# Patent

## Title
Microbial production of alkanolamides and amidoamines and uses thereof

## Abstract

The disclosure relates to a recombinant microorganism engineered to express an enzyme which catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide. The disclosure further encompasses a method of producing a fatty amide by culturing the recombinant microorganism in the presence of a carbon source.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is the National Phase of International Application No. PCT/US2013/30502 filed 12 Mar. 2013, which designated the U.S. and that International Application was published under PCT Article 21(2) in English, which claims the benefit of priority to U.S. Provisional Application Ser. No. 61/623,711, filed 13 Apr. 2012, all of which applications are incorporated herein by reference in their entirety.


FIELD
The disclosure relates to a microorganism that is engineered to express an enzyme in order to produce fatty amides when cultured in the presence of a carbon source.
BACKGROUND
Fatty amides are endogenous components of animal and plant lipids that have a wide variety of biochemical and physiological functions (Bachur et al. (1965) J. Biol. Chem. 240:1019-1024). Endogenous fatty amides such as N-palmitoylethanolamine (PEA), N-arachidonoyl ethanolamide (anandamide), N-oleoyl ethanolamide (OEA), and N-arachidonoyl dopamine (NADA) function as signaling molecules in the central and peripheral nervous system (see, e.g., Tan et al. (2006) AAPS J. 8 (3): E461-E465; and Lo Verme et al. (2004) Mol. Pharmacol. 67(1):15-19). PEA has been demonstrated to exert anti-inflammatory and anti-nociceptive activities, and pharmaceutical formulations of PEA for the treatment of pain are available in Europe under the trade name NORMAST (Petrosino et al. (2010) Biochimie 92 (6):724-7; and Bacci et al. (2011) ISRN Surgery, Volume 2011, Article ID 917350, 6 pages; doi:10.5402/2011/917350).
Fatty amides, such as fatty alkanolamides and fatty aminoamides, also have a wide variety of non-pharmaceutical commercial uses. Fatty alkanolamides and fatty aminoamides are useful as foaming agents, surfactants, or intermediates thereof in the production of personal care products (e.g., shampoos, body washes, and facial cleansers), cosmetic formulations (e.g., blushes, mascaras, and lipsticks), and household cleaning products (e.g., laundry detergents, dishwashing liquids, and surface cleaning compositions). Fatty alkanolamides and fatty aminoamides also are useful as fuel additives. It is estimated that 100,000 tons of alkanolamides are consumed in the global market each year (Adlercreutz et al. (2010) Industrial Biotechnology 6 (4):204-211).
Fatty alkanolamides for commercial use classically have been produced via costly synthetic organic reactions between a fatty acid or fatty acid methyl ester derived from feedstocks such as natural oils or fats and crude oil and an alkanolamine (Adlercreutz et al., supra, and Frost & Sullivan, “Nonionic Surfactants in the Industrial Triad” (2002)). For example, PEA can be produced by reacting palmitoyl fatty acids derived from coconut oils with monoethanolamine in a Schotten-Baumann reaction, as follows:




Fatty alkanolamides have also been produced biosynthetically. For example, OEA can be produced from phosphatidylethanolamine (PE) and sn-1-oleoyl-phosphatidylcholine (PC) precursors via a two enzyme process, wherein PE and sn-1-oleoyl-PC are reacted with N-acyl transferase to form N-acyl phosphatidylethanolamine (NAPE) which is then combined with lyso-PC and reacted with NAPE-specific phospholipase D to form OEA and phosphatidic acid (see Astarita et al. (2006) Am. J. Physiol. Regul. Integr. Comp. Physiol 290:R1407-R1412).
These methods, as well as other methods known in the art for synthesizing fatty amides, often involve inefficient reaction steps and are thus costly, from both an economical and environmental perspective. Hence, there is a need for improved methods and reagents for the production of fatty amides, wherein the length and saturation of fatty chain as well as the type of the amide head group can be controlled efficiently.
SUMMARY
One aspect of the present disclosure provides a recombinant microorganism including a nucleic acid sequence encoding a polypeptide that catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide, wherein the microorganism is cultured in the presence of a carbon source. Herein, the microorganism is engineered to express the nucleic acid sequence that encodes the polypeptide that catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide when the microorganism is cultured in the presence of a carbon source. In one embodiment, the carbon source is a carbohydrate. In another embodiment, the polypeptide is a palmitoylputrescine synthase (PPS) polypeptide. In still another embodiment, the polypeptide is a N-(4-amino-2-hydroxylbutyl)tetradecanamide synthase (AhtS) polypeptide.
Another aspect of the disclosure provides a palmitoylputrescine synthase (PPS) polypeptide that has the amino acid sequence of SEQ ID NO: 1. In one embodiment, the PPS polypeptide includes an amino acid sequence that has at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 1. In another embodiment, the PPS polypeptide is encoded by a nucleic acid sequence comprising the nucleic acid sequence of SEQ ID NO: 2.
Another aspect of the disclosure provides a N-(4-amino-2-hydroxylbutyl)tetradecanamide synthase (AhtS) polypeptide that has the amino acid sequence of SEQ ID NO: 3. In one embodiment, the AhtS polypeptide includes an amino acid sequence that has at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 3. In another embodiment, the AhtS polypeptide is encoded by a nucleic acid sequence comprising the nucleic acid sequence of SEQ ID NO: 22.
Yet, another aspect of the disclosure provides a recombinant microorganism, wherein the primary amine includes, but is not limited to, 3-dimethylamino-1-propylamine, (±)-1-amino-2-propanol, 2-methoxyethylamine, 3-amino-1-propanol, 2-amino-1,3-propanediol, 3-methoxypropylamine, N-(2-hydroxyethyl)ethylenediamine, and butylamine, 1,4-diaminobutane, or a combination thereof.
Still, another aspect of the disclosure provides a recombinant microorganism, wherein the acyl thioester is a fatty acyl-ACP or a fatty acyl-CoA. The fatty acyl-ACP or the fatty acyl-CoA is produced by the microorganism.
The disclosure further encompasses a recombinant microorganism that includes a nucleic acid sequence encoding one or more of a fatty acid biosynthetic polypeptide, a thioesterase polypeptide (EC 3.1.2.14 or EC 3.1.1.5) and an acyl-CoA synthase polypeptide (EC 2.3.1.86). In one embodiment, the nucleic acid sequence encoding the thioesterase polypeptide is tesA. In another embodiment, the nucleic acid sequence encoding the acyl-CoA synthase polypeptide is fadD. In yet another embodiment, the microorganism includes a nucleic acid sequence encoding a fatty acid biosynthetic polypeptide, including, but not limited to accABCD, FabD, FabH, FabG, FabB, FabA, FabZ, FabF, FabI, and/or FadR.
The disclosure further contemplates a microorganism including, but not limited to, bacteria, cyanobacteria, algae, and fungi. In one embodiment, the bacteria is E. coli. In another embodiment, the fungi is yeast or filamentous fungi. In yet another embodiment, the microorganism includes, but is not limited to, Saccharomyces cerevisiae, Candida lipolytica, Escherichia coli, Arthrobacter, Rhodotorula glutinins, Acinetobacter, Candida lipolytica, Botryococcus braunii, Vibrio furnissii, Micrococcus leuteus, Stenotrophomonas maltophilia, Bacillus subtilis, Bacillus lichenoformis, Psuedomonus putida, Psuedomonas florescens, Streptomyces coelicolor, Synechococcus sp. PCC7002, Thermosynechococcus elongatus BP-1, Prototheca moriformis, Prototheca krugani, Prototheca stagnora, Prototheca zopfii, or Chorella protothecoide cell. In still another embodiment, the microorganism includes, but is not limited to Arthrobacter AK 19, Acinetobacter sp. strain M-1, E. coli B, E. coli C, E. coli K, or E. coli W cell.
Another aspect of the disclosure provides a recombinant microorganism including a nucleic acid sequence encoding a polypeptide that catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide, wherein the polypeptide that catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide is endogenous to the microorganism.
Another aspect of the disclosure provides a recombinant microorganism including a nucleic acid sequence encoding a polypeptide that catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide, wherein the polypeptide that catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide is exogenous to the microorganism.
Still, another aspect of the disclosure provides a recombinant microorganism including a nucleic acid sequence encoding an enzyme that catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide. In one embodiment, the fatty amide is a fatty alkanolamide and/or a fatty amidoamine. In another embodiment, the fatty amide is a C14, C16, and/or C18 fatty alkanolamide and/or a C14, C16, or C18 fatty amidoamine. In yet another embodiment, the fatty amide is a C8, C9, C10, C11, C12, C13, C14, C15, C16, C17, C18, C19 or C20 fatty alkanolamide and/or a C8, C9, C10, C11, C12, C13, C14, C15, C16, C17, C18, C19 or C20 fatty amidoamine.
Yet, another aspect of the disclosure provides a recombinant microorganism including a nucleic acid sequence encoding a polypeptide that catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide, wherein the microorganism expresses a serine decarboxylase polypeptide.
The disclosure further encompasses a method of producing a fatty amide including: (a) providing a recombinant microorganism including a nucleic acid sequence encoding a polypeptide that catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide; and (b) culturing the recombinant microorganism in a culture medium under conditions suitable for expression of the nucleic acid sequence encoding the polypeptide that catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide in the presence of at least one substrate for the polypeptide. This method may further include isolating the fatty amide from the culture medium. The method can be used to produce fatty amides. In one embodiment, the fatty amide is a fatty alkanolamide and/or a fatty amidoamine. In another embodiment, the fatty amide is a C8, C9, C10, C11, C12, C13, C14, C15, C16, C17, C18, C19 or C20 fatty alkanolamide and/or a C8, C9, C10, C11, C12, C13, C14, C15, C16, C17, C18, C19 or C20 fatty amidoamine.



BRIEF DESCRIPTION OF THE FIGURES
The present disclosure is best understood when read in conjunction with the accompanying figures, which serve to illustrate the preferred embodiments. It is understood, however, that the disclosure is not limited to the specific embodiments disclosed in the figures.
FIG. 1 is a representative gas chromatography-mass spectroscopy (GC-MS) chromatogram of the fatty species produced by E. coli MG1655 strain DG5 transformed with an expression vector encoding a palmitoylputrescine synthase (PPS) cultured in the presence of ethanolamine. The upper panel depicts a peak having a GC retention time of 13.1 min which was identified as N-palmitoylethanolamide by MS analysis depicted in the lower panel.
FIGS. 2A-2D are GC-MS chromatograms of the N-palmitoylethanolamide product following derivatization with N,O-bis(trimethylsilyl)-trifluoroacetamide (BSTFA). FIG. 2A depicts a peak having a GC retention time of 13.3 min which was identified as trimethylsilyl (TMS)-protected N-palmitoylethanolamide by MS analysis depicted in FIG. 2E. FIGS. 2B-2D are control chromatograms of BSTFA alone, N-palmitoylethanolamide without BSTFA derivatization, and blank reaction, respectively.
FIG. 3 is a GC-MS chromatogram of the fatty N-(3-dimethylamino-1-propylamine)amides produced by E. coli MG1655 strain DG5 transformed with an expression vector encoding a PPS cultured in the presence of 3-dimethylamino-1-propylamine.
FIG. 4 depicts the fatty amide products obtained from E. coli MG1655 cells transformed with an expression vector encoding a PPS and cultured in the presence of the indicated primary amine feeds.
FIG. 5 is a representative GC-MS chromatogram of the fatty species produced by an E. coli MG1655 strain transformed with an expression vector encoding the enzyme N-(4-amino-2-hydroxylbutyl)tetradecanamide synthase (AhtS) cultured in the presence of 3-dimethylamino-1-propylamine. The upper panel depicts a peak having a GC retention time of 11.4 min which was identified as C14:0 fatty N-(3-dimethylamino-1-propylamide) by MS analysis depicted in the lower panel.
FIG. 6 is a schematic diagram of metabolic pathways which can be genetically modified according to the methods of the disclosure.



