WO2012106579A1 - Acide aminé déshydrogénase et son utilisation dans la préparation d'acides aminés à partir de cétoacides - Google Patents

Acide aminé déshydrogénase et son utilisation dans la préparation d'acides aminés à partir de cétoacides Download PDF

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WO2012106579A1
WO2012106579A1 PCT/US2012/023740 US2012023740W WO2012106579A1 WO 2012106579 A1 WO2012106579 A1 WO 2012106579A1 US 2012023740 W US2012023740 W US 2012023740W WO 2012106579 A1 WO2012106579 A1 WO 2012106579A1
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aadh
amino acid
seq
gdh
polypeptide
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PCT/US2012/023740
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Animesh Goswami
Steven L. Goldberg
Robert M. Johnston
Ronald L. Hanson
William Lawrence Parker
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Bristol-Myers Squibb Company
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y104/00—Oxidoreductases acting on the CH-NH2 group of donors (1.4)
    • C12Y104/01—Oxidoreductases acting on the CH-NH2 group of donors (1.4) with NAD+ or NADP+ as acceptor (1.4.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0012—Oxidoreductases (1.) acting on nitrogen containing compounds as donors (1.4, 1.5, 1.6, 1.7)
    • C12N9/0014—Oxidoreductases (1.) acting on nitrogen containing compounds as donors (1.4, 1.5, 1.6, 1.7) acting on the CH-NH2 group of donors (1.4)
    • C12N9/0016—Oxidoreductases (1.) acting on nitrogen containing compounds as donors (1.4, 1.5, 1.6, 1.7) acting on the CH-NH2 group of donors (1.4) with NAD or NADP as acceptor (1.4.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P13/00—Preparation of nitrogen-containing organic compounds
    • C12P13/005—Amino acids other than alpha- or beta amino acids, e.g. gamma amino acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P13/00—Preparation of nitrogen-containing organic compounds
    • C12P13/04—Alpha- or beta- amino acids

Definitions

  • This invention relates to novel compositions that can be used in the process of preparing amino acids from keto acids. This invention also relates to methods of synthesizing amino acids through the use of said novel compositions.
  • AD Alzheimer's disease
  • a progressive neurodegenerative disease which begins with memory loss and progresses to include severe cognitive impairment, altered behavior, and decreased motor function (Grundman, M. et al, Arch Neurol, 61 :59-66 (2004); Walsh, D.M. et al, Neuron, 44: 181-193 (2004)).
  • the cost of AD is enormous and includes not only the suffering of the patients and families but also the lost productivity of patients and caregivers. No treatment that effectively prevents AD or reverses the clinical symptoms and underlying pathophysiology is currently available.
  • a definitive diagnosis of AD for a demented patient requires a
  • Plaques primarily consist of ⁇ -amyloid ( ⁇ ) peptides that are formed by a stepwise proteolytic cleavage of the amyloid precursor protein (APP) by ⁇ -site APP-cleaving enzyme (BACE), to generate the N-terminus, and ⁇ -secretase, to generate the C-terminus (Selkoe, D.J., Physiol.
  • APP amyloid precursor protein
  • BACE ⁇ -site APP-cleaving enzyme
  • ⁇ -Secretase is a transmembrane protein complex that includes Nicastrin, Aph-1, PEN-2, and either Presenilin-1 (PS-1) or Presenilin-2 (PS-2) (Wolfe, M.S. et al., Science, 305: 11 19-1 123 (2004)). PS-1 and PS-2 are believed to contain the catalytic sites of ⁇ -secretase.
  • ⁇ 40 is the most abundant form of ⁇ synthesized (80-90%), while ⁇ 42 is most closely linked with AD pathogenesis.
  • mutations in the APP, PS-1, and PS-2 genes that lead to rare, familial forms of AD implicate ⁇ 42 aggregates as the primary toxic species (Selkoe, D.J., Physiol. Rev., 81 :741-766 (2001)).
  • Current evidence suggests that oligomeric, protofibrillar and intracellular ⁇ 42 play a significant role in the disease process (Cleary, J.P. et al, Nat. Neurosci., 8:79-84 (2005)).
  • Inhibitors of the enzymes that form ⁇ 42 such as ⁇ -secretase, represent potential disease-modifying therapeutics for the treatment of AD.
  • AADH amino acid dehydrogenase
  • the co-factor for this reaction may be regenerated in situ by using another enzyme, e.g., glucose dehydrogenase (GDH).
  • GDH oxidizes glucose to gluconolactone with the concomitant reduction of NAD or NADP to NADH or NADPH, respectively.
  • Performing the AADH- catalyzed reaction in the presence of GDH and one equivalent of glucose also utilizes much less co-factor for the reaction.
  • the chiral amino acid, (R)-5,5,5-trifluoronorvaline is a key intermediate for a ⁇ -secretase inhibitor that can be used for the treatment of Alzheimer's disease.
  • the intermediate also known as (R)-5,5,5-trifluoro-2-aminopentanoic acid, can be prepared from the corresponding keto acid, 5,5,5-trifluoro-2-oxopentanoic acid, via an AADH catalyzed reaction. This enzymatic reaction generates the amino acid (R)-5,5,5- trifluoronorvaline which can then be isolated from the reaction mixture. Alternatively, the amino acid from the AADH reaction may be converted to a sulfonamide and isolated.
  • the instant invention provides a novel AADH and a recombinantly cloned GDH that can be utilized to convert keto acids to amino acids more efficiently and in a more cost effective manner.
  • the instant invention also provides knock-out
  • Escherichia coli E. coll cells which lack glutamate dehydrogenase (gdhA).
  • the invention provides an isolated nucleic acid molecule comprising a nucleotide sequence according to SEQ ID NO: 12.
  • the invention provides a recombinant vector comprising the isolated nucleic acid molecule comprising a nucleotide sequence according to SEQ ID NO: 12.
  • the invention provides a recombinant host cell comprising said recombinant vector.
  • the recombinant host cell is an E. coli cell.
  • the E. coli cell does not express glutamate dehydrogenase (gdhA).
  • the invention provides an isolated polypeptide comprising an amino acid sequence according to SEQ ID NO: 1 1.
  • the polypeptide has amino acid dehydrogenase (AADH) activity.
  • the invention provides a recombinant vector comprising the isolated nucleic acid molecule comprising a nucleotide sequence according to SEQ ID NO: 12 and a glucose dehydrogenase (GDH) gene according to SEQ ID NO: 13.
  • the invention provides a recombinant host cell comprising said vector.
  • the host cell is E. coli.
  • the E. coli cell does not express gdhA.
  • the invention provides a method of converting a keto acid to an amino acid using the AADH of the present invention.
  • the amino acid is (R)-5,5,5-trifluoronorvaline.
  • the invention provides a bacterial cell which expresses the isolated nucleic acid molecules according to SEQ ID NO: 12 and SEQ ID NO: 13. In a preferred embodiment, the bacterial cell does not express gdhA.
  • the invention provides a method of making an amino acid, said method comprising: contacting a keto acid with a polypeptide comprising an amino acid sequence according to SEQ ID NO: 1 1 in the presence of a nicotinamide cofactor, said polypeptide being capable of catalyzing the conversion of the keto acid into its corresponding amino acid.
  • the polypeptide comprises SEQ ID NO: 11.
