# Patent

## Title
Bioconversion process for producing nylon-7, nylon-7,7 and polyesters

## Abstract

Embodiments of the present invention relate to methods for the biosynthesis of di- or trifunctional C7 alkanes in the presence of isolated enzymes or in the presence of a recombinant host cell expressing those enzymes. The di- or trifunctional C7 alkanes are useful as intermediates in the production of nylon-7, nylon-7,x, nylon-x,7, and polyesters.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Appl. Ser. No. 61/503,043, filed Jun. 30, 2011, and U.S. Provisional Appl. Ser. Nos. 61/578,265; 61/578,272; and 61/578,289, all of which were filed Dec. 21, 2011, the entireties of all of which are incorporated by reference as if fully set forth herein.


FIELD OF THE INVENTION
Embodiments of the present invention relate to methods for the biosynthetic production of di- or trifunctional C7 alkanes in the presence of one or more isolated enzymes or in the presence of a recombinant host cell expressing one or more enzymes. The di- or trifunctional C7 alkanes are useful as intermediates in the production, for example, of nylon-7, nylon-7,x and/or nylon-x,7.
BACKGROUND OF THE INVENTION
The promotion of sustainable practices by the chemical industry is focused on lowering energy usage, recycling raw materials, and reducing by-products produced during the production of goods. However, the chemical industry vitally depends upon petroleum and natural gas as basic feedstocks. Given the state of optimization associated with major petrochemical processes, a significant shift in feedstock use and manufacturing designs will be required to lower energy, emissions, and costs to below their current level. Biotechnology offers a new approach for the production of industrial chemical intermediates and end-products from renewable carbohydrates, such as plant derived sugars, or other renewable feedstocks such as fatty acids. In addition, biotechnology also offers a way to utilize waste or low value streams such as glycerol from biodiesel production, or to transform petrochemical-derived feedstocks such as benzene, toluene, and polycyclic aromatic hydrocarbons (PAHs) to useful products in bioprocesses that are more benign to the environment than existing chemical processes.
US2010/0203600 and WO2011/031147 are incorporated by reference in their entirety. There is a need in the art for cost-effective biosynthetic routes to chemical intermediates to nylon-7, nylon-7,x nylon-x,7, and polyesters and the end-products nylon-7, nylon-7,x nylon-x,7, and polyesters especially from a variety renewable and non-renewable feedstocks.
SUMMARY OF THE INVENTION
This disclosure is based at least in part of the development of enzymatic systems and recombinant hosts for biosynthesizing di- or trifunctional C7 alkanes that are useful intermediates (monomers) for producing nylon-7, nylon-x,7, nylon-7,x, and polyesters. In particular, as described herein, intermediates useful in the production of nylon-7, and nylon-7,x, nylon-x,7, and polyesters can be biosynthetically produced from renewable feedstocks, such as plant-derived sugars and glycerol, or from petrochemical-derived feedstocks such as benzene or cyclohexane carboxylate. In some embodiments, production of the di- or trifunctional C7 alkanes ultimately proceeds through a common intermediate, pimelic acid semialdehyde (also known as 7-oxoheptanoate), even though there are a number of different feedstocks that can be used and a number of ways to produce pimelic acid semialdehyde. FIG. 1 is a schematic depicting the biotransformation of pimelic acid semialdehyde to various difunctional C7 alkanes.
For example, pimelic acid semialdehyde can be derived from pimeloyl-coenzyme A (CoA), pimeloyl-[acyl carrier protein (acp)], pimelic acid (also known as heptane 1,7-dioate), or α-ketosuberate. As described herein, pimeloyl-CoA and pimeloyl-[acp] can be derived from a number of sources, including from a diverse number of naturally occurring metabolic pathways that form pimeloyl-CoA or pimeloyl-[acp] as an intermediate in the naturally occurring metabolic pathway.
In addition, pimeloyl-CoA and pimelic acid also can be derived from the corresponding enoate 2-heptene-dioic acid or its corresponding CoA ester. In some embodiments, these C7 2-enoates are derived from D,L-diaminopimelate. In some embodiments, the production of difunctional C7 alkanes (e.g., 7 amino heptanoic acid) proceeds through α-ketosuberate or α-aminosuberate, which can be derived from D,L-diaminopimelate. In other embodiments, the α-ketosuberate or α-aminosuberate is derived from α-ketopimelate.
More specifically, the present document provides a variety of methods of converting compounds in order to produce intermediates useful for the manufacture of nylon-7, nylon-7,7, and polyester. It is not required that at all possible steps of any one method be performed and any of the methods can be terminated when a desired compound is obtained. Thus, any method can be terminated after the production of, for example, pimelic acid, 7-amino-heptanoic acid, enantholactam, 1,7-diaminoheptane, or 7-hydroxy-heptanoic acid.
A first method of converting a compound can include contacting a compound selected from 2,6 diaminopimelate (2,6 DAP) and α-amino-pimelate (AAP) with an enzyme that catalyzes the reductive deamination of 2,6 DAP to 6-amino-2-heptenedioic acid (6A2HA) or the reductive deamination of AAP to 2-heptene dioic acid (2 HDA), such that 6A2HA or 2 HDA is produced.
The compound can be 2,6 DAP and the first method can further involve contacting the 6A2HA with an enzyme that catalyzes the enoate reduction of the 6A2HA to AAP, such that AAP is produced.
The AAP can be contacted with an enzyme that catalyzes the reductive deamination of the AAP to 2 HDA, such that 2 HDA is produced.
The 2 HDA can be contacted with an enzyme that catalyzes the enoate reduction of the 2 HDA to pimelic acid (PA), such that PA is produced.
The PA can be contacted with an enzyme that catalyzes the carboxylic acid reduction of the PA to pimelic acid semialdehyde (PAS), such that PAS is produced.
The PAS can be contacted with an enzyme that catalyzes the semialdehyde amination of the PAS to 7-amino-heptanoic acid (7 AHA), such that 7 AHA is produced.
The 7 AHA can be contacted with an enzyme that catalyzes the amide hydrolysis of the 7 AHA to enatholactam (ENTL), such that ENTL is produced.
A second method of converting compound can include, after performing all the steps of the first method up to the production of 7 AHA, contacting the 7 AHA with an enzyme that catalyzes the aldehyde dehydrogenation of the 7 AHA to 7-amino-heptanal (7 AHT), such that AHT is produced.
The 7 AHT can be contacted with an enzyme that catalyzes the transfer of an amino group to the 7 AHT to produce 1,7-diaminoheptane (1,7 DAH), such that 1,7 DAH is produced.
A third method of converting compound can include, after performing all the steps of the first method up to the production of 2 HDA, contacting the 2 HDA with an enzyme that catalyzes the transfer of Coenzyme A (CoA) to the 2 HDA to produce 2-heptene diacid-CoA (2 HDA-CoA), such that 2 HDA-CoA is produced.
The 2 HDA-CoA can be contacted with an enzyme that catalyzes the enoate reduction of the 2 HDA-CoA to pimeloyl-CoA (PCoA), such that PCoA is produced.
The PCoA can be contacted with an enzyme that catalyzes the thioester hydrolysis of the PCoA to PA, such that PA is produced.
The PA can be contacted with an enzyme that catalyzes the carboxylic acid reduction of the PA to PAS, such that PAS is produced.
The PAS can be contacted with an enzyme that catalyzes the semialdehyde amination of the PAS to 7 AHA, such that 7 AHA is produced.
The 7 AHA can be contacted with an enzyme that catalyzes the amide hydrolysis of the 7 AHA to ENTL, such that ENTL is produced.
A fourth method of converting a compound can include, after performing all the steps of the third method up to production of 7 AHA, contacting the 7 AHA with an enzyme that catalyzes the aldehyde dehydrogenation of the 7 AHA to 7 AHT, such that 7 AHT is produced.
The 7 AHT can be contacted with an enzyme that catalyzes the transfer of an amino group to the 7 AHT to produce 1,7 DAH, such that 1,7 DAH is produced.
A fifth method of converting a compound can include, after performing all the steps of the first method up to the production of AAP, contacting the AAP with an enzyme that catalyzes the transfer of an amino group to the AAP to produce α-keto-pimelate (AKP), such that AKP is produced.
The AKP can be contacted with one or more enzymes that catalyze the ketone reduction of the AKP to α-hydroxy-pimelate (AHP), such that AHP is produced.
The AHP can be contacted with an enzyme that catalyzes the transfer of CoA to the AHP to produce α-hydroxy-pimelate (AHP-CoA), such that AHP-CoA is produced.
The AHP-CoA can be contacted with an enzyme that catalyzes the dehydration of the AHP-CoA to 2 HDA-CoA, such that 2 HDA-CoA is produced.
The 2 HDA-CoA can be contacted with an enzyme that catalyzes the enoate reduction of the 2 HDA-CoA to PCoA, such that PCoA is produced.
The PCoA can be contacted with an enzyme that catalyzes the thioester hydrolysis of the PCoA to PA, such that PA is produced.
The PA can be contacted with an enzyme that catalyzes the carboxylic acid reduction of the PA to PAS, such that PAS is produced.
The PAS with can be contacted with an enzyme that catalyzes the semialdehyde amination of the PAS to 7 AHA, such that 7 AHA is produced.
The 7 AHA can be contacted with an enzyme that catalyzes the amide hydrolysis of the 7 AHA to ENTL, wherein ENTL is produced.
A sixth method of converting a compound can include, after performing all the steps of the fifth method up to the production of 7 AHA, contacting the 7 AHA with an enzyme that catalyzes the aldehyde dehydrogenation of the 7 AHA to 7 AHT, such that 7 AHT is produced.
The 7 AHT can be contacted with an enzyme that catalyzes the transfer of an amino group to the 7 AHT to produce 1,7 DAH, such that 1,7 DAH is produced.
A seventh method of converting a compound can include, after performing all the steps of the fifth method up to the production of AHP, contacting the AHP with an enzyme that catalyzes the dehydration of the AHP to 2 HDA, such that 2 HDA is produced.
The 2 HDA can be contacted with an enzyme that catalyzes the enoate reduction of the 2 HDA to pimelic acid (PA), such that PA is produced.
The PA can be contacted with an enzyme that catalyzes the carboxylic acid reduction of the PA to PAS, such that PAS is produced.
The PAS can be contacted with an enzyme that catalyzes the semialdehyde amination of the PAS to 7 AHA, such that 7 AHA is produced.
The 7 AHA can be contacted with an enzyme that catalyzes the amide hydrolysis of the 7 AHA to ENTL, such that ENTL is produced.
An eighth method of converting a compound can include, after performing all the steps of the fifth method up to the production of 7 AHA, contacting the 7 AHA with an enzyme that catalyzes the aldehyde dehydrogenation of the 7 AHA to 7 AHT, such that 7 AHT is produced.
The 7 AHT can be contacted with an enzyme that catalyzes the transfer of an amino group to the 7 AHT to produce 1,7 DAH, such that 1,7 DAH is produced.
A ninth method of converting a compound can include, after performing all the steps of the seventh method up to the production of 2 HDA, contacting the 2 HDA with an enzyme that catalyzes the transfer of CoA to 2 HDA to produce 2 HDA-CoA, such that 2 HDA-CoA is produced.
The 2 HDA-CoA can be contacted with an enzyme that catalyzes the enoate reduction of the 2 HDA-CoA to PCoA, such that PCoA is produced.
The PCoA can be contacted with an enzyme that catalyzes the thioester hydrolysis of the PCoA to PA, such that PA is produced.
The PA can be contacted with an enzyme that catalyzes the carboxylic acid reduction of the PA to PAS, such that PAS is produced.
The PAS can be contacted with an enzyme that catalyzes the semialdehyde amination of the PAS to 7 AHA, such that 7 AHA is produced.
The 7 AHA can be contacted with an enzyme that catalyzes the amide hydrolysis of the 7 AHA to ENTL, such that ENTL is produced.
A tenth method of converting a compound can include, after performing all the steps of the ninth method up to the production of 7 AHA, contacting the 7 AHA with an enzyme that catalyzes the aldehyde dehydrogenation of the 7 AHA to 7 AHT, such that 7 AHT is produced.
The 7 AHT can be contacted with an enzyme that catalyzes the transfer of an amino group to the 7 AHT to produce 1,7 DAH, such that 1,7 DAH is produced.
An eleventh method of converting a compound can include, after performing all the steps of the fifth method up to the production of AKP, contacting the AKP with an enzyme that catalyzes the α-keto acid chain elongation of the AKP to α-keto-suberate (AKS), such that AKS is produced.
The AKS can be contacted with an enzyme that catalyzes the transfer of an amino group to the AKS to produce α-amino suberate (AAS), such that AAS is produced. The AAS can be contacted with an enzyme that catalyzes the α-keto acid decarboxylation of the AAS to 7 AHA, such that 7 AHA is produced.
The 7 AHA can be contacted with an enzyme that catalyzes the amide hydrolysis of the 7 AHA to ENTL, such that ENTL is produced.
A twelfth method of converting a compound can include, after performing all the steps of the eleventh method up to the production of 7 AHA, contacting the 7 AHA with an enzyme that catalyzes the aldehyde dehydrogenation of the 7 AHA to 7 AHT, such that 7 AHT is produced.
The 7 AHT can be contacted with an enzyme that catalyzes the transfer of an amino group to the 7 AHT to produce 1,7 DAH, such that 1,7 DAH is produced.
A thirteenth method of converting a compound can include, after performing all the steps of the eleventh method up to the production of AKS, contacting the AKS with an enzyme that catalyzes the α-keto acid decarboxylation of the AKS to PAS, such that PAS is produced.
The PAS can be contacted with an enzyme that catalyzes the semialdehyde amination of the PAS to 7 AHA, such that 7 AHA is produced.
The 7 AHA can be contacted with an enzyme that catalyzes the amide hydrolysis of the 7 AHA to ENTL, such that ENTL is produced.
A fourteenth method of converting a compound can include, after performing all the steps of the thirteenth method up to the production of 7 AHA, contacting the 7 AHA with an enzyme that catalyzes the aldehyde dehydrogenation of the 7 AHA to 7 AHT, such that 7 AHT is produced.
The 7 AHT can be contacted with an enzyme that catalyzes the transfer of an amino group to the 7 AHT to produce 1,7 DAH, such that 1,7 DAH is produced.
A fifteenth method of converting a compound can include, after performing all the steps of the fifth method up to the production of PCoA, contacting the PCoA with an enzyme that catalyzes the reduction of the PCoA to PAS, such that PAS is produced.
The PAS can be contacted with an enzyme that catalyzes the semialdehyde amination of the PAS to 7 AHA, such that 7 AHA is produced.
The 7 AHA can be contacted with an enzyme that catalyzes the amide hydrolysis of the 7 AHA to ENTL, such that ENTL is produced.
A sixteenth method of converting a compound can include, after performing all the steps of the fifteenth method up to the production of 7 AHA, contacting the 7 AHA with an enzyme that catalyzes the aldehyde dehydrogenation of the 7 AHA to 7 AHT, such that 7 AHT is produced.
The 7 AHT can be contacted with an enzyme that catalyzes the transfer of an amino group to the 7 AHT to produce 1,7 DAH, such that 1,7 DAH is produced.
A seventeenth method of converting a compound can include, after performing all the steps of the ninth method up to the production of PCoA, contacting the PCoA with an enzyme that catalyzes the reduction of the PCoA to PAS, such that PAS is produced.
The PAS can be contacted with an enzyme that catalyzes the semialdehyde amination of the PAS to 7 AHA, such that 7 AHA is produced.
The 7 AHA can be contacted with an enzyme that catalyzes the amide hydrolysis of the 7 AHA to ENTL, such that ENTL is produced.
An eighteenth method of converting a compound can include, after performing all the steps of the seventeenth method up to the production of 7 AHA, contacting the 7 AHA with an enzyme that catalyzes the aldehyde dehydrogenation of the 7 AHA to 7 AHT, such that 7 AHT is produced.
The 7 AHT can be contacted with an enzyme that catalyzes the transfer of an amino group to the 7 AHT to produce 1,7 DAH, such that 1,7 DAH is produced.
A nineteenth method of converting a compound can include contacting a compound selected from 6A2HA and 2 HDA with an enzyme that catalyzes the enoate reduction of 6A2HA to AAP or for the enoate reduction of 2 HDA to PA, such that AAP or PA is produced. It is understood that, following the production of AAP or PA, any of the steps after the production of AAP or PA described above in the first to eighteenth methods can be performed.
A twentieth method of converting a compound can include contacting a compound selected from PCoA and pimeloyl [acp] (PACP) with an enzyme that catalyzes the thioesterase hydrolysis PCoA or PACP to PA, wherein PA is produced.
The PA can be contacted with an enzyme that catalyzes the carboxylic acid reduction of the PA to PAS, such that PAS is produced.
The PAS can be contacted with an enzyme that catalyzes the semialdehyde amination of the PAS to 7 AHA, such that 7 AHA is produced.
The 7 AHA with an enzyme that catalyzes the amide hydrolysis of the 7 AHA to ENTL, such that ENTL is produced.
A twenty first method of converting a compound can include, after performing all the steps of the twentieth method up to the production of 7 AHA, contacting the 7 AHA with an enzyme that catalyzes the aldehyde dehydrogenation of the 7 AHA to 7 AHT, such that 7 AHT is produced.
The 7 AHT can be contacted with an enzyme that catalyzes the transfer of an amino group to the 7 AHT to produce 1,7 DAH, such that 1,7 DAH is produced.
A twenty second method of converting a compound can include contacting AKP with one or more enzymes that catalyze the ketone reduction of AKP to AHP, such that AHP is produced. The AKP can have been produced by chain elongation of α-keto adipate or α-keto glutarate. The AHP can then be converted to PA or to PCoA. It is understood that, following the production of PA or PCoA, any of the steps after the production of PA or PCoA described above in the first to eighteenth methods can be performed.
A twenty third method of converting a compound can include converting AKP to AKS by α-keto acid chain elongation. The AKP can have been produced by chain elongation of α-keto adipate or α-keto glutarate. It is understood that, following the production of AKS, any of the steps after the production of AKS described above in the first to eighteenth methods can be performed.
A twenty fourth method of converting a compound can include contacting PAS with an enzyme that catalyzes the semialdehyde amination of PAS to 7 AHA, such that 7 AHA is produced. The PAS can have been obtained by conversion from 2,6 DAP, AKG, PCoA, or PACP. It is understood that, following the production of AHA, any of the steps after the production of AHA described above in the first to eighteenth methods can be performed.
A twenty fifth method of converting a compound can include contacting a compound selected from PCoA and PACP with an enzyme that catalyzes the reduction of the compound to PAS, such that PAS is produced. It is understood that, following the production of PAS, any of the steps after the production of PAS described above in the first to eighteenth methods can be performed. Moreover, any of the steps described in the first to eighteenth and the twenty second method leading to the production of PCoA can be performed prior to the twenty fifth method.
A twenty sixth method of converting a compound can include contacting PAS with an enzyme that catalyzes the alcohol dehydrogenation of PAS to 7-hydroxy-heptanoic acid (7 HHA), such that 7 HHA is produced. It is understood that any of the steps described in the first to eighteenth and the twentieth, twenty second, twenty third, and twenty fifth methods leading to the production of PAS can be performed prior to the twenty sixth method.
In any of the described methods the enzyme(s) can be used in purified form. Alternatively, the enzyme(s) can be used in the form of a cell lysate or a partially purified cell lysate. In addition, the enzyme(s) can be in a cell recombinantly expressing it/them.
In the described methods, an enzyme that catalyzes reductive deamination can include an ammonia lyase. The ammonia lyase can be in EC 4.3.1, e.g., EC 4.3.1.1; EC 4.3.1.2; EC 4.3.1.3; EC 4.3.1.12; EC 43.1.13; or EC 4.3.1.24.
In the described methods, an enzyme that catalyzes enoate reduction can include an enoate reductase. The enoate reductase can be in EC 1.3.1, e.g., EC 1.3.1.31.
In the described methods, an enzyme that catalyzes carboxylic acid reduction can include a carboxylic acid reductase. The carboxylic acid reductase can be in EC 1.2.99, e.g., EC 1.2.99.6.
In the described methods, an enzyme that catalyzes semialdehyde amination can include an ω transaminase. The ω transaminase can be in EC 2.6.1, e.g., EC 2.6.1.18; EC 2.6.1.19; EC 2.6.1.2; EC 2.6.1.7; EC 2.6.1.29; EC 2.6.1.36; EC 2.6.1.39; EC 2.6.1.42; or EC 2.6.1.68.
In the described methods, an enzyme that catalyzes thioester hydrolysis can include a thioesterase, an acid-thiol ligase, or a CoA transferase. The thioesterase can be in EC 3.1.2, e.g.,
EC 3.1.2.18; EC 3.1.2.19; or EC 3.1.2.20. The acid-thiol ligase can be in EC 6.2.1, e.g., EC 6.2.1.3; EC 6.2.1.14; or EC 6.2.1.23. The CoA transferase can be in EC 2.8.3, e.g., EC 2.8.3.12 or EC 2.8.3.13.
In the described methods, an enzyme that catalyzes the transfer of an amino group can include an aminotransferase. The aminotransferase can be in EC 2.6.1, e.g., EC 2.6.1.67.
In the described methods, an enzyme that catalyzes ketone reduction can be a carbonyl reductase. The carbonyl reductase can include EC.1.1.1.184.
In the described methods, an enzyme that catalyzes α-keto acid decarboxylation can be an α-keto acid decarboxylase.
In the described methods, an enzyme that catalyzes reduction (of, for example, PCoA to PAS) can be a fatty-acyl-CoA reductase. The fatty-acyl-CoA reductase can be in EC 1.2.1, e.g., EC 1.2.1.50.
In the described methods, an enzyme that catalyzes aldehyde dehydrogenation can be an aldehyde dehydrogenase. The aldehyde dehydrogenase can be in EC 1.2.1, e.g., EC 1.2.1.4 or EC 1.2.1.63.
In the described methods, an enzyme that catalyzes the transfer of CoA can include a CoA transferase. The CoA transferase can be in EC 2.8.3, e.g., EC 2.8.3.12 or EC 2.8.3.13.
In the described methods, an enzyme that catalyzes amide hydrolysis can be an amino hydrolase.
In the described methods, an enzyme that catalyzes dehydration (of, for example, AHP or AHP-CoA) can be a hydro-lyase. The hydro-lyase can be in EC 4.2.1, e.g., EC 4.2.1.2; EC 4.2.1.59; 4.2.1.61; 4.1.2.17 or 4.1.2.18.
In the described methods, enzymes that catalyzes α-keto acid chain elongation can include one of more of the set of enzymes including AksA, AksD, AksE and AksF. The AksA can be in EC 2.3.3, e.g., EC 2.3.3.13 or 2.3.3.14. The AksD can be in EC 4.2.1, e.g., EC 4.2.1.33. The AksF can be in EC 1.1.1, e.g., EC 1.1.1.85. One or more (e.g., two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, ten or more, 12 or more, 14 or more, 18, or more, or 20 or more) of the α-keto acid chain elongation enzymes can be from methanogenic bacteria.
In the described methods, an enzyme that catalyzes alcohol dehydrogenation can include an alcohol dehydrogenase. The alcohol dehydrogenase can include EC. 1.1.1.1 or EC 1.1.1.2. It can also be, for example, adhA from Zymomonas mobilis, adhB from Zymomonas mobilis, butanol dehydrogenase from Clostridium acetobutylicum, Saccharomyces ADHIV, and ADH6 from S. cerevisiae. 
PCoA or PACP used in the methods of the document can be derived from acetyl-CoA or benzoyl-CoA. The acetyl-CoA can be derived from renewable feedstocks comprising cellulosic feedstocks, sugars, glycerol, or fatty acids. Moreover, the acetyl-CoA can be derived from SynGas, methane or methanol. The benzoyl-CoA can be derived from polycyclic aromatic hydrocarbons.
The 2,6 DAP used in the methods of the document can be produced by a lysine-producing organism lacking diaminopimelate decarboxylase. The 2,6 DAP is derived from renewable feedstocks, which can contain sugars.
The present document features a bioderived nylon-7, nylon-7, x nylon-x,7, and polyester. It also includes a Nylon-7 produced by a process that includes polymerizing 7 AHA, where the 7 AHA is derived from PAS or AAS. Also provided by the document is a nylon-7,7 produced by a process that includes polymerizing PA and 1,7 DHA, where the PA is derived from PCoA; PACP; or 2 HDA and the 1,7 DHA is derived from 7 AHA. The document also embodies nylon-7 produced by a process that includes polymerizing 7 AHA made by any of the methods described above that lead to the production of 7 AHA. Another aspect of the invention is a nylon 7,7 produced by a process comprising polymerizing 1,7 DHA and PA, where the 1,7 DHA is made by any of the methods described above that lead to the production of 1,7 DHA and the PA is made by any of the methods described above that lead to the production of PA.
The present document also provides a substantially pure culture of host cells, a substantial number of which comprise and express one or more exogenous nucleic acids encoding one or more enzymes involved in the biosynthesis of one or more polymer monomers selected from 7 AHA; PA; 1,7 DAH; ENTL; and 7 HHA. These enzymes include acyl-CoA reductases, acyl-[acp] reductases, thioester hydrolases, ammonia lyases, enoate reductases, aminotransferases, CoA transferases, thioesterases, acid-thiol ligases, hydro-lyases, carbonyl reductases, carboxylic acid reductases, fatty-acyl CoA reductases, ω-transaminases, α-keto acid decarboxylases, aldehyde dehydrogenases, alcohol dehydrogenases, and enzymes catalyzing α-keto acid chain elongation. As used herein, a “substantial number” is at least 10% (e.g., at least: 20%; 30%; 40%; 50%; 60%; 70%; 75%; 80%; 85%; 90%; 95%; 97%; 98%; 99%; or even 100%) of the cells in the culture.
The cells of the culture can be prokaryotic cells, such as, without limitation, Escherichia coli, Rhodopseudomonas palustris, sphingomonads, pseudomonads, methanogenic bacteria (e.g., Methanobacterium autotrophicum), Corynebacterium, Salmonella, Burkholderia, Moraxella, Alcaligenes, Psychrobacter, Thermotoga, Acinetobacteria, Rhodobacter, Azoarcus, Rhodospirillum, Brevibacterium, streptococci, lactobacilli, Nocardia, Bacillus, Rhodococcus, Clostridium, Streptomyces, and Arthobacter. 
Alternatively, the cells of the culture can be eukaryotic cells, e.g., fungal cells such as yeast cells. The yeast cells can be of a yeast such as, without limitation, Yarrowia lipolytica, Candida, Rhodotorula, Rhizopus, Saccharomyces, Pichia, Trichosporon, Issatchenka, Kluyveromyces, Debaryomyces, Hansenula, Schizosaccharomyces, Schwanniomyces, and Lipomyces. The Candida cells can be of a yeast such as, without limitation, C. tropicalis, C. albicans, C. cloacae, C. guillermondii, C. intermedia, C. maltosa, C. parapsilosis, and C. zeylenoides. Other fungal cells can be of a fungus such as, without limitation, Aspergillus, Exophiala, Mucor, Trichoderma, Cladosporium, Phanerochaete, Cladophialophora, Paecilomyces, Scedosporium, and Ophiostoma. 
Exogenous enzymes that can be expressed by the cells are as follows. The ammonia lyases can include an ammonia lyase in EC 4.3.1, e.g., EC 4.3.1.1; EC 4.3.1.2; EC 4.3.1.3; EC 4.3.1.12; EC 4.3.1.13; or EC 4.3.1.24. The enoate reductases can include an enoate reductase in EC 1.3.1, e.g., EC 1.3.1.31. The carboxylic acid reductases include a carboxylic acid reductase in EC 1.2.99, e.g., EC 1.2.99.6. The ω-transaminases can include a transaminase in EC 2.6.1, e.g., EC 2.6.1.18; EC 2.6.1.19; EC 2.6.1.2; EC 2.6.1.7; EC 2.6.1.29; EC 2.6.1.36; EC 2.6.1.39; EC 2.6.1.42; or EC 2.6.1.68. The thioesterases can include a thioesterase in EC 3.1.2, e.g., EC 3.1.2.18; EC 3.1.2.19; or EC 3.1.2.20. The acid-thiol ligases can include an acid-thiol ligase in EC 6.2.1, e.g., EC 6.2.1.3; EC 6.2.1.14; or EC 6.2.1.23. The CoA transferases can include a CoA transferase in EC 2.8.3, e.g., EC 2.8.3.12 or EC 2.8.3.13. The aminotransferases can include an aminotransferase in EC 2.6.1, e.g., EC 2.6.1.67. The carbonyl reductases can include EC.1.1.1.184. The fatty-acyl-CoA reductases can include a fatty-acyl-CoA reductase in EC 1.2.1, e.g., EC 1.2.1.50. The aldehyde dehydrogenases can include an aldehyde dehydrogenase in EC 1.2.1, e.g., EC 1.2.1.4 or EC 1.2.1.63. The hydro-lyases include a hydro-lyase in EC 4.2.1, e.g., EC 4.2.1.2; EC 4.2.1.59; 4.2.1.61; 4.1.2.17 or 4.1.2.18. The enzymes catalyzing α-keto acid chain elongation can include one or more enzymes of the set including AksA, AksD, AksE and AksF enzymes. The AksA can include an AksA enzyme in EC 2.3.3, e.g., EC 2.3.3.13 or 2.3.3.14. The AksD can include an AksD enzyme in EC 4.2.1, e.g., EC 4.2.1.33. The AksF can include an AksF enzyme in EC 1.1.1, e.g., EC 1.1.1.85. The alcohol dehydrogenases can include, e.g., EC. 1.1.1.1 or EC 1.1.1.2. In addition the alcohol dehydrogenases can include, for example, adhA from Zymomonas mobilis, adhB from Zymomonas mobilis, butanol dehydrogenase from Clostridium acetobutylicum, Saccharomyces ADHIV, and ADH6 from S. cerevisiae. 
Another aspect of the present document is an isolated host cell comprising and expressing one or more exogenous nucleic acids encoding one or exogenous nucleic acids involved in the biosynthesis of one or more polymer monomers selected from 7 AHA; PA; 1,7 DAH; ENTL; and 7 HHA. The enzymes include acyl-CoA reductases, acyl-[acp] reductases, thioester hydrolases, ammonia lyases, enoate reductases, aminotransferases, CoA transferases, thioesterases, acid-thiol ligases, hydro-lyases, carbonyl reductases, carboxylic acid reductases, fatty-acyl CoA reductases, ω-transaminases, α-keto acid decarboxylases, aldehyde dehydrogenases, alcohol dehydrogenases, and enzymes catalyzing α-keto acid chain elongation. The cell and enzymes can be any of those described above for a substantially pure culture of host cells.
Other objects and advantages will become apparent to those skilled in the art from a consideration of the ensuing detailed descriptions set forth herein.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a schematic showing the biotransformation of pimelic acid semialdehyde, to various difunctional C7 alkanes useful for nylon 7, nylon 7,7 and nylon 7,x production, as well as polyesters.
FIG. 2 is a schematic of the formation of pimelic acid semialdehyde from pimeloyl-CoA, pimeloyl-[acp], or α-ketosuberate, all of which are intermediates in naturally occurring pathways as indicated.
FIG. 3 is a schematic of the series of reactions in α-ketoacid chain elongation. Three basic reactions are involved: a condensation between an α-ketodiacid and acetyl-CoA to form a citrate homolog, isomerization of the citrate homolog to an isocitrate homolog, and oxidative decarboxylation of the isocitrate homolog to an α-ketodiacid containing an additional methylene group [Howell98: Howell D M, Harich K, Xu H, White RH (1998). Alpha-keto acid chain elongation reactions involved in the biosynthesis of coenzyme B (7-mercaptoheptanoyl threonine phosphate) in methanogenic Archaea.” Biochemistry 1998; 37(28); 10108-17.]
These reactions are analogous to the reactions catalyzed by citrate synthase, aconitase, and isocitrate dehydrogenase in the TCA cycle I (prokaryotic) and the reactions catalyzed by (R)-homocitrate synthase, homoaconitase and (−)-threo-isohomocitrate dehydrogenase in lysine biosynthesis V [Howell, 1998, supra].
FIG. 4 is a schematic of the formation of pimeloyl-CoA through condensation of three malonyl-CoAs.
FIG. 5 is a schematic of the formation of pimeloyl-CoA from pimelic acid or other precursors in 7-keto-8-aminopelargonate biosynthesis in biotin biosynthesis pathway II. 7-keto-8-aminopelargonate is the key intermediate for biotin biosynthesis. Degradation of pimeloyl-CoA in the host organism can be prevented by deletion or inactivation of BioF, the gene encoding 7-keto-8-aminopelargonic acid synthetase (E.C. 2.3.1.47).
FIG. 6 is a schematic of the formation of pimeloyl-[acp] or its methyl ester in 7-keto-8-aminopelargonate biosynthesis in biotin biosynthesis pathway I. The key intermediate in biotin biosynthesis. Pimelic acid or pimelic acid semialdehyde can be prepared from these precursors by the action of aaaS (acyl-ACP synthetase), FatA (fatty acyl-ACP thioesterase A), FatB (fatty acyl-ACP thioesterase B), or acyl-[acp] reductase as shown in bold text.
FIG. 7 is a scheme showing formation of pimeloyl-CoA from benzoate or cyclohexane carboxylate degradation.
FIG. 8 is a scheme showing the formation of pimelic acid semialdehyde in the tetralin degradation pathway in Sphingomonas and Corynebacterium spp.
FIG. 9 is a scheme showing formation of pimeloyl-CoA in the cyclohexane carboxylate pathway from crotonate by methanogens. See Mouttaki et al., Applied and Environmental Microbiology, pages 930-938 (2001).
FIG. 10 is a schematic showing examples of engineered pathways to pimelic acid semialdehyde and 7-aminoheptanoic acid from D,L-diaminopimelate as a starting point via 2-aminoheptanedioic acid. There are 2 routes from 2-aminoheptanedioic acid to pimelic acid semialdehyde, either via reductive deamination by an ammonia lyase to 2-heptenedioic acid or via follnation of the α-keto-acid that can subsequently be converted to pimelic acid or its CoA ester. Alternatively, α-keto-pimelate derived from 2-aminoheptanedioic acid can undergo one round of chain elongation to α-keto-suberate, which can either be decarboxylated to form pimelic acid semialdehyde, or converted to α-aminosuberate, which will lead directly to 7-aminoheptanoic acid upon decarboxylation. α-keto-pimelate also can be derived from α-keto-adipate, which in turn can be derived from α-keto-glutarate, through two successive rounds of α-keto-acid chain elongation.
FIG. 11A shows an SDS-PAGE analysis on soluble and insoluble fractions from expression of the Citrobacter amalonaticus ammonia lyase protein.
FIG. 11B shows an SDS-PAGE analysis on soluble and insoluble fractions from expression of the Clostridium tetanomorphum (I5) and Aspergillus oryzae (I6) ammonia lyase proteins.
FIG. 12 shows an SDS-PAGE analysis on soluble and insoluble fractions from expression of the Nocardia sp. carboxylic acid reductase gene.
FIG. 13 shows a change in absorbance over time due to reduction of pimelic acid to pimelic acid semialdehyde by Nocardia CAR reductase activity.
FIG. 14 shows an SDS-PAGE analysis on soluble fraction and insoluble fraction from expression of the Haemophilus influenzae YciA thioesterase protein (I8)
FIG. 15 shows an SDS-PAGE analysis of the aminotransferase IlvE-Omega Vf fusion (pING2022) and IlvE-Ad optimized omega fusion (pING2030) proteins.
FIG. 16 shows Results of the biotransformation of sodium pyruvate and 7-aminoheptanoic acid with the measured concentrations of 7-aminoheptanoic acid substrate and L-alanine product.
FIG. 17 shows a Summary of the HPLC results from the L- and D-2-aminosuberic acid enantiomer concentrations in the six biotransformations after 48 and 96 hours.
FIG. 18 shows an SDS-PAGE analysis on soluble and insoluble fractions from the bead lysis of expression of the E. coli GadA (I29), E. coli LysA (I30), E. coli GadA ilvE (I31) and E. coli LysA ilvE (I32) proteins.
FIG. 19 shows the formation of 7-aminoheptanoic acid from the decarboxylation of 2-aminosuberate.
FIG. 20 shows protein alignment using the ClustalW algorithm showing significant homology between MJ0277 (SEQ ID NO:22) and comD (SEQ ID NO:41)/comE (SEQ ID NO:42) proteins.
FIG. 21 shows homology of MJ0277 (SEQ ID NO:22) to LACLA acetolactate synthase from Lactococcus lactis (SEQ ID NO:43).
FIG. 22 shows an analysis of the functional domains in LACLA acetolactate synthese, comD/comE from Methanocella paludicola and the hypothetical acetolactate synthase MJ0277 showed that all of them have a similar structure containing a thiamine phosphate binding site.
FIG. 23 depicts a map of pING2022 vector, containing the IlvE-Omega Vf fusion gene.
FIG. 24 depicts a map of pING2030 vector containing the IlvE-Ad optimized omega fusion gene.
FIG. 25 sets forth the SEQ. ID 1-40



