Carboxylic acid reductase polypeptide, nucleotide sequence encoding same and methods of use

[0001] Microorganism-produced enzymes are widely used as a class of biocatalytic reagents in production of synthetic, aromatic, aliphatic and alicyclic aldehydes and alcohols are useful chemical intermediates in chemical, agrochemical, pharmaceutical and food industries. These enzymes are useful in a wide variety of reactions including, e.g., oxidations, reductions, hydrolyses, and carbon—carbon bond ligations.

[0002] Biocatalysts are valued for their intrinsic abilities to bind organic substrates and to catalyze highly specific and selective reactions under the mildest of reaction conditions. These selectivities and specificities are realized because of highly rigid interactions occurring between the enzyme active site and the substrate molecule. Biocatalytic reactions are particularly useful when they may be used to overcome difficulties encountered in catalysis achieved by the use of traditional chemical approaches.

[0003] Carboxylic acid reductases are complex, multicomponent enzyme systems, requiring the initial activation of carboxylic acids via formation of AMP and often coenzyme A intermediates (see, e.g., Hempel et al., Protein Sci. 2:1890–1900 (1993). Chemical methods for carboxylic acid reductions are generally poor usually requiring prior derivatization and product deblocking with multifunctional reactants.

[0004] An enzymatic reaction offers significant advantages over existing methods used in chemical reductions of carboxylic acids, or their derivatives. Unlike many substrates subjected to biocatalytic reactions, carboxylic acids are generally water soluble, rendering them of potentially broad application to this class of enzyme. The carboxylic acid reduction reaction appears to bear the usual desirable features of functional group specificity. It also functions well under mild reaction conditions and produces a high yield of product. The reduction of the activated carboxylic acid intermediate occurs step-wise to give aldehyde products (Gross et al., Eur. J. Biochem. 8:413–419; 420–425 (1969); Gross, Eur. J. Biochem. 31:585–592 (1972)).

[0005] The reduction of carboxylic acids by microorganisms is a relatively new biocatalytic reaction that has not yet been widely examined or exploited. Jezo and Zemek reported the reduction of aromatic acids to their corresponding benzaldehyde derivatives by Actinomycetes in Chem. Papers 40(2):279–281 (1986). Kato et al. reported the reduction of benzoate to benzyl alcohol by Nocardia asteroides JCM 3016 (Agric. Biol. Chem. 52(7):1885–1886 (1988)), and Tsuda et al. described the reduction of 2-aryloxyacetic acids (Agric. Biol. Chem. 48(5): 1373–1374 (1984)) and arylpropionates (Chem. Pharm. Bull. 33(11):4657–4661 (1985)) by species of Glomerella and Gloeosporium. Microbial reductions of aromatic carboxylic acids, typically to their corresponding alcohols, have also been observed with whole cell biotransformations by Clostridium thermoaceticum (White et al., Eur. J. Biochem. 184:89–96 (1989)), and by Neurospora (Bachman et al., Arch. Biochem. Biophys. 91:326 (1960)). More recently, carboxylic acid reduction reactions have reportedly been catalyzed by whole cell preparations of Aspergillus niger, Corynespora melonis and Coriolus (Arfmann et al., Z. Naturforsch 48c:52–57 (1993); cf., Raman et al., J. Bacterial 84:1340–1341 (1962)), and by Nocardia asteriodes (Chen and Rosazza, Appl. Environ. Microbiol. 60(4):1292–1296 (1994)).

[0006] Biocatalytic reductions of carboxylic acids are attractive to traditional chemical catalysis because the substrates are water soluble, blocking chemistry is not necessary, reductions are enantioselective (7), and the scope of the reaction is very broad (23, 32).

[0007] Aldehyde oxidoreductases are also known as carboxylic acid reductases (CAR), require ATP, Mg²⁺, and NADPH as cofactors during carboxylic acid reduction (15, 16, 20, 23). The reduction reaction is a stepwise process involving initial binding of both ATP and the carboxylic acid to the enzyme, to form mixed 5′-adenylic acid-carbonyl anhydride intermediates (8, 14, 24, 26, 40) that are subsequently reduced by hydride delivery from NADPH to form the aldehyde product (15, 24).

[0008] Aromatic carboxylic acid reductases have been purified to homogeneity only from Neurospora (16) and Nocardia (20, 23). Although details of N- and internal amino acid sequences have been reported for the Nocardia asteriodes enzyme (23), complete gene sequences for these or any other carboxylic acid reductases are unknown.

[0009] It is an object of the present invention to provide a purified and isolated bacterial carboxylic acid reductase (CAR) gene and the protein encoded thereby.

[0010] It is yet another object of the invention to provide homologous nucleotide sequences and/or amino acid sequences which encode CAR.

[0011] It is yet another object of the invention to provide recombinant DNA using expression constructs, vectors, and recombinant cells using the sequences of the invention for production of recombinant CAR.

[0012] It is yet another object of the invention to provide for large scale production of and recovery of recombinant CAR, for use in production of synthetic, aromatic, aliphatic and alicyclic aldehydes and alcohols.

[0013] It is yet another embodiment of the invention to provide methods of synthesis of chemical compounds such as those for biocatalytically reducing a carboxylic acid, or a derivative thereof, to its corresponding aldehyde product(s), to provide a method of biocatalytically reducing a carboxylic acid, or a derivative thereof, to its corresponding intermediary by-product(s), as exemplified by acyl-AMP analogs, or to provide a method of biocatalytically reducing vanillic acid, or a precursor or derivative thereof, to vanillin, all using recombinant CAR as described the invention disclosed herein.