  • a GDH enzyme is added for nicotinamide cofactor regeneration.
  • the amino acid sequence of the GDH enzyme comprises SEQ ID NO: 14.
  • both the AADH and GDH are expressed in the same recombinant E coli cells.
  • the E coli cells do not express gdhA.
  • an ammonia or a source of ammonia is added.
  • the keto acid is 5,5,5-trifluoro-2-oxopentanoic acid.
  • the amino acid is (R)-2-amino-5,5,5-trifluoropentanoic acid (which is also known as (R)-5,5,5-trifluoronorvaline).
  • the amino acid is further converted to an amino acid derivative selected from the group consisting of (R)-2- (4-chlorophenylsulfonamido)-5,5,5-trifluoropentanoic acid, (R)-2-(4- chlorophenylsulfonamido)-5,5,5-trifluoropentanoic acid chloride and (R)-2-(4- chlorophenylsulfonamido)-5,5,5-trifluoropentanamide.
  • an amino acid derivative selected from the group consisting of (R)-2- (4-chlorophenylsulfonamido)-5,5,5-trifluoropentanoic acid, (R)-2-(4- chlorophenylsulfonamido)-5,5,5-trifluoropentanamide.
  • Table 1 shows the results of protein extracts assayed for their ability to catalyze the oxidative deamination of meso-2,6-diaminopimelate (DAP A) to (S)-a- amino-e-ketopimelate.
  • Table 2 shows the oligonucleotide primers prepared based upon the putative Gluconobacter oxydans (G. oxydans) GDH sequence.
  • Table 3 shows the results of protein samples assayed for the ability to catalyze reductive amination.
  • Table 4 shows the results of the AADH and gdhA assay
  • Table 5 shows the results of the gdhA assay from wild type and gdhA knockout cells.
  • Table 6 shows the yields of various compounds from conversion reactions.
  • Figure 1 shows the process used for generating an amino acid from a keto acid and the subsequent conversions of the amino acid to the sulfonamide, to the sulfonamide acid chloride, and to the sulfonamide amide.
  • Figures 2A and 2B show the nucleotide sequence (SEQ ID NO:3,
  • Figure 3 shows the amino acid alignment of DAPD isolated from B.
  • Figure 4 shows the amino acid sequence of the AADH of the present invention (SEQ ID NO: 11). The amino acids that were mutated from the B. sphaericus DAPD enzyme are underlined.
  • Figure 5 shows the nucleotide sequence of the AADH of the present invention (SEQ ID NO: 12).
  • the start codon (ATG) and the stop codon (TAA) are underlined.
  • Figure 6 shows the nucleotide sequence of GDH (SEQ ID NO: 13) cloned from G. oxydans.
  • Figure 7 shows the amino acid sequence of GDH (SEQ ID NO: 14) cloned from G. oxydans.
  • the present invention is directed to novel polynucleotides and polypeptides that are capable of catalyzing the conversion of a keto acid to an amino acid.
  • the present invention is also directed to methods of producing amino acids by reductive amination of the corresponding keto acid through the use of these novel polypeptides.
  • Wild-type DAPD enzyme from B. sphaericus has little or no activity toward the reductive amination of keto acids to produce amino acids.
  • the present invention is based on the discovery that certain mutated forms of the B. sphaericus DAPD enzyme are capable of catalyzing the stereoselective reductive amination of a keto acid to produce an amino acid ( Figure 1).
  • the present invention provides a novel AADH enzyme that has been generated by evolution of the meso- ⁇ , ⁇ - diaminopimelate dehydrogenase (DAPD) enzyme of B. sphaericus through mutagenesis.
  • the amino acid and nucleic acid sequences are represented in SEQ ID NOs: l 1 and 12, respectively.
  • the AADH of the present invention has activity to convert a keto acid to an amino acid as demonstrated in Table 1.
  • Rozell et al. have demonstrated that it is possible to evolve a DAPD enzyme capable of catalyzing the reductive amination of 2-keto acids to (R)-amino acids (Rozell, J.D. et al., J. Am. Chem. Soc, 128: 10923-10929 (2006)) into a broad host.
  • the native enzyme in that study bore very little resemblance to that of B. sphaericus DAPD from which the AADH of the present invention was evolved.
  • Rozell's AADH was only 50% identical at the amino acid level to the DAPD enzyme of B.
  • the AADH polynucleotides and/or polypeptides of the invention are useful in the amination of a keto acid to form an amino acid.
  • the AADH enzyme of the present invention can be utilized to generate a key intermediate for a gamma secretase inhibitor.
  • the present invention encompasses a novel AADH polypeptide comprising the amino acid sequence of SEQ ID NO: 1 1 as shown in Figure 4. More specifically, the AADH polypeptide of SEQ ID NO: 11 is 326 amino acids in length and has 95% amino acid identity with the DAPD enzyme of B. sphaericus from which it was evolved.
  • the AADH enzyme of the present invention requires a nicotinamide cofactor (NADPH or NADH) which is recycled by an appropriate nicotinamide cofactor recycle system.
  • NADPH nicotinamide cofactor
  • the nicotinamide cofactors can be used in equimolar quantities relative to the target ketone, keto acid, amine or amino acid, or the cofactors may be recycled, if desired. Numerous methods for the recycling of nicotinamide cofactors are well-known in the art, and any of these methods may be used in the practice of the present invention. Some of the methods for recycling nicotinamide cofactors are described in Lemiere, G.L.
  • An example of such a nicotinamide cofactor recycle system includes an NAD + or NADP + -dependent formate dehydrogenase using inexpensive formate as the reductant, an NAD + or NADP + -dependent GDH and glucose as the reductant or any other similar system.
  • One advantage of this recycle system is that the reaction allows amino acids to be prepared in a single step.
  • Other advantages of this recycle system include the use of inexpensive, readily available starting materials, a 100% theoretical yield, a 100% enantiomeric excess of the chiral amino acid, and no harmful by-products (other than volatile CO 2, , or water soluble gluconic acid) that must be removed in downstream purification steps.
  • the enzymes are tested for activity on the desired substrate, or target compound. Because many enzymes such as AADH require nicotinamide cofactors for optimal activity, detection of the oxidation or reduction of the cofactor can be used as a signal of enzyme activity.
  • polynucleotide sequences that are capable of hybridizing to the novel AADH nucleic acid sequence as set forth in SEQ ID NO: 12 under various conditions of stringency.
  • Hybridization conditions are typically based on the melting temperature (T m ) of the nucleic acid binding complex or probe (see, Wahl, G.M. et al, Meth. Enzymol, 152:399-407 (1987) and Kimmel, A.R., Meth.
  • moderate stringency conditions include prewashing solution of 2X SSC, 0.5% SDS, l .OmM EDTA, pH 8.0, and hybridization conditions of 50 °C, 5XSSC, overnight.
  • polynucleotide sequences or portions thereof which encode an AADH polypeptide or peptides can comprise recombinant DNA molecules to direct the expression of AADH polypeptide products, peptide fragments, or functional equivalents thereof, in appropriate host cells.
  • AADH polypeptide-encoding nucleotide sequences possessing non-naturally occurring codons it may be advantageous to produce AADH polypeptide-encoding nucleotide sequences possessing non-naturally occurring codons.