DETAILED DESCRIPTION OF THE INVENTION
In general, this disclosure relates to methods and materials for biosynthetically producing di- or trifunctional C7 alkanes that are useful as intermediates in the production of nylon-7, nylon-7,x and nylon-x,7, as well as the production of polyesters.
In some embodiments, one or more (e.g., two or more; three or more; four or more; five or more; six or more; seven or more; eight or more; nine or more; ten or more; eleven or more; twelve or more; thirteen or more; fourteen or more; fifteen or more; sixteen or more; seventeen or more; eighteen or more; nineteen or more; twenty or more; or even more) isolated enzymes (e.g., an ammonia lyase, enoate reductase, aminotransferase, CoA transferase, thioestesterase, acid-thiol ligase, hydro-lyase, carbonyl reductase, thioesterase, carboxylic acid reductase, fatty-acyl CoA reductase, ω-transaminase, α-keto acid decarboxylase, enzymes catalyzing α-keto acid chain elongation, acyl-ACP synthetase, FatA (fatty acyl-ACP thioesterase A), FatB (fatty acyl-ACP thioesterase B), or acyl-[acp] reductase) can be used to biosynthetically produce the di- or trifunctional C7 alkanes. Such enzymes can be isolated from recombinant cells expressing exogenous nucleic acids encoding the enzyme(s) or non-recombinant cells naturally expressing the enzymes.
In some embodiments, a recombinant host that includes one or more (e.g., two or more; three or more; four or more; five or more; six or more; seven or more; eight or more; nine or more; ten or more; eleven or more; twelve or more; thirteen or more; fourteen or more; fifteen or more; sixteen or more; seventeen or more; eighteen or more; nineteen or more; twenty or more; or even more) exogenous nucleic acids encoding one or more (e.g., two or more; three or more; four or more; five or more; six or more; seven or more; eight or more; nine or more; ten or more; eleven or more; twelve or more; thirteen or more; fourteen or more; fifteen or more; sixteen or more; seventeen or more; eighteen or more; nineteen or more; twenty or more; or even more) enzymes (e.g., one or more (as above) of an ammonia lyase, enoate reductase, aminotransferase, CoA transferase, thioestesterase, acid-thiol ligase, hydro-lyase, carbonyl reductase, thioesterase, carboxylic acid reductase, fatty-acyl CoA reductase, ω-transaminase, α-keto acid decarboxylase, enzymes catalyzing α-keto acid chain elongation, acyl-ACP synthetase, FatA, FatB, or acyl-[acp] reductase), or a lysate prepared from such a recombinant host or a non-recombinant cell naturally expressing the enzyme(s) can be used to biosynthetically produce the di- or trifunctional C7 alkanes. A recombinant host also may have a deficiency in one or more endogenous enzymes in order to divert metabolic intermediates towards the production of the di- or trifunctional C7 alkanes.
As described herein, the biosynthetically produced di- or trifunctional C7 alkanes can be used to produce nylon-7, nylon-7,x, or nylon-x,7, as well as polyesters. The term “nylon-7” is a polyamide produced by polymerization of the monomer 7-aminoheptanoic acid or by ring-opening condensation enantholactam. Nylon-7 also is known as “polyenanthamide” or “polyheptanamide.”
The term “nylon-x,7” refers to the family of polyamides that are produced by the polymerization of heptane-1,7-dioic acid (also known as pimelic acid or pimelate) with a diamine. The integer x indicates the number of carbon atoms in the diamine with which the heptane-1,7-dioic acid is reacted. In some embodiments, the integer x is an integer greater than 3, e.g., greater than 5, greater than 7, or greater than 9. For example, nylon-5,7 is produced by reacting heptane-1,7-dioic acid and 1,5-pentanediamine. Nylon 7,7 is produced by reacting heptane-1,7-dioic acid and 1,7 diaminoheptane.
The term “nylon-7,x” refers to the family of polyamides that are produced by the polymerization reaction of heptamethylenediamine with a dicarboxylic acid. The integer x indicates the number of carbon atoms in the dicarboxylic acid with which the heptamethylenediamine is reacted. For example, nylon-7,5 is produced by the reaction of heptamethylenediamine (also known as 1,7-diaminoheptane or 1,7-heptanediamine) and pentane-1,5-dioic acid. In some embodiments, the integer x is an integer greater than 3, e.g., greater than 5, greater than 7 or greater than 9.
The term “polyester” refers to a category of polymers which contains an ester functional group in their main chain. Polyesters can be homopolymers, for example polycaprolactone, that is produced by ring-opening condensation of caprolactone. Copolymer polyesters are formed by the esterification condensation of polyfunctional alcohols and acids. For example, adipic acid and ethylene glycol are used to produce polyethylene adipate. Pimelic acid can be used in the place of adipic acid in such copolymers. Alternatively, 7-hydroxyheptanoic acid can be used to produce polyenantholactone.
The foregoing and other aspects of the present invention will now be described in more detail with respect to embodiments described herein. It should be appreciated that the invention can be embodied in different forms and should not be construed as limited to the embodiments set forth herein. Rather, these embodiments are provided so that this disclosure will be thorough and complete, and will convey the scope of the invention to those skilled in the art.
1.1 Definitions
The terminology used in the description of the invention herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention. As used in the description of the embodiments of the invention and the appended claims, the singular forms “a,” “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. Also, as used herein, “and/or” refers to, and encompasses, any and all possible combinations of one or more of the associated listed items. Unless otherwise defined, all terms, including technical and scientific terms used in the description, have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.
As used herein, the term “enzyme” or “enzymes” refers to a protein catalyst capable of catalyzing a reaction. Herein, the term does not mean only an isolated enzyme, but also includes a host cell expressing that enzyme. Accordingly, the conversion of A to B by enzyme C should also be construed to encompass the conversion of A to B by a host cell expressing enzyme C.
As used herein, the term “difunctional C7 alkane” refers to straight or branched, saturated or unsaturated, hydrocarbon having seven carbon atoms and two functional groups. The functional groups may be positioned at any point along the hydrocarbon chain. In some embodiments, the functional groups are located at the terminal ends of the hydrocarbon chain (e.g., one functional group at each terminus). The term is also intended to encompass cyclic compounds such as enantholactam. Exemplary difunctional C7 alkanes include, but are not limited to, pimeloyl-CoA, pimeloyl-[acp], heptane-1,7-dioic acid (pimelic acid or pimelate), 7-aminoheptanoic acid, 7-hydroxyheptanoic acid, heptamethylenediamine, 1,7-heptanediol, 7-aminoheptanol, 7-aminoheptanal, enantholactam, pimelic acid semialdehyde (also known as 7-oxoheptanoate), 2-heptenediacid, and 2-heptene diacid-CoA.
As used herein, the terms “-oate” and “-oic acid”, for example heptanoate and heptanoic acid, are used interchangeably. Moreover, it should be understood that “-ate”, “-oate” and “-oic acid” can be used interchangeably throughout to refer to the compound in any of its neutral or ionized forms, and so-called “zwitterionic” forms.
As used herein, the term “trifunctional C7 alkane” refers to straight or branched, saturated or unsaturated, hydrocarbon having seven carbon atoms and three functional groups. The functional groups may be positioned at any point along the hydrocarbon chain. In some embodiments, two of the three functional groups are located at the terminal ends of the hydrocarbon (e.g., one functional group at each terminus). Exemplary trifunctional C7 alkanes include, but are not limited to, 2-oxopimelate (α-ketopimelate), 2-aminopimelate α-aminopimelate), 2-hydroxypimelate (α-hydroxypimelate), and 2-hydroxypimelate-CoA α-hydroxypimelate-CoA).
As used herein, the term “functional group” refers to an amine group, a carboxylic acid group, an aldehyde group, an alcohol group, a co-enzyme A group or a keto group. The term “amine group” refers to the radical —NH2. The term “carboxylic acid group” refers to the radical —COOH. The term “aldehyde group” refers to the radical —C(O)H. The term “alcohol group” refers to the radical —OH. The term “keto group” refers to the radical C(O).
The term “co-enzyme A group” refers to the organic cofactor, or prosthetic group (nonprotein portion of an enzyme), whose presence is required for the activity of many enzymes (the apoenzyme) to form an active enzyme system. Coenzyme A functions in certain condensing enzymes, acts in acetyl or other acyl group transfer and in fatty acid synthesis and oxidation, pyruvate oxidation and in other acetylation.
The term “acp” or “acyl carrier protein” refers to a protein (which typically is active in fatty acid synthesis) that picks up acetyl and malonyl groups from acetyl coenzyme A and malonyl coenzyme A and links them by condensation to form β-keto acid acyl carrier protein, releasing carbon dioxide and the sulfhydryl form of the acyl carrier protein.
The functional groups on a di- or trifunctional C7 alkane can be the same or different. For example, in some embodiments with a difunctional C7 alkane, both functional groups can be amine groups, both functional groups can be carboxylic acid groups, or both functional groups can be alcohol groups.
In some embodiments, one of the functional groups on a difunctional C7 alkane is an amine group and the other is a carboxylic acid group. In some embodiments, one of the functional groups on a difunctional C7 alkane is an alcohol group and the other is a carboxylic acid group. In some embodiments, one of the functional groups on a difunctional C7 alkane is an alcohol group and the other is an amine group.
In some embodiments with a trifunctional C7 alkane, two of the functional groups are carboxylic acid groups and one functional group is a keto group or a hydroxyl group or an amino group.
The term “heterologous” is used herein to refer to any nucleic acid or polypeptide, that is not derived from a cell of the same species as the host cell. Accordingly, as used herein, “homologous” nucleic acids or proteins are those that occur in, or are produced by, a cell of the same species as the host cell.
The term “exogenous” as used herein with reference to nucleic acid and a particular host cell refers to any nucleic acid that does not occur in (and cannot be obtained from) that particular cell as found in nature. Thus, a non-naturally-occurring nucleic acid is considered to be exogenous to a host cell once introduced into the host cell. 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 that 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 cell, 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 cell. 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.
It will be clear from the above that “exogenous” nucleic acids can be “homologous” or “heterologous” nucleic acids. In contrast, the term “endogenous” as used herein with reference to nucleic acids or genes (or proteins encoded by the nucleic acids or genes) and a particular cell refers to any nucleic acid or gene that does occur in (and can be obtained from) that particular cell as found in nature.
As used herein, the term “recombinant host” refer to a host, the genome of which has been augmented by at least exogenous nucleic acid sequence. Such nucleic acid sequences include, but are not limited to, nucleic acids that are not naturally present in the host (i.e., a heterologous nucleic acid), DNA sequences that are not normally transcribed into RNA or translated into a protein (“expressed”), and other nucleic acid sequences which one desires to introduce into the non-recombinant host (e.g., a regulatory region to alter expression of a particular nucleic acid sequence). It will be appreciated that typically the genome of a recombinant host described herein is augmented through the stable introduction of one or more exogenous nucleic acids. Generally, the exogenous nucleic acid is not originally resident in the host that is the recipient of the DNA (i.e., it is a heterologous nucleic acid), but it is within the scope of the invention to isolate a nucleic acid from a given host, and to subsequently introduce one or more additional copies of that nucleic acid into the same host, e.g., to enhance production of an encoded product or alter the expression pattern of a nucleic acid. In some instances, the exogenous nucleic acid will modify or even replace an endogenous gene or DNA sequence by, e.g., homologous recombination or site-directed mutagenesis. Modification or replacement of an endogenous gene can result in a deficiency in a particular encoded product, e.g., an enzyme. Suitable recombinant hosts are described below. Recombinant hosts can also contain nucleic acids that are not incorporated into the genome of the host cell but exist (and preferably replicate) episomally in the cell.
As used herein, a “promoter” refers to a DNA sequence that enables a gene to be transcribed. The promoter is recognized by RNA polymerase, which then initiates transcription. Thus, a promoter contains a DNA sequence that is either bound directly by, or is involved in the recruitment, of RNA polymerase. A promoter sequence can also include “enhancer regions,” which are one or more regions of DNA that can be bound with proteins (namely, the trans-acting factors, much like a set of transcription factors) to enhance transcription levels of genes (hence the name) in a gene-cluster. An enhancer, while typically at the 5′ end of a coding region, can also be separate from a promoter sequence and can be, e.g., within an intronic region of a gene or 3′ to the coding region of the gene.
As used herein, “operably linked” means incorporated into a genetic construct so that expression control sequences effectively control expression of a coding sequence of interest.
1.2 Feedstocks
A variety of different feedstocks can be used to produce di- or trifunctional alkanes. In some embodiments, a recombinant host cell, or a lysate prepared from a cell (e.g., a recombinant host cell), is contacted with a renewable feedstock to produce a di- or trifunctional C7 alkane, such as 7-aminoheptanoic acid. Examples of renewable feedstocks which may be used as a carbon source include, but are not limited to, cellulosic feedstocks, plant-derived carbohydrates and fatty acids. In some embodiments, the feedstock with which the recombinant host cell is contacted is glucose, sucrose, xylose, fatty acids or glycerol.
In addition to renewable feedstocks, such as those listed above, the recombinant host cell can be modified for growth on synthesis gas, also known as SynGas, as a source of carbon. In this specific embodiment, the recombinant host cells of the invention are engineered to provide an efficient metabolic pathway for utilization of SynGas, or other gaseous carbon sources, to produce di- or trifunctional C7 alkanes.
Additionally, recombinant hosts described herein, or a lysate prepared from a recombinant host cell, can be contacted with an aromatic hydrocarbon feedstock. The use of aromatic hydrocarbon feedstocks, rather than renewable feedstocks, provides a way to convert such petroleum derived materials to compounds that are more benign to the environment, reducing environmental impact. Examples of suitable aromatic hydrocarbon feedstocks include, but are not limited to, toluene, benzene, benzoic acid and shikimate.
1.3. Routes to Difunctional C7 Alkanes Comprising Enzyme-Catalyzed Steps
As stated above, embodiments of the present invention relate to methods for producing di- or trifunctional C7 alkanes in the presence of one or more isolated enzymes, in the presence of a recombinant host cell expressing that/those enzyme(s), or in the presence of a cell lysate (or a partially purified lysate) of cell (e.g., recombinant cell) that expresses the enzyme(s). In some embodiments, the production of the di- or trifunctional C7 alkanes starts with pimelate or pimeloyl-CoA and proceeds through a common intermediate, namely, pimelic acid semialdehyde. Specifically, in some embodiments, the invention relates to a method of producing the difunctional C7 alkane 7-aminoheptanoic acid by using an enzyme that catalyzes the semialdehyde amination of pimelic acid semialdehyde to 7-aminoheptanoic acid. See FIG. 1. A semialdehyde aminotransferase such as an ω-transanimase can be used. Exemplary transaminases include, but are not limited to transaminases classified under EC 2.6.1 such as EC 2.6.1.18; EC 2.6.1.19; EC 2.6.1.2; EC 2.6.1.7; EC 2.6.1.29; EC 2.6.1.36; EC 2.6.1.39; EC 2.6.1.42; and EC 2.6.1.68. In some embodiments, the aminotransferase is β-alanine aminotransferase classified in EC 2.6.1.18 from V. fluvialis, B. weihenstephanensis, P. aureginosa, B. subtilis, or P. syringae. See WO2011/031147, which is incorporated herein in its entirety.
In some embodiments, 7-aminoheptanal can be produced using an enzyme that catalyzes the aldehyde dehydrogenation of 7-aminoheptanoic acid to 7-aminoheptanal. See, FIG. 1. An aldehyde dehydrogenases classified under EC 1.2.1, such as EC 1.2.1.4 or EC 1.2.1.63, can be used to produce 7-aminoheptanal from 7-aminoheptanoic acid.
In some embodiments, heptamethylenediamine (also known as 1,7-diaminoheptane) can be produced from 7-aminoheptanal using an enzyme that catalyzes the transfer of an amino group. See FIG. 1. Suitable aminotransferases include, but are not limited to, aminotransferases in EC 2.6.1 such as EC 2.6.1.18; EC 2.6.1.19; EC 2.6.1.2; EC 2.6.1.7; EC 2.6.1.29; EC 2.6.1.36; EC 2.6.1.39; EC 2.6.1.42; and EC 2.6.1.68. In some embodiments, the aminotransferase is β-alanine aminotransferase classified in EC 2.6.1.18 from V. fluvialis, B. weihenstephanensis, P. aureginosa, B. subtilis, or P. syringae. See WO2011/031147, which is incorporated herein in its entirety.
In some embodiments, enantholactam can be produced from 7-aminoheptanoic acid using an enzyme that catalyzes the amide hydrolysis of 7-aminoheptanoic acid. See, FIG. 1. Suitable amidohydrolases include amidotransferases classified under EC 3.5.2 such as EC 3.5.2.12 or EC 3.5.2.11 can be used.
In some embodiments, 7-hydroxyheptanoate is produced from pimelic acid semialdehyde or 7-aminoheptanol is produced from 7-aminoheptanal using an enzyme that catalyzes the reduction of an aldehyde. See FIG. 1. For example, an alcohol dehydrogenase classified under EC 1.1.1 such as EC 1.1.1.21 can be used.
In some embodiments, 1,7 heptanediol can be produced from 7-hydroxyheptanoate using an aldehyde dehydrogenase and an alcohol dehydrogenase. A suitable aldehyde dehydrogenase can be classified under EC 1.2.1 (e.g., EC 1.2.1.4). See, FIG. 1. A suitable alcohol dehydrogenase can be classified under E.C. 1.1.1. such as EC 1.1.1.1
In embodiments in which the C7 di- or trifunctional alkanes may be toxic to the host (e.g., semialdehydes such as 7-oxoheptanoate or 7-aminoheptanal), the conversion to the toxic compound can be performed in vitro using isolated enzymes or a lysate from the recombinant host. In some embodiments, the toxic compound is produced by the host and then subsequently converted (using isolated enzymes, a recombinant host expressing an enzyme, or chemically converted) to enantholactam.
1.5 Biosynthetic Pathways to Pimelate and/or Pimeloyl-CoA
Pimelate and/or pimeloyl-CoA can be obtained via a number of different ways including: (i) α-ketosuberate produced from the α-keto acid chain elongation pathway, or (ii) the biotin biosynthesis pathway I; (iii) biotin biosynthesis pathway II; (iv) the condensation of three malonyl-CoA molecules into a single pimeloyl-CoA molecule; (v) the benzoate degradation pathway; (vi) cyclohexane carboxylate pathway, (vi) D,L-diaminopimelate pathway; and (vii) a biosynthetic pathway where the starting carbon source is crotonate. See FIG. 2. These pathways to pimelate and/or pimeloyl-CoA are described in greater detail below.
In any of these pathways, pimelate can be produced from pimeloyl-CoA using an enzyme that catalyzes the hydrolysis of a thioester. For example, enzymes that can hydrolyze a thioester include, but are not limited to, thioesterases, acid-thiol ligases, and CoA transferases. Suitable thioesterases include thioesterases classified in EC 3.1.2 such as EC 3.1.2.18; EC 3.1.2.19; or EC 3.1.2.20. For example, one of the following enzymes can be used: a thioester hydrolases/acyl-CoA thioesterase classified in EC 3.1.2 such as an ADP-dependent medium-chain-acyl-CoA hydrolase in EC 3.1.2.19 and 3.1.2.18, an acyl-CoA hydrolase in EC 3.1.2.20; or a hydrolase in EC 3.1.2.3. Suitable acid-thiol ligases include acid-thiol ligases classified in EC 6.2.1 such as EC 6.2.1.3; EC 6.2.1.14; and EC 6.2.1.23. Suitable CoA transferases include CoA transferases classified under EC 2.8.3 such as EC 2.8.3.6, EC 2.8.3.8, EC 2.8.3.12 or EC 2.8.3.13.
Heptane-1,7-dioic acid can be obtained from pimeloyl-[acp] by the use of enzymes acting on [acp]-thioesters, such as EC 2.3.1.38 ([acyl-carrier-protein] S-acetyltransferase) or hydrolases in EC 3.1.2.14, such as fatA and fatB. Alternatively, pimelic acid can be obtained form pimeloyl-[acp]methyl ester by hydrolysis of the ester bond by AaasaS (acyl-ACP synthetase), followed by removal of the methyl group by a lipase/esterase.
Pimelate can be transformed to pimelic acid semialdehyde using an enzyme that catalyzes the reduction of a carboxylic acid. Suitable reductases include, but are not limited to, carboxylic acid reductases classified in EC 1.2.99 or fatty acyl-CoA reductases classified in EC 1.2.1 such as EC 1.2.1.50. In some embodiments, a fatty-acyl-CoA reductase can directly convert pimeloyl-CoA or pimeloyl-[acp] to pimelic acid semialdehyde. Exemplary carbonyl reductases in EC 1.2.99 include, but are not limited to EC 1.2.99.6 from Norcardia sp. (Aimin et al., Appl. Environ. Microbiol. 70: 1874-1881 (2004), incorporated by reference) or S. griseus (Suzuki et al., J. Antibiot. (Tokyo) 60: 380-387 (2007) incorporated by reference). Exemplary carbonyl reductases in EC 1.2.1 include, but are not limited to EC 1.2.1.75 from, e.g., C. aurantiacus (Bugler, M, et al., J Bacteriology 184: 2404-2410 (2002), incorporated by reference), M sedula (Kockelkorn, D. and Fuchs, G., J. Bacteriology 191: 6352-6362 (2009), incorporated by reference), or S. tokodai (Alber, B. et al., J. Bacteriology 188: 8551-8559 (2006), incorporated by reference); and 1.2.1.50 from, e.g., Acinetobacter sp., A. platyrhynchos (Ishige, T., et al., Appl. Envtl. Microbiology 68: 1192-1195 (2002), incorporated by reference), A. thaliana (Doan, T. T., et al., Journal Plant Physiology 166: 787-796 (2009) and Hooks, M. A., et al., Plant J. 20:1-13 (1999), both of which are incorporated by reference); Homo sapiens (McAndrew, R. P. et al., J. Biol. Chem. 283: 9435-9443 (2008), incorporated by reference), M. Musculis, P. leiognathi, P. phosphoreum, P. sativum, or S. chinesis. 
1.5.1 α-Keto Acid Chain Elongation
Difunctional alkanes can be produced from α-ketoglutarate via successive chain elongation reactions to α-ketoadipate, α-ketopimelate or α-ketosuberate known in the art. See, e.g., FIG. 3 and WO2010/068944. Decarboxylation of the α-keto dioic acid (Cn, n=5-8) or the corresponding 2-amino-dioic acid then provides precursors to α,ω-difunctional alkanes of Cn-1, e.g., C4-7. These successive alpha-keto acid chain elongation reactions occur in the Coenzyme B biosynthesis pathway as elucidated in methanogenic bacteria such as Methanocaldococcus jannaschii, Methanococcus voltae, and Methanosarcina thermophila. 
The three successive rounds of chain elongation from α-ketoglutarate (C5) to α-ketosuberate are catalyzed by the same three enzymes acting three times (and in the case of EC 4.2.1.114 (AksD (3-isopropylmalate dehydratase large subunit)/AksE (3-isopropylmalate dehydratase small subunit)) six times) on substrates, each time increasing chain length. See FIG. 3. These enzymes include, but are not limited to: EC 2.3.3.14:homocitrate synthase/AksA (alpha-isopropylmalate synthase), which acts on α-ketoglutarate, α-ketoadipate, and α-ketopimelate; EC 4.2.1.114: homoaconitase or AksD/AksE, which catalyzes the dehydration reactions of (R)-homocitrate, dihomocitrate and trihomocitrate, as well as the hydration reactions of cis-homoaconitate, cis-(homo)2aconitate and cis-(homo)3aconitate; and EC 1.1.1.87: homoisocitrate dehydrogenase or AksF (multifunctional 3-isopropylmalate dehydrogenase/D-malate dehydrogenase_, which catalyzes the NAD(P)+ dependent oxidative decarboxylation of homoisocitrate, threo-iso(homo)2citrate and threo-iso(homo)3citrate.
Exemplary AksA enzymes include, but are not limited to, those in EC 2.3.3 such as EC 2.3.13 or 2.3.3.14. Exemplary AksD enzymes include those in EC 4.2.1 such as EC 4.2.1.33. Exemplary AksF enzymes include, but are not limited to enzymes in EC 1.1.1 such as EC 1.1.1.85.
In some embodiments, the chain elongation enzyme is AksA MTH1630, AksD MTH1631, AksE MTH0829 or AksF MTH1388. See, e.g., WO2010/104391, which is incorporated by reference herein.
The advantage of this pathway is that it only requires the recombinant expression of three heterologous proteins in a host. Chain elongation from α-ketoglutarate to α-ketoadipate also occur in the lysine biosynthesis V pathway of archae, including Aeropyrum pernix, Deinococcus radiodurans, Pyrococcus abyssi, Pyrococcus horikoshii, Sulfolobus solfataricus, Sulfolobus tokodaii, and Thermus thermophilus; and in the lysine biosynthesis IV pathway of yeast and fungi including Euglena gracilis, Aspergillus, Penicillium chrysogenum and Saccharomyces cerevisiae. 
In the lysine biosynthesis IV and V pathways, the reactions from α-ketoglutarate to α-ketoadipate are catalyzed by the consecutive action of four enzymes, namely: EC 2.3.3.14: homocitrate synthase (hcs/LYS20/LYS21/nifV); EC 4.2.1.114: methanogen HACN; EC 4.2.1.36: homoaconitase hydratase; and EC 1.1.1.87-homoisocitrate dehydrogenase (hicDH or LYS12).
1.5.3 Malonyl-CoA Condensation Pathway
In some embodiments, malonyl-CoA can be used as the source of pimeloyl-CoA as certain organisms are able to condense three malonyl-CoA molecules into a single pimeloyl-CoA molecule. See FIG. 4. See also Lin, S, and Cronan, J. E., Molecular Biosystems 7: 1811-21 (2011), which is incorporated by reference herein. Accordingly, a recombinant host can be produced in which pimeloyl-CoA is produced from malonyl-CoA. In some embodiments, the host cell is an organism other than Achromobacter. In some embodiments, the pimeloyl-CoA may be subsequently converted to pimelic acid or other difunctional C7 alkanes.
1.5.4 Biotin Biosynthesis Pathways I (Gram Negative Bacteria) and II (Gram Positive Bacteria)
In one embodiment, a recombinant host cell produces pimelic acid and/or pimeloyl-[acp] from acetyl-CoA derived from glycerol and/or fatty acids. See, e.g., Lin, S., Nature Chem. Biol. 6: 682-688 (2010); and Cronan, J. E. and Lin, S., Current Opinion in Chem. Biology 15: 1-7 (2011), both of which are incorporated by reference herein. FIG. 5 shows formation of pimeloyl-CoA from pimelic acid or other precursors in biotin biosynthesis II (gram positive bacteria). FIG. 6 shows formation of pimelyl-[acp] or its methyl esters in biotin biosynthesis I (gram negative bacteria). FIG. 6 also shows pathways for the conversion of pimeloyl-[acp] methyl ester into pimelate monomethyl ester. The pimelate monomethyl ester is subsequently converted to pimelic acid (heptane-1,7-dioic acid) in the presence of, e.g., a lipase in EC 3.1.1. FIG. 6 also shows the conversion of pimeloyl-[acp] methyl ester into pimeloyl-[acp] in the presence of an esterase (e.g., an enzyme in EC 3.1.1, such as EC 3.1.1.85, BioH). The pimeloyl-[acp] is subsequently converted into pimelic acid (heptane-1,7-dioic acid) in the presence of a thioesterase, e.g., an enzyme in EC 3.1.2.14, such as FatA or FatB. In some embodiments, the invention contemplates a recombinant host cell capable of producing pimelic acid (heptane-1,7-dioic acid) that comprises one or all of the enzymes shown in FIG. 6. In some embodiments, the recombinant host cell does has a deficiency in 7-keto-8-aminopelargonic acid synthetase, an enzyme capable of converting 6-carboxyhexanoyl-CoA (pimeloyl-CoA) into 7-keto-8-aminopelargonic acid (KAPA), and encoded by the BioF gene in host organisms with a native biotin biosynthesis pathway so that the pimeloyl-CoA cannot be shuttled into biotin biosynthesis.
Pimeloyl-[acp] methyl ester can also be produced as a result of the metabolism of long-chain acyl-[acp] and/or free fatty acids by BioI (for example BioI from Bacillus subtilis).
1.5.5 Eukaryotic Biosynthesis Pathway
Pimelic acid and/or pimeloyl-CoA can also be obtained from eukaryotic biotin biosynthesis pathways. See, e.g., Roje, S., Phytochemistry 68: 1904-1921 (2007); and Charles R. Hall, The Contribution of Horizontal Gene Transfer to the Evolution of Fungi (May 10, 2007) (unpublished Ph.D. dissertation, Duke University) (on file with Duke University Libraries), both of which are incorporated by reference herein. In the eukaryotic pathway, acetyl-CoA is biotransformed to acetoacetyl CoA using an enzyme classified under EC 2.3.1.9; acetoacetyl-CoA is biotransformed into (S)-3-hydroxybutanoyl-CoA using an enzyme classified under E.C. 1.1.1.157; (S)-3-hydroxybutanoyl-CoA is biotransfored to crotonyl-CoA using an enzyme classified under EC 4.2.1.17; crotonyl-CoA is biotransformed into glutaconyl-1-CoA using an enzyme classified under EC 4.1.1.70; glutaconyl-1-CoA is biotransformed to glutaryl-CoA using an enzyme classified under EC 1.3.99.7; glutaryl-CoA is biotranformed into 3-ketopimelyl-CoA using an enzyme classified under EC 2.3.1.43; 3-ketopimelyl-CoA is biotransformed into 3-hydroxypimelyl-CoA using an enzyme classified under EC 1.1.1.4259; 3-hydroxypimelyl-CoA is biotransformed into 2,3-didehydro-pimeloyl-CoA using an enzyme classified under EC 4.2.1.-, and 2,3-didehydro-pimeloyl-CoA is biotransformed into pimeloyl-CoA using an enzyme classified under EC 1.3.1.62. The pimeloyl-CoA is subsequently transformed into pimelic acid.
In some embodiments, acetyl-CoA can be fed into the tricarboxylic acid (TCA) cycle, in which acetyl-CoA is transformed into succinic acid (butan-1,4-dioic acid). The succinic acid is then diverted from the TCA cycle into a pathway for synthesizing pimelic acid starting with the biotransformation of 2-oxoglutarate into 2-hydroxy-1,2,4-butanetricarboxylic acid (homocitrate) (e.g., by an enzyme in EC 2.3.3.14); biotransformation of homocitrate to homo cis aconitase and homo cis aconitase to homoisocitrate using an enzyme classified under EC 4.2.1.36; biotransformation of homoisocitrate to oxaloglutarate using an enzyme classified under EC 1.1.1.87; biotransformation of oxaloglutarate to 2-oxoadipate using an enzyme classified under EC 1.1.1.87, and biotransformation of 2-oxoadipate to glutaryl-CoA using an enzyme classified under EC 1.2.4.2. Glutaryl-CoA can be converted to pomeloyl-CoA as discussed above. The homocitrate is ultimately converted to pimeloyl-CoA and, subsequently, into pimelic acid as described herein.
Thus, in some embodiments, the invention provides a recombinant host cell comprising the enzymes for converting acetyl CoA into heptane-1,7-dioic acid. In some embodiments, the recombinant host cell has a deficiency in 7-keto-8-aminopelargonic acid synthetase, an enzyme capable of converting 6-carboxyhexanoyl-CoA (pimeloyl-CoA) into 7-keto-8-aminopelargonic acid (KAPA), and encoded by the BioF gene in the host, if the host organisms has a native biotin biosynthesis pathway, so that the pimeloyl-CoA cannot be shuttled into biotin biosynthesis. The embodiments of the invention also provide a method of producing heptane-1,7-dioic acid comprising the use of such recombinant host cells.
1.5.6 Benzoyl-CoA Degradation Pathway
One additional source of pimeloyl-CoA and/or pimelic acid contemplated herein is the benzoate degradation pathway shown in FIG. 7. See, e.g., Bernsteinb, J. R., et al., Metabolic Eng'g 10: 131-140 (2008); Harwood, C. S., et al., FEMS Microbiology Reviews 22: 439-458 (1999); and Harrison, F. H. and Harwood, C. S., Microbiology 151: 727-736 (2005), all of which are incorporated by reference herein. A number of transformations are illustrated in FIG. 7, where benzoate is converted into benzoyl-CoA using an enzyme classified under EC 6.2.1.25, and ultimately into pimeloyl-CoA. Benzoyl-CoA is converted to cyclohexa-1,5-dienecarbonyl CoA using an enzyme classified under EC 1.3.99.15. In some embodiments, cyclohexa-1,5-dienecarbonyl CoA is biotransformed to 6-hydroxycyclohex-1-ene-1-carboxyl-CoA using an enzyme classified under EC 4.2.1.100; 6-hydroxycyclohex-1-ene-1-carboxyl-CoA is biotransformed to 6-ketoxycyclohex-1-ene-1-carboxyl-CoA using an enzyme classified under EC 1.1.1-; 6-ketoxycyclohex-1-ene-1-carboxyl-CoA is biotransformed to 3-hydroxypimelyl-CoA using an enzyme classified under EC 3.7.1.-; 3-hydroxypimelyl-CoA is biotransformed to 6-carboxylhex-2-enoyl-CoA using an enzyme classified under EC 4.2.1.-; 3-hydroxypimelyl-CoA is biotransformed to pomelyol-CoA using an enzyme classified under EC 1.3.1.62. The pimeloyl-CoA, in turn, is converted into pimelic acid (heptane-1,7-dioic acid). In some embodiments, cyclohexa-1,5-dienecarbonyl CoA is biotransformed to cyclohex-1-ene-1-carboxyl-CoA, cyclohex-1-ene-1-carboxyl-CoA is biotransformed to 2-hydroxycyclohexane-1-carboxyl CoA using an enzyme classified under EC 4.2.1.-; 2-hydroxycyclohexane-1-carboxyl CoA is biotransformed to 2-ketocyclohexane-1-carboxyl-CoA using an enzyme classified under E.C. 1.1.1.-, and 2-ketocyclohexanecarboxyl-CoA is biotransformed to pimeloyl-CoA using an enzyme classified under EC 3.1.2.-_ (e.g., a-ketocyclohexanecarboxyl-CoA hydrolase Rp-badl, an enzyme classified under EC 3.1.2.-).
In some embodiments, the recombinant host cell capable of producing heptane-1,7-dioic acid includes one or more of the enzymes listed in FIG. 7 or in this section.
1.5.7 2,6-Diaminopimelate Pathway
Yet another source of pimelate is D,L diaminopimelate, also known as 2,6-diaminopimelate. D,L-diaminopimelate is an intermediate in the production of lysine. In some embodiments, an endogenous lysine pathway can be modified to preferentially produce pimelate by creating recombinant host cells that have a deficiency in diaminopimilate decarboxylase., See, e.g., FIG. 10. The D,L diaminopimelate can be biotransformed into an unsaturated monoaminopimelic acid by an enzyme that catalyzes the reductive deamination of D,L diaminopimelate to 6-amino-2-heptenedioic acid. Examples of enzymes that catalyze reductive deamination of D,L diaminopimilate include ammonia lyases classified in EC 4.3.1 such as EC 4.3.1.1; EC 4.3.1.2; EC 4.3.1.3; EC 4.3.1.12; EC 4.3.1.13; and EC 4.3.1.24. In some embodiments, the ammonia lyase is a methyl aspartate ammonia lyase classified under EC 4.3.1.2 from C. amalonaticus, C. tetanomorphum or A. oryzae. See, e.g., Botting, Biochemistry 27: 2953-2955 (1988); and Kato, Appl. Microbial. Biotechnol. 50: 468-474 (1998), the entireties of which are incorporated by reference herein.
6-amino-2-heptenedioic acid can be biotransformed into 2-amino-2-heptenedioic acid using an enzyme that catalyzes the enoate reduction of 6-amino-2-heptenedioic acid to 2-amino-2-heptanedioic acid (also known as 2-aminopimelic acid or alpha aminopimelate). Examples of enzymes that catalyze the enoate reduction of 6-amino-2-heptenedioic acid include enoate reductases classified in EC 1.3.1 such as EC 1.3.1.31. In some embodiments, the enoate reductase is YqjM or OPR1/3 in EC 1.3.1.31 from B. subtilis or L. esculentum, respectively. See, e.g., Stueckler, Org. Lett. 9: 5409-5411 (2007); Kitzing, J. Biol. Chem. 280: 27904-27913 (2005); Hall, Angew. Chem. Int. Ed. 46: 3934-3937 (2007); and Breithaupt, Proc. Natl. Acad. Sci. USA 103: 14337-14342 (2006), the entireties of which are incorporated by reference herein.
The 2-aminopimelic acid can be converted to the corresponding 2-heptenedioic acid (also known as 2,3-didehydropimelic acid) by an enzyme that catalyzes the reductive deamination of 2-aminopimelic acid. Examples of enzymes that catalyze reductive deamination of 2-aminopimelic acid include ammonia lyases classified in EC 4.3.1 such as EC 4.3.1.1; EC 4.3.1.2; EC 4.3.1.3; EC 4.3.1.12; EC 4.3.1.13; or EC 4.3.1.24 as described above. The 2-heptene dioic acid can be transformed to 2-heptene dioic acid CoA using a CoA transferase (e.g., a CoA transferase classified in EC2.8.3 such EC 2.8.3.12 or EC 2.8.3.13) and an acid thiol ligase (e.g., an acid-thiol ligases classified n EC 6.2.1 such as EC 6.2.1.3; EC 6.2.1.14; or EC 6.2.1.23).
2-heptene dioic acid CoA is then converted to pimelate-CoA by an enzyme that catalyzes the enoate reduction of 2-heptene dioic acid such as an enoate reductase enzyme classified in EC 1.3.1. Pimelate-CoA can be converted to pimelate as described above.
As shown in FIG. 10 and in FIG. 3, a keto pimelate also can undergo one round of chain elongation to α-keto-suberate, which can either be decarboxylated to form pimelic acid semialdehyde, or converted to α-aminosuberate, which will lead directly to 7-aminoheptanoic acid upon decarboxylation. Exemplary decarboxylases include those in EC 4.1.1 such as EC 4.1.1.11; EC 4.1.1.15; EC 4.1.1.17; EC 4.1.1.18; EC 4.1.1.19; EC 4.1.1.20 and EC 4.1.1.86. In some embodiments, the decarboxylase comprises ketoisovalerate decarboxylase kivD in EC 4.1.1.1 from L. lactis; benzoylformate decarboxylase mdIC A460I or BFD in EC4.1.1.7 from P. putida; pyruvate decarboxylase isozymes 1 and 2 Pdc1 in EC 4.1.1.1 from S. cereivisae; pyruvate decarboxylase Pdc (I472A) from Z. mobilis; or branched chain alpha-keto acid decarboxylase kdcA in EC 4.1.1.72 from L. lactis, as described in WO2011/031147, the entirety of which is incorporated by reference herein.
The α-amino suberate can be converted to 7-aminoheptanoic acid using chain elongation enzymes, such as those present in methanogenic bacteria (e.g., Methanobacterium autotrophicum). Such chain elongation enzymes include, but are not limited to AksA, AksD, and AksE or F as discussed above. Exemplary AksA enzymes include, but are not limited to, those in EC 2.3.3. Exemplary enzymes in EC 2.3.3 include, but are not limited to EC 2.3.13 or 2.3.3.14. Exemplary AksD enzymes include those in EC 4.2.1. An exemplary enzyme in EC 4.2.1 includes, but is not limited to EC 4.2.1.33. Exemplary AksF enzymes include, but are not limited to enzymes in EC 1.1.1. An exemplary enzyme in EC 1.1.1 includes, but is not limited to EC 1.1.1.85. And, in this instance, the fourth set of enzymes comprises a decarboxylase. Exemplary decarboxylases include those in EC 4.1.1. Exemplary decarboxylases in EC 4.1.1 include, but are not limited to EC 4.1.1.11; EC 4.1.1.15; EC 4.1.1.17; EC 4.1.1.18; EC 4.1.1.19; EC 4.1.1.20 and EC 4.1.1.86.
In one embodiment, α keto pimelate can be contacted with one or more enzymes that catalyze the ketone reduction to α hydroxypimelate (e.g., a carbonyl reductase such as EC1.1.1.184), which in turn can be converted to α-hydroxypimelate CoA using an enzyme that catalyzes the transfer of CoA (e.g., a CoA transferase described above). The α-hydroxypimelate CoA can be converted to 2-heptene dioic acid CoA with an enzyme that catalyzes the dehydration of the α-hydroxypimelate-CoA (e.g., a hydrolyase classified under EC 4.2.1. such as EC 4.2.1.2, EC 4.2.1.59, EC 4.2.1.61). The 2-heptene dioic acid CoA can be converted to pimelic CoA using an enzyme that catalyzes the enoate reduction of 2-heptene dioic acid CoA. Suitable enoate reductases are described above.
In some embodiments, the invention provides a recombinant host cell comprising one or more enzymes necessary to convert D,L-diaminopimelate preferentially to pimelate.
1.5.8 Crotonate Pathway
A source of pimeloyl-CoA, and ultimately a source of pimelate, is a biosynthetic pathway where the starting carbon source is crotonate. That biosynthetic pathway is illustrated in FIG. 9. See, e.g., Mouttaki, H., et al., Applied Envtl. Microbiology 73: 930-938 (2001). The crotonate is broken down to acetyl-CoA. It has been reported that two thirds of the acetyl-CoA produced in the biosynthetic pathway shown in FIG. 9 is transformed into acetate. In some embodiments, the invention provides a recombinant host cell that is deficient in the enzymes that would convert acetyl-CoA into acetate (e.g., a phosphate acetyltransferase and acetate kinase such that the acetyl-CoA is instead converted to acetoacetyl-CoA and subsequently to glutaconyl-CoA in a number of metabolic steps as shown in FIG. 9. The glutaconyl-CoA is subsequently converted to glutaryl-CoA. The glutaryl-CoA is chain-extended to form 3-oxopimelyl-CoA. Following a reduction, dehydration, and a second reduction, pimelyl-CoA is obtained.
In the biosynthetic pathway shown in FIG. 9, the pimelyl-CoA is ultimately transformed into cyclohexane carboxylate. Such a biosynthetic pathway has been observed in S. aciditrophicus. Thus, in some embodiments, the invention provides a recombinant host cell in which the genes encoding the enzymes that would convert pimeloyl-CoA into cyclohex-1-ene-1-carboxyl-CoA and ultimately into cyclohexane carboxylate, are “knocked out”, such that the metabolic pathway ends at pimeloyl-CoA.
1.5.9 Tetralin Degradation Pathway
In some embodiments, pimelic acid semialdehyde is produced using the tetralin (benzocyclohexane) degradation pathway from Sphingomonas and Corynebacterium spp. 7-oxoheptanoic acid is produced as an intermediate is the tetralin degradation pathway in Sphingomonas macrogolitabid. López-Sánchez, A., et al., Appl. Environ. Microbiol. 76:110-118 (2010). Tetralin is metabolized by cleavage of both aromatic rings yielding pyruvate and pimelic acid semialdehyde. Tetralin, an organic solvent, is a complex starting material that is derived from naphthalene. Naphthalene is currently produced from coal tar, but biosynthetic pathways for naphthalene synthesis are known to occur in termites, fungi and some types of plants. Chen, J. et al., Nature 392: 558-559 (1998); Daisy, B. H., et al., Microbiology 148: 3737-3741 (2002); and Azuma, H., et al., Phytochemistry 42: 999-1004 (1996). Pimelic acid semialdehyde can be converted to 7-amino heptanoic acid or 7-hydroxyheptanoic acid as discussed above.
1.11 Hexamethylenediamine from 2-oxopimelate
Some embodiments of the invention also provides a method of producing hexamethylenediamine from 2-oxopimelate comprising using recombinant host cells. 2-oxopimelate is a known intermediate in the Coenzyme B biosynthesis pathway in methanogenic Archae.
Thus the invention provides a recombinant host cell comprising: an enzyme capable of converting 2-oxopimelate into 2-aminopimelate (e.g., an aminotransferase enzyme in EC 2.6.1.67), an enzyme capable of converting 2-aminopimelate to 2-amino-7-oxoheptanoate (e.g., a reductase enzyme in EC 1.4.1), an enzyme capable of converting 2-amino-7-oxoheptanoate to 2,7-diaminoheptanoate (e.g., a 1-aminotransferase enzyme in EC 2.6.1), and an enzyme capable of converting 2,7-diaminoheptanoate to hexamethylenediamine (e.g., a decarboxylase enzyme in EC 4.1.1). In some embodiments, the recombinant host cell capable of producing hexamethylenediamine comprises any or all of these enzymes. Embodiments of the invention also provide a method of producing hexamethylenediamine comprising the use of these recombinant host cells.
In some embodiments, the invention provides a method for producing hexamethylenediamine from renewable feedstocks such as sugars, fatty acids, glycerol, and SynGas. In some embodiments, the non-naturally occurring host cell capable of producing hexamethylenediamine comprises any or all of the enzymes required to convert renewable feedstocks to hexamethylenediamine.
2.2 Recombinant Host Cells
This disclosure features recombinant host cells that recombinantly express one or more (e.g., two or more; three or more; four or more; five or more; six or more; seven or more; eight or more; nine or more; ten or more; eleven or more; twelve or more; thirteen or more; fourteen or more; fifteen or more; sixteen or more; seventeen or more; eighteen or more; nineteen or more; twenty or more; or even more) of the enzymes used for producing a compound in one of the pathways described herein and methods of using such host cells to produce di- and trifunctional C7 alkanes. For example, a host cell can include one or more (as above) exogenous nucleic acids encoding one or more (as above) of the following: an enzyme that catalyzes the reductive deamination of D,L diaminopimelate or alpha-aminopimielate; an enzyme that catalyzes the enoate reduction of 2-heptenedioic acid to pimelic acid; an enzyme that catalyzes the carboxylic acid reduction of pimelic acid to pimelic acid semialdehyde, an enzyme that catalyzes the semialdehyde amination of pimelic acid semialdehyde to 7-aminoheptanoic acid, an enzyme that catalyzes the amido hydrolysis of 7-aminoheptanoic acid to enantholactam, an enzyme that catalyzes the aldehyde dehydrogenation of 7-aminoheptanoic acid to 7-aminoheptanal; an enzyme that catalyzes the transfer of an amino group to 7-aminoheptanal to produce 1,7-diaminoheptane; an enzyme that catalyzes the transfer of CoA to 2-heptenedioic acid to produce 2-heptene diacid-CoA; an enzyme that catalyzes the enoate reduction of 2-heptene dioic acid-CoA to pimeloyl-CoA; an enzyme that catalyzes the thioester hydrolysis of pimeloyl-CoA to produce pimelic acid; an enzyme that catalyzes the carboxylic acid reduction of pimelic acid to pimelic acid semialdehyde; an enzyme that catalyzes the transfer of an amino group from alpha amino pimelate to produce alpha keto pimelate; an enzyme that catalyzes the carbonyl reduction of alpha keto pimelate to alpha hydroxy pimelate; an enzyme that catalyzes the transfer of CoA to alpha hydroxy pimelate to produce alpha hydroxypimelate CoA; an enzyme that catalyzes the reduction of alpha hydroxypimelate to 2-heptenedioic acid; an enzyme that catalyzes the alpha keto acid chain elongation of alpha ketopimelate to alpha ketosuberate, an enzyme that catalyzes the transfer of an amino group to alpha ketosuberate to produce alpha-aminosuberate, an enzyme that catalyzes the alpha keto acid decarboxylation of alpha aminosuberate to 7-aminoheptanoic acid; an enzyme that catalyzes the alpha keto acid decarboylation of alpha ketosuberate to produce pimelic acid semialdehyde; an enzyme that catalyzes the enoate reduction of 6-amino-2-heptendioic acid to produce pimelic acid; or an enzyme that catalyzes the thioester hydrolysis of pimeloyl [ac[p] to pimelic acid. Recombinant host cells can contain any subgroup consisting of one or more (as above) nucleic acids encoding one or more of the above-listed enzymes.
The host cells that are used typically possess a number of properties: they may be easily genetically modified, are tolerant of the conditions used in the method of the invention, and grow to cells densities which are industrially useful.
Optionally the host cell may be a single celled microorganism, or may be a cell of a cell line. The host cell may be of a wild type genotype. In this instance, the enzyme that is used to catalyze one or more steps in the method of the invention is naturally present in the host cell and is expressed at a level that has industrial use in the methods of the invention. In an alternative, the host cell has been genetically modified to express the enzyme at a level that has industrial use in the methods of the embodiments of invention. The enzyme may be sourced from the cell in which it is expressed. In an alternative, the enzyme is sourced from a different strain or species of cell.
In one alternative, the host cell is a prokaryote. In another alternative it is a eukaryote. Typically single celled microorganisms are used.
The term prokaryotic cell includes gram positive and gram negative bacteria. Examples of suitable gram negative bacteria include Escherichia coli, Rhodopseudomonas palustris, sphingomonads, pseudomonads, and other bacteria belonging to Corynebacterium, Salmonella, Burkholderia, Moraxella, Acaligenes, Psychrobacter, Thermotoga, Acinetobacteria, Rhodobacter, Azoarcus, and Rhodospirillum genera. Examples of suitable gram positive bacteria include streptococci, lactobacilli, and other bacteria belonging to Nocardia, Bacillus, Rhodococcus, Clostridium, Streptomyces, and Arthobacter genera.
Eukaryotic host cells include those from yeast and other fungi, as well as, for example, insect, mouse, rat, primate, or human cells. Examples of suitable eukaryotic host cells include the yeasts Yarrowia lipolytica, Candida genera such as Candida tropicalis, C. albicans, C. cloacae, C. guillermondii, C. intermedia, C. maltosa, C. parapsilosis, C. zeylenoides, yeasts belonging to the Rhodotorula, Rhizopus, Trichosporon, and Lipomyces genera, and other fungi belonging to Aspergillus, Exophiala, Mucor, Trichoderma, Cladosporium, Phanerochaete, Cladophialophora, Paecilomyces, Scedosporium, and Ophiostoma genera.
The host cells may be provided in a variety of different forms. The cells may be resting cells. That is to say that the cells are grown up in cultures and removed from the culture medium before being employed as the biocatalyst. The cells may be used directly following growth, or they may be stored before use. Typical methods of storage include freezing. In an alternative, the cells are lyophilized prior to use. In a further alternative, the cells are growing cells. That is to say that the cells perform their biocatalytic action while being cultured. If the substrate for a particular biocatalytic reaction cannot cross the cell membrane to be transformed by host cells, then in one alternative, a crude lysate may be used. A crude lysate is the initial suspension of cellular components produced following lysis of the cells. Lysis of the cells may be performed by any means, including chemical or mechanical. Further methods of lysis will be evident to the skilled person in light of their general knowledge and the teachings herein. In another alternative, a clarified lysate may be used. A clarified lysate may be prepared by centrifuging the crude lysate to pellet unlysed cells and other cellular debris.
In some embodiments, substantially pure cultures of recombinant host cells are provided. As used herein, a “substantially pure culture” of a recombinant cell is a culture of that cell in which less than about 40% (i.e., less than about: 35%; 30%; 25%; 20%; 15%; 10%; 5%; 2%; 1%; 0.5%; 0.25%; 0.1%; 0.01%; 0.001%; 0.0001%; or even less) of the total number of viable cells in the culture are viable cells other than the recombinant cells, e.g., bacterial, fungal (including yeast), mycoplasmal, or protozoan cells. The term “about” in this context means that the relevant percentage can be 15% percent of the specified percentage above or below the specified percentage. Thus, for example, about 20% can be 17% to 23%. Such a culture of recombinant cells includes the cells and a growth, storage, or transport medium. Media can be liquid, semi-solid (e.g., gelatinous media), or frozen. The culture includes the cells growing in the liquid or in/on the semi-solid medium or being stored or transported in a storage or transport medium, including a frozen storage or transport medium. The cultures are in a culture vessel or storage vessel or substrate (e.g., a culture dish, flask, or tube or a storage vial or tube).
In one embodiment, the recombinant cells of this disclosure can be harvested from a fermentation process by conventional methods such as filtration or centrifugation and formulated into a dry pellet or dry powder formulation while maintaining high activity. Processes for production of a dry powder whole recombinant cell composition exhibiting one or more of the activities disclosed herein can include spray-drying, freeze-drying, fluidised bed drying, vacuum drum drying, or agglomeration and the like. The compositions can be a shelf-stable, dry biocatalyst composition suitable for the biosynthetic methods described herein. Drying methods such as freeze-drying, fluidised bed drying or a method employing extrusion/spheronisation pelleting followed by fluidised bed drying can be particularly useful. Temperatures for these processes may be <100° C. but typically <70° C. to maintain high residual activity and stereoselectivity. The dry powder formulation should have a water content of 0-10% w/w, typically 2-5% w/w. Stabilising additives such as salts (e.g. KCl), sugars, proteins and the like may be included to improve thermal tolerance or improve the drying characteristics of the recombinant cells during the drying process.
In some embodiments, partially or wholly purified enzymes may be used instead of or in combination with recombinant hosts or lysates of recombinant or non-recombinant cells. Wholly or partially purified enzymes can be wholly or partially purified lysates of any of the recombinant cells described here or non-recombinant cells. Methods of purification are well known in the art. Partial or complete purification has the advantage that the enzyme of interest is separated from other cellular components which may interfere with the reaction catalyzed by that enzyme (either by also reacting with the substrate or by converting intermediates or the desired product to an unwanted compound). Purification does add further steps to any biocatalyst preparation, however, and therefore may not be suitable in all instances. The determination of the suitability of the use of partially or wholly purified enzymes will be well within the grasp of the skilled person following the teaching herein.
In some embodiments one or more of the conversions in the method of the invention will be performed by the biocatalyst under aerobic conditions. In an alternative one or more of the conversions in the method of the invention will be performed under anaerobic conditions. In a further alternative, some steps of the method of the invention will be performed under aerobic conditions and some steps will be performed under anaerobic conditions.
2.3 Modification of Whole Cell Biocatalysts
The biocatalysts used in the methods of the invention may be unmodified host cells of the species in which the enzyme naturally occurs. Typically, however, it is necessary to modify genetically the host cell to produce a non-naturally occurring (i.e., recombinant or engineered) host cell.
2.4 Chromosomal Modification of the Host Cell Genome
In some embodiments, the chromosome of the whole cell biocatalyst (i.e., the host cell) has been modified. This modification may be an insertion, a deletion or a substitution of a nucleic acid in the chromosome. Methods of effecting modifications to the chromosome of a cell are well known, e.g., transposon mutagenesis, Cre-Lox mediated recombination, lambda Red and RecET mediated recombination.
Stable integration into the chromosome of a nucleic acid is advantageous because it allows the maintenance of the nucleic acid without the need for a selectable marker.
By performing repeated insertions, it is possible to integrate stably a number of different nucleic acids into a host cell biocatalyst's chromosome. Stable integration means that the host cell can be cultured for greater than five generations without loss of the alteration. Generally, stable genetic alterations include modifications that persist greater than 10 generations, particularly stable modifications will persist more than about 25 generations, and more particularly, stable genetic modifications will be greater than 50 generations, including indefinitely.
2.5 Episomal Modification of the Host Cell Biocatalyst's Genome
In some embodiments, the episomal composition of the host cell genome is modified. By episome is meant any autonomously replicating element, for example a plasmid (which may be linear or circular), a cosmid, a yeast artificial chromosome (YAC), etc. Episomal elements frequently place a metabolic load on their host cell, and accordingly, in the absence of any active partitioning mechanism to ensure that at least one copy of the episome is present in each daughter cell following cell division it is necessary to include a selectable marker.
2.6 Introduced Nucleic Acid Sequences
The nucleic acids introduced into the cell may comprise one or more (e.g., two or more; three or more; four or more; five or more; six or more; seven or more; eight or more; nine or more; ten or more; eleven or more; twelve or more; thirteen or more; fourteen or more; fifteen or more; sixteen or more; seventeen or more; eighteen or more; nineteen or more; twenty or more; or even more) of a number of elements. Typically one of the elements encodes an enzyme that is used to produce di- or trifunctional C7 alkanes or precursors to such molecules. In some alternatives, the nucleic acid encodes a protein which is not an enzyme that functions in the method of the invention.
Typically, a promoter is operably linked to a nucleic acid. The choice of promoter will depend on the intended application, and can readily be determined by the skilled person. For example, if an enzyme catalyzed reaction may be detrimental to a particular host cell, it may be desirable to use a regulated or inducible promoter, such that gene expression can be turned on or off as necessary. Alternatively, it may be preferred to have expression driven by either a weak or strong constitutive promoter to ensure that the enzyme is expressed at all stages of growth. Exemplary promoters suitable for eukaryotic cell systems include the SV40 early promoter, the cytomegalovirus (CMV) promoter, the mouse mammary tumor virus (MMTV) steroid-inducible promoter, and the Moloney murineleukemia virus (MMLV) promoter. Exemplary yeast promoters include 3-phosphoglycerate kinase promoter, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) promoter, galactokinase (GAL1) promoter, galactoepimerase promoter, and alcohol dehydrogenase (ADH) promoter. Other suitable promoters in yeast are known to those skilled in the art. Exemplary promoters suitable for bacterial cell systems include but are not limited to: T7, T3, SP6, lac and trp promoters.
If necessary to ensure expression, the introduced nucleic acid also can be operably linked to comprise 5′ untranslated region (UTR), 3′ UTR, enhancer and/or teiminator regions, as required. Such elements will be known to the skilled person.
2.7 Expression of Multiple Enzymes in a Host Cell
In some embodiments, a single strain of host cell is used to express more than one (e.g., two or more; three or more; four or more; five or more; six or more; seven or more; eight or more; nine or more; ten or more; eleven or more; twelve or more; thirteen or more; fourteen or more; fifteen or more; sixteen or more; seventeen or more; eighteen or more; nineteen or more; twenty or more; or even more) of the enzymes used in the methods of the invention. In this instance, the multiple enzymes may be encoded by the same introduced nucleic acid. In an alternative, the enzymes may be encoded on separate introduced nucleic acid fragments. The enzymes may all be expressed from a single promoter (for example by arranging the enzymes in the form of an operon). In an alternative, the enzymes may be expressed from multiple separate promoters. In some instances, the multiple separate promoters may be induced by the same chemical (for example, each of the multiple enzymes may be expressed from the yeast GAL promoter, thus meaning that each gene is inducible with galactose). Other suitable promoters are known in the art. In an alternative, each of the genes encoding an enzyme used in the method of the invention is under the control of a different promoter. Thus, different enzymes can be introduced individually through the use of different inducing compounds. In another alternative, an intermediate approach is used, wherein a number of enzymes are under the control of the same promoter, and a number of enzymes are under the control of different promoters. This alternative may be particularly advantageous when numerous enzyme pathways have been generated in a host cell and it is desirous to control each member of a pathway in concert with the other pathway members, but to control each pathway separately.
Further considerations can be made with regard to whether the multiple enzymes are expressed from the chromosome or from the plasmid. In instances where the enzyme is expressed from the plasmid, advantageously each plasmid comprises a different origin and/or a different selectable marker.
The expression of multiple enzymes in a single cell is advantageous because, if the co-expressed enzymes act directly after one another in a reaction pathway, it ensures that the product of the upstream enzyme reaction is immediately available to be acted upon by the downstream enzyme. This avoids the need for either (i) purification of the intermediate and the setting up of second reaction vessel to perform the second reaction; or (ii) the need for the product to be exported from the cell comprising the upstream enzyme into the culture medium where it may be acted upon by a cell comprising the downstream enzyme.
2.8 Chaperone Systems
When a cell has been engineered to express a protein under non-natural conditions (for example, when a protein that is native to a species is expressed at levels above the natural level, or in an alternative, when a protein from a different species is expressed in a host cell) in some instances that protein will not be expressed in an active form. Instead it may fold incorrectly, and accumulate as a non-functional “inclusion body” aggregates. In this instance, the cells used to express the protein may be subjected to genetic modification to further express chaperone proteins which are able either to prevent the mis-folding of the protein, or are able to refold it from the aggregated state. The inclusion of such chaperone proteins is advantageous because it increases the quantity of active protein per cell, and therefore increases the overall efficiency of the method of the invention. The expressed chaperone may be a chaperone protein of the host cell. In an alternative, the chaperone may be from the same species/strain as the protein. Typical chaperone proteins for expression include members of the GroEL/GroES family, and members of the DnaJ/DnaK/GrpE family. Homologs of the archetypal E. coli GroEL/GroES and DnaJ/DnaK/GrpE proteins have been identified in other prokaryotic species (see, for example), and eukaryotic homologs are also known (GroEL and GroES correspond to the eukaryotic proteins Hsp60 and Hsp10, and DnaJ, DnaK and GrpE correspond to the eukaryotic proteins Hsp70, Hsp40 and Hsp24, respectively). These proteins have been identified in a number of species of yeast (for example, Saccharomyces cerevisiae). The choice of appropriate chaperone proteins for coexpression with an enzyme used in the method of the invention will be evident to the skilled person following the teachings herein.
2.9 Metabolic Engineering of Host Cells
Metabolic engineering is the process of optimizing the parameters in a host cell in order to increase the ability of a cell to produce a compound. The host cells used in the method of the present invention optionally have been engineered to optimize the output of the difunctional C7 alkanes discussed above.
Metabolic engineering to increase the ability of a cell to produce a compound is principally performed via two avenues. The first is to optimize the enzymes in the pathway producing the desired product from the starting material. In a multi-enzyme pathway resulting in the production of a difunctional C7 alkanes (as shown in the figures and described in the preceding sections), it is possible to determine the concentration of each intermediate in the pathway using techniques known to the skilled person (for example, two dimensional electrophoresis, the use of isotopically labeled precursors, and nuclear magnetic resonance (NMR) spectroscopy), and therefore determine which of the enzyme conversions is the rate limiting step—that is to say which step in the reaction scheme is the slowest. This can be determined by observing a build up of an intermediate, which indicates that the enzyme acting upon this intermediate is limiting the overall rate of conversion. In this instance, the rate at which this intermediate is reacted should therefore be increased. This can be performed by a number of means. Firstly, the expression level of the limiting enzyme may be increased. Optionally this may be achieved by placing the gene encoding the enzyme under the control of a strong promoter, e.g., the T7 promoter if the enzyme is being expressed in E. coli or the TEF promoter if the enzyme is being expressed in yeast. The second option is to increase the number of copies of the gene encoding the enzyme that are present in cell, for instance by placing the gene on a multicopy plasmid, or by incorporating multiple copies of the gene into the chromosome of the host cell (these copies may be incorporated at the same location in the chromosome or in different locations in the chromosome).
The production of difunctional C7 alkanes (as shown in the figures and described in the preceding sections) can also be increased by inactivating or reducing the activity of any enzymes which are capable of diverting the substrate, any of the intermediates, or the product into a metabolic pathway other than that which is the aim of the method. Therefore, the activity of the enzyme may be lowered to increase the yield of the difunctional C7 alkanes. Thus in some embodiments, the recombinant host cells disclosed herein can have a deficiency in one or more enzymes (e.g., by deleting the nucleic acid encoding an enzyme of interest or reducing expression of the nucleic acid) that are capable of diverting the starting material of the method of the invention, or any intermediates produced in the reaction pathway producing difunctional C7 alkanes, to a different, unwanted, end product. In an alternative, the enzyme is not deleted, but is instead altered so that it can acts against the substrate, intermediates, or product, at a rate that is less than the rate of the wild type enzyme. In the instance where the enzyme catalyses a reversible reaction, then the enzyme should be altered so that it acts only in the desired direction of reaction.
For example, in some embodiments, a recombinant host cell can have a deficiency in an enzyme capable of converting pimeloyl-[acp] into 7-keto-8-aminopelargonic acid (KAPA) or converting 6-carboxyhexanoyl-CoA (pimeloyl-CoA) into KAPA (e.g., a deletion or inactivation of BioF, the gene encoding 7-keto-8-aminopelargonic acid synthetase (E.C. 2.3.1.47).
In some embodiments, a recombinant host cell can have a deficiency in diaminopimilate decarboxylase, which creates a lysine auxotroph. A lysine auxotroph can be particularly useful for deregulating carbon flux to D,L diaminopimelate, the immediate precursor to lysine. A lysine auxotroph would require fed-batch fermentation.
2.10 Growing Whole Cell Biocatalysts
In some embodiments of the invention, host cells are used which are growing (L e., dividing) at the time the cells perform the conversions in the method of the invention. In these embodiments the cells are cultured under conditions which optimize the production of desired difunctional C7 alkane. Any of the recombinant host cells described herein can be cultured to produce and/or secrete the biosynthetic products of the invention. As used herein, the term culture is equivalent with fermentor and bioreactor.
2.10.1 Media
In some instances, the carbon source used for growth will be provided in the form of a nutrient broth, for example Luria medium or yeast extract medium. In other instances, a defined medium (that is to say, a medium in which the concentration of each component is known) appropriate for growth of the host cell may be used. In one alternative, the growth medium comprises glucose as a carbon source. In another alternative, the carbon source used by the host cells in the medium is glucose, sucrose, xylose, fatty acids and glycerol.
2.10.2 Growth of Multiple Strains in the Same Culture
In some embodiments, the enzymes which catalyze the conversions in the method of the invention are present in more than one strain/species of cell, wherein those more than one strain/species of cell are used simultaneously. In the instance where the multiple strains/species are growing when the conversions in the method of the invention are performed (i.e., the cells are in co-culture), then the strains/species that are chosen must be selected such that one strain does not outcompete the other strain. Such a relationship can be obtained by introducing an artificial symbiosis into the co-culture. That is to say that the two stains/species that are used are each auxotrophic for an essential nutrient, but for different nutrients. Furthermore, the other strain should be engineered to produce an excess of that nutrient so that both strains can survive together in a culture when the growth medium of the culture does not comprise the two essential nutrients. Selection of appropriate auxotrophies will be well within the grasp of the skilled person following the teachings herein.
2.10.3 Fermentations
The culture conditions described herein can be scaled up and grown continuously for manufacturing of heptane-1,7-dioic acid, 7-oxoheptanoic acid, 7-hydroxyheptanoic acid, 7-hydroxyheptanal, 7-aminoheptanoic acid, heptamethylenediamine, 1,7-heptandiol, 7-aminoheptanal, 7-aminoheptanol or enantholactam. Exemplary growth procedures include, for example, fed-batch fermentation and batch separation; fed-batch fermentation and continuous separation, or continuous fermentation and continuous separation. All of these processes are well known in the art. Fermentation procedures are particularly useful for the biosynthetic production of commercial quantities of di- and trifunctional C7 alkanes. Generally, and as with non continuous culture procedures, the continuous and/or near-continuous production of heptane-1,7-dioic acid, 7-oxoheptanoic acid, 7-hydroxyheptanoic acid, 7-hydroxyheptanal, 7-aminoheptanoic acid, heptamethylenediamine, 1,7-heptandiol, 7-aminoheptanal, 7-aminoheptanol or enantholactam described previously include culturing a recombinant host cell producing heptane-1,7-dioic acid, 7-oxoheptanoic acid, 7-hydroxyheptanoic acid, 7-hydroxyheptanal, 7-aminoheptanoic acid, heptamethylenediamine, 1,7-heptandiol, 7-aminoheptanal, 7-aminoheptanol or enantholactam described herein in the presence of sufficient nutrients and medium to sustain and/or nearly sustain growth in an exponential phase. Continuous culture under such conditions can include, for example, 1 day, 2, 3, 4, 5, 6 or 7 days or more. Additionally, continuous culture can include 1 week, 2, 3, 4 or 5 or more weeks and up to several months. Alternatively, recombinant cells can be cultured for hours, if suitable for a particular application. It is to be understood that the continuous and/or near-continuous culture conditions also can include all time intervals in between these exemplary periods. It is further understood that the time of culturing the host cell of the invention is for a sufficient period of time to produce a sufficient amount of product for a desired purpose.
Fermentation procedures are well known in the art. Briefly, fermentation for the biosynthetic production of heptane-1,7-dioic acid, 7-oxoheptanoic acid, 7-hydroxyheptanoic acid, 7-hydroxyheptanal, 7-aminoheptanoic acid, heptamethylenediamine, 1,7-heptandiol, 7-aminoheptanal, 7-aminoheptanol or enantholactam described previously can be utilized in, for example, fed-batch fermentation and batch separation; fed-batch fermentation and continuous separation, or continuous fermentation and continuous separation. Examples of batch and continuous fermentation procedures are well known in the art.
In addition to the above fermentation procedures using the heptane-1,7-dioic acid, 7-oxoheptanoic acid, 7-hydroxyheptanoic acid, 7-hydroxyheptanal, 7-aminoheptanoic acid, heptamethylenediamine, 1,7-heptandiol, 7-aminoheptanal, 7-aminoheptanol or enantholactam producers described herein for continuous production of substantial quantities of these, the heptane-1,7-dioic acid, 7-oxoheptanoic acid, 7-hydroxyheptanoic acid, 7-hydroxyheptanal, 7-aminoheptanoic acid, heptamethylenediamine, 1,7-heptandiol, 7-aminoheptanal, 7-aminoheptanol or enantholactam producers also can be, for example, simultaneously subjected to further procedures to convert the product to other compounds or the product can be separated from the fermentation culture and sequentially subjected to chemical or biocatalytic conversions to convert the product to other compounds, if desired.
2.11 Compositions of the Invention
The invention also provides compositions comprising recombinant host cells according to the invention and heptane-1,7-dioic acid, 7-oxoheptanoic acid, 7-hydroxyheptanoic acid, 7-hydroxyheptanal, 7-aminoheptanoic acid, heptamethylenediamine, 1,7-heptandiol, 7-aminoheptanal, 7-aminoheptanol and enantholactam. The invention also provides a composition comprising a recombinant host cell according to the invention and a feedstock. In some embodiments the feedstock is a renewable feedstock, for example wherein the feedstock is selected from the group consisting of glucose, sucrose, xylose, fatty acids and glycerol. In some embodiments the feedstock is a polyaromatic hydrocarbon, for example benzene, toluene or shikimate.
3.1 Examples
Having now generally described the invention, the same will be more readily understood by reference to the following examples, which are provided by way of illustration and are not intended as limiting. It is understood that various modifications and changes can be made to the herein disclosed exemplary embodiments without departing from the spirit and scope of the invention.
3.1.1 Conversion of 2,6-diaminopimelate to 2-amino-5,6-dehydro Pimelic Acid (6-amino-2-heptene Dioic Acid) and of 2-aminoheptanedioic Acid to 2-heptenedioic Acid by Ammonia Lyases (EC 4.3.1.-) (See, FIG. 10)
3.1.1.1 Selection of MAL Enzyme Gene Targets
Upon identification of the pathways involved in conversion of 2,6-diamino pimelic acid into pimelic acid, which is used in the production of nylon 7,7, and conversion of pimelic acid into 7-amino heptaonic acid, gene targets from these pathways were selected. In particular, enzyme targets were selected from the ammonia lyase family (EC 4.3.1), including methylaspartate ammonia lyase (MAL; EC 4.3.1.2), based on its broad substrate specificity, presence in a wide range of hosts, ability to be cloned and expressed exogenously, and available crystal structure for rational design protein engineering. The MAL genes from Citrobacter amalonaticus, Clostridium tetanomorphum and Aspergillus oryzae were selected. The MAL enzymes encoded by C. amalonaticus (GeneBank AB005294; fragment 1641-2882878596.879060NM_NM) and C. tetanomorphum (GeneBank 548141; fragment 756-1997) have significant dissimilarity (57% identity). The Aspergillus oryzae MAL gene (GeneBank XM_001827609) is evolutionarily divergent (44% identity with Citrobacter amalonaticus MAL, 39% identity with Clostridium tetanomorphum MAL), which may show different catalytic properties and/or selectivities. Another unusual ammonia lyase that is a potential enzyme for the reductive deamination of 2,6-diaminopimelate and 2-aminoheptanedioic acid, is the D-glucosaminate ammonia lyase (EC 4.3.1.9) from Pseudomonas fluorescens (accession number BAD69624). This is an unusual ammonia lyase that catalyzes an α,β-elimination:




