Patent Application
20140193862
This invention relates to methods for biosynthesizing one or more of pimelic acid, 7-hydroxyheptanoate, 7-aminoheptanoate, heptamethylenediamine and 1,7-heptanediol (hereafter “C7 building blocks”) using one or more isolated enzymes such as β-ketothiolases, dehydrogenases, reductases, thioesterases, decarboxylases, hydratases, synthases, thioesterases, CoA-ligases, CoA-transferases, deacetylases, or transaminases or using recombinant host cells expressing one or more such enzymes or using recombinant host cells expressing one or more such enzymes.
Nylons are polyamides which are generally synthesized by the condensation polymerisation of a diamine with a dicarboxylic acid. Similarly, Nylons may be produced by the condensation polymerisation of lactams. A ubiquitous Nylon is Nylon 6,6, which is produced by reaction of hexamethylenediamine (HMD) and adipic acid. Nylon 6 can be produced by a ring opening polymerisation of caprolactam (Anton & Baird, Polyamides Fibers, Encyclopedia of Polymer Science and Technology, 2001).
Nylon 7 and Nylon 7,7 represent novel polyamides with value-added characteristics compared to Nylon 6 and Nylon 6,6. Nylon 7 is produced by polymerisation of 7-aminoheptanoic acid, whereas Nylon 7,7 is produced by condensation polymerisation of pimelic acid and heptamethylenediamine. No economically viable petrochemical routes exist to producing the monomers for Nylon 7 and Nylon 7,7.
Given no economically viable petrochemical monomer feedstocks; biotechnology offers an alternative approach via biocatalysis. Biocatalysis is the use of biological catalysts, such as enzymes, to perform biochemical transformations of organic compounds.
Both bioderived feedstocks and petrochemical feedstocks are viable starting materials for the biocatalysis processes.
Accordingly, against this background, it is clear that there is a need for sustainable methods for producing one or more of pimelic acid, 7-hydroxyheptanoate, 7-aminoheptanoate, heptamethylenediamine and 1,7-heptanediol (hereafter “C7 building blocks”) wherein the methods are biocatalyst based.
However, no wild-type prokaryote or eukaryote naturally overproduces or excretes such C7 building blocks to the extracellular environment. Nevertheless, the metabolism of pimelic acid has been reported.
The dicarboxylic acid, pimelic acid, is converted efficiently as a carbon source by a number of bacteria and yeasts via β-oxidation into central metabolites. β-oxidation of Coenzyme A (CoA) activated pimelate to CoA activated 3-oxopimelate facilitates further catabolism via, for example, pathways associated with aromatic substrate degradation. The catabolism of 3-oxopimeloyl-CoA to acetyl-CoA and glutaryl-CoA by several bacteria has been characterized comprehensively (Harwood and Parales, Annual Review of Microbiology, 1996, 50:553-590).
The optimality principle states that microorganisms regulate their biochemical networks to support maximum biomass growth. Beyond the need for expressing heterologous pathways in a host organism, directing carbon flux towards C7 building blocks that serve as carbon sources rather than as biomass growth constituents, contradicts the optimality principle. For example, transferring the 1-butanol pathway from Clostridium species into other production strains has often fallen short by an order of magnitude compared to the production performance of native producers (Shen et al., Appl. Environ. Microbiol., 2011, 77(9):2905-2915).
The efficient synthesis of the seven carbon aliphatic backbone precursor is a key consideration in synthesizing one or more C7 building blocks prior to forming terminal functional groups, such as carboxyl, amine or hydroxyl groups, on the C7 aliphatic backbone.
This document is based at least in part on the discovery that it is possible to construct biochemical pathways for producing a seven carbon chain aliphatic backbone precursor in which one or two functional groups, i.e., carboxyl, amine or hydroxyl, can be formed, leading to the synthesis of one or more of pimelic acid, 7-aminoheptanoic acid, 7-hydroxyheptanoic acid, heptamethylenediamine, and 1,7-heptanediol (hereafter “C7 building blocks). Pimelic acid and pimilate, 7-hydroxyheptanoic acid and 7-hydroxyheptanoate, and 7-aminoheptanoic and 7-aminoheptanoate are used interchangeably herein to refer to the compound in any of its neutral or ionized forms, including any salt forms thereof. It is understood by those skilled in the art that the specific form will depend on pH. These pathways, metabolic engineering and cultivation strategies described herein rely on carbon chain elongation enzymes or homologs associated with cyclohexane carboxylate biosynthesis in Synthrophus aciditrophicus or 2-aminoadipate lysine biosynthesis.
In the face of the optimality principle, it surprisingly has been discovered that appropriate non-natural pathways, feedstocks, host microorganisms, attenuation strategies to the host's biochemical network, and cultivation strategies may be combined to efficiently produce one or more C7 building blocks.
In some embodiments, the C7 aliphatic backbone for conversion to a C7 building block is 3-ketopimeloyl-CoA (also can be referred to as 3-oxopimeloyl-CoA) or pimeloyl-CoA, which can be formed from acetyl-CoA using enzymes associated with cyclohexane carboxylate biosynthesis in in Synthrophus aciditrophicus or 2-aminoadipate lysine biosynthesis. See
In some embodiments, a terminal carboxyl group can be enzymatically formed using a thioesterase, an aldehyde dehydrogenase, a 7-oxoheptanoate dehydrogenase, a CoA-transferase, or a reversible CoA-ligase. See
In some embodiments, a terminal amine group can be enzymatically formed using a ω-transaminase or a deacetylase. See
In some embodiments, a terminal hydroxyl group can be enzymatically formed using an alcohol dehydrogenase. See
In one aspect, this document features a method for biosynthesizing a product selected from the group consisting of pimelic acid, 7-aminoheptanoic acid, 7-hydroxyheptanoic acid, heptamethylenediamine, and 1,7-heptanediol. The method includes enzymatically synthesizing a seven carbon chain aliphatic backbone using enzymes associated with cyclohexane carboxylate biosynthesis or the 2-aminoadipate lysine biosynthesis pathway, and enzymatically forming one or two terminal functional groups selected from the group consisting of carboxyl, amine, and hydroxyl groups in the backbone, thereby forming the product. The seven carbon chain aliphatic backbone can be pimeloyl-CoA. Pimeloyl-CoA can be enzymatically synthesized from acetyl-CoA or 2-oxoglutarate via 3-ketopimeloyl-CoA. A β-ketothiolase or a β-ketoacyl[acp] synthase can convert glutaryl-CoA to 3-ketopimeloyl-CoA. Glutaryl-CoA can be produced from crotonyl-CoA using a glutaconyl-CoA decarboxylase or a glutaryl-CoA dehydrogenase. 3-ketopimeloyl-CoA can be converted to 3-hydroxypimeloyl-CoA using a 3-hydroxyadipyl-CoA dehydrogenase; 3-hydroxypimeloyl-CoA can be converted to 6-ketocyclohex-1-ene-1-carboxyl-CoA by a 6-oxo-cyclohex-1-ene-carbonyl-CoA hydrolase or 3-hydroxypimeloyl-CoA can be converted to 2,3-dehydropimeloyl-CoA by an enoyl-CoA hydratase.
The two terminal functional groups can be the same (e.g., amine or hydroxyl) or can be different (e.g., a terminal amine and a terminal carboxyl group; or a terminal hydroxyl group and a terminal carboxyl group).
A ω-transaminase or a deacetylase can enzymatically form an amine group. The ω-transaminase can have at least 70% sequence identity to any one of the amino acid sequences set forth in SEQ ID NO. 8-13.
A 6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, a 4-hydroxybutyrate dehydratase, or an alcohol dehydrogenase can enzymatically form a hydroxyl group.
A thioesterase, an aldehyde dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a CoA-transferase (e.g. a glutaconate CoA transferase), or a reversible CoA-ligase (e.g., a reversible succinate-CoA ligase) can enzymatically forms a terminal carboxyl group. The thioesterase can have at least 70% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1.
A carboxylate reductase and a phosphopantetheinyl transferase can form a terminal aldehyde group as an intermediate in forming the product. The carboxylate reductase can have at least 70% sequence identity to any one of the amino acid sequences set forth in SEQ ID NO. 2-7.
Any of the methods can be performed in a recombinant host by fermentation. The host can be subjected to a cultivation strategy under aerobic, anaerobic, micro-aerobic or mixed oxygen/denitrification cultivation conditions. The host can be cultured under conditions of nutrient limitation. The host can be retained using a ceramic hollow fiber membrane to maintain a high cell density during fermentation.
In any of the methods, the host's tolerance to high concentrations of a C7 building block can be improved through continuous cultivation in a selective environment.
The principal carbon source fed to the fermentation can derive from biological or non-biological feedstocks. In some embodiments, the biological feedstock is, includes, or derives from, monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin, levulinic acid and formic acid, triglycerides, glycerol, fatty acids, agricultural waste, condensed distillers' solubles, or municipal waste.
In some embodiments, the non-biological feedstock is or derives from natural gas, syngas, CO2/H2, methanol, ethanol, benzoate, non-volatile residue (NVR) or a caustic wash waste stream from cyclohexane oxidation processes, or a terephthalic acid/isophthalic acid mixture waste stream.
In another aspect, this document features a recombinant host that includes at least one exogenous nucleic acid encoding i) a β-ketothiolase or a β-ketoacyl[acp] synthase, (ii) a 6-oxo-cyclohex-1-ene-carbonyl-CoA hydrolase or an enoyl-CoA hydratase, and (iii) a trans-2-enoyl-CoA reductase, an enoyl[acp] reductase, or a 2-ketocyclohexanecarboxyl-CoA hydrolase, the host producing pimeloyl-CoA. The host further can include a glutaconyl-CoA decarboxylase or a glutaryl-CoA dehydrogenase.
A recombinant host producing pimeloyl-CoA further can include at least one exogenous nucleic acid encoding one or more of a thioesterase, an aldehyde dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a glutaconate CoA-transferase, a reversible succinyl-CoA ligase, an acetylating aldehyde dehydrogenase, or a carboxylate reductase, the host producing pimelic acid or pimelate semialdehyde.
A recombinant host producing pimelate semialdehyde further can include at least one exogenous nucleic acid encoding a ω-transaminase, and producing 7-aminoheptanoate.
A recombinant host producing pimelate semialdehyde further can include at least one exogenous nucleic acid encoding a 4-hydroxybutyrate dehydrogenase, a 5-hydroxypentanoate dehydrogenase or a 6-hydroxyhexanoate dehydrogenase, the host producing 7-hydroxyheptanoic acid.
A recombinant host producing pimelate semialdehyde, 7-aminoheptanoate, or 7-hydroxyheptanoic acid further can include a carboxylate reductase, a ω-transaminase, a deacetylase, an N-acetyl transferase, or an alcohol dehydrogenase, the host producing heptamethylenediamine.
A recombinant host producing 7-hydroxyheptanoic acid further can include at least one exogenous nucleic acid encoding a carboxylate reductase or an alcohol dehydrogenase, the host producing 1,7-heptanediol.