DETAILED DESCRIPTION
The natural antibiotic palmitoylputrescine can be produced by bacteria which express palmitoylputrescine synthase (PPS) (GenBank Accession No. AAV33349.1 (hereinafter “AAV33349”)) (SEQ ID NO: 1) encoded by the nucleic acid sequence of GenBank Accession No. AY632377.1 (hereinafter “AY632377”) (SEQ ID NO: 2) (Brady et al. (2004) J. Nat. Prod. 67:1283-1286). When overexpressed in E. coli, the PPS encoded by AY632377 was demonstrated to produce only one major N-acyl derivative of putrescine (1,4-diaminobutane), namely palmitoylputrescine (Brady et al., supra). A homologue encoding the enzyme, N-(4-amino-2_hydroxylbutyl)tetradecanamide synthase (AhtS) (GeneBank Accession No. ACX33975.1) (SEQ ID NO: 3), has an amino acid sequence that is 38% identical to the amino acid sequence of PPS. The N-(4-amino-2-hydroxybutyl)tetradecanamide synthase (AhtS) gene from uncultured bacterium RM44 (GenBank GQ869386) is shown in (SEQ ID NO: 22).
The disclosure is based, at least in part, on the discovery that a microorganism (e.g., bacteria) expressing a PPS or AhtS can produce fatty amides from acyl thioester precursors when cultured in the presence of a carbon source. Without wanting to be bound by theory, it is believed that PPS directly catalyzes the amidation between an acyl thioester and a primary amine. This is the first time that a microorganism has been specifically engineered to express an enzyme such as PPS or AhtS in order to produce fatty amides. This is advantageous because the microorganism thereby serves as a convenient biological factory that generates fatty amides of desired chain length, including in branched or unbranched form. In addition, various different feedstocks (e.g., corn, sugar cane, glycerol, switchgrass) can be used interchangeably to supply the necessary carbon source for the microorganism, allowing for flexibility. As such, the microorganism can be used to produce fatty amides upon demand that can be harvested via fermentation, thereby bypassing the cumbersome and costly prior art systems that still rely on expensive natural oils and complicated synthetic chemistry. Fatty amides are needed for the production of numerous products including, but not limited to, foaming agents, cationic surfactants, intermediates for use as shampoos and bath products, emulsifying agents in cosmetics and pharmaceuticals, fuel additives, and the like.
The disclosure provides a recombinant microorganism engineered to express a nucleic acid sequence encoding a polypeptide that catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide, wherein the microorganism is cultured in the presence of a carbon source. In one embodiment, the carbon source is a carbohydrate. More specifically, the microorganism was engineered such that an enzyme like PPS or AhtS is expressed in order to catalyze the amidation between any primary amine (e.g, ethanolamine, amine 3-dimethylamino-1-propylamine) with an acyl thiol-ester (e.g., acyl-CoA or acyl-ACP) in order to produce fatty amides such as alkanolamides and amidoamines. This is a novel process because fatty alkanolamides (e.g., intermediates used in the synthesis of cocamidopropyl betaine) and amidoamines have so far been produced synthetically from feed stocks such as natural oils (or fats) and crude oil, which is an inefficient process because it relies on refining the raw materials until the desired materials are achieved. In comparison, the present disclosure provides a production method, wherein a microorganism is engineered to express enzymes such that, for example, alkanolamides and fatty N-(3-dimethylamino-1-propylamine)amides are synthesized biochemically, which is a much more effective process for producing fatty amides. Amino acids or carbohydrates can be added to the fermentation medium of the microorganism to supply the necessary carbon source (see Examples 3-7). Alternatively, the microorganism can be engineered to generate its own primary amine in vivo. For example, the biosynthesis of ethanolamine can be achieved by genetically increasing serine biosynthesis and serine decarboxylation pathways (see Example 8). Enzymatically, AhtS produces the same amide compounds as PPS but with a preference for C14:0 fatty thioester substrates. Both enzymes belong to EC family 2.3.1.X.X.
The disclosure further provides a method of producing a fatty amide in a recombinant microorganism. Fatty amides produced by this method include, but are not limited to, fatty alkanolamides and fatty amidoamines. In one embodiment, the fatty amide is a C14, C16, and/or C18 fatty alkanolamide. In another embodiment, the fatty amide is a C14, C16, and/or C18 fatty amidoamine. The method involves the steps of (a) providing a recombinant microorganism engineered to express a nucleic acid sequence encoding a polypeptide such as PPS or AhtS which catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide; and (b) culturing the recombinant microorganism under conditions suitable for expression of the polypeptide in the presence of at least one substrate for the polypeptide, thereby producing the fatty amide. The microorganism is cultured in the presence of a carbon source. The carbon source can be selected from a wide variety of different sources, including but not limited to, amino acids, carbohydrates, and lipids. In one embodiment, the carbon source is a carbohydrate. The fatty amide that is produced by the microorganism can be isolated from the culture broth (e.g., fermentation broth). In one embodiment, the fatty amide is isolated from the extracellular environment of the microorganism. In another embodiment, the fatty amide is spontaneously secreted, partially or completely, from the microorganism. In another embodiment, the fatty amide is transported into the extracellular environment, optionally with the aid of one or more suitable transport proteins. In yet another embodiment, the fatty amide is passively transported into the extracellular environment.
The terms “fatty amide” and “alkyl amide” refer to a compound having the formula R1CONHR2, wherein R1 represents an aliphatic group derived from a fatty acid, and R2 represents a substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted alkenyl, or substituted or unsubstituted heteroalkenyl group derived from a primary amine.
An “acyl thioester” refers to a fatty acid which has been “activated” by a fatty acid biosynthetic pathway of the production host microorganism. The acyl thioester can be generated from a fatty acid endogenous to the microorganism, or the acyl thioester can be generated from a fatty acid provided to the microorganism exogenously. Non-limiting examples of acyl thioesters are acyl-coenzyme A (CoA) and acyl-acyl carrier protein (ACP).
The term “acyl-CoA” refers to an acyl thioester formed between the carbonyl carbon of an alkyl chain and the sulfhydryl group of the 4′-phosphopantetheine moiety of CoA, which has the formula R1—C(O)S-CoA, where R1 is an aliphatic group. The term “acyl-ACP” refers to an acyl thioester formed between the carbonyl carbon of an alkyl chain and the sulfhydryl group of a 4′-phosphopantetheine moiety attached to ACP, which has the formula R1—C(O)S-ACP, where R1 is an aliphatic group.
The term “fatty acid” means a carboxylic acid having the formula R1COOH. R1 represents an aliphatic group, preferably an alkyl group. R1 can comprise between 4 and 26 carbon atoms. In certain embodiments, R1 is at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 carbons in length. Alternatively, or in addition, the R1 group is 22 or less, 21 or less, 20 or less, 19 or less, 18 or less, 17 or less, 16 or less, 15 or less, 14 or less, 13 or less, 12 or less, 11 or less, 10 or less, 9 or less, 8 or less, 7 or less, or 6 or less carbons in length. Thus, the R1 group can have an R1 group bounded by any two of the above endpoints. For example, the R1 group can be 6-16 carbons in length, 10-14 carbons in length, or 12-18 carbons in length. In some embodiments, the fatty acid is a C6, C7, C8, C9, C10, C11, C12, C13, C14, C15, C16, C17, C18, C19, C20, C21, C22, C23, C24, C25, or C26 fatty acid. In certain embodiments, the fatty acid is a C6, C8, C10, C12, C13, C14, C15, C16, C17, or C18 fatty acid. In one preferred embodiment, the fatty amide is a C14, C16, or C18 fatty alkanolamide. In another preferred embodiment, the fatty amide is a C14, C16, or C18 fatty amidoamine. In still another preferred embodiment, the fatty amide is a C8, C9, C10, C11, C12, C13, C14, C15, C16, C17, C18, C19 or C20 alkanolamide. In yet another preferred embodiment, the fatty amide is a C8, C9, C10, C11, C12, C13, C14, C15, C16, C17, C18, C19 or C20 amidoamine.
The R1 group of a fatty acid can be a straight chain or a branched chain. Branched chains may have more than one point of branching and may include cyclic branches. In some embodiments, the branched fatty acid is a C6, C7, C8, C9, C10, C11, C12, C13, C14, C15, C16, C17, C18, C19, C20, C21, C22, C23, C24, C25, or C26 branched fatty acid. In particular embodiments, the branched fatty acid is a C6, C8, C10, C12, C13, C14, C15, C16, C17, or C18 branched fatty acid. In certain embodiments, the hydroxyl group of the branched fatty acid is in the primary (C1) position.
In certain embodiments, the branched fatty acid is an iso-fatty acid or an anteiso-fatty acid. In exemplary embodiments, the branched fatty acid is selected from iso-C7:0, iso-C8:0, iso-C9:0, iso-C10:0, iso-C11:0, iso-C12:0, iso-C13:0, iso-C14:0, iso-C15:0, iso-C16:0, iso-C17:0, iso-C18:0, iso-C19:0, anteiso-C7:0, anteiso-C8:0, anteiso-C9:0, anteiso-C10:0, anteiso-C11:0, anteiso-C12:0, anteiso-C13:0, anteiso-C14:0, anteiso-C15:0, anteiso-C16:0, anteiso-C17:0, anteiso-C18:0, and anteiso-C19:0 branched fatty acid.
The R1 group of a branched or unbranched fatty acid can be saturated or unsaturated. If unsaturated, the R1 group can have one or more than one point of unsaturation. In some embodiments, the unsaturated fatty acid is a monounsaturated fatty acid. In certain embodiments, the unsaturated fatty acid is a C6:1, C7:1, C8:1, C9:1, C10:1, C11:1, C12:1, C13:1, C14:1, C15:1, C16:1, C17:1, C18:1, C19:1, C20:1, C21:1, C22:1, C23:1, C24:1, C25:1, or C26:1 unsaturated fatty acid. In other embodiments, the unsaturated fatty acid is a C10:1, C12:1, C14:1, C16:1, or C18:1 unsaturated fatty acid. In yet other embodiments, the unsaturated fatty acid is unsaturated at the omega-7 position. In certain embodiments, the unsaturated fatty acid comprises a cis double bond.
The primary amine can be any primary amine capable of serving as a substrate for PPS having the formula R2NH2, wherein R2 represents a substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted alkenyl, or substituted or unsubstituted heteroalkenyl chain. In certain embodiments, R2 is substituted with a hydroxyl group, and the fatty amide may be referred to as an “alkanolamide” or a “fatty alkanolamide.” In other embodiments, R2 contains an amino group, and the fatty amide may be referred to as an “amidoamine” or a “fatty amidoamine.”
R2 can comprise between 1 and 12 carbon atoms. In certain embodiments, R2 comprises at least 2, at least 3, at least 4, at least 5, at least 6, or at least 7 carbons. Alternatively, or in addition, R2 comprises 12 or less, 11 or less, 10 or less, 9 or less, 8 or less, 7 or less, 6 or less, 5 or less, or 4 or less carbons. Thus, the R2 group can comprise carbons bounded by any two of the above endpoints. For example, the R2 group can comprise 2-8 carbons, 4-10 carbons, or 3-6 carbons. In some embodiments, the R2 group contains 3, 4, 5, or 6 carbon atoms.
The R2 group of a primary amine can be a straight chain or a branched chain. Branched chains may have more than one point of branching and may include cyclic branches.
The term “alkyl,” by itself or as part of another substituent means, unless otherwise stated, a straight chain or branched chain, or cyclic hydrocarbon radical, or combination thereof. This definition also applies wherever “alkyl” occurs as part of a group, such as, e.g., in hydroxyalkyl, haloalkyl, aminoalkyl, alkylamino, dialkylamino, etc.
The term “alkenyl,” by itself or as part of another substituent means, unless otherwise stated, a straight chain or branched chain, or cyclic hydrocarbon radical, or combination thereof, containing, for example, about 2 to about 12 carbon atoms and containing at least one carbon-carbon double bond.
The terms “heteroalkyl” and “heteroalkenyl” refer to, unless otherwise stated, a straight or branched chain, or cyclic hydrocarbon radical, or combinations thereof, consisting of the stated number of carbon atoms and at least one heteroatom selected from the group consisting of O, N, Si, and S, and wherein the nitrogen and sulfur atoms may optionally be oxidized, and the nitrogen heteroatom may optionally be quaternized. The heteroatom(s) O, N, Si, and S may be placed at any interior position of the heteroalkyl or heteroalkenyl group. Exemplary heteroalkyl groups for the R2 group include, but are not limited to, —CH2—CH2—OH, —CH2—CH2—O—CH3, —CH2—CHOH—CH3, —CH2—CH2—CH2—O—CH3, —CH2—CH2—CH2—N(CH3)2, CH2—CH2—CH2—NH—CH2—CH3, —CH2—CH2—CH2—NH—CH2—CH2—OH, —CH—(CH2—OH)2, and —Si(CH3)3. Up to two heteroatoms may be consecutive, such as, for example, —CH2—CH2—O—Si(CH3)3.
The terms alkyl, heteroalkyl, alkenyl, and heteroalkenyl are meant to include both substituted and unsubstituted forms of the indicated radical. Exemplary substituents for the alkyl, heteroalkyl, alkenyl, and heteroalkenyl radicals of the R2 group can be one or more of a variety of groups selected from, but not limited to, —OR′, ═O, ═NR′, ═N—OR′, —NR′R′′, —SR′, -halogen, —SiR′R′′R′′′, —OC(O)R′, —C(O)R′, —CO2R′, —CN and —NO2 in a number ranging from zero to (2m′+1), where m′ is the total number of carbon atoms in such radical. Each of R′, R′′, and R′′′ independently refers to hydrogen, unsubstituted or substituted alkyl, unsubstituted or substituted heteroalkyl, unsubstituted or substituted alkenyl, unsubstituted or substituted heteroalkenyl, alkoxy or thioalkoxy groups, or arylalkyl groups.
In some embodiments, the substituent for the R2 group is —OH. In certain embodiments, the R2 group is a polyhydroxy alkyl or a polyhydroxy heteroalkyl moiety containing 2, 3, or 4 hydroxyl groups.
The alkyl, heteroalkyl, alkenyl, or heteroalkenyl chain of the R2 group also can be interrupted with a polyethylene oxide moiety. In certain embodiments, the R2 group contains a polyethylene oxide moiety comprising 2 or more, 3 or more, 4 or more, 5 or more, or 6 or more, or 7 or more ethylene oxide moieties. In other embodiments, the R2 group contains a polyethylene oxide moiety comprising 12 or less, 11 or less, 10 or less, 9 or less, 8 or less, 7 or less, 6 or less, or 5 or less ethylene oxide moieties. Thus, the R2 group can contain a polyethylene oxide moiety having a number of ethylene oxide moieties bounded by any two of the above endpoints. For example, the R2 group can contain a polyethylene oxide moiety having 2-10, 4-8, or 3-5 ethylene oxide moieties.
The primary amine may be produced in the microorganism from a fermentable carbon source. For example, monoethanolamine can be generated in vivo from serine by the action of serine decarboxylase (SDC) (Rontein et al. (2001) J. Biol. Chem. 276 (38):35523-35529). In some embodiments, the microorganism expresses an endogenous SDC polypeptide. In other embodiments, the microorganism is engineered to overexpress a SDC polypeptide.
Putrescine (1,4-diaminobutane) can be generated in vivo from arginine by the actions of arginine decarboxylase (ADC) and agmatine ureohydrolase (AUH), which convert arginine to agmatine, and agmatine to putrescine, respectively (Moore et al. (1990) J. Bacteriol 172(8): 4631-4640). In some embodiments, the microorganism expresses endogenous ADC and AUH polypeptides. In other embodiments, the microorganism is engineered to overexpress an ADC polypeptide, an AUH polypeptide, or ADC and AUH polypeptides. In certain embodiments, the ADC is encoded by the speA gene from E. coli MG1655 (GenBank Accession No. NC_000913).