3.1.1.2 Cloning Expression Vectors Containing Gene Targets
The selected MAL gene targets from Citrobacter amalonaticus, Clostridium tetanomorphum, and Aspergillus oryzae were then cloned into the IPTG inducible pET21-a backbone using in ABLE technology to generate I4 (pET21-a with the Citrobacter amalonaticus MAL gene), I5 (pET21-a with the Clostridium tetanomorphum MAL gene), and 16 (pET21-a with the Aspergillus oryzae MAL gene). First, the gene and vector DNA are split into truncated parts using software analysis. Potential restriction enzyme, e.g., EarI, sites in the selected MAL genes and pET21 vector were identified and disrupted by introducing mutations. EarI restriction sites located within coding sequences were disrupted, e.g., by incorporation of a silent mutation, as to avoid altering the encoded protein sequence. The resulting DNA was free of EarI sites, and was used the input sequence for software analysis to design corresponding truncated parts flanked by EarI (ordered through DNA 2.0), long and short linker oligonucleotides (ordered through Sigma-Aldrich), and long and short part oligonucleotides (ordered through Sigma-Aldrich). The 5′-end of the part and linker oligonucleotides were phosphorylated by incubating the primer in the present of T4 kinase under suitable reaction conditions (6 μM oligo, 1 PNK buffer, 1 mM ATP, 10 U T4 kinase, 5 mM DTT, 5% (w/v) PEG8000) at 37° C. for 30 minutes, followed by inactivation of the enzyme at 65° C. for 20 minutes.
Next, the phosphorylated linker oligos and phosphorylated part oligos were annealed by mixing equimolar amounts of each oligo (50 μL at 6 μM) and then heating the mixture to 65° C. in a thermocycler before gradually lowering the temperature down to 20° C. to form partially double-strand part oligos and partially double-strand linker oligos having specific 16 bp overhangs (melting temperature above 75° C.). The resulting annealed part oligos (POA) and annealed linker oligos (LOA) were then diluted to a final concentration of 1 μM with TE buffer (Tris-EDTA).
Then, the part/linker fragments corresponding to the selected genes (Citrobacter amalonaticus, Clostridium tetanomorphum and Aspergillus oryzae MAL) were generated by successive cycles of EarI digestion of the cloned truncated parts followed by ligation of their respective annealed part oligos (POA28, POA29 or POA30), their truncated part (TP28, TP29 or TP30), and the annealed linker oligos from the vector backbone (LOA31). Part linker fusions corresponding to the vector backbone were prepared by ligation of its annealed part oligos (POA31), its truncated part (TP31) and the annealed linker oligos from either genes (LOA28, LOA29 or LOA30). Ten and twenty-fold molar excesses of LOA and POA compared to the truncated part were used in the gene and vector reactions respectively to favor ligation between the truncated part and the oligonucleotides during each EarI digestion/ligation cycle. The reactions were performed in a total volume of 50 μL and were incubated in a thermocycler (Eppendorf Mastercycler Gradient). Cycles of EarI digestion/ligation were achieved by alternating the temperature between 37° C. and 16° C., which correspond to the optimum temperatures for the EarI digestion and for the ligation using the T4 DNA ligase respectively. The samples were loaded on a 0.7% agarose gel, and the part linker was purified from the residual backbone through agarose gel separation and gel extraction (QIAGEN QIAquick Gel Extraction Kit). Expected size fragments were observed after agarose gel electrophoresis for the preparation of part linker fragments. Ligation of the digested fragment with the annealed oligonucleotides displaying compatible 3 bp overhangs resulted in the formation of a non-cleavable part/linker fragment.
The gene part/linker fusions were then combined with their respective vector part/linker fusion using a 2-part assembly to construct an E. coli expression vector using the part linkers previously generated. The gene and vector part linker fusions were mixed together in an equimolar amount (0.1 μmol each), which resulted in the expected DNA fragment assembly due to the specific complementary overhangs formed in the annealed part oligonucleotide and the annealed linker oligonucleotide from each part. Reactions were incubated at room temperature for 30 min prior to transformation of high efficiency chemically competent NEB10β E. coli cells using 2 μl of the assembly reaction and 10 μl of the competent cells. Transformed cells were plated on LB-Amp-agar and incubated at 37° C. overnight. Five hundred clones were obtained for each assembly. Two random clones were then picked from each assembly and the corresponding vectors were isolated using the QIAGEN QIAprep Miniprep Kit.
Restriction analysis was performed on the previously isolated vectors to confirm the construction of the correct assembly, e.g., assembly of the Citrobacter amalonaticus gene into the pET21-a backbone. Clones obtained from the assembly of the Citrobacter amalonaticus gene into the E. coli expression vector were analyzed using PvuI and BmgBI to identify positive clones for the insertion. Clones obtained from the assembly of the Clostridium tetanomorphum gene into the E. coli expression vector were analyzed using PstI and AlwNI (Figure 30, Table 10) to identify positive clones for the insertion. Clones obtained from the assembly of the Aspergillus oryzae gene into the E. coli expression vector were analyzed using SphI and EcoRV to identify positive clones for the insertion. The restriction products from each sample were analyzed using agarose gel electrophoresis. The expected band pattern was observed for both clones from each assembly confirming the construction of E. coli expression vectors harbouring the Citrobacter amalonaticus, Clostridium tetanomorphum and Aspergillus oryzae MAL genes. Assembly of the I7 negative control vector (pET21-a control) was performed using the part/linker fusion pET21-a part/pET21-a linker was performed as a negative control, and clones from the generation of the negative control gene-free construct were analyzed using XmnI and AlwNI. To further confirm proper assembly of the expression vectors, the part junctions between the 3′-end of the vector backbone and the 5′-end of the genes as well as between the 3′-end of the gene and the 5′-end of the vector backbone were sequenced from one of the two clones from each assembly.
3.1.1.3 Expression of Exogenous MAL Genes in E. coli 
The E. coli constructs previously obtained were used to study the expression of the Citrobacter amalonaticus, Clostridium tetanomorphum and Aspergillus oryzae MAL genes in E. coli. The vectors (10 ng DNA from each assembly) were used to transform electrocompetent BL21 (DE3) E. coli cells, and transformation samples were plated on LB-Amp-Agar. Transformants were obtained after overnight incubation at 37° C.
A single clone was picked from each assembly plate, and was used to inoculate 5 ml of LB-Amp medium as a starting culture. The OD600 was measured after overnight incubation at 37° C. and 250 rpm. Two mL of each starting culture (approximately 4.5×107-6.2×107 cells) were used to inoculate 100 mL of LB-Amp, and the cultures were incubated in a 500 mL baffled shake flask at 37° C. and 250 rpm until an OD600 of 0.6 to 0.8 was reached. Protein expression, which is controlled by the T7 promoter in pET21-a, was induced by addition of 1 mM IPTG (final concentration) and cultures were further incubated at 37° C. and 250 rpm. 1 mL of each sample was taken prior to induction, 4 h post-induction, and 24 h post-induction. Cell growth was checked by measuring OD600. The remaining culture left after 24 h post-induction incubation was transferred to a 50 mL falcon tube, harvested by centrifugation at 5000 rpm for 10 minutes and the cell pellets stored at −20° C.
Next, the time-point samples from each assembly were processed for SDS-PAGE analysis. The samples were centrifuged at 13000 rpm for 2 min before the supernatant was removed and the cells were lysed using the Bugbuster protein extraction reagent supplemented with lysozyme (15 mg/mL) and benzonase (3.4 U/μL). The lysis reactions were then centrifuged at 13000 rpm for 2 min, and the soluble fraction was transferred to a new tube and the insoluble fraction was re-suspended in water. 20 μl of each fraction was mixed with 80 μl SDS-Sample buffer (SDS-Loading Buffer, 9% DTT and water) and the mixture was heated in a heatblock for 5 minutes at 95° C. 10 μl of each sample was then loaded on SDS-PAGE 4-20% Tricene gels to analyze the protein content of the soluble and insoluble fractions. A protein band at the expected size (45 kDa) was clearly visible in the soluble fraction after IPTG induction. No corresponding protein was observed in the negative control experiment suggesting that the expected 45 kDa Citrobacter amalonaticus MAL protein and 45 kDa Clostridium tetanomorphum MAL protein were successfully expressed as soluble proteins in E. coli from the assembled expression vector constructs No significant protein was observed in the insoluble fraction of any sample after induction. The 45 kDa Aspergillus oryzae MAL protein was also expressed in E. coli from the assembled expression vector construct, but it was expressed as an insoluble protein (a 45 kDa band was visible in the insoluble fraction after induction) (See, FIGS. 11A and 11B).
In order to improve the solubility of the Aspergillus oryzae MAL protein, the temperature of induction and/or the concentration of inducer was reduced, which in some cases has been shown to result in increased protein solubility due to a slower rate in protein synthesis and therefore a higher efficiency in protein folding. These parameters were reduced using the same expression and induction procedure described above, but SDS-PAGE analysis shows that the Aspergillus oryzae MAL protein was still insoluble (a 45 kDa band was visible in the insoluble fraction after induction). A yeast expression vector containing the Aspergillus oryzae MAL protein may be used to express the protein in soluble form.
Cultures of E. coli expressing the Citrobacter amalonaticus or Clostridium tetanomorphum MAL genes were scaled up to increase production of the soluble proteins for use in enzymatic assays. The cultures were grown, induced, and harvested as previously described. Briefly, a single clone was picked from each transformation plate previously prepared, and 20 ml of LB-Amp medium were inoculated as starting cultures. The OD600 was measured after overnight incubation at 37° C. and 250 rpm. 16 mL of each starting culture (approximately 4.4×108 cells) were used to inoculate 800 mL of LB-Amp, and the cultures were incubated in a 2 L baffled shake flask at 37° C. and 250 rpm until an OD600 of 0.6 to 0.8 was reached. Protein expression was induced by addition of 1 mM IPTG (final concentration), and cultures were further incubated at 37° C. and 250 rpm. After 24 h post-induction incubation, the remaining culture was transferred to four 50 mL falcon tubes, harvested by repeated centrifugation at 5000 rpm for 10 minutes (4 rounds of centrifugation per tube; 50 mL of medium per round) and the cell pellets stored at −20° C.
Glass bead lysis was used to disrupt the cells for collecting the Citrobacter amalonaticus, Clostridium tetanomorphum and Aspergillus oryzae MAL protein. Cell pellets from the 24 hour post-induction samples were re-suspended in bead lysis buffer consisting of 0.1 mM Tris, 1 mg/ml Pepstatin A and 200 mM PMSF protease inhibitors. Acid washed 212-300 μm glass beads (0.4 g per 1 mL of lysis buffer) were added to each tube, and lysed in a sonicating water bath in parallel. 250 μl samples from each of the 4 tubes were taken prior to sonication and after 5 minutes and 10 minutes of cell lysis. The 250 μl samples from each time point were pooled to give a total sample of 1 mL. Cell free extracts were prepared by centrifugation for 10 minutes at 5000 rpm and transfer of the supernatants to new tubes. Insoluble samples were prepared after re-suspension of the cell pellet isolated after 10 min of sonication with an equivalent volume of water. The remaining pellets and supernatant were stored at −20° C. 20 μl of each pooled fraction was mixed with 80 μl SDS-Sample buffer (SDS-loading buffer, 9% DTT and water) and the mixture was heated in a heatblock for 5 minutes at 95° C. 10 μl of each SDS-sample preparation was then loaded on SDS-PAGE 4-20% Tricene gels to analyze the protein content of the soluble and insoluble fractions. Protein bands were clearly detected in the samples from expression of the Citrobacter amalonaticus MAL and the Clostridium tetanomorphum MAL.
3.1.1.4 Functionality of Exogenously Expressed MAL
The activity of the methyl aspartate ammonia lyase derived from Citrobacter amalonaticus, Clostridium tetanomorphum, and Aspergillus oryzae was assayed using the I4, I5, and I6 strains towards beta-methyl aspartate, in the first place. In subsequent studies described herein, the activity of these strains were assayed in the context of different substrates, namely, 2-aminopimelate, D,L-lysine, and, finally, 2,6-diaminopimelic acid. A negative control biotransformation of 2-aminopimelate with I17 was also conducted.
3.1.1.4.1 Biotransformation Screening of I4, I5, and I6 Strains Toward beta-methyl Aspartate