  • codons preferred by a particular prokaryotic or eukaryotic host can be selected to increase the rate of protein expression or to produce a recombinant RNA transcript having desirable properties, such as a half-life which is longer than that of a transcript generated from the naturally occurring sequence.
  • nucleotide sequences of the present invention can be engineered using methods generally known in the art in order to alter the AADH polypeptide-encoding sequences for a variety of reasons, including, but not limited to, alterations which modify the cloning, processing, and/or expression of the gene product.
  • DNA shuffling by random fragmentation, PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences.
  • site-directed mutagenesis may be used to insert new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, or introduce mutations, and the like.
  • natural, modified, or recombinant nucleic acid sequences encoding the AADH polypeptide may be ligated to a heterologous sequence to encode a fusion (or chimeric or hybrid) protein.
  • a fusion protein may comprise an amino acid sequence that differs from SEQ ID NO: 1 1 only by conservative substitutions.
  • a fusion protein may also be engineered to contain a cleavage site located between the AADH protein-encoding sequence and the heterologous protein sequence, for example a GDH sequence, so that the AADH protein may be cleaved and purified away from the heterologous moiety.
  • sequences encoding the AADH polypeptide may be synthesized in whole, or in part, using chemical methods well known in the art (see, for example, Caruthers, M.H. et al, Nucl. Acids Res. Symp. Ser., 215-223 (1980) and Horn, T. et al., Nucl. Acids Res. Symp. Ser., 225-232 (1980)).
  • the AADH protein itself, or a fragment or portion thereof may be produced using chemical methods to synthesize the amino acid sequence of the AADH polypeptide, or a fragment or portion thereof.
  • peptide synthesis can be performed using various solid-phase techniques (Roberge, J.Y. et al, Science, 269:202-204 (1995)) and automated synthesis can be achieved, for example, using the ABI 431 A Peptide Synthesizer (PE Biosystems).
  • the newly synthesized AADH polypeptide or peptide can be substantially purified by preparative high performance liquid chromatography (e.g., Creighton, T., Proteins, Structures and Molecular Principles, W.H. Freeman and Co., New York, NY (1983)), by reverse-phase high performance liquid chromatography (HPLC), or other purification methods as known and practiced in the art.
  • the composition of the synthetic peptides may be confirmed by amino acid analysis or sequencing (e.g., the Edman degradation procedure; Creighton, supra).
  • the amino acid sequence of an AADH polypeptide, or any portion thereof can be altered during direct synthesis and/or combined using chemical methods with sequences from other proteins, or any part thereof, to produce a variant polypeptide.
  • nucleotide sequences encoding the AADH polypeptide, or functional equivalents may be inserted into an appropriate expression vector, i.e., a vector, which contains the necessary elements for the transcription and translation of the inserted coding sequence.
  • an expression vector contains an isolated and purified polynucleotide sequence as set forth in SEQ ID NO: 12 encoding AADH, or a functional fragment thereof, in which the AADH comprises the amino acid sequence as set forth in SEQ ID NO: 11.
  • an expression vector can contain the complement of the aforementioned AADH nucleic acid sequence.
  • Expression vectors derived from retroviruses, adenovirus, herpes or vaccinia viruses, or from various bacterial plasmids can be used for the delivery of nucleotide sequences to a target organ, tissue or cell population. Methods, which are well known to those skilled in the art, may be used to construct expression vectors containing sequences encoding the AADH polypeptide along with appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Such techniques are described in the most recent edition of Sambrook, J.
  • a variety of expression vector/host systems may be utilized to contain and express sequences encoding the AADH polypeptide or peptides.
  • Such expression vector/host systems include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with virus expression vectors (e.g., baculovirus); plant cell systems transformed with virus expression vectors (e.g., cauliflower mosaic virus (CaMV) and tobacco mosaic virus (TMV)), or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems, including mammalian cell systems.
  • microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors
  • yeast transformed with yeast expression vectors insect cell systems infected with virus expression vectors (e.g., baculovirus)
  • the host cell employed is not limiting to the present invention.
  • the host cell of the invention contains an expression vector comprising an isolated and purified polynucleotide having a nucleic acid sequence selected from SEQ ID NO: 12 and encoding the AADH of this invention, or a functional fragment thereof, comprising an amino acid sequence as set forth in SEQ ID NO: 11.
  • Bacterial artificial chromosomes may be used to deliver larger fragments of DNA that can be contained and expressed in a plasmid vector.
  • BACs are vectors used to clone DNA sequences of 100-300kb, on average 150kb, in size in E. coli cells.
  • BACs are constructed and delivered via conventional delivery methods (e.g., liposomes, polycationic amino polymers, or vesicles) for therapeutic purposes.
  • Control elements are those non-translated regions of the vector, e.g., enhancers, promoters, 5' and 3' untranslated regions, which interact with host cellular proteins to carry out transcription and translation. Such elements may vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used. Specific initiation signals may also be used to achieve more efficient translation of sequences encoding an AADH polypeptide. Such signals include the ATG initiation codon and adjacent sequences.
  • a number of expression vectors may be selected, depending upon the use intended for the expressed AADH product. For example, when large quantities of expressed protein are needed, vectors that direct high level expression of fusion proteins that can be readily purified may be used.
  • vectors include, but are not limited to, the multifunctional E. coli cloning and expression vectors such as
  • BLUESCRIPT® (Stratagene), in which the sequence encoding the AADH polypeptide can be ligated into the vector in- frame with sequences for the amino-terminal Met and the subsequent 7 residues of B-galactosidase, so that a hybrid protein is produced; pIN vectors (see, Van Heeke, G. et al, J. Biol. Chem., 264:5503-5509 (1989)); and the like.
  • pGEX vectors (Promega, Madison, WI) can also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST).
  • fusion proteins are soluble and can be easily purified from lysed cells by adsorption to glutathione-agarose beads followed by elution in the presence of free glutathione.
  • Proteins made in such systems can be designed to include heparin, thrombin, or factor XA protease cleavage sites so that the cloned polypeptide of interest can be released from the GST moiety at will.
  • a number of viral-based expression systems can be utilized.
  • sequences encoding the AADH polypeptide may be ligated into an adenovirus transcription/ translation complex containing the late promoter and tripartite leader sequence. Insertion into a non-essential El or E3 region of the viral genome may be used to obtain a viable virus which is capable of expressing an AADH polypeptide in infected host cells (Logan, J. et al, Proc. Natl. Acad. Set, 81 :3655-3659 (1984)).
  • transcription enhancers such as the Rous sarcoma virus (RSV) enhancer
  • RSV Rous sarcoma virus
  • Other expression systems can also be used, such as, but not limited to yeast, plant, and insect vectors.
  • a host cell strain may be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed protein in the desired fashion.
  • modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation.
  • Post-translational processing which cleaves a "prepro" form of the protein may also be used to facilitate correct insertion, folding and/or function.
  • Different host cells having specific cellular machinery and characteristic mechanisms for such post-translational activities e.g., CHO, HeLa, MDCK, HEK293, and W138 are available from the
  • ATCC American Type Culture Collection
  • Host cells transformed with vectors containing nucleotide sequences encoding an AADH protein, or fragments thereof may be cultured under conditions suitable for the expression and recovery of the protein from cell culture.
  • the protein produced by a recombinant cell may be secreted or contained intracellularly depending on the sequence and/or the vector used.