The recombinant host can be a prokaryote, e.g., from the genus Escherichia such as Escherichia coli; from the genus Clostridia such as Clostridium ljungdahlii, Clostridium autoethanogenum or Clostridium kluyveri; from the genus Corynebacteria such as Corynebacterium glutamicum; from the genus Cupriavidus such as Cupriavidus necator or Cupriavidus metallidurans; from the genus Pseudomonas such as Pseudomonas fluorescens, Pseudomonas putida or Pseudomonas oleavorans; from the genus Delftia acidovorans, from the genus Bacillus such as Bacillus subtillis; from the genes Lactobacillus such as Lactobacillus delbrueckii; from the genus Lactococcus such as Lactococcus lactis or from the genus Rhodococcus such as Rhodococcus equi.
The recombinant host can be a eukaryote, e.g., a eukaryote from the genus Aspergillus such as Aspergillus niger; from the genus Saccharomyces such as Saccharomyces cerevisiae; from the genus Pichia such as Pichia pastoris; from the genus Yarrowia such as Yarrowia lipolytica, from the genus Issatchenkia such as Issathenkia orientalis, from the genus Debaryomyces such as Debaryomyces hansenii, from the genus Arxula such as Arxula adenoinivorans, or from the genus Kluyveromyces such as Kluyveromyces lactis.
Any of the recombinant hosts described herein further can include one or more of the following attenuated enzymes: a phosphotransacetylase generating acetate, an acetate kinase; a lactate dehydrogenase; a menaquinol-fumarate oxidoreductase; an alcohol dehydrogenase producing ethanol; a pyruvate decarboxylase; a 2-oxoacid decarboxylase generating isobutanol; a polymer synthase; a NADPH-specific L-glutamate dehydrogenase; a NADPH/NADH L-glutamate dehydrogenase; a NADH-consuming transhydrogenase, a pimeloyl-CoA dehydrogenase; an acyl-CoA dehydrogenase that degrades C7 building blocks and their precursors; a glutaryl-CoA dehydrogenase; or a pimeloyl-CoA synthetase.
Any of the recombinant hosts described herein further can overexpress one or more genes encoding: an acetyl-CoA synthetase, a formate dehydrogenase, a PEP carboxykinase, a PEP carboxylase, a pyruvate carboxylase, a PEP synthase, a L-alanine dehydrogenase; a NADH-specific L-glutamate dehydrogenase; a diamine transporter; a dicarboxylate transporter; and/or a multidrug transporter.
The reactions of the pathways described herein can be performed in one or more cell (e.g., host cell) strains (a) naturally expressing one or more relevant enzymes, (b) genetically engineered to express one or more relevant enzymes, or (c) naturally expressing one or more relevant enzymes and genetically engineered to express one or more relevant enzymes. Alternatively, relevant enzymes can be extracted from any of the above types of host cells and used in a purified or semi-purified form. Extracted enzymes can optionally be immobilized on a solid substrate such as the floors and/or walls of appropriate reaction vessels. Moreover, such extracts include lysates (e.g. cell lysates) that can be used as sources of relevant enzymes. In the methods provided by the document, all the steps can be performed in cells (e.g., host cells), all the steps can be performed using extracted enzymes, or some of the steps can be performed in cells and others can be performed using extracted enzymes.
Many of the enzymes described herein catalyze reversible reactions, and the reaction of interest may be the reverse of the described reaction. The schematic pathways shown in
In some embodiments, the host microorganism's endogenous biochemical network is attenuated or augmented to (1) ensure the intracellular availability of acetyl-CoA (2) create an NADH imbalance that may only be balanced via the formation of a C7 building block, (3) prevent degradation of central metabolites or central precursors leading to and including C7 building blocks and (4) ensure efficient efflux from the cell.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although methods and materials similar or equivalent to those described herein can be used to practice the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.
The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and the drawings, and from the claims. The word “comprising” in the claims may be replaced by “consisting essentially of” or with “consisting of,” according to standard practice in patent law.
This document provides enzymes, non-natural pathways, cultivation strategies, feedstocks, host microorganisms and attenuations to the host's biochemical network, which generates a seven carbon chain aliphatic backbone from central metabolites in which one or two terminal functional groups may be formed leading to the synthesis of one or more of pimelic acid, 7-hydroxyheptanoic acid, 7-aminoheptanoic acid, heptamethylenediamine, and 1,7-heptanediol (referred to as “C7 building blocks” herein). As used herein, the term “central precursor” is used to denote any metabolite in any metabolic pathway shown herein leading to the synthesis of a C7 building block. The term “central metabolite” is used herein to denote a metabolite that is produced in all microorganisms to support growth.
Host microorganisms described herein can include endogenous pathways that can be manipulated such that one or more C7 building blocks can be produced. In an endogenous pathway, the host microorganism naturally expresses all of the enzymes catalyzing the reactions within the pathway. A host microorganism containing an engineered pathway does not naturally express all of the enzymes catalyzing the reactions within the pathway but has been engineered such that all of the enzymes within the pathway are expressed in the host.
The term “exogenous” as used herein with reference to a nucleic acid (or a protein) and a host refers to a nucleic acid that does not occur in (and cannot be obtained from) a cell of that particular type as it is found in nature or a protein encoded by such a nucleic acid. Thus, a non-naturally-occurring nucleic acid is considered to be exogenous to a host once in the host. It is important to note that non-naturally-occurring nucleic acids can contain nucleic acid subsequences or fragments of nucleic acid sequences that are found in nature provided the nucleic acid as a whole does not exist in nature. For example, a nucleic acid molecule containing a genomic DNA sequence within an expression vector is non-naturally-occurring nucleic acid, and thus is exogenous to a host cell once introduced into the host, since that nucleic acid molecule as a whole (genomic DNA plus vector DNA) does not exist in nature. Thus, any vector, autonomously replicating plasmid, or virus (e.g., retrovirus, adenovirus, or herpes virus) that as a whole does not exist in nature is considered to be non-naturally-occurring nucleic acid. It follows that genomic DNA fragments produced by PCR or restriction endonuclease treatment as well as cDNAs are considered to be non-naturally-occurring nucleic acid since they exist as separate molecules not found in nature. It also follows that any nucleic acid containing a promoter sequence and polypeptide-encoding sequence (e.g., cDNA or genomic DNA) in an arrangement not found in nature is non-naturally-occurring nucleic acid. A nucleic acid that is naturally-occurring can be exogenous to a particular host microorganism. For example, an entire chromosome isolated from a cell of yeast x is an exogenous nucleic acid with respect to a cell of yeast y once that chromosome is introduced into a cell of yeast y.
In contrast, the term “endogenous” as used herein with reference to a nucleic acid (e.g., a gene) (or a protein) and a host refers to a nucleic acid (or protein) that does occur in (and can be obtained from) that particular host as it is found in nature. Moreover, a cell “endogenously expressing” a nucleic acid (or protein) expresses that nucleic acid (or protein) as does a host of the same particular type as it is found in nature. Moreover, a host “endogenously producing” or that “endogenously produces” a nucleic acid, protein, or other compound produces that nucleic acid, protein, or compound as does a host of the same particular type as it is found in nature.
For example, depending on the host and the compounds produced by the host, one or more of the following enzymes may be expressed in the host in addition to (i) a β-ketothiolase or a β-ketoacyl[acp] synthase; (ii) a 6-oxo-cyclohex-1-ene-carbonyl-CoA hydrolase or an enoyl-CoA hydratase accepting 3-hydroxypimeloyl-CoA as substrate, and (iii) a trans-2-enoyl-CoA reductase, an enoyl-[acp] reductase, or a 2-ketocyclohexanecarboxyl-CoA hydrolase: a glutaconyl-CoA decarboxylase, a glutaryl-CoA dehydrogenase, a 3-hydroxyacyl-CoA dehydrogenase, a 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase, a cyclohexa-1,5-dienecarbonyl-CoA hydratase, a cyclohex-1-ene-1-carboxyl-CoA dehydrogenase, a cyclohex-1-ene-1-carboxyl-CoA hydratase, a 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase, a thioesterase, an aldehyde dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a 4-hydroxybutyrate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, a 6-hydroxyhexanoate dehydrogenase, a CoA-transferase, a reversible CoA-ligase, an acetylating aldehyde dehydrogenase, a ω-transaminase, a carboxylate reductase, a deacetylase, a lysine N-acetyl transferase, or an alcohol dehydrogenase. In recombinant hosts expressing a carboxylate reductase, a phosphopantetheinyl transferase also can be expressed as it enhances activity of the carboxylate reductase.
For example, a recombinant host can include a β-ketothiolase or a β-ketoacyl[acp] synthase; a 6-oxo-cyclohex-1-ene-carbonyl-CoA hydrolase or an enoyl-CoA hydratase accepting 3-hydroxypimeloyl-CoA as substrate; and a trans-2-enoyl-CoA reductase, an enoyl-[acp] reductase, or a 2-ketocyclohexanecarboxyl-CoA hydrolase, and produce pimeloyl-CoA. The host further can include a glutaconyl-CoA decarboxylase or a glutaryl-CoA dehydrogenase.
A recombinant host producing pimeloyl-CoA further can include one or more of an aldehyde dehydrogenase, a 6-oxohexanoate dehydrogenase, a thioesterase, a 7-oxoheptanoate dehydrogenase, a reversible succinyl-CoA-ligase, a glutaconate CoA transferase, a carboxylate reductase, or an acetylating aldehyde dehydrogenase, and produce pimelate or pimelate semialdehyde. For example, a recombinant host producing pimeloyl-CoA can include a thioesterase, a CoA-transferase, or a reversible CoA-ligase and produce pimelic acid. For example, a recombinant host producing pimeloyl-CoA can include an acetylating aldehyde dehydrogenase and either an aldehyde dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase and produce pimelic acid. For example, a recombinant host producing pimeloyl-CoA can include an acetylating aldehyde dehydrogenase or a carboxylate reductase and produce pimelate semialdehyde.
A recombinant host producing pimelic acid or pimelate semialdehyde further can include at least one exogenous nucleic acid encoding a ω-transaminase and produce 7-aminoheptanoate.
A recombinant host producing pimelate semialdehyde further can include a 6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase or a 4-hydroxybutyrate dehydrogenase, and produce 7-hydroxyheptanoic acid.
A recombinant host producing pimelate semialdehyde, 7-aminoheptanoate, or 7-hydroxyheptanoate further can include at least one exogenous nucleic acid encoding a carboxylate reductase, a ω-transaminase, a deacetylase, a lysine N-acetyl transferase, or an alcohol dehydrogenase, and produce heptamethylenediamine. For example, a recombinant host producing 7-hydroxyheptanoate can include a carboxylate reductase, a ω-transaminase and an alcohol dehydrogenase.
A recombinant host producing 7-hydroxyheptanoic acid further can include a carboxylate reductase or an alcohol dehydrogenase, and produce 1,7-heptanediol.
Within an engineered pathway, the enzymes can be from a single source, i.e., from one species or genus, or can be from multiple sources, i.e., different species or genera. Nucleic acids encoding the enzymes described herein have been identified from various organisms and are readily available in publicly available databases such as GenBank or EMBL.