Six biotransformations were prepared at either 5 g/L or 20 g/L whole cell equivalent of the I4, I5 and I6 lyase strains. The enzyme concentration was calculated based on whole cell equivalent which is the pelleted cell mass after centrifugation (wet cell weight) divided by the volume of buffer used to resuspend the cells during lysis. The biotransformations were conducted in 3 ml volumes with 10 mM DL-threo-beta methyl aspartate.
Reactions were incubated at 30° C. in an orbital incubator and samples removed for analysis by HPLC after 1, 5 and 18 hours. The 1 ml aliquots were prepared for analysis by heat treatment to remove heat labile proteins. The samples were subsequently centrifuged at 10,000 rpm for 2 minutes and filtered through a 0.2 micron filter. Analysis of the samples was carried out by HPLC using a Phenomenex Rezex column with 5 mM sulfuric acid mobile phase using RID and UV detection. Confirmation of lyase activity was affirmed by detection of mesaconic acid in the samples. The concentration of mesaconic acid formed in each biotransformation was determined by measurement of an external standard mesaconic acid from Aldrich.
Mesaconic acid was detected in all the I4 and I5 strain biotransformations, confirming functional expression of the lyase enzyme was present in these cell extracts. No activity was observed in the 16 strain which is consistent with the results observed by SDS PAGE analysis of the expressed protein which showed the protein was expressed in insoluble form. The yield of mesaconic acid in all samples analyzed from the I4 and I5 strains was  ̃5 mM, which is consistent with the anticipated activity on 10 mM DL-threo-beta methyl aspartate, since the wild type enzyme is L-enantioselective. In the I4 and I5 strains complete conversion was observed after just 1 hour incubation.
3.1.1.4.2 Biotransformation Screening of I4 and I5 Strains Toward 2-aminopimelate




Eight biotransformations were prepared varying levels of enzyme and substrate concentrations (2 variable, 2 level stat design) to examine I4 and I5 enzyme activity towards 2-aminopimelate. The biotransformations were conducted in 3 ml volumes with varying loadings as indicated below:
I4 strain 5 g/L; 2-aminopimelate concentration 5 mM
I4 strain 5 g/L; 2-aminopimelate concentration 10 mM
I4 strain 20 g/L; 2-aminopimelate concentration 5 mM
I4 strain 20 g/L; 2-aminopimelate concentration 10 mM
I5 strain 5 g/L; 2-aminopimelate concentration 5 mM
I5 strain 5 g/L; 2-aminopimelate concentration 10 mM
I5 strain 20 g/L; 2-aminopimelate concentration 5 mM
I5 strain 20 g/L; 2-aminopimelate concentration 10 mM
The biotransformations were placed in a falcon tube at 30° C. in a shaker incubator. Aliquots (1 ml) were removed from the biotransformations after 7, 14 and 21 days. Prolonged incubation was operated to provide best possible chance of observing lyase activity. The 1 ml aliquots were prepared for analysis by heat treatment to remove heat labile proteins. The samples were subsequently centrifuged at 10,000 rpm for 2 minutes and filtered through a 0.2 micron filter. Analysis of the samples was carried out by HPLC using a precolumn derivatisation method. This method comprises forming a chiral adduct with a Boc-cysteine and ortho-phthaldehyde reagent to form a diastereomeric pair of L- and D-2-aminopimelate derivatives. The diastereomers (representing the enantiomers of 2-aminopimelate) can then be separated by HPLC using a C18 column and a 5 mM potassium phosphate buffer pH 7.0 and acetonitrile gradient at 338 nm. The peak areas for L- and D-2-aminopimelate signals in each sample were recorded and observed decrease in the L-2-aminopimelate standard is expressed as % relative to the D-2-aminopimelate.
The data show L-2-aminopimelate being degraded in all the biotransformations. The increase in enantiomeric excess is consistent with the natural L-enantioselectivity expeected for these lyase enzymes which preferentially acts on L-beta-methyl aspartate. The lower substrate loadings (5 mM) also showed a greater enantio-enrichment (ie higher conversion of the available substrate) compared to the higher substrate loadings which is consistent with the anticipated lyase activity.
The presence of unreacted 2-aminopimelate was confirmed via mass spectrometry. The M+H equal to 176.09 was observed in the sample and matched the simulated mass spectrum for C7H13NO4. On the full sweep mass spectrum, the enoic acid product (M+H=159.06) was not observed. However, when the MS accumulated ions for 20 seconds over a 20 m/z wide mass isolation the correct product signal was observed and matched with the simulated mass spectrum for C7H10O4.
A sample of the rac-2-aminopimelic acid starting material was also analyzed. Using the same MS methods carried out on this standard clearly displayed the expected molecular ion for 2-aminopimelate. However, repeating the MS ion accumulation for 20 seconds over a 20 m/z wide mass isolation (as had been carried out on the previous biotransformation sample) revealed the presence of the enoic acid product as a mass fragment.
3.1.1.4.3 Negative Control Biotransformation of 2-aminopimelate with I17 Strain
Four biotransformations were prepared with varying level of cell extract and substrate to match the levels used in the experiment described in 3.1.1.4.1. The biotransformations were conducted in 3 ml reaction volumes as indicated below:
I7 strain 5 g/L; 2-aminopimelate concentration 5 mM
I7 strain 5 g/L; 2-aminopimelate concentration 10 mM
I7 strain 20 g/L; 2-aminopimelate concentration 5 mM
I7 strain 20 g/L; 2-aminopimelate concentration 10 mM
The biotransformations were incubated at 30° C. in a shaker incubator and samples taken after 8, 13 and 21 days. Analysis of the reaction was carried out by HPLC following the method described in the experiment described above in 3.1.1.4.1.
The data show there is some loss of the L-enantiomer in the I17 strain. However the relative decrease in the L-enantiomer is less than the equivalent biotransformations with the I4 and I5 strains, particular when the second time points incubating for 2 weeks are compared. The trend depicted below clearly shows the I4 and I5 strains in the biotransformations have a consistently higher level of L-2-aminopimelate degradation compared to the I17 negative control strain across the 2×2 statistical design experiment examining cell extract and substrate loadings.
3.1.1.4.4 Biotransformation Screening of I4 and I5 CFE with DL-lysine




