaction may particular be performed in the presence of a biocatalyst, catalysing this reaction step, in particular a biocatalyst that is capable of catalysing the reduction of an oxo group, in particular a carbonyl group to a hydroxy group.
In a specific embodiment, the 3-oxoadipate is present as its thioester with co-enzyme A (hereinafter, the thioester of 3-oxoadipate and co-enzyme A will be referred to as 3-oxoadipyl-CoA).
In a preferred method of the invention, the preparation comprises a biocatalytic reaction in the presence of a biocatalyst capable of catalysing the reduction of a 3-oxoacyl (ester or thioester) to a 3-hydroxyacyl (ester or thioester).
An enzyme having such catalytic activity may therefore be referred to as a 3-hydroxyacyl (ester or thioester) dehydrogenase. An enzyme having such catalytic activity toward the 3-hydroxyacyl CoA-thioester may therefore be referred to as a 3-hydroxyacyl-CoA dehydrogenase. Preferably, the said 3-hydroxyacyl-CoA dehydrogenase is selective towards the substrate 3-oxoadipyl-CoA.
An enzyme capable of catalysing the reduction of 3-oxoacyl (ester or thioester) to a 3-hydroxyacyl (ester or thioester) may in particular be selected from the group of dehydrogenases (E.C. 1.1.1), preferably from the group 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35 and EC 1.1.1.36), 3-hydroxybutanoyl-CoA dehydrogenase (EC 1.1.1.157), 3-hydroxypimeloyl-CoA dehydrogenase (EC 1.1.1.259) and long-chain-3-hydroxyacyl-CoA dehydrogenases (EC 1.1.1.211). The enzymes may use NADH or NADPH as cofactor. 3-Hydroxyacyl-CoA dehydrogenase activity has been described, for example, in fatty acid metabolism, polyketide biosynthesis, polyhydroxyalkanoate metabolism, butanoate metabolism, as well as degradation of aromatic compounds according to the KEGG (Kyoto Encyclopedia of Genes and Genomes) database.
In particular, microorganisms that are able to degrade an organic compound, as identified above (see ‘reaction 1’), in particular an aromatic compound, an alicyclic compound or a dicarboxylic acid.
Other preferred organisms for providing a biocatalyst capable of catalysing the preparation of 3-hydroxyadipate (ester or thioester) include: Acinetobacter (in particular Acinetobacter sp. Strain ADP1 and A. calcoaceticus), Alicaligenes (in particular Alicaligenes strain D2 and A. eutrophus), Arzoarcus (in particular A. evansii), Bacillus (in particular B. halodurans), Bordetella (in particular B. pertussis), Burkholderia (in particular B. pseudomallei and B. xenovorans), Corynebacterium (in particular C. glutamicum, C. aurantiacum and C. efficiens), Deinococcus (in particular D. radiodurans), E. coli, Flavobacterium, Klebsiella (in particular K. pneumonia), Pseudomonas (in particular P. putida and P. fluorescens), Rhodopseudomonas (in particular R. palustris), Rodococcus (in particular R. erythropolis, R. opacus, and Rodococcus sp strain RHA1), Aspergillus (in particular A. niger), Neurospora (in particular N. crassa), Penicillium (in particular P. chrysogenum), Saccharomyces (in particular S. cerevisiae).
A suitable organism for providing an enzyme of EC1.1.1.35, acting on 3-ketohexanoyl-CoA may be from any organism including mammals, in particular mammals selected from the group of Bos taurus, Rattus norvegicus, Sus scrofa, and Homo sapiens.
At suitable biocatalyst involved in (anaerobic) fatty acid synthesis, polyketide biosynthesis or polyhydroxyalkanoate metabolism may be from any organism, in particular microorganisms including: Clostridia (in particular C. acetobutylicum and C. kluyven), Euglenozoa (in particular Euglena gracilis), Megasphera (in particular Megasphera elsdenii), Raistonia (in particular Raistonia eutropha), and Zoogloea (in particular Zoogloea ramigera).
In a specific embodiment, the biocatalyst (catalysing ‘reaction 2’) comprises an enzyme comprising an amino acid sequence as identified in any of the SEQUENCE ID's 15-26, 29 or a homologue thereof. It is envisaged that in particular an enzyme comprising an amino acid sequence according to SEQUENCE ID 26 may catalyse both ‘reaction 2’ and ‘reaction 3’.
The Preparation of 2,3-Dehydro Adipate (Ester or Thioester) (‘Reaction 3’)
In an embodiment, 2,3-dehydro adipate (5-carboxy-2-pentenoate) (ester or thioester) is prepared from 3-hydroxyadipate (ester or thioester). Optionally, the 2,3-dehydro adipate and the 3-hydroxyadipate are coupled to a co-enzyme, ACP or another activating group, as indicated above.
In an embodiment of the invention, the 2,3-dehydro adipate (ester or thioester) is prepared by converting 3-hydroxyadipate (ester or thioester) chemically, e.g. by dehydration in a water free environment in the presence of e. g. sulphuric acid.
The 2,3-dehydro adipate may in particular be prepared from 3-hydroxyadipate using at least one biocatalyst.
A preferred biocatalyst is a biocatalyst that is capable of catalysing the dehydration of a 3-hydroxyacyl ester or thioester to a 2-enoyl ester or 2-enoyl thioester thereof.
In a specific embodiment, the 2,3-dehydro adipate is present as its thioester with co-enzyme A (hereinafter, the thioester of 2,3-dehydro adipate and co-enzyme A will be referred to as 5-carboxy-2-pentenoyl-CoA).
In a specific embodiment, the biocatalyst catalyses the dehydration of 3-hydroxyadipyl-CoA to 5-carboxy-2-pentenoyl-CoA.
In particular, the biocatalytic reaction may be carried out in the presence of a biocatalyst capable of catalysing the dehydration of a 3-hydroxyacyl (thio)ester to a 2,3-dehydroacyl thioester.
An enzyme having such catalytic activity may therefore be referred to as a 3-hydroxyacyl (ester or thioester) dehydratase. An enzyme having such catalytic activity toward the 3-hydroxyacyl CoA-thioester may therefore be referred to as a 3-hydroxyacyl-CoA dehydratase. Preferably, the said 3-hydroxyacyl-CoA dehydratase is selective towards the substrate 3-hydroxyadipyl-CoA.
An enzyme capable of catalysing the dehydration of 3-hydroxyacyl (ester or thioester) to a 2,3-dehydroacyl (ester or thioester) may in particular be selected from the group of hydrolyases (E.C. 4.2.1), preferably from the group of preferably from the group of enoyl-CoA hydratases (EC 4.2.1.17), 3-hydroxybutyryl-CoA dehydratases (EC 4.2.1.55) and long-chain-enoyl-CoA hydratases (EC 4.2.1.74). 3-Hydroxyacyl-CoA dehydratase activity has been described, for example, in fatty acid metabolism, polyketide synthesis, or butanoate metabolism, as well as degradation of aromatic compounds according to the KEGG database.
A 3-hydroxyacyl (ester or thioester) dehydratase may be a 3-hydroxyacyl (ester or thioester) dehydratase of an organism selected from the group of archaea, bacteria, and eukaryotes, for instance from the group of yeasts, fungi and mammals.
In particular, microorganisms that are able to degrade an organic compound, as identified above (see ‘reaction 1’), in particular an aromatic compound, an alicyclic compound or a dicarboxylic acid, are preferred sources for a biocatalyst catalysing the preparation of 2,3-dehydro adipate (ester or thioester).
Microorganisms capable of degrading an aromatic compound, an alicyclic compound or a dicarboxylic acid include Acinetobacter (in particular Acinetobacter sp. strain ADP1 and A. calcoaceticus), Alicaligenes (in particular Alicaligenes D2), Aspergillus (in particular A. niger), Azoarcus (in particular A. evansii), Bacillus (in particular B. halodurans), Corynebacterium (in particular C. glutamicum and C. aurantiacum), E. coli, Flavobacterium, Neurospora (in particular N. crassa), Penicillium (in particular P. chrysogenum), Pseudomonas (in particular P. putida and P. fluorescens), Rhodopseudomonas (in particular R. palustris), Rhodococcus (in particular Rhodococcus sp strain RHA1).
A preferred organism for providing an enzyme of EC4.2.1.17, acting on 3-hydroxyhexanoyl-CoA includes an organism selected from the group of mammals and microorganisms. A suitable enzyme of EC4.2.1.17 from a mammal may in particular be from a mammal selected from the group of Bos taurus, Homo sapiens, Rattus norvegicus, and Sus scrofa. A suitable enzyme of EC4.2.1.17 from a microorganism may in particular be from a microorganism selected from the group of Aeromonas (in particular A. caviae), Clostridium (in particular C. acetobutylicumi), Gossypium (in particular G. hirsutum), Rhodospirillum (in particular R. rubrumi), and Raistonia (in particular Raistonia eutropha).
Preferred also are microorganisms capable of (anaerobic) fatty acid biosynthesis. Such micro-organisms include Clostridia, in particular (C. acetobutylicum and C. kluyven), Euglenozoa (in particular Euglena gracilis, Megasphera (in particular M. elsdenii), and Saccharomyces (in particular S. cerevisiae).