  • expression vectors containing polynucleotides which encode an AADH protein can be designed to contain signal sequences which direct secretion of the AADH protein through a prokaryotic or eukaryotic cell membrane.
  • nucleic acid sequences encoding an AADH protein to a nucleotide sequence encoding a polypeptide domain, which will facilitate purification of soluble proteins.
  • purification facilitating domains include, but are not limited to, metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilized metals; protein A domains that allow purification on immobilized immunoglobulin; and the domain utilized in the FLAGS extension/ affinity purification system (Immunex Corp., Seattle, WA).
  • cleavable linker sequences such as those specific for Factor XA or enterokinase (Invitrogen, San Diego, CA) between the purification domain and the AADH protein may be used to facilitate purification.
  • One such expression vector provides for expression of a fusion protein containing AADH and a nucleic acid encoding 6 histidine residues preceding a thioredoxin or an enterokinase cleavage site. The histidine residues facilitate purification on IMAC (immobilized metal ion affinity chromatography) as described by Porath, J. et al, Prot. Exp.
  • enterokinase cleavage site provides a means for purifying the 6 histidine residue tag from the fusion protein.
  • HSV TK Herpes Simplex Virus thymidine kinase
  • Wigler, M. et al, Cell, 1 1 :223-232 (1977) and adenine
  • phosphoribosyltransferase (Lowy, I. et al, Cell, 22:817-823 (1980)) genes which can be employed in tk “ or aprt " cells, respectively.
  • anti-metabolite, antibiotic or herbicide resistance can be used as the basis for selection; for example, dhfr, which confers resistance to methotrexate (Wigler, M. et al, Proc. Natl. Acad. Set, 77:3567-3570 (1980)); npt, which confers resistance to the aminoglycosides neomycin and G-418 (Colbere-Garapin, F. et al, J. Mol.
  • markers as the anthocyanins, B-glucuronidase and its substrate GUS, and luciferase and its substrate luciferin, which are widely used not only to identify trans formants, but also to quantify the amount of transient or stable protein expression that is attributable to a specific vector system (Rhodes, C.A. et al, Methods Mol. Biol, 55: 121-131 (1995)).
  • the presence or absence of marker gene expression suggests that the gene of interest is also present, the presence and expression of the desired gene of interest may need to be confirmed.
  • the nucleic acid sequence encoding the AADH polypeptide is inserted within a marker gene sequence, recombinant cells containing a polynucleotide sequence encoding the AADH polypeptide can be identified by the absence of marker gene function.
  • a marker gene can be placed in tandem with a sequence encoding the AADH polypeptide under the control of a single promoter. Expression of the marker gene in response to induction or selection typically indicates co-expression of the tandem gene.
  • a wide variety of labels and conjugation techniques are known and employed by those skilled in the art and may be used in various nucleic acid and amino acid assays.
  • Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides encoding an AADH polypeptide include oligo-labeling, nick translation, end-labeling, or PCR amplification using a labeled nucleotide.
  • the sequences encoding an AADH polypeptide of this invention, or any portion or fragment thereof can be cloned into a vector for the production of an mRNA probe.
  • RNA polymerase such as T7, T3, or SP(6)
  • labeled nucleotides such as T7, T3, or SP(6)
  • RNA polymerase such as T7, T3, or SP(6)
  • Suitable reporter molecules or labels which can be used include radionucleotides, enzymes, fluorescent, chemiluminescent, or chromogenic agents, as well as substrates, cofactors, inhibitors, magnetic particles, and the like.
  • host cells which contain the nucleic acid sequence coding for an AADH polypeptide of the invention and which express the AADH polypeptide product may be identified by a variety of procedures known to those having skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridizations and protein bioassay or immunoassay techniques, including membrane, solution, or chip based technologies, for the detection and/or quantification of nucleic acid or protein.
  • polynucleotide sequences encoding AADH polypeptides can be detected by DNA-DNA or DNA-RNA hybridization, or by amplification using probes, portions, or fragments of polynucleotides encoding an AADH polypeptide.
  • Nucleic acid amplification based assays involve the use of oligonucleotides or oligomers based on the nucleic acid sequences encoding an AADH polypeptide to detect transformants containing DNA or RNA encoding an AADH polypeptide.
  • the invention provides a GDH enzyme which is a common enzyme of glucose metabolism and is also necessary for the conversion reaction of Figure 1.
  • GDH enzymes have been reported as early as 1963 (Okamoto, K., J. Biochem., 53 :346-353 (1963)).
  • the soluble GDH enzyme from G. oxydans has been well known and well characterized (Adachi, O. et al, Agric. Biol. Chem., 44:301 (1980)).
  • the complete gene sequence of G. oxydans was reported in 2005 (Prust, C. et al, Nature Biotechnology, 23 : 195-200 (2005); Shinjoh, M., PCT International Patent Application No.
  • WO 2007/028601 Al in which a soluble GDH with the open reading frame (ORF) designation of GOX2015 was described and details of the GENBANK® deposition of the genomic DNA sequence was given.
  • ORF open reading frame
  • the chromosomal sequence for ORF GOX2015 was provided and the nucleotide and amino acid sequences were highlighted.
  • the nucleotide sequence (SEQ ID NO: 13) and amino acid sequence (SEQ ID NO: 14) of an exemplary GDH are shown in Figures 6 and 7, respectively.
  • the instant invention also includes cloning of the NADP dependent GOX2015 and its expression in E. coli. A separate fermentation of this recombinant E. coli strain followed by processing gave a cell-free extract containing GDH.
  • both the GDH and AADH genes were cloned and expressed in the same E. coli strain. Any of the above mentioned expression vectors could be utilized to express these genes.
  • the AADH gene and the GDH gene are cloned into same vector thus generating a bicistronic plasmid.
  • the main advantage of expressing both the GDH and the AADH in the same bacterial strain is that there only needs to be a single fermentation of the bacterial strain to obtain a cell-free extract containing both AADH and GDH enzymes. By utilizing this system, it reduces the cost of enzyme preparation considerably.
  • endogenous gdhA can convert some keto acid to amino acid with varying selectivity.
  • the presence of endogenous gdhA in conjunction with AADH enzyme can cause lowering of the enantiomeric excess of the amino acid that would have otherwise been obtained with the AADH alone.
  • the advantage of utilizing a cell with no endogenous gdhA activity is that the gdhA does not interfere with the exogenously expressed AADH activity.
  • the invention provides a cell in which the endogenous gdhA is knocked out resulting in a cell which does not express gdhA and, therefore, does not have gdhA activity.
  • the cell is E. coli.
  • both AADH and GDH enzymes are cloned and then expressed in this gdhA deficient E. coli strain.
  • the amino acid sequence of the AADH is the amino acid sequence according to SEQ ID NO: 1 1.
  • the amino acid sequence of the GDH is the amino acid sequence according to SEQ ID NO: 14.
  • Fermentation followed by processing will give a cell-free extract containing both AADH and GDH enzymes with no gdhA activity.
  • These knockout cells can be generated according to procedures known to one of ordinary skill in the art.
  • the endogenous gdhA gene can be disrupted by the insertion of an intron into the chromosomal gdhA gene.
  • the insertion of an intron, a large polynucleotide (e.g., ⁇ 1000bp size), in the gdhA gene disrupts its function to produce gdhA activity.