[0014] Additional objects, advantages and novel features of the invention will be set forth in part in the description which follows, and in part will become apparent to those skilled in the art on examination of the following, or may be learned by practice of the invention.

[0015] The present invention provides polynucleotides, related polypeptides and all conservatively modified variants of purified and isolated CAR. The nucleotide sequence of CAR comprises the sequence found in SEQ ID NO: 1, 3, and 5. Sequences 3 and 5 provide examples of conservatively modified polynucleotides of SEQ ID NO: 1 and sequences 7, and 9, 11, are examples of sequences with 80, 90, and 95% sequence identity to SEQ ID NO:1 as also described herein.

[0016] Therefore, in one aspect, the present invention relates to an isolated nucleic acid comprising an isolated polynucleotide sequence encoding a CAR enzyme. In a further aspect, the present invention includes a nucleic acid selected from: (a) an isolated polynucleotide encoding a polypeptide of the present invention; (b) a polynucleotide having at least 80%, 90% or 95% identity to a polynucleotide of the present invention; (c) a polynucleotide comprising at least 25 nucleotides in length which hybridizes under high stringency conditions to a polynucleotide of the present invention; (d) a polynucleotide comprising a polynucleotide of the present invention; and (e) a polynucleotide which is complementary to the polynucleotide of (a) to (d).

[0017] In another aspect, the present invention relates to a recombinant expression cassette comprising a nucleic acid as described, supra. Additionally, the present invention relates to a vector containing the recombinant expression cassette. Further, the vector containing the recombinant expression cassette can facilitate the transcription and translation of the nucleic acid in a host cell. The present invention also relates to host cells able to express the polynucleotide of the present invention. A number of host cells could be used, such as but not limited to, microbial, mammalian, plant, or insect. In a preferred embodiment the host cell is a bacterial cell. In a more preferred embodiment the bacterial host cell is E. Coli. Thus the invention is also directed to transgenic cells, containing the nucleic acids of the present invention as well as cells, strains and lines derived therefrom.

[0018] This invention also provides an isolated polypeptide comprising (a) a polypeptide comprising at least 80%, 90% or 95% sequence identity to a polypeptide of the present invention (SEQ ID NO:2); (b) a polypeptide encoded by a nucleic acid of the present invention; and (c) a polypeptide comprising CAR activity and modeled and designed after SEQ ID NO:1.

[0019] Another embodiment of the subject invention comprises a methods for biocatalytically reducing a carboxylic acid, or a derivative thereof, to its corresponding aldehyde product(s), to provide a method of biocatalytically reducing a carboxylic acid, or a derivative thereof, to its corresponding intermediary by-product(s), as exemplified by acyl-AMP analogs, or to provide a method of biocatalytically reducing vanillic acid, or a precursor or derivative thereof, to vanillin, all using recombinant cells, extracts, CAR protein purified therefrom or derivatives and modifications of this CAR protein.

[0020] Yet another embodiment of the invention comprises a method of making a polypeptide of a recombinant gene comprising:

• • [0021] a) providing a population of these host cells; and
  • [0022] b) growing the population of cells under conditions whereby the polypeptide encoded by the coding sequence of the expression cassette is expressed;
  • [0023] c) isolating the resulting polypeptide.

[0024] A number of expression systems using the said host cells could be used, such as but not limited to, microbial, mammalian, plant, or insect.

[0031] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Unless mentioned otherwise, the techniques employed or contemplated herein are standard methodologies well known to one of ordinary skill in the art. The materials, methods and examples are illustrative only and not limiting. The following is presented by way of illustration and is not intended to limit the scope of the invention.

[0032] The practice of the present invention will employ, unless otherwise indicated, conventional techniques of botany, microbiology, tissue culture, molecular biology, chemistry, biochemistry and recombinant DNA technology, which are within the skill of the art. Such techniques are explained fully in the literature. See, e.g., The Microbial World, (1986) 5th Ed., Prentice-Hall; O. D. Dhringra and J. B. Sinclair, Basic Plant Pathology Methods, (1985) CRC Press; Maniatis, Fritsch & Sambrook, Molecular Cloning: A Laboratory Manual (1982); DNA Cloning, Vols. I and II (D. N. Glover ed. 1985); Oligonucleotide Synthesis (M. J. Gait ed. 1984); Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. 1984); and the series Methods in Enzymology (S. Colowick and N. Kaplan, eds., Academic Press, Inc.).

[0033] Units, prefixes, and symbols may be denoted in their SI accepted form. Unless otherwise indicated, nucleic acids are written left to right in 5′ to 3′ orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively. Numeric ranges are inclusive of the numbers defining the range. Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes. The terms defined below are more fully defined by reference to the specification as a whole.

[0034] In describing the present invention, the following terms will be employed, and are intended to be defined as indicated below.

[0035] By “amplified” is meant the construction of multiple copies of a nucleic acid sequence or multiple copies complementary to the nucleic acid sequence using at least one of the nucleic acid sequences as a template. Amplification systems include the polymerase chain reaction (PCR) system, ligase chain reaction (LCR) system, nucleic acid sequence based amplification (NASBA, Cangene, Mississauga, Ontario), Q-Beta Replicase systems, transcription-based amplification system (TAS), and strand displacement amplification (SDA). See, e.g., Diagnostic Molecular Microbiology: Principles and Applications, D. H. Persing et al., Ed., American Society for Microbiology, Washington, D.C. (1993). The product of amplification is termed an amplicon.