Eight biotransformations were prepared in a similar fashion as used to test for lyase activity towards 2-aminopimelate. The I4 and I5 lyase strains were tested at varying concentrations of cell extract and DL-lysine substrate as follows:
I4 strain 5 g/L; DL-lysine concentration 5 mM
I4 strain 5 g/L; DL-lysine concentration 10 mM
I4 strain 20 g/L; DL-lysine concentration 5 mM
I4 strain 20 g/L; DL-lysine concentration 10 mM
I5 strain 5 g/L; DL-lysine concentration 5 mM
I5 strain 5 g/L; DL-lysine concentration 10 mM
I5 strain 20 g/L; DL-lysine concentration 5 mM
I5 strain 20 g/L; DL-lysine concentration 10 mM
The biotransformations were placed in a falcon tube at 30° C. in a shaker incubator. Aliquots (1 ml) were removed from the biotransformations after 7, 14 and 21 days. Prolonged incubation was operated to provide best possible chance of observing lyase activity. The 1 ml aliquots were prepared for analysis by heat treatment to remove heat labile proteins. The samples were subsequently centrifuged at 10,000 rpm for 2 minutes and filtered through a 0.2 micron filter. DL-lysine samples were analyzed using a chiral HPLC column (Chirobiotic T2 Astec) to monitor enantiomer ratios to determine lyase activity. Samples were removed from the biotransformations after 7, 14 and 21 days.
The results indicate loss of L-lysine in all the biotransformations with 5 mM lysine. Some variations in enantioselective action on DL-lysine was observed, where the concentration of L-lysine exceeded the concentration of D-lysine. Owing to the poor UV absorbance (detector set to 210 nm) and low signal to noise ratio of lysine in the HPLC chromatogram the possibility of a false positive L-lysine detection cannot be excluded from these results. However, in general degradation of L-lysine from DL-lysine was observed across the eight biotransformations which is consistent with the expected stereoselectivity of potential lytic activity arising from lyase functioning in the I4 and I5 strains.
In order to gather further evidence to support the functioning of lyase activity in these biotransformations, a sample was analyzed by MS to attempt to detect the desired enoic acid product in the sample. The MS signal corresponding to the unreacted lysine (M+H=176.09) was observed in the sample and matched the simulated mass spectrum for C6H14N2O2.
On the full sweep mass spectrum, the enoic acid product (M+H=130.09) was not observed. However, as for the amino-pimelic acid reactions, when the MS accumulated ions for 20 seconds over a 20 m/z wide mass isolation the correct product signal was observed and matched with the simulated mass spectrum for C6H11NO2.
A sample of the DL-lysine starting material was also analyzed. Using the same MS methods carried out on this standard clearly displayed the expected molecular ion for DL-lysine. However, repeating the MS ion accumulation for 20 seconds over a 20 m/z wide mass isolation (as had been carried out on the previous biotransformation sample) revealed the presence of the enoic acid product as a mass fragment.
3.1.1.4.5 Biotransformation Screening of I4 and I5 CFE with meso-2,6-diaminopimelic acid




Six biotransformations were prepared to test for lyase activity towards meso-2,6-diaminopimelic acid. The I4, I5 and 17 strains were tested with 5 mM meso-2,6-diaminopimelic acid. Varying concentrations of cell extract were examined as follows:
I4 strain 5 g/L; meso-2,6-diaminopimelic acid concentration 5 mM
I4 strain 20 g/L; meso-2,6-diaminopimelic acid concentration 5 mM
I5 strain 5 g/L; meso-2,6-diaminopimelic acid concentration 5 mM
I5 strain 20 g/L; meso-2,6-diaminopimelic acid concentration 5 mM
I17 strain 5 g/L; meso-2,6-diaminopimelic acid concentration 5 mM
I17 strain 20 g/L; meso-2,6-diaminopimelic acid concentration 5 mM
The biotransformations were placed in a falcon tube at 30° C. in a shaker incubator. Aliquots (1 ml) aliquots were removed from the biotransformations after 4 days, further sample acquisitions are pending prior to HPLC analysis.
A sample acquired after 4 days was analyzed by MS. The analysis confirmed the presence of meso-2,6-diaminopimelic acid which matched the simulated mass signal for C7H14N2O4.
The desired enoic acid signal was not observed in this mass spectrum in the biotransformation sample. However, when ion accumulation was introduced for 0.5 sec then the corresponding enoic acid signal (M+H=174.08) was observed in one of the samples.
3.1.2 Conversion of 2-amino-5,6-dehydro Pimelic Acid (6-amino-2-heptenedioic acid) to 2-amino-heptane Dioic Acid and 2-heptenedioic Acid or its CoA ester to Pimelic acid or its CoA Ester by Enoate Reductases (EC 1.3.1.31) or Enoyl-CoA Dehydrogenases (EC 1.3.1.62) (See, FIG. 10)
3.1.2.1 Selection of Enoate Reductase Targets
Upon identification of the pathways involved in the conversion of two unsaturated intermediates of pimelic acid, i.e., 2-amino-5,6-dehydro pimelic acid and 2-heptenedioic acid, into their corresponding saturated compounds 2-aminoheptanedioic acid and pimelic acid, enzyme targets were selected from the enoate reductase family (EC 1.3.1), such as EC 1.3.1.31, based on to their different substrate specificity towards α,β-unsaturated carboxylic acids and their stability (Stereocomplementary bioreduction of α,β-unsaturated dicarboxylic acids and dimethyl esters using enoate reductases—Enzyme- and substrate-based stereocontrol: Stueckler et al. Org. Lett. 2007, 9, 5409-5411).
In particular, the enoatereductase genes from Bacillus subtilis (YqjM) (GeneBank D84432; fragment 242791-243807) and Solanum lycopersicum (OPR1 and OPR3) (GeneBank NM_001247852, fragment 108-1238 and GeneBank NM_001246944; fragment 94-1284, respectively) were selected because they had been previously cloned and successfully expressed in E. coli, crystal structures of the YqjM and OPR3 enzymes were reported, which enables protein engineering through rational design (The 1.3 A crystal structure of the flavoprotein YqjM reveals a novel class of old yellow enzyme: Kitzing et al. J. Biol. Chem. 2005, 280, 27904-27913; Asymmetric bioreduction of activated alkenes using cloned 12-oxophytodienoate reductase isoenzymes OPR-1 and OPR-3 from Lycopersicon esculentum (Tomato): A striking switch of stereopreference: Hall et al. Angew. Chem. Int. Ed. 2007, 46, 3934-3937; Crystal structure of 12-oxophytodienoate reductase 3 from tomato—Self inhibition by dimerization: Breithaupt et al. PNAS 2006, 103, 14337-14342).
Enoate reductases from Clostridium species are also considered due to their broad substrate specificity (Chiral compounds synthesized by biocatalytic reductions: Simon et al. Angew. Chem. Ed. Engl. 1985, 24, 539-553; Properties and mechanistic aspects of newly found redox enzymes from anaerobes suitable for bioconversions on preparatory scales: Simon et al. Pure & Appl. Chem. 1992, 64, 1181-1186). However, those enzymes were not cloned and expressed for initial proof of concept due to their high sensitivity towards oxygen (Enoate reductases of Clostridia—Cloning, sequencing and expression: Rohdich et al. J. Biol. Chem. 2001, 276, 5779-5787), but may be useful catalysts for the final pathway construction in an anaerobic host. In particular, the following enoate reductases should be useful for the reduction of the double bonds in the target 2-enoyl C7 compounds:
enr 2-Enoate reductase (Y16137) EC 1.3.1.31 from Clostridium kluyveri: Whole cells of Clostridium kluyveri were found to reduce a broad range of 2-enoates in the presence of molecular hydrogen. The substrates were: tiglic acid, acrylic acid, methacrylic acid, dimethylacrylic acid, (E)-pentenoic acid, (E)-hexenoic acid, sorbic acid, cinnamic acid [19], (E)-2-butenoic acid and (E)-2-methyl-2-butenoic acid, (E)- and (Z)-3-methyl-2-pentenoic acid, p-methoxy-cinnamic acid and p-nitro-cinnamic acid [Bühler, M., Giesel, H., Tischer, W. and Simon, H. (1980) Occurrence and the possible physiological role of 2-enoate reductases. FEBS Lett. 109, 244-246]. A partial sequence of the gene encoding the enzyme was identified [Rohdich, F., Wiese, A., Feicht, R., Simon, H. and Bacher, A. (2001) Enoate reductases of Clostridia. Cloning, sequencing, and expression. J. Biol. Chem. 276, 5779-5787]. Since the genome of C. kluyveri has been sequenced, we found the full sequence of the gene (YP_001394144.1, GENEBANK).
enr 2-Enoate reductase (Y09960) EC 1.3.1.31 from C. tyrobutyricum (previously Clostridium sp. La 1): 2-Enoate reductase was found in Clostridium sp. growing on (E)-butenoate and purified to homogeneity. It accepted (E)-2-methylbutenoate and cinnamate [Elshahed M S, Bhupathiraju V K, Wofford N Q, Nanny M A, McInerney M J. (2001) Metabolism of benzoate, cyclohex-1-ene carboxylate, and cyclohexane carboxylate by “Syntrophus aciditrophicus” strain SB in syntrophic association with H(2)-using microorganisms. Appl Environ Microbiol. 67: 1728-1738], (E)-alpha-formylamino-cinnamate, and 4-methyl-2-pentenoate [Bühler, M., Giesel, H., Tischer, W. and Simon, H. (1980) Occurrence and the possible physiological role of 2-enoate reductases. FEBS Lett. 109, 244-246]. The gene encoding enr reductase was identified and the enzyme was overexpressed in E. coli under anaerobic conditions [Rohdich, F., Wiese, A., Feicht, R., Simon, H. and Bacher, A. (2001) Enoate reductases of Clostridia. Cloning, sequencing, and expression. J. Biol. Chem. 276, 5779-5787].
enr 2-Enoate reductase (Y16136) EC 1.3.1.31 from Moorella thermoacetica (previously Clostridium thermoaceticum): An antiserum against enoate reductase from C. tyrobutyricum cross-reacted with a protein of the thermophilic Clostridium thermoaceticum. The gene encoding the reductase was identified and the enzyme was successfully overexpressed in E. coli [Rohdich, 2001].
Other potential enoate reductase candidates were identified from Saccharomyces cerevisiae and Pseudomonas putida but no evidence of gene characterization and no activity towards α,β-unsaturated carboxylic acids were reported respectively for those two enzymes.
In addition to enoate reductases, pimeloyl-CoA dehydrogenases (EC 1.3.1.62) should catalyse the reduction of the double bond in 2-heptenedioic acids and the corresponding CoA esters. Pimeloyl-CoA dehydrogenase activity was found in cell extracts of Syntrophus aciditrophicus grown in a co-culture with Desulfovibrio sp. strain G11 with benzoate or in a pure culture with crotonate and is involved in the benzoate degradation pathway (Elshahed M S, Bhupathiraju V K, Wofford N Q, Nanny M A, McInerney M J. (2001) Metabolism of benzoate, cyclohex-1-ene carboxylate, and cyclohexane carboxylate by “Syntrophus aciditrophicus” strain SB in syntrophic association with H(2)-using microorganisms. Appl Environ Microbiol. 67: 1728-1738). Other hypothetical pimeloyl-CoA dehydrogenases found in databases include ThnJ (D9PTN0) and ThnK (D9PTM9) from Sphingomonas macrogolitabida—found in the gene cluster for tetralin degradation via the beta-oxidation pathway, PimC (Q6N3I0) and PimD (Q6N3I1) from Rhodopseudomonas palustris and PimC (A5ES10) and PimD (A5ES09) from Bradyrhizobium sp.
Other dehydrogenases useful to the invention include GDH Glutaryl-Coenzyme A Dehydrogenase Desulfococcus multivorans, a non-decarboxylating glutaconyl-coenzyme A-forming glutaryl-coenzyme A dehydrogenase was characterized in the obligately anaerobic bacteria Desulfococcus multivorans [Wischgoll S, Demmer U, Warkentin E, Günther R, Boll M, Ermler U. (2010) Structural basis for promoting and preventing decarboxylation in glutaryl-coenzyme A dehydrogenases. Biochemistry. 49: 5350-5357]. The enzyme was overexpressed and its crystal structure was determined.
3.1.2.2 Cloning Expression Vectors Containing Gene Targets
The selected YqjM, OPR1, and OPR3 gene targets from Bacillus subtilis and Solanum lycopersicum were then cloned into the IPTG inducible pET21-a backbone using in ABLE technology, as described in detail in Section 3.1.1.2) to generate I1 (Bacillus subtilis YqjM gene in pET21-a), I2 (Solanum lycopersicum OPR1 gene in pET21-a), and I3 (Solanum lycopersicum OPR3 gene in pET21-a).
Briefly, potential EarI sites in the selected genes and the vector backbone were disrupted to prevent interference with the part/linker fusion preparation involving EarI digestion/ligation cycles. No EarI sites were observed in the Bacillus subtilis YqjM enoate reductase gene, but one and two EarI sites were detected in the Solanum lycopersicum OPR1 and OPR3 genes, respectively, which were disrupted by incorporating silent mutation(s) in the restriction site. Disruption of the EarI sites 1 and 2 in the Solanum lycopersicum OPR3 gene sequence resulted in an inadvertent EarI site being created, which was only discovered after the sequences were synthesized. The residual EarI site was removed using the Quikchange single-site directed mutagenesis kit from Strategene. Forward and reverse primers were designed to disrupt the residual EarI site, and the primers were phosphorylated as described in the section 3.1.1.2 prior to the Quikchange reaction. The Quikchange and the negative control reactions were prepared as follows:















TP27
Negative



Reagent
Quikchange
control








10x Pfu turbo Reaction
5 μl
5 μl



Buffer





TP27
1 μl
1 μl



Forward Primer
3 μl
3 μl



Reverse Primer
3 μl
3 μl



dNTP solution
5 μl
5 μl



Molecular Biology Grade
32 μl 
33 μl 



Water





Pfu turbo enyme
1 μl
—



Total Volume
50 μl 
50 μl 









The reactions were run in a thermocycler (95° C. 0.5 minutes; 35 cycles of 95° C. 0.5 minutes, 55° C. 1 minute, 68° C. 10 minutes; 68° C. 1 minutes, 4° C. hold), and then treated with DpnI (1 μL) to digest the methylated parental DNA at 37° C. for 2 hours. The digestion reactions (3 μL) were used to transform TOP10 electrocompetent E. coli cells, and the transformation samples (100 μL) were plated onto LB-Kan-Agar. About 100 clones were obtained on the Quikchange reaction plate compared to none on the negative control plate after overnight incubation at 37° C. Ten clones were picked from the plate, the corresponding plasmids were purified, and analyzed by EarI digestion. The absence of a 300 bp band on the agarose gel indicated that the EarI site located in the OPR3 gene was deleted. EarI digestion showed that several clones were positive for the removal of the residual EarI site. DNA sequencing confirmed the clone's sequence.
Vector from clone 3 (a clone positive for removal of EarI) was used to transform electrocompetent TOP10 E. coli cells. QIAGEN Hi-Speed Plasmid Purification Midi Kit was used to prepare a large DNA stock from the culture, and the DNA sample was subsequently concentrated using the QIAGEN PCR purification kit. The final DNA concentration and the volume of the sample was 470.0 ng/μl in 120 μl (DNA conc. 199.8 nM).
Three EarI sites were detected in the vector backbone pET21-a, which were disrupted by mutating the last guanidine base of the restriction site into a thymine (corresponding to the first cytosine into an adenine on the reverse complement sequence).
The EarI free sequences were then used as input sequences in the part designer software to design the corresponding truncated parts flanked by EarI sites, as discussed in Section 3.1.1.2. The synthesized Bacillus subtilis YqjM (TP25), Solanum lycopersicum OPR1 (TP26), and Solanum lycopersicum OPR3 (TP27) truncated parts were inserted into the DNA2.0 pJ201 vector. The pET21-a truncated part vector was fully synthesized with introduction of a fragment including the chloramphenicol resistance gene to produce the vector TP31.
Phosphorylation and subsequent annealing of the in ABLE oligonucleotides were performed as described in section 3.1.1.2.
Next, part linker fusions were prepared by ligating the 5′-end of the truncated part with its corresponding part oligo annealed fragment, and the 3′-end of the truncated part with the linker oligo annealed fragment, as previously described in section 3.1.1.2. Part linker fusions corresponding to the Bacillus subtilis YqjM, Solanum lycopersicum OPR1 and Solanum lycopersicum OPR3 genes were prepared by ligation of their respective annealed part oligos, their truncated part, and the annealed linker oligos from the vector backbone. Part linker fusions corresponding to the vector backbone were prepared by ligation of its annealed part oligos, its truncated part, and the annealed linker oligos from either genes. A negative control gene-free assembly was also prepared by ligation of the vector backbone annealed part oligos, its truncated part, and its annealed linker oligos, resulting in self-assembly of the vector backbone.
A ten and twenty-fold molar excesses of linker and part oligos to the truncated part was used in the gene and vector reactions to favor ligation between the truncated part and the oligonucleotides during each EarI digestion/ligation cycle. The 50 μL EarI digestion/ligation reactions were incubated in a thermocycler (Eppendorf Mastercycler Gradient), alternating the temperature between 37° C. and 16° C. Upon completion of the cycles, samples were loaded on a 0.7% agarose gels, and the expected size fragments were observed for preparation of the part/linker fusions, e.g., Bacillus subtilis YqjM part/pET21-a linker and Solanum lycopersicum OPR1 part/pET21-a linker as well as the 3 kb vector backbone; or pET21-a part/Solanum lycopersicum OPR3 linker—5.3 kb and Solanum lycopersicum OPR3 part/pET21-a linker—1.2 kb as well as a 1.8 kb band corresponding to the vector backbone. The correct size bands were then excised from the gel, and the DNA was gel extracted using the QIAGEN QIAquick Gel Extraction Kit. The DNA concentration ranged from 14.4 ng/μl to 49.6 μg/μl in a total volume of 30 μl (DNA conc. range 5.4 nM to 35.6 nM).
Combination of the gene part/linker fusions with their respective vector part/linker fusion was then carried out through a 2-part assembly as described in section 3.1.1.2. Briefly, the gene part linkers and the vector part linkers were incubated at room temperature for 30 min prior to transformation of high efficiency OPR3 chemically competent NEB10β E. coli cells using 2 μl of the assembly reaction and 10 μl of the competent cells. Transformed cells were plated on LB-Amp-agar, and incubated at 37° C. overnight. Five hundred clones were obtained for each assembly. One or two random clones were selected from each assembly, and the corresponding vectors were isolated using the QIAGEN QIAprep Miniprep Kit.
Restriction was performed to confirm vector construction, as described in section 3.1.1.2. Briefly, clones obtained from the assembly I1 were analyzed using PstI and HincII to identify positive clones for the insertion of the Bacillus subtilis YqjM gene into the E. coli pET21-1 expression vector, clones obtained from the assembly 12 were analyzed using PvuI and PsiI, and clones obtained from the assembly I3 were analyzed using BglII and MluI. The restriction products were run on an agarose gel, and the expected band pattern was observed for the clones tested from each assembly, confirming the construction of E. coli pET21-a expression vectors harbouring the Bacillus subtilis YqjM, the Solanum lycopersicum OPR1 and Solanum lycopersicum OPR3 enoate reductase genes. In addition, the part junctions between the 3′-end of the vector backbone and the 5′-end of the genes as well as between the 3′-end of the gene and the 5′-end of the vector backbone were sequenced to confirm the construction.
3.1.2.3 Expression of Exogenous Enoate Reducatase Genes in E. coli 
Initially, the cloned enoate reductase genes were expressed in E. coli using 1 mM IPTG and 37° induction temperature, as described above in Section 3.1.1.3. Briefly, the OD600 was measured for each culture pre-induction and at various time points after induction. The remaining culture left after 24 h post-induction incubation was transferred to a 50 mL falcon tube, harvested by centrifugation at 5000 rpm for 10 minutes, and the protein content of the samples were analyzed using SDS-PAGE. A large protein band at the expected size (35 kDa) was clearly visible in the soluble fraction from the expression study of the Bacillus subtilis YqjM enaoate reductase after IPTG induction. A large band was visible in the insoluble fraction from the expression of the Solanum lycopersicum OPR1 enoate reducatase after IPTG induction, suggesting that the expected 42 kDa OPR1 protein expressed from 12 was insoluble in E. coli. A protein band at the expected size (44 kDa) was clearly detected in the soluble portion after IPTG induction of Solanum lycopersicum OPR3 enoate reductase I3, as well as in the insoluble fraction, suggesting that the expected 44 kDa Solanum lycopersicum OPR3 enoate reductase protein was expressed in E. coli as partial soluble form.
Based on reports of expression functional expression of the Solanum lycopersicum OPR1 enoate reductase in E. coli optimized in the literature, the conditions for IPTG concentration (range of 0.1-1 mM IPTG) and induction temperature (range of 16-37° C.) were optimized in an attempt to improve the solubility of Solanum lycopersicum OPR1 enoate reductase in E. coli. (Strassner et al. JBC 1999, 274, p. 35067-35073; Hall et al. Angew. Chem. Int. Ed. 2007, 46, p. 3934-3937). The same expression protocol and the same SDS-PAGE sample preparation as described in section 3.1.1.3. was used for the solubility optimization experiments.
The time-point samples from each assembly were then processed for and analyzed using SDS-PAGE analysis, as described in section 3.1.1.3, which showed that lowering the induction temperature to 16° C. and the inducer concentration to 0.1 mM was effective to partially solubilize the Solanum lycopersicum OPR1 enoate reductase expressed in E. coli. 
E. coli strains expressing the 3 enoate reductases were scaled up to 800 ml cultures and assayed for activity.
3.1.3 Conversion of pimeloyl-CoA and pimeloyl-[acp] to Pimelic Acid Semialdehyde by Fatty acyl-CoA Reductases (Aldehyde Forming FAR) (EC 1.2.1.50) or acyl-[acp] Reductases (EC 1.2.1.80) (See, FIG. 2).
3.1.3.1 Selection of Target Enzymes
Fatty acyl CoA reductases are involved in wax ester synthesis in plants and other higher eukaryotes for cuticle wax formation. In Archaea and bacteria, these enzymes are involved in long-chain alkane biosynthesis, although their physiological function in these organisms is still not always clear. The formation of wax esters in plants begins with the elongation of acyl CoAs to form long-chain fatty acids (LFCA) (or fatty acyl-CoAs), which are then reduced via the decarbonylation pathway or acyl CoA reduction pathways (Cheesbrough and Kolattukudy, 1984).
Hydrocarbons are formed via the decarbonylation pathway. This pathway is initiated by a fatty acyl-CoA reductase-catalysed reaction to produce the aldehyde, followed by decarbonylation catalysed by an aldehyde decarbonylase to yield the [Cn-1] alkane (Cheesbrough and Kolattukudy, 1984).
The acyl CoA reduction pathway is also initiated by a reduction of LCFAs to aldehydes, followed by a further reduction of aldehydes by an aldehyde reductase to produce even-chained primary alcohols (Millar et al., 1999) (Kolattukudy, 1971). Similar pathways are thought to exist in prokaryotes (Schirmer et al., 2010).
Both pathways are initiated by reduction of long-chain acyl-CoAs to aldehydes catalysed by fatty acyl-CoA reductase (FAR; EC 1.2.1.50) in a reversible reaction. In the acyl CoA reduction pathway, the aldehydes are reduced further to the alcohols. This can be achieved in either one or two steps, depending on the organism. The two step reduction is initiated using the acyl-CoA reductase-catalysed reaction, which releases the fatty aldehyde for a second reduction catalysed by a fatty aldehyde reductase. The one step reduction is catalysed by a bi-functional acyl CoA reductase which reduces the acyl CoA directly to the alcohol without releasing the aldehyde intermediate. Thus, fatty acyl CoA reductases can be broadly divided into two types: (1) alcohol-forming acyl-CoA reductases and (2) aldehyde generating acyl-CoA reductases. There are examples of both types in prokaryotes and eukaryotes. Since the target is pimelic semialdehyde, the aldehyde-generating fatty acyl CoA reductases are the most promising candidates for reduction of pimeloyl CoA.
Preliminary literature and database searches revealed that the overwhelming majority of acyl-CoA reductases studied or identified by sequence homology were alcohol-forming FARs in both eukaryotes and prokaryotes. However, one of the early examples of an aldehyde-generating reductase came from Acinetobacter calcoaceticus—Acr1. Therefore, the primary sequence of this enzyme was used in database searches for other aldehyde-generating enzymes.
A general rule for acyl-CoA reductases seems to be that the shorter proteins (295-350 aa) tend to be aldehyde-generating enzymes, whereas longer polypeptides (500+ aa) are alcohol producers. However, most of the shorter enzymes deposited in databases had putative or hypothetical annotations with no further information beyond sequence data and, for this reason, they were not considered.
The candidates were chosen using the following criteria:—(1) The enzyme must generate aldehyde only or there must be scope to eliminate alcohol formation by protein engineering; (2) The must be evidence of existence of the protein i.e. protein has been identified and purified or isolated in cellular fractions; (3) The enzyme was tested using acyl-CoA or acyl-ACP substrates; (4) The enzyme must not be part of multi-enzyme complex unless activity has been demonstrated independently of the complex. Once candidates were identified, further bioinformatics and literature searches were perfoinied to provide additional data to rank the selections.
Table 1 shows the results of database searches carried out against a known aldehyde-forming enzyme (Acr1). Each of the candidates has been purified and assayed in vitro. The candidates were ranked and grouped according to their suitability. The top ranking enzymes (1-3) are considered the best candidates for further study, the intermediate ranked enzymes (4 and 5) are considered to be good candidates but may require further investigation and the lower ranked enzyme (6) would require more effort to obtain enzyme activity data, due to the absence of the protein sequence and the lack of a sequenced genome.







TABLE 1







Candidate Acyl-CoA reductases from various organisms.














Protein

Shortest






name or

substrate






Pubmed

tested (no.
No. of





accession

carbon
amino
Reduction to
Level of


Rank
number
Organism
atoms)
acids
alcohol
Evidence*
















1
P94129
Acinetobacter
14
295
No
Enzyme




calcoaceticus



activity


2
YP_400611
Synechococcus
18
341
No
Enzyme




elongatus PCC



activity




7942






3
BAF92773
Photobacterium
14
488
No
Enzyme




phosphoreum



activity


4
YP_959769
Marinobacter
8
661
Yes, but may
Enzyme




aquaoelei VT8


be possible to
activity







truncate



5
YP_959486
Marinobacter
ND
513
Yes, but may
Enzyme




aquaoelei VT8


be possible to
activity







truncate



6
AAB35106
Botryococcus
16
26
No
Enzyme



(partial)
braunii



activity





*Level of evidence - Enzyme activity means enzyme has been purified either heterologously or homologously, or activity has been measured in crude extracts or other cellular fractions