Any of the enzymes described herein that can be used for production of one or more C7 building blocks can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100%) to the amino acid sequence of the corresponding wild-type enzyme. It will be appreciated that the sequence identity can be determined on the basis of the mature enzyme (e.g., with any signal sequence removed).
For example, a thioesterase described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100%) to the amino acid sequence of an Escherichia coli thioesterase encoded by tesB (see GenBank Accession No. AAA24665.1, SEQ ID NO: 1). See
For example, a carboxylate reductase described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Mycobacterium marinum (see Genbank Accession No. ACC40567.1, SEQ ID NO: 2), a Mycobacterium smegmatis (see Genbank Accession No. ABK71854.1, SEQ ID NO: 3), a Segniliparus rugosus (see Genbank Accession No. EFV11917.1, SEQ ID NO: 4), a Mycobacterium smegmatis (see Genbank Accession No. ABK75684.1, SEQ ID NO: 5), a Mycobacterium massiliense (see Genbank Accession No. EIV 11143.1, SEQ ID NO: 6), or a Segniliparus rotundus (see Genbank Accession No. ADG98140.1, SEQ ID NO: 7) carboxylate reductase. See, FIG. 7.
For example, a ω-transaminase described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 8), a Pseudomonas aeruginosa (see Genbank Accession No. AAG08191.1, SEQ ID NO: 9), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 10), a Rhodobacter sphaeroides (see Genbank Accession No. ABA81135.1, SEQ ID NO: 11), an Escherichia coli (see Genbank Accession No. AAA57874.1, SEQ ID NO: 12), or a Vibrio fluvialis (see Genbank Accession No. AEA39183.1, SEQ ID NO: 13) ω-transaminase. Some of these ω-transaminases are diamine ω-transaminases. See,
For example, a phosphopantetheinyl transferase described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Bacillus subtilis phosphopantetheinyl transferase (see Genbank Accession No. CAA44858.1, SEQ ID NO:14) or a Nocardia sp. NRRL 5646 phosphopantetheinyl transferase (see Genbank Accession No. ABI83656.1, SEQ ID NO:15). See
The percent identity (homology) between two amino acid sequences can be determined as follows. First, the amino acid sequences are aligned using the BLAST 2 Sequences (B12seq) program from the stand-alone version of BLASTZ containing BLASTP version 2.0.14. This stand-alone version of BLASTZ can be obtained from Fish & Richardson's web site (e.g., www.fr.com/blast/) or the U.S. government's National Center for Biotechnology Information web site (www.ncbi.nlm.nih.gov). Instructions explaining how to use the Bl2seq program can be found in the readme file accompanying BLASTZ. Bl2seq performs a comparison between two amino acid sequences using the BLASTP algorithm. To compare two amino acid sequences, the options of Bl2seq are set as follows: -i is set to a file containing the first amino acid sequence to be compared (e.g., C:\seql.txt); -j is set to a file containing the second amino acid sequence to be compared (e.g., C:\seq2.txt); -p is set to blastp; -o is set to any desired file name (e.g., C:\output.txt); and all other options are left at their default setting. For example, the following command can be used to generate an output file containing a comparison between two amino acid sequences: C:\B12seq -i c:\seql.txt -j c:\seq2.txt -p blastp -o c:\output.txt. If the two compared sequences share homology (identity), then the designated output file will present those regions of homology as aligned sequences. If the two compared sequences do not share homology (identity), then the designated output file will not present aligned sequences. Similar procedures can be following for nucleic acid sequences except that blastn is used.
Once aligned, the number of matches is determined by counting the number of positions where an identical amino acid residue is presented in both sequences. The percent identity (homology) is determined by dividing the number of matches by the length of the full-length polypeptide amino acid sequence followed by multiplying the resulting value by 100. It is noted that the percent identity (homology) value is rounded to the nearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 is rounded down to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 is rounded up to 78.2. It also is noted that the length value will always be an integer.
It will be appreciated that a number of nucleic acids can encode a polypeptide having a particular amino acid sequence. The degeneracy of the genetic code is well known to the art; i.e., for many amino acids, there is more than one nucleotide triplet that serves as the codon for the amino acid. For example, codons in the coding sequence for a given enzyme can be modified such that optimal expression in a particular species (e.g., bacteria or fungus) is obtained, using appropriate codon bias tables for that species.
Functional fragments of any of the enzymes described herein can also be used in the methods of the document. The term “functional fragment” as used herein refers to a peptide fragment of a protein that has at least 25% (e.g., at least: 30%; 40%; 50%; 60%; 70%; 75%; 80%; 85%; 90%; 95%; 98%; 99%; 100%; or even greater than 100%) of the activity of the corresponding mature, full-length, wild-type protein. The functional fragment can generally, but not always, be comprised of a continuous region of the protein, wherein the region has functional activity.
This document also provides (i) functional variants of the enzymes used in the methods of the document and (ii) functional variants of the functional fragments described above. Functional variants of the enzymes and functional fragments can contain additions, deletions, or substitutions relative to the corresponding wild-type sequences. Enzymes with substitutions will generally have not more than 50 (e.g., not more than one, two, three, four, five, six, seven, eight, nine, ten, 12, 15, 20, 25, 30, 35, 40, or 50) amino acid substitutions (e.g., conservative substitutions). This applies to any of the enzymes described herein and functional fragments. A conservative substitution is a substitution of one amino acid for another with similar characteristics. Conservative substitutions include substitutions within the following groups: valine, alanine and glycine; leucine, valine, and isoleucine; aspartic acid and glutamic acid; asparagine and glutamine; serine, cysteine, and threonine; lysine and arginine; and phenylalanine and tyrosine. The nonpolar hydrophobic amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine. The polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine. The positively charged (basic) amino acids include arginine, lysine and histidine. The negatively charged (acidic) amino acids include aspartic acid and glutamic acid. Any substitution of one member of the above-mentioned polar, basic or acidic groups by another member of the same group can be deemed a conservative substitution. By contrast, a nonconservative substitution is a substitution of one amino acid for another with dissimilar characteristics.
Deletion variants can lack one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid segments (of two or more amino acids) or non-contiguous single amino acids. Additions (addition variants) include fusion proteins containing: (a) any of the enzymes described herein or a fragment thereof; and (b) internal or terminal (C or N) irrelevant or heterologous amino acid sequences. In the context of such fusion proteins, the term “heterologous amino acid sequences” refers to an amino acid sequence other than (a). A heterologous sequence can be, for example a sequence used for purification of the recombinant protein (e.g., FLAG, polyhistidine (e.g., hexahistidine), hemagglutinin (HA), glutathione-S-transferase (GST), or maltosebinding protein (MBP)). Heterologous sequences also can be proteins useful as detectable markers, for example, luciferase, green fluorescent protein (GFP), or chloramphenicol acetyl transferase (CAT). In some embodiments, the fusion protein contains a signal sequence from another protein. In certain host cells (e.g., yeast host cells), expression and/or secretion of the target protein can be increased through use of a heterologous signal sequence. In some embodiments, the fusion protein can contain a carrier (e.g., KLH) useful, e.g., in eliciting an immune response for antibody generation) or ER or Golgi apparatus retention signals. Heterologous sequences can be of varying length and in some cases can be a longer sequences than the full-length target proteins to which the heterologous sequences are attached.
Engineered hosts can naturally express none or some (e.g., one or more, two or more, three or more, four or more, five or more, or six or more) of the enzymes of the pathways described herein. Thus, a pathway within an engineered host can include all exogenous enzymes, or can include both endogenous and exogenous enzymes. Endogenous genes of the engineered hosts also can be disrupted to prevent the formation of undesirable metabolites or prevent the loss of intermediates in the pathway through other enzymes acting on such intermediates. Engineered hosts can be referred to as recombinant hosts or recombinant host cells. As described herein recombinant hosts can include nucleic acids encoding one or more of a dehydrogenase, a β-ketothiolase, a β-ketoacyl-[acp] synthase, a reductase, a hydratase, a thioesterase, a CoA-ligase, a reversible CoA-ligase, a CoA-transferase, an N-acetyl transferase, a deacetylase, or a ω-transaminase as described in detail herein.
In addition, the production of one or more C7 building blocks can be performed in vitro using the isolated enzymes described herein, using a lysate (e.g., a cell lysate) from a host microorganism as a source of the enzymes, or using a plurality of lysates from different host microorganisms as the source of the enzymes.
As depicted in
C7 building block, can be formed from the central metabolites acetyl-CoA or 2-oxoglutarate via carbon chain elongation (i) associated with cyclohexane carboxylate biosynthesis in Synthrophus aciditrophicus or (ii) associated with lysine biosynthesis via α-aminoadipate.
In some embodiments, glutaryl-CoA is formed via CoA-dependent carbon chain elongation associated with cyclohexane carboxylate biosynthesis in Synthrophus aciditrophicus which comprises using (i) a β-ketothiolase or an acetyl-carboxylase in combination with an acetoacetyl-CoA synthase, (ii) a 3-hydroxybutyryl-CoA dehydrogenase, (iii) an enoyl-CoA hydratase, and either (iv) a glutaryl-CoA dehydrogenase in combination with an enoyl-CoA reductase or a trans-2-enoyl-CoA reductase or (v) a glutaconyl-CoA decarboxylase.
In some embodiments, glutaryl-CoA is formed via C1 carbon chain elongation associated with lysine biosynthesis via α-aminoadipate, which comprises using (i) a homocitrate synthase, (ii) a homocitrate dehydratase and a homoaconitate hydratase, (iii) an isohomocitrate dehydrogenase, (iv) an indolepyruvate decarboxylase, (vi) a glutarate-semialdehyde dehydrogenase and (v) a glutarate: CoA ligase.
In some embodiments, pimeloyl-CoA is formed from glutaryl-CoA via CoA dependent chain elongation using (i) a β-ketothiolase or β-ketoacyl[acp] synthase, (ii) a 3-hydroxyacyl-CoA dehydrogenase, (iii) an enoyl-CoA hydratase, and (iv) an enoyl-CoA reductase.
In some embodiments, pimeloyl-CoA is formed from 3-hydroxypimeloyl-CoA via aromatic intermediates associated with cyclohexane carboxylate biosynthesis in Synthrophus aciditrophicus using (i) a 6-oxo-cyclohex-1-ene-carbonyl-CoA hydrolase, (ii) a 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase, (iii) a cyclohexa-1,5-dienecarbonyl-CoA hydratase, (iv) a cyclohex-1-ene-1-carboxyl-CoA dehydrogenase, (v) a cyclohex-1-ene-1-carboxyl-CoA hydratase, (vi) a 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase and (vi) a 2-ketocyclohexanecarboxyl-CoA hydrolase.