[0036] The term “conservatively modified variants” applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refer to those nucleic acids that encode identical or conservatively modified variants of the amino acid sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations” and represent one species of conservatively modified variation. Every nucleic acid sequence herein that encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of ordinary skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, one exception is Micrococcus rubens, for which GTG is the methionine codon (Ishizuka, et al., J. Gen'l Microbiol, 139:425–432 (1993)) can be modified to yield a functionally identical molecule. Accordingly, each nucleic acid disclosed herein also includes each silent variation of the nucleic acid, which encodes a polypeptide of the present invention, it is implicit in each described polypeptide sequence and incorporated herein by reference. Examples of conservatively modified variants with silent mutations are SEQ ID NO:37 (where some gca codons have been replaced with gcg condons both of which code for Alanine) and 38 (where a tca codon has been replaced with an agt codon both of which code for serine).

[0037] As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservatively modified variant” when the alteration results in the substitution of an amino acid with a chemically similar amino acid. Thus, any number of amino acid residues selected from the group of integers consisting of from 1 to 15 can be so altered. Thus, for example, 1, 2, 3, 4, 5, 7, or 10 alterations can be made. Conservatively modified variants typically provide similar biological activity as the unmodified polypeptide sequence from which they are derived. For example, substrate specificity, enzyme activity, or ligand/receptor binding is generally at least 80%, or 95%, preferably 80–95% of the native protein for it's native substrate. Conservative substitution tables providing functionally similar amino acids are well known in the art. Sequence ID no 39 is a protein sequence with a conservative substitution of A for S.

[0038] The following six groups each contain amino acids that are conservative substitutions for one another:

• [0039] 1) Alanine (A), Serine (S), Threonine (T);
• [0040] 2) Aspartic acid (D), Glutamic acid (E);
• [0041] 3) Asparagine (N), Glutamine (Q);
• [0042] 4) Arginine (R), Lysine (K);
• [0043] 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and
• [0044] 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).
  See also, Creighton (1984) Proteins W.H. Freeman and Company. Examples of proteins with conservatively modified variants are SEQ ID NO:______.

[0045] By “encoding” or “encoded”, with respect to a specified nucleic acid, is meant comprising the information for translation into the specified protein. A nucleic acid encoding a protein may comprise non-translated sequences (e.g., introns) within translated regions of the nucleic acid, or may lack such intervening non-translated sequences (e.g., as in cDNA). The information by which a protein is encoded is specified by the use of codons. Typically, the amino acid sequence is encoded by the nucleic acid using the “universal” genetic code. However, variants of the universal code, such as is present in some plant, animal, and fungal mitochondria, the bacterium Mycoplasma capricolum (Proc. Natl. Acad. Sci. (USA), 82: 2306–2309 (1985)), or the ciliate Macronucleus, may be used when the nucleic acid is expressed using these organisms.

[0046] When the nucleic acid is prepared or altered synthetically, advantage can be taken of known codon preferences of the intended host where the nucleic acid is to be expressed.

[0047] As used herein, “heterologous” in reference to a nucleic acid is a nucleic acid that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention. For example, a promoter operably linked to a heterologous structural gene is from a species different from that from which the structural gene was derived, or, if from the same species, one or both are substantially modified from their original form. A heterologous protein may originate from a foreign species or, if from the same species, is substantially modified from its original form by deliberate human intervention.

[0048] By “host cell” is meant a cell, which contains a vector and supports the replication and/or expression of the expression vector. Host cells may be prokaryotic cells such as E. coli, or eukaryotic cells such as yeast, insect, plant, amphibian, or mammalian cells. Preferably, host cells are bacterial cells to provide for production of the enzyme in large quantities. A particularly preferred bacterial host cell is an E. coli host cell.

[0049] The term “hybridization complex” includes reference to a duplex nucleic acid structure formed by two single-stranded nucleic acid sequences selectively hybridized with each other.

[0050] The term “introduced” in the context of inserting a nucleic acid into a cell, means “transfection” or “transformation” or “transduction” and includes reference to the incorporation of a nucleic acid into a eukaryotic or prokaryotic cell where the nucleic acid may be incorporated into the genome of the cell (e.g., chromosome, plasmid, plastid or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).

[0051] The terms “isolated” refers to material, such as a nucleic acid or a protein, which is substantially or essentially free from components which normally accompany or interact with it as found in its naturally occurring environment. The isolated material optionally comprises material not found with the material in its natural environment. Nucleic acids, which are “isolated”, as defined herein, are also referred to as “heterologous” nucleic acids.

[0052] Unless otherwise stated, the term “CAR nucleic acid” means a nucleic acid, including all conservatively modified variants, encoding an CAR polypeptide. The term CAR, unless otherwise stated encompasses CAR and its functional, conservatively modified variants.

[0053] As used herein, “nucleic acid” includes reference to a deoxyribonucleotide or ribonucleotide polymer in either single- or double-stranded form, and unless otherwise limited, encompasses known analogues having the essential nature of natural nucleotides in that they hybridize to single-stranded nucleic acids in a manner similar to naturally occurring nucleotides (e.g., peptide nucleic acids).

[0054] By “nucleic acid library” is meant a collection of isolated DNA or RNA molecules, which comprise and substantially represent the entire transcribed fraction of a genome of a specified organism. Construction of exemplary nucleic acid libraries, such as genomic and cDNA libraries, is taught in standard molecular biology references such as Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology, Vol. 152, Academic Press, Inc., San Diego, Calif. (Berger); Sambrook et al., Molecular Cloning—A Laboratory Manual, 2nd ed., Vol. 1–3 (1989); and Current Protocols in Molecular Biology, F. M. Ausubel et al., Eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc. (1994 Supplement).