Acinetobacter calcoaceticus Acr1 (P94129) (Reiser, S., and Somerville, C. (1997): Isolation of mutants of Acinetobacter calcoaceticus deficient in wax ester synthesis and complementation of one mutation with a gene encoding a fatty acyl coenzyme A reductase. J Bacteriol 179, 2969-2975): An aldehyde-generating acyl-CoA reductase has been purified and contains 295 amino acids, with a molecular weight of 32.5 kDa. This enzyme has been expressed in E. coli and cell-free extracts were shown to contain acyl-CoA reductase activity. Acyl-CoA substrates ranging from C12 to C24 in length were assayed (but not the C-odd substrates). The corresponding aldehyde was generated in all cases except for the C12 substrate. It would be worth examining the substrate range of this enzyme further and testing its activity on shorter length acyl-CoAs. Even if pimeloyl CoA is not a substrate, there is scope for directed evolution to extend the substrate range. This enzyme has been named directly in a patent about enhancing production of fatty acid derivatives (US20110256599).
AAR from Synechococcus elongatus PCC 7942 (YP_400611) (Schirmer, A., Rude, M. A., Li, X., Popova, E., and Del Cardayre, S. B. (2010). Microbial Biosynthesis of Alkanes. Science 329, 559-562): This acyl-ACP reductase is in the cyanobacterium S. elongatus and designated AAR. The enzyme is thought to be involved in alkane biosynthesis. It has been expressed and purified in E. coli MG1655. Both CoA and ACP derivatives are substrates. Thus, octadecanal is formed from either oleoyl-CoA and oleoyl-ACP without fatty alcohol formation. However, oleoyl-ACP was the preferred substrate, with a KM of 8 μM compared to 130 μM for oleoyl-CoA. The enzyme is NADPH-dependent and requires magnesium for activity. No other substrates have been tested. The selectivity for aldehyde formation and the activity with CoA derivatives makes this enzyme a good candidate for testing for pimeloyl-CoA reduction. Furthermore, there are a number of orthologues of this gene in closely related organisms (Schirmer et al., 2010), although AAR is the best studied. The following patents are associated with the work from (Schirmer et al., 2010): WO 2009/140695 and WO 2009/140696.
LuxC (BAF92773) from Photobacterium phosphoreum (Boylan, M., Miyamoto, C., Wall, L., Graham, A., and Meighen, E. (1989). Lux C, D and E genes of the Vibrio fischeri luminescence operon code for the reductase, transferase, and synthetase enzymes involved in aldehyde biosynthesis. Photochemistry and photobiology 49, 681-688; Lee, C. Y., and Meighen, E. A. (1997). Cysteine-286 as the site of acylation of the Lux-specific fatty acyl-CoA reductase. Biochim Biophys Acta 1338, 215-222; Wang, X., and Kolattukudy, P. E. (1995). Solubilization and purification of aldehyde-generating fatty acyl-CoA reductase from green alga Botryococcus braunii. FEBS Lett 370, 15-18): LuxC is part of a multi-enzyme complex (LuxCDE) consisting of a fatty acyl-CoA reductase, fatty acyl synthetase and fatty acyl thioesterase, and is involved in bioluminescence. LuxC is a well-studied enzyme and has been cloned, expressed and purified in E. coli. The enzyme exhibits acyl-CoA reductase activity with the C14 substrate, tetradecanoyl-CoA (myristoyl-CoA), which is reduced to the corresponding aldehyde, tetradecanal. No other substrates have been tested. Although the LuxC is part of a multisubunit complex in vivo, the enzyme has been successfully purified from the wild-type organism and has been expressed and partially purified from E. coli. In both cases, LuxC was active independently of the other subunits. This makes LuxC a good candidate to convert pimeloyl-CoA to pimelic acid semialdehyde.
FAcoAR from Marinobacter aquaeolei VT8 (YP_959769.1) (Willis, R. M., Wahlen, B. D., Seefeldt, L. C., and Barney, B. M. (2011). Characterization of a fatty acyl-CoA reductase from Marinobacter aquaeolei VT8: a bacterial enzyme catalyzing the reduction of fatty acyl-CoA to fatty alcohol. Biochemistry 50, 10550-10558): This fatty acyl CoA reductase (designated FAcoAR) was recently discovered in the gamma proteobacterium Marinobacter aquaeolei VT8. It is the first prokaryotic example of a bi-functional acyl-CoA reductase, catalyzing reduction of acyl-CoA derivatives to alcohol. Crucially it is the only enzyme that has been tested with substrates below C12, and shows activity with octanoyl-CoA in vitro (Willis et al., 2011). Although this enzyme generates alcohol from acyl-CoA, the rationale for its inclusion is that there is clear evidence that it has a broad substrate range from octanoyl-CoA (C8) to arachidonoyl-CoA (C20). Furthermore, the C-terminal end shows high sequence homology to the Acr1 enzyme, so the N-terminal region may be the alcohol-forming domain. Therefore, it would be worthwhile to test the effect of removing the portion of the gene coding for the N-terminal region of the polypeptide, with the aim of generating a functional, aldehyde-generating enzyme. A potential problem with this approach is that the enzyme might be inactive or the aldehyde may not be released from the truncated enzyme complex. This enzyme has not been tested for activity against acyl ACP derivatives.
FAR from Marinobacter aquaeolei VT8 (YP_959486) (Hofvander, P., Doan, T. T. P., and Hamberg, M. (2011). A prokaryotic acyl-CoA reductase performing reduction of fatty acyl-CoA to fatty alcohol. FEBS Letters 585, 3538-3543): This fatty acyl CoA reductase (designated FAR) was originally identified as a fatty aldehyde reductase (Wahlen, B. D., Oswald, W. S., Seefeldt, L. C., and Barney, B. M. (2009). Purification, characterization, and potential bacterial wax production role of an NADPH-dependent fatty aldehyde reductase from Marinobacter aquaeolei VT8. Appl Environ Microbiol 75, 2758-2764), but has since been shown to have acyl-CoA reductase activity (Hofvander, P., Doan, T. T. P., and Hamberg, M. (2011). A prokaryotic acyl-CoA reductase performing reduction of fatty acyl-CoA to fatty alcohol. FEBS Letters 585, 3538-3543). It is very similar to the fatty acyl-CoA reductase described above, but it is also known to act on acyl ACP derivatives Activity was observed with C16-CoA up to C20-CoA, but has not been tested with shorter substrates. The enzyme is 513 amino acids long and has the same C-terminal domain associated with aldehyde generation as Acr1. It is possible that this enzyme could also be truncated, which would mean cleaving off the N-terminal region as described previously. It is not clear whether or not FAR and FAcoR are entirely different enzymes, since two separate (and competing) research groups have studied them.
Aldehyde-generating acyl-CoA reductase from Botryococcus braunii (AAB35106) (Wang, X., and Kolattukudy, P. E. (1995). Solubilization and purification of aldehyde-generating fatty acyl-CoA reductase from green alga Botryococcus braunii. FEBS Left 370, 15-18): This enzyme is an aldehyde-generating acyl-CoA reductase from the microalga, Botryococcus braunii. The enzyme has been purified from the wild-type organism and assayed using labeled activated fatty acid, [1-14C]-palmitoyl-CoA. The enzyme was shown to produce the corresponding aldehyde and was NADH-dependent. The substrate range has not been studied and this would need to be addressed. Furthermore, the protein needs to be cloned, expressed and purified in E. coli. Accession number AAB35106 refers to a partial 26 amino acid N-terminal sequence from the purified enzyme. The full protein sequence is not deposited on UNIPROT, BRENDA or NCBl databases. Sequencing of the genome is underway. There might be scope to isolate the gene using primers for the N terminal sequence, but the general lack of information about the enzyme may complicate its exploitation for metabolic engineering.
Thus, a number of acyl-CoA reductases have been identified that are suitable candidates to be tested for reduction of pimeloyl-CoA to pimelic semialdehyde. The enzyme from Acinetobacter calcoaceticus, Acr1, appears to be the best candidate, as it is the best characterized of the enzymes identified even though there is no information on activity with short chain, C-odd substrates. If initial tests turn out to be negative, the enzyme would still be a good target for directed evolution to obtain pimeloyl CoA reduction.
AAR from S. elongatus and its orthologues as well as LuxC are also promising candidates. Although these enzymes operate on relatively long chain fatty acyl CoA substrates, they have not been tested with short chain substrates. Again, directed evolution may provide a promising route to obtain the desired substrate selectivity if the initial tests are negative.
The two enzymes from M. aquaeolei VT8 may also be promising, although some protein engineering is likely to be required to prevent oxidation of the aldehyde. These enzymes are suitable candidates because they are known to act on the shortest chain fatty acyl CoAs out of all the fatty acyl CoA reductases identified. The gene encoding the enzyme from B. braunii has not yet been identified. This makes it the most difficult of the enzymes to work with, but it could be investigated if other options are not successful. Similar enzymes are also known in higher plants (e.g. Pisum sativum) and provide further options for testing, but, again, are not well characterised.
Thus, the above six enzymes have been selected because there are literature reports that they have been prepared, purified (partially of fully) either recombinantly or natively in cellular fractions and assayed in vitro. Their nucleotide and primary amino acid sequences are deposited on the main protein databases BRENDA and UNIPROT, except for the enzyme from Botyrococcus braunii. Results from the studies have been published in peer-reviewed journals. The substrates tested range from octanoyl-CoA (C8) up to arachinadoyl-CoA (C20) and also included acyl-ACP as substrate in the case of AAR from Synechococcus elongates. The corresponding aldehydes are formed as products. However, to date, none of the enzymes have been tested with pimeloyl-CoA or any other C-odd number substrates, presumably because the metabolism of these substrates is invariably assumed to follow the same pattern as the C-even number substrates and, until now, there has been no reason to test them against these substrates. Therefore, it is highly likely that the enzymes will catalyse the reduction of pimeloyl-CoA. Even if pimeloyl CoA is not a substrate, the enzymes would provide a good starting points for directed evolution or targeted protein engineering.
Other candidates amongst the long fatty acyl-CoA reductase for the conversion of pimeloyl-CoA to pimelic acid semialdehyde include, but is not limited to, reductases from the following organisms: Pisum sativum (Vioque et al., 1997. Resolution and purification of an aldehyde-generating and an alcohol-generating fatty acyl-CoA reductase from Pea leaves (Pisum sativum L.), Archives of Biochemistry and Biophysics, 340 (1), 64-72); Vibrio fischeri (P12748) (Boylan et al., 1985. Functional identification of the fatty acid reductase components encoded in the luminescence operon of Vibrio fischeri, Journal of Bacteriology, 163(3), 1186-1190); Brassica oleracea and B. napus (Q39342) (Kolattukudy, 1971. Enzymatic synthesis of fatty alcohols in Brassica oleracea. Archives of Biochemistry and Biophysics, 142(2), 701-709); Clostridium butyricum (Day et al., 1978. Partial purification and properties of acyl-CoA reductase from Clostridium butyricum, Archives of Biochemistry and Biophysics, 190(1), 322-331); Anas platyrhynchos (Ishige, T.; Tani, A.; Takabe, K.; Kawasaki, K.; Sakai, Y.; Kato, N. Wax Ester Production from n-Alkanes by Acinetobacter sp. Strain M-1: Ultrastructure of Cellular Inclusions and Role of Acyl Coenzyme A Reductase. Appl Environ Microbiol 2002, 68, 1192-1195); Arabidopsis thaliana (Doan, T. T. P.; Carlsson, A. S.; Bamberg, M.; Bülow, L.; Stymne, S.; Olsson, P. Functional expression of five Arabidopsis fatty acyl-CoA reductase genes in Escherichia coli. Journal of plant physiology 2009, 166, 787-796; Hooks, M. A.; Kellas, F.; Graham, I. A. Long-chain acyl-CoA oxidases of Arabidopsis. Plant J. 1999, 20, 1-13); Homo sapiens, R. P.; Wang, Y.; Mohsen, A. W.; He, M.; Vockley, J.; Kim, J. J. P. Structural basis for substrate fatty acyl chain specificity: crystal structure of human very-long-chain acyl-CoA dehydrogenase. J Biol Chem 2008, 283, 9435-9443); Simmondsia chinensis (Q9XGY7), and Mus musculus (Q7TNT2, Q922J9).
3.1.4 Conversion of Pimelic Acid to Pimelic Acid Semialdehyde by Carboxylaic Acid Reductases (EC 1.2.99.-)
3.1.4.1 Selection, Cloning, and Expression of Carboxylic Acid Reducatse Targets
Enzyme targets for the reduction of pimelic acid into pimelic acid semialdehyde were selected from the carboxylic acid reductase family (EC 1.2.99.-, such as EC 1.2.99.6). In particular, the Nocardia carboxylic acid reducatse is a monomeric enzyme that displays a large substrate specificity towards aromatic substrates and was successfully cloned and expressed in E. coli (Nocardia sp. Carboxylic acid reductase: Cloning, expression, and characterization of a new aldehyde oxidoreductase family: He et al. Appl. Environ. Microbiol. 2004, 70, 1874-1881). The enzyme was therefore a good candidate for an initial screening to monitor conversion of pimelic acid to pimelic acid semialdehyde.
The Nocardia sp. carboxylic acid reductase (CAR) gene (GeneBank AY495697) was previously cloned into the pHAT-10 vector (Clontech). The E. coli strain BL-21 (DE3) RP 1pPV2-85 harbouring the carboxylic acid reductase from Nocardia species was used (He et al. (2004). Expression study was then initiated using standard conditions (1 mM IPTG, 37° C. pre- and post-induction temperatures) and was expressed in E. coli under IPTG induction according to the previously reported protocol, and scaled up to produce enough protein for the activity assay.
3.1.4.2 Cell Lysis and SDS-PAGE Analysis
The cell pellet was lysed to provide material for the activity assays. Due to the large scale glass bead lysis in conjunction with lysozyme treatment was employed to break the cells. The cell pellet from the 4 hour post-induction sample was re-suspended in bead lysis buffer consisting of 0.1 mM Tris, 1 mg/ml Pepstatin A and 200 mM PMSF protease inhibitors (161 μL of the mixture should be used for the lysis of the cell pellet from 1 mL of culture at an OD600 of 5) supplemented with 1.5 mg/mL lysozyme. Acid washed 212-300 μm glass beads (0.4 g per 1 mL of lysis buffer) were added to each sample, and lysed by vortexing (cycles of 30 s vortex and 30 s on ice for 10 cycles). The lysis reaction was then centrifuged at 13000 rpm for 20 min. The soluble fraction was transferred to a new tube and the insoluble fraction re-suspended in the same volume of water as the volume of lysis buffer previously used. 20 μl of each fraction was mixed with 80 μl SDS-Sample buffer (SDS-Loading Buffer, 9% DTT and water) and the mixture was heated in a heatblock for 5 minutes at 95° C. 20 μl of each SDS-sample preparation was then loaded on SDS-PAGE 4-20% Tricene gels to analyze the protein content of the soluble and insoluble fractions (FIG. 12).
Protein bands at the expected size (128 kDa) were clearly visible in the soluble and insoluble fractions (FIG. 1: Lanes 3 and 4 respectively) after 4 h post-induction. A larger amount of expressed proteins was observed in the soluble fractions (FIG. 12: Lane 3) showing that a large fraction of the protein was expressed in soluble form.
3.1.4.3 Activity Assays
The activity assay was based on spectrophotometric detection of CAR activity towards sodium benzoate as positive control and sodium pimelate. The conditions for the assay were taken from Applied and Environmental Microbiology 2004, 70, p 1874-1881.
The following stock solutions were prepared: 50 mM sodium benzoate, 50 mM sodium pimelate, 100 mM MgCl2, 50 mM Tris.HCl pH7.5 with 1 mM DTT, 1 mM EDTA in 10 v/v % glycerol buffer, 10 mM ATP, 1.5 mM NADPH (reduced form).
In a quartz cuvette the following reagents were added: 100 μL MgCl2, 100 μL ATP, 100 μl NADPH, 2004 Tris.HCl buffer. The absorbance at 340 nm was measured and recorded and 100 μL of CAR cell free extract was added. The absorbance was monitored and recorded. After 2 minutes 100 μL of 100 mM of either sodium benzoate or sodium pimelate was added, and the absorbance was again monitored and recorded. The absorbance monitored over time was subtracted from the initial measurement. The best line fit for the data was plotted to generate a gradient of the rate of change in absorbance at 340 nm and is presented in FIG. 13 and Table 2 below to determine the relative rate of change in absorbance compared to that of benzoic acid:










TABLE 2






gradient of
Adjusted for
Relative rate %


Substrate
trend line
background
compared to benzoate


















sodium benzoate
0.0141
0.00133
 100%


sodium pimelate
0.0076
0.0068
51.1%









Thus, CAR from Nocardia catalysed the reduction of pimelic acid to pimelic acid semialdehyde with >50% of the activity for benzoic acid. Other suitable enzymes for the reduction of pimelic acid from EC 1.2.99.6 include for example that of Streptomyces griseus (Suzuki et al., 2007. GriC and GriD constitute a carboxylic acid reductase involved in grixazone biosynthesis in Streptomyces griseus. J Antibiot (Tokyo). Jun; 60(6):380-7).
3.1.5 Conversion of Pimeloyl-CoA to Pimelic Acid by Thioester Hydrolases (EC 3.2.1.-), Pimeloyl-CoA Ligases (EC 6.2.1.-) such as EC 6.2.1.14 and 6.2.1.23, or CoA Transferases, (EC 2.8.3.-) and Pimeloyl-[acp] to Pimelic Acid by oleoyl-[acp] hydrolase (EC 3.1.2.14)
Enzymes that are able to catalyse the hydrolysis or transfer of CoASH include thioester hydrolases from EC 3.2.1.-, such as EC 3.1.2.2, EC 3.1.2.3, EC 3.1.2.18; 3.1.2.19, 3.1.2.20 EC 3.1.2.21, EC 3.1.2.27, acid-thiol ligases from EC 6.2.1.-, such as EC 6.2.1.3, EC 6.2.1.14, EC 6.2.1.23 and CoA transferases from EC 2.8.3.-, such as EC 2.8.3.12 and EC 2.8.3.13. Amongst those three families, thioesterases present the best candidates for the hydrolysis of pimeloyl-CoA due to the large number of characterized enzymes and their broad substrate specificity in terms of chain length (C-3 to C-26) and in terms of functional groups (Dicarboxylyl-CoA substrate).
3.1.5.1 Acid-thiol Ligases
Acid thiol ligases catalyse the formation of carbon-sulfur bonds with concomitant hydrolysis of adenosine triphosphate (ATP). Hydrolysis of Acyl-CoA would therefore require the generation of ATP during the acid thiol ligase-catalysed reaction which is thermodynamically disfavored compared to the reverse reaction:




However, these enzymes are still useful and several CoA ligases are known to act on pimeloyl-CoA:























Over-









expres-
Purifi-


Enzyme
EC
Source
Reaction
Gene
Size
sion
cation






















bioW
6.2.1.14
Lysinibacillus
pimelic acid →
Yes
28
Yes,
Yes,


(P22822)
6-carboxy-
(Bacillus
pimeloyl-CoA

kDA
E. coli
homo-



hexanoate--
sphaericus)




geneity



CoA ligase









AMP forming









(pimeloyl-CoA









synthase)








pauA
6.2.1.n
Pseudomonas
pimelic acid →
Yes
74
Yes,
Yes,


(AJ012480)
catabolic
mendocina35
pimeloyl-CoA

kDa
E. coli
homo-



pimeloyl-CoA

adipic acid →



geneity



synthase

adipoyl-CoA









azelaic acid →









azelaoyl-CoA






??
6.2.1.n
Bacillus
pimelic acid →
No
?
No
Yes, 34-



pimeloyl-CoA
megaterium
pimeloyl-CoA



fold



synthetase








??
pimeloyl-CoA
Lavandula vera
pimelic acid →
No
?
No
No



synthase
L.
pimeloyl-CoA






??
plant soluble
Pisum sativum
pimelic acid →
No
53
No
No



acyl-CoA
L.
pimeloyl-CoA

kDa





synthetase

azelaic acid →









azelaoyl-CoA






??
plant
Pisum sativum
pimelic acid →
No
?
No
No



peroxisomal
L.
pimeloyl-CoA







acyl-CoA









synthetase








??
6.2.1.23 -
Rattus
C5-C16
No
?
No
No



microsomal
norvegicus
dicarboxylates → 







dicarboxylate-

CoA esters







CoA ligase








??
6.2.1.23
LP-1 strain
pimelic acid →
No
?
No
No



pimeloyl-CoA

pimeloyl-CoA







synthetase









BioW (Uniprot:P22822)—from Lysinibacillus sphaericus (Bacillus sphaericus)

Pimelic acid CoA synthase (6-carboxyhexanoate-CoA ligase) was discovered in Bacillus sphaericus using cell free extracts. It is involved in the biotin biosynthesis pathway. The enzyme activity was determined indirectly by a reaction coupled with 7-keto-8-aminopelargonic acid synthetase and microbiological assay using Saccharomyces cerevisiae[1]. The gene encoding pimelic acid CoA synthase (bioW) was identified together with 7-keto-8-aminopelargonic acid synthetase (bioF) by complementation studies of E. coli mutants with the library carrying sequences from the B. sphaericus genome [Gloeckler R, Ohsawa I, Speck D, Ledoux C, Bernard S, Zinsius M, Villeval D, Kisou T, Kamogawa K, Lemoine Y. (1990) Cloning and characterization of the Bacillus sphaericus genes controlling the bioconversion of pimelate into dethiobiotin. Gene. 87:63-70]. BioW was overexpressed in E. coli and purified to homogeneity [Ploux O, Soularue P, Marquet A, Gloeckler R, Lemoine Y. (1992) Investigation of the first step of biotin biosynthesis in Bacillus sphaericus. Purification and characterization of the pimeloyl-CoA synthase, and uptake of pimelate. Biochem J. 287: 685-690]. The enzyme was active in the presence of disodium pimelate, ATP, CoASH and MgCl2. The products of the reaction were pimeloyl-CoA and AMP, no ADP was detected. The enzyme was specific only for ATP and pimelate. Other nucleotides (such as GTP, AMP) and alternative substrates (succinate, glutarate, adipate, suberate) were not accepted.
PauA (GenBank: AJ012480.1) from Pseudomonas mendocina 35
Catabolic pimeloyl-CoA ligase, pauA, is involved in degradation of dicarboxylic acids (C6-C10) in Pseudomonas mendocina 35 [Binieda A, Fuhrmann M, Lehner B, Rey-Berthod C, Frutiger-Hughes S, Hughes G, Shaw N M. (1999) Purification, characterization, DNA sequence and cloning of a pimeloyl-CoA synthetase from Pseudomonas mendocina 35. Biochem J. 340:793-801]. The enzyme activates dicarboxylic acids which are subsequently metabolized via the beta-oxidation pathway. The enzyme was purified to homogeneity and the partial amino acid sequence was determined. PauA showed a broader substrate range than bioW, and accepts pimelate (100% relative activity), adipate (72%) and azelate (18%). The enzyme was between one and two orders of magnitude more active than bioW involved in the biotin biosynthesis pathways. The gene pauA was identified and the ligase was successfully overexpressed in E. coli. 
Pimeloyl-CoA Synthetase from Bacillus megaterium 
The enzyme was purified about 34-fold with 79% recovery [Izumi Y, Morita H, Tani Y, Ogata K. (1974) The pimeloyl-CoA synthetase responsible for the first step in biotin biosynthesis by microorganisms. Agr. Biol. Chem. 38, 2257-2262]. The reaction required pimelate, ATP, CoASH and MgCl2. The enzyme was specific towards pimelate only, and other dicarboxylic acids were not accepted. Interestingly, ATP could be replaced with ADP, suggesting that pyrophosphate cleavage is not essential. The amino acid and nucleotide sequences are not known. However three complete genomes of Bacillus megaterium have been published since 1974. Therefore, a BLAST search for bioW homologs was undertaken. Unfortunately, this did not show any matches.
Plant Pimeloyl-CoA Synthase from Lavandula vera L.
Pimeloyl-CoA synthase activity in lavender cell cultures has been described [6]. Although [3H]-pimelic acid was found to be a precursor in biotin biosynthesis, there are no data available about the enzyme or the gene.
Plant Soluble acyl-CoA Synthetase from Pisum sativum L.
The activity was found in the soluble fraction of pea protein extracts [7]. The enzyme required ATP/Mg2+ and CoASH. The molecular weight of the ligase was determined by western blot technique using polyclonal antibodies against the ligase from Lysinibacillus sphaericus. The enzyme accepted pimelic acid as well as azelaic acid, but not nonanoic acid. GTP could be used instead of ATP, but no reaction was observed for ADP. The gene encoding the soluble pimeloyl-CoA synthetase was not identified.
Plant Peroxisomal acyl-CoA Synthetase from Pisum sativum L.
The enzyme was located in the peroxisomal protein fraction [GerblingH, AxiotisS, Douce R. (1994) A new acyl-CoA synthetase, located in higher plant cytosol. J Plant Physiol. 143: 561-564.]. Pimelic acid was activated to pimeloyl-CoA and subsequently degraded to acetyl-CoA and malonyl-CoA by the beta-oxidation pathway. The substrate range of this enzyme was not tested. It showed a higher pH-optimum than soluble acyl-CoA synthetase from the same organism.
Dicarboxylate-CoA Ligase from Rattus norvegicus 
Dicarboxylic acids (C5-C16) were converted into their CoA esters by a dicarboxylyl-CoA synthetase from the microsomal protein fraction from a rat liver [Vamecq J, de Hoffmann E, Van Hoof F. (1985) The microsomal dicarboxylyl-CoA synthetase. Biochem J. 230:683-693.]. The enzyme uses ATP, but not GTP. The reaction is inhibited by its products, and AMP is more inhibitory than pyrophosphate. The enzyme showed the highest activity for the C12 substrate. In some assays of dicarboxylyl-CoA synthetase, the plateau of CoA consumption was followed by CoA release. This is an important observation because it suggests that the reaction might be reversible. However, this suggestion should be treated with some caution, because the protein sample may have been contaminated with CoA thioesterase. Whilst this enzyme may be promising, BLAST searching of the R. norvegicus genome sequence did not reveal any bioW or pauA homologues. An alternative approach would be needed to identify the gene, for example, enzyme purification, N-terminal sequencing, primer design and PCR amplification.
Pimeloyl-CoA Synthetase from Unidentified Bacterium, LP-1 Strain
The activity was found in environmental cultures of denitrifying bacteria from activated sludge enriched to grow on sodium nitrate and pimelate [Gallus C, Schink B. (1994) Anaerobic degradation of pimelate by newly isolated denitrifying bacteria. Microbiology. 140: 409-416.]. The enzyme was active in the presence of ATP and Mg2+. The product of the reaction was AMP rather than ADP. The enzyme did not accept benzoic acid.
The CoA ligases have not been tested rigorously or systematically for reversibility. No crystal structures are available, so the active site structure is not known. Therefore, it is not clear whether AMP, pyrophosphate or magnesium ions would be needed for the reverse reaction, and in vitro assays should be done in the presence and absence of combinations of these cofactors. Of course, the ultimate goal is to obtain the reverse reaction in whole cells, and this might be more challenging. The later reactions in the pathway will, of course, pull the equilibrium in the thiolytic direction. Nevertheless, this might be a difficult reaction to reverse because the hydrolysis of ATP and subsequent hydrolysis of pyrophosphate make the forward reaction exergonic. Therefore, it is important to measure the effect of different ATP:AMP ratios on reversibility of the reaction in vitro before attempting to engineer the cells. If the ATP:AMP ratio is critical, it might be necessary to manipulate the cellular energy charge to make the intracellular ATP concentration low enough to allow the reverse reaction to proceed. This, in turn, may cause further difficulties with obtaining good productivity, since it might be necessary to use ATP synthase inhibitors or uncouplers to achieve low enough ATP concentrations. In principle, none of these problems is insurmountable, but development of the engineered biocatalysts might become complicated. Therefore, simpler enzyme systems such as thioesterases were investigated as a higher priority.
3.1.5.2 CoA Transferases (EC 2.8.3.-)
CoA transferases are less attractive candidates than thioesterases, due to either a narrow substrate specificity or a lack of gene/protein characterization such as for the succinate-hydroxymethylglutarate CoA transferase despite showing activity towards the C-6 derivative of pimeloyl-CoA, adipyl-CoA (EC 2.8.3.13—Substrate specificity of a dicarboxyl-CoA:dicarboxylic acid coenzyme A transferase from rat liver mitochondria: Deana et al. Biochem Int. 1992, 26, 767-773). Some enzymes from this family may still be useful, since it had been possible to change the activity of the enzyme glutaconate CoA transferase from Acidaminococcus fermentans (EC 2.8.3.12-Glutaconate CoA-transferase from Acidaminococcus fermentans: Buckel et al. Eur. J. Biochem. 1981, 118, 315-321) from a CoA transferase to CoA esterase by site-directed mutagenesis (Mack M, Buckel W. (1997) Conversion of glutaconate CoA-transferase from Acidaminococcus fermentans into an acyl-CoA hydrolase by site-directed mutagenesis. FEBS Lett. 405: 209-212). This enzyme was successfully expressed in E. coli and used for enzymatic biosynthesis of glutaconyl-CoA, 3-methylglutaconyl-CoA, butynedioyl-CoA, 2-hydroxyadpioyl-CoA, oxalocrotonyl-CoA and muconyl-CoA (Parthasarthy A, Pierik A, Kahnt J, Zelder O, Buckel W. (2011) Substrate specificity of 2-hydroxyglutaryl-CoA dehydratase from Clostiridium symbiosum: Toward a bio-based production of adipic acid. Biochemistry. 50: 3540-35500). The crystal structure of GctAB was also published (Jacob U, Mack M, Clausen T, Huber R, Buckel W, Messerschmidt A., (1997) Glutaconate CoA-transferase from Acidaminococcus fermentans: the crystal structure reveals homology with other CoA-transferases. Structure. 5:415-426). This transferase binds the terminal carboxylate anion via several hydrogen bonds to serine residues, which may adjust to the different chain lengths. The CoA transferase from Rattus norvegious (Succinate-hydroxymethylglutarate CoA-transferase EC 2.8.3.13) is also a good candidate, since it accepts adipyl-CoA as substrate, with higher affinity than that observed for succinyl-CoA, malonyl-CoA, glutaryl-CoA (Substrate specificity of a dicarboxyl-CoA:dicarboxylic acid coenzyme A transferase from rat liver mitochondria (Deana Biochem Int. 1992, 26, 767-773).
3.1.5.3 Thioester Hydrolases (EC 2.3.1.-)
3.1.5.3.1 Selection of Suitable Enzymes
Thioesterases are hydrolytic enzymes that catalyze the hydrolysis of thioesters:




There are very large numbers of thioesterases listed in the databases, but it seems that only two thioesterases (ACOT8 and ACOT4) have been tested for activity towards dicarboxylyl-mono-CoA esters.























Over-








Size
expres-
Purifi-


Enzyme
EC
Source
Substrates
Gene
(kDa)
sion
cation






















ACOT8
3.1.2.27
Mus
Broad range
Yes
50
Yes
Yes,


(PTE-2)

musculus
straight-CoA,



his-tag





bile acids CoA



fusion,





and branched-



homoge-





chain acyl-CoA



neity


ACOT5
3.1.2.2
Mus
Medium chain
Yes
46.6
Yes
Yes,


(PTE-Ic)
palmitoyl-CoA 
musculus
acyl-CoA



his-tag



hydrolase





fusion,









homoge-









neity


ACOT3
3.1.2.2
Mus
Long chain
Yes
47.4
Yes
Yes,


(PTE-Ia)
palmitoyl-CoA
musculus
acyl-CoAs



his-tag



hydrolase





fusion,









homoge-









neity


ACOT4
3.1.2.3
Mus
Succinyl-CoA
Yes
36
Yes
Yes,


(PTE-1b)
Succinyl-CoA
musculus
and glutaryl-

(active

his-tag



thioester-ase

CoA ONLY.

as

fusion,







dimer)

homoge-









neity









ACOT8 Peroxisomal acyl-CoA Thioesterase 8 (Formerly PTE-2) from Mus musculus 

ACOT8 is a homologue of human PET1 thioesterase. The enzyme was overexpressed as a His-Tag fusion protein in E. coli and purified to homogeneity using HisTrap column chromatography [Westin M A, Hunt M C, Alexson S E. (2005) The identification of a succinyl-CoA thioesterase suggests a novel pathway for succinate production in peroxisomes. J Biol. Chem. 280: 38125-38132]. The activity was inhibited at substrate concentrations >5-10 μM for long-chain acyl-CoAs, but addition of BSA prevented inhibition. The substrate range of the thioesterase was tested using saturated and unsaturated straight-chain acyl-CoAs (C2-C20). The highest activity was for C10-C18, bile acids (trihydroxycoprostanoyl-CoA, choloyl-CoA and chenodeoxycholoyl-CoA and branched-chain acyl-CoAs. Km values for most of the substrates tested were rather low, strongly suggesting that ACOT8 has very broad substrate specificity and can accept most of them. ACOT8 was strongly inhibited by CoASH with an IC50 of 10-15 μM. ACOT8 was also tested for activity towards dicarboxylyl-mono-CoA derivatives and preferentially hydrolyzed the longer-chain substrates (activity increase with C chain length from C3 to C12) [Hunt M C, Solaas K, Kase B F, Alexson S E. (2002) Characterization of an acyl-coA thioesterase that functions as a major regulator of peroxisomal lipid metabolism. J Biol. Chem. 277: 1128-1138].
ACOT3 (Formerly PTE-1a) from Mus musculus 
ACOT3 was expressed in E. coli and purified to homogeneity [19]. The enzyme showed activity for monocarboxylic acid esters from C8 to C26, with the highest activity towards longer chain substrates (C16). The enzyme did not accept bile acid esters. There was no inhibition with free CoASH. Dicarboxylic acid esters were not tested.
ACOT5 (Formerly PTE-1c) from Mus musculus 
ACOT5 was expressed in E. coli and purified to homogeneity [Westin M A, Alexson S E, Hunt M C. (2004) Molecular cloning and characterization of two mouse peroxisome proliferator-activated receptor alpha (PPARalpha)-regulated peroxisomal acyl-CoA thioesterases. J Biol Chem. 279: 21841-21848]. The enzyme showed activity for monocarboxylic acid esters from C6 to C20, with the highest activity towards medium chain substrates (C10). The enzyme did not accept bile acid esters. There was no inhibition with free CoASH. Dicarboxylic acid esters were not tested.
ACOT4 Peroxisomal acyl-CoA Thioesterase 4 (Formerly PTE-1b) from Mus musculus 
ACOT4 was expressed in E. coli and purified to homogeneity [18]. The enzyme showed a narrow substrate range, accepting succinyl-CoA and glutaryl-CoA. The reaction was not inhibited by CoASH at concentrations up to 500 μM.
ACOT8, ACOT5 and ACOT3 are thus excellent candidates for the hydrolysis of dicarboxylyl-CoAs and other acyl-CoAs that are involved in the pimelic acid biosynthesis pathway.
3.1.5.3.2 Cloning, Expression and Biotransformations with Selected Thioesterases
Thioesterases from Mus musculus Acot8 (WT mRNA sequence GeneBank NM_133240; mRNA fragment 65-1027) and the Haemophilus influenzae YciA (WT gene sequence (GeneBank L42023 fragment 878596-879060) were selected as examples for the conversion of pimeloyl-CoA to pimelic acid, due their specificity towards dicarboxylyl-CoA substrates (The identification of a succinyl-CoA thioesterase suggests a novel pathway for succinate production in peroxisomes: Westin J. et al. Biol. Chem. 2005, 280, 38125-38132; Divergence of function in the hot dog fold enzyme superfamily—the bacterial thioesterase YciA: Zhuang et al. Biochemistry 2008, 47, 2789-2796). Both genes were identified from their respective host genome and successfully cloned and expressed in Escherichia coli (Characterization of an acyl-CoA thioesterase that functions as a major regulator of peroxisomal lipid metabolism: Hunt et al. J. Biol. Chem. 277, 1128-1138; Divergence of function in the hot dog fold enzyme superfamily—the bacterial thioesterase YciA: Zhuang et al. Biochemistry 2008, 47, 2789-2796).
Both genes were selected as wild-type sequences for the construction of the corresponding E. coli expression vectors and used to transform E. coli BL21 (DE3). Expression of Haemophilus influenzae YciA thioesterase was achieved in E. coli, (FIG. 14h) but not of the Mus musculus Acot8 thioesterase. A protein band at the expected size (17 kDa) was clearly detected after IPTG induction in the soluble fraction (Lanes 2 to 3) and in the insoluble fraction (Lanes 6 and 7). No corresponding protein was observed in the negative control experiment (Lanes 4 and 8) suggesting that the expected 17 kDa Haemophilus influenzae YciA thioesterase protein was successfully expressed in E. coli from the assembly construct I8. Soluble expression of the YciA protein appeared to increase over time between 4 h and 24 h post-induction incubation (Lanes 2 and 3) whereas insoluble expression appeared to decrease in the same period (Lanes 6 and 7). Therefore, the 24 h soluble sample seemed to be the best candidate for monitoring activity of the Haemophilus influenzae YciA thioesterase.
Since no expression of the Mus musculus Acot8 protein was detected in E. coli using the pET21-a/IPTG expression system, Saccharomyces cerevisiae was selected as an alternative system to produce and test the thioesterase enzyme. Transformation with the S. cerevisiae expression vector was carried out and expression from the constitutive promoter ADH1p was monitored on SDS-PAGE after cell lysis.
3.1.6 Conversion of Pimelic Acid Semialdehyde to 7-aminoheptanoic Acid and Conversion of α-ketosuberate to α-aminosuberate by Aminotransferases (EC 2.6.1.19; EC 2.6.1.39)
Transaminases or aminotransferases are enzymes that catalyse the reaction between an amino acid and a keto acid. This reaction involves removing the amino group from the amino donor, leaving behind an α-keto acid, and transferring it to the acceptor α-keto acid and converting it into an amino acid. They are important enzymes in the synthesis of amino acids and are ubiquitous throughout nature. Many of these enzymes contain pyridoxal-phosphate (PLP) as cofactor. These enzymes belong to a large diverse family covering a wide range of cellular functions, using a wide range of substrates.
3.1.6.1 Conversion of Pimelic Acid Semialdehyde to 7-aminoheptanoic Acid
A number of candidates, identified by literature searching, BLAST searching and protein database searching are suitable enzymes for to conversion of pimelic acid semialdehyde to 7-aminoheptanoic acid.