A suitable enzyme may in particular comprise an amino acid sequence according to any of the SEQUENCE ID's 14, 27, 28, 30-41, 92, or a homologue thereof
The Preparation of Adipate (Ester or Thioester) from 2,3-Dehydro Adipate (Ester or Thioester) (‘Reaction 4’)
In an embodiment, adipate (ester or thioester) is prepared from 2,3-dehydro adipate (ester or thioester). Adipate (ester or thioester) may be prepared chemically from 2,3-dehydro adipate (ester or thioester), e.g. by selective hydrogenation of the C2-C3 doublebond, or biocatalytically.
Usually, the 2,3-dehydro adipate is provided with an activating group, as indicated above.
The adipate (ester or thioester) preferably is prepared from 2,3-dehydro adipate (ester or thioester) using at least one biocatalyst, catalysing the hydrogenation of the carbon-carbon double bond of 5-carboxy-2-pentenoate (ester or thioester).
In a preferred method of the invention, the preparation comprises a biocatalytic reaction in the presence of a biocatalyst capable of catalysing the reduction of a cis or a trans 2-enoyl (ester or thioester) to an acyl (ester or thioester). The biocatalyst may use a range of electron donors, for example, an electron donor selected from the group of NADH, NADPH, FADH2 and reduced ferredoxin. The electrons may be transferred directly from the electron donor to the biocatalyst, or, alternatively, mediated, in particular by the so-called electron transfer flavoprotein (ETF). An enzyme having such catalytic activity may therefore be referred to as a 2-enoyl (ester or thioester) reductase (ER). An enzyme having such catalytic activity toward the 2-enoyl CoA-thioester may therefore be referred to as a 2-enoyl-CoA reductase. Preferably, the said 2-enoyl-CoA reductase is selective towards the substrate 2,3-dehydroadipyl-CoA.
An enzyme capable of catalysing the reduction of 2-enoyl (ester or thioester) may in particular be selected from the group of oxidoreductases (EC 1.3.1 and EC 1.3.99), preferably from the group of enoyl-CoA reductases EC 1.3.1.8, EC 1.3.1.38 and EC 1.3.1.44, from the group of enoyl-[acyl-carrier-protein] reductases EC 1.3.1.9, EC 1.3.1.10 and EC 1.3.1.39, and from the group butyryl-CoA dehydrogenase (EC 1.3.99.2), acyl-CoA dehydrogenase (1.3.99.3) and long-chain-acyl-CoA dehydrogenase (EC 1.3.99.13). Trans-2-enoyl (ester or thioester) reductase activity has been described, for example, in fatty acid metabolism, polyketide synthesis, butanoate metabolism and mitochondrial fatty acid biosynthesis according to the KEGG database.
An 2-enoyl (ester or thioester) reductase may in principle be obtained or derived from any organism. In particular the organism can be selected from bacteria, archaea, or eukariotes, such as from the group of yeasts, fungi, protists, plants and animals (including human).
In an embodiment, the organism may be selected from the following bacteria: E. coli, Vibrio, Bacillus (in particular B. subtilis), Clostridia (in particular C. kluyveri, C. acetobutylicum, C. beijerinckii and C. perfringens), Streptomyces (in particular S. coelicolor and S. avermitilis), Pseudomonas (in particular P. putida and P. aeruginosa), Shewanella, Xanthomonas, Xylella, Yersinia, Treponema (in particular T. denticola), Aeromonas (in particular Aeromonas hydrophila), Microscilla (in particular Microscilla marina), Megasphera (in particular Megasphera elsdenii), Deinococcus (in particular Deinococcus radiourans), Yarrowia (in particular Y. lypolytica) and Eubacterium (in particular E. pyruvativorans).
In an embodiment an 2-enoyl (ester or thioester) reductase is from an organism selected from the group of Euglenozoa, in particular Euglena gracilis)
In an embodiment an 2-enoyl (ester or thioester) reductase is from an organism selected from the group of Saccharomyces (in particular S. cerevisiae), Kluyveromyces (in particular K. lactis), Schizosaccharomyces (in particular S. pombe), Candida (in particular C. tropicalis)
In an embodiment an 2-enoyl (ester or thioester) reductase is from an organism selected from the group of Aspergillus (in particular A. niger and A. nidulans), and Penicillium (in particular P. chrysogenum).
In an embodiment an 2-enoyl (ester or thioester) reductase is from an organism selected from the group of Arabidopsis (in particular A. thaliana).
In an embodiment an 2-enoyl (ester or thioester) reductase is from an organism selected from the group of Homo sapiens, Rattus norvegicus, Bos Taurus, Cavia sp., Caenorhabditis elegans, and Drosophila melanogaster.
A suitable enzyme may in particular comprise an amino acid sequence according to any of the SEQUENCE ID's 42-67, 94, 96, 98, 100, 105, 107, 109, 111, 113, or a homologue thereof, in particular an amino acid sequence according to any of the SEQUENCE ID's 60, 63, 96, 100 or a homologue thereof. Exemplary nucleotide sequences encoding a suitable enzyme for catalysing ‘reaction 4’ are represented by 2-enoyl (ester or thioester) reductase 93, 95, 97, 99, 104, 106, 108, 110 and 112.
In an advantageous embodiment, in addition to the 2-enoyl (ester or thioester) reductase an ETF is used, which may be beneficial to the activity of said reductase. Such ETF may be obtained or derived from an organism from which a reductase can be obtained or derived, as identified above. In particular it may be obtained or derived from an organism of the same genus, more in particular of the same species, as the reductase that is used. Specific ETF's comprise a amino acid sequences represented by SEQUENCE ID's 102, 103, 115, 116. SEQUENCE ID's 101 and 114 represent nucleotide sequences encoding a specific ETF. Usually, such ETFs comprise two subunits (etfA and etfB) encoded by two different genes. These are generally used together to make the ETF protein active. E.g. the following combinations could be used: Sequence ID 102 with Sequence ID 103 or Sequence ID 116 with Sequence ID 115. The skilled person will be able to select other suitable ETF combinations, known in the art per se.
In an embodiment of the invention a biocatalyst not per se having a desired activity or substrate specificity may be modified by methods known in the art, e.g. by rational design or molecular evolution to create mutants able to catalyse the conversion of 2,3-dehydro adipate (ester or thioester) to adipate (ester or thioester) at a desirable rate or selectivity. Biocatalysts having activity with 2-enoyl-CoA derivatives with a chain length of 6, in particular such biocatalysts from C. kluyveri, Bos taurus, Euglena gracilis, Cavia sp., S. cerevisiae, C. tropicalis, Homo sapiens, and E. pyruvativorans are preferred.
The Preparation of Adipic Acid (‘Reaction 7’)
In accordance with the invention an adipate ester or thioester may be used to prepare adipic acid, by hydrolysis of the ester or thioester bond. This may be accomplished chemically, e.g. by chemical hydrolysis in the presence of acid or base or biocatalytically.
In a preferred method of the invention, the preparation comprises a biocatalytic reaction in the presence of a biocatalyst capable of catalysing the hydrolysis of an acyl (thio)ester.
An enzyme having such catalytic activity may therefore be referred to as an acyl (thio)ester hydrolase. An enzyme having such catalytic activity toward the acyl-CoA thioester may therefore be referred to as an acyl-CoA hydrolase. Preferably, the said acyl-CoA hydrolase is selective towards the substrate adipyl-CoA.
An enzyme capable of catalysing the hydrolysing an acyl (thio)ester may in particular be selected from the group of hydrolases (EC 3.1.2), preferably from the group of acyl-CoA hydrolase (EC 3.1.2.20), acetyl-CoA hydrolase (EC 3.1.2.1), long-chain fatty-acyl-CoA hydrolase (EC 3.1.2.2), succinyl-CoA hydrolase (EC 3.1.2.3) and acyl-[acyl-carrier-protein]-hydrolase (EC 3.1.2.14).
The biocatalyst may comprise an enzyme originating from any organism, including archaea, bacteria or eukaryotes.
In particular, the biocatalyst may comprise an enzyme of a bacterium selected from the group of E. coli, Brucella, (in particular Brucella melitensis), Agrobacterium (in particular A. tumefaciens), Xanthomonas, Sinorhizobium (in particular Sinorhizobium meliloti), Mesorhizobium (in particular Mesorhizobium loti), Vibrio, Streptomyces (in particular S. coelicolor and S. avermitilis), Rhodopseudomonas (in particular Rhodopseudomonas palustris), Xylella, Yersinia, Pseudomonas (in particular P. putida and P. aeruginosa), Shewanella, Shigella, Salmonella, Corynebacterium, Mycobacterium, Hyphomonas (in particular Hyphomonas neptunium) and Propionibacterium.
A suitable biocatalyst may in particular be found in a yeast selected from the group of Saccharomyces (in particular Saccharomyces cerevisiae) and Kluyveromyces (in particular K. lactis).
A suitable biocatalyst may in particular be found in a fungus selected from the group of Aspergillus (in particular A. niger, A. fumigatus and A. nidulans) and Penicillium (in particular P. chrysogenum).
In a further embodiment, the organism is selected from the group of Arabidopsis (in particular A. thaliana), Muridae (in particular Rattus norvegicus, Mus musculus), Bovidae (in particular Bos taurus, Ovis aries), Homo sapiens, and Caenorhabditis (in particular Caenorhabditis elegans).