[0055] As used herein “operably linked” includes reference to a functional linkage between a first sequence, such as a promoter and a second sequence, wherein the promoter sequence initiates and mediates transcription of the DNA sequence corresponding to the second sequence. Generally, operably linked means that the nucleic acid sequences being linked are contiguous and, where necessary to join two protein coding regions, contiguous and in the same reading frame.

[0056] As used herein, “polynucleotide” includes reference to a deoxyribopolynucleotide, ribopolynucleotide, or analogs thereof that have the essential nature of a natural ribonucleotide in that they hybridize, under stringent hybridization conditions, to substantially the same nucleotide sequence as naturally occurring nucleotides and/or allow translation into the same amino acid(s) as the naturally occurring nucleotide(s). A polynucleotide can be full-length or a subsequence of a native or heterologous structural or regulatory gene. Unless otherwise indicated, the term includes reference to the specified sequence as well as the complementary sequence thereof. Thus, DNAs or RNAs with backbones modified for stability or for other reasons are “polynucleotides” as that term is intended herein. Moreover, DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritylated bases, to name just two examples, are polynucleotides as the term is used herein. It will be appreciated that a great variety of modifications have been made to DNA and RNA that serve many useful purposes known to those of skill in the art. The term polynucleotide as it is employed herein embraces such chemically, enzymatically or metabolically modified forms of polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including inter alia, simple and complex cells.

[0057] The terms “polypeptide”, “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical analogue of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers.

[0058] As used herein “promoter” includes reference to a region of DNA upstream from the start of transcription and involved in recognition and binding of RNA polymerase and other proteins to initiate transcription. An “inducible” or “regulatable” promoter is a promoter, which is under environmental control. Examples of environmental conditions that may effect transcription by inducible promoters include anaerobic conditions or the presence of light. Another type of promoter is a developmentally regulated or tissue specific promoter. Tissue preferred, cell type specific, developmentally regulated, and inducible promoters constitute the class of “non-constitutive” promoters. A “constitutive” promoter is a promoter, which is active under most environmental conditions.

[0059] The term “CAR polypeptide” refers to one or more amino acid sequences. The term is also inclusive of conservatively modified variants, fragments, homologs, alleles or precursors (e.g., preproproteins or proproteins) thereof. A “CAR protein” comprises a CAR polypeptide.

[0060] As used herein “recombinant” includes reference to a cell or vector, that has been modified by the introduction of a heterologous nucleic acid or that the cell is derived from a cell so modified. Thus, for example, recombinant cells express genes that are not found in identical form within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all as a result of deliberate human intervention. The term “recombinant” as used herein does not encompass the alteration of the cell or vector by naturally occurring events (e.g., spontaneous mutation, natural transformation/transduction/transposition) such as those occurring without deliberate human intervention.

[0061] As used herein, a “recombinant expression cassette” is a nucleic acid construct, generated recombinantly or synthetically, with a series of specified nucleic acid elements, which permit transcription of a particular nucleic acid in a target cell. The recombinant expression cassette can be incorporated into a plasmid, chromosome, mitochondrial DNA, plastid DNA, virus, or nucleic acid fragment. Typically, the recombinant expression cassette portion of an expression vector includes, among other sequences, a nucleic acid to be transcribed, and a promoter.

[0062] The term “residue” or “amino acid residue” or “amino acid” are used interchangeably herein to refer to an amino acid that is incorporated into a protein, polypeptide, or peptide (collectively “protein”). The amino acid may be a naturally occurring amino acid and, unless otherwise limited, may encompass known analogs of natural amino acids that can function in a similar manner as naturally occurring amino acids.

[0063] The term “selectively hybridizes” includes reference to hybridization, under stringent hybridization conditions, of a nucleic acid sequence to a specified nucleic acid target sequence to a detectably greater degree (e.g., at least 2-fold over background) than its hybridization to non-target nucleic acid sequences and to the substantial exclusion of non-target nucleic acids. Selectively hybridizing sequences typically have about at least 40% sequence identity, preferably 60–90% sequence identity, and most preferably 100% sequence identity (i.e., complementary) with each other.

[0064] The terms “stringent conditions” or “stringent hybridization conditions” include reference to conditions under which a probe will hybridize to its target sequence, to a detectably greater degree than other sequences (e.g., at least 2-fold over background). Stringent conditions are sequence-dependent and will be different in different circumstances. By controlling the stringency of the hybridization and/or washing conditions, target sequences can be identified which can be up to 100% complementary to the probe (homologous probing). Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing). Optimally, the probe is approximately 500 nucleotides in length, but can vary greatly in length from less than 500 nucleotides to equal to the entire length of the target sequence.

[0065] Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide or Denhardt's. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C., and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1×SSC at 60 to 65° C. Specificity is typically the function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. For DNA-DNA hybrids, the T_m can be approximated from the equation of Meinkoth and Wahl, Anal. Biochem., 138:267–284 (1984): T_m=81.5° C.+16.6 (log M)+0.41 (% GC)−0.61 (% form)−500/L; where M is the molarity of monovalent cations, % GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. The T_m is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. T_m is reduced by about 1° C. for each 1% of mismatching; thus, T_m, hybridization and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with ≧90% identity are sought, the T_m can be decreased 10° C. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (T_m) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4° C. lower than the thermal melting point (T_m); moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than the thermal melting point (T_m); low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower than the thermal melting point (T_m). Using the equation, hybridization and wash compositions, and desired T_m, those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. If the desired degree of mismatching results in a T_m of less than 45° C. (aqueous solution) or 32° C. (formamide solution) it is preferred to increase the SSC concentration so that a higher temperature can be used. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes, Part I, Chapter 2 “Overview of principles of hybridization and the strategy of nucleic acid probe assays”, Elsevier, New York (1993); and Current Protocols in Molecular Biology, Chapter 2, Ausubel, et al., Eds., Greene Publishing and Wiley-Interscience, New York (1995). Unless otherwise stated, in the present application high stringency is defined as hybridization in 4×SSC, 5× Denhardt's (5 g Ficoll, 5 g polyvinylpyrrolidone, 5 g bovine serum albumin in 500 ml of water), 0.1 mg/ml boiled salmon sperm DNA, and 25 mM Na phosphate at 65° C., and a wash in 0.1×SSC, 0.1% SDS at 65° C.