The primary amine can also be provided to the microorganism exogenously.
Exemplary primary amines suitable for use in the disclosure include, but are not limited to, ethanolamine (monoethanolamine), 3-dimethylamino-1-propylamine, (±)-1-amino-2-propanol, 2-methoxyethylamine, 3-amino-1-propanol, 2-amino-1-3-propanediol, 3-methoxypropylamine, N-(2-hydroxyethyl)ethylenediamine, butylamine, 1,4-diaminobutane, and combinations thereof. In certain embodiments, the primary amine is 3-dimethylamino-1-propylamine.
The nucleic acid suitable for use in the recombinant microorganisms and methods of the disclosure can be any nucleic acid having a sequence which encodes a polypeptide capable of converting a primary amine and an acyl thioester to a fatty amide when the nucleic acid is expressed and the microorganism is cultured in the presence of a carbon source.
In one embodiment, the polypeptide is a PPS polypeptide. In certain embodiments, the PPS polypeptide comprises, consists essentially of, or consists of the amino acid sequence of SEQ ID NO: 1, i.e., the amino acid sequence of AAV33349. In some embodiments, the PPS polypeptide is encoded by a nucleic acid sequence comprising the nucleic acid sequence of SEQ ID NO: 2. In other embodiments, the PPS polypeptide is a homologue of the PPS polypeptide having the amino acid sequence of SEQ ID NO: 1. The PPS polypeptide preferably comprises, consists essentially of, or consists of an amino acid sequence that is at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to the amino acid sequence of SEQ ID NO: 1.
In other embodiments, the polypeptide is a N-(4-amino-2-hydroxylbutyl)tetradecanamide synthase (AhtS) polypeptide. In certain embodiments, the AhtS polypeptide comprises, consists essentially of, or consists of the amino acid sequence of SEQ ID NO: 3, i.e., the amino acid sequence of GenBank Accession No. ACX33975. In some embodiments, the AhtS polypeptide is encoded by a nucleic acid sequence comprising the nucleic acid sequence of SEQ ID NO: 22. In other embodiments, the AhtS polypeptide is a homologue of the AhtS polypeptide having the amino acid sequence of SEQ ID NO: 3. The AhtS polypeptide preferably comprises, consists essentially of, or consists of an amino acid sequence that is at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to the amino acid sequence of SEQ ID NO: 3.
In certain embodiments, the polypeptide that catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide is endogenous to the microorganism. In such embodiments, the recombinant microorganism is engineered to overexpress the endogenous polypeptide that catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide.
In other embodiments, the polypeptide that catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide is exogenous to the microorganism. In such embodiments, the recombinant microorganism is engineered to express the exogenous polypeptide such that it catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide. For example, the exogenous nucleic acid encoding the exogenous polypeptide can be integrated into the microorganism through standard molecular biology procedures. Providing the microorganism with a carbon source will allow the microorganism to increase fatty amide production.
The terms “homolog,” “homologue,” and “homologous” as used herein refer to a polynucleotide or a polypeptide comprising a sequence that is at least about 70% homologous to the corresponding polynucleotide or polypeptide sequence. One of ordinary skill in the art is well aware of methods to determine homology between two or more sequences. For example, the comparison of sequences and determination of percent homology between two sequences can be accomplished using a mathematical algorithm, such as Basic Local Alignment Search Tool (BLAST) (Altschul et al. (1990) J. Mol. Biol. 215 (3): 403-410).
The term “polynucleotide” refers to a polymer of DNA or RNA, which can be single-stranded or double-stranded and which can contain non-natural or altered nucleotides. The terms “polynucleotide,” “nucleic acid,” and “nucleic acid molecule” are used herein interchangeably to refer to a polymeric form of nucleotides of any length, either ribonucleotides (RNA) or deoxyribonucleotides (DNA).
The terms “polypeptide” and “protein” refer to a polymer of amino acid residues. The term “recombinant polypeptide” refers to a polypeptide that is produced by recombinant DNA techniques, wherein generally DNA encoding the expressed protein or RNA is inserted into a suitable expression vector that is in turn used to transform a host cell to produce the polypeptide or RNA.
In the compositions and methods of the disclosure, the production of a desired fatty acid or acyl thioester derivative thereof can be enhanced by altering the expression of one or more genes involved in the regulation of fatty acid production, degradation and/or secretion in the recombinant microorganism.
In some embodiments, the recombinant microorganism comprises a nucleic acid sequence encoding a fatty acid biosynthetic polypeptide. As used herein, the term “fatty acid biosynthetic polypeptide” refers to any polypeptide involved in fatty acid biosynthesis. The fatty acid biosynthetic pathway in host cells uses the precursors acetyl-CoA and malonyl-CoA. The steps in this pathway are catalyzed by enzymes of the fatty acid biosynthesis (fab) and acetyl-CoA carboxylase (acc) gene families (see, e.g., Heath et al. (2001) Prog. Lipid Res. 40 (6):467-497). Acetyl-CoA is carboxylated by acetyl-CoA carboxylase (EC 6.4.1.2) to form malonyl-CoA. Acetyl-CoA carboxylase (EC 6.4.1.2) is a multi-subunit enzyme encoded by four separate genes (accA, accB, accC, and accD) in most prokaryotes. In some bacteria, such as Corynebacterium glutamicus, acetyl-CoA carboxylase includes two subunits, AccDA [YP_225123.1] and AccBC [YP_224991], encoded by accDA and accBC, respectively. Depending upon the desired fatty acid or fatty acid derivative product, specific fab and/or acc genes (or combinations thereof) may be overexpressed, modified, attenuated, or deleted in an engineered host cell.
In some embodiments, the nucleic acid sequence encoding a fatty acid biosynthetic polypeptide encodes accABCD. In other embodiments, the nucleic acid sequence encoding a fatty acid biosynthetic polypeptide encodes FabD, FabH, FabG, FabB, FabA, FabZ, FabF, FabI, or a functional homologue of Fab from another organism, such as FabV. Exemplary GenBank Accession numbers for the fatty acid biosynthetic polypeptides suitable for use in the compositions and methods of the disclosure include FabD (AAC74176), FabH (AAC74175), FabG (AAC74177), FabB (POA953), FabA (ACY27485.1), FabZ (ACY27493.1), FabF (AAC74179), and FabI (NP_415804).
In some embodiments, the recombinant microorganism comprises nucleic acid sequences encoding two or more (e.g., 3 or more, 4 or more) biosynthetic polypeptides (e.g., accABCD and FabD; FabD, FabH, and FabG; or FabI, FabG,H,D, FabA,B, and FabZ).
FadR is a transcription factor involved in fatty acid degradation and fatty acid biosynthesis pathways (Cronan et al. (1998) Mol. Microbiol. 29 (4):937-943). FadR is known to modulate the expression and/or activity of numerous genes, including fabA, fabB, iclR, fadA, fadB, fadD, fadE, fadl, fadJ, fadL, fadM, uspA, aceA, aceB, and aceK. Exemplary GenBank accession numbers for polypeptides encoded by the FadR target genes include fabA (NP_415474), fabB (BAA16180), (NP_418442), fadA (YP_026272.1), fadB (NP_418288.1), fadD (AP_002424), fadE (NP_414756.2), fadl (NP_416844.1), fadJ (NP_416843.1), fadL (AAC75404), fadM (NP_414977.1), uspA (AAC76520), aceA (AAC76985.1), aceB (AAC76984.1), and aceK (AAC76986.1).
In some embodiments, the recombinant microorganism includes a nucleic acid sequence encoding a fatty acid biosynthetic polypeptide, and the nucleic acid sequence encoding FadR. In certain embodiments, the nucleic acid sequence encodes FadR from E. coli MG1655 (NP_415705).
Thioesterases (EC 3.1.2.14 or EC 3.1.1.5) hydrolyze fatty acids from acyl-ACP thioesters. The chain length of an acyl thioester substrate can be selected for by modifying the expression of selected thioesterases. In certain embodiments, a host cell is engineered to express, overexpress, have attenuated expression, or not to express one or more selected thioesterases to increase the production of a preferred fatty acid derivative substrate. For example, C10 fatty acids can be produced by expressing a thioesterase that has a preference for producing C10 fatty acids and attenuating thioesterases that have a preference for producing fatty acids other than C10 fatty acids (e.g., a thioesterase which prefers to produce C14 fatty acids). This would result in a relatively homogeneous population of fatty acids that comprise 10 carbons. In other instances, C14 fatty acids can be produced by attenuating endogenous thioesterases that produce non-C14 fatty acids and expressing the thioesterases that have a preference for C14-ACP. In some situations, C12 fatty acids can be produced by expressing thioesterases that have a preference for C12-ACP and attenuating thioesterases that preferentially produce non-C12 fatty acids. Acetyl-CoA, malonyl-CoA, and fatty acid overproduction can be verified using methods known in the art, for example, by using radioactive precursors, HPLC, or GC-MS.
Non-limiting examples of thioesterase genes (and corresponding GenBank Accession number(s)) whose expression can be altered in the compositions and methods of the disclosure include tesA without leader sequence ('tesA) from E. coli (AAC73596), tesB from E. coli (AAC73555), fatB from Umbellularia california (Q41635, AAA34215), fatB2 from Cuphea hookeriana (AAC49269), fatB3 from Cuphea hookeriana (Q39513; AAC72881), fatB from Cinnamonum camphorum (Q39473, AAC49151), fatB [M 141T] from Arabidopsis thaliana (CAA85388) (Mayer et al. (2007) BMC Plant Biology 7:1-11), fatA from Arabidopsis thaliana (NP 189147; NP 193041), fatA from Bradyrhiizobium japonicum (CAC39106), fatA from Cuphea hookeriana (AAC72883), and fatA1 from Helianthus annus (AAL79361).
In certain embodiments, the recombinant microorganism includes a nucleic acid sequence encoding a thioesterase, and the nucleic acid sequence is 'tesA from E. coli MG1655 (AAC73596).
Acyl-CoA synthases (EC 2.3.1.86) activate fatty acids by catalyzing the formation of acyl-CoA thioesters. Non-limiting examples of acyl-CoA synthase genes whose expression can be altered in the compositions and methods of the disclosure include fadD, fadK, BH3103, yhfL, Pfl-4354, EAV15023, fadD1, fadD2, RPC_4074, fadDD35, fadDD22, faa3p or the gene encoding the protein ZP_01644857. Specific examples of acyl-CoA synthase genes include fadDD35 from M. tuberculosis H37Rv [NP_217021], fadDD22 from M. tuberculosis H37Rv [NP_217464], fadD from E. coli [NP_416319], fadK from E. coli [YP_416216], fadD from Acinetobacter sp. ADP1 [YP_045024], fadD from Haemophilus influenza RdkW20 [NP_438551], fadD from Rhodopseudomonas palustris Bis B 18 [YP_533919], BH3101 from Bacillus halodurans C-125 [NP_243969], Pfl-4354 from Pseudomonas fluorescens Pfo-1 [YP_350082], EAV15023 from Comamonas testosterone KF-1 [ZP_01520072], yhfL from B. subtilis [NP_388908], fadD1 from P. aeruginosa PAO1 [NP_251989], fadD1 from Ralstonia solanacearum GM1 1000 [NP_520978], fadD2 from P. aeruginosa PAO1 [NP_251990], the gene encoding the protein ZP_01644857 from Stenotrophomonas maltophilia R551-3, faa3p from Saccharomyces cerevisiae [NP_012257], faalp from Saccharomyces cerevisiae [NP_014962], lcfA from Bacillus subtilis [CAA99571], and those described in Shockey et al. (2002) Plant. Physiol. 129:1710-1722); Caviglia et al. (2004) J. Biol. Chem. 279:1163-1169); Knoll et al. (1994) J. Biol. Chem. 269(23):16348-56); Johnson et al. (1994) J. Biol. Chem. 269:18037-18046); and Black et al. (1992) J. Biol. Chem. 267:25513-25520).
In some embodiments, the recombinant microorganism comprises a nucleic acid sequence encoding an acyl-CoA synthase polypeptide, and the acyl-CoA synthase polypeptide is FadD from E. coli MG1655 [NP_416319].
The recombinant microorganism can comprise nucleic acids encoding any combination of fatty acid biosynthetic polypeptides, thioesterase polypeptides, and acyl-CoA synthase polypeptides. In certain embodiments, the microorganism comprises a nucleic acid sequence encoding a thioesterase polypeptide and a nucleic acid sequence encoding an acyl-CoA synthase polypeptide.
One of ordinary skill in the art will understand that, depending upon the purpose (e.g., desired fatty acid or acyl thioester derivative thereof), specific genes (or combinations of genes) involved in fatty acid metabolism may be overexpressed, modified, attenuated, or deleted in a recombinant microorganism engineered to comprise a nucleic acid sequence encoding a polypeptide capable of catalyzing the conversion of a primary amine and an acyl thioester to a fatty amide. Additional examples of genes involved in fatty acid metabolism suitable for use in the disclosure are described, for example, in U.S. Patent Application Publication 2011/0162259, which is incorporated in its entirety by reference herein.
In some embodiments, the polypeptide is a fragment of any of the polypeptides described herein. The term “fragment” refers to a shorter portion of a full-length polypeptide or protein ranging in size from four amino acid residues to the entire amino acid sequence minus one amino acid residue. In certain embodiments of the invention, a fragment refers to the entire amino acid sequence of a domain of a polypeptide or protein (e.g., a substrate binding domain or a catalytic domain).
In some embodiments, the polypeptide is a mutant or a variant of any of the polypeptides described herein. The terms “mutant” and “variant” as used herein refer to a polypeptide having an amino acid sequence that differs from a wild-type polypeptide by at least one amino acid. For example, the mutant can comprise one or more of the following conservative amino acid substitutions: replacement of an aliphatic amino acid, such as alanine, valine, leucine, and isoleucine, with another aliphatic amino acid; replacement of a serine with a threonine; replacement of a threonine with a serine; replacement of an acidic residue, such as aspartic acid and glutamic acid, with another acidic residue; replacement of a residue bearing an amide group, such as asparagine and glutamine, with another residue bearing an amide group; exchange of a basic residue, such as lysine and arginine, with another basic residue; and replacement of an aromatic residue, such as phenylalanine and tyrosine, with another aromatic residue. In some embodiments, the mutant polypeptide has about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, or more amino acid substitutions, additions, insertions, or deletions.
Preferred fragments or mutants of a polypeptide retain some or all of the biological function (e.g., enzymatic activity) of the corresponding wild-type polypeptide. In some embodiments, the fragment or mutant retains at least about 75%, at least about 80%, at least about 90%, at least about 95%, or at least about 98% or more of the biological function of the corresponding wild-type polypeptide. In other embodiments, the fragment or mutant retains about 100% of the biological function of the corresponding wild-type polypeptide. Guidance in determining which amino acid residues may be substituted, inserted, or deleted without affecting biological activity may be found using computer programs well known in the art, for example, LASERGENETM software (DNASTAR, Inc., Madison, Wis.).