In an embodiment of the invention a biocatalysts not per se having the desired activity or substrate specificity may be modified by methods known in the art, e.g. by rational design or molecular evolution, to create mutants able to efficiently convert an adipate ester or thioester to adipate. A biocatalyst having initial activity with a acyl-CoA derivative of a C4-C8 acid, preferably including dicarboxylic acids, are preferred. For instance a mutant may be created based on an acyl-CoA-thioesterase from Mus musculus (e.g. as given in Seq ID 73).
In a specific embodiment of the invention, the preparation comprises a biocatalytic reaction in the presence of a biocatalyst capable of catalysing the transfer of an activating group, in particular an ester or thio-ester, most particular CoA.
An enzyme having such catalytic activity may therefore be referred to as a CoA transferase. Preferably, the said CoA transferase is selective towards a dicarboxylic-CoA as CoA-donating substrate. More preferably, the said dicarboxylic-CoA is adipyl-CoA. Preferably, the said CoA transferase is selective towards or acetate as the CoA-accepting substrate.
An enzyme capable of catalysing the transfer of a CoA group may in particular be selected from the group of CoA transferases (EC 2.8.3), preferably from the group of dicarboxylic acid-CoA:dicarboxylic acid CoA transferase, adipate:succinyl-CoA CoA transferase, 3-oxoacid CoA-transferase (EC 2.8.3.5), 3-oxoadipate CoA-transferase (EC 2.8.3.6) and acetate CoA-transferase (EC 2.8.3.8).
A CoA transferase may in principle be obtained or derived from any organism. The organism may be bacteria, archaea or eukaryotes. In particular, organisms that are able to degrade dicarboxylic acids, in particular adipic acid, are preferred.
The organism may in particular be a bacterium selected from the group of Acinetobacter (in particular Acinetobacter strain ADP1, A. calcoaceticus), Clostridium (in particular C. kluyveri, C. acetobutylicum or C. beijerinckii), Pseudomonas (in particular P. putida and P. fluorescens), Agrobacterium, Alcaligenes, Athrobacter, Azomonas, Azospirillum, Azotobacter, Bacillus, Beijerinckia, Bradyrhizobium, Burkholderia, Comamonas, Corynebacterium, Norcadia, Rhizobium, Rhodotorula, Rodococcus, Trichosporon, and Roseburia sp.,
The organism may in particular be a yeast or fungus selected from the group of Aspergillus (in particular A. niger), Penicillium (in particular P. chrysogenum), and Neurospora.
In particular, a suitable CoA transferase may be obtained or derived from a species from the family of Hominidea, more in particular from Homo sapiens.
A suitable enzyme for reaction 7 may in particular comprise an amino acid sequence according to any of the SEQUENCE ID's 68-73, 85, 116, 117, 119-124 or a homologue thereof.
The preparation of adipic acid from a thioester may in particular be catalysed by a biocatalyst comprising an acyl-CoA hydrolase comprising an amino acid sequence according to any of the SEQUENCE ID's 68-73, 117, 119 or a homologue thereof.
The preparation of adipic acid from a thioester may in particular be catalysed by a biocatalyst comprising a CoA transferase comprising an amino acid sequence according to any of the SEQUENCE ID's 85, 121, 122, 123, 124, 125, 126 or a homologue thereof.
The CoA-transferase can be encoded by a single gene or by more than one gene. For instance, some CoA-transferases comprise two subunits encoded by two different genes. These are generally used together to make the CoA transferase protein active. E.g. the following combinations could be used: Sequence ID 121 with Sequence ID 122, or Sequence ID 125 with Sequence ID 126.
The preparation of 5-FVA from an adipate ester or an adipate thioester (‘Reaction 5’)
In an embodiment, 5-formylpentanoate (5-FVA) is prepared from an adipate ester or an adipiate thioester. This may be done chemically, or biocatalytically. The adipate may in particular be coupled to CoA or another activating group, as indicated above.
In particular, the present invention also provides a method for preparing 5-FVA from an adipate ester or an adipate thioester, in particular a method for preparing 5-FVA from adipyl-CoA thioester, in the presence of a biocatalyst capable of catalysing the reduction of an acyl ester or thioester to an aldehyde.
An enzyme having such catalytic activity may therefore be referred to as an aldehyde dehydrogenase. An enzyme having such catalytic activity toward an acyl ester or acyl thioester—for instance acyl-CoA thioester—may therefore be referred to as an aldehyde dehydrogenase (acetylating). Preferably, the biocatalyst—comprising an aldehyde dehydrogenase (acetylating)—is selective towards the substrate adipate-ester or thioester.
An enzyme capable of catalysing the reduction of an acyl (thio)ester may in particular be selected from the group of oxidoreductases (EC 1.2.1), preferably from the group of aldehyde dehydrogenases (acetylating) (EC 1.2.1.10), fatty acyl-CoA reductases (EC 1.2.1.42), long-chain-fatty-acyl-CoA reductases (EC 1.2.1.50), butanal dehydrogenases (EC 1.2.1.57) and succinate semialdehyde dehydrogenases (acetylating) (see e.g. Sohling et al. 1996. J Bacteriol. 178: 871-880)
An aldehyde dehydrogenase may in principle be obtained or derived from any organism. It is understood that the enzyme can also be obtained from metagenomic sources by direct isolation of the encoding nucleic acid and subsequent determination of activity in a heterologous host or by sequence homology found in the metagenomic DNA. The organism may be bacteria, archaea or eukaryotes. In particular the organism can be selected from bacteria, more in particular amongst the group of E. coli, Clostridium (in particular C. kluyveri, C. beijerinckii, C. acetobutylicum, C. botylicum, C. tetani, C. perfringens and C. novyi), Porphyromonas gingivalis, Listeria, Propionibacterium (in particular P. freudenreichii), Enterococcus, Fusobacterium, Lactobacillus (in particular L. lactis), Bacillus (in particular B. thuringiensis), Burkholderia (in particular B. thailandensis and B. mallei), Pseudomonas (in particular P. putida), Rhodococcus (in particular R. sp. RHA1) and Salmonella (in particular S. typhimurium). The organism can also be selected from eukaryotes, more in particular amongst the group of Giardia (in particular G. lamblia), Entamoeba (in particular E. Histolytica), Mastigamoeba balamuthi, Chlamydomonas reinhardtii, Polytomella, Piromyces, Cryptosporidium, and Spironucleus barkhanus.
A suitable dehydrogenase, may in particular comprise an amino acid sequence according to any of the SEQUENCE ID's 74-81, 139-148, or a homologue thereof.
In an embodiment of the invention a biocatalyst not per se having the desired activity or substrate specificity may be modified by methods known in the art, e.g. by rational design or molecular evolution, to create mutants able to convert adipate ester or thioester to 5-FVA. Biocatalysts having acylating aldehyde dehydrogenase activity with acyl-CoA derivatives with a chain length of 4-8, including but not limited to biocatalysts such as succinate semialdehyde dehydrogenase (acetylating) from C. kluyveri (Sequence ID 74) or P. gingivialis (Sequence ID 75) and butylaldehyde dehydrogenase (acetylating) from C. acetobutylicum (Sequence ID 80, 81) or Propionibacterium freudenreichii (Sequence ID 79) are preferred.
The Preparation of 5-FVA from Adipic Acid (‘Reaction 8’)
In accordance with the invention adipic acid may be used to prepare 5-FVA, by reduction of one of the carboxylic acid groups. This may be accomplished chemically, e.g. by selective chemical reduction optionally including protection of one carboxylic acid group or biocatalytically. In a preferred method of the invention, the preparation comprises a biocatalytic reaction in the presence of a biocatalyst capable of catalysing the reduction a carboxylic acid. The biocatalyst may use NADH or NADPH as electron donor.
An enzyme having such catalytic activity may therefore be referred to as an aldehyde dehydrogenase. Preferably, the said aldehyde dehydrogenase is selective towards the substrate adipate.
An enzyme capable of catalysing the reduction of a carboxylic acid may in particular be selected from the group of oxidoreductases (EC 1.2.1), preferably from the group of aldehyde dehydrogenase (EC 1.2.1.3, EC 1.2.1.4 and EC 1.2.1.5), malonate-semialdehyde dehydrogenase (EC 1.2.1.15), succinate-semialdehyde dehydrogenase (EC 1.2.1.16 and EC 1.2.1.24); glutarate-semialdehyde dehydrogenase (EC 1.2.1.20), aminoadipate semialdehyde dehydrogenase (EC 1.2.1.31), adipate semialdehyde dehydrogenase (EC 1.2.1.63), which may also be referred to as 6-oxohexanoate dehydrogenase. Adipate semialdehyde dehydrogenase activity has been described, for example, in the caprolactam degradation pathway in the KEGG database. In particular a 6-oxohexanoate dehydrogenase may be used. Examples of 6-oxohexanoate dehydrogenases are enzymes comprising a sequence as represented by SEQUENCE ID 127, 128 or a homologue thereof.
An aldehyde dehydrogenase may in principle be obtained or derived from any organism. The organism may be prokaryotic or eukaryotic. In particular the organism can be selected from bacteria, archaea, yeasts, fungi, protists, plants and animals (including human).