  • Such an insertion can be performed through the cloning techniques described herein.
  • B. sphaericus (ATCC 4525) was used to inoculate 100 mL of sterile Luria Bertani (LB) broth. The flask was grown at 30 °C on a shaker platform until late-log phase. The cells were harvested by centrifugation, washed one time with sterile distilled water, and repelleted. Chromosomal DNA was prepared from the cell paste using a standard proteinase K/SDS/NaCl/CTAB bacterial DNA purification protocol (Ausubel et al, Current Protocols in Molecular Biology, Vol. 2, John Wiley and Sons, New York, NY (2001)).
  • the resulting crude preparation was extracted 3 times with an equal volume of phenol/chloroform/isoamyl alcohol (25:24: 1).
  • the aqueous phase was retained and the DNA was precipitated using 0.6 volume isopropyl alcohol.
  • the precipitated DNA was washed with 70% ethanol (in water) and recentrifuged.
  • the DNA pellet was air dried, resuspended in 1 mL TE buffer (10 mM Tris, 1 mM EDTA, pH 7.0) containing 50 ⁇ g/mL RNase, and incubated at 37 °C for 15 minutes to digest contaminating RNA.
  • One tenth volume 3M sodium acetate (pH 4.8) and two volume 100% ethanol were added to precipitate the chromosomal DNA.
  • the DNA pellet was concentrated by
  • the GENBANK® amino acid sequence submission for a comparable B. sphaericus DAPD protein (GENBANK® accession number BAB07799) was used to design synthetic oligonucleotides to prime amplification of the DAPD gene from chromosomal DNA.
  • the N-terminal primer (sense strand) was 5'- GACCATATGAGTGGAATTCGAGTAG-3 ' (SEQ ID NO: 1), representing the N- terminal amino acid sequence MSAIRVG (SEQ ID NO:20) with an added Ndel restriction endonuclease cutting site (underlined in SEQ ID NO: 1) encompassing the initiator methionine ATG codon.
  • the C-terminal primer (antisense strand) was 5"- GCAGGTACCTTATAATAGTTCCTTACG-3 ' (SEQ ID NO:2) representing the C- terminal amino acid sequence RKELLStop (SEQ ID NO:28) with an added Kpnl restriction endonuclease cutting site (underlined in SEQ ID NO:2) downstream of the translational stop codon TAA. Both of these primers were synthesized, purified, resuspended in TE buffer at 100 ⁇ / ⁇ and used as PCR primers using the B. sphaericus chromosomal DNA as the target.
  • a PCR reaction was prepared using standard Taq reagents and Taq polymerase.
  • a 20 ⁇ ⁇ reaction contained 1 ⁇ g of chromosomal DNA as the target, 200 picomoles of each primer and 0.2 units of Taq polymerase.
  • the "touchdown" cycling conditions were 94 °C/1 min/1 cycle, 94 °C/30 sec/55 °C/30 sec/72 °C/30 sec. (5 cycles); 94 °C/30 sec/65 °C (minus 1 °C per successive cycle) 30 sec/72 °C/30 sec. (16 cycles); 94 °C/30 sec/50 °C/30 sec/72 °C/30 sec.
  • Cloning vector pCR4-TOPO+DAPD was digested with restriction enzymes Ndel and Kpnl. The digest products were separated by agarose gel electrophoresis and the DAPD insert (984 nt) was excised from the gel and purified. This DNA fragment was ligated into Ndel/Kpnl digested expression vector pET30a, placing the putative DAPD coding sequence downstream of an IPTG-inducible promoter sequence. The ligation product (pET30a+ DAPD) was used to transform competent BL21(DE3)-GOLD
  • Isopropyl ⁇ -D-thiogalactoside (IPTG) was added to a final concentration of 200 ⁇ to induce transcription of the DAPD gene from the tac promoter and the culture was continued overnight at 30 °C.
  • the cells were collected by centrifugation, resuspended in water at 10% wt/vol, and lysed by vortexing with glass beads.
  • the resulting cellular proteins were analyzed by SDS/PAGE containing a protein molecular weight standard.
  • the proteins derived from the DAPD expression culture displayed a novel highly overexpressed protein with a MW of -36 kD.
  • Protein extracts were assayed for the ability to catalyze the oxidative deamination of DAP A to (5)-a-amino-8-ketopimelate (reaction shown below).
  • Enzyme assay mixtures were prepared containing 100 mM glycine-KCl buffer (pH 10.5), 25 mM DAPA, 10 ⁇ ⁇ of cell lysate and water to a final volume of 990 ⁇ ⁇ .
  • the reactions were initiated by the addition of 10 ⁇ ⁇ of lOOmM NADP.
  • Activity levels were determined by monitoring the change in absorption over 2 minutes at 340 nM in a twin beam scanning spectrophotometer. Lysates tested were 10% wt/vol aqueous suspensions of B. sphaericus ATCC 4525 (positive control), untrans formed E.
  • the oxidative deamination activity level in the recombinant DAPD E. coli expression strain was about 1000-fold higher than the level observed in the native strain used to isolate the DAPD gene clearly demonstrating that the cloned gene encoded a DAPD.
  • the product produced by this reaction had a 100% ee of the (5)-keto acid.
  • a QUIKCHANGE® Multisite Mutagenesis kit (Stratagene) was used to introduce nucleotide substitutions into the B. sphaericus DAPD gene, altering the amino acid sequence of the encoded protein to include five amino acid mutations.
  • T173I 5'GGGGCGATGGCCTAAGTCTGGGACATTCAGGCGCTGTTCGTCGTATTGAAG G-3' (SEQ ID NO:7), with the two codon substitutions underlined.
  • the nucleotide sequence of T173I is:
  • the nucleotide sequence of R199M is:
  • H249N 5'-CAACACGTGAAAAACATGCAATGGAATGTTGGGTTGTATTAGAAG-3' (SEQ ID NO: 9).
  • the nucleotide sequence of H249N is:
  • the mutagenic PCR reaction was conducted following the QUIKCHANGE® manufacturer's protocol, including 100 ng of pET30+DAPD target and 200 picomoles of each of the four mutagenic primers in a total reaction volume of 25 ⁇ ⁇ .
  • the QUIKCHANGE® manufacturer's protocol including 100 ng of pET30+DAPD target and 200 picomoles of each of the four mutagenic primers in a total reaction volume of 25 ⁇ ⁇ .
  • thermocycling parameters were 95 °C/1 minute (1 cycle); 95 °C/1 minute/55 °C/1 minute/65 °C/1 1 minutes (30 cycles); 4 °C/5 minutes.
  • the mutagenized PCR product was purified and concentrated on a silica membrane microcentrifuge spin column, eluting into 10 ⁇ ⁇ of sterile distilled water.
  • This mutagenized plasmid was used to transform competent E. coli strain XL10-GOLD selecting transformants by growth on LB/kan agar plates. Plasmid DNA was prepared from 20 isolates and used for DNA sequencing reactions using the N- terminal and C-terminal DAPD oligonucleotides as primers.
  • Plasmid pET30+AADH was used to transform E. coli strain BL21(DE3)- GOLD. A single colony was inoculated into LB/kan broth and grown at 37 °C until late log-phase. The cell density was determined by measuring the OD 6 oo and the cells were subcultured into MT5mod2/kan at an initial cell density of 0.2. The culture was placed on a 30 °C shaker platform and the fermentation was continued until an OD 600 of ⁇ 1.0. IPTG (0.2 mM) was added to induce expression of the AADH enzyme.