Enzyme






Name/EC
Accession

Gene
Protein


No.
number
Source
available
purified







EC 2.6.1.19
YP_001823341.1
Streptomyces
Yes
Yes




griseus




LysN
Q72LL6
Thermus
Yes
Yes




thermophillus




AADaT
Q64602
Rattus norvegicus
Yes
Yes









EC 2.6.1.19

4-Aminobutyrate Transaminase from Streptomyces griseus 

This enzyme was first studied in 1985 and was found to catalyse the reaction 4-aminobutanoate+2-oxoglutarate→4-oxobutanoate+glutamate.
The enzyme has a relatively wide substrate range, including 6-aminohexanoate and 7-aminoheptanoate, using 2-oxoglutatarate as the amino acceptor, and forming the corresponding semialdehydes (Yonaha, K., K. Suzuki, and S. Toyama, 4-Aminobutyrate:2-oxoglutarate aminotransferase of Streptomyces griseus: purification and properties. Eur J Biochem, 1985. 146(1): p. 101-6). Although this is very promising, the reversibility of these reactions has not been tested. Therefore, the reverse reactions are tested in vitro, using glutamate as the amino donor, since this would provide 7-aminoheptanoic acid from 7-oxoheptanoate. The enzyme was purified in S. griseus IFO 3102 (S. griseus subsp. griseus) and was found to be 100 kDa, consisting of two identical subunits approx. 50 kDa each. The cofactor is pyridoxal 5′-phosphate. A protein is deposited on the Pubmed database (Table 1). The gene encoding this (SGR_1829), annotated as a putative 4-aminotransferase, is present in the genome sequence of S. griseus IFO 13350, which is closely related to IFO 3102. Although not clear, it is highly likely that this protein is a close homologue of the enzyme described and studied (Yonaha, K., K. Suzuki, and S. Toyama, 4-Aminobutyrate:2-oxoglutarate aminotransferase of Streptomyces griseus: purification and properties. Eur J Biochem, 1985. 146(1): p. 101-6). In light of the substrate range data available, this protein is a very good candidate for testing as a suitable aminotransferase enzyme.

EC 2.6.1.39

Aminoadipate Transaminase from Thermus thermophilus (Q72LL6)

This is an enzyme with homology to the alpha-aminoadipate aminotransferases (AAAAT) from mammals and is thought to be involved in lysine synthesis in the bacterium Thermus thermophilus HB27 [2, 3]. Kinetic data are available for substrates such as 2-oxoadipate, 2-oxoisocaproate, alpha-aminoadipate and even aromatic amino acids [3]. The protein has been expressed and purified in E. coli and was found to exist in vitro mainly as a homodimer, with each subunit  ̃44 kDa in size (Miyazaki, T., et al., alpha-Aminoadipate aminotransferase from an extremely thermophilic bacterium, Thermus thermophilus. Microbiology, 2004. 150(Pt 7): p. 2327-34). The broad substrate specificity, its prokaryotic origin and the availability of the encoding gene suggest that it may be a good candidate for testing with 1. It is a very well studied enzyme and its crystal structure is available (PDB ID: 2ZP7), which offers mechanistic insights into substrate specificity (Ouchi, T., et al., Dual roles of a conserved pair, Arg23 and Ser20, in recognition of multiple substrates in alpha-aminoadipate aminotransferase from Thermus thermophilus. Biochem Biophys Res Commun, 2009. 388(1): p. 21-7; Tomita, T., et al., Mechanism for multiple-substrates recognition of alpha-aminoadipate aminotransferase from Thermus thermophilus. Proteins, 2009. 75(2): p. 348-59).
Aminoadipate Aminotransferase from Rattus norvegicus (Q64602)
This enzyme is similar to the enzyme from Thermus thermophilus described previously. It is annotated as a kynurenine/aminoadipate aminotransferase, although there is some evidence to suggest that two distinct proteins carry out these reactions (Mawal, M. R. and D. R. Deshmukh, Alpha-aminoadipate and kynurenine aminotransferase activities from rat kidney. Evidence for separate identity. J Biol Chem, 1991. 266(4): p. 2573-5). The protein has been purified from rat kidney and expressed in human embryonic kidney fibroblast cells and was found to be around 100 kDa in size. The enzyme can accept 2-oxoadipate as a substrate. EarIier studies (presumably on the same enzyme) indicate that it is able to use DL-2-aminopimelic acid as an amino donor, with 2-oxoglutarate as acceptor in a reaction that is apparently reversible (Deshmukh, D. R. and S. M. Mungre, Purification and properties of 2-aminoadipate: 2-oxoglutarate aminotransferase from bovine kidney. Biochem J, 1989. 261(3): p. 761-8). The same paper indicated that pimelic acid may be an inhibitor of activity with a 30% reduction in activity in the presence of pimelic acid.
The above three enzymes should be suitable for the final transamination to yield 7-aminoheptanoic acid. The enzyme from S. griseus is a good candidate and the process of cloning, expression and purification would not be particularly difficult. The same is true of LysN from T. thermophiles, which seems to have a broad substrate range. The enzyme from Rattus norvegicus would be more challenging but activity data suggest that this enzyme may be able to use the specific substrates required.
3.1.6.2 Expression of Selected Aminotransferases
Two genes were selected for the conversion of both pimelic acid semialdehyde to 7-aminoheptanoic acid, and the conversion of α-ketosuberate to α-aminosuberate: (1) IlvE-Omega Vf fusion (SEQ ID 1 and 2) and (2) IlvE-Ad optimized omega fusion (SEQ ID 3 and 4). These genes were prepared in plasmids that incorporate fusion of the omega aminotransferase with the 5′-end of the branched chain amino transferase IlvE, which previously showed high expression level in E. coli (See, FIG. 23 and FIG. 24). It was demonstrated that introduction of the IlvE fragment increases significantly the expression of the aminotransferase genes. Another heat induced plasmid containing a branched chain aminotransferase gene with the IlvE fragment was also tested (ING66) in the activity assays.
A further 5 genes (Bacillus weihenstephanensis KBAB4, Pseudomonas aeruginosa (gi9951072), Bacillus subtilis (gi16078032), Pseudomonas syringae class III, Rhodobacter sphaeroides class III) were selected (DSM patent (Preparation of 6-aminocaproic acid from 5-formyl valeric acid: DSM—US2011-0171699 A1 patent). These enzymes showed some activity in the conversion of α-keto pimelic acid into α-amino pimelic acid and may also be active in the conversion of pimelic acid semialdehyde into 7-amino heptanoic acid. (See, SEQ ID 5-14).
SDS-PAGE analysis of IlvE-Omega Vf fusion (pING2022) (FIG. 23) and IlvE-Ad optimized omega fusion (pING2030) (FIG. 24) proteins expressed in E. coli BL21 as before. A clear band of the expected size is observed in both the IlvE-Omega Vf fusion (pING2022) (FIG. 15, Lanes 5 and 6) and IlvE-Ad optimized omega fusion (pING2030) (FIG. 15, Lanes 8 and 9) proteins. There is no corresponding band in the negative control, confirming the expression of the IlvE-Omega Vf fusion and the IlvE-Ad optimized omega fusion proteins.
Activity assay of IlvE-Omega Vf Fusion (pING2022) and IlvE-Ad Optimized Omega Fusion (pING2030) Aminotransferase Proteins
Recombinant Vf aminotransferase was used to assay for activity on 7-aminoheptanoic acid. Three biotransformations were prepared examining the effect of enzyme loading on conversion of 7-aminoheptanoic acid and sodium pyruvate to L-alanine. Detection of L-alanine in the biotransformation would provide positive evidence for the desired aminotransferase specificity on 7-aminoheptanoic acid. The reaction scheme depicting aminotransferase conversion of 7-aminoheptanoic acid to pimelic acid semialdehyde is depicted below:.




The three biotransformations (3 ml volume) contained 50 mM sodium pyruvate and 10 mM 7-aminoheptanoic acid. The reactions were held in a 30° C. orbital incubator and aliquots removed periodically from the biotransformations for analysis.














sodium
7-aminoheptanoic
Enzyme loading


Sample ID
pyruvate/mM
acid/mM
v/v %







rc0212-40-1
50
10
0.33


rc0212-40-2
50
10
0.66


rc0212-40-3
50
10
1.67









The aliquots (1 ml) were removed from the biotransformations and heat to 95° C. for 5 minutes to precipitate soluble protein. The sample was subsequently centrifuged and the supernatant filtered through a 0.2 micron filter prior to HPLC analysis. The HPLC analysis used a precolumn derivatisation method based on chemical adduct formation with beta-mercaptoethanol and orthophthaldehyde. External standards of L-alanine and 7-aminoheptanoic acid were used to determine the concentration of 7-aminoheptanoic acid and L-alanine in the biotransformations.
The results (FIG. 16) clearly show the formation of L-alanine in the biotransformation providing compelling evidence for aminotransferase activity and specificity with Vf aminotransferase. The 7-aminoheptanoic acid concentration decreases over time which is consistent with the expected aminotransferase activity. The rate of 7-aminoheptanoic acid increases with increased concentration of enzyme which is again consistent with expected transaminase activity. The amount of L-alanine formed is not matched by the 7-aminoheptanoic consumed, this could be caused by alternative biochemical degradation of the L-alanine formed by other non-aminotransferase enzymes present in the E. coli extract.
A further examination of the aminotransferases was performed to assess for activity towards 2-aminosuberate.




An aminotransferase conversion of L-2-aminosuberic acid to 2-ketosuberic acid provides an opportunity to modulate biotransformations.
Six biotransformations were carried out examining pING 2022, pING2030 and ING66 (Ilve branched chain aminotransferase, E.C.2.6.1.42, construct already in strain collection). Each biotransformation contained 10 mM DL-2-aminosuberic acid, 50 mM sodium pyruvate and high or low loading of cell free extract (CFE) as indicated below, N.B. ING 66 used as whole cells:
















whole cell





equivalents



lab book ID
aminotransferase
g/L



















rc0212-44-5
pING2022
5



rc0212-44-6
pING2030
5



rc0212-44-7
pING2022
20



rc0212-44-8
pING2030
20



rc0212-46-1
ING66
25



rc0212-46-2
ING66
5









The six biotransformations (3 ml volume) were held in a 30° C. orbital incubator and aliquots removed periodically from the biotransformations for analysis. The aliquots (1 ml) were removed from the biotransformations and heat to 95° C. for 5 minutes to precipitate soluble protein. The sample was subsequently centrifuged and the supernatant filtered through a 0.2 micron filter prior to HPLC analysis. The HPLC analysis used a precolumn derivatisation method based on chemical adduct formation with Boc-cysteine and orthophthaldehyde. External standards of DL-2-aminosuberic acid and L-alanine were used to determine the retention times of the 2-aminosuberic acid enantiomers.
The results indicate a reduction in the L-2-aminosuberic acid concentration and an enantioenrichment in the D-2-aminosuberic acid across all six biotransformations. This effect is consistent with the action of the aminotransferase on the L-enantiomer, since the aminotransferases tested here are known to exhibit L-stereoselectivity. No measurable L-alanine was observed by HPLC which should result from the transamination of pyruvate, however it is likely that the L-alanine formed has been degraded further by the other host proteins present in the biotransformation as has been previously observed in the 7-aminoheptanoic acid reactions.
The ING66 biotransformations (rc0212-46-1 and -2) showed significantly higher levels of L-2-aminosuberic acid degradation compared to the pING2022 and pING2030 aminotransferases. ING 66 branched chain aminoacid aminotransferase is already known to exhibit excellent selectivity for L-2-aminoglutarate (L-glutamic acid) which is a shorter (C5) homologue of L-2-aminosuberic acid so this preference in activity for ING 66 is not unexpected.
3.1.7 Conversion of α-amino Suberic Acid to 7-amino Heptanoic Acid by α-amino decarboxylases (EC 4.1.1.-) (See, FIG. 10)
Suitable catalysts were selected from the α-amino acid decarboxylases as candidates for the decarboxylation of α-amino suberic acid, in particular the aspartate 4-decarboxylase (EC 4.1.1.11), the glutamate decarboxylase (EC 4.1.1.15), the lysine decarboxylase (EC 4.1.1.18), the diaminopimelate decarboxylase (EC 4.1.1.20), and the diaminobutyrate decarboxylase (EC 4.1.1.86).
The Escherichia coli GadA glutamate decarboxylase and Escherichia coli LysA diaminopimelate decarboxylase were initially selected from those groups of proteins. Other suitable enzymes include LysA from Methanocaldococcus jannaschii (AAB99100) (EC 4.1.1.20) (Ray, S. S., et al., Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor. Structure, 2002. 10(11): p. 1499-508), and the lysine decarboxylases present in E. coli: CadA (AAA23536), which is inducible under anaerobic conditions and by lysine, and has a very high activity and Ldc (accession D87518) that is constitutively expressed but has lower activity for lysine (Kikuchi, Y., et al., Characterization of a second lysine decarboxylase isolated from Escherichia coli. J Bacteriol, 1997. 179(14): p. 4486-9).
The DNA sequences corresponding to the selected genes as well as their related protein sequence are shown in SEQ ID 15-18. Sequence of the Escherichia coli LysA diaminopimelate decarboxylase was selected as an E. coli codon optimized gene as previously described (Preparation of 6-aminocaproic acid from 5-formyl valeric acid: DSM—US2011-0171699 A1 patent). The Escherichia coli GadA glutamate decarboxylase was selected as wild type sequence. The genes were cloned and expressed using methods described in previous examples.
In addition to the previously prepared constructs (I29:pET21-GadA and I30:pET21-LysA, 2 further constructs were prepared by introduction of the ilvE fragment (assemblies I31 and I32 below) using the in ABLE technology. Introduction of the 15 amino acid Nter peptide of the E. coli branched amino acid aminotransferase (IlvE) upstream of the protein of interest has previously been shown to result in an increase in expression of some protein targets in E. coli. 
The expression results are summarized below:













Soluble
Insoluble



fraction
fraction












Assembly
Protein
4 h
24 h
4 h
24 h





I29
E. coli GadA
++
+
+++
+++


I30
E. coli LysA
+
+
+
+


I31
E. coli GadA ilvE
+
++
+++
++


I32
E. coli LysA ilvE
+++
++
+
+









Preparation of Protein Extracts for Activity Assay

The previously frozen cell pellets from the 24 hour post-induction samples were re-suspended in bead lysis buffer consisting of 0.1 mM Tris, 1 mg/ml Pepstatin A and 200 mM PMSF protease inhibitors (161 μL of the mixture should be used for the lysis of the cell pellet from 1 mL of culture at an OD600 of 5), supplemented with 1.5 mg lysozyme. Acid washed 212-300 μm glass beads (0.4 g per 1 mL of lysis buffer) were added to each sample. Lysis was performed by 30 second bursts of vortexing on full speed, followed by 30 second incubation on ice, repeated to a total time of 10 minutes.
1 mL samples were taken and the remainder of the culture used for the activity assays. The 1 mL samples were centrifuged at 13000 rpm, for 2 minutes and the supernatant separated. SDS samples were prepared and analyzed on SDS-PAGE gels as described above (FIG. 18). Following lysis, there is a large band in the soluble fraction for the E. coli GadA ilvE (I31) protein (FIG. 18, Lane 4) that was not present in the 1 mL sample, lysed by bugbuster. The E. coli LysA (I32) protein, which showed high soluble expression previously, did not show much soluble expression in the bead lysis (FIG. 18, Lane 5). This may indicate a large variability in the lysis methods. Crude cell extracts were then used to monitor the activity of proteins expressed from the 4 constructs I29 to I32.
Biotransformations were performed to assay activity for 2-aminosuberate. Each biotransformation comprised of 1 mM 2-mercaptoethanol and 10□g/ml pyridoxal phosphate as described (Biochem. J. (1965) 96, 75). All substrates included in the biotransformations were at 10 mM concentration and crude cell extract loading was at 20 g/L whole cell equivalent. Biotransformations were incubated in falcon tubes at 37 degC and 250 rpm.
Samples were removed after 18 and 24 hours incubation. The aliquots were heated to 95 degC for 5 minutes to denatured the soluble protein. Any precipitates were removed by centrifugation at 12,000 rpm and 0.2 micron filtration of the supernatant. The filtered samples were analysed by HPLC in order to confirm whether decarboxylation of the relevant substrates had occurred.




The conversion of DL-2-aminosuberic acid should yield 7-aminoheptanoic acid by the action of α-amino acid decarboxylase. The HPLC traces showed little change in the DL-2-aminosuberic acid concentration over the duration of this experiment. A peak corresponding to 7-aminoheptanoic acid however was observed in the 24 hour aliquots. The concentration of the observed peak corresponding to 7-aminoheptanoic acid is shown in FIG. 19.
3.1.8 Conversion of α-keto Suberic Acid to Pimelic Acid Semialdehyde by α-keto Decarboxylases (EC 4.1.1.-)
3.1.8.1 Selection of Suitable Catalysts
Amongst the family of decarboxylase, the α-keto acid decarboxylases emerged as the best candidates for the decarboxylation of α-keto suberic acid, in particular the pyruvate decarboxylase EC 4.1.1.1), the benzoylformate decarboxylase (EC 4.1.1.7) and the branched-chain-2-oxoacid decarboxylase (EC 4.1.1.72).
Genes encoding proteins from each of those four groups have been identified from a broad range of hosts and their products characterized biochemically and in some cases structurally (The crystal structure of benzoylformate decarboxylase at 1.6 A resolution—Diversity of catalytic residues in ThDP-dependent enzymes: Hasson et al. Biochemistry 1998, 37, 9918-9930; High resolution crystal structure of pyruvate decarboxylase from Zymomonas mobilis: Dobritzsch et al. J. Biol. Chem. 1998, 273, 20196-20204; Structure of the branched-chain keto acid decarboxylase (KdcA) from Lactococcus lactis provides insights into the structural basis for the chemoselective and enantioselective carboligation reaction: Berthold et al. Acta Crystallographica Sec. D 2007. D63, 1217-1224).
The following enzymes were then selected amongst those groups according to their substrate specificity: Lactococcus lactis kivD 2-ketoisovalerate decarboxylase (GeneBank JA114157); Lactococcus lactis kdcA branched chain alpha-keto acid decarboxylase (GeneBank JA114154), Saccharomyces cerevisiae pdc1 pyruvate decarboxylase (GeneBank JA114148), Zymomonas mobilis pdc (I472A) pyruvate decarboxylase mutant (GeneBank JA114151), Pseudomonas putida mdlC (A460I) benzoylformate mutant (GeneBank AY143338; fragment 2860-4446).
The first four enzymes previously showed some activity in the decarboxylation of the α-keto pimelic acid, the C-7 derivative of the target compound, α-keto suberic acid (Preparation of 6-aminocaproic acid from 5-formyl valeric acid: DSM—US2011-0171699 A1 patent).
Characterization of the A460I mutant of the benzoylformate decarboxylase from Pseudomonas putida displayed increased selectivity towards 2-keto hexanoic acid (Exchanging the substrate specificities of pyruvate decarboxylase from Zymomonas mobilis and benzoylformate decarboxylase from Pseudomonas putida: Siegert et al. Port. Eng. Des. Sel. 2005, 18, 345-357) compared to the wild-type enzyme which showed low activity towards 2-keto octanoic acid (Comparative characterisation of ThPP-dependent decarboxylases: Gocke et al. J. Mol. Cat. B: Enzymatic 2009, 61, 30-35).
3.1.8.1 Synthesis of 2-ketopimelic Acid and 2-ketosuberic Acid
In order to characterise the alpha-keto acid decarboxylase activity of 2-ketosuberate and 2-ketopimelate these substrates were synthesised since they are not commercially available. The route and method used was taken from JOC 1986 51, p 2389-2391, 3.77 g of 2-ketosuberic acid and 1.72 grams of 2-ketopimelic acid were prepared. The chemical structure of the two respective products was determined by 1H and 13C-NMR.




3.1.9 Conversion of α-ketosuberic Acid to Pimelic Acid Semialdehyde by α-keto Decarboxylases (EC 4.1.1.-)

The pathway for synthesis of coenzyme B [(7-hercaptoheptanoyl)threonine phosphate] has been postulated by White [White R H (1989) Biosynthesis of the 7-mercaptoheptanoic acid subunit of component B [(7-mercaptoheptanoyl)threonine phosphate] of methanogenic bacteria, Biochemistry, 28: 860-865] based on the analysis of other metabolic pathways in Archea and the mass spectroscopic analysis of incorporation of 2H and 13C labeled precursors into the final product. The pathway contains a nonoxidative decarboxylation step of 2-ketosuberic acid to 7-oxoheptanoic acid (pimelate semialdehyde) mediated by a postulated 2-ketoacid decarboxylase. In the next step, 7-mercaptoheptanoic acid is formed. Since this product only is formed (and not the C5 and C6 equivalents), this indicates that at least one of the upstream enzymes in the pathway will only accept C8, but not C6 and C7 substrates.
The pathway was verified by confirmation of the 2-ketodicarboxylic acid elongation reaction from 2-ketoglutarate to 2-ketosuberate using GC-MS [White R H (1989) A novel biosynthesis of medium chain length alpha-ketodicarboxylic acids in methanogenic archaebacteria. Archivers of Biochemistry and Biophysics, 270: 691-697] and synthesis of 7-mercaptoheptanoic acid and coenzyme B from 7-oxoheptanoic acid [White R H (1989) Steps in the conversion of a-ketosuberate to 7-mercaptoheptanoic acid in methanogenic bacteria, Biochemistry, 28: 9417-9423; White R H (1994) Biosynthesis of 7-mercaptoheptanoylthreonine phosphate, Biochemistry, 33: 7077-7081]. The genes encoding enzymes responsible for the some of the steps of the pathway (aksA, aksD, aksE and aksF) have been identified, cloned and expressed in E. coli, but not the gene encoding 2-ketosuberic acid decarboxylase [Howell D M, Harich K, Xu H, White R H. (1998) Alpha-keto acid chain elongation reactions involved in the biosynthesis of coenzyme B (7-mercaptoheptanoyl threonine phosphate) in methanogenic Archaea. Biochemistry, 37: 10108-10117; Howell D M, Graupner M, Xu H, White R H. (2000) Identification of enzymes homologous to isocitrate dehydrogenase that are involved in coenzyme B and leucine biosynthesis in methanoarchaea. J Bacteriol. 182: 5013-5016; Drevland R M, Jia Y, Palmer D R, Graham D E. (2008) Methanogen homoaconitase catalyzes both hydrolyase reactions in coenzyme B biosynthesis. J Biol Chem. 283: 28888-28896], Nothing is known about nonoxidative decarboxylation of 2-ketosuberic acid to 7-oxoheptanoic acid and this activity has not been reported in vitro. However 2-ketosuberic acid was converted to coenzyme B by whole cells [White R H (1989)].
Methodology
Work done by White and Graham showed that Archaebacteria (like Methanocaldococcus jannaschii) are likely to possess an enzyme responsible for nonoxidative decarboxylation of 2-ketosuberic acid to 7-oxoheptanoic acid. Other enzymes involved in the coenzyme B pathway were identified by analysis of the genomes of M. jannaschii [Bult C J, White O, Olsen G J, Zhou L, Fleischmann R D, Sutton G G, Blake J A, FitzGerald L M, Clayton R A, Gocayne J D, Kerlavage A R, Dougherty B A, Tomb J F, Adams M D, Reich C I, Overbeek R, Kirkness E F, Weinstock K G, Merrick J M, Glodek A, Scott J L, Geoghagen N S, Venter J C. (1996) Complete genome sequence of the methanogenicarchaeon, Methanococcus jannaschii. Science. 273: 1058-1073] and Methanobacterium thermoautotrophicum ΔH [Smith D R, Doucette-Stamm L A, Deloughery C, Lee H, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, Harrison D, Hoang L, Keagle P, Lumm W, Pothier B, Qiu D, Spadafora R, Vicaire R, Wang Y, Wierzbowski J, Gibson R, Jiwani N, Caruso A, Bush D, Reeve J N, (1997) Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J Bacteriol. 179: 7135-7155]. The genomes were analyzed for the presence of the target gene clusters and were BLAST searched for proteins showing homology to existing enzymes. We took a similar approach to identify the gene encoding 2-ketosuberic acid decarboxylase.
Results
Analysis of the Gene Clusters
Bacterial genomes can show a high level of organization in which genes encoding enzymes playing a role in specific pathways are localized in operons and/or gene clusters. Because other enzymes of the coenzyme B pathway have been identified and the sequences of some archaebacterial genomes are published, an attempt was made to identify 2-ketosuberic acid decarboxylase. The table below shows the genes and enzymes involved in the pathway.












Genes












Methanocaldococcus
Methanobacterium


Enzyme
Reaction
jannaschii
thermoautotrophicum





AksA
condensation of α-ketoglutarate and
MJ0503
MTH1630


(R)-homocitrate
acetyl-CoA; condensation of α-




synthase
ketoadipate and α-ketopimelate to





acetyl-CoA;




AksDAksE
dehydration of (R)-homocitrate and
MJ1003
MTH1113


homocitrate
analogs to cis-homoaconitate or the
MJ1271
MTH1631


synthase/
respective analogs, and the




dehydratase and
hydration of the products to




cis-
homoisocitrate and its respective




homoaconitatehydratase
analog




AksF
NAD-dependent decarboxylation of
MJ1596
MTH0184


NAD-dependent
(-)-threo-isohomocitrate, (-)-threo-




threo-isocitrate
iso(homo)2citrate and (-)-threo-




dehydrogenase
iso(homo)3citrate




2-ketosuberic
2-ketosuberic acid decarboxylation
??
??


acid





decarboxylase





mercaptoheptanoate

??
??


synthase





mercaptoheptanoylthreonine

??
??


synthase





N-(7-

??
??


mercaptoheptanoyl)-





3-O-





phosphono-L-





threonine





synthase









The coenzyme B biosynthetic genes from M. jannaschii and M. thermoautotrophicum did not appear to reside in gene clusters, except for the genes encoding (R)-homocitrate synthase (MTH1630) and homocitrate synthase/dehydratase large subunit (MTH1631) in M. thermoautotrophicum. The analysis of hypothetical operons containing any of the genes listed above did not show the presence of any protein with homology to known decarboxylases. Therefore, a search was made for analogous decarboxylations in related metabolic pathways in M. jannaschii. 
Analysis of Methanocaldococcus jannaschii Genome
Analysis of other metabolic pathways in M. jannaschii showed that a similar decarboxylation is present in the coenzyme M pathway [Graupner M, Xu H and White R H. (2000) Identification of the gene encoding sulfopyruvate decarboxylase, an enzyme involved in biosynthesis of coenzyme M. J Bacteriol. 182: 4862-4867].




Nonoxidative decarboxylation of 3-sulfopyruvate to sulfoacetaldehyde is catalyzed by sulfopyruvate decarboxylase (EC.4.1.1.79) containing two subunits, comD (SEQ ID 19) and comE (SEQ ID 20). As both coenzyme B and coenzyme M are involved in methanogenesis and the reactions downstream of the decarboxylation are analogous, it is possible that the decarboxylases evolved together and show high homology to each other.
ComD, comE and their orthologues found in the BRENDA database were used as queries to BLAST search the Methanocaldococcus jannaschii. The best match was obtained using comD/comE decarboxylase from Methanocella paludicola (SEQ ID 21).
Only two open reading frames (MJ0277 and MJ0663) encoded by the M. jannaschii genome showed significant homology to comD/comE with the E-value <0.0001. Both of them were annotated as acetolactate synthases (SEQ ID 22 and SEQ ID 23).
Another search was performed using sequences of decarboxylases accepting similar substrates that are deposited in the BRENDA database (2-ketoglutarate decarboxylase, oxaloacetate decarboxylase, α-ketoisovalerate decarboxylase, transaminated amino acid decarboxylase, benzoylformate decarboxylase, 2-ketoarginine decarboxylase, phosphonopyruvate decarboxylase, pyruvate decarboxylase and indole-3-pyruvate decarboxylase).













QUERY





(Name &





UNIPROT





entry)
Substrate
Source
Hits (E-value <10−4)







Kgd
2-ketoglutarate
Mycobacterium
No hits


Q9CC97
decarboxylase
leprae




4.1.1.71




citM
oxaloacetate
Lactococcus
No hits


Q7X4Z5
decarboxylase
lactis



kivd
α-ketoisovalerate
Lactococcus
NP_247250.1 acetolactate synthase


Q684J7
decarboxylase
lactis
catalytic subunit E-value: 8e−29



4.1.1.1

NP_247647.1 acetolactate synthase





large subunit IlvB5e−19


ARO10
transaminated
Saccharomyces
NP_247250.1 acetolactate synthase


Q06408
amino acid
cerevisiae
catalytic subunit 2e−17



decarboxylase 4.1.1.-

NP_247647.1 acetolactate synthase





large subunit IlvB9e−12





P58416.1 Sulfopyruvate





decarboxylase subunit beta 4e−04


MdlC
benzoylformate
Sulfolobus
NP_247250.1 acetolactate synthase


Q97XR3
decarboxylase
solfataricus
catalytic subunit 3e−23



4.1.1.7

NP_247065.1 signal recognition





particle protein Srp54 6e−04





2V3C_C Crystal Structure Of The





Srp54-Srp19-7s.S SrpRna6e−04





3NDB_B Crystal Structure Of A





Signal Sequence Bound To The





Signal 6e−04


aruI
2-ketoarginine
Pseudomonas
NP_247250.1 acetolactate synthase


B7V368
decarboxylase
aeruginosa
catalytic subunit 4e−71





NP_247647.1 acetolactate synthase





large subunit 2e−38





NP_248425.1cobyrinic acid a,c-





diamide synthase 4e−05


fom2
phosphonopyruvate
Erwinia
P58416.1 Sulfopyruvate


Q6D9X5
decarboxylase
carotovora
decarboxylase subunit beta 3e−20




subsp.
P58415.1Sulfopyravate




atroseptica
decarboxylase subunit alpha 2e−11




(Pectobacterium
NP_247516.1 2-oxoglutarate




atrosepticum)
ferredoxinoxidoreductase subunit





beta 2e−05





NP_247250.1 acetolactate synthase





catalytic subunit 6e−04


PDC6
Pyruvate
Saccharomyces
NP_247250.1 acetolactate synthase


P26263
decarboxylase
cerevisiae
catalytic subunit 6e−23



isozyme 3

NP_247647.1 acetolactate synthase



4.1.1.1

large subunit IlvB9e−14





P58416.1Sulfopyruvate





decarboxylase subunit beta 6e−04





NP_247310.1 hypothetical protein





MJ_0337 9e−04


IpdC
Indole-3-pyruvate
Pantoea
NP_247250.1 acetolactate synthase


F2EPZ5
decarboxylase
ananatis
catalytic subunit 6e−22





NP_247647.1 acetolactate synthase





large subunit 7e−12





NP_247516.1 2-oxoglutarate





ferredoxinoxidoreductase subunit





beta 9e−05









MJ0277 (accession number NP_247250) and MJ0663 (NP_247647) were good hits for almost all the queries used to search the genome. The protein alignment using the ClustalW algorithm showed significant homology between MJ0277 and comD/comE proteins (FIG. 20). However, MJ0277 showed even higher homology to LACLA acetolactate synthase from Lactococcus lactis (FIG. 21).
Analysis of the functional domains in LACLA acetolactate synthese, comD/comE from Methanocella paludicola and the hypothetical acetolactate synthase MJ0277 showed that all of them have a similar structure containing a thiamine phosphate binding site (FIG. 22). Almost identical results were obtained for the second open reading frame MJ0663 from Methanocaldococcus jannaschii. 
The acetolactate synthase (ALS) enzyme (also known as acetohydroxy acid synthase) catalyzes the conversion of pyruvate to α-acetolactate.