In an embodiment the bacterium is selected from the group of Acinetobacter (in particular Acinetobacter sp. NCIMB9871), Ralstonia, Bordetella, Burkholderia, Methylobacterium, Xanthobacter, Sinorhizobium, Rhizobium, Nitrobacter, Brucella (in particular B. melitensis), Pseudomonas, Agrobacterium (in particular Agrobacterium tumefaciens), Bacillus, Listeria, Alcaligenes, Corynebacterium, and Flavobacterium.
In an embodiment the organism is selected from the group of yeasts and fungi, in particular from the group of Aspergillus (in particular A. niger and A. nidulans) and Penicillium (in particular P. chrysogenum)
In an embodiment, the organism is a plant, in particular Arabidopsis, more in particular A. thaliana.
The Preparation of 6-ACA (‘Reaction 6’)
In an embodiment of the invention, 5-FVA is used to prepare 6-ACA.
In an embodiment, 6-ACA is obtained by hydrogenation over PtO2 of 6-oximocaproic acid, prepared by reaction of 5-FVA and hydroxylamine. (see e.g. F. O. Ayorinde, E. Y. Nana, P. D. Nicely, A. S. Woods, E. O. Price, C. P. Nwaonicha J. Am. Oil Chem. Soc. 1997, 74, 531-538 for synthesis of the homologous 12-aminododecanoic acid).
6-ACA can be prepared in high yield by reductive amination of 5-FVA with ammonia over a hydrogenation catalyst, for example Ni on SiO2/Al2O3 support, as described for 9-aminononanoic acid (9-aminopelargonic acid) and 12-aminododecanoic acid (12-aminolauric acid) in EP-A 628 535 or DE 4 322 065.
In a further embodiment 6-ACA is biocatalytically prepared. In a preferred method, the preparation of 6-ACA from 5-FVA comprises an enzymatic reaction in the presence of an enzyme capable of catalysing a transamination reaction in the presence of an amino donor, selected from the group of aminotransferases (E.C. 2.6.1).
In general, a suitable aminotransferase has 6-ACA 6-aminotransferase activity, capable of catalysing the conversion of 5-FVA into 6-ACA.
The aminotransferase may in particular be selected amongst aminotransferases from a mammal; Mercurialis, in particular Mercurialis perennis, more in particular shoots of Mercurialis perennis; Asplenium, more in particular Asplenium unilaterale or Asplenium septentrionale; Ceratonia, more in particular Ceratonia siliqua; Rhodobacter, in particular Rhodobacter sphaeroides, Staphylococcus, in particular Staphylococcus aureus; Vibrio, in particular Vibrio fluvialis; Pseudomonas, in particular Pseudomonas aeruginosa; Rhodopseusomonas; Bacillus, in particular Bacillus weihenstephanensis and Bacillus subtilis; Legionella; Nitrosomas; Neisseria; or yeast, in particular Saccharomyces cerevisiae.
In case the enzyme is of a mammal, it may in particular originate from mammalian kidney, from mammalian liver, from mammalian heart or from mammalian brain. For instance a suitable enzyme may be selected amongst the group of β-aminoisobutyrate:α-ketoglutarate aminotransferase from mammalian kidney, in particular β-aminoisobutyrate:α-ketoglutarate aminotransferase from hog kidney; β-alanine aminotransferase from mammalian liver, in particular β-alanine aminotransferase from rabbit liver; aspartate aminotransferase from mammalian heart; in particular aspartate aminotransferase from pig heart; 4-amino-butyrate aminotransferase from mammalian liver, in particular 4-amino-butyrate aminotransferase from pig liver; 4-amino-butyrate aminotransferase from mammalian brain, in particular 4-aminobutyrate aminotransferase from human, pig, or rat brain; α-ketoadipate-glutamate aminotransferase from Neurospora, in particular α-ketoadipate:glutamate aminotransferase from Neurospora crassa; 4-amino-butyrate aminotransferase from E. coli, or α-aminoadipate aminotransferase from Thermus, in particular α-aminoadipate aminotransferase from Thermus thermophilus, and 5-aminovalerate aminotransferase from Clostridium in particular from Clostridium aminovalericum. A suitable 2-aminoadipate aminotransferase may e.g. be provided by Pyrobaculum islandicum.
In a specific embodiment, an aminotransferase is used comprising an amino acid sequence according to Sequence ID 82, Sequence ID 83, Sequence ID 84, Sequence ID 134, Sequence ID 136, Sequence 138, or a homologue of any of these sequences. Sequence ID's 86 (wild-type) and 88 (codon optimised) represent sequence encoding an enzyme represented by Sequence ID 82 (=87). Sequence ID's 89 (wild-type) and 91 (codon optimised) represent sequence encoding an enzyme represented by Sequence ID 83 (=90). Sequence ID 133, Sequence ID 135, Sequence 137 represent encoding sequences for Sequence ID 134, Sequence ID 136, Sequence 138, respectively.
In particular, the amino donor can be selected from the group of ammonia, ammonium ions, amines and amino acids. Suitable amines are primary amines and secondary amines. The amino acid may have a D- or L-configuration. Examples of amino donors are alanine, glutamate, isopropylamine, 2-aminobutane, 2-aminoheptane, phenylmethanamine, 1-phenyl-1-aminoethane, glutamine, tyrosine, phenylalanine, aspartate, β-aminoisobutyrate, β-alanine, 4-aminobutyrate, and α-aminoadipate.
In a further preferred embodiment, the method for preparing 6-ACA comprises a biocatalytic reaction in the presence of an enzyme capable of catalysing a reductive amination reaction in the presence of an ammonia source, selected from the group of oxidoreductases acting on the CH—NH2 group of donors (EC 1.4), in particular from the group of amino acid dehydrogenases (E.C. 1.4.1). In general, a suitable amino acid dehydrogenase has 6-aminocaproic acid 6-dehydrogenase activity, catalysing the conversion of 5-FVA into 6-ACA or has α-aminopimelate 2-dehydrogenase activity, catalysing the conversion of AKP into AAP. In particular a suitable amino acid dehydrogenase be selected amongst the group of diaminopimelate dehydrogenases (EC 1.4.1.16), lysine 6-dehydrogenases (EC 1.4.1.18), glutamate dehydrogenases (EC 1.4.1.3; EC 1.4.1.4), and leucine dehydrogenases (EC 1.4.1.9).
In an embodiment, an amino acid dehydrogenase may be selected amongst an amino acid dehydrogenases classified as glutamate dehydrogenases acting with NAD or NADP as acceptor (EC 1.4.1.3), glutamate dehydrogenases acting with NADP as acceptor (EC 1.4.1.4), leucine dehydrogenases (EC 1.4.1.9), diaminopimelate dehydrogenases (EC 1.4.1.16), and lysine 6-dehydrogenases (EC 1.4.1.18).
An amino acid dehydrogenase may in particular originate from an organism selected from the group of Corynebacterium, in particular Corynebacterium glutamicum; Proteus, in particular Proteus vulgaris; Agrobacterium, in particular Agrobacterium tumefaciens; Geobacillus, in particular Geobacillus stearothermophilus; Acinetobacter, in particular Acinetobacter sp. ADP1; Ralstonia, in particular Ralstonia solanacearum; Salmonella, in particular Salmonella typhimurium; Saccharomyces, in particular Saccharomyces cerevisiae; Brevibacterium, in particular Brevibacterium flavum; and Bacillus, in particular Bacillus sphaericus, Bacillus cereus or Bacillus subtilis. For instance a suitable amino acid dehydrogenase may be selected amongst diaminopimelate dehydrogenases from Bacillus, in particular Bacillus sphaericus; diaminopimelate dehydrogenases from Brevibacterium sp.; diaminopimelate dehydrogenases from Corynebacterium, in particular diaminopimelate dehydrogenases from Corynebacterium glutamicum; diaminopimelate dehydrogenases from Proteus, in particular diaminopimelate dehydrogenase from Proteus vulgaris; lysine 6-dehydrogenases from Agrobacterium, in particular Agrobacterium tumefaciens, lysine 6-dehydrogenases from Geobacillus, in particular from Geobacillus stearothermophilus; glutamate dehydrogenases acting with NADH or NADPH as cofactor (EC 1.4.1.3) from Acinetobacter, in particular glutamate dehydrogenases from Acinetobacter sp. ADP1; glutamate dehydrogenases (EC 1.4.1.3) from Ralstonia, in particular glutamate dehydrogenases from Ralstonia solanacearum; glutamate dehydrogenases acting with NADPH as cofactor (EC 1.4.1.4) from Salmonella, in particular glutamate dehydrogenases from Salmonella typhimurium; glutamate dehydrogenases (EC 1.4.1.4) from Saccharomyces, in particular glutamate dehydrogenases from Saccharomyces cerevisiae; glutamate dehydrogenases (EC 1.4.1.4) from Brevibacterium, in particular glutamate dehydrogenases from Brevibacterium flavum; and leucine dehydrogenases from Bacillus, in particular leucine dehydrogenases from Bacillus cereus or Bacillus subtilis.
In an embodiment, 6-ACA prepared in a method of the invention is used for preparing caprolactam. Such method comprises cyclising the 6 amino-caproic acid, optionally in the presence of a biocatalyst.