  • G. oxydans chromosomal DNA was prepared using a known procedure with the following modification (Ausubel, F.M. et al., eds., Current Protocols in Molecular Biology, Vol. 2, John Wiley & Sons, New York, NY (2001)). The cell pellet was resuspended in 9.5 mL GTE buffer (50 mM glucose, 25 mM Tris-HCl pH 8.0, 10 mM NaEDTA) containing 2 mg/mL lysozyme and incubated at 37 °C for 30 min before adding SDS and Proteinase K. [0074] A putative NAD(P)-dependent glucose 1 -dehydrogenase gene was identified from the sequenced genome of G. oxydans (NCBI accession number NC 006677).
  • Oligonucleotide primers prepared based upon the putative G. oxydans GDH sequence
  • the primers were used for polymerase chain reaction (PCR) along with the FailSafe series of buffers (Epicentre Technologies, Madison, WI) and G. oxydans chromosomal DNA (10 ng per reaction) as template in 10 ⁇ ⁇ reactions.
  • Amplification was carried out in a Hybaid PCR Express thermocycler (ThermoSavant, Holbrook, NY). The amplification conditions included incubation at 94 °C for 1 min, followed by 30 cycles at 94 °C for 0.5 min; 50 °C for 0.5 min; and 72 °C for 0.5 min. Samples were electrophoresed on a 1.0% agarose gel for 2 hr at 100 v in TAE buffer (0.04 M
  • TRIZMA® base 0.02 M acetic acid, and 0.001 M EDTA, pH 8.3) containing 0.5 ⁇ g/mL ethidium bromide.
  • the amplified gene was named GDH.
  • Colonies containing recombinant plasmids were selected on LB agar plates containing 50 ⁇ g/mL kanamycin sulfate (Sigma Chemicals, St. Louis, MO).
  • kanamycin sulfate Sigma Chemicals, St. Louis, MO.
  • kanamycin-resistant colonies were screened for the presence of the GDH gene by colony PCR using oligos 819 + 820 under previously described conditions; eight amplified a fragment of the expected size.
  • Plasmid DNA was prepared from a liquid culture of a colony that contained the insert and was verified to possess the expected 807-bp Ndel-BamHl fragment after digestion with these enzymes and named pBMS2004-GDH.
  • the DNA sequence of the insert was determined and showed completed homology to that obtained from genomic sequencing of G.
  • BL21(DE3)/pET30A+AADH culture were assayed for the ability to catalyze the reductive amination of (2) to (R)-2-amino-5,5,5-trifluoro-pentanoic acid (T).
  • the initial assays were performed on a dual beam spectrophotometer measuring the change in absorbance at 340 nm over a two minute test period.
  • the reaction mixture for the initial 1 mL assays contained 5 mg/mL (2), 53.5 mg NH 4 C1, 10.6 mg Na 2 C0 3 in -800 of water. After adjusting the pH to 9.0 with 10 N NaOH, additional water was added to a final volume of 970 ⁇ ⁇ .
  • Plasmid pBMS2004+AADH was used to transform E. coli expression strain BL21-GOLD selecting transformants on LB/kan agar plates. A single transformant colony was used to inoculate LB/kan broth, which was grown overnight at 37 °C. This overnight culture was subcultured into MT5mod2/kan and grown at 30 °C and induced 0.2 mM IPTG.
  • BL21-GOLD/pBMS2004+AADH was used to inoculate 1L of MT5mod2/kan broth in a 4L shake flask. The flask was placed on a 30 °C shaker platform and grown overnight at 225 RPM. The OD 6 oo was measured and the entire 1L volume was used to inoculate 100L of MT5mod2/kan in a 150L Braun fermentor (B. Braun Biotech
  • Enzyme assays were done using 1 cm path length cuvets in a
  • the (R)-AADH assay solution contained 5 mg/mL (29.4 mM) keto acid (2), 1 M NH 4 C1, 0.1 M Na 2 C0 3, 0.2 mM NADPH at pH 9.0 in a volume of 1 mL.
  • the absorbance decrease/min at 340 nm was used to calculate enzyme activity.
  • a blank was run with no keto acid.
  • the GDH assay solution contained 0.1 M potassium phosphate buffer pH 8, 0.5 mM NADP, and 0.1 M glucose in a volume of 1 mL. After addition of diluted enzyme solution, the absorbance increase/min at 340 nm was used to calculate enzyme activity. A blank was run with no enzyme.
  • pBMS2004-GDH was transformed into competent E. coli expression strain BL21 by electroporation as described above.
  • a single kanamycin-resistant colony was initially grown in MT5-M2 + kanamycin for 20-24 hr, 30 °C, 250 rpm.
  • MT5-M2 medium contains Hy-Pea (Quest International) 2.0%;
  • TASTONE® 154 (Quest), 1.85%; Na 2 HP0 4 , 0.6%; (NH 4 ) 2 S0 4 , 0.125%; glycerol, 4.0%; pH adjusted to 7.2 w/10 N NaOH before autoclaving.
  • the optical density at 600 nm (OD 6 oo) was recorded and fresh medium inoculated with the culture to a starting OD 6 oo of 0.30.
  • the flask was incubated as described above until the OD 6 oo reached -0.8-1.0.
  • IPTG was added from a 1 M filter-sterilized stock in d3 ⁇ 40 to a final concentration of 50 ⁇ or 1 mM and the culture allowed to grow for an additional 22 hr. Cells were harvested by centrifugation at 5,000 x g at 4 °C in a Beckman JA 5.3 rotor.
  • GDH activity was measured spectrophotometrically by following the rate of NADPH formation at 340 nm.
  • Standard conditions were 200 mM Tris-HCl pH 9.0, 10 mM D-glucose, 20 mM MgCi 2 , 1.25 mM NADP, and enzyme.
  • the increase in absorbance was recorded for 3 min and units of activity per mL calculated using the formula AOD340 nm X enzyme dilution factor/6.22 x time (min) x enzyme used (mL).
  • GDH from Gluconobacter oxydans expressed in E. coli was prepared by microfluidization, ammonium sulfate fractionation and lyophilization, then stored at 4 °C. GDH activity was 21.8 U/mg.
  • 5,5,5-Trifluoro-2-oxopentanoic acid (2) (1 g, 5.88 mmoles), NH 4 C1 (1.07 g, 20 mmoles), glucose (1.44 g, 7.99 mmoles) and water (16.2 mL) were charged to a 20-mL jacketed reactor and the mixture was stirred with a magnet at 30 °C to dissolve the solids. NaOH (0.65 mL of 10 N) was added to raise the pH to about 8.
  • the GDH insert of expression vector pBMS2004-GDH was modified by PCR amplification using primers that substituted a Kpnl restriction endonuclease cutting site for the C-terminal BamHI site contained in the original construct.
  • the resulting product contained an Ndel site prior to the initiation codon and a Kpnl site immediately following the termination codon.
  • This fragment was purified and ligated into NdeLKpnl cut pBMS2004, creating an alternate GDH expression plasmid.
  • This expression vector served as a starting point for the creation of a bicistronic E. coli expression plasmid designed to produce both the AADH and the GDH from the same IPTG-inducible mRNA.