The first step of the reaction is decarboxylation of pyruvate (which is a 2-ketoacid) to an enzyme-bound intermediate that is further condensed with the second pyruvate molecule resulting in acetolactate. Thus, 2-ketoacid decarboxylases and acetolactate synthases are likely to show high homology to each other.
Conclusions
Analysis of the M. jannaschii genome showed the presence of two proteins annotated as acetolactate synthases (MJ0277 and MJ0663) that may be the previously unidentified 2-ketosuberic acid nonoxidative decarboxylase involved in coenzyme B biosynthesis. It is very likely that one of them is the real acetolactate synthase. This enzymatic activity has been shown in many archaebacteria, and M. jannaschii encodes the acetolactate synthase regulatory subunit, MJ0161. However, one of the enzymes may be the unidentified 2-ketoacid decarboxylase and has simply been misannotated. Alternatively, 2-ketosuberic acid might be decarboxylated by the enzyme responsible for decarboxylation of 3-sulfopyruvate in the coenzyme M pathway. Therefore, comD/comE decarboxylase should also be considered as a target enzyme.
The proteins annotated as acetolactate synthases MJ0277 (NP_247250) and MJ0663 (NP_247647) were identified as prime candidates for nonoxidative decarboxylation of 2-ketoadipic acid, 2-ketopimelic acid and 2-ketosuberic acid. In addition: 3-sulfopyruvate decarboxylase comD/comE (P58415/P58416), Kgd (Q9CC97), citM (Q7X4Z5), kivd (Q684J7), ARO10 (Q06408), MdlC (Q97XR3), aruI (B7V368), fom2 (Q6D9×5), PDC6 (P26263) and IpdC (F2EPZ5) are excellent candidates for the conversion of 2-ketosuberic acid to pimelic acid semialdehyde (SEQ ID 24-40).
3.1.10 Conversion of α-keto Pimelic Acid to α-keto Suberic Acid by α-keto Acid Chain Elongation (See, FIG. 10)
3.1.10.1 Selection of Enzyme Gene Targets
Conversion of α-ketopimelic acid into α-ketosuberic acid was previously reported to be part of the biosynthesis of the Coenzyme B in methanogenic archaebacteria, such as Methanocaldococcus janaschii, Methanocaldococcus vannielii, Methanocaldococcus maripaludis, Methanobacterium thermoautotrophicum, Methanosarcina termophila and others (White, Arch. Biochem. Biophys. 270: 691-697 (1989)). Genes encoding the enzymes involved in the multi cycles of chain elongation from α-ketoglutaric acid to suberic acid, homologous to enzymes involved in the leucin and lysine biosynthesis, were idientifed from Methanocaldococcus janaschii and their corresponding proteins characterized α-keto acid chain elongation reactions involved in the biosynthesis of coenzyme B (7-mercaptoheptanoyl threonine phosphate) in Howell et al., Biochemistry 37: 10108-10117 (1998); Drevland et al., Bacteriol. 189: 4391-4400 (2007); Howell et al., J. Bacteriol. 182: 5013-5016 (2000); Drevland et al., J. Biol. Chem. 283: 28888-28896 (2008); and Jeyakanthan et al., Biochemistry 49: 2687-2696 (2010).
Orthologous genes were also identified from Methanobacterium thermoautotrophicum, but their products have not been characterized yet. At least two isogenes were reported in this archaebacteria for each of the required activity (AskA, AksD/E and AksF) as previously reported in Methanocaldococcus janaschii (Smith et al. 1997, 179, 7135-7155). The table below presents the orthology of the corresponding Methanobacterium thermoautotrophicum proteins with the well-characterized Methanocaldococcus janaschii proteins based on the literature previously mentioned and their potential deduced function
















Orthologous



M. janaschii
Functions of M. janaschii
M. thermoautotrophicum


Enzyme activity
proteins
proteins
proteins







AksA:
MJ0503
Condensation of α-
MTH1630


2-isopropylmalate

ketoglutarate and acetyl-



synthase/homocitrate synthase

CoA to form trans-





homoaconitate; functions





in the α-ketosuberate





synthesis




MJ1195
Formation of 2-
MTH1481




isopropylmalate from





acetyl-CoA and





2-oxoisovalerate in





leucine biosynthesis



AksD:
MJ1003
Formation of cis-homon
MTH1631


3-isopropylmalate

aconitate (n = 1-4) when



dehydratase/homoaconitase

coupled with MJ1271;



(Large subunit)

involved in the production





of α-keto suberic acid




MJ0499
Involved in the leucine
MTH1386




biosynthesis



AksE:
MJ1271
Formation of cis-homon
MTH0829: Contains


3-isopropylmalate

aconitate (n = 1-4) when
the YLTR consensus


dehydratase or

coupled with MJ1003;
sequence


isomerase/homoaconitase

involved in the production
characteristic of


(Small subunit)

of α-keto suberic acid
homoaconitase



MJ1277
Involved in the leucine
MTH1387: Contains




biosynthesis
the YLVM consensus





sequence





characteristic of





isopropylmalate





isomerase


AksF:
MJ1596
Involved in the
MTH1388


3-isopropylmalate

production of



dehydrogenase/homoisocitrate

α-keto suberic acid



dehydrogenase
MJ0720
Involved in the leucine
MTH0184




biosynthesis









Identification of orthologs to the chain elongation proteins in Methanobacterium thermoautotrophicum was reported in the literature from comparative genomics data between Methanocaldococcus janaschii and Methanobacterium thermoautotrophicum genomes, sequence analysis of the corresponding proteins and activity assay. Potential application of the alternative Methanobacterium thermoautotrophicum gene products and their corresponding Methanocaldococcus janaschii orthologs for the synthesis of alpha-keto pimelic acid was reported (WO2010-104391 A2). Therefore, eight Methanobacterium thermoautotrophicum proteins were selected for the exemplification of the chain elongation reaction between pimelic acid and suberic acid, i.e., AksA 2-isopropylmalate synthase/homocitrate synthases MTH1630 and MTH1481, fragment 1337346-1338863; AksD 3-isopropylmalate dehydratase/homoaconitases (Large subunit) MTH1386 fragment 1253910-1255169; and MTH1631 (fragment 1495715-1497001; AksE 3-isopropylmalate dehydratase or isomerase/homoaconitases (Small subunit) MTH 0829 fragment 752586-753098; and MTH1387 fragment 1255181-1255669; and AksF 3-isopropylmalate dehydrogenase/homoisocitrate dehydrogenases MTH0184 fragment 130396-131391; and MTH 1388 fragment 1255666-1256655.
Wild-type genes were selected for the construction of the corresponding E. coli expression vectors, except for the genes AksA(1)-MTH1630, AksD(2)-MTH1631 and AksF(2)-MTH1388 in which the starting codons GTG or TTG were changed to ATG.
3.1.10.2 Cloning Expression Vectors Containing Gene Targets
The selected gene targets from Methanobacterium thermoautotrophicum were then cloned into the IPTG inducible pET21-a backbone using in ABLE technology, as described in detail in Section 3.1.1.2) to generate I9 (M. thermoautotrophicum AksA(1)-MTH1630 gene in pET21-a), I10 (M. thermoautotrophicum AksA(2)-MTH1481 gene in pET21-a), I11 (M. thermoautotrophicum AksD(1)-MTH1386 gene pET21-a gene in pET21-a), I12 (M. thermoautotrophicum AksD(2)-MTH1631 gene in pET21-a), I13 (M. thermoautotrophicum AksE(1)-MTH0829 gene in pET21-a), I14 (M. thermoautotrophicum AksE(2)-MTH1387 gene in pET21-a), I15 (M. thermoautotrophicum AksF(1)-MTH0184 gene in pET21-a), and I16 (M. thermoautotrophicum AksF(2)-MTH1388 gene in pET21-a).
Briefly, potential EarI sites in the selected genes and the vector backbone were disrupted to prevent interference with the part/linker fusion preparation involving EarI digestion/ligation cycles. No EarI sites were observed in AksD(1)-MTH1386, AksD(2)-MTH1631 and AksE(2)-MTH1387. One EarI site was observed in each of the AksA(1)-MTH1630, AksA(2)-MTH1481, AksE(1)-MTH0829 and AksF(2)-MTH1388 genes, and two EarI sites were observed in the AksF(1)-MTH0184 gene three EarI sites were detected in the vector backbone pET21-a. The EarI sites were disrupted by introducing a silent mutation(s) into the restriction site. The three EarI sites in the vector were disrupted by mutating the last guanidine base of the restriction site into a thymine.
The EarI free sequences were then used as input sequences in the part designer software to design the corresponding truncated parts flanked by EarI sites, as discussed in Section 3.1.1.2. The synthesized Methanobacterium thermoautotrophicum AksA(1)-MTH1630 (TP48), AksA(2)-MTH1481 (TP49), AksD(1)-MTH1386 (TP50), AksD(2)-MTH1631 (TP51), AksE(1)-MTH0829 (TP52), AksE(2)-MTH1387 (TP53), AksF(1)-MTH0184 (TP54) and AksF(2)-MTH1388 (TP55) truncated parts were inserted into the DNA2.0 pJ201 vector. The pET21-a truncated part vector was fully synthesized with introduction of a fragment including the chloramphenicol resistance gene to produce the vector TP31.
Phosphorylation and subsequent annealing of the in ABLE oligonucleotides were performed as described in section 3.1.1.2. Briefly, the oligos were incubated with T4 kinase at 37° C. for 30 minutes, followed by inactivation of the enzyme at 65° C. for 20 minutes.
Next, part linker fusions were prepared by ligating the 5′-end of the truncated part with its corresponding part oligo annealed fragment, and the 3′-end of the truncated part with the linker oligo annealed fragment, as previously described in section 3.1.1.2. Part linker fusions corresponding to the selected genes (Methanobacterium thermoautotrophicum AksA(1)-MTH1630, AksA(2)-MTH1481, AksD(1)-MTH1386, AksD(2)-MTH1631, AksE(1)-MTH0829, AksE(2)-MTH1387, AksF(1)-MTH0184 and AksF(2)-MTH1388) were prepared by ligation of their respective annealed part oligos (POA48, POA49, POA50, POA51, POA52, POA53, POA54 or POA55), their truncated part (TP48, TP49, TP50, TP51, TP52, TP53, TP54 or TP55) and the annealed linker oligos from the vector backbone. Part linker fusions corresponding to the vector backbone were prepared by ligation of its annealed part oligos, its truncated part, and the annealed linker oligos from either genes. A negative control gene-free assembly was also prepared by ligation of the vector backbone annealed part oligos, its truncated part, and its annealed linker oligos, resulting in self-assembly of the vector backbone.
A ten and twenty-fold molar excesses of linker and part oligos to the truncated part was used in the gene and vector reactions to favor ligation between the truncated part and the oligonucleotides during each EarI digestion/ligation cycle. The 50 μL EarI digestion/ligation reactions were incubated in a thermocycler (Eppendorf Mastercycler Gradient), alternating the temperature between 37° C. and 16° C. Upon completion of the cycles, samples were loaded on a 0.7% agarose gels, and the expected size fragments were observed for preparation of the part/linker fusions. The correct size bands were then excised from the gel, and the DNA was gel extracted using the QIAGEN QIAquick Gel Extraction Kit. The DNA concentration ranged from 13.6 ng/μl to 24.8 μg/μl in a total volume of 30 μl (DNA conc. range 4.9 nM to 53.9 nM). Self-assembly of the part/linker fusion (pET21-a part/pET21-a linker) for the generation of the negative control gene-free construct was also performed.
Combination of the gene part/linker fusions with their respective vector part/linker fusion was then carried out through a 2-part assembly, as described in section 3.1.1.2. Briefly, the gene part linkers and the vector part linkers were incubated at room temperature for 30 min prior to transformation of high efficiency chemically competent NEB10β E. coli cells using 2 μl of the assembly reaction and 10 μl of the competent cells. Transformed cells were plated on LB-Amp-agar, and incubated at 37° C. overnight. About one thousand clones were obtained for each assembly. Two random clones were selected from each assembly, and the corresponding vectors were isolated using the QIAGEN QIAprep Miniprep Kit.
Restriction was performed to confirm vector construction, as described in section 3.1.1.2. Briefly, clones obtained from I9 were analyzed using BglII and XmnI to identify positive clones for the insertion of the Methanobacterium thermoautotrophicum AksA(1)-MTH1630 gene into pET21-a, clones obtained from I10 assembly were analyzed using PstI and XmaI/XbaI to identify insertion of AksA(2)-MTH1481 gene into pET21-a, clones obtained from I11 assembly were analyzed using HindIII and AlwNI to identify insertion of AksD(1)-MTH1386 gene, clones obtained from I12 assembly were analyzed using NcoI and BglII to identify insertion of AksD(2)-MTH1631 gene, clones obtained from I13 assembly I13 were analyzed using MluI and XmnI to identify insertion of AksE(1)-MTH0829 into pET21-a, clones obtained from I14 assembly I14 were analyzed using PsiI and XmaI/AlwNI to identify insertion of AksE(2)-MTH1387 gene into the E. coli expression vector, clones obtained from I15 assembly were analyzed using AlwNI and HincII to identify insertion of AksF(1)-MTH0184 gene into the E. coli expression vector, and clones obtained from 116 assembly were analyzed using BsaI and HindIII/AlwN1 to identify insertion of the AksF(2)-MTH1388. The restriction products were am on an agarose gel, and the expected band pattern was observed for the clones tested from each assembly, confirming the construction of E. coli pET21-a expression vectors harbouring the Methanobacterium thermoautotrophicum chain elongation genes. In addition, the part junctions between the 3′-end of the vector backbone and the 5′-end of the genes as well as between the 3′-end of the gene and the 5′-end of the vector backbone were sequenced to confirm the construction.
3.1.10.3 Expression of Exogenous Thioesterase Genes in E. coli 
Expression of exogenous Methanobacterium thermoautotrophicum AksA(1)-MTH1630, AksA(2)-MTH1481, AksD(1)-MTH1386, AksD(2)-MTH1631, AksE(1)-MTH0829, AksE(2)-MTH1387, AksF(1)-MTH0184 and AksF(1)-MTH0184 chain elongation genes gene products in E. coli was performed as described in section 3.1.1.3. Briefly, electrocompetent BL21 (DE3) cells were transformed with 10 ng DNA, and the transformation samples were plated on LB-Amp-Agar. Transformants were obtained after overnight incubation at 37° C. A single clone was picked from each assembly, and 5 ml of LB-Amp medium were inoculated as a starting culture. The OD600 of the culture was measured after overnight incubation at 37° C. and 250 rpm, 2 mL culture (approximately 8×107) were used to inoculate 100 mL of LB-Amp, which were incubated in a 500 mL baffled shake flask at 37° C. and 250 rpm.
Protein expression was induced by addition of 1 mM IPTG (final conc.), and cultures were incubated at 37° C. and 250 rpm. A 1 mL sample was taken prior to induction and after 4 h and 24 h post-induction incubation, and the OD600 measured to determine cell growth. After 24 h post-induction incubation, the remaining culture was transferred to a 50 mL falcon tube, harvested by centrifugation at 5000 rpm for 10 minutes, and the cell pellets used for further analysis or stored at −20° C.
For SDS-PAGE analysis, the samples were centrifuged at 13000 rpm for 2 min, the supernatant was removed, and the cells were lysed using the Bugbuster protein extraction reagent supplemented with lysozyme (15 mg/mL) and benzonase (3.4 U/μL). The lysis reactions were then centrifuged at 13000 rpm for 2 min, the soluble fraction was transferred to a new tube, and the insoluble fraction re-suspended in water. 20 μl of each fraction was mixed with 80 μl SDS-Sample buffer (SDS-Loading Buffer, 9% DTT and water), heated in a heatblock for 5 minutes at 95° C., and 10 μl of each SDS-sample preparation was then loaded on SDS-PAGE 4-20% Tricene gels to analyze the protein content of the soluble and insoluble fractions.
Only the AksE(2)-MTH1387 protein was successfully expressed in soluble form, i.e., an 18 kD bank in the soluble fraction after IPTG induction. The AksA(1)-MTH1630, AksD(2)-MTH1631, AksF(1)-MTH0184 and AksF(2)-MTH1388 proteins were expressed in insoluble forms, i.e., a 44, 36, and 46 kD bands, respectively, were detected in the insoluble portion. No expression was detected for the AksA(2)-MTH1481, AksD(1)-MTH1386 and AksE(2)-MTH1387 proteins. Therefore, expression optimization was performed for AksA(1)-MTH1630, AksD(2)-MTH1631, AksF(1)-MTH0184, AksF(2)-MTH1388, AksA(2)-MTH1481, AksD(1)-MTH1386, and AksE(2)-MTH1387, based on reports of successful expression of Methanocaldococcus jannaschii orthologs in the literature. In particular, literature data on the expression of the M janaschii orthologs revealed a set of different conditions in particular in terms of inducer concentration and induction temperature. The IPTG conc. was varied between 0.1 and 1 mM (initial conditions 1 mM) and the temperature of induction was varied between 16 and 37 C (initial conditions 37 C). The same expression protocol and the same SDS-PAGE sample preparation, as described in the section 3.1.1.3 was used for the solubility optimization experiments.
The level of AksA(1)-MTH1630 protein expression was improved after decreasing 10-fold the IPTG concentration, but the protein remained insoluble; optimization of the temperature did not affect expression or solubility. No significant improvement in AksD(2)-MTH1631 and AksF(2)-MTH1388 solubility by lowering 10-fold the IPTG concentration since both proteins were only visible in the insoluble fractions after induction. No significant improvement in solubility was observed for AksD(2)-MTH1631 and AksF(2)-MTH1388 by lowering the induction temperature to 16° C. since both proteins were only visible in the insoluble fractions after induction. However, AksF(1)-MTH0184 solubility was improved by lowering the induction temperature to 30° C. Therefore, AksA(1)-MTH1630 (19), AksD(2)-MTH1631 (112) and AksF(2)-MTH1388 (116) may be expressed in different hosts, e.g., eukaryotic system like Saccharomyces cerevisiae or in a thermophile bacteria like Bacillus stearothermophilus. 
Since the Methanobacterium thermoautotrophicum AksA(1)-MTH1630, AksA(2)-MTH1481, AksD(2)-MTH1631 and AksE(1)-MTH0829 gene products were not expressed in a soluble foiin in E. coli using the pET21-a/IPTG expression system, these genes was cloned for expression using the Saccharomyces cerevisiae expression system. The expression vector was assembled using the in ABLE technology described above, except the SapI restriction enzyme instead of EarI in the preparation of the part/linker fusion of the yeast vector backbone, comprising the constitutive promoter ADH1p, the transcription terminator CYC1t, and the high copy number vector backbone derived from the YEplac195 plasmid. Electrocompetent TOP10 E. coli cells were transformed with each part/linker assembly and a large DNA stock for was prepared using the QIAGEN Hi-Speed Plasmid Purification Midi Kit (67.4-173.0 nM in 120 μl). The expected size fragment was observed for the preparation of the yeast vector part/ADH1 promoter linker, despite the use of SapI, after agarose gel electrophoresis. The correct bands were then excised from the gel, and the DNA was gel extracted using the QIAGEN QIAquick Gel Extraction Kit (14.1-138.1 nM in 30 μl).
The final constructs were then prepared incubating the 4-part assembly reaction, i.e., the ADH1 promoter, each of the Methanobacterium thermoautotrophicum genes AksA(1)-MTH1630, AksA(2)-MTH1481, AksD(2)-MTH1631 and AksE(1)-MTH0829, the CYC1 terminator and the yeast vector backbone, at 37° C. Then, 10 μl high efficiency chemically competent NEB10β E. coli cells were transformed with 2 μl of the assembly reaction, plated on LB-Kan-agar, and incubated at 37° C. overnight. Between two hundred and two hundred and fifty clones were obtained for the 4-part assemblies. Five random clones were then picked from the plates, and the corresponding vectors were isolated using the QIAGEN QIAprep Miniprep Kit.
The isolated constructs were analyzed using restriction analysis. A preliminary analysis was performed using PmeI/SapI to identify any truncated vector contaminants. The clones did not contain truncated vector contaminants, so they were then analyzed using the restriction enzymes XhoI/NdeI, BsaI and MluI in order to confirm the insertion of the 4 part/linker fusions. The expected band pattern was observed for both clones confirming the construction of S. cerevisiae expression vector harbouring the ADH1 promoter, the gene of interest, the CYC1 terminator and the yeast vector backbone. Lastly, the junctions between the 4 parts were sequenced to confirm proper assembly.
Transformation with the S. cerevisiae I24-I27 expression vectors can be performed as described herein, and expression from the constitutive promoter ADH1p can monitored after cell lysis using SDS-PAGE. The I24 construct includes the ADH1 promoter, the Methanobacterium thermoautotrophicum AksA(1)-MTH1630 gene, and the CYC1 terminator inserted in the yeast vector backbone. The I25 construct includes the ADH1 promoter, the Methanobacterium thermoautotrophicum AksA(2)-MTH1481 gene, and the CYC1 terminator. The I26 construct includes the ADH1 promoter, the Methanobacterium thermoautotrophicum AksD(2)-MTH1631 gene, and the CYC1 terminator. The I27 construct includes the ADH1 promoter, the Methanobacterium thermoautotrophicum AksE(1)-MTH0829 gene, and the CYC1 terminator.
Patents, patent applications, publications, product descriptions, and protocols cited throughout this application are incorporated herein by reference in their entireties for all purposes.

## Claims

1. A method of converting a compound, the method comprising (a) contacting pimeloyl acyl carrier protein (PACP) with an enzyme that catalyzes the thioester hydrolysis of PACP to pimelic acid (PA), wherein PA is produced, and
(b) further contacting the PA with an enzyme that catalyzes the carboxylic acid reduction of PA to pimelic acid semialdehyde (PAS), wherein PAS is produced.

2. The method of claim 1, wherein the enzyme that catalyzes the thioester hydrolysis of PACP to PA is a thioesterase, an acid-thiol ligase, or a CoA transferase.

3. The method of claim 2, wherein:
the thioesterase is a thioesterase in EC 3.1.2;
the acid-thiol ligase is an acid-thiol ligase in EC 6.2.1, and
the CoA transferase is a CoA transferase in EC 2.8.3.

4. The method of claim 3, wherein:
the thioesterase in EC 3.1.2 is one more of
the thioesterase in EC 3.1.2.18, EC 3.1.2.19, or EC 3.1.2.20,
the gene product of yciA,
a thioesterase in EC 3.1.2.14, and
the gene product of fatA or fatB;

the acid-thiol ligase in EC 6.2,1 is
an acid-thiol ligase in EC 6.2,1,14, or EC 6.2.1.23; and

the CoA transferase in EC 2.8.3 is
a CoA transferase in EC 2.8.3.12, EC 2.8.3.13, or EC 2.8.3.14.

5. The method of claim 1, wherein the PACP is produced by a process comprising one or more steps of
the biotin biosynthesis pathway I (see FIG. 6).

6. The method of claim 1, wherein the enzyme that catalyzes the carboxylic acid reduction of PA to PAS is one or more of
a carboxylic acid reductase, and
a carboxylic acid reductase in EC 1.2.99.

7. The method of claim 6, wherein the carboxylic acid reductase in EC 1.2.99 is a carboxylic acid reductase in EC 1.2.99.6.

8. The method of claim 1, the method further comprising contacting PACP with an enzyme that catalyzes the reduction of PACP to PAS, wherein PAS is produced.

9. The method of claim 8, wherein the enzyme that catalyzes the reduction of PACP to PAS is one or more of
a fatty-acyl-CoA reductase or an aldehyde dehydrogenase;
a fatty-acyl-CoA reductase or an aldehyde dehydrogenase is a reductase in EC 1.2.1,
a fatty-acyl-CoA reductase or aldehyde dehydrogenase in EC 1.2.1.4, EC 1.2.1.50, EC 1.2.1.83, or EC 1.2.1.80.

10. The method of claim 8, wherein the PACP is produced by a process comprising one or more steps of:
the biotin biosynthesis pathway I (see FIG. 6).

11. The method of claim 8, wherein the enzyme, or one or more enzymes, is or are:
(i) isolated; (ii) in cell lysate, a partially purified cell lysate, cell lysates, or partially purified cell lysates; or (iii) in one or more host cell strains recombinantly expressing it or them.

12. The method of claim 1, the method further comprising contacting α-ketosuberate (AKS) with an enzyme that catalyzes the α-keto decarboxylation of AKA to PAS, wherein PAS is produced.

13. The method of claim 12, wherein the enzyme that catalyzes the α-keto decarboxylation of AKS to PAS is one or more of
a decarboxylase or an acetolactate synthase, and
an enzyme in EC.4.1.1.

14. The method of claim 13, wherein the AKS is produced by a process comprising one or more steps of:
(a) a pathway shown in FIG. 10; or
(b) the coenzyme B pathway of methanogenic archae (see FIG. 3).

15. The method of claim 12, wherein the AKS is produced by a process comprising one or more steps of:
(a) a pathway shown in FIG. 10; or
(b) the coenzyme B pathway of methanogenic archae (see FIG. 3).

16. The method of claim 12, wherein the enzyme, or one or more enzymes, is or are:
(i) isolated; (ii) in a cell lysate or partially purified cell lysate; or (iii) in a host cell recombinantly expressing it or them.

17. The method of claim 1, the method further comprising contacting AKS with an enzyme that catalyzes the transfer of an amino group to the AKS to produce α-amino suberate (AAS), wherein AAS is produced.

18. The method of claim 17, wherein the enzyme that catalyzes the transfer of an amino group to the AKS to produce α-amino suberate (AAS) is one or more of
an amino acid aminotransferase,
an aminotransferase in EC 2.6.1, or
an amino acid aminotransferase in EC 2.6.1.39, EC 2.6.1.42, or EC 2.6.1.67.

19. The method of claim 17, further comprising contacting the AAS with an enzyme that catalyzes the α-amino acid decarboxylation of the AAS to 7-amino-heptanoic acid (7 AHA), wherein 7 AHA is produced.

20. The method of claim 19, wherein the enzyme that catalyzes the α-amino acid decarboxylation of the AAS to 7-amino-heptanoic acid (7 AHA) is one or more of
a decarboxylase or an acetolactate synthase, or
an enzyme in EC.4.1.1.

21. The method of claim 19, further comprising contacting the 7 AHA with an enzyme that catalyzes the amide hydrolysis of the 7 AHA to enantholactam (ENTL), wherein ENTL is produced.

22. The method of claim 19, further comprising contacting the 7 AHA with an enzyme that catalyzes the aldehyde dehydrogenation of the 7 AHA to 7-amino-heptanal (7 AHT), wherein 7 AHT is produced.

23. The method of claim 22, further comprising contacting the 7 AHT with an enzyme that catalyzes the transfer of an amino group to the 7 AHT to produce 1,7-diaminoheptane (1,7 DAH), wherein 1,7 DAH is produced.

24. The method of claim 17, wherein the enzyme, or one or more enzymes, is or are:
(i) isolated; (ii) in a cell lysate or partially purified cell lysate; or (iii) in a host cell recombinantly expressing it or them.

25. The method of claim 1, the method further comprising contacting PAS with an enzyme that catalyzes the semialdehyde amination of the PAS to 7-amino-heptanoic acid (7 AHA), wherein 7 AHA is produced.

26. The method of claim 25, further comprising contacting the 7 AHA with an enzyme that catalyzes the amide hydrolysis of the 7 AHA to enantholactam (ENTL), wherein ENTL is produced.

27. The method of claim 25, further comprising:
contacting the 7 AHA with an enzyme that catalyzes the aldehyde dehydrogenation of the 7 AHA to 7-amino-heptanal (7 AHT), wherein AHT is produced; and
contacting the 7 AHT with an enzyme that catalyzes the transfer of an amino group to the 7 AHT to produce 1,7-diaminoheptane (1,7 DAH), wherein 1,7 DAH is produced.

28. The method of claim 25, wherein the PAS is produced by a process comprising:
(1) contacting a-ketosuberate (AKS) with an enzyme that catalyzes the α-keto decarboxylation of AKS to PAS; or
(2) one or more steps of the Tetralin degradation pathway (see FIG. 8).

29. The method of claim 25, wherein the enzyme, or one or more enzymes, is or are:
(i) isolated; (ii) in a cell lysate or partially purified cell lysate; or (iii) in a host cell recombinantly expressing it or them.

30. The method of claim 1, the method further comprising contacting 7 AHT with an enzyme that catalyzes the transfer of an amino group to the 7 AHT to produce 1,7-diaminoheptane (1,7 DAH), wherein 1,7 DAH is produced.

31. The method of claim 30, wherein the enzyme that catalyzes the transfer of an amino group to the 7 AHT to produce 1,7-diaminoheptane (1,7 DAH) is one or more of
an amino acid aminotransferase or an ω-transaminase,
an amino acid aminotransferase in EC 2.6.1 or an ω-transaminase in EC.2.6.1,
an amino acid aminotransferase in EC 2.6.1.39, EC 2.6.1.42, or EC 2.6.1.67, and
an ω-transaminase in EC 2.6.1.18, EC 2.6.1.19, or EC 2.6.1.39.

32. The method of claim 30, wherein the 7 AHT is produced by aldehyde dehydrogenation of 7 AHA, which is produced by one or steps of a pathway shown in FIG. 10.

33. The method of claim 30, wherein the enzyme, or one or more enzymes, is or are:
(i) isolated; (ii) in a cell lysate or partially purified cell lysate; or (iii) in a host cell recombinantly expressing it or them.

34. The method of claim 1, wherein the enzyme in (a) or (b) is:
(i) isolated; (ii) in a cell lysate or partially purified cell lysate; or (iii) in a host cell recombinantly expressing it.

35. An isolated cell comprising one or more exogenous nucleic acid encoding:
(a) (I) a thiosterase, an acid thiol ligase, or a CoA transferase that catalyzes the thioester hydrolysis of PACP to PA; and (ii) a carboxylic acid reductase that catalyzes the carboxylic acid reduction of PA to PAS; and comprising PACP; and
optionally further comprising one or more exogenous nucleic acid encoding:
(b) (i) a fatty-acyl-CoA reductase or an aldehyde dehydrogenase; and (ii) an enzyme that catalyzes a reaction whose product is PACP;
(c) (i) a keto add decarboxylase or an acetolactate synthase; and (ii) and enzyme that catalyzes a reaction whose product is AKS;
(d) (i) an aminotransferase; and (ii) a decarboxylase or an acetolactate synthase; or
(e) (i) an aminotransferase or a ω-transaminase; and (ii) an enzyme that catalyzes a reaction whose product is 7 AHT.

36. The cell of claim 35, wherein the cell is a prokaryotic cell or a eukaryotic cell.

37. The isolated cell of claim 35, wherein the exogenous nucleic acid encoding the thiosterase is selected from the group consisting of fatA and fatB; and wherein the exogenous nucleic acid encoding the carboxylic acid reductase is car from Nocardia.

38. The isolated cell of claim 37, wherein the isolated cell is a prokaryotic cell or a eukaryotic cell.

39. A method of converting a compound, the method comprising contacting PACP with an enzyme that catalyzes the thioester hydrolysis of PACP to PA, wherein the enzyme is the gene product of fatA or fatB.

40. The method of claim 39, wherein the PACP is produced by a process comprising one or more steps of the biotin biosynthesis pathway I (see FIG. 6).

41. The method of claim 39, further comprising contacting the PA with the gene product of car that catalyzes the carboxylic acid reduction of PA to PAS, wherein PAS is produced.

42. The method of claim 39 wherein the enzyme is: (i) isolated; (ii) in a cell lysate or partially purified cell lysate; or (iii) in a host cell recombinantly expressing it.