Reaction conditions for any biocatalytic step in the context of the present invention may be chosen depending upon known conditions for the biocatalyst, in particular the enzyme, the information disclosed herein and optionally some routine experimentation.
In principle, the pH of the reaction medium used may be chosen within wide limits, as long as the biocatalyst is active under the pH conditions. Alkaline, neutral or acidic conditions may be used, depending on the biocatalyst and other factors. In case the method includes the use of a micro-organism, e.g. for expressing an enzyme catalysing a method of the invention, the pH is selected such that the micro-organism is capable of performing its intended function or functions. The pH may in particular be chosen within the range of four pH units below neutral pH and two pH units above neutral pH, i.e. between pH 3 and pH 9 in case of an essentially aqueous system at 25° C. A system is considered aqueous if water is the only solvent or the predominant solvent (>50 wt. %, in particular >90 wt. %, based on total liquids), wherein e.g. a minor amount (<50 wt. %, in particular <10 wt. %, based on total liquids) of alcohol or another solvent may be dissolved (e.g. as a carbon source) in such a concentration that micro-organisms which may be present remain active. In particular in case a yeast and/or a fungus is used, acidic conditions may be preferred, in particular the pH may be in the range of pH 3 to pH 8, based on an essentially aqueous system at 25° C. If desired, the pH may be adjusted using an acid and/or a base or buffered with a suitable combination of an acid and a base.
In principle, the incubation conditions can be chosen within wide limits as long as the biocatalyst shows sufficient activity and/or growth. This includes aerobic, micro-aerobic, oxygen limited and anaerobic conditions.
Anaerobic conditions are herein defined as conditions without any oxygen or in which substantially no oxygen is consumed by the biocatalyst, in particular a micro-organism, and usually corresponds to an oxygen consumption of less than 5 mmol/l·h, in particular to an oxygen consumption of less than 2.5 mmol/l·h, or less than 1 mmol/l·h.
Aerobic conditions are conditions in which a sufficient level of oxygen for unrestricted growth is dissolved in the medium, able to support a rate of oxygen consumption of at least 10 mmol/l·h, more preferably more than 20 mmol/l·h, even more preferably more than 50 mmol/l·h, and most preferably more than 100 mmol/l·h.
Oxygen-limited conditions are defined as conditions in which the oxygen consumption is limited by the oxygen transfer from the gas to the liquid. The lower limit for oxygen-limited conditions is determined by the upper limit for anaerobic conditions, i.e. usually at least 1 mmol/l·h, and in particular at least 2.5 mmol/l·h, or at least 5 mmol/l·h. The upper limit for oxygen-limited conditions is determined by the lower limit for aerobic conditions, i.e. less than 100 mmol/l·h, less than 50 mmol/l·h, less than 20 mmol/l·h, or less than to 10 mmol/l·h.
Whether conditions are aerobic, anaerobic or oxygen limited is dependent on the conditions under which the method is carried out, in particular by the amount and composition of ingoing gas flow, the actual mixing/mass transfer properties of the equipment used, the type of micro-organism used and the micro-organism density.
In principle, the temperature used is not critical, as long as the biocatalyst, in particular the enzyme, shows substantial activity. Generally, the temperature may be at least 0° C., in particular at least 15° C., more in particular at least 20° C. A desired maximum temperature depends upon the biocatalyst. In general such maximum temperature is known in the art, e.g. indicated in a product data sheet in case of a commercially available biocatalyst, or can be determined routinely based on common general knowledge and the information disclosed herein. The temperature is usually 90° C. or less, preferably 70° C. or less, in particular 50° C. or less, more in particular or 40° C. or less.
Further, solvents, additional reagents and further aids, e.g. cofactors (for instance FAD/FADH and/or NAD/NADH cofactor) may be chosen based on known reaction principles, to accomplish or accelerate a specific reaction and/or measures may be taken to shift the equilibrium to the desired side. In particular if a biocatalytic reaction is performed outside a host organism, a reaction medium comprising an organic solvent may be used in a high concentration (e.g. more than 50%, or more than 90 wt. %), in case an enzyme is used that retains sufficient activity in such a medium.
Succinate (ester or thioester) and acetate (ester or thioester) used in a method of the invention may in principle be obtained in any way.
Succinate is, e.g. naturally formed as an intermediate of the citric acid cycle (Krebs cycle) or an end product in cellular metabolism. Thus, it may be obtained from a renewable carbon source by using a suitable biocatalyst. Biocatalysts, in particular microorganisms, can be used for producing succinate from a suitable carbon source. The microorganism can be a prokaryote or a eukaryote. The microorganism may be recombinant or wild type.
In a recombinant microorganism, the metabolism may be altered to increase the yield and productivity of succinate on a suitable carbon source. Methods for increasing succinate production have been described for prokaryotes in Song and Lee, Enzyme and Microbial Technology, 2006, 39: 352-361. Succinate may also be produced in a eukaryote. In addition and alternatively, adaptive evolutionary can be applied, such as described in US application 2007/111294.
Succinate ester or thioester can be obtained from succinate in any way. In particular, succinate ester or thioester can be obtained from succinate by using a biocatalyst. In particular, succinyl-CoA can be obtained from succinate by using a biocatalyst comprising an enzyme selected from the group of acid thiol ligase (EC 6.2.1), preferably from the group of succinyl-CoA synthase (EC 6.2.1.4 and EC 6.2.1.5). In addition or alternatively, succinyl-CoA can be obtained from succinate by using a biocatalyst comprising an enzyme selected from the group of CoA transferases (EC 2.8.3) as specified for reaction 7.
Succinate ester or thioester can also be obtained from molecules other than succinate in any way. In particular, succinyl-CoA can be obtained from 2-oxoglutarate using a biocatalyst comprising a 2-oxoglutarate dehydrogenase complex. 2-Oxoglutarate dehydrogenase complex is a multi-enzyme complex participating in the TCA cycle, known to person skilled in the art. In addition or alternatively, succinyl-CoA can be obtained from 2-oxoglutarate using a biocatalyst comprising a 2-oxoglutarate: ferredoxin oxidoreductase (EC 1.2.7.3).
Acetate is a natural intermediate or end product in cellular metabolism. Thus, it may be obtained from a renewable carbon source by using a suitable biocatalyst. Biocatalysts, in particular microorganisms, can be used for producing succinate from a suitable carbon source. The microorganism can be a prokaryote or a eukaryote. The microorganism may be recombinant or wild type.
Acetate ester or thioester can be obtained from acetate in any way. In particular, acetyl-CoA can be obtained from acetate by using a biocatalyst comprising an enzyme selected from the group of acid thiol ligase (EC 6.2.1), preferably acetyl-CoA synthase (EC 6.2.1.1 and EC 6.2.1.13). In addition or alternatively, acetyl-CoA can be obtained from acetate using a biocatalyst comprising of an enzyme selected from the group of CoA transferases (EC 2.8.3) as specified for reaction 7.
Acetate ester or thioester can also be obtained from molecules other than acetate in any way. In particular, acetyl-CoA can be obtained from pyruvate using a biocatalyst comprising an enzyme selected from the group of pyruvate dehydrogenase complex, pyruvate dehydrogenase (NADP+) (EC 1.2.1.51), pyruvate formate lyase (EC 2.3.1.54) or a biocatalyst or enzyme effectively converting pyruvate to acetyl-CoA. Pyruvate dehydrogenase complex is a multi-enzyme complex converting pyruvate into acetyl-CoA, known to person skilled in the art.
Acetyl-CoA can also be obtained from acetaldehyde using a biocatalyst comprising an enzyme selected from the group of oxidoreductases (EC 1.2.1), preferably from the group of aldehyde dehydrogenases (acetylating) (EC 1.2.1.10), fatty acyl-CoA reductases (EC 1.2.1.42), butanal dehydrogenases (EC 1.2.1.57) and succinate semialdehyde dehydrogenases (acetylating) (as described in Sohling et al. 1996. J Bacteriol. 178: 871-880).
When the biocatalyst is a eukaryote, the supply of acetyl-CoA, preferably in the cytosolic compartment in the host cell, may be increased by overexpressing homologous and/or heterologous genes encoding enzymes that catalyze the conversion of a precursor molecule to acetyl-CoA. The precursor molecule may for example be acetate, as described by Shiba et al., Metabolic Engineering, 2007, 9: 160-8.
In an advantageous method of the invention, in particular a method for preparing 6-ACA, adipic acid or an intermediate compound for 6-ACA or adipic acid, use is made of a whole cell biotransformation of the substrate for 6-ACA, adipic acid or an intermediate thereof, comprising the use of a micro-organism wherein one or more enzymes catalysing any of the above reactions are produced, and a carbon source for the micro-organism.
The carbon source may in particular contain at least one compound selected from the group of monohydric alcohols, polyhydric alcohols, carboxylic acids, carbon dioxide, fatty acids, glycerides, including mixtures comprising any of said compounds. Suitable monohydric alcohols include methanol and ethanol, Suitable polyols include glycerol and carbohydrates. Suitable fatty acids or glycerides may in particular be provided in the form of an edible oil, preferably of plant origin.