[0066] “Transgenic” is used herein to include any cell, cell line, or tissue, the genotype of which has been altered by the presence of heterologous nucleic acid including those transgenics initially so altered as well as those created by sexual crosses or asexual propagation from the initial transgenic. The term “transgenic” as used herein does not encompass the alteration of the genome (chromosomal or extra-chromosomal) by conventional breeding methods or by naturally occurring events such as random cross-fertilization, non-recombinant viral infection, non-recombinant bacterial transformation, non-recombinant transposition, or spontaneous mutation.

[0067] As used herein, “vector” includes reference to a nucleic acid used in transfection of a host cell and into which can be inserted a polynucleotide. Vectors are often replicons. Expression vectors permit transcription of a nucleic acid inserted therein.

[0068] The following terms are used to describe the sequence relationships between two or more nucleic acids or polynucleotides or polypeptides: (a) “reference sequence”, (b) “comparison window”, (c) “sequence identity”, (d) “percentage of sequence identity”, and (e) “substantial identity”.

[0069] (a) As used herein, “reference sequence” is a defined sequence used as a basis for sequence comparison. A reference sequence may be a subset or the entirety of a specified sequence; for example, as a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence.

[0070] (b) As used herein, “comparison window” means includes reference to a contiguous and specified segment of a polynucleotide sequence, wherein the polynucleotide sequence may be compared to a reference sequence and wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. Generally, the comparison window is at least 20 contiguous nucleotides in length, and optionally can be 30, 40, 50, 100, or longer. Those of skill in the art understand that to avoid a high similarity to a reference sequence due to inclusion of gaps in the polynucleotide sequence a gap penalty is typically introduced and is subtracted from the number of matches.

[0071] Methods of alignment of nucleotide and amino acid sequences for comparison are well known in the art. The local homology algorithm (Best Fit) of Smith and Waterman, Adv. Appl. Math may conduct optimal alignment of sequences for comparison. 2: 482 (1981); by the homology alignment algorithm (GAP) of Needleman and Wunsch, J. Mol. Biol. 48: 443 (1970); by the search for similarity method (Tfasta and Fasta) of Pearson and Lipman, Proc. Natl. Acad. Sci. 85: 2444 (1988); by computerized implementations of these algorithms, including, but not limited to: CLUSTAL in the PC/Gene program by Intelligenetics, Mountain View, Calif., GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis., USA; the CLUSTAL program is well described by Higgins and Sharp, Gene 73: 237–244 (1988); Higgins and Sharp, CABIOS 5: 151–153 (1989); Corpet, et al., Nucleic Acids Research 16: 10881–90 (1988); Huang, et a., Computer Applications in the Biosciences 8: 155–65 (1992), and Pearson, et al., Methods in Molecular Biology 24: 307–331 (1994). The preferred program to use for optimal global alignment of multiple sequences is PileUp (Feng and Doolittle, Journal of Molecular Evolution, 25:351–360 (1987) which is similar to the method described by Higgins and Sharp, CABIOS, 5:151–153 (1989) and hereby incorporated by reference). The BLAST family of programs which can be used for database similarity searches includes: BLASTN for nucleotide query sequences against nucleotide database sequences; BLASTX for nucleotide query sequences against protein database sequences; BLASTP for protein query sequences against protein database sequences; TBLASTN for protein query sequences against nucleotide database sequences; and TBLASTX for nucleotide query sequences against nucleotide database sequences. See, Current Protocols in Molecular Biology, Chapter 19, Ausubel, et al., Eds., Greene Publishing and Wiley-Interscience, New York (1995).

[0072] GAP uses the algorithm of Needleman and Wunsch (J. Mol. Biol. 48: 443–453, 1970) to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. GAP considers all possible alignments and gap positions and creates the alignment with the largest number of matched bases and the fewest gaps. It allows for the provision of a gap creation penalty and a gap extension penalty in units of matched bases. GAP must make a profit of gap creation penalty number of matches for each gap it inserts. If a gap extension penalty greater than zero is chosen, GAP must, in addition, make a profit for each gap inserted of the length of the gap times the gap extension penalty. Default gap creation penalty values and gap extension penalty values in Version 10 of the Wisconsin Genetics Software Package are 8 and 2, respectively. The gap creation and gap extension penalties can be expressed as an integer selected from the group of integers consisting of from 0 to 100. Thus, for example, the gap creation and gap extension penalties can be 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, or greater.

[0073] GAP presents one member of the family of best alignments. There may be many members of this family, but no other member has a better quality. GAP displays four figures of merit for alignments: Quality, Ratio, Identity, and Similarity. The Quality is the metric maximized in order to align the sequences. Ratio is the quality divided by the number of bases in the shorter segment. Percent Identity is the percent of the symbols that actually match. Percent Similarity is the percent of the symbols that are similar. Symbols that are across from gaps are ignored. A similarity is scored when the scoring matrix value for a pair of symbols is greater than or equal to 0.50, the similarity threshold. The scoring matrix used in Version 10 of the Wisconsin Genetics Software Package is BLOSUM62 (see Henikoff & Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915).