  • Plasmid pBMS2004+AADH was used as the target for a PCR amplification to add a Kpnl restriction site at the N-terminal and introduce a ribosome binding site between Kpnl site and the AADH initiation codon, and add a BamHI restriction site downstream of the termination codon.
  • the N-terminal (sense) primer was:
  • sphaericus chromosomal DNA 5 '-GCAGGTACCTTATAATAGTTCCTTACG-3 ' (SEQ ID NO: 16), with the C-terminal Kpnl site underlined.
  • a PCR reaction was performed using the thermocycler conditions described for the initial isolation of the DAPD native gene. Agarose gel electrophoresis of the completed reaction revealed a single amplified product of -980 bp. This fragment was excised from the gel, purified and used as an insert fragment for a ligation into the Kpnl cut pBMS2004-GDH vector. The ligation reaction was used to transform E. coli strain BL21-Gold, and transformants were selected by plating on LB kan agar.
  • Nucleotides 1-27 of SEQ ID NO: 17 encode for the eight C-terminal amino acids of the GDH protein (SEQ ID NO: 14) which are DFENNWSS Stop (SEQ ID NO: 18). GA4TAAATAAAACATATGAGTGCAATTCGAGTAGGT ... (AADH gene) ...3" (SEQ ID NO: 19)
  • Nucleotides of 16-36 SEQ ID NO: 19 encode for the seven N-terminal amino acids of the AADH protein (SEQ ID NO: 1 1) which are MSAIRVG (SEQ ID NO:20).
  • Transformant BL21 -Gold/pBMS2004-GDH+AADH was used to inoculate a shake flask containing 25 mL of MT5(mod 2)/kan broth. The flask was placed on a 37 °C shaker at 250 RPM and grown until OD 600 ⁇ 1.0. IPTG was added to a final concentration of 0.5 mM and the culture was continued overnight ( ⁇ 16 hrs).
  • MT5mod2/kan broth in a 4L shake flask was placed on a 37 °C shaker platform and grown overnight at 225 RPM.
  • the OD 60 o was measured and the entire 1L volume was used to inoculate 250L of MT5mod2/kan in a 275L Braun fermentor (B. Braun Biotech International GMBH, Melsungen, Germany) yielding an initial OD 600 of -0.15.
  • the cells were grown at 37 °C, 150 LPM air input, 10 psig pressure, 320 RPM, at pH 7.2. Based on prior shake flask fermentations, the pH level was not controlled and drifted downward during the course of the fermentation.
  • OD 6 oo of the culture reached ⁇ 5
  • sterile IPTG was added to a final concentration of 1.0 mM.
  • the fermentation was continued until the CO 2 off-gas dropped precipitously, indicating depletion of the growth medium.
  • the cells were harvested by centrifugation and the cell paste was analyzed for both GDH and (R)-AADH activity.
  • the pH was maintained at 9.00 with 5 N NaOH from a pH stat, and the reaction temperature was kept at 30 °C. After 22h the pH was adjusted to 1.98 with 63.5 mL cone. HC1.
  • the final reaction mixture contained 44.54 g (260.3 mmoles, 88.5% solution yield, 98.9% ee) of (R)-5,5,5-trifluoro-2- aminopentanoic acid (1) in 1 100 mL by HPLC analysis.
  • Extract from cells expressing (R)-AADH and GDH was prepared by sonication of 835 mg cells in 5 mL of 50 mM potassium phosphate buffer, pH 7. All further steps were carried out at 4 °C.
  • the extract was centrifuged for 10 min at 43000xg and 2 niL of the supernatant was added to a 1-mL column of Q-SEPHAROSE® equilibrated with 20 mM tris chloride pH 7.4.
  • the column was eluted with 2-mL portions of 20 mM tris chloride pH 7.4 containing 0, 0.1, 0.2, 0.3 and 0.4 M NaCl and 2-mL fractions were collected.
  • each fraction was assayed for glutamate dehydrogenase, (R)- AADH and ee of (R)-5,5,5-trifluoronorvaline produced by the fraction.
  • the fractions giving a product with low ee had the highest amount of glutamate dehydrogenase activity, and the elevated activity in these fractions was believed to result from endogenous L- glutamate dehydrogenase found in E. coli.
  • Low levels of glutamate dehydrogenase activity in the other fractions can result from (R)-AADH.
  • the reaction mixture contained in a total volume of 1 mL at pH 9.0: 5 mg/mL (29.4 mM) keto acid (2), 0.5 M NH 4 C1, 0.347 M glucose, 0.5 mM NADP, and 0.1 mL of the fraction being assayed at pH 9.0 in a volume of 1 mL. After 15 h incubation at 30 °C the (R)-5,5,5-trifluoronorvaline was analyzed by HPLC using a Regis Davankov column as described above.
  • gdhA assay 5 mg/mL (29.4 mM) keto acid (2), 0.5 M NH 4 C1, 0.347 M glucose, 0.5 mM NADP, and 0.1 mL of the fraction being assayed at pH 9.0 in a volume of 1 mL. After 15 h incubation at 30 °C the (R)-5,5,5-trifluoronorvaline was analyzed by HPLC using a Regis Davankov column as described
  • the gdhA assay solution contained 5 mg/mL (29.7 mM) a-ketoglutarate monosodium salt, 1 M NH 4 C1, 0.1 M Na 2 C0 3, 0.2 mM NADPH at pH 9.0 in a volume of 1 mL.
  • the absorbance decrease/min at 340 nm was used to calculate enzyme activity.
  • a blank was run with no keto acid.
  • nucleotide sequence of the gdhA gene from E. coli strain B was obtained from the GENBANK® sequence database. Based on this sequence, an N-terminal (sense) primer:
  • 5'-ATGGATCAGACATATTCTCTGG-3' SEQ ID NO:21
  • a C-terminal (antisense) primer 5 '-AATTTAGTGTGGGACGCGGTCG-3 ' (SEQ ID NO:22)
  • 5 '-AATTTAGTGTGGGACGCGGTCG-3 ' SEQ ID NO:22
  • a colony of BL21 - Gold was picked from a LB agar plate and resuspended in 25 of sterile distilled water.
  • Two microliters of the cell suspension plus 200 picomoles of each gdhA primer were used to prepare a 20 ⁇ L PCR amplification reaction using standard reagents and 0.2 units of Taq polymerase.
  • the "touchdown" cycling conditions were 94 °C/1 min/lX, 94 °C/30 sec/55 °C/30 sec/72 °C/30 sec. (5 cycles); 94 °C/30 sec/65 °C (minus 1 °C per successive cycle) 30 sec/72 °C/30 sec. (16 cycles); 94 °C/30 sec/50 °C/30 sec/72 °C/30 sec. (5 cycles), 94 °C/30 sec/50 °C/30 sec/72 °C/5 min. (1 cycle).
  • the completed PCR reaction was analyzed by ethidium bromide stained agarose gel electrophoresis. A single band of ca. 1350 base pairs was strongly amplified, consistent with the expected size of an E.