In particular a carbohydrate may be used, because usually carbohydrates can be obtained in large amounts from a biologically renewable source, such as an agricultural product, for instance an agricultural waste-material. Preferably a carbohydrate is used selected from the group of glucose, fructose, sucrose, lactose, saccharose, starch, cellulose and hemi-cellulose. Particularly preferred are glucose, oligosaccharides comprising glucose and polysaccharides comprising glucose.
In a specific method of the invention, the method is a fermentation method. Such method may in particular, comprise contacting cells comprising a biocatalyst—optionally a host cell as described herein—with a fermentable carbon source, wherein the carbon source contains any of said compounds which are to be converted into the compound to be prepared or wherein the cells prepare the compound to be converted into the compound to be prepared from the carbon source.
A cell comprising one or more enzymes for catalysing a reaction step in a method of the invention can be constructed using molecular biological techniques, which are known in the art per se. For instance, if one or more biocatalysts are to be produced in a heterologous system, such techniques can be used to provide a vector which comprises one or more genes encoding one or more of said biocatalysts. A vector comprising one or more of such genes can comprise one or more regulatory elements, e.g. one or more promoters, which may be operably linked to a gene encoding an biocatalyst.
As used herein, the term “operably linked” refers to a linkage of polynucleotide elements (or coding sequences or nucleic acid sequence) in a functional relationship. A nucleic acid sequence is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence. For instance, a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the coding sequence.
As used herein, the term “promoter” refers to a nucleic acid fragment that functions to control the transcription of one or more genes, located upstream with respect to the direction of transcription of the transcription initiation site of the gene, and is structurally identified by the presence of a binding site for DNA-dependent RNA polymerase, transcription initiation sites and any other DNA sequences, including, but not limited to transcription factor binding sites, repressor and activator protein binding sites, and any other sequences of nucleotides known to one of skilled in the art to act directly or indirectly to regulate the amount of transcription from the promoter. A “constitutive” promoter is a promoter that is active under most environmental and developmental conditions. An “inducible” promoter is a promoter that is active under environmental or developmental regulation. The term “homologous” when used to indicate the relation between a given (recombinant) nucleic acid or polypeptide molecule and a given host organism or host cell, is understood to mean that in nature the nucleic acid or polypeptide molecule is produced by a host cell or organisms of the same species, preferably of the same variety or strain.
The promoter that could be used to achieve the expression of the nucleotide sequences coding for an enzyme for use in a method of the invention such as described herein above may be native to the nucleotide sequence coding for the enzyme to be expressed, or may be heterologous to the nucleotide sequence (coding sequence) to which it is operably linked. Preferably, the promoter is homologous, i.e. endogenous to the host cell.
If a heterologous promoter (to the nucleotide sequence encoding for the enzyme of interest) is used, the heterologous promoter is preferably capable of producing a higher steady state level of the transcript comprising the coding sequence (or is capable of producing more transcript molecules, i.e. mRNA molecules, per unit of time) than is the promoter that is native to the coding sequence. Suitable promoters in this context include both constitutive and inducible natural promoters as well as engineered promoters, which are well known to the person skilled in the art.
A “strong constitutive promoter” is one which causes mRNAs to be initiated at high frequency compared to a native host cell. Examples of such strong constitutive promoters in Gram-positive micro-organisms include SP01-26, SP01-15, veg, pyc (pyruvate carboxylase promoter), and amyE.
Examples of inducible promoters in Gram-positive micro-organisms include, the IPTG inducible Pspac promoter, the xylose inducible PxylA promoter.
Examples of constitutive and inducible promoters in Gram-negative microorganisms include, tac, tet, trp-tet, lpp, lac, lpp-lac, laclq, T7, T5, T3, gal, trc, ara (PBAD), SP6, λ-PR, and λ-PL.
The term “heterologous” when used with respect to a nucleic acid (DNA or RNA) or protein refers to a nucleic acid or protein that does not occur naturally as part of the organism, cell, genome or DNA or RNA sequence in which it is present, or that is found in a cell or location or locations in the genome or DNA or RNA sequence that differ from that in which it is found in nature. Heterologous nucleic acids or proteins are not endogenous to the cell into which it is introduced, but has been obtained from another cell or synthetically or recombinantly produced. Generally, though not necessarily, such nucleic acids encode proteins that are not normally produced by the cell in which the DNA is transcribed or expressed. Similarly exogenous RNA encodes for proteins not normally expressed in the cell in which the exogenous RNA is present. Heterologous nucleic acids and proteins may also be referred to as foreign nucleic acids or proteins. Any nucleic acid or protein that one of skill in the art would recognize as heterologous or foreign to the cell in which it is expressed is herein encompassed by the term heterologous nucleic acid or protein.
A method according to the invention may be carried out using an organism, which may be a host organism, in particular a host micro-organism, or a wild-type micro-organism. Accordingly, the invention also relates to a novel (host) cell, which may be a microorganism, comprising a biocatalyst capable of catalysing at least one reaction step in a method of the invention, preferably the cell is capable of producing an enzyme or a plurality of enzymes, whereby two or more reaction steps in a method of the invention are catalysed. The invention also relates to a novel vector comprising one or more genes encoding for one or more enzymes capable of catalysing at least one reaction step in a method of the invention.
In an embodiment, a cell or a vector is provided comprising a nucleic acid sequence, which may be recombinant, encoding an enzyme with 5-carboxy-2-pentenoyl ester or thioester hydrogenase activity, in particular 5-carboxy-2-pentenoyl hydrogenase activity.
Preferably, the cell further comprises at least one (recombinant vector comprising a) nucleic acid sequence encoding an enzyme selected from the group of enzymes capable of catalysing the conversion of an adipyl ester or thioester, in particular adipyl-Coa, into 5-FVA and enzymes catalysing the conversion of adipyl ester or thioester, in particular adipyl-Coa, into adipic acid.
In particular in an embodiment wherein the cell comprises an enzyme capable of catalysing the conversion of an adipyl ester or thioester into 5-FVA, the cell may advantageously comprise (a recombinant vector comprising) a nucleic acid sequence encoding an enzyme capable of catalysing the conversion of 5-FVA into 6-ACA. Such enzyme may in particular be an enzyme with 5-FVA aminotransferase activity.
In addition or alternatively, the (host) cell respectively vector comprises at least one of the following nucleic acid sequences:
One or more suitable genes may in particular be selected amongst genes encoding an enzyme as mentioned herein above, more in particular amongst genes encoding an enzyme according to any of the Sequence ID's 1-67, 94, 96, 98, 100, 102, 103, 105, 107, 109, 111, 113, 115, 116 or a homologue thereof.
The host cell may be a prokaryote or an eukaryote. In particular the host cell can be selected from bacteria, archaea, yeasts, fungi, protists, plants and animals (including human).
In particular a host cell according to the invention may be selected from the group of genera consisting of Aspergillus, Bacillus, Corynebacterium, Escherichia, Saccharomyces, Pseudomonas, Gluconobacter, Penicillium, Pichia. In particular a host strain and, thus, a host cell may be selected from the group of E. coli, Bacillus subtilis, Bacillus amyloliquefaciens, Corynebacterium glutamicum, Aspergillus niger, Penicillium chrysogenum, Pichia pastoris, Saccharomyces cerevisiae.
Host cells able to produce short chain fatty acids such as succinate and/or acetate and/or esters or thio-esters thereof may be advantageous. Organisms capable thereof are generally present in the rumen of ruminants. In particular an organism able of coproduction of succinate and acetate or esters or thioesters thereof is preferred.
The microorganism may be recombinant or wild type. In particular, microorganisms capable of producing succinate include E. coli, Actinobacillus (in particular A. succinogenes), Mannheimia (in particular M. succiniciproducens), Saccharomyces cerevisiae, Aspergillus (in particular A. niger), Penicillium (in particular P. chrysogenum and P. simplicissimum) and other organisms mentioned in Kaemwich Jantama, M. J. Haupt, Spyros A. Svoronos, Xueli Zhang, J. C. Moore, K. T. Shanmugam, L. O. Ingram. Biotechnology and Bioengineering (2007) 99, 5: 1140-1153.
In particular, microorganisms capable of producing acetate include Enterobacteriaceae (in particular E. coli, Salmonella, and Shigella), acetic acid bacteria (Includes Acetobacter (in particular Acetobacter aceti), Gluconobacter (in particular Gluconobacter oxidans), Acidomonas, Gluconacetobacter, Asaia, Kozakia, Swaminathania, Saccharibacter, Neoasaia, Granulibacter, Clostridium (in particular C. aceticum, C. thermoaceticum, C. thermoautotrophicum, C. formicoaceticum, C. kluyveri, C. propionicum), Megasphaera (in particular M. elsdenii), Acetobacterium (In particular A. woodii and A. wieringae), Lactobacillus (in particular L. plantarum, L. brevum), Bifidobacterium (In particular B. bifidum), and Leuconostoc.
The invention further relates to a novel polypeptide, respectively to a nucleotide sequence encoding such polypeptide. In particular, the invention further relates to a polypeptide comprising an amino acid sequence according to any of the Sequence ID's 57, 68-72, 79, 85 and homologues thereof. In particular, the invention further relates to a polynucleotide encoding a polypeptide comprising an amino acid sequence according to any of the Sequence ID's 57, 68-72, 79, 85 and homologues thereof.