In some embodiments, a β-ketothiolase may be classified under EC 2.3.1.—(e.g., EC 2.3.1.9, EC 2.3.1.16, or EC 2.3.174). For example, a β-ketothiolase may be classified under EC 2.3.1.9, such as the gene product of atoB or phaA. The β-ketothiolase encoded by atoB or phaA accepts acetyl-CoA as substrates, forming butanoyl-CoA (see, Haywood et al., 1988, supra; Slater et al., 1998, supra). The β-ketothiolase encoded by paaJ can be classified under, for example, EC 2.3.1.174. The β-ketothiolase encoded by paaJ condenses acetyl-CoA and succinyl-CoA to 3-oxoadipyl-CoA (see, for example, Fuchs et al., 2011, Nature Reviews Microbiology, 9, 803-816). A homologue of paaJ in Synthrophus aciditrophicus catalyses the condensation of acetyl-CoA and glutaryl-CoA to 3-oxopimeloyl-CoA such as Genbank Accession No. ABC78517.1 or Genbank Accession No. ABC78881.1. Alternately, a β-ketoacyl[acp] homologue of paaJ in S. aciditrophicus catalyses the condensation of acetyl-CoA and glutaryl-CoA to 3-oxopimeloyl-CoA.
A β-ketoacyl[acp] synthase can be classified, for example, under, EC 2.3.1.41, EC 2.3.1.179, or EC 2.3.1.180. The β-ketothiolases and β-ketoacyl-[acp] synthases involved in fatty acid synthesis in S. aciditrophicus likely accept CoA activated dicarboxylic acids (Mouttaki et al., Appl. Environ. Microbiol., 2007, 73(3), 930-938).
An acetyl-CoA carboxylase can be classified under EC 6.4.1.2 and an acetoacetyl-CoA synthase can be classified under EC 2.3.1.194. Conversion of acetyl-CoA to malonyl-CoA by an acetyl-CoA carboxylase has been shown to increase the rate of fatty acid synthesis (Davis et al., J. Biol. Chem., 2000, 275(37), 28593-28598). It has been demonstrated that acetoacetyl-CoA synthase may be used as an irreversible substitute for the gene product of phaA in the carbon chain elongation associated with polyhydroxybutyrate synthesis (Matsumoto et al., Biosci. Biotechnol. Biochem., 2011, 75(2), 364-366).
In some embodiments, a 3-hydroxybutyryl-CoA dehydrogenase (also can be referred to as a 3-hydroxyacyl-CoA dehydrogenase) may be classified under EC 1.1.1.157 such as the gene product hbd (see, for example, Shen et al., 2011, supra; Budde et al., J. Bacteriol., 2010, 192(20), 5319-5328).
In some embodiments, an enoyl-CoA hydratase can be classified under EC 4.2.1.17, such as the gene product of crt (see, for example, Shen et al., 2011, supra; Fukui et al., J. Bacteriol., 1998, 180(3), 667-673) or the gene product of paaF (see, for example, Fuchs et al., 2011, supra). Homologs of paaF in S. aciditrophicus include the enoyl-CoA hydratase of Genbank Accession No. ABC77794.1 or the enoyl-CoA dehydratase of Genbank Accession No. ABC78950.1.
In some embodiments, an enoyl[acp] reductase can be classified under EC 1.3.1.—(e.g., EC 1.3.1.9) such as the enoyl[acp] reductase obtained from S. aciditrophicus or the gene product of FabI (Genbank Accession No: CAB13029.2) from Bacillus subtillis (see, for example, Heath et al., 2000, J. Biol. Chem., 275(51), 40128-33). The enoyl-[acp] reductase involved in fatty acid synthesis in S. aciditrophicus likely accepts CoA activated dicarboxylic acids (Mouttaki et al., 2007, supra).
In some embodiments, a trans-2-enoyl-CoA reductase can be classified, for example, under EC 1.3.1.44, such as the gene product of ter (Genbank Accession No. AAW66853.1) (Hoffmeister et al., 2005, J. Biol. Chem., 280(6), 4329-4338; Shen et al., 2011, supra) or tdter (Genbank Accession No. AAS11092.1) (Bond-Watts et al., Biochemistry, 2012, 51, 6827-6837).
In some embodiments, a reversible glutaconyl-CoA decarboxylase that relies on a Na+ membrane pump can be classified, for example, under EC 4.1.1.70 (see Mouttaki et al., 2007, supra). The EC 4.1.1.70 enzyme activity is associated with the following subunits in S. aciditrophicus, viz. Genbank Accession Nos. (1) ABC77900.1, (2) ABC76114.1 and (3) ABC77898.1.
In some embodiments, a glutaryl-CoA dehydrogenase from S. aciditrophicus subject to electron bifurcation via NADH can be classified under EC 1.3.8.6 such as the dehydrogenases in Genbank Accession Nos. (1) ABC77899.1, (2) ABC76101.1, (3) ABC76260.1, (4) ABC76949.1 or (5) ABC78863.1.
In some embodiments, a homocitrate synthase can be classified, for example, under EC 2.3.3.14 or EC 2.3.3.13, such as the gene product of LYS20 and LYS21 from Saccharomyces cerevisiae or hcs from Thermus thermophiles.
In some embodiments, the combination of homocitrate dehydratase and homoaconitate hydratase may be classified, for example, under EC 4.2.1.—(e.g., EC 4.2.1.114, EC 4.2.1.36 or EC 4.2.1.33), such as the gene product of LYS4 from
Saccharomyces cerevisiae or lysT and LysU from Thermus thermophiles.
In some embodiments, an isohomocitrate dehydrogenase may be classified, for example, under EC 1.1.1.—such as EC 1.1.1.85, EC 1.1.1.87 or EC 1.1.1.286, such as the gene product of LYS12 from Saccharomyces cerevisiae or hicdh from Thermus thermophiles.
In some embodiments, a 5-oxopentanoate dehydrogenase may be classified, for example under EC 1.2.1.—such as the gene product of CpnE (see, for example, Iwaki et al., 2002, Appl. Environ. Microbiol., 68(11):5671-5684).
In some embodiments, an indolepyruvate decarboxylase can be classified, for example, under EC 4.1.1.43 or EC 4.1.1.74 such as the indole-3-pyruvate decarboxylase from Salmonella typhimurium (see, for example, Genbank Accession No. CAC48239.1 in which residue 544 can be a leucine or an alanine). A mutant variant of the indolepyruvate decarboxylase from Salmonella typhimurium has been engineered successfully to selectively accept longer chain length substrates. The L544A mutation of Genbank Accession No. CAC48239.1 allowed for 567 times higher selectivity towards the C7 2-oxoacid than towards the C5 2-oxoacid (see, Xiong et al., 2012, Scientific Reports, 2: 311).
In some embodiments, a 3-hydroxyadipyl-CoA dehydrogenase (also can be referred to as 3-hydroxyacyl-CoA:NAD+ oxidoreducatase) may be classified under EC 1.1.1.157 such as the gene product of paaH (see, for example, Fuchs et al., 2011, Nature Reviews Microbiology, 9, 803-816). Homologues of paaH in S. aciditrophicus include the 3-hydroxyacyl-CoA dehydrogenase of Genbank Accession No. ABC77793.1.
In some embodiments, a 6-oxo-cyclohex-1-ene-carbonyl-CoA hydrolase can be classified under EC 3.7.1.—such as the gene product of Oah or BamA (see, for example, Fuchs et al., 2011, supra).
In some embodiments, a 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase can be classified under EC 1.1.1.—such as the gene product of Had or BamA (see, for example, Fuchs et al., 2011, supra).
In some embodiments, a cyclohexa-1,5-dienecarbonyl-CoA hydratase can be classified under EC 4.2.1.100 such as the gene product of Dch or BamR (see, for example, Fuchs et al., 2011, supra).
In some embodiments, a cyclohex-1-ene-1-carboxyl-CoA dehydrogenase can be classified under EC 1.3.8.—such as the acyl-CoA dehydrogenase of Genbank Accession No. ABC76101.1 from S. aciditrophicus (see, for example, Kung et al., 2013, J. Bacteriol., 195(14), 3193-3200). This enzyme was reassigned to class EC 1.3.8.—from EC 1.3.99.—.
In some embodiments, a cyclohex-1-ene-1-carboxyl-CoA hydratase can be classified under EC 4.2.1.—such as the gene product of badK (see, for example, Harwood et al., 1999, FEMS Microbiol. Reviews, 22, 439-458). Homologues of badK in S. aciditrophicus include the enoyl-CoA hydratase of Genbank Accession No. ABC77794.1.
In some embodiments, a 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase can be classified under EC 1.1.1.—such as the gene product of badH (see, for example, Harwood et al., 1999, FEMS Microbiol. Reviews, 22, 439-458). Homologs of badH in S. aciditrophicus include the 3-oxoacyl-ACP reductase of Genbank Accession No. ABC76948.1.
In some embodiments, a 2-ketocyclohexanecarboxyl-CoA hydrolase can be classified under EC 4.1.3.36 such as the gene product of badl (see, for example, Harwood et al., 1999, supra). Homologs of badl in S. aciditrophicus such as encoded by Genbank Accession No. ABC78756.1.
As depicted in
In some embodiments, the second terminal carboxyl group leading to the synthesis of a C7 building block (e.g., pimelic acid) is enzymatically formed by a thioesterase classified under EC 3.1.2.—, such as the gene product of YciA, tesB (Genbank Accession No. AAA24665.1, SEQ ID NO: 1) or Acot13 (see, for example, Cantu et al., Protein Science, 2010, 19, 1281-1295; Zhuang et al., Biochemistry, 2008, 47(9), 2789-2796; or Naggert et al., J. Biol. Chem., 1991, 266(17), 11044-11050).
In some embodiments, the second terminal carboxyl group leading to the synthesis of pimelic acid is enzymatically formed by an aldehyde dehydrogenase classified, for example, under EC 1.2.1.3 (see, for example, Guerrillot & Vandecasteele, Eur. J. Biochem., 1977, 81, 185-192).
In some embodiments, the second terminal carboxyl group leading to the synthesis of pimelic acid is enzymatically formed by a 6-oxohexanoate dehydrogenase or a 7-oxoheptanoate dehydrogenase classified under EC 1.2.1.—, such as the gene product of ChnE from Acinetobacter sp. or ThnG from Sphingomonas macrogolitabida (see, for example, Iwaki et al., Appl. Environ. Microbiol., 1999, 65(11), 5158-5162; or López-Sanchez et al., Appl. Environ. Microbiol., 2010, 76(1), 110-118). For example, a 6-oxohexanoate dehydrogenase can be classified under EC 1.2.1.63. For example, a 7-oxoheptanoate dehydrogenase can be classified under EC 1.2.1.—.
In some embodiments, the second terminal carboxyl group leading to the synthesis of pimelic acid is enzymatically formed by a CoA-transferase such as a glutaconate CoA-transferase classified, for example, under EC 2.8.3.12 such as from Acidaminococcus fermentans. See, for example, Buckel et al., 1981, Eur. J. Biochem., 118:315-321.
In some embodiments, a terminal carboxyl group leading to the synthesis of pimelic acid is enzymatically formed by a reversible CoA-ligase classified under EC 6.2.1.5.
In some embodiments, the second terminal carboxyl group leading to the synthesis of pimelic acid is enzymatically formed by a reversible CoA-ligase such as a succinate-CoA-ligase classified, for example, under EC 6.2.1.5 such as from Thermococcus kodakaraensis. See, for example, Shikata et al., 2007, J. Biol. Chem., 282(37):26963-26970.