In yet other embodiments, a fragment or mutant has an “increased level of activity.” By “increased level of activity” is meant that a polypeptide has a higher level of biochemical or biological function (e.g., DNA binding or enzymatic activity) in an engineered cell as compared to its level of biochemical and/or biological function in a corresponding wild-type host cell under the same conditions. The degree of enhanced activity can be about 10% or more, about 20% or more, about 50% or more, about 75% or more, about 100% or more, about 200% or more, about 500% or more, about 1000% or more, or any range therein.
In some embodiments, a polypeptide or polynucleotide having an altered or modified level of expression is “overexpressed” or has an “increased level of expression.” As used herein, “overexpress” and “increasing the level of expression” mean to express or cause to be expressed a polynucleotide or polypeptide in an engineered cell at a greater concentration than is normally expressed in a corresponding wild-type cell under the same conditions. For example, a polypeptide can be “overexpressed” in an engineered cell when the polypeptide is present in a greater concentration in the engineered cell as compared to its concentration in a non-engineered host cell of the same species under the same conditions.
In other embodiments, a polypeptide or polynucleotide having altered level of expression is “attenuated” or has a “decreased level of expression.” As used herein, “attenuate” and “decreasing the level of expression” mean to express or cause to be expressed a polynucleotide or polypeptide in an engineered cell at a lesser concentration than is normally expressed in a corresponding wild-type cell under the same conditions.
The degree of overexpression or attenuation can be 1.5-fold or more, e.g., 2-fold or more, 3-fold or more, 5-fold or more, 10-fold or more, or 15-fold or more. Alternatively, or in addition, the degree of overexpression or attenuation can be 500-fold or less, e.g., 100-fold or less, 50-fold or less, 25-fold or less, or 20-fold or less. Thus, the degree of overexpression or attenuation can be bounded by any two of the above endpoints. For example, the degree of overexpression or attenuation can be 1.5-500-fold, 2-50-fold, 10-25-fold, or 15-20-fold.
A polynucleotide or polypeptide can be attenuated using methods known in the art. In some embodiments, the expression of a gene or polypeptide encoded by the gene is attenuated by mutating the regulatory polynucleotide sequences which control expression of the gene. In other embodiments, the expression of a gene or polypeptide encoded by the gene is attenuated by overexpressing a repressor protein, or by providing an exogenous regulatory element that activates a repressor protein. In still yet other embodiments, DNA- or RNA-based gene silencing methods are used to attenuate the expression of a gene or polynucleotide. In some embodiments, the expression of a gene or polypeptide is completely attenuated, e.g., by deleting all or a portion of the polynucleotide sequence of a gene.
A polynucleotide or polypeptide can be overexpressed using methods known in the art. In some embodiments, overexpression of a polypeptide is achieved by the use of an exogenous regulatory element. The term “exogenous regulatory element” generally refers to a regulatory element originating outside of the host cell. However, in certain embodiments, the term “exogenous regulatory element” can refer to a regulatory element derived from the host cell whose function is replicated or usurped for the purpose of controlling the expression of an endogenous polypeptide. For example, if the recombinant microorganism is an E. coli cell which comprises a nucleic acid sequence encoding a fatty acid biosynthetic polypeptide, and the fatty acid biosynthetic polypeptide is FadR encoded by an endogenous fadR gene, then expression of the endogenous fadR can be controlled by a promoter derived from another E. coli gene.
In some embodiments, the exogenous regulatory element is a chemical compound, such as a small molecule. As used herein, the term “small molecule” refers to a substance or compound having a molecular weight of less than about 1,000 g/mol.
In some embodiments, the exogenous regulatory element which controls the expression of a nucleic acid sequence is an expression control sequence which is operably linked to the nucleic acid sequence. Expression control sequences are known in the art and include, for example, promoters, enhancers, polyadenylation signals, transcription terminators, internal ribosome entry sites (IRES), ribosome binding sites (RBS), and the like, that provide for the expression of the nucleic acid sequence in a host cell. Expression control sequences interact specifically with cellular proteins involved in transcription (Maniatis et al. (1987) Science 236:1237-1245). Exemplary expression control sequences are described in, for example, Goeddel, Gene Expression Technology: Methods in Enzymology, Vol. 185, Academic Press, San Diego, Calif. (1990).
By “operably linked” is meant that a nucleic acid sequence and an expression control sequence(s) are connected in such a way as to permit gene expression when the appropriate molecules (e.g., transcriptional activator proteins) are bound to the expression control sequence(s). Operably linked promoters are located upstream of the selected nucleic acid sequence in terms of the direction of transcription and translation. Operably linked enhancers can be located upstream, within, or downstream of the selected nucleic acid sequence.
In some embodiments, the nucleic acid sequence is provided to the host cell by way of a recombinant vector, which comprises a promoter operably linked to the polynucleotide sequence. In certain embodiments, the promoter is an inducible, a constitutive, or an organelle specific promoter. In certain embodiments, the expression control sequence is operably linked to an endogenous nucleic acid sequence by integration of the expression control sequence into the genome of a host cell by homologous recombination using methods known in the art (e.g., Datsenko et al. (2000) Proc. Natl. Acad. Sci. U.S.A. 97 (12): 6640-6645).
As used herein, the term “vector” refers to a nucleic acid molecule capable of transporting another nucleic acid sequence to which it has been linked. One type of useful vector is an episome (i.e., a nucleic acid capable of extra-chromosomal replication). Useful vectors are those capable of autonomous replication and/or expression of nucleic acids to which they are linked. Vectors capable of directing the expression of genes to which they are operatively linked are referred to herein as “expression vectors.” In general, expression vectors of utility in recombinant DNA techniques are often in the form of “plasmids,” which refer generally to circular double stranded DNA loops that, in their vector form, are not bound to the chromosome. However, also included are such other forms of expression vectors that serve equivalent functions and that become known in the art subsequently hereto.
In some embodiments, the recombinant vector comprises at least one sequence selected from the group consisting of (a) an expression control sequence operatively coupled to the nucleic acid sequence; (b) a selection marker operatively coupled to the nucleic acid sequence; and (c) a targeting sequence operatively coupled to the nucleic acid sequence.
It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of polypeptide desired, etc. The expression vectors described herein can be introduced into host cells to produce polypeptides, including fusion polypeptides, encoded by the polynucleotide sequences as described herein.
Suitable expression systems for both prokaryotic and eukaryotic cells are well known in the art; see, e.g., Sambrook et al., “Molecular Cloning: A Laboratory Manual,” second edition, Cold Spring Harbor Laboratory (1989). Examples of inducible, non-fusion E. coli expression vectors include pTrc (Amann et al. (1988) Gene 69:301-315) and PET 11d (Studier et al., Gene Expression Technology Methods in Enzymology 185, Academic Press, San Diego, Calif., pp. 60-89 (1990)). In certain embodiments, a polynucleotide sequence of the disclosure is operably linked to a promoter derived from bacteriophage T5. Examples of vectors for expression in yeast include pYepSec1 (Baldari et al. (1987) EMBO J. 6:229-234), pMFa (Kurjan et al. (1982) Cell 30:933-943), pJRY88 (Schultz et al. (1987) Gene 54:113-123), pYES2 (Invitrogen Corp., San Diego, Calif.), and picZ (Invitrogen Corp., San Diego, Calif.).
Vectors can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques. As used herein, the terms “transformation” and “transfection” refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, or electroporation. Suitable methods for transforming or transfecting host cells as well as methods to select for cells which have taken up the vector can be found in, for example, Sambrook et al. (supra).
A “recombinant microorganism” is a host cell used to produce a product described herein (e.g., a fatty amide). A recombinant microorganism, also referred to herein as a “recombinant host cell,” an “engineered microorganism,” or an “engineered host cell,” is a host cell wherein the expression of one or more nucleic acids or polypeptides are altered or modified as compared to their expression in a corresponding wild-type host cell under the same conditions. In any of the aspects of the disclosure described herein, the host cell can include, but is not limited to, a bacteria cell, a cyanobacteria cell, an algae cell, and a fungus cell (e.g., a filamentous fungus cell or a yeast cell).
In some embodiments, the host cell is a Gram-positive bacterial cell. In other embodiments, the host cell is a Gram-negative bacterial cell.
In some embodiments, the host cell is selected from the genus Escherichia, Bacillus, Lactobacillus, Rhodococcus, Pseudomonas, Aspergillus, Trichoderma, Neurospora, Fusarium, Humicola, Rhizomucor, Kluyveromyces, Pichia, Mucor, Myceliophtora, Penicillium, Phanerochaete, Pleurotus, Trametes, Chrysosporium, Saccharomyces, Stenotrophamonas, Schizosaccharomyces, Synechococcus, Yarrowia, or Streptomyces. 
In certain embodiments, the host cell is a Saccharomyces cerevisiae, Candida lipolytica, Escherichia coli, Arthrobacter, Rhodotorula glutinins, Acinetobacter, Candida lipolytica, Botryococcus braunii, Vibrio furnissii, Micrococcus leuteus, Stenotrophomonas maltophilia, Bacillus subtilis, Bacillus lichenoformis, Psuedomonus putida, Psuedomonas florescens, Streptomyces coelicolor, Prototheca moriformis, Prototheca krugani, Prototheca stagnora, Prototheca zopfii, or Chorella protothecoide cell.
In some embodiments, the host cell is an Arthrobacter AK 19, Acinetobacter sp. strain M-1, E. coli B, E. coli C, E. coli K, or E. coli W cell.
In other embodiments, the host cell is a Bacillus lentus cell, a Bacillus brevis cell, a Bacillus stearothermophilus cell, a Bacillus lichenformis cell, a Bacillus alkalophilus cell, a Bacillus coagulans cell, a Bacillus circulans cell, a Bacillus pumilis cell, a Bacillus thuringiensis cell, a Bacillus clausii cell, a Bacillus megaterium cell, or a Bacillus amyloliquefaciens cell.
In other embodiments, the host cell is a Trichoderma koningii cell, a Trichoderma viride cell, a Trichoderma reesei cell, a Trichoderma longibrachiatum cell, an Aspergillus awamori cell, an Aspergillus fumigates cell, an Aspergillus foetidus cell, an Aspergillus nidulans cell, an Aspergillus niger cell, an Aspergillus oryzae cell, a Humicola insolens cell, a Humicola lanuginose cell, a Rhodococcus opacus cell, a Rhizomucor miehei cell, or a Mucor michei cell.
In yet other embodiments, the host cell is a Streptomyces lividans cell or a Streptomyces murinus cell.
In yet other embodiments, the host cell is an Actinomycetes cell.
In other embodiments, the host cell is a cell from an eukaryotic plant, algae, cyanobacterium, green-sulfur bacterium, green non-sulfur bacterium, purple sulfur bacterium, purple non-sulfur bacterium, extremophile, yeast, fungus, an engineered organism thereof, or a synthetic organism. In some embodiments, the host cell is light-dependent or fixes carbon. In some embodiments, the host cell is light-dependent or fixes carbon. In some embodiments, the host cell has autotrophic activity. In some embodiments, the host cell has photoautotrophic activity, such as in the presence of light. In some embodiments, the host cell is heterotrophic or mixotrophic in the absence of light. In certain embodiments, the host cell is a cell from Avabidopsis thaliana, Panicum virgatum, Miscanthus giganteus, Zea mays, Chlamydomonas reinhardtii, Dunaliela salina, Synechococcus Sp. PCC 7002, Synechococcus Sp. PCC 7942, Synechocystis Sp. PCC 6803, Thermosynechococcus elongates BP-1, Chlorobium tepidum, Chlorojlexus auranticus, Chromatiumm vinosum, Rhodospirillum rubrum, Rhodobacter capsulatus, Rhodopseudomonas palusris, Clostridium ljungdahlii, Clostridiuthermocellum, Penicillium chrysogenum, Pichia pastoris, Schizosaccharomyces pombe, Pseudomonasjluorescens, or Zymomonas mobilis. 
As used herein, the term “conditions permissive for the production” means any conditions that allow a host cell to produce a desired product, such as a fatty amide. Similarly, the term “conditions suitable for expression” means any conditions that allow a host cell to synthesize a polypeptide. Suitable conditions include, for example, fermentation conditions. Fermentation conditions can comprise many parameters, such as temperature ranges, levels of aeration, and media composition. Each of these conditions, individually and in combination, allows the host cell to grow. Exemplary culture media include broths or gels. Generally, the medium includes a carbon source that can be metabolized by a host cell directly. In addition, enzymes can be used in the medium to facilitate the mobilization (e.g., the depolymerization of starch or cellulose to fermentable sugars) and subsequent metabolism of the carbon source.
As used herein, the phrase “carbon source” refers to a substrate or compound suitable to be used as a source of carbon for prokaryotic or simple eukaryotic cell growth. Carbon sources can be in various forms, including, but not limited to polymers, carbohydrates, acids, alcohols, aldehydes, ketones, amino acids, peptides, and gases (e.g., CO and CO2). Exemplary carbon sources include, but are not limited to, monosaccharides, such as glucose, fructose, mannose, galactose, xylose, and arabinose; oligosaccharides, such as fructo-oligosaccharide and galacto-oligosaccharide; polysaccharides such as starch, cellulose, pectin, and xylan; disaccharides, such as sucrose, maltose, and turanose; cellulosic material and variants such as methyl cellulose and sodium carboxymethyl cellulose; saturated or unsaturated fatty acid esters, succinate, lactate, and acetate; alcohols, such as ethanol, methanol, and glycerol, or mixtures thereof. The carbon source can also be a product of photosynthesis, such as glucose. In certain preferred embodiments, the carbon source is biomass. In other preferred embodiments, the carbon source is glucose.
The term “biomass” refers to any biological material from which a carbon source is derived. In some embodiments, a biomass is processed into a carbon source, which is suitable for bioconversion. In other embodiments, the biomass does not require further processing into a carbon source. The carbon source can be converted into a biofuel. An exemplary source of biomass is plant matter or vegetation, such as corn, sugar cane, or switchgrass. Another exemplary source of biomass is metabolic waste products, such as animal matter (e.g., cow manure). Further exemplary sources of biomass include algae and other marine plants. Biomass also includes waste products from industry, agriculture, forestry, and households, including, but not limited to, fermentation waste, ensilage, straw, lumber, sewage, garbage, cellulosic urban waste, food leftovers, and glycerol. The term “biomass” also can refer to sources of carbon, such as carbohydrates (e.g., monosaccharides, disaccharides, or polysaccharides).