[0074] Unless otherwise stated, sequence identity/similarity values provided herein refer to the value obtained using the BLAST 2.0 suite of programs using default parameters. Altschul et al., Nucleic Acids Res. 25:3389–3402 (1997).

[0075] As those of ordinary skill in the art will understand, BLAST searches assume that proteins can be modeled as random sequences. However, many real proteins comprise regions of nonrandom sequences, which may be homopolymeric tracts, short-period repeats, or regions enriched in one or more amino acids. Such low-complexity regions may be aligned between unrelated proteins even though other regions of the protein are entirely dissimilar. A number of low-complexity filter programs can be employed to reduce such low-complexity alignments. For example, the SEG (Wooten and Federhen, Comput. Chem., 17:149–163 (1993)) and XNU (Claverie and States, Comput. Chem., 17:191–201 (1993)) low-complexity filters can be employed alone or in combination.

[0076] (c) As used herein, “sequence identity” or “identity” in the context of two nucleic acid or polypeptide sequences includes reference to the residues in the two sequences, which are the same when aligned for maximum correspondence over a specified comparison window. When percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g. charge or hydrophobicity) and therefore do not change the functional properties of the molecule. Where sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Sequences, which differ by such conservative substitutions, are said to have “sequence similarity” or “similarity”. Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., according to the algorithm of Meyers and Miller, Computer Applic. Biol. Sci., 4: 11–17 (1988) e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, Calif., USA).

[0077] (d) As used herein, “percentage of sequence identity” means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity.

[0078] (e) (i) The term “substantial identity” of polynucleotide sequences means that a polynucleotide comprises a sequence that has between 50–100% sequence identity, preferably at least 50% sequence identity, preferably at least 60% sequence identity, preferably at least 87%, more preferably at least 90%, more preferably at least 95%, compared to a reference sequence using one of the alignment programs described using standard parameters. One of skill will recognize that these values can be appropriately adjusted to determine corresponding identity of proteins encoded by two nucleotide sequences by taking into account codon degeneracy, amino acid similarity, reading frame positioning and the like. Substantial identity of amino acid sequences for these purposes normally means sequence identity of between 55–100%, preferably at least 75%, preferably at least 80%, more preferably at least 90%, and most preferably at least 95%.

[0079] Another indication that nucleotide sequences are substantially identical is if two molecules hybridize to each other under stringent conditions. The degeneracy of the genetic code allows for many amino acids substitutions that lead to variety in the nucleotide sequence that code for the same amino acid, hence it is possible that the DNA sequence could code for the same polypeptide but not hybridize to each other under stringent conditions. This may occur, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. One indication that two nucleic acid sequences are substantially identical is that the polypeptide, which the first nucleic acid encodes, is immunologically cross reactive with the polypeptide encoded by the second nucleic acid.

[0080] (e) (ii) The terms “substantial identity” in the context of a peptide indicates that a peptide comprises a sequence with between 55–100% sequence identity to a reference sequence preferably at least 55% sequence identity, preferably 60% preferably 70%, more preferably 80%, most preferably at least 90% or 95% sequence identity to the reference sequence over a specified comparison window. Preferably, optimal alignment is conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443 (1970). An indication that two peptide sequences are substantially identical is that one peptide is immunologically reactive with antibodies raised against the second peptide. Thus, a peptide is substantially identical to a second peptide, for example, where the two peptides differ only by a conservative substitution. In addition, a peptide can be substantially identical to a second peptide when they differ by a non-conservative change if the epitope that the antibody recognizes is substantially identical. Peptides, which are “substantially similar” share sequences as, noted above except that residue positions, which are not identical, may differ by conservative amino acid changes.

[0081] Carboxylic acid reductase (CAR) catalyzes the first and rate limiting step in the reduction of carboxylic acids to aldehydes, and later alcohols. According to the invention, analysis of a cloned 6.9 Kb sequence revealed that the entire open reading frame of Nocardia CAR and its 5′ and 3′ flanking regions had been cloned. ATG was identified as the translation start codon by matching the N-terminal amino acid sequence from purified Nocardia CAR (23) with an amino acid sequence deduced from the DNA sequence. The assignment of ATG as the start codon is supported by 5′ flank region analysis: 6 bp upstream from the start codon ATG lies a conserved Streptomyces ribosomal binding site (GGGAGG) (27, 35). The 2.5 Kb sequence upstream of CAR showed fair homology to a putative transmembrane efflux protein (33% identity) in S. avermitilis, and a putative efflux protein (32% identity) in M. tuberculosis. The sequence downstream of Nocardia car showed 40%, 35%, 34% and 28% identities to putative membrane proteins in Corynebacterium efficiens, M. tuberculosis, M. leprae, and S. coelicolor, respectively. Although the CAR gene was flanked by genes encoding membrane proteins, the actual function of CAR in Nocardia remains unknown at this time.

[0082] BLAST analysis also showed that CAR contained two major domains and a possible phosphopantetheine attachment site. The N-terminal domain (aa 90–544) showed high homology to AMP-binding proteins. The C-terminal showed high homology to NADPH binding proteins. If a 4′-phosphopantetheine prosthetic group exists in active CAR, it likely acts as a “swinging arm” for transferring acyl-AMP intermediates to the C-terminal reductase domain. This arrangement of the CAR protein would reflect its sequential catalytic mechanism wherein the N-terminal domain catalyzes substrate activation by formation of an initial acyl-AMP intermediate, while the C-terminal portion then catalyzes the reduction of acyl-AMP by cofactor NADPH to finish a catalytic cycle. The existence of a possible 4′-phosphopantetheine prosthetic group for the catalytic process remains to be shown.