As depicted in
In some embodiments, the first terminal amine group leading to the synthesis of 7-aminoheptanoic acid is enzymatically formed by a ω-transaminase classified, for example, under EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as that obtained from Chromobacterium violaceum (Genbank Accession No. AAQ59697.1, SEQ ID NO: 8), Pseudomonas aeruginosa (Genbank Accession No. AAG08191.1, SEQ ID NO: 9), Pseudomonas syringae (Genbank Accession No. AAY39893.1, SEQ ID NO: 10), Rhodobacter sphaeroides (Genbank Accession No. ABA81135.1, SEQ ID NO: 11), Vibrio Fluvialis (Genbank Accession No. AAA57874.1, SEQ ID NO: 13), Streptomyces griseus, or Clostridium viride. An additional ω-transaminase that can be used in the methods and hosts described herein is from Escherichia coli (Genbank Accession No. AAA57874.1, SEQ ID NO: 12). Some of the ω-transaminases classified, for example, under EC 2.6.1.29 or EC 2.6.1.82 are diamine ω-transaminases (e.g., SEQ ID NO:12).
The reversible ω-transaminase from Chromobacterium violaceum (Genbank Accession No. AAQ59697.1, SEQ ID NO: 8) has demonstrated analogous activity accepting 6-aminohexanoic acid as amino donor, thus forming the first terminal amine group in adipate semialdehyde (Kaulmann et al., Enzyme and Microbial Technology, 2007, 41, 628-637).
The reversible 4-aminobubyrate:2-oxoglutarate transaminase from Streptomyces griseus has demonstrated analogous activity for the conversion of 6-aminohexanoate to adipate semialdehyde (Yonaha et al., Eur. J. Biochem., 1985, 146, 101-106).
The reversible 5-aminovalerate transaminase from Clostridium viride has demonstrated analogous activity for the conversion of 6-aminohexanoate to adipate semialdehyde (Barker et al., J. Biol. Chem., 1987, 262(19), 8994-9003).
In some embodiments, the second terminal amine group leading to the synthesis of heptamethylenediamine is enzymatically formed by a diamine transaminase. For example, the second terminal amino group can be enzymatically formed by a diamine transaminase classified, for example, under EC 2.6.1.29 or classified, for example, under EC 2.6.1.82, such as the gene product of YgjG from E. coli (Genbank Accession No. AAA57874.1, SEQ ID NO: 12).
The gene product of ygiG accepts a broad range of diamine carbon chain length substrates, such as putrescine, cadaverine and spermidine (Samsonova et al., BMC Microbiology, 2003, 3:2).
The diamine transaminase from E. coli strain B has demonstrated activity for 1,7 diaminoheptane (Kim, The Journal of Chemistry, 1964, 239(3), 783-786).
In some embodiments, the second terminal amine group leading to the synthesis of heptamethylenediamine is enzymatically formed by a deacetylase classified, for example, under EC 3.5.1.62 such as an acetylputrescine deacetylase. The acetylputrescine deacetylase from Micrococcus luteus K-11 accepts a broad range of carbon chain length substrates, such as acetylputrescine, acetylcadaverine and N8-acetylspermidine (see, for example, Suzuki et al., 1986, BBA—General Subjects, 882(1):140-142).
As depicted in
In some embodiments, the terminal hydroxyl group leading to the synthesis of 1,7 heptanediol is enzymatically formed by an alcohol dehydrogenase classified, for example, under EC 1.1.1.—(e.g., EC 1.1.1.1, 1.1.1.2, 1.1.1.21, or 1.1.1.184).
In some embodiments, glutaryl-CoA is synthesized from the central metabolite, acetyl-CoA, by conversion of acetyl-CoA to acetoacetyl-CoA by a β-ketothiolase classified, for example, under EC 2.3.1.9 such as the gene product of atoB or phaA or by an acetyl-CoA carboxylase classified under, for example, EC 6.4.1.2 and an acetoacetyl-CoA synthase classified, for example, under EC 2.3.1.194; followed by conversion to 3-hydroxybutanoyl-CoA by a 3-hydroxyacyl-CoA dehydrogenase classified, for example, under EC 1.1.1.—such as EC 1.1.1.157 such as the gene product of hbd; followed by conversion to crotonyl-CoA by an enoyl-CoA reductase classified, for example, under EC 4.2.1.—(e.g., EC 4.2.1.17) such as the gene product of crt, followed by conversion to either a) glutaconyl-CoA by a glutaconyl-CoA decarboxylase classified, for example, under EC 4.1.1.70; followed by conversion to glutaryl-CoA by either (i) an enoyl-[acp] reductase classified, for example, under EC 1.3.1.9 or (ii) a trans-2-enoyl-CoA reductase classified, for example, under EC 1.3.1.44 such as the gene product of ter or tdter or (b) glutaryl-CoA by a glutaryl-CoA dehydrogenase subject to electron bifurcation from Synthrophus aciditrophicus such as the dehydrogenases of Genbank Accession Nos. (1) ABC77899.1, (2) ABC76101.1, (3) ABC76260.1, (4) ABC76949.1 or (5) ABC78863.1. See,
In some embodiments, glutaryl-CoA can be synthesized from the central metabolite, 2-oxoglutarate, by conversion of 2-oxoglutrate to (Homo)1citrate by a homocitrate synthase classified, for example, under EC 2.3.3.14 or EC 2.3.3.13 such as the gene product of LYS20 and LYS21 from Saccharomyces cerevisiae or hcs from Thermus thermophiles; followed by conversion to iso(homo)1citrate by a homocitrate dehydratase and a homoaconitate hydratase classified, for example, under EC 4.2.1.114, EC 4.2.1.36 or EC 4.2.1.33 such as the gene product of LYS4 from Saccharomyces cerevisiae or lysT and LysU from Thermus thermophiles; followed by conversion to 2-oxoadipate by an iso(homo)ncitrate dehydrogenase classified, for example, under EC 1.1.1.85, EC 1.1.1.87 or EC 1.1.1.286 such as the gene product of LYS12 from Saccharomyces cerevisiae or hicdh from Thermus thermophiles; followed by conversion to glutarate semialdehyde by an indolepyruvate decarboxylase classified under EC 4.1.1.43 or EC 4.1.1.74 (e.g., GenBank Accession No. CAC48239.1); followed by conversion to glutarate by a glutarate semialdehyde dehydrogenase classified, for example, under EC 1.2.1.20, EC 1.2.1.16 or EC 1.2.1.79 such as the gene product of CpnE; followed by conversion to glutaryl-CoA by a glutarate:CoA ligase classified, for example, under EC 6.2.1.6. See, e.g.,
In some embodiments, pimeloyl-CoA can be synthesized from glutaryl-CoA produced as described above by conversion of glutaryl-CoA to 3-ketopimeloyl-CoA by a β-ketothiolase classified under EC 2.3.1.—, e.g., EC 2.3.1.174 or EC 2.3.1.16 such as the gene product of paaJ or homologs of paaJ (e.g., Genbank Accession No. ABC78517.1 or Genbank Accession No. ABC78881.1) or by a β-ketoacyl-[acp] synthase classified, for example, under EC 2.3.1.41, EC 2.3.1.179, EC 2.3.1.180; followed by conversion to 3-hydroxypimeloyl-CoA by a 3-hydroxyadipyl-CoA dehydrogenase classified, for example, under EC 1.1.1.157 such as the gene product of paaH or homologs of paaH (e.g., Genbank Accession No. ABC77793.1); followed by conversion to 2,3-dehydropimeloyl-CoA by an enoyl-CoA hydratase such as the gene product of paaF or homologs of paaF (e.g., Genbank Accession No. ABC77794.1 or Genbank Accession No. ABC78950.1); followed by conversion to pimeloyl-CoA by an enoyl-[acp] reductase from S. aciditrophicus classified, for example, under EC 1.3.1.9 or a trans-2-enoyl-CoA reductase classified, for example, under EC 1.3.1.44 such as the gene product of ter or tdter. See, e.g.,
In some embodiments, pimeloyl-CoA can be synthesized from glutaryl-CoA produced as described above by conversion of glutaryl-CoA to 3-ketopimeloyl-CoA by a β-ketothiolase classified under EC 2.3.1.—, e.g., EC 2.3.1.174 or EC 2.3.1.16 such as the gene product of paaJ or homologs of paaJ (e.g., Genbank Accession No. ABC78517.1 or Genbank Accession No. ABC78881.1) or by a β-ketoacyl-[acp] synthase classified, for example, under EC 2.3.1.41, EC 2.3.1.179, EC 2.3.1.180; followed by conversion to 6-ketocyclohex-1-ene-1-carboxyl-CoA by a 6-oxo-cyclohex-1-ene-carbonyl-CoA hydrolase classified, for example, under EC 3.7.1.—such as the gene product of Oah or BamA; followed by conversion to 6-hydroxycyclohex-1-ene-1-carboxyl-CoA by a 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase classified, for example, under EC 1.1.1.- such as the gene product of Had or BamQ; followed by conversion to cyclohexa-1,5-diene-1-carbonyl-CoA by a cyclohexa-1,5-dienecarbonyl-CoA hydratase classified under, for example, EC 4.2.1.100 such as the gene product of Dch or BamR; followed by conversion to cyclohex-1-ene-1-carboxyl-CoA by a cyclohex-1-ene-1-Carboxyl-CoA dehydrogenase classified under EC 1.3.8.—such as Genbank Accession No. ABC76100.1; followed by conversion to 2-hydroxycyclohexane-1-carboxyl-CoA by a cyclohex-1-ene-1-carboxyl-CoA hydratase classified under, for example, EC 4.2.1.—such as the gene product of badK or homologs of badK (e.g., Genbank Accession No. ABC77794.1); followed by conversion to 2-ketocyclohex-1-ene-1-carboxyl-CoA by a 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase classified, for example, under EC 1.1.1.—such as the gene product of badH or homologs of badH (e.g., Genbank Accession No. ABC76948.1); followed by conversion to pimeloyl-CoA by a 2-ketocyclohexanecarboxyl-CoA hydrolase classified, for example, under, EC 4.1.3.36 such as the gene product of badI or homologs of badI (e.g., Genbank Accession No. ABC78756.1).