To determine if conditions are sufficient to allow production of a product or expression of a polypeptide, a host cell can be cultured, for example, for about 4, 8, 12, 24, 36, 48, 72, or more hours. During and/or after culturing, samples can be obtained and analyzed to determine if the conditions allow production or expression. For example, the host cells in the sample or the medium in which the host cells were grown can be tested for the presence of a desired product. When testing for the presence of a fatty amide, assays, such as, but not limited to, MS, thin layer chromatography (TLC), high-performance liquid chromatography (HPLC), liquid chromatography (LC), GC coupled with a flame ionization detector (FID), GC-MS, and LC-MS can be used. When testing for the expression of a polypeptide, techniques such as, but not limited to, Western blotting and dot blotting may be used.
In the methods of the invention, the production and isolation of fatty amides can be enhanced by optimizing fermentation conditions. In some embodiments, fermentation conditions are optimized to increase the percentage of the carbon source that is converted to hydrocarbon products. During normal cellular lifecycles, carbon is used in cellular functions, such as producing lipids, saccharides, proteins, organic acids, and nucleic acids. Reducing the amount of carbon necessary for growth-related activities can increase the efficiency of carbon source conversion to product. This can be achieved by, for example, first growing host cells to a desired density (for example, a density achieved at the peak of the log phase of growth). At such a point, replication checkpoint genes can be harnessed to stop the growth of cells. Specifically, quorum sensing mechanisms (reviewed in Camilli et al. (2006) Science 311:1113; Venturi (2006) FEMS Microbiol. Rev. 30:274-291; and Reading et al. (2006) FEMS Microbiol. Lett. 254:1-11) can be used to activate checkpoint genes, such as p53, p21, or other checkpoint genes.
Genes that can be activated to stop cell replication and growth in E. coli include umuDC genes. The overexpression of umuDC genes stops the progression from stationary phase to exponential growth (Murli et al. (2000) J. Bacteriol. 182:1127-1135). UmuC is a DNA polymerase that can carry out translesion synthesis over non-coding lesions which commonly result from ultraviolet (UV) and chemical mutagenesis. The umuDC gene products are involved in the process of translesion synthesis and also serve as a DNA sequence damage checkpoint. The umuDC gene products include UmuC, UmuD, umuD′, UmuD′2C, UmuD′2, and UmuD2. Simultaneously, product-producing genes can be activated, thereby minimizing the need for replication and maintenance pathways to be used while a fatty amide or intermediate thereof is being made. Host cells can also be engineered to express umuC and umuD from E. coli in pBAD24 under the prpBCDE promoter system through de novo synthesis of this gene with the appropriate end-product production genes.
The host cell can be additionally engineered to express a recombinant cellulosome, which can allow the host cell to use cellulosic material as a carbon source. Exemplary cellulosomes suitable for use in the methods of the disclosure include, e.g., the cellulosomes described in International Patent Application Publication WO 2008/100251. The host cell also can be engineered to assimilate carbon efficiently and use cellulosic materials as carbon sources according to methods described in U.S. Pat. Nos. 5,000,000; 5,028,539; 5,424,202; 5,482,846; and 5,602,030. In addition, the host cell can be engineered to express an invertase so that sucrose can be used as a carbon source.
In some embodiments of the fermentation methods of the disclosure, the fermentation chamber encloses a fermentation that is undergoing a continuous reduction, thereby creating a stable reductive environment. The electron balance can be maintained by the release of carbon dioxide (in gaseous form). Efforts to augment the NAD/H and NADP/H balance can also facilitate in stabilizing the electron balance. The availability of intracellular NADPH can also be enhanced by engineering the host cell to express an NADH:NADPH transhydrogenase. The expression of one or more NADH:NADPH transhydrogenases converts the NADH produced in glycolysis to NADPH, which can enhance the production of fatty amides and intermediates thereof.
For small scale production, the engineered host cells can be grown in batches of, for example, about 100 mL, 500 mL, 1 L, 2 L, 5 L, or 10 L; fermented; and induced to express a desired nucleic acid sequence, such as a nucleic acid sequence encoding a PPS. For large scale production, the engineered host cells can be grown in batches of about 10 L, 100 L, 1000 L, 10,000 L, 100,000 L, 1,000,000 L or larger; fermented; and induced to express a desired nucleic acid sequence.
The fatty amides produced by the methods of disclosure generally are isolated from the host cell. The term “isolated” as used herein with respect to products, such as fatty amides, refers to products that are separated from cellular components, cell culture media, or chemical or synthetic precursors. The fatty amides produced by the methods described herein can be relatively immiscible in the fermentation broth, as well as in the cytoplasm. Therefore, the fatty amides and derivatives thereof can collect in an organic phase either intracellularly or extracellularly. The collection of the products in the organic phase can lessen the impact of the fatty amide on cellular function and can allow the host cell to produce more product.
In some embodiments, the fatty amides produced by the methods of disclosure are purified. As used herein, the term “purify,” “purified,” or “purification” means the removal or isolation of a molecule from its environment by, for example, isolation or separation. “Substantially purified” molecules are at least about 60% free (e.g., at least about 70% free, at least about 75% free, at least about 85% free, at least about 90% free, at least about 95% free, at least about 97% free, at least about 99% free) from other components with which they are associated. As used herein, these terms also refer to the removal of contaminants from a sample. For example, the removal of contaminants can result in an increase in the percentage of a fatty amide in a sample. For example, when a fatty amide is produced in a host cell, the fatty amide can be purified by the removal of host cell proteins. After purification, the percentage of a fatty amide in the sample is increased.
As used herein, the terms “purify,” “purified,” and “purification” are relative terms which do not require absolute purity. Thus, for example, when a fatty amide is produced in host cells, a purified fatty amide is a fatty amide that is substantially separated from other cellular components (e.g., nucleic acids, polypeptides, lipids, carbohydrates, or other hydrocarbons).
Additionally, a purified fatty amide preparation is a fatty amide preparation in which the fatty amide is substantially free from contaminants, such as those that might be present following fermentation. In some embodiments, a fatty amide is purified when at least about 50% by weight of a sample is composed of the fatty amide. In other embodiments, a fatty amide is purified when at least about 60%, e.g., at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 92%, by weight of a sample is composed of the fatty amide. Alternatively, or in addition, a fatty amide is purified when less than about 100%, e.g., less than about 99%, less than about 98%, less than about 95%, less than about 90%, or less than about 80%, by weight of a sample is composed of the fatty amide. Thus, a purified fatty amide can have a purity level bounded by any two of the above endpoints. For example, a fatty amide can be purified when at least about 80%-95%, at least about 85%-99%, or at least about 90%-98% of a sample is composed of the fatty amide.
The fatty amide may be present in the extracellular environment, or it may be isolated from the extracellular environment of the host cell. In certain embodiments, a fatty amide is secreted from the host cell. In other embodiments, a fatty amide is transported into the extracellular environment. In yet other embodiments, the fatty amide is passively transported into the extracellular environment. A fatty amide can be isolated from a host cell using methods known in the art, such as those disclosed in International Patent Application Publications WO 2010/042664 and WO 2010/062480.
The methods described herein can result in the production of homogeneous compounds wherein at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 95%, of the fatty amides produced will have fatty chains that vary by less than 6 carbons, less than 5 carbons, less than 4 carbons, less than 3 carbons, or less than about 2 carbons. Alternatively, or in addition, the methods described herein can result in the production of homogeneous compounds wherein less than about 98%, less than about 95%, less than about 90%, less than about 80%, or less than about 70% of the fatty amides produced will have fatty chains that vary by less than 6 carbons, less than 5 carbons, less than 4 carbons, less than 3 carbons, or less than about 2 carbons. Thus, the fatty amides can have a degree of homogeneity bounded by any two of the above endpoints. For example, the fatty amide can have a degree of homogeneity wherein about 70%-95%, about 80%-98%, or about 90%-95% of the fatty amides produced will have fatty chains that vary by less than 6 carbons, less than 5 carbons, less than 4 carbons, less than 3 carbons, or less than about 2 carbons. These compounds also can be produced with a relatively uniform degree of saturation.
As a result of the methods of the invention, one or more of the titer, yield, or productivity of the fatty amide produced by the recombinant microorganism engineered to comprise a nucleic acid sequence encoding a polypeptide that catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide is increased relative to that of the corresponding wild-type microorganism.
The term “titer” refers to the quantity of fatty amide produced per unit volume of host cell culture. In any aspect of the compositions and methods described herein, a fatty amide is produced at a titer of 25 mg/L or more, 50 mg/L or more, 75 mg/L or more, 100 mg/L or more, 125 mg/L or more, 150 mg/L or more, 175 mg/L or more, 200 mg/L or more, 250 mg/L or more, 300 mg/L or more, 350 mg/L or more, 400 mg/L or more, 450 mg/L or more, 500 mg/L or more, 600 mg/L or more, 700 mg/L or more, 800 mg/L or more, 900 mg/L or more, or 1000 mg/L or more. Alternatively, or in addition, the fatty amide is produced at a titer of 2000 mg/L or less, 1900 mg/L or less, 1800 mg/L or less, 1700 mg/L or less, 1600 mg/L or less, 1500 mg/L or less, 1400 mg/L or less, 1300 mg/L or less, 1200 mg/L or less, 1100 mg/L or less, 1000 mg/L or less, 900 mg/L or less, 800 mg/L or less, 700 mg/L or less, 600 mg/L or less, 500 mg/L or less, 400 mg/L or less, 300 mg/L or less, or 200 mg/L or less. Thus, the fatty amide is produced at a titer bounded by any two of the above endpoints. For example, the fatty amide can be produced at a titer of 150-1000 mg/L, 200-500 mg/L, 500-1500 mg/L, or 300-1300 mg/L. In other embodiments, a fatty amide is produced at a titer of more than 2000 mg/L, more than 5000 mg/L, more than 10,000 mg/L, or higher, such as 50 g/L, 70 g/L, 100 g/L, 120 g/L, 150 g/L, or 200 g/L.
The term “yield” refers to the efficiency by which an input carbon source is converted to product (i.e., fatty amide) in a host cell. For oxygen-containing carbon sources (e.g., glucose and other carbohydrate based sources), the oxygen must be released in the form of carbon dioxide. Thus, for every two oxygen atoms released, a carbon atom is also released leading to a maximal theoretical metabolic efficiency of approximately 34% (w/w) (for fatty acid derived products). This figure, however, changes for other organic compounds and carbon sources. Typical yield reported in the literature are approximately less than 5%. Host cells engineered to produce fatty amides according to the methods of the disclosure can have a yield of about 3% or more, about 5% or more, about 10% or more, about 15% or more, about 18% or more, or about 20% or more. Alternatively, or in addition, the yield is about 30% or less, about 27% or less, about 25% or less, about 22% or less, about 20% or less, about 17% or less, about 13% or less, or about 10% or less. Thus, the yield can be bounded by any two of the above endpoints. For example, the yield of the fatty amide produced by the recombinant microorganism of the disclosure can be about 5% to about 25%, about 10% to about 25%, about 10% to about 22%, about 15% to about 27%, or about 18% to about 22%. In other embodiments, the yield is greater than 30%.
The term “productivity” refers to the quantity of fatty amide produced per unit volume of host cell culture per unit density of host cell culture. In any aspect of the compositions and methods described herein, the productivity of a fatty amide produced by a recombinant microorganism is about 3 mg/L/OD600 or more, about 6 mg/L/OD600 or more, about 9 mg/L/OD600 or more, about 12 mg/L/OD600 or more, about 15 mg/L/OD600 or more, about 18 mg/L/OD600 or more, or about 20 mg/L/OD600 or more. Alternatively, or in addition, the productivity is about 50 mg/L/OD600 or less, about 40 mg/L/OD600 or less, about 30 mg/L/OD600 or less, about 25 mg/L/OD600 or less, about 20 mg/L/OD600 or less, about 17 mg/L/OD600 or less, or about 10 mg/L/OD600 or less. Thus, the productivity can be bounded by any two of the above endpoints. For example, the productivity can be about 3 to about 30 mg/L/OD600, about 6 to about 20 mg/L/OD600, or about 15 to about 30 mg/L/OD600.
The disclosure also provides a fatty amide produced by the recombinant microorganisms and methods described herein. A bioproduct (e.g., a fatty amide) produced by the recombinant microorganisms and methods of the disclosure can be distinguished from organic compounds derived from petrochemical carbon on the basis of dual carbon-isotopic fingerprinting or 14C dating. Additionally, the specific source of biosourced carbon (e.g., glucose vs. glycerol) can be determined by dual carbon-isotopic fingerprinting (see, e.g., U.S. Pat. No. 7,169,588).
The ability to distinguish bioproducts from petroleum-based organic compounds is beneficial in tracking these materials in commerce. For example, organic compounds or chemicals comprising both biologically-based and petroleum-based carbon isotope profiles may be distinguished from organic compounds and chemicals made only of petroleum-based materials. Hence, the fatty amides prepared in accordance with the inventive methods may be followed in commerce on the basis of their unique carbon isotope profile.
Bioproducts can be distinguished from petroleum-based organic compounds by comparing the stable carbon isotope ratio (13C/12C) in each fuel. The 13C/12C ratio in a given bioproduct is a consequence of the 13C/12C ratio in atmospheric carbon dioxide at the time the carbon dioxide is fixed. It also reflects the precise metabolic pathway. Regional variations also occur. Petroleum, C3 plants (the broadleaf), C4 plants (the grasses), and marine carbonates all show significant differences in 13C/12C and the corresponding δ13C values. Furthermore, lipid matter of C3 and C4 plants analyze differently than materials derived from the carbohydrate components of the same plants as a consequence of the metabolic pathway.
The 13C measurement scale was originally defined by a zero set by Pee Dee Belemnite (PDB) limestone, where values are given in parts per thousand deviations from this material. The “δ13C” values are expressed in parts per thousand (per mil), abbreviated, % o, and are calculated as follows:

δ13C(%o)=[(13C/12C)sample—(13C/12C)standard]/(13C/12C)standard×1000

In some embodiments, a fatty amide produced according to the methods of the disclosure has a δ13C of about −30 or greater, about −28 or greater, about −27 or greater, about −20 or greater, about −18 or greater, about −15 or greater, about −13 or greater, or about −10 or greater. Alternatively, or in addition, a fatty amide has a δ13C of about −4 or less, about −5 or less, about −8 or less, about −10 or less, about −13 or less, about −15 or less, about −18 or less, or about −20 or less. Thus, the fatty amide can have a δ13C bounded by any two of the above endpoints. For example, the fatty amide can have a δ13C of about −30 to about −15, about −27 to about −19, about −25 to about −21, about −15 to about −5, about −13 to about −7, or about −13 to about −10. In some embodiments, the fatty amide can have a δ13C of about −10, −11, −12, or −12.3. In other embodiments, the fatty amide has a δ13C of about −15.4 or greater. In yet other embodiments, the fatty amide has a δ13C of about −15.4 to about −10.9, or a δ13C of about −13.92 to about −13.84.
Bioproducts can also be distinguished from petroleum-based organic compounds by comparing the amount of 14C in each compound. Because 14C has a nuclear half life of 5730 years, petroleum based fuels containing “older” carbon can be distinguished from bioproducts which contain “newer” carbon (see, e.g., Currie, “Source Apportionment of Atmospheric Particles”, Characterization of Environmental Particles, J. Buffle and H. P. van Leeuwen, Eds., Vol. I of the IUPAC Environmental Analytical Chemistry Series, Lewis Publishers, Inc., pp. 3-74 (1992)).
14C can be measured by accelerator mass spectrometry (AMS), with results given in units of “fraction of modern carbon” (fM). fM is defined by National Institute of Standards and Technology (NIST) Standard Reference Materials (SRMs) 4990B and 4990C. As used herein, “fraction of modem carbon” or fM has the same meaning as defined by National Institute of Standards and Technology (NIST) Standard Reference Materials (SRMs) 4990B and 4990C, known as oxalic acids standards HOxI and HOxII, respectively. The fundamental definition relates to 0.95 times the 14C/12C isotope ratio HOxI (referenced to AD 1950). This is roughly equivalent to decay-corrected pre-Industrial Revolution wood. For the current living biosphere (plant material), fM is approximately 1.1.
In some embodiments, a fatty amide produced according to the methods of the disclosure has a fM14C of at least about 1, e.g., at least about 1.003, at least about 1.01, at least about 1.04, at least about 1.111, at least about 1.18, or at least about 1.124. Alternatively, or in addition, the fatty amide has an fM14C of about 1.130 or less, e.g., about 1.124 or less, about 1.18 or less, about 1.111 or less, or about 1.04 or less. Thus, the fatty amide can have a fM14C bounded by any two of the above endpoints. For example, the fatty amide can have a fM14C of about 1.003 to about 1.124, a fM14C of about 1.04 to about 1.18, or a fM14C of about 1.111 to about 1.124.
Another measurement of 14C is known as the percent of modem carbon, i.e., pMC. For an archaeologist or geologist using 14C dates, AD 1950 equals “zero years old.” This also represents 100 pMC. “Bomb carbon” in the atmosphere reached almost twice the normal level in 1963 at the peak of thermo-nuclear weapons testing. Its distribution within the atmosphere has been approximated since its appearance, showing values that are greater than 100 pMC for plants and animals living since AD 1950. It has gradually decreased over time with today's value being near 107.5 pMC. This means that a fresh biomass material, such as corn, would give a 14C signature near 107.5 pMC. Petroleum-based compounds will have a pMC value of zero. Combining fossil carbon with present day carbon will result in a dilution of the present day pMC content. By presuming 107.5 pMC represents the 14C content of present day biomass materials and 0 pMC represents the 14C content of petroleum-based products, the measured pMC value for that material will reflect the proportions of the two component types. For example, a material derived 100% from present day soybeans would have a radiocarbon signature near 107.5 pMC. If that material was diluted 50% with petroleum-based products, the resulting mixture would have a radiocarbon signature of approximately 54 pMC.
A biologically-based carbon content is derived by assigning “100%” equal to 107.5 pMC and “0%” equal to 0 pMC. For example, a sample measuring 99 pMC will provide an equivalent biologically-based carbon content of 93%. This value is referred to as the mean biologically-based carbon result and assumes that all of the components within the analyzed material originated either from present day biological material or petroleum-based material.
In some embodiments, a fatty amide produced according to the methods of the disclosure has a pMC of at least about 50, at least about 60, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 96, at least about 97, or at least about 98. Alternatively, or in addition, the fatty amide has a pMC of about 108 or less, about 105 or less, about 102 or less, about 99 or less, about 96 or less, about 93 or less, about 90 or less, about 85 or less, or about 80 or less. Thus, the fatty amide can have a pMC bounded by any two of the above endpoints. For example, a fatty amide can have a pMC of about 50 to about 100; about 60 to about 105; about 70 to about 100; about 80 to about 105; about 85 to about 100; about 87 to about 98; or about 90 to about 95. In other embodiments, a fatty amide described herein has a pMC of about 90, about 91, about 92, about 93, about 94, or about 94.2.
A fatty amide produced by any of the recombinant microorganisms and methods described herein can be used directly as a surfactant or detergent per se, or the fatty amide can be formulated into a personal, pet, or household cleaning composition. Surfactant, detergent, and cleaning compositions and methods for the production thereof are well known to those of skill in the art, and are described in more detail in, e.g., U.S. Patent Application Publication 2011/0206630, which is incorporated in its entirety by reference herein.
Thus, the disclosure provides surfactant, detergent, and cleaning compositions comprising a fatty amide produced by any of the methods described herein. One of ordinary skill in the art will appreciate that, depending upon the intended purpose of the surfactant, detergent, or cleaning composition, different fatty amides can be produced and used. For example, when the fatty amides described herein are used as a feedstock for surfactant or detergent production, one of ordinary skill in the art will appreciate that the characteristics of the fatty amide feedstock will affect the characteristics of the surfactant or detergent composition produced. Hence, the characteristics of the surfactant or detergent composition can be selected for by producing particular fatty amides for use as a feedstock.
A fatty amide-based surfactant or detergent of the disclosure can be mixed with other surfactants and/or detergents well known in the art. The fatty amide can be present in the mixture in an amount of 10 weight percent (wt. %) or more, 15 wt. % or more, 20 wt. % or more, 30 wt. % or more, 40 wt. % or more, 50 wt. % or more, 60 wt. % or more, or 70 wt. % or more, based on the total weight of the mixture. Alternatively, or in addition, the fatty amide can be present in the mixture in an amount of 95 wt. % or less, 90 wt. % or less, 80 wt. % or less, 70 wt. % or less, 60 wt. % or less, 50 wt. % or less, or 40 wt. % or less, based on the total weight of the mixture. Thus, the fatty amide can be present in the mixture in an amount bounded by any two of the above endpoints. For example, the fatty amide can be present in the mixture in an amount of 15-40%, 30-90%, 50-95%, or 40-50%.
A fatty amide-based surfactant can be formulated into a cleaning composition to impart detergency and cleaning power to the cleaning composition. The fatty amide can be present in the cleaning composition in an amount of 0.001 wt. % or more, 0.1 wt. % or more, 1 wt. % or more, 10 wt. % or more, 20 wt. % or more, or 40 wt. % or more, based on the total weight of the cleaning composition. Alternatively, or in addition, the fatty amide can be present in the cleaning composition in an amount of 60 wt. % or less, 50 wt. % or less, 40 wt. % or less, 30 wt. % or less, 15 wt. % or less, or 5 wt. % or less, based on the total weight of the cleaning composition. Thus, the fatty amide can be present in the cleaning composition in an amount bounded by any two of the above endpoints. For example, the fatty amide can be formulated into a cleaning composition in an amount of 0.1-10 wt. %, 10-15 wt. %, 20-40 wt. %, or 0.001-5 wt. %.
A cleaning composition of the disclosure can be in solid form, such as a tablet, granule, powder, or compact. The cleaning composition also can be in liquid form, such as a fluid, gel, paste, emulsion, or concentrate.
In certain embodiments, the cleaning composition of the disclosure is a liquid or solid laundry detergent composition. In some embodiments, the cleaning composition is a hard surface cleaning composition, wherein the hard surface cleaning composition preferably impregnates a nonwoven substrate. As used herein, “impregnate” means that the hard surface cleaning composition is placed in contact with a nonwoven substrate such that at least a portion of the nonwoven substrate is penetrated by the hard surface cleaning composition. For example, the hard surface cleaning composition preferably saturates the nonwoven substrate. In other embodiments, the cleaning composition of the disclosure is a car care composition, which is useful for cleaning various surfaces such as hard wood, tile, ceramic, plastic, leather, metal, and/or glass. In some embodiments, the cleaning composition is a dishwashing composition, such as, for example, a liquid hand dishwashing composition, a solid automatic dishwashing composition, a liquid automatic dishwashing composition, and a tab/unit dose form automatic dishwashing composition.
In other embodiments, the cleaning composition can be used in industrial environments for cleaning various equipment and machinery, and for use in oil drilling operations. For example, the cleaning composition of the disclosure can be particularly suited in environments wherein it comes into contact with free hardness and in compositions that require hardness tolerant surfactant systems, such as when used to aid oil drilling.
In some embodiments, a fatty amide produced by any of the recombinant microorganisms and methods of the disclosure is formulated into personal or pet care composition such as a shampoo, body wash, face wash, or liquid or solid soap.
A cleaning composition containing a fatty amide produced by any of the recombinant microorganisms and methods of the disclosure can comprise other cleaning adjuncts which are well known to those of skill in the art. Common cleaning adjuncts applicable to most cleaning compositions, including household cleaning compositions, personal care compositions, and the like, include solvents, solubilizing agents, carriers, builders, enzymes, polymers, suds boosters, suds suppressors (antifoam), dyes, fillers, germicides, hydrotropes, anti-oxidants, perfumes, pro-perfumes, enzyme stabilizing agents, pigments, and the like. In some embodiments, the cleaning composition is a liquid cleaning composition, wherein the composition comprises one or more selected from solvents, chelating agents, dispersants, and water. In other embodiments, the cleaning composition is a solid, wherein the composition further comprises, for example, an inorganic filler salt. Inorganic filler salts are conventional ingredients of solid cleaning compositions, present in substantial amounts, varying from, for example, about 10 wt. % to about 35 wt. %. Suitable filler salts include, for example, alkali and alkaline-earth metal salts of sulfates and chlorides. An exemplary filler salt is sodium sulfate.
Household cleaning compositions (e.g., laundry detergents and household surface cleaners) can comprise one or more additional ingredients selected from bleaches, bleach activators, catalytic materials, dispersant polymers, silvercare, anti-tarnish and/or anti-corrosion agents, alkalinity sources, processing aids, dye transfer inhibiting agents, brighteners, structure elasticizing agents, fabric softeners, anti-abrasion agents, and other fabric care agents. The cleaning adjuncts particularly useful for household cleaning compositions and the levels of use have been described in, e.g., U.S. Pat. Nos. 5,576,282, 6,306,812 and 6,326,348. A list of suitable laundry or other household cleaning adjuncts is described in, e.g., International Patent Application Publication WO 99/05245.
Personal care, pet care, or cosmetic compositions (e.g., shampoos, facial cleansers, hand sanitizers, blushes, bronzers, and the like) can comprise one or more additional ingredients selected from conditioning agents (e.g., vitamins, silicone, silicone emulsion stabilizing components), cationic cellulose, or polymers (e.g., guar polymers), anti-dandruff agents, antibacterial agents, gel-forming agents, suspending agents, viscosity modifiers, dyes, non-volatile solvents or diluents (water soluble or insoluble), foam boosters, pediculicides, pH adjusting agents, perfumes, preservatives, chelators, proteins, skin active agents, sunscreens, UV absorbers, minerals, herbal/fruit/food extracts, sphingolipid derivatives, and clay.
The disclosure also provides a fuel additive comprising a fatty amide produced by any of the recombinant microorganisms and methods described herein. In certain embodiments, the fuel additive is selected from an engine performance additive, detergent, dispersant, anti-wear agent, viscosity index modifier, friction modifier, antioxidant, rust inhibitor, antifoaming agent, seal fix, lubricity additive, pour point depressant, cloud point reducer, smoke suppressant, drag reducing additive, metal deactivator, biocide and demulsifier. Fuel additives are described in more detail in U.S. Patent Application Publication 2010/0257777, which is incorporated by reference herein.
In certain embodiments, the fuel additive comprising a fatty amide produced by any of the recombinant microorganisms and methods is blended into a package comprising the fatty amide and one or more base oils used as a solvent for the fatty amide. Depending on grade and/or type, the base oil may provide a varying degree of performance benefit to an additive package, including, for example, extreme temperature benefits, anti-oxidative benefits, or a suitable pour point.
The disclosure also provides a pharmaceutical composition comprising a fatty amide produced by any of the recombinant microorganisms and methods described herein and a pharmaceutically acceptable carrier. The pharmaceutical composition can contain additional components, such as, for example, diluents, adjuvants, excipients, preservatives, pH adjusting agents, and the like, as well as additional therapeutic agents, such as, for example, therapeutic agents useful in the treatment of a particular indication (e.g., pain or inflammation).
The pharmaceutical composition can be a solid (e.g., tablet, capsule, sublingual tablet, powder, sachet) composition. The pharmaceutical composition also can be a liquid (e.g., aqueous liquid, gel, lotion, cream) composition. The pharmaceutical composition can be formulated for administration by any suitable route, such as, for example, an administration route selected from the group consisting of oral, topical, intravenous, intramuscular, intraperitoneal, intrathecal, epidural, percutaneous, subcutaneous, transmucosal, and intranasal routes.
The disclosure also provides a method of preventing or treating a disease or condition in a subject in need thereof comprising administering to the subject an effective amount of a fatty amide produced by any of the recombinant microorganisms and methods described herein, thereby preventing or treating the disease or condition in the subject.
By “effective amount” or “therapeutically effective amount,” it is meant an amount that relieves (to some extent, as judged by a skilled medical practitioner) one or more symptoms of the disease or condition in a human or animal subject. Additionally, by “effective amount” or “therapeutically effective amount,” it is meant an amount that returns to normal, either partially or completely, physiological or biochemical parameters associated with or causative of a disease or condition. A clinician skilled in the art can determine the therapeutically effective amount of a composition in order to treat or prevent a particular disease condition, or disorder when it is administered. The precise amount of the composition required to be therapeutically effective will depend upon numerous factors, e.g., such as the specific activity of the active substance, the delivery device employed, physical characteristics of the substance, purpose for the administration, in addition to many patient specific considerations. The determination of amount of a composition that must be administered to be an effective amount or a therapeutically effective amount is routine in the art and within the skill of an ordinarily skilled clinician.
In some embodiments, an effective amount may be 1 ng or more, e.g., 10 ng or more, 100 ng or more, 1 μg or more, 10 μg or more, 100 μg or more, 1 mg or more, 10 mg or more, 50 mg or more, or 100 mg or more of a fatty amide of the disclosure per dosage unit. Alternatively, or in addition, an effective amount may be 5 g or less, 1 g or less, 500 mg or less, 250 mg or less, 100 mg or less, 75 mg or less, 25 mg or less, 10 mg or less, or 1 mg or less of a fatty amide of the disclosure per dosage unit. Thus, the fatty amide can be present in a dosage unit in an amount bounded by any two of the above endpoints. For example, the fatty amide can be present in a dosage unit in an amount of 100 ng-10 mg, 50 mg-250 mg, 1 μg-1 mg, or 100 mg-500 mg. A dosage unit comprising an effective amount of a fatty amide of the disclosure may be administered in a single daily dose, or the total daily dosage may be administered in divided doses of two, three, four times or more daily, as needed.
The disease or condition can be any disease or condition having one or more symptoms and/or physiological or biochemical parameters responsive to therapy with a fatty amide of the invention. In some embodiments, the disease is an inflammatory disease, and the fatty amide of the disclosure is administered in an amount sufficient to reduce inflammation. In certain embodiments, the inflammatory disorder is autoimmune disease, rheumatoid arthritis, multiple sclerosis, or Crohn's disease.
In certain embodiments, the condition is pain, and the fatty amide of the disclosure is administered in an amount sufficient to provide analgesia.
In other embodiments, the condition is hypertension, and the fatty amide of the disclosure is administered in an amount sufficient to cause the reduction of blood pressure.
Anandamide is an endogenous agonist of the cannabinoid (CB) 1 receptor and, to a lesser extent, the CB2 receptor and the vanilloid 1 receptor (Tan et al., supra). Administration of anandamide to human and animal subjects has been demonstrated to have myriad physiological effects, including regulating food intake and body weight, decreasing blood pressure, decreasing heart rate, protecting against myocardial reperfusion injury, reducing acute pain elicited by chemical, mechanical, or thermal stimuli, reducing chronic pain of neuropathic or inflammatory origin, reducing inflammation, providing neuroprotection in acute neuronal injury (e.g., traumatic brain injury, stroke, and epilepsy) and in chronic neurodegenerative disorders, (e.g., multiple sclerosis, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and Alzheimer's disease), promoting bronchodilation, reducing intraocular pressure (e.g., in glaucoma patients), and promoting tumor cell apoptosis (see, e.g., Pacher et al. (2006) Pharmacol. Rev. 58 (3):389-462).
In some embodiments, the fatty amide is anandamide produced by the recombinant microorganisms and methods described herein, and the disease or condition is one of the aforementioned diseases or conditions capable of being treated or prevented by the administration of an effective amount of anandamide.
PEA and OEA are endogenous agonists of peroxisome proliferator-activated receptor-α (PPAR-α) (Fu et al. (2003) Nature 425 (6953): 90-93; and Lo Verme et al., supra). Administration of PEA or OEA to human and animal subjects has been demonstrated to evoke many of the same responses elicited by anandamide, including regulating food intake and body weight, reducing pain and inflammation, providing neuroprotection, and reducing intraocular pressure (see, e.g., Fu et al., supra, Tan et al., supra, Lo Verme et al., supra, and U.S. Pat. Nos. 6,348,498 and 6,656,972).
In some embodiments, the fatty amide is PEA produced by the recombinant microorganisms and methods described herein, and the disease or condition is one of the aforementioned diseases or conditions capable of being treated or prevented by the administration of an effective amount of PEA. In other embodiments, the fatty amide is OEA produced by the recombinant microorganisms and methods described herein, and the disease or condition is one of the aforementioned diseases or conditions capable of being treated or prevented by the administration of an effective amount of OEA.
EXAMPLES
The following specific examples are intended to illustrate the disclosure and should not be construed as limiting the scope of the claims.
Example 1
This example illustrates the construction of a genetically engineered microorganism in which the expression of an acyl-CoA dehydrogenase, an outer membrane protein receptor, a pyruvate formate lyase, a lactate dehydrogenase, and a transcriptional repressor were attenuated.
E. coli MG1655 DV4 is a genetically engineered E. coli K strain comprising fadE (an acyl-CoA dehydrogenase), fhuA (an outer membrane protein receptor), pflB (a pyruvate formate lyase), and IdhA (a lactate dehydrogenase) gene deletions (see U.S. Patent Application Publications 2011/0072714 and 2011/0162259, which are incorporated by reference herein). The fabR gene of E. coli MG1655 (GenBank Accession No. AAC76945), which encodes a transcriptional repressor was deleted from E. coli MG1655 DV4 using the Lambda Red System according to Datsenko et al. (2000) Proc. Natl. Acad. Sci. USA 97:6640-6645, with the following modifications described herein.
The two primers used to create the deletion strain were:







fabR_del_F:


(SEQ ID NO: 4)


5′-ATGTTTTATTGCGTTACCGTTCATTCACAATACTGGAGCAATCCAGT


 


ATGATTCCGGGGATCCGTCGACC-3′;


and


 


fabR_del_R:


(SEQ ID NO: 5)


5′-CGTACCTCTATCTTGATTTGCTTGTTTCATTACTCGTCCTTCACATT


 


TCCTGTAGGCTGGAGCTGCTTCG-3′.