[0083] By BLAST analysis, the deduced amino acid sequence of Nocardia CAR showed high similarity to those of the putative enzymes in M. tuberculosis (fadD9, 61% identity), M. leprae (acyl-CoA synthetase, 57% identity), M. smegmatis (unnamed hypothetical protein on contig:3313, 61.8% identity), M. bovis strain BCG (unnamed hypothetical protein at bases 2,885,319–2,888.822, 60.3% identity), suggesting that possible functions of these proteins may relate to carboxylic acid reduction.

[0084] The present invention provides, inter alia, isolated nucleic acids of RNA, DNA, and analogs and/or chimeras thereof, comprising a CAR nucleic acid.

[0085] The present invention also includes polynucleotides optimized for expression in different organisms. For example, for expression of the polynucleotide in a maize plant, the sequence can be altered to account for specific codon preferences and to alter GC content as according to Murray et al, supra. Maize codon usage for 28 genes from maize plants is listed in Table 4 of Murray, et al., supra.

[0086] The CAR nucleic acids of the present invention comprise isolated CAR nucleic acid sequences which, are inclusive of:

[0087] (a) an isolated polynucleotide encoding a polypeptide of the present invention; (b) a polynucleotide having at least 80%, 90% or 95% identity to a polynucleotide of the present invention; (c) a polynucleotide comprising at least 25 nucleotides in length which hybridizes under high stringency conditions to a polynucleotide of the present invention; (d) a polynucleotide comprising a polynucleotide of the present invention; and (e) a polynucleotide which is complementary to the polynucleotide of (a) to (d).

[0088] The following description sets forth the general procedures involved in practicing the present invention. To the extent that specific materials are mentioned, it is merely for purposes of illustration and is not intended to limit the invention. Unless otherwise specified, general cloning procedures, such as those set forth in Sambrook et al., Molecular Cloning, Cold Spring Harbor Laboratory (1989) (hereinafter “Sambrook et al.”) or Ausubel et al. (eds) Current Protocols in Molecular Biology, John Wiley & Sons (1999) (hereinafter “Ausubel et al.” are used.

[0089] A. Preparation of CAR, Antibodies Specific for CAR and Nucleic Acid Molecules Encoding CAR

[0090] 1. Proteins and Antibodies

[0091] CAR may be prepared in a variety of ways, according to a variety of methods that have been developed for purifying CAR from bacteria which are detailed in the materials incorporated herein by reference. Alternatively, the availability of amino acid sequence information, such as (SEQ ID NO: 2), enables the isolation of nucleic acid molecules encoding CAR. This may be accomplished using anti-CAR antibodies to screen a cDNA expression library from a selected species, according to methods well known in the art. Alternatively, a series of degenerate oligonucleotide probes encoding parts or all of (SEQ ID NO: 1) FIG. 2 may be used to screen cDNA or genomic libraries, as described in greater detail below.

[0092] Once obtained, a cDNA or gene may be cloned into an appropriate in vitro transcription vector, such a pSP64 or pSP65 for in vitro transcription, followed by cell-free translation in a suitable cell-free translation system, such as wheat germ or rabbit reticulocytes. In vitro transcription and translation systems are commercially available, e.g., from Promega Biotech, Madison, Wis. or BRL, Rockville, Md. The pCITE in vitro translation system (Novagen) also may be utilized.

[0093] According to a preferred embodiment, larger quantities of the proteins may be produced by expression in a suitable procaryotic or eucaryotic system. This is particularly beneficial for CAR as Nocardia sp. are difficult to propagate and maintain in culture. For example, part or all of a CAR-encoding DNA molecule may be inserted into a vector adapted for expression in a bacterial cell (such as E. coli) or a yeast cell (such as Saccharomyces cerevisiae), or a mammalian cell. Such vectors comprise the regulatory elements necessary for expression of the DNA in the host cell, positioned in such a manner as to permit expression of the DNA in the host cell. Such regulatory elements required for expression include operably linked promoter sequences, transcription initiation sequences and, optionally, enhancer sequences.

[0094] CAR produced by gene expression in a recombinant procaryotic or eukaryotic system may be purified according to methods known in the art and incorporated herein. In a preferred embodiment, a commercially available expression/secretion system can be used, whereby the recombinant protein is expressed and thereafter secreted from the host cell, to be easily purified from the surrounding medium. If expression/secretion vectors are not used, an alternative approach involves purifying the recombinant protein by affinity separation, such as by immunological interaction with antibodies that bind specifically to the recombinant protein or with expression/secretion systems (e.g. a C-terminal tag on a secreted protein). Such methods are commonly used by skilled practitioners.

[0095] The present invention also provides antibodies capable of binding to CAR from one or more selected species. Polyclonal or monoclonal antibodies directed toward part or all of a selected CAR may be prepared according to standard methods. Monoclonal antibodies may be prepared according to general methods of Kohler and Milstein, following standard protocols. In a preferred embodiment, antibodies are prepared, which react immunospecifically with selected epitopes of CAR distinguishing it from other enzymes.

[0096] 2. Nucleic Acid Molecules

[0097] Once sequence information is obtained, nucleic acid molecules encoding CAR may be prepared by two general methods: (1) they may be synthesized from appropriate nucleotide triphosphates, or (2) they may be isolated from biological sources. Both methods utilize protocols well known in the art.