In some embodiments, pimelic acid is synthesized from the central precursor, pimeloyl-CoA, by conversion of pimeloyl-CoA to pimelate by a thioesterase classified under EC 3.1.2.—such as the gene products of YciA, tesB (Genbank Accession No. AAA24665.1, SEQ ID NO: 1) or Acot13. See
In some embodiments, pimelic acid is synthesized from the central precursor, pimeloyl-CoA, by conversion of pimeloyl-CoA to pimelate by a reversible CoA ligase such as a succinate CoA-ligase classified, for example, under EC 6.2.1.5. See
In some embodiments, pimelic acid is synthesized from the central precursor, pimeloyl-CoA, by conversion of pimeloyl-CoA to pimelate by a CoA-transferase classified, for example, under EC 2.8.3.12 such as a glutaconate CoA-transferase. See
In some embodiments, pimeloyl-CoA can be converted to pimelate semialdehyde by an acetylating aldehyde dehydrogenase classified, for example, under EC 1.2.1.10 such as the gene product of PduB or PduP; followed by conversion to pimelic acid by a dehydrogenase classified, for example, under EC 1.2.1.- such as a 7-oxoheptanoate dehydrogenase (e.g., the gene product of ThnG), a 6-oxohexanoate dehydrogenase (e.g., the gene product of ChnE), or an aldehyde dehydrogenase classified under EC 1.2.1.3. See
In some embodiments, 7-aminoheptanoate is synthesized from the central precursor, pimelate or pimeloyl-CoA. For example, pimelate, formed as described above, can be converted to pimelate semialdehyde by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as the gene product of car in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia) or the gene products of GriC and GriD from Streptomyces griseus (see Suzuki et al., J. Antibiot., 2007, 60(6), 380-387); followed by conversion of pimelate semialdehyde to 7-aminoheptanoate by a ω-transaminase (classified, for example, under EC 2.6.1.—EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.48, EC 2.6.1.82, see SEQ ID NOs:8-13). See
The carboxylate reductase encoded by the gene product of car and enhancer npt or sfp has broad substrate specificity, including terminal difunctional C4 and C5 carboxylic acids (Venkitasubramanian et al., Enzyme and Microbial Technology, 2008, 42, 130-137).
In some embodiments, pimeloyl-CoA formed as described above is converted to pimelate semialdehyde by an acetylating aldehyde dehydrogenase classified, for example, under EC 1.2.1.10 such as the gene product of PduB or PduP; followed by conversion of pimelate semialdehyde to 7-aminoheptanoate by a ω-transaminase classified, for example, under EC 2.6.1.—such as EC 2.6.1.18, EC 2.6.1.19, or EC 2.6.1.48, see). See
In some embodiments, heptamethylenediamine is synthesized from the central precursor, 7-aminoheptanoate, by conversion of 7-aminoheptanoate to 7-aminoheptanal by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as the gene product of car (see above) in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia) or the gene products of GriC and GriD from Streptomyces griseus (Suzuki et al., 2007, supra); followed by conversion of 7-aminoheptanal to heptamethylenediamine by a ω-transaminase (e.g., EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.48, EC 2.6.1.82 such as SEQ ID NOs:8-13). See
The carboxylate reductase encoded by the gene product of car and enhancer npt has broad substrate specificity, including terminal difunctional C4 and C5 carboxylic acids (Venkitasubramanian et al., Enzyme and Microbial Technology, 2008, 42, 130-137).
In some embodiments, heptamethylenediamine is synthesized from the central precursor, 7-hydroxyheptanoate (which can be produced as described in
In some embodiments, heptamethylenediamine is synthesized from the central precursor, 7-aminoheptanoate, by conversion of 7-aminoheptanoate to N7-acetyl-7-aminoheptanoate by an N-acetyltransferase such as a lysine N-acetyltransferase classified, for example, under EC 2.3.1.32; followed by conversion to N7-acetyl-7-aminoheptanal by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as the gene product of car (see above) in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia) or the gene product of GriC & GriD; followed by conversion to N7-acetyl-1,7-diaminoheptane by a ω-transaminase classified, for example, under EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as SEQ ID NOs:8-13, see above; followed by conversion to heptamethylenediamine by an acetylputrescine deacetylase classified, for example, under EC 3.5.1.62. See,
In some embodiments, heptamethylenediamine is synthesized from the central precursor, pimelate semialdehyde, by conversion of pimelate semialdehyde to heptanedial by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as the gene product of car (see above) in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia) or the gene product of GriC & GriD; followed by conversion to 7-aminoheptanal by a ω-transaminase classified, for example, under EC 2.6.1.18, EC 2.6.1.19, or EC 2.6.1.48; followed by conversion to heptamethylenediamine by a ω-transaminase classified, for example, under EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as SEQ ID NOs:8-13. See
Pathways using Pimelate or Pimelate Semialdehyde as central precursors to 7-hydroxyheptanoate or 1,7-heptanediol
In some embodiments, 7-hydroxyheptanoate is synthesized from the central precursor, pimelate, by conversion of pimelate to pimelate semialdehyde by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as the gene product of car (see above) in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia) or the gene product of GriC & GriD; followed by conversion to 7-hydroxyheptanoate by a 6-hydroxyhexanoate dehydrogenase classified, for example, under EC 1.1.1.258 such as the gene product of ChnD, a 5-hydroxypentanoate dehydrogenase classified, for example, under EC 1.1.1.—such as the gene product of CpnD (see, for example, Iwaki et al., 2002, Appl. Environ. Microbiol., 68(11):5671-5684) or a 4-hydroxybutyrate dehydrogenase such as gabD (see, for example, Lütke-Eversloh & Steinbüchel, 1999, FEMS Microbiology Letters, 181(1):63-71). See
In some embodiments, 7-hydroxyheptanoate is synthesized from the central precursor, pimeloyl-CoA, by conversion of pimeloyl-CoA to pimelate semialdehyde by an acetylating aldehyde dehydrogenase classified, for example, under EC 1.2.1.10 such as the gene product of PduB or PduP; followed by conversion to 7-hydroxyheptanoate by a 6-hydroxyhexanoate dehydrogenase classified, for example, under EC 1.1.1.258 such as the gene product of ChnD, a 5-hydroxypentanoate dehydrogenase classified, for example, under EC 1.1.1.- such as the gene product of CpnD (see, for example, Iwaki et al., 2002, Appl. Environ. Microbiol., 68(11):5671-5684) or a 4-hydroxybutyrate dehydrogenase such as gabD (see, for example, Lüke-Eversloh & Steinbüchel, 1999, FEMS Microbiology Letters, 181(1):63-71). See
In some embodiments, pimeloyl-CoA formed as described above is converted to pimelate semialdehyde by an acetylating aldehyde dehydrogenase (classified, for example, under EC 1.2.1.10) such as the gene product of PduB; followed by conversion of pimelate semialdehyde to 7-hydroxyheptanoate by an alcohol dehydrogenase classified for example, under EC 1.1.1.—(e.g., EC 1.1.1.1, EC 1.1.1.2, EC 1.1.1.21, or EC 1.1.1.184). See
In some embodiments, 1,7 heptanediol is synthesized from the central precursor, 7-hydroxyheptanoate, by conversion of 7-hydroxyheptanoate to 7-hydroxyheptanal by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as the gene product of car (see above) in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia) or the gene products of GriC and GriD from Streptomyces griseus (Suzuki et al., 2007, supra); followed by conversion of 7-hydroxyheptanal to 1,7 heptanediol by an alcohol dehydrogenase classified, for example, under EC 1.1.1.—such as EC 1.1.1.1, EC 1.1.1.2, EC 1.1.1.21, or EC 1.1.1.184) such as the gene product of YMR318C or YqhD (from E. coli, GenBank Accession No. AAA69178.1) (see, e.g., Liu et al., Microbiology, 2009, 155, 2078-2085; Larroy et al., 2002, Biochem J., 361(Pt 1), 163-172; or Jarboe, 2011, Appl. Microbiol. Biotechnol., 89(2), 249-257) or the protein having GenBank Accession No. CAA81612.1 (from Geobacillus stearothermophilus). See
In some embodiments, the cultivation strategy entails achieving an anaerobic cultivation, micro-aerobic, or mixed oxygen/denitrification condition. Enzymes characterized in vitro as being oxygen sensitive require a micro-aerobic cultivation strategy maintaining a very low dissolved oxygen concentration (See, for example, Chayabatra & Lu-Kwang, Appl. Environ. Microbiol., 2000, 66(2), 493 0 498; Wilson and Bouwer, 1997, Journal of Industrial Microbiology and Biotechnology, 18(2-3), 116 -130).
In some embodiments, the cultivation strategy entails nutrient limitation such as nitrogen, phosphate or oxygen limitation.
In some embodiments, a final electron acceptor other than oxygen such as nitrates can be utilized.
In some embodiments, a cell retention strategy using, for example, ceramic hollow fiber membranes can be employed to achieve and maintain a high cell density during either fed-batch or continuous fermentation.
In some embodiments, the principal carbon source fed to the fermentation in the synthesis of one or more C7 building blocks can derive from biological or non-biological feedstocks.
In some embodiments, the biological feedstock can be, can include, or can derive from, monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin, levulinic acid and formic acid, triglycerides, glycerol, fatty acids, agricultural waste, condensed distillers' solubles, or municipal waste.
The efficient catabolism of crude glycerol stemming from the production of biodiesel has been demonstrated in several microorganisms such as Escherichia coli, Cupriavidus necator, Pseudomonas oleavorans, Pseudomonas putida and Yarrowia lipolytica (Lee et al., Appl. Biochem. Biotechnol., 2012, 166, 1801-1813; Yang et al., Biotechnology for Biofuels, 2012, 5:13; Meijnen et al., Appl. Microbiol. Biotechnol., 2011, 90, 885-893).
The efficient catabolism of lignocellulosic-derived levulinic acid has been demonstrated in several organisms such as Cupriavidus necator and Pseudomonas putida in the synthesis of 3-hydroxyvalerate via the precursor propanoyl-CoA (Jaremko and Yu, Journal of Biotechnology, 2011, 155, 2011, 293-298; Martin and Prather, Journal of Biotechnology, 2009, 139, 61-67).
The efficient catabolism of lignin-derived aromatic compounds such as benzoate analogues has been demonstrated in several microorganisms such as Pseudomonas putida, Cupriavidus necator (Bugg et al., Current Opinion in Biotechnology, 2011, 22, 394-400; Pérez-Pantoja et al., FEMS Microbiol. Rev., 2008, 32, 736-794).
The efficient utilization of agricultural waste, such as olive mill waste water has been demonstrated in several microorganisms, including Yarrowia lipolytica (Papanikolaou et al., Bioresour. Technol., 2008, 99(7), 2419-2428).
The efficient utilization of fermentable sugars such as monosaccharides and disaccharides derived from cellulosic, hemicellulosic, cane and beet molasses, cassava, corn and other agricultural sources has been demonstrated for several microorganism such as Escherichia coli, Corynebacterium glutamicum and Lactobacillus delbrueckii and Lactococcus lactis (see, e.g., Hermann et al, Journal of Biotechnology, 2003, 104, 155-172; Wee et al., Food Technol. Biotechnol., 2006, 44(2), 163-172; Ohashi et al., Journal of Bioscience and Bioengineering, 1999, 87(5), 647-654).
The efficient utilization of furfural, derived from a variety of agricultural lignocellulosic sources, has been demonstrated for Cupriavidus necator (Li et al., Biodegradation, 2011, 22, 1215-1225).
In some embodiments, the non-biological feedstock can be or can derive from natural gas, syngas, CO2/H2, methanol, ethanol, benzoic acid, non-volatile residue (NVR), a caustic wash waste stream from cyclohexane oxidation processes, or terephthalic acid/isophthalic acid mixture waste streams.
The efficient catabolism of methanol has been demonstrated for the methylotrophic yeast Pichia pastoris.
The efficient catabolism of ethanol has been demonstrated for Clostridium kluyveri (Seedorf et al., Proc. Natl. Acad. Sci. USA, 2008, 105(6) 2128-2133).