  • coli gdhA gene The amplified fragment was purified, ligated into cloning vector pCR4-TOPO, and used to transform E. coli strain TOP 10. Transformants were selected by growth on LB agar plates and the gdhA insert was verified by PCR analysis of individual colonies. A PCR positive transformant was used to inoculate 10 mL of LB media. The culture was grown overnight at 37 °C then used to prepare purified plasmid DNA. The plasmid DNA was sequenced. The sequence of the PCR insert was compared to the GENBANK® database and shown to be a match for the expected gdhA sequence.
  • a TargeTron Gene Knockout System (Sigma Aldrich) was used to disrupt the chromosomal gdhA gene in BL21-Gold.
  • the nucleotide sequence from the gdhA gene was submitted to Sigma and analyzed using their proprietary algorithm to determine the optimal region for insertion of an intron intended to disrupt the gdhA coding sequence.
  • This primer set was designed to adapt the intron to insert between nucleotides 903 and 904 of the gdhA gene. All subsequent gene knockout experiments: amplification of a gdhA-modified intron fragment, cloning of the modified intron into the pACD4 vector and transformation of BL21 -Gold to disrupt the native gdhA gene were conducted according to the TargeTron manufacturer's protocol.
  • colony PCR using the original gdhA terminal primers was used to detect which colonies contained disrupted gdhA genes. Approximately 20% of the colonies amplified a PCR product -1000 bp larger than the control (the purified pCR4-TOPO+gdhA vector) indicating they had incorporated the intron within the gdhA coding region. One of these colonies, named BL21-Gold(gdhA minus ) was selected for further analysis.
  • Both BL21 -Gold and BL21 -Gold(gdhA minus ) were grown in shake flasks containing MT5(mod2) medium at 37 °C. When the cultures had reached late-log phase, the cells were harvested, resuspended in 50 mM NaP0 4 (pH 8.0) at 10% (wt/vol), and lysed. The lysates were tested for glutamate dehydrogenase activity.
  • gdhA activity in knockouts measured in this assay was ⁇ 10% of wild type control activity.
  • the residual AA340/min found in the knockouts may be a result of ketoreductase activity and not glutamate dehydrogenase.
  • the gdhA knockout strain BL21 -Gold(gdhA minus ) was used as an expression strain for the bicistronic GDH+AADH plasmid construct.
  • BL21 -Gold(gdhA minus ) was transformed with plasmid pBMS2004- GDH+AADH.
  • Transformants were identified by growth on LB/kan agar plates and verified by colony PCR specific for amplification of the GDH+AADH gene cassette.
  • BL21 -Gold(gdhA minus )/pBMS2004GDH+AADH was used to inoculate 500 mL of MT5mod2 kan broth in a 2L shake flask. The flask was placed on a 37 °C shaker platform and grown overnight at 225 RPM. The OD 600 was measured and the entire 500 mL volume was used to inoculate 15L of MT5mod2/kan in a 21L Braun fermentor (B. Braun Biotech International GMBH, Melsoder, Germany) yielding an initial OD 600 of -0.25. The cells were grown at 37 °C, 150 LPM air input, 10 psig pressure, 320 RPM, at pH 7.2.
  • reaction mixture was stirred at 30 °C and maintained at pH 9.00 by addition of 1 N NaOH from a pH stat. After 20 h the solution yield of (R)-5,5,5-trifluoro-2-aminopentanoic acid (T) was 0.889 g, 89% yield, 100% ee.
  • Enzyme reaction samples of 0.02 mL were diluted with 0.98 mL water and placed in a boiling water bath for 2 min to precipitate proteins. After cooling, samples were filtered into HPLC vials. Samples were analyzed with a PHENOMENEX® Chirex 3126 (D-Penicillamine Ligand Exchange) 50x4.6-mm column. The mobile phase was 2 mM CuS0 4 in 5% isopropanol/ 95% water, flow rate was 1 mL/min, detection was at 235 nm, temperature was 40 °C, and injection volume was 10 ⁇ . Retention times were (5)- enantiomer of 5,5,5-trifluoronorvaline 3.75 min, (R)- 5,5,5-trifluoronorvaline (T) 5.86 min, keto acid (2) 26.3 min.
  • reaction mixture 1200 g, pH 2.0, containing 44.5 g of (R)-trifluoronorvaline
  • the residue (containing the acid chloride (4)) was dissolved in 156 mL of MeTHF and poured into an ice-cold stirred mixture of 780 mL of MeTHF, 520 mL of water and 260 mL of 15M ammonia. After 10 min the lower phase was separated, back extracting with 400 mL of MeTHF. The combined upper phase was washed with 50-mL portions of 0.5 M sulfuric acid until the washes were acidic and then with 50-mL portions of water until neutral. The organic phase was concentrated in vacuo, chasing with 200 mL of n-butanol.
  • the product (5) was filtered out, washed with 100 mL of ice-cold n-butanol and dried by suction on the funnel and in vacuo at room temperature, giving 68 g of .(R)-2-(4-Chlorophenylsulfonamido)-5,5,5- trifluoropentanamide (5), mp 21 1-212.5 °C, ee 99.1%, 66% yield.
  • (R)-2-(4-Chlorophenylsulfonamido)-5,5,5-trifluoropentanamide (5) was prepared from 15 kg of an enzymatic reaction solution containing (R)-2-amino-5,5,5- trifluoropentanoic acid (1), ee 98.95, derived from 600 g, 3.53 moles, of 5,5,5-trifluoro-2- oxopentanoic acid (2).
  • the solution was acidified to pH 2.10 (HC1), and after holding at 5 °C for several days, precipitated protein was filtered out.
  • the filtrate was concentrated in vacuo to 8.5 L, adjusted to pH 12.30 (NaOH) and further concentrated in vacuo with addition of water to remove ammonia.
  • the resulting solution 6.5 L, contained 556 g (3.25 moles) of (R)-2-amino-5,5,5-trifluoropentanoic acid (T), ee 98.95, by HPLC analysis.
  • the solution was concentrated in vacuo, adding portions of 2- methyltetrahydrofuran (MeTHF) until the water content in the distillate was ⁇ 0.1 weight%.
  • the solution was diluted to 4 L with MeTHF, and oxalyl chloride, 335 mL, 3.96 moles, was added in 30-mL portions at 1 min intervals. After 30 min, four 26-mL portions of a 5 vol% solution of DMF in MeTHF were added at 10-minute intervals. By 75 min gas evolution (CO and CO 2 ) had stopped.
  • the solution was concentrated in vacuo with addition of MeTHF until the distillate gave negligible gas evolution when mixed with water.
  • the mother liquor/wash contained 68 g of 2-(4-chlorophenylsulfonamido)- 5,5,5-trifluoropentanamide (5).
  • the mother liquor therefore contained 59 g of the (R) enantiomer.
  • a second crop was obtained by crystallization from 1-butanol, giving 30 g of (R)-2-(4-chlorophenylsulfonamido)-5,5,5-trifluoropentanamide (5), ee 99.6%, potency 98.9 w%.

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Abstract

La présente invention concerne une nouvelle acide aminé déshydrogénase qui peut être utilisée pour convertir des cétoacides en acides aminés plus efficacement et d'une manière plus économique. La présente invention concerne également des cellules ayant un gène inactivé qui sont dépourvues de glutamate déshydrogénase.
PCT/US2012/023740 2011-02-03 2012-02-03 Acide aminé déshydrogénase et son utilisation dans la préparation d'acides aminés à partir de cétoacides WO2012106579A1 (fr)

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