Next, the invention is illustrated by the following examples.
Molecular and Genetic Techniques
Standard genetic and molecular biology techniques are generally known in the art and have been previously described (Maniatis et al. 1982 “Molecular cloning: a laboratory manual”. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.; Miller 1972 “Experiments in molecular genetics”, Cold Spring Harbor Laboratory, Cold Spring Harbor; Sambrook and Russell 2001 “Molecular cloning: a laboratory manual” (3rd edition), Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press; F. Ausubel et al, eds., “Current protocols in molecular biology”, Green Publishing and Wiley Interscience, New York 1987).
Plasmids and Strains
pBAD/Myc-His C and pET21d were obtained from Invitrogen (Carlsbad, Calif., USA) and EMD Biosciences (Darmstadt, Germany) respectively. pF113 (a derivative of pJF119EH (Fürste, J. P., W. Pansegrau, R. Frank, H. Blocker, P. Scholz, M. Bagdasarian, and E. Lanka. 1986. Molecular cloning of the plasmid RP4 primase region in a multi-host-range tacP expression vector. Gene 48:119-131.) which contains two NotI sites at positions 515 and 5176 respectively with the tac promoter being the start of the numbering), pACYC-tac (Krämer, M. (2000). Untersuchungen zum Einfluss erhöhter Bereitstellung von Erythrose-4-Phosphat and Phosphoenolpyruvat auf den Kohlenstofffluss in den Aromatenbiosyntheseweg von Escherichia coli. Berichte des Forschungszentrums Jülich, 3824. ISSN 0944-2952 (PhD Thesis, University of Düsseldorf) and pMS470 (Balzer, D.; Ziegelin, G.; Pansegrau, W.; Kruft, V.; Lanka, E. Nucleic Acids Research 1992, 20(8), 1851-1858.) have been described previously. E. coli TOP10 (Invitrogen, Carlsbad, Calif., USA) was used for all cloning procedures. E. coli strains Top10 (Invitrogen, Carlsbad, Calif., USA), Rv308 (ATCC31608), Rv308ΔaraB, and BL21 A1 (Invitrogen, Carlsbad, Calif., USA) were used for protein expression.
All vectors were adapted by inserting a common linker to allow an identical cloning strategy. The adaptation and general cloning scheme is shown in
Media
2xTY medium (16 g/l tryptopeptone, 10 g/l yeast extract, 5 g/l NaCl) was used for growth of E. coli. Antibiotics (100 μg/ml ampicillin) were supplemented to maintain plasmids. For induction of gene expression arabinose (for pBAD derivatives), IPTG (for pMS470 and pF113 derivatives), and a combination of arabinose and IPTG (for pET21d derivatives in E. coli BL21-A1) were used at 0.005-0.2% (arabinose) and 0.1-0.5 mM (IPTG) final concentrations.
Identification of Plasmids
Plasmids carrying the different genes were identified by genetic, biochemical, and/or phenotypic means generally known in the art, such as resistance of transformants to antibiotics, PCR diagnostic analysis of transformant or purification of plasmid DNA, restriction analysis of the purified plasmid DNA or DNA sequence analysis.
HPLC-MS Analysis Method for the Determination of CoA-Derivatives
Adipyl-Coa and 6-carboxy-2,3-ene hexanoyl-CoA concentrations were determined by LC-MS. An Agilent SB-C18 2.1*50 mm column was used for separation with acetonitrile/water buffered with 750 mg/l octylammonium acetate (pH=7.5) as mobile phase. Flow was 300 μl/min and elution was done with a gradient (Start: 70% water, decrease to 58% in 3 min, step to 45%, further decrease to 20% in 1.5 min, followed by reequilibration of the column, in such a way that the total runtime was 7 min). A LTQ orbitrap was used in electrospray negative ionization mode, scanning from m/z 765-900. adipyl-Coa and 6-carboxy-2,3-ene hexanoyl-CoA eluted at 2.25 min and 2.5 min respectively. The selectivity of the method was enhanced by observing the accurate protonated molecules of the compounds requested (adipyl-Coa: 894.15123-894.16017, 6-carboxy-2,3-ene hexanoyl-CoA: 892.13437-892.14329). To determine concentrations a standard curve of synthetically prepared compounds was run to calculate a response factor for the respective ions. This was used to calculate the concentrations in unknown samples.
Adipate can be detected and quantified as described in Kippenberger, M.; Winterhalter, R.; Moortgat, G. K. Anal. Bioanal. Chem. 2008, 392(7-8), 1459-1470.
Expression Constructs
Putative 6-carboxy-2,3-ene-hexanoyl-CoA reductases were selected from databases (Table 1).
Target genes encoding the selected proteins were codon pair optimized (using methodology described in WO08000632) and constructed synthetically (Geneart, Regensburg, Germany). Before optimization, targeting sequences (e.g secretion signals or peroxisomal/mitochondrial targeting sequences) were removed from the amino acid sequence. Such targeting sequences can be identified by bioinformatics tools well known in the art, such as described in Emanuelsson et al. 2007. Nature protocols, 2: 953-971). In the optimization procedure internal restriction sites were avoided and common restriction sites were introduced at the start and stop to allow cloning according to the strategy shown in
Protein Expression in E. coli
Starter cultures were grown overnight in 96-well plates with 200 μl medium/well. 40-160 μl were transferred to fresh 24-deep-well plates with 4 ml media. For pBAD constructs in E. coli TOP10 or E. coli Rv308ΔaraB this medium directly contained 0.005% arabinose for inductions. Plates were incubated on an orbital shaker (Infors, 550 rpm) at 25° C. After 4-6 h inducers were added (0.5 mM IPTG for pF113 and pMS470 in E. coli Rv308, E. coli BL21 or E. coli TOP10; 0.5 mM IPTG and 0.2% arabinose for pET21d in E. coli BL21A1) and plates were incubated for another 4-48 h until cells were collected by centrifugation.
Preparation of Cell Free Extract and His-Tag Purification
Cells from small scales growth (see previous paragraph) were harvested by centrifugation and the supernatant was discarded. The cell pellets formed during centrifugation were frozen at −20° C. for at least 16 h and then thawed on ice. 2 ml of freshly prepared lysis buffer (50 mM potassium phosphate pH7.5, 0.1 mg/ml DNAse I (Roche, Almere, NL), 2 mg/ml Lysozyme, 0.5 mM MgSO4, 1 mM dithiothreitol, and protease inhibitors (Complete Mini EDTA-free Tablets™, Roche, Almere, NL, were used according to the manufacturers specification) were added to each well and cells were resuspended by vigorously vortexing the plate for 2-5 min. To achieve lysis, the plate was incubated at room temperature for 30 min. To remove cell debris, the plate was centrifuged at 4° C. and 6000 g for 20 min. The supernatant was transferred to a fresh plate and kept on ice until further use. For purification of His-tagged proteins His Multitrap HP filter plates (GE Healthcare bioscience AB, Uppsala, Sweden) were used according to the manufacturer's instructions.
Synthesis of Substrates
Substrate (J. R. Stern, A. del Campillo, J. Biol. Chem., 1956, 985. A. K. Das, M. D. Uhler, A. K. Hajra, J. Biol. Chem., 2000, 24333. H. Oku, N. Futamori, K. Masuda, Y. Shimabukuro, T. Omine, H. Iwasaki, Biosc. Biotech. Biochem., 2003, 2107. Elvidge et. al, J. Chem. Soc., 1953, 1793. F. Liu, H-Y. Zha, Z-J. Yao, J. Org. Chem., 2003, 6679-6684) and product (WO2004/106347) of the desired biochemical reaction and were synthesized by Syncom (Groningen, NL) according to published procedures.
Enzymatic Enoyl-CoA Assay
A reaction mixture was prepared comprising 50 mM potassium buffer (pH7.5), 0.7 mM NADH and NADPH each, and approximately 20 μM of the substrate 6-carboxylic 2,3-ene hexanoyl-CoA. 190 μl of the reaction mixture were dispensed into each well of 96-wellplates. The same way 10 μl of cell free extract prepared from the respective strain carrying the empty vector was used in control reactions. To start the reaction, 10 μl of the cell free extracts or purified protein were added, to each of the wells. Reaction mixtures were incubated at room temperature (20-25 C) for 15 min to 24 h with online monitoring of UV absorption at 340 nm. At the end reactions were stopped by adding an equal volume of MeOH and samples were centrifuged. Supernatant was transferred to a fresh plate and stored at −80 C until further analysis by HPLC-MS. adipyl-Coa was found as shown in Table 1.
1If the resulting polypeptide after modification does not start with a methionine at the N-terminus, the resulting polypeptide is further modified by adding a methionine at the N-terminus.
2Results shown were obtained with E. coli BL21 containing the adi gene cloned in pMS470 after 20 h incubation. Positive results were also obtained with other expression vectors and host strains (such as pET21d in E. coli BL21-A1, pBAD//Myc-His C in E. coli Rv308 and pF113 in E. coli BL21) and different incubation periods (e.g. 2 h).
Construction of an Adipate Biosynthetic Pathway
A synthetic pathway was designed consisting of the enzymatic activities shown in
For reactions 1, 2, and 3 the combinations of adi21+22+23 or adi26+27+28 were used. For reaction 7 adi29, adi30 or a combination of adi24+25 were used. For reaction 4 adi1-20 can be used with adi8, adi6, adi13+12.