The efficient catabolism of CO2 and H2, which may be derived from natural gas and other chemical and petrochemical sources, has been demonstrated for Cupriavidus necator (Prybylski et al., Energy, Sustainability and Society, 2012, 2:11).
The efficient catabolism of syngas has been demonstrated for numerous microorganisms, such as Clostridium ljungdahlii and Clostridium autoethanogenum (Köpke et al., Applied and Environmental Microbiology, 2011, 77(15), 5467-5475).
The efficient catabolism of the non-volatile residue waste stream from cyclohexane processes has been demonstrated for numerous microorganisms, such as Delftia acidovorans and Cupriavidus necator (Ramsay et al., Applied and Environmental Microbiology, 1986, 52(1), 152-156).
In some embodiments, the host microorganism is a prokaryote. For example, the prokaryote can be a bacterium from the genus Escherichia such as Escherichia coli; from the genus Clostridia such as Clostridium ljungdahlii, Clostridium autoethanogenum or Clostridium kluyveri; from the genus Corynebacteria such as Corynebacterium glutamicum; from the genus Cupriavidus such as Cupriavidus necator or Cupriavidus metallidurans; from the genus Pseudomonas such as Pseudomonas fluorescens, Pseudomonas putida or Pseudomonas oleavorans; from the genus Delftia such as Delftia acidovorans; from the genus Bacillus such as Bacillus subtillis; from the genus Lactobacillus such as Lactobacillus delbrueckii; or from the genus Lactococcus such as Lactococcus lactis. Such prokaryotes also can be a source of genes to construct recombinant host cells described herein that are capable of producing one or more C7 building blocks.
In some embodiments, the host microorganism is a eukaryote. For example, the eukaryote can be a filamentous fungus, e.g., one from the genus Aspergillus such as Aspergillus niger. Alternatively, the eukaryote can be a yeast, e.g., one from the genus Saccharomyces such as Saccharomyces cerevisiae; from the genus Pichia such as Pichia pastoris; or from the genus Yarrowia such as Yarrowia lipolytica; from the genus Issatchenkia such as Issathenkia orientalis; from the genus Debaryomyces such as Debaryomyces hansenii; from the genus Arxula such as Arxula adenoinivorans; or from the genus Kluyveromyces such as Kluyveromyces lactis. Such eukaryotes also can be a source of genes to construct recombinant host cells described herein that are capable of producing one or more C7 building blocks.
The present document provides methods involving less than all the steps described for all the above pathways. Such methods can involve, for example, one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve or more of such steps. Where less than all the steps are included in such a method, the first, and in some embodiments the only, step can be any one of the steps listed.
Furthermore, recombinant hosts described herein can include any combination of the above enzymes such that one or more of the steps, e.g., one, two, three, four, five, six, seven, eight, nine, ten, or more of such steps, can be performed within a recombinant host. This document provides host cells of any of the genera and species listed and genetically engineered to express one or more (e.g., two, three, four, five, six, seven, eight, nine, 10, 11, 12 or more) recombinant forms of any of the enzymes recited in the document. Thus, for example, the host cells can contain exogenous nucleic acids encoding enzymes catalyzing one or more of the steps of any of the pathways described herein.
In addition, this document recognizes that where enzymes have been described as accepting CoA-activated substrates, analogous enzyme activities associated with [acp]-bound substrates exist that are not necessarily in the same enzyme class.
Also, this document recognizes that where enzymes have been described accepting (R)-enantiomers of substrate, analogous enzyme activities associated with (S)-enantiomer substrates exist that are not necessarily in the same enzyme class.
This document also recognizes that where an enzyme is shown to accept a particular co-factor, such as NADPH, or a co-substrate, such as acetyl-CoA, many enzymes are promiscuous in terms of accepting a number of different co-factors or co-substrates in catalyzing a particular enzyme activity. Also, this document recognizes that where enzymes have high specificity for e.g., a particular co-factor such as NADH, an enzyme with similar or identical activity that has high specificity for the co-factor NADPH may be in a different enzyme class.
In some embodiments, the enzymes in the pathways outlined herein are the result of enzyme engineering via non-direct or rational enzyme design approaches with aims of improving activity, improving specificity, reducing feedback inhibition, reducing repression, improving enzyme solubility, changing stereo-specificity, or changing co-factor specificity.
In some embodiments, the enzymes in the pathways outlined herein can be gene dosed (i.e., overexpressed by having a plurality of copies of the gene in the host organism), into the resulting genetically modified organism via episomal or chromosomal integration approaches.
In some embodiments, genome-scale system biology techniques such as Flux Balance Analysis can be utilized to devise genome scale attenuation or knockout strategies for directing carbon flux to a C7 building block.
Attenuation strategies include, but are not limited to; the use of transposons, homologous recombination (double cross-over approach), mutagenesis, enzyme inhibitors and RNA interference (RNAi).
In some embodiments, fluxomic, metabolomic and transcriptomal data can be utilized to inform or support genome-scale system biology techniques, thereby devising genome scale attenuation or knockout strategies in directing carbon flux to a C7 building block.
In some embodiments, the host microorganism's tolerance to high concentrations of a C7 building block can be improved through continuous cultivation in a selective environment.
In some embodiments, the host microorganism's endogenous biochemical network can be attenuated or augmented to ensure the intracellular availability of acetyl-CoA (2) create an NADH imbalance that may only be balanced via the formation of a C7 building block, (3) prevent degradation of central metabolites or central precursors leading to and including C7 building blocks and (4) ensure efficient efflux from the cell.
In some embodiments requiring the intracellular availability of acetyl-CoA for C7 building block synthesis, an endogenous gene encoding a phosphotransacetylase, which generates acetate, such as pta is attenuated (Shen et al., Appl. Environ. Microbiol., 2011, 77(9), 2905-2915).
In some embodiments requiring the intracellular availability of acetyl-CoA for C7 building block synthesis, an endogenous gene encoding an acetate kinase in an acetate synthesis pathway, such as ack, is attenuated.
In some embodiments requiring the intracellular availability of acetyl-CoA and NADH for C7 building block synthesis, an endogenous gene encoding an enzyme that catalyzes the degradation of pyruvate to lactate such as ldhA is attenuated (Shen et al., Appl. Environ. Microbiol., 2011, 77(9), 2905-2915).
In some embodiments requiring the intracellular availability of acetyl-CoA and NADH for C7 building block synthesis, an endogenous gene encoding an enzyme that catalyzes the degradation of phophoenolpyruvate to succinate such as frdBC is attenuated (see, e.g., Shen et al., 2011, supra).
In some embodiments requiring the intracellular availability of acetyl-CoA and NADH for C7 building block synthesis, an endogenous gene encoding an enzyme that catalyzes the degradation of acetyl-CoA to ethanol such as the alcohol dehydrogenase encoded by adhE is attenuated (Shen et al., 2011, supra).
In some embodiments, an endogenous gene encoding an enzyme that catalyzes the degradation of pyruvate to ethanol such as pyruvate decarboxylase is attenuated.
In some embodiments requiring the intracellular availability of acetyl-CoA for C7 building block synthesis, a gene encoding an acetyl-CoA synthetase such as the gene acs is overexpressed in the microorganism (Satoh et al., Journal of Bioscience and Bioengineering, 2003, 95(4), 335-341).
In some embodiments, where a pathway requires excess NADH for C7 building block synthesis, carbon flux is directed into the pentose phosphate cycle by attenuating an endogenous gene encoding a glucose-6-phosphate isomerase (EC 5.3.1.9).
In some embodiments, where a pathway requires excess NADH co-factor for C7 building block synthesis, a gene encoding a formate dehydrogenase is overexpressed in the host organism (Shen et al., 2011, supra).
In some embodiments, endogenous enzymes facilitating the conversion of NADH to NADPH are attenuated, such as the NADPH generation cycle that may be generated via inter-conversion of glutamate dehydrogenases in EC 1.4.1.2 (NADH-specific) and EC 1.4.1.4 (NADPH-specific). Similarly, transhydrogenases such as classified, for example, under EC 1.6.1.1, EC 1.6.1.2 or EC 1.6.1.3, may be attenuated.
In some embodiments, an endogenous gene encoding a glutamate dehydrogenase (EC 1.4.1.3) that utilizes both NADH and NADPH as co-factors is attenuated.
In some embodiments, membrane-bound enoyl-CoA reductases are solubilized via truncation of the amino acid residues that anchor the protein in the membrane (Hoffmeister et al., J. Biol. Chem., 2005, 280(6) 4329-4338).
In some embodiments, membrane-bound enoyl-CoA reductases are solubilized via expression as a fusion protein (Gloerich et al., FEBS Letters, 2006, 580, 2092-2096).
In some embodiments, an enoyl-[acp] reductase from fatty acid synthesis or a trans-2-enoyl-CoA reductase is subjected to enzyme engineering with the aim of modifying the tunnel-like hydrophobic cavity to accept CoA activated dicarboxylic acids as substrate (Roujeinikova et al., J. Mol. Biol., 2007, 365, 135-145).
In some embodiments using hosts that naturally accumulate polyhydroxyalkanoates, an endogenous gene encoding a polymer synthase enzyme can be attenuated in the host strain.
In some embodiments, a L-alanine dehydrogenase can be overexpressed in the host to regenerate L-alanine from pyruvate as amino donor for ω-transaminase reactions.
In some embodiments, a NADH-specific L-glutamate dehydrogenase can be overexpressed in the host to regenerate L-glutamate from 2-oxoglutarate as amino donor for ω-transaminase reactions.
In some embodiments, enzymes such as pimeloyl-CoA dehydrogenase classified under, for example, EC 1.3.1.62 and/or an acyl-CoA dehydrogenase classified under, for example, EC 1.3.8.7 or EC 1.3.8.1 that degrade central metabolites and central precursors leading to and including C7 building blocks can be attenuated.
In some embodiments, endogenous enzymes activating C7 building blocks via Coenzyme A esterification such as CoA-ligases such as pimeloyl-CoA synthetase classified under, for example, EC 6.2.1.14 can be attenuated.
In some embodiments, the efflux of a C7 building block across the cell membrane to the extracellular media can be enhanced or amplified by genetically engineering structural modifications to the cell membrane or increasing any associated transporter activity for a C7 building block.
The efflux of heptamethylenediamine can be enhanced or amplified by overexpressing broad substrate range multidrug transporters such as Blt from Bacillus subtilis (Woolridge et al., 1997, J. Biol. Chem., 272(14):8864-8866); AcrB and AcrD from Escherichia coli (Elkins & Nikaido, 2002, J. Bacteriol., 184(23), 6490-6499) or NorA from Staphylococcus aereus (Ng et al., 1994, Antimicrob Agents Chemother, 38(6), 1345-1355) or Bmr from Bacillus subtilis (Neyfakh, 1992, Antimicrob Agents Chemother, 36(2), 484-485).
The efflux of 7-aminoheptanoate and heptamethylenediamine can be enhanced or amplified by overexpressing the solute transporters such as the lysE transporter from Corynebacterium glutamicum (Bellmann et al., 2001, Microbiology, 147, 1765-1774).