The fabR_del_F and fabR_del_R primers were used to amplify the kanamycin resistance (KmR) cassette from plasmid pKD13 by PCR, as described by Datsenko et al., supra. The resulting PCR product was then used to transform electro-competent E. coli MG1655 DV4 cells containing plasmid pKD46, which cells were previously induced with arabinose for 3-4 hours, as described by Datsenko et al., supra. Following a 3 hour outgrowth in SOC medium at 37° C., the cells were plated on Luria agar plates containing 50 μg/mL of kanamycin. Colonies that were resistant to kanamycin were identified and isolated after an overnight incubation at 37° C. Disruption of the fabR gene was confirmed using primers flanking the E. coli fabR gene.
Confirmation of the deletion of fabR was performed using the following primers:









fabR_3:



(SEQ ID NO: 6)



5′-GCGACGCGCGCACCTTGCTTAACCAGGCCC-3′



 



fabR_4:



(SEQ ID NO: 7)



5′-CGCATCTTCGCGCCAATCCAGAACACC-3′.






After the deletions were confirmed, a single colony was used to remove the KmR marker in accordance with the method described by Datsenko et al., supra. The resulting MG1655 E. coli strain having fadE, fhuA, pflB, IdhA, and fabR gene deletions was named E. coli MG1655 ΔfadE_ΔfhuA_ΔpflB_ΔldhA_ΔfabR or E. coli MG1655 DG5.
This example shows the construction of E. coli MG1655 DG5, which is a genetically engineered microorganism in which the expression of an acyl-CoA dehydrogenase, an outer membrane protein receptor, a pyruvate formate lyase, a lactate dehydrogenase, and a transcriptional repressor were attenuated.
Example 2
This example illustrates the construction of a genetically engineered microorganism in which nucleotide sequences encoding a thioesterase ('tesA) and an acyl-CoA synthase (fadD) were integrated into the microorganism's chromosome under the control of an inducible promoter.
'tesA is a nucleotide sequence comprising a leaderless E. coli tesA gene (GenBank entry AAC73596, Accession U00096.2). 'tesA encodes an E. coli thioesterase (EC 3.1.1.5, 3.1.2.-) in which the first twenty-five amino acids were deleted and the amino acid in position 26, alanine, was replaced with methionine. That methionine then became the first amino acid of 'tesA (Cho et al. (1995) J. Biol. Chem. 270:4216-4219). E. coli fadD (GenBank entry AAC74875; Accession U00096.2) encodes an acyl-CoA synthase.
Construction of pACYC-Ptrc Plasmid Containing 'tesA or 'tesA-fadD
The 'tesA gene was obtained from a pETDuet-1-'tesA plasmid, which was constructed by cloning the 'tesA gene into an NdeI/AvrII digested pETDuet-1 plasmid (Novagen, Madison, Wis.) as described previously (see U.S. Patent Application Publication 2010/0242345 and International Patent Application Publication WO 2007/136762, which are incorporated in their entireties by reference herein). The fadD gene was obtained from a pHZ1.61 plasmid (SEQ ID NO: 8), which was constructed by cloning the fadD gene into a pCDFDuet-1 plasmid (Novagen, Madison, Wis.) as described previously (see also U.S. Patent Application Publication 2010/0257777, which is incorporated in its entirety by reference herein). The 'tesA and fadD genes were amplified from pETDuet-1-'tesA and pHZ1.61, respectively, using high fidelity PHUSIONTM polymerase (New England Biolabs, Inc., Ipswich, Mass.) and the following primers:









′tesAForward-



(SEQ ID NO: 9)



5′-CTCTAGAAATAATTTAACTTTAAGTAGGAGAUAGGTAC



 



CCATGGCGGACACGTTATTGAT-3′



 



′tesAReverse-



(SEQ ID NO: 10)



5′-CTTCGAATTCCATTTAAATTATTTCTAGAGTCATTATGAGTC



 



ATGATTTACTAAAGGC-3′



 



fadDForward-



(SEQ ID NO: 11)



5′-CTCTAGAAATAATTTTAGTTAAGTATAAGAAGGAGATATACC



 



ATGGTGAAGAAGGTTTGGCTTAA-3′



 



fadDReverse-



(SEQ ID NO: 12)



5′-CTTCGAATTCCATTTAAATTATTTCTAGAGTTATCAGGCTTTA



 



TTGTCCAC-3′.






To construct the pACYC-'tesA plasmid, the 'tesA PCR product and a pACYC-Ptrc vector (SEQ ID NO: 13) were digested with NcoI and EcoRI. Following overnight ligation with T4 DNA ligase (New England Biolabs, Ipswich, Mass.), the DNA product was transformed into TOP10® ONE SHOT® cells (Invitrogen, Carlsbad, Calif.). The insertion of 'tesA into the pACYC-Ptrc vector was confirmed by restriction digestion. A SwaI restriction site and overlapping fragments for IN-FUSIONTM cloning (Clontech, Mountain View, Calif.) also were created at the 3′-end of the 'tesA insert.
To construct the pACYC-Ptrc-'tesA-fadD plasmid, the pACYC-Ptrc-'tesA plasmid was subjected to an overnight restriction digestion by SwaI. The fadD PCR product amplified from pHZ1.61 was cloned downstream from the 'tesA gene using the IN-FUSIONTM PCR Cloning System (Clontech, Mountain View, Calif.). The insertion of fadD was verified with restriction digestion. The insertion of fadD destroys the SwaI site following the 'tesA gene, but recreates a new SwaI site at the 3′-end of fadD.
Construction of Tn7tes and Tn7tesfad Plasmids
The pACYC-Ptrc-'tesA and pACYC-Ptrc-'tesA-fadD plasmids were used as templates to generate Ptrc-'tesA and Ptrc-'tesA-fadD cassettes, respectively. The following primers were used to obtain the cassettes:









IFF:



(SEQ ID NO: 14)



5′-GGGTCAATAGCGGCCGCCAATTCGCGCGCGAAGGCG-3′



 



IFR:



(SEQ ID NO: 15)



5′-TGGCGCGCCTCCTAGGGCATTACGCTGACTTGACGGG-3′.






Plasmid pGRG25 (GenBank Accession No. DQ460223) was purified and subjected to restriction digestions by NotI and AvrII (New England Biolabs, Inc., Ipswich, Mass.). The Ptrc-'tesA cassette was cloned into the NotI and AvrII restriction sites of pGRG25 using the IN-FUSIONTM PCR cloning system (Clontech, Mountain View, Calif.), creating the Tn7tes plasmid (SEQ ID NO: 16), wherein the lacIq and Ptrc-'tesA genes are flanked by the left and right Tn7 ends. The Ptrc-'tesA-fadD cassette was cloned into the NotI and AvrII restriction sites of pGRG25 similarly, thereby creating the Tn7tesfad plasmid (SEQ ID NO: 17), wherein the lacIq and Ptrc-'tesA-fadD genes are flanked by the left and right Tn7 ends.
Generation of E. coli MG1655 DG5 Tn7-'tesA and E. coli MG1655 DG5 Tn7-'tesA-fadD
The plasmids Tn7tes and Tn7tesfad were each electroporated separately into strain E. coli MG1655 DG5 (described in Example 1) using a protocol described by McKenzie et al., BMC Microbiology, 6:39 (2006). After electroporation, ampicillin-resistant cells were selected by growth in an LB medium containing 0.1% glucose and 100 μg/mL carbenicilin at 32° C. overnight, followed by selection for cells comprising the Tn7-transposition fractions by growth on LB plates containing 0.1% arabinose overnight at 32° C. Single colonies were streaked onto LB medium plates with or without ampicillin and grown overnight at 42° C. to cure of Tn7tes or Tn7tesfad plasmids. Thus, the lacIq and Ptrc-'tesA or lacIq and Ptrc-'tesA-fadD genes were integrated into the attTn7 site on the E. coli MG1655 chromosome located between the pstS and glmS genes. Integration of these genes was confirmed by PCR and sequencing using the following primers:









attTn7.A:



(SEQ ID NO: 18)



5′-GATGCTGGTGGCGAAGCTGT-3′



 



attTn7.C:



(SEQ ID NO: 19)



5′-GTTGCGACGGTGGTACGCATAAC-3′.