Construction of an Adipate Producing E. coli Strain
To construct adipate producing E. coli strains plasmids encoding a complete adipate pathway were transformed into the appropriate host strains for expression of the cloned genes. pMS470 constructs containing full pathways, were transformed into E. coli BL21, TOP10 and Rv308. pBAD/Myc-His C constructs were transformed into E. coli TOP10 and Rv308ΔaraB. Constructs in pF113 or pACYC-tac were transformed together with compatible pF113, pACYC-tac or pMS470 constructs in a way that the final strain contained a complete adipate pathway. These plasmids were co-transformed to E. coli TOP10, BL21, and Rv308.
Production of Adipate
For production of adipate, starter cultures were grown over night in 96-well plates with 200 μl medium at 30 C. 50 μl were transferred to a fresh plate 24-well plate with 4 ml medium and grown for 4-6 h at 25 C and then inducers to induce expression of the adipate pathway were added. Cultures were incubated for another 12 h-72 h at 25 C. Plates were centrifuged and samples prepared for LC-MS analysis. Supernatant was mixed 1:1 with MeOH to precipitate proteins and then directly analyzed. Metabolites from cells were extracted by resuspending the pellet in 1 ml Ethanol. The cell suspension was transferred to a tube with a screw top and heated in a boiling water bath for 3 min. After centrifugation the supernatant was transferred to a fresh tube and evaporated in a speed-vac. Dry samples were resuspended in 100 μl mobile phase prior to analysis.
HPLC-MS Analysis Method for the Determination of 5-FVA
5-FVA was detected by selective reaction monitoring (SRM)-MS, measuring the transition m/z 129→83. Concentrations for 5-FVA were calculated by measuring the peak area of the 5-FVA peak eluting at approximately 6 min. Calibration was performed by using an external standard procedure. All the LC-MS experiments were performed on an Agilent 1200 LC system, consisting of a quaternary pump, autosampler and column oven, coupled with an Agilent 6410 QQQ triple quadrupole MS.
LC Conditions:
Expression Constructs
Putative adipyl-CoA-reductases were selected (SeqID 74, 75, 77, 79, 80, 139-148). Expression constructs are designed and prepared in the same way as described before in example 2 using pBAD/Myc-His C and pET21d.
Protein Expression, Extraction and Purification
All steps are carried out as described in example 2.
Enzymatic Adipyl-CoA Reductase Assay
A reaction mixture is prepared comprising 50 mM potassium buffer (pH7.5), 0.7 mM NADH and NADPH each, and 10 μM-10 mM of the substrate adipyl-CoA. 190 μl of the reaction mixture are dispensed into each well of 96-wellplates. Adipyl-CoA was prepared as described in example 2. To start the reaction, 10 μl of the cell free extracts or purified protein are added to each of the wells. The same way 10 μl of cell free extract prepared from the respective strain carrying the empty vector is used in control reactions. Reaction mixtures are incubated at room temperature (20-25 C) for 15 min-24 h with online monitoring of UV absorption at 340 nm. At the end reactions are stopped by adding an equal volume of MeOH and samples are centrifuged. Supernatant is transferred to a fresh plate and stored at −80 C until detection of 5-FVA by HPLC-MS. Measurement of 5-FVA demonstrates adipyl-CoA reductase activity of the selected enzymes.
HPLC-MS Analysis for the Determination of 6-ACA
Calibration:
The calibration was performed by an external calibration line of 6-ACA (m/z 132→m/z 114, Rt 7.5 min). All the LC-MS experiments were performed on an Agilent 1100, equipped with a quaternary pump, degasser, autosampler, column oven, and a single-quadrupole MS (Agilent, Waldbronn, Germany). The LC-MS conditions were:
Cloning of Target Genes
Design of Expression Constructs
attB sites were added to all genes upstream of the ribosomal binding site and start codon and downstream of the stop codon to facilitate cloning using the Gateway technology (Invitrogen, Carlsbad, Calif., USA).
Gene Synthesis and Construction of Plasmids
Synthetic genes were obtained from DNA2.0 and codon optimised for expression in E. coli according to standard procedures of DNA2.0. The aminotransferase genes from Vibrio fluvialis JS17 [SEQ ID No. 86] and Bacillus weihenstephanensis KBAB4 [SEQ ID No. 89] encoding the amino acid sequences of the V. fluvialis JS17 ω-aminotransferase [SEQ ID No. 82] and the B. weihenstephanensis KBAB4 aminotransferase (ZP_01186960) [SEQ ID No. 83], respectively, were codon optimised and the resulting sequences [SEQ ID No. 88] and [SEQ ID No. 91] were obtained by DNA synthesis.
Cells provided with said genes are referred to herein below as E. coli TOP10/pBAD-Vfl_AT and E. coli TOP10/pBAD-Bwe_AT respectively
Cloning by PCR
Various genes encoding a biocatalyst were amplified from genomic DNA by PCR using PCR Supermix High Fidelity (Invitrogen) according to the manufacturer's specifications
PCR reactions were analysed by agarose gel electrophoresis and PCR products of the correct size were eluted from the gel using the QIAquick PCR purification kit (Qiagen, Hilden, Germany). Purified PCR products were cloned into pBAD/Myc-His-DEST expression vectors using the Gateway technology (Invitrogen) via the introduced attB sites and pDONR-zeo (Invitrogen) as entry vector as described in the manufacturer's protocols. The sequence of genes cloned by PCR was verified by DNA sequencing. This way the expression vectors, pBAD-Bsu_gi16077991_AT (comprising a gene as represented by Sequence ID 133, encoding peptide represented by Sequence ID 134), pBAD-Pae_gi9946143_AT (using primers as identified in sequence ID's 130 and 131), pBAD-Pae_gi9951072_AT (comprising a gene as represented by Sequence ID 135, encoding peptide represented by Sequence ID 136), pBAD-Pae_gi9951630_AT (comprising a gene as represented by Sequence ID 137, encoding peptide represented by Sequence ID 138) were obtained. The corresponding expression strains were obtained by transformation of chemically competent E. coli TOP10 (Invitrogen) with the pBAD constructs.
Enzymatic Reactions for Conversion of 5-Formylpentanoic Acid to 6-ACA
Unless specified otherwise, a reaction mixture was prepared comprising 10 mM 5-formylpentanoic acid, 20 mM racemic α-methylbenzylamine, and 200 μM□ pyridoxal 5′-phosphate in 50 mM potassium phosphate buffer, pH 7.0. 100 μl of the reaction mixture were dispensed into each well of the well plates. To start the reaction, 20 μl of the cell free extracts were added, to each of the wells. Reaction mixtures were incubated on a shaker at 37° C. for 24 h. Furthermore, a chemical blank mixture (without cell free extract) and a biological blank (E. coli TOP10 with pBAD/Myc-His C) were incubated under the same conditions. Samples were analysed by HPLC-MS. The results are summarised in the following table.
E. coli TOP10/pBAD-Vfl_AT
E. coli TOP10/pBAD-Pae_pBAD-
E. coli TOP10/pBAD-Pae_AT
E. coli TOP10/pBAD-Bwe_AT
E. coli TOP10/pBAD-Bsu_gi16077991_AT
E. coli TOP10/pBAD-Pae_gi9951072_AT
E. coli TOP10/pBAD-Pae_gi9951630_AT
E. coli TOP10 with pBAD/Myc-His C
It is shown that 6-ACA is formed from 5-FVA in the presence of an aminotransferase, and that E. coli is capable of catalysing this formation.
| Number | Date | Country | Kind |
|---|---|---|---|
| 08152595 | Mar 2008 | EP | regional |
This application is a division of U.S. patent application Ser. No. 15/140,384, filed Apr. 27, 2016, now issued U.S. Pat. No. 10,435,723, which is a continuation of U.S. patent application Ser. No. 14/082,000, filed Nov. 15, 2013, now abandoned, which is a continuation of U.S. patent application Ser. No. 13/841,142, filed Mar. 15, 2013, now abandoned, which is a continuation of U.S. patent application Ser. No. 13/572,346, filed Aug. 10, 2012, now abandoned, which is a continuation of U.S. patent application Ser. No. 12/921,547, now issued U.S. Pat. No. 9,096,873, issued Aug. 4, 2015, which is a U.S. National Stage Application under 35 U.S.C. § 371 of International Patent Application No. PCT/NL2009/050115, filed Mar. 11, 2009, which claims the benefit of priority to European Patent Application No. 08152595.8, filed Mar. 11, 2008, the entire contents of which are each incorporated herein by reference.
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| Number | Date | Country | |
|---|---|---|---|
| 20200239917 A1 | Jul 2020 | US |
| Number | Date | Country | |
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| Parent | 15140384 | Apr 2016 | US |
| Child | 16573796 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 14082000 | Nov 2013 | US |
| Child | 15140384 | US | |
| Parent | 13841142 | Mar 2013 | US |
| Child | 14082000 | US | |
| Parent | 13572346 | Aug 2012 | US |
| Child | 13841142 | US | |
| Parent | 12921547 | US | |
| Child | 13572346 | US |