The efflux of pimelic acid can be enhanced or amplified by overexpressing a dicarboxylate transporter such as the SucE transporter from Corynebacterium glutamicum (Huhn et al., Appl. Microbiol. & Biotech., 89(2), 327-335).
Typically, one or more C7 building blocks can be produced by providing a host microorganism and culturing the provided microorganism with a culture medium containing a suitable carbon source as described above. In general, the culture media and/or culture conditions can be such that the microorganisms grow to an adequate density and produce a C7 building block efficiently. For large-scale production processes, any method can be used such as those described elsewhere (Manual of Industrial Microbiology and Biotechnology, 2nd Edition, Editors: A. L. Demain and J. E. Davies, ASM Press; and Principles of Fermentation Technology, P. F. Stanbury and A. Whitaker, Pergamon). Briefly, a large tank (e.g., a 100 gallon, 200 gallon, 500 gallon, or more tank) containing an appropriate culture medium is inoculated with a particular microorganism. After inoculation, the microorganism is incubated to allow biomass to be produced. Once a desired biomass is reached, the broth containing the microorganisms can be transferred to a second tank. This second tank can be any size. For example, the second tank can be larger, smaller, or the same size as the first tank. Typically, the second tank is larger than the first such that additional culture medium can be added to the broth from the first tank. In addition, the culture medium within this second tank can be the same as, or different from, that used in the first tank.
Once transferred, the microorganisms can be incubated to allow for the production of a C7 building block. Once produced, any method can be used to isolate C7 building blocks. For example, C7 building blocks can be recovered selectively from the fermentation broth via adsorption processes. In the case of pimelic acid and 7-aminoheptanoic acid, the resulting eluate can be further concentrated via evaporation, crystallized via evaporative and/or cooling crystallization, and the crystals recovered via centrifugation. In the case of heptamethylenediamine and 1,7-heptanediol, distillation may be employed to achieve the desired product purity.
The invention is further described in the following example, which does not limit the scope of the invention described in the claims.
A sequence encoding an N-terminal His tag was added to the tesB gene from Escherichia coli that encodes a thioesterase (SEQ ID NO 1, see
The pellet from the induced shake flask culture was harvested via centrifugation. The pellet was resuspended and lysed in Y-per™ solution (ThermoScientific, Rockford, Ill.). The cell debris was separated from the supernatant via centrifugation. The thioesterase was purified from the supernatant using Ni-affinity chromatography and the eluate was buffer exchanged and concentrated via ultrafiltration.
The enzyme activity assay was performed in triplicate in a buffer composed of 50 mM phosphate buffer (pH=7.4), 0.1 mM Ellman's reagent, and 667 μM of pimeloyl-CoA (as substrate). The enzyme activity assay reaction was initiated by adding 0.8 μM of the tesB gene product to the assay buffer containing the pimeloyl-CoA and incubating at 37° C. for 20 min. The release of Coenzyme A was monitored by absorbance at 412 nm. The absorbance associated with the substrate only control, which contained boiled enzyme, was subtracted from the active enzyme assay absorbance and compared to the empty vector control. The gene product of tesB accepted pimeloyl-CoA as substrate as confirmed via relative spectrophotometry (see
A sequence encoding an N-terminal His-tag was added to the genes from Chromobacterium violaceum, Pseudomonas syringae, Rhodobacter sphaeroides, and Vibrio Fluvialis encoding the ω-transaminases of SEQ ID NOs: 8, 10, 11 and 13, respectively (see
The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation and the cell free extract was used immediately in enzyme activity assays.
Enzyme activity assays in the reverse direction (i.e., 7-aminoheptanoate to pimelate semialdehyde) were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM 7-aminoheptanoate, 10 mM pyruvate and 100 μM pyridoxyl 5′ phosphate. Each enzyme activity assay reaction was initiated by adding cell free extract of the ω-transaminase gene product or the empty vector control to the assay buffer containing the 7-aminoheptanoate and incubated at 25° C. for 4 h, with shaking at 250 rpm. The formation of L-alanine from pyruvate was quantified via RP-HPLC.
Each enzyme only control without 7-aminoheptanoate demonstrated low base line conversion of pyruvate to L-alanine See
Enzyme activity in the forward direction (i.e., pimelate semialdehyde to 7-aminoheptanoate) was confirmed for the transaminases of SEQ ID NO 10, SEQ ID NO 11 and SEQ ID NO 13. Enzyme activity assays were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM pimelate semialdehyde, 10 mM L-alanine and 100 μM pyridoxyl 5′ phosphate. Each enzyme activity assay reaction was initiated by adding a cell free extract of the ω-transaminase gene product or the empty vector control to the assay buffer containing the pimelate semialdehyde and incubated at 25° C. for 4 h, with shaking at 250 rpm. The formation of pyruvate was quantified via RP-HPLC.
The gene product of SEQ ID NO 10, SEQ ID NO 11 and SEQ ID NO 13 accepted pimelate semialdehyde as substrate as confirmed against the empty vector control. See
A sequence encoding a HIS-tag was added to the genes from Segniliparus rugosus and Segniliparus rotundus that encode the carboxylate reductases of SEQ ID NOs: 4 and 7, respectively (see
The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication, and the cell debris was separated from the supernatant via centrifugation. The carboxylate reductases and phosphopantetheine transferases were purified from the supernatant using Ni-affinity chromatography, diluted 10-fold into 50 mM HEPES buffer (pH=7.5), and concentrated via ultrafiltration.
Enzyme activity assays (i.e., from pimelate to pimelate semialdehyde) were performed in triplicate in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 2 mM pimelate, 10 mM MgCl2, 1 mM ATP and 1 mM NADPH. Each enzyme activity assay reaction was initiated by adding purified carboxylate reductase and phosphopantetheine transferase gene products or the empty vector control to the assay buffer containing the pimelate and then incubated at room temperature for 20 min. The consumption of NADPH was monitored by absorbance at 340 nm. Each enzyme only control without pimelate demonstrated low base line consumption of NADPH. See
The gene products of SEQ ID NO 4 and SEQ ID NO 7, enhanced by the gene product of sfp, accepted pimelate as substrate, as confirmed against the empty vector control (see
A sequence encoding a His-tag was added to the genes from Mycobacterium marinum, Mycobacterium smegmatis, Segniliparus rugosus, Mycobacterium smegmatis, Mycobacterium massiliense, and Segniliparus rotundus that encode the carboxylate reductases of SEQ ID NOs: 2-7—respectively (see
Each expression vector was transformed into a BL21[DE3] E. coli host and the resulting recombinant E. coli strains were cultivated at 37° C. in a 250 mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 37° C. using an auto-induction media.
The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation. The carboxylate reductases and phosphopantetheine transferase were purified from the supernatant using Ni-affinity chromatography, diluted 10-fold into 50 mM HEPES buffer (pH=7.5) and concentrated via ultrafiltration.
Enzyme activity (i.e., 7-hydroxyheptanoate to 7-hydroxyheptanal) assays were performed in triplicate in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 2 mM 7-hydroxyheptanal, 10 mM MgCl2, 1 mM ATP, and 1 mM NADPH. Each enzyme activity assay reaction was initiated by adding purified carboxylate reductase and phosphopantetheine transferase or the empty vector control to the assay buffer containing the 7-hydroxyheptanoate and then incubated at room temperature for 20 min. The consumption of NADPH was monitored by absorbance at 340 nm. Each enzyme only control without 7-hydroxyheptanoate demonstrated low base line consumption of NADPH. See
The gene products of SEQ ID NO 2-7, enhanced by the gene product of sfp, accepted 7-hydroxyheptanoate as substrate as confirmed against the empty vector control (see
Example 5
A nucleotide sequence encoding an N-terminal His-tag was added to the Chromobacterium violaceum, Pseudomonas syringae and Rhodobacter sphaeroides genes encoding the ω-transaminases of SEQ ID NOs: 8, 10 and 11, respectively (see
The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation and the cell free extract was used immediately in enzyme activity assays. Enzyme activity assays in the reverse direction (i.e., 7-aminoheptanol to 7-oxoheptanol) were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM 7-aminoheptanol, 10 mM pyruvate, and 100 μM pyridoxyl 5′ phosphate. Each enzyme activity assay reaction was initiated by adding cell free extract of the ω-transaminase gene product or the empty vector control to the assay buffer containing the 7-aminoheptanol and then incubated at 25° C. for 4 h, with shaking at 250 rpm. The formation of L-alanine was quantified via RP-HPLC.
Each enzyme only control without 7-aminoheptanol had low base line conversion of pyruvate to L-alanine See
The gene products of SEQ ID NO 8, 10 & 11 accepted 7-aminoheptanol as substrate as confirmed against the empty vector control (see
A sequence encoding an N-terminal His-tag was added to the Chromobacterium violaceum, Pseudomonas aeruginosa, Pseudomonas syringae, Rhodobacter sphaeroides, Escherichia coli, and Vibrio fluvialis genes encoding the ω-transaminases of SEQ ID NOs: 8-13, respectively (see
The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation and the cell free extract was used immediately in enzyme activity assays.
Enzyme activity assays in the reverse direction (i.e., heptamethylenediamine to 7-aminoheptanal) were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM heptamethylenediamine, 10 mM pyruvate, and 100 μM pyridoxyl 5′ phosphate. Each enzyme activity assay reaction was initiated by adding cell free extract of the ω-transaminase gene product or the empty vector control to the assay buffer containing the heptamethylenediamine and then incubated at 25° C. for 4 h, with shaking at 250 rpm. The formation of L-alanine was quantified via RP-HPLC.
Each enzyme only control without heptamethylenediamine had low base line conversion of pyruvate to L-alanine See
The gene products of SEQ ID NO 8-13 accepted heptamethylenediamine as substrate as confirmed against the empty vector control (see
The activity of each of the N-terminal His-tagged carboxylate reductases of SEQ ID NOs: 3, 6, and 7 (see Examples 4, and
The gene products of SEQ ID NO 3, 6, and 7, enhanced by the gene product of sfp, accepted N7-acetyl-7-aminoheptanoate as substrate as confirmed against the empty vector control (see
The activity of the N-terminal His-tagged ω-transaminases of SEQ ID NOs: 8-13 (see Example 6, and
Each enzyme only control without N7-acetyl-1,7-diaminoheptane demonstrated low base line conversion of pyruvate to L-alanine See
The gene product of SEQ ID NOs: 8 - 13 accepted N7-acetyl-1,7-diaminoheptane as substrate as confirmed against the empty vector control (see
Given the reversibility of the ω-transaminase activity (see example 2), the gene products of SEQ ID NOs: 8-13 accept N7-acetyl-7-aminoheptanal as substrate forming N7-acetyl-1,7-diaminoheptane.
The N-terminal His-tagged carboxylate reductase of SEQ ID NO 7 (see Example 4 and
It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.
This application claims priority of U.S. Provisional Application Ser. No. 61/747,409, filed Dec. 31, 2012, and U.S. Provisional Application Ser. No. 61/829,092, filed May 30, 2013. The contents of the prior applications are incorporated herein by reference in their entirety.
| Number | Date | Country | |
|---|---|---|---|
| 61747409 | Dec 2012 | US | |
| 61829092 | May 2013 | US |