The resulting strains were given the names E. coli MG1655 DG5 Tn7-'tesA and E. coli MG1655 DG5 Tn7-'tesA-fadD, accordingly.
The results of this example illustrate the generation of genetically engineered microorganisms in which nucleotide sequences encoding a thioesterase (i.e., E. coli MG1655 DG5 Tn7-'tesA) or a thioesterase and an acyl-CoA synthase (i.e., E. coli MG1655 DG5 Tn7-'tesA-fadD) were integrated into the host cell's chromosome under the control of an inducible promoter.
Example 3
This example illustrates a method of producing N-palmitoylethanolamide by expressing a gene encoding a palmitoylputrescine synthase in a genetically engineered microorganism.
A gene encoding a bacterial palmitoylputrescine synthase (PPS), identified as GenBank Accession No. AY632377 (Brady, S. F., et al. (2004) J. Nat. Prod., 67:1283-1286) (SEQ ID NO: 2), was synthesized by DNA2.0 (Menlo Park, Calif.). The DNA2.0 plasmid, termed pJ201:30127, was designed to contain an NcoI site flanking the start codon and a PmeI site flanking the stop codon. The PPS encoding gene in pJ201:30127 was not codon optimized. The PPS encoding gene was subcloned into the expression vector OP80, which has been described previously (see U.S. Patent Application Publication No. 2010/0154293, which is incorporated in its entirety by reference herein). The OP80 vector is based upon pCL1920, which is a low copy plasmid that expresses operably linked genes under the control of the IPTG-inducible trc promoter. To construct the OP80 vector expressing the PPS gene, plasmids OP80 and pJ201:30127 were purified and subjected to restriction digestions with NcoI/PmeI (New England Biolabs, Inc., Ipswich, Mass.). The PPS encoding gene was ligated with T4 DNA ligase into the NcoI/PmeI digested OP80 plasmid. The ligation reaction was transformed into TOP10® E. coli cells, and the cells were plated onto LB agar containing spectinomycin. Ten colonies were selected and tested for the PPS encoding insert by culturing the colonies, isolating plasmid DNA, and digesting the plasmid DNA with NcoI/PmeI. One colony was positive for plasmid containing the PPS encoding insert by restriction digestion. The plasmid was confirmed to contain the PPS encoding gene by sequence analysis, and was termed “OP80-PPS.” The OP80-PPS plasmid was then transformed into E. coli MG1655 strains DG5 (described in Example 1), DG5 Tn7-'tesA (described in Example 2), and DG5 Tn7-'tesA-fadD (described in Example 2). As a control, the OP80 empty vector was transformed into E. coli MG1655 strains DG5, DG5 Tn7-'tesA, and DG5 Tn7-'tesA-fadD. All six strains were cultured in LB broth with no additional glucose. When each culture reached an OD600 of 1.2, IPTG was added to a final concentration of 1 mM, along with ethanolamine (0.1% (v/v)). After 24 hrs, the cultures were harvested and extracted with ethyl acetate (2 volumes of culture to 1 volume of ethyl acetate), and the organic fraction was collected and utilized for analysis of fatty species by GC-MS.
All samples were analyzed by GC-MS (Agilent 6850 GC with 5975B VL MSD) equipped with a 30 m×0.25 mm 0.25 μm film Agilent HP-5-MS column for separation, with the mass detectors electron ionization (EI) in full scan mode (50-500 m/z). One μL of the ethyl acetate extraction was injected on the Agilent splitless inlet set at 300° C. The column was temperature programmed as follows: 100° C. for 5 min, increase to 320° C. at 20° C./min, and hold at 320° C. for 5 min. The carrier gas helium was set at a flow rate of 1.2 mL/min. A representative chromatogram with an interpretation of the mass spectra of E. coli MG1655 strain DG5 transformed with OP80-PPS is shown in FIG. 1. A peak having a retention time of 13.1 min was identified in the GC-MS traces of all E. coli MG1655 strains DG5, DG5 Tn7-'tesA, and DG5 Tn7-'tesA-fadD transformed with OP80-PPS. This peak was identified as N-palmitoylethanolamide. The peak identified as N-palmitoylethanolamide was not present in any of the control strains transformed with empty vector.
It was estimated that approximately 200 mg/L of N-palmitoylethanolamide was produced in E. coli MG1655 strain DG5 transformed with OP80-PPS. E. coli MG1655 strain DG5 is engineered to produce fatty acyl-ACP, whereas DG5 Tn7-'tesA is engineered to produce free fatty acid and DG5 Tn7-'tesA-fadD is engineered to produce fatty acyl-CoA. Since these results demonstrated that all three strains produced N-palmitoylethanolamide, the production of N-palmitoylethanolamide in the parental DG5 strain suggests that the PPS enzyme encoded by gene AY632377 uses C16:0 acyl-ACP as a substrate in the presence of the primary ethanolamine. The N-palmitoylethanolamide identified in FIG. 1 was further characterized by derivatization with N,O-bis(trimethylsilyl)-trifluoroacetamide (BSTFA), in which the hydroxyl group was trimethylsilyl-protected. As shown in FIG. 2A, a peak in the GC-MS trace having a retention time of 13.3 min was identified as the trimethylsilyl (TMS)-protected product.
The results of this example illustrate a method of producing N-palmitoylethanolamide by expressing a PPS enzyme encoded by gene AY632377 in a bacterial strain that was engineered to produce fatty acyl-ACP. In addition, these results suggest that a single enzyme (i.e., PPS) can perform a secondary amidation directly from acyl-ACP and a primary amine head group in vivo.
Example 4
This example shows a method of producing N-palmitoylethanolamide by expressing a gene encoding a palmitoylputrescine synthase in a genetically engineered microorganism.
The OP80 empty vector or OP80-PPS plasmid was transformed into E. coli MG1655 strains DG5, DG5 Tn7-'tesA, and DG5 Tn7-'tesA-fadD, as described in Example 3. Each of the six strains was cultured overnight in LB broth with no additional glucose. Then, each of the overnight cultures was inoculated in nutrient rich media containing glucose. More specifically, 1 mL of each of the overnight cultures was inoculated in triplicate into nutrient rich 2N-BT (2% glucose, nitrogen limited medium, 0.2M Bis-Tris, pH 7.0, 0.1% Triton): LB media (1:10) containing 1 mM IPTG, antibiotics, and 1% ethanolamine, and cultured in a pH-controlled incubator. After 48 hrs, the OD600 of each culture was recorded, and the cells were harvested and extracted with ethyl acetate (2 volumes of culture to 1 volume of ethyl acetate). The organic fractions were collected and utilized for GC-MS analysis as described in Example 3. A peak having a retention time of 13.1 min was found to be most abundant in the GC-MS trace for E. coli MG1655 strain DG5 Tn7-'tesA-fadD transformed with OP80-PPS. The peak having a retention time of 13.1 was second most abundant in strain DG5 transformed with OP80-PPS, and third most abundant in strain DG5 Tn7-'tesA transformed with OP80-PPS. The 13.1 min peak was identified as N-palmitoylethanolamide from all strains. The peak identified as N-palmitoylethanolamide was not present in any of the control DG5 strains transformed with empty vector.
As noted above, E. coli MG1655 strain DG5 Tn7-'tesA-fadD is engineered to produce fatty acyl-CoA. Therefore, the production of N-palmitoylethanolamide in the DG5 Tn7-'tesA-fadD strain suggests that the PPS enzyme encoded by gene AY632377 also can use fatty acyl-CoA as a substrate in the presence of ethanolamine.
The results of this example show a method of producing N-palmitoylethanolamide by expressing a PPS enzyme encoded by gene AY632377 in a bacterial strain that was engineered to produce fatty acyl-CoA. In addition, these results suggest that a single enzyme (i.e., PPS) can perform a secondary amidation directly from a fatty thioester and a primary amine head group in vivo.
Example 5
This example shows a method of producing saturated and unsaturated fatty amides by expressing a gene encoding a PPS in a genetically engineered microorganism.
Fatty 3-dimethylamino-1-propylamide is a precursor in the synthesis of the amphoteric detergent cocamidopropyl betaine (CAPB). To determine whether fatty N-(3-dimethylamino-1-propylamine)amides could be produced in a microorganism genetically engineered to express a PPS, E. coli MG1655 strain DG5 cells were transformed with OP80 empty vector or OP80-PPS plasmid, and cultured overnight in LB broth with no additional glucose. Then, each of the overnight cultures was inoculated in nutrient rich media containing glucose. More specifically, 1 mL of each of the overnight cultures was inoculated in triplicate into nutrient rich 2N-BT (2% glucose, nitrogen limited medium, 0.2M Bis-Tris, pH 7.0, 0.1% Triton): LB (1:10) media containing 1 mM IPTG, antibiotics, and 1% primary amine 3-dimethylamino-1-propylamine, and cultured in a pH-controlled incubator. After 60 hrs, the OD600 of each culture was recorded, and the cells were harvested and extracted with ethyl acetate (2 volumes of culture to 1 volume of ethyl acetate). The organic fractions were collected and utilized for GC-MS analysis as described in Example 3. The chromatogram was analyzed by extraction ion chromatogram for ion 58, which is a common ion for fatty N-(3-dimethylamino-1-propylamine)amides. Fatty N-(3-dimethylamino-1-propylamine)amides containing C12:0 (12.8 min), C14:0 (13.2 min), C16:1 (13.5 min), C16:0 (13.6 min), and C18:1 (14.3 min) fatty chains were identified in the GC-MS trace (FIG. 3). Fatty amides containing a C16:0 fatty chain were identified as being the most abundant in the GC-MS trace (FIG. 3).
The results of this example show a method of producing fatty amides with various fatty chain lengths having either zero or one unsaturation by culturing an E. coli strain that was engineered to produce acyl-ACP and which further expressed a PPS enzyme encoded by gene AY632377 in a medium containing 3-dimethylamino-1-propylamine.
Example 6
This example illustrates a method for producing various fatty amides by feeding a variety of primary amines to a genetically engineered microorganism.
The OP80 empty vector or OP80-PPS plasmid was transformed into E. coli MG1655 strains DG5, DG5 Tn7-'tesA, and DG5 Tn7-'tesA-fadD, as described in Example 3. Each of the six strains was cultured overnight in LB broth with no additional glucose. Then, each of the overnight cultures was inoculated in nutrient rich media containing glucose. More specifically, 1 mL of each of the overnight cultures was inoculated into nutrient rich 2N-BT (2% glucose, nitrogen limited medium, 0.2M Bis-Tris, pH 7.0, 0.1% Triton): LB (1:10) media containing 1 mM IPTG, antibiotics, and 1% of one of the following primary amines: (±)-1-amino-2-propanol, 2-methoxyethylamine, 3-amino-1-propanol, 2-amino-1-3-propanediol, 3-methoxypropylamine, N-(2-hydroxyethyl)ethylenediamine, or butylamine. The cultures were incubated in a pH-controlled environment for 60 hrs. The OD600 of each culture was recorded, and the cells were harvested and extracted with ethyl acetate (2 volumes of culture to 1 volume of ethyl acetate). The organic fractions were collected and utilized for GC-MS analysis as described in Example 3. Fatty amides were obtained from each of the PPS-expressing E. coli strains fed with a primary amine. The fatty amide product obtained from each feed substrate is depicted in FIG. 4. The fatty amide products were not detected in E. coli strains transformed with empty vector.
The results of this example demonstrate a method of producing distinct species of fatty amides in an E. coli strain that was genetically engineered to produce fatty thioesters and which further expressed a PPS enzyme encoded by gene AY632377 by varying the primary amine feed type.
Example 7
This example shows that expression of a homolog of PPS in a genetically engineered microorganism produced the same fatty amide compounds that are produced when PPS is expressed.
The PPS encoded by AY632377 (SEQ ID NO: 2) was previously determined not to have a sequence identity of greater than 20% to any other known sequence by BLAST analysis (see Brady et al. (2004) J. Nat. Prod., 67: 1283-1286). The amino acid sequence of the PPS enzyme encoded by gene AY632377, i.e., GenBank Accession No. AAV33349 (SEQ ID NO: 1) was subjected to a BLAST search of the National Center for Biotechnology Information (NCBI) database. A homologue, encoding the enzyme, N-(4-amino-2-hydroxylbutyl)tetradecanamide synthase (AhtS) (GenBank Accession No. ACX33975.1) (SEQ ID NO: 3), was identified as having an amino acid sequence that is 38% identical to the amino acid sequence of PPS encoded by gene AY632377. The gene encoding AhtS was synthesized by GENEARTTM (Life Technologies, Grand Island, N.Y.) and cloned into the expression vector OP80, as follows. Plasmid OP80 was purified and subjected to restriction digestions with NcoI/PmeI (New England Biolabs, Inc., Ipswich, Mass.). The AhtS gene was cloned into OP80 using the IN-FUSIONTM PCR Cloning System (Clontech, Mountain View, Calif.) with the following primers:









3.10.10-2_InfusF:



(SEQ ID NO: 20)



5′-GAGGAATAAACCATGCCCATTCTTGAAAGCGTGGG-3′



and



 



3.10.10-2_InfusR:



(SEQ ID NO: 21)



5′-AGCTGGAGACCGTTTAAACTTATAAACCGCTGTTTGTCGCAA



 



CCG-3′.






Two colonies were positive for plasmid containing the AhtS-encoding insert by restriction digestion. The plasmid was confirmed to contain the AhtS-encoding gene by sequence analysis, and was termed “OP80-AhtS.” The OP80-AhtS plasmid was transformed into E. coli MG1655 strains DG5, DG5 Tn7-'tesA, and DG5 Tn7-'tesA-fadD. The three strains were cultured and induced as described in Example 4, and each culture was fed either 3-dimethylamino-1-propylamine, (±)-1-amino-2-propanol, or ethanolamine to a final concentration of 1%. After 60 hrs of culture in a pH-controlled incubator, the cultures were harvested and extracted with ethyl acetate (2 volumes of culture to 1 volume of ethyl acetate). The organic fractions were collected and utilized for GC-MS analysis as described in Example 3.
Fatty amides were obtained from each of the AhtS-expressing E. coli strains fed with each of the primary amines. A representative GC-MS trace of the products produced by E. coli MG1655 DG5 Tn7-'tesA-fadD transformed with OP80-AhtS fed with 3-dimethylamino-1-propylamine is provided as FIG. 5. The peak having a GC retention time of 11.4 min was confirmed as C14:0 fatty N-(3-dimethylamino-1-propylamide) by MS analysis (FIG. 5). Fatty amide products were not detected in E. coli strains transformed with empty vector. The highest amount of amides were produced in E. coli MG1655 strain DG5 Tn7-'tesA-fadD, whereas the lowest amount of amides were produced in E. coli MG1655 strain DG5 Tn7-'tesA. The increased production of amides in the DG5 Tn7-'tesA-fadD strain suggests that the AhtS enzyme has a preference for C14:0 fatty thioester substrates. These data also suggest that both AhtS and PPS can use each of the two fatty thioester substrates (i.e., fatty-ACPs and fatty-CoAs) in E. coli to make fatty amides.
The results of this example demonstrate that the AhtS enzyme can catalyze the same type of reaction between primary amines and fatty thioester substrates as the PPS enzyme. In addition, the data shown in this example indicated that the AhtS enzyme has a preference for C14:0 fatty thioester substrates.
Example 8
This example provides an in vivo method for generating a primary amine useful as a starting material in the generation of a fatty amide according to the present disclosure.
In vivo production of ethanolamine can be achieved by genetically increasing serine biosynthesis and serine decarboxylation pathways. To do so, the glycolytic intermediate 3-phosphoglycerate is increased by engineering E. coli strain MG1655 to overexpress phosphoglycerate mutases (gpm AB). The serine production pathway is engineered by overexpressing phosphoglycerate dehydrogenase (serA), 3-phosphoserine aminotransferase (serC), and 3-phosphoserine phosphate (serB). A heterologous serine decarboxylase (SDC), which decarboxylates serine to ethanolamine, is expressed in the host. In order to prevent the strain from metabolizing ethanolamine and serine, the genes encoding the degradation enzymes ethanolamine ammonia-lyase (eutABC) and serine deaminases (sdaAB) are deleted (FIG. 6). Fatty amides can then be produced in the recombinant microorganism which produces ethanolamine by overexpressing a polypeptide, such as PPS or AhtS, which catalyzes the conversion of ethanolamine and an acyl thioester to a fatty amide.
Various modifications and variations of the present disclosure will be apparent to those skilled in the art without departing from the scope and spirit of the disclosure. Although the disclosure has been described in connection with specific preferred embodiments, it should be understood that the claims should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the disclosure, which are understood by those skilled in the art are intended to be within the scope of the claims.

## Claims

1. A recombinant microorganism comprising an exogenous nucleic acid sequence encoding a palmitoylputrescine synthase (PPS) haying at least 90% sequence identity to the amino acid sequence of SEQ. ID. NO.: 1, wherein the PPS catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide, wherein the microorganism further expresses an exogenous thioesterase (EC 3.12.14 or EC 3.1.1.5) and is cultured in the presence of a carbon source.

2. The recombinant microorganism of claim 1, wherein the PPS polypeptide has an amino acid sequence comprising SEQ ID NO: 1.

3. The recombinant microorganism of claim 1, wherein the PPS polypeptide is encoded by an exogenous nucleic acid sequence comprising SEQ ID NO: 2.

4. The recombinant microorganism of claim 1, wherein the carbon source is a carbohydrate.

5. The recombinant microorganism of claim 1, wherein the primary amine is selected from the group consisting of 3-dimetylamino-1-propylamine, ±-1-amino-2-propanol, 2-methoxyethylamine, 3-amino-l-propanol, 2-amino-1,3-propanediol, 3-methoxypropylamine, N-(2-hydroxyethyl)ethylenediamine, butylamine, and 1,4-diaminobutane, or a combination thereof.

6. The recombinant microorganism of claim 5, wherein the acyl thioester is a fatty acyl-ACP or a fatty acyl-CoA.

7. The recombinant microorganism of claim 6, wherein the fatty acyl-ACP or the fatty acyl-CoA is produced by the microorganism.

8. The recombinant microorganism of claim 1, wherein the recombinant microorganism comprises exogenous nucleic acid sequences encoding one or more of a fatty acid biosynthetic polypeptide and an acyl-CoA synthase polypeptide (EC 2.3.1.86).

9. The recombinant microorganism of claim 8, wherein the microorganism comprises exogenous nucleic acid sequences encoding a thioesterase polypeptide and an acyl-CoA synthase polypeptide.

10. The recombinant microorganism of claim 8, wherein the exogenous nucleic acid sequence encoding the thioesterase polypeptide comprises a nucleic acid sequence of ′tesA.

11. The recombinant microorganism of claim 1, wherein the microorganism is a bacteria, a cyanobacteria, an algae, or a fungi.

12. The recombinant microorganism of claim 11, wherein the microorganism is a fungi.

13. The microorganism of claim 12, wherein the fungi is a yeast or a filamentous fungi.

14. The recombinant microorganism of claim 1, wherein the microorganism is a Saccharomyces cerevisiae, Candida lipolytica, Escherichia coli, Arthrobacter, Rhodotorula glutinins , Acinetobacter, Candida lipolytica, Botryococcus braunii, Vibrio furnissii, Micrococcus leuteus, Stenotrophomonas maltophilia, Bacillus subtilis, Bacillus lichenoformis, Psuedomonus putida, Psuedomonas florescens, Streptomyces coelicolor, Synechococcus sp. PCC7002, Thermosynechococcus elongatesBP-1, Prototheca moriformis, Prototheca krugani, Prototheca stagnora, Prototheca zopfii, or Chorella protothecoide cell.

15. The recombinant microorganism of claim 14, wherein the microorganism is an Arthrobacter AK 19, Acinetobacter sp. strain M-1, E. coli B, E. coli C, E. coli K, or E. coli W cell.

16. The recombinant microorganism claim 5, wherein the fatty amide is a fatty alkanolamide or a fatty amidoamine.

17. The recombinant microorganism of claim 1, wherein the microorganism expresses a serine decarboxylase polypeptide.

18. A method of producing a fatty amide comprising:
(a) providing a recombinant microorganism according to claim 1; and
(b) culturing the recombinant microorganism in a culture medium under conditions suitable for expression of the nucleic acid sequence encoding the polypeptide that catalyzes the conversion of the primary amine and the acyl thioester to the fatty amide in the presence of at least one substrate for the polypeptide.

19. The method of claim 18, further comprising isolating the fatty amide from the culture medium.

20. The method of claim 18, wherein the fatty amide is a C8, C9, C10, C11, C12, C13, C14, C15, C16, C17, C18, C19, or C20 fatty alkanolamide.

21. The method of claim 18, wherein the fatty amide is a C8, C9, C10, C11, C12, C13, C14, C15, C16, C17, C18, C19, or C20 fatty amidoamine.