[0098] The availability of nucleotide sequence information enables preparation of an isolated nucleic acid molecule of the invention by oligonucleotide synthesis. Synthetic oligonucleotides may be prepared by the phosphoramadite method employed in the Applied Biosystems 38A DNA Synthesizer or similar devices. The resultant construct may be purified according to methods known in the art, such as high performance liquid chromatography (HPLC). Long, double-stranded polynucleotides, such as a DNA molecule of the present invention, must be synthesized in stages, due to the size limitations inherent in current oligonucleotide synthetic methods. Thus, for example, a long double-stranded molecule may be synthesized as several smaller segments of appropriate complementarity. Complementary segments thus produced may be annealed such that each segment possesses appropriate cohesive termini for attachment of an adjacent segment. Adjacent segments may be ligated by annealing cohesive termini in the presence of DNA ligase to construct an entire long double-stranded molecule. A synthetic DNA molecule so constructed may then be cloned and amplified in an appropriate vector.

[0099] Nucleic acid molecules encoding CAR also may be isolated from microorganisms of interest using methods well known in the art. Nucleic acid molecules from a selected species may be isolated by screening cDNA or genomic libraries with oligonucleotides designed to match a nucleic acid sequence specific to a CAR-encoding gene. If the gene from a species is desired, the genomic library is screened. Alternatively, if the protein coding sequence is of particular interest, the cDNA library is screened. In positions of degeneracy, where more than one nucleic acid residue could be used to encode the appropriate amino acid residue, all the appropriate nucleic acids residues may be incorporated to create a mixed oligonucleotide population, or a neutral base such as inosine may be used. The strategy of oligonucleotide design is well known in the art (see also Sambrook et al., Molecular Cloning, 1989, Cold Spring Harbor Press, Cold Spring Harbor N.Y.).

[0100] Alternatively, PCR (polymerase chain reaction) primers may be designed by the above method to encode a portion of CAR protein, and these primers used to amplify nucleic acids from isolated cDNA or genomic DNA. In a preferred embodiment, the oligonucleotides used to isolate CAR-encoding nucleic acids are designed to encode sequences unique to CAR, as opposed to other homologous proteins.

[0101] In accordance with the present invention, nucleic acids having the appropriate sequence homology with a CAR-encoding nucleic acid molecule may be identified by using hybridization and washing conditions of appropriate stringency. For example, hybridizations may be performed, according to the method of Sambrook et al. (1989, supra), using a hybridization solution comprising: 5×SSC, 5× Denhardt's reagent, 1.0% SDS, 100 μg/ml denatured, fragmented salmon sperm DNA, 0.05% sodium pyrophosphate and up to 50% formamide. Hybridization is carried out at 37–42° C. for at least six hours. Following hybridization, filters are washed as follows: (1) 5 minutes at room temperature in 2×SSC and 1% SDS; (2) 15 minutes at room temperature in 2×SSC and 0.1% SDS; (3) 30 minutes–1 hour at 37° C. in 1×SSC and 1% SDS; (4) 2 hours at 42–65° in 1×SSC and 1% SDS, changing the solution every 30 minutes.

[0102] Nucleic acids of the present invention may be maintained as DNA in any convenient cloning vector. In a preferred embodiment, clones are maintained in plasmid cloning/expression vector, such as pGEM-T (Promega Biotech, Madison, Wis.) or pBluescript (Stratagene, La Jolla, Calif.), either of which is propagated in a suitable E. coli host cell.

[0103] CAR-encoding nucleic acid molecules of the invention include cDNA, genomic DNA, RNA, and fragments thereof which may be single- or double-stranded. Thus, this invention provides oligonucleotides (sense or antisense strands of DNA or RNA) having sequences capable of hybridizing with at least one sequence of a nucleic acid molecule of the present invention. Such oligonucleotides are useful as probes for detecting CAR-encoding genes or mRNA in test samples, e.g. by PCR amplification.

[0104] B. Uses of CAR Protein

[0105] CAR can reduce many types of carboxylic acids. Previous work by the inventors(23, 32) showed that CAR from Nocardia has wide ranging substrate capabilities and that the enzyme is enantioselective versus racemic carboxylic acid substrates such as ibuprofen (7). Recombinant CAR shown in the examples herein indicate that CAR effectively reduced benzoic acid, vanillic acid and ferulic acid in preparative scale reactions. However, CAR is different than coniferyl aldehyde dehydrogenase, which uses NAD⁺ as the cofactor to catalyze the oxidation of aldehydes to acids, which does not use ATP, and which has no homology with CAR (1). ATP-dependent CAR catalyzes the energetically unfavorable reduction of acids to aldehdyes by using ATP as an energy source to drive the reaction forward. It can also catalyze the oxidation of aldehyde to acid without ATP, but the cofactor for CAR is NADP(H) instead of NAD(H). From the gene sequence, we know that CAR (3.5 kb) is much larger than aldehyde dehydrogenases (1.5 kb) (1). The enzyme also differs from fatty acid reductases in luminescent bacteria which contains three polypeptide components (31).

[0106] 1. Proteins and Antibodies

[0107] Purified CAR, or fragments thereof, may be used to produce polyclonal or monoclonal antibodies which may serve as sensitive detection reagents for the presence and accumulation of the proteins in cultured cells or tissues and in intact organisms. Recombinant techniques enable expression of fusion proteins containing part or all of a selected CAR. The full length protein or fragments of the protein may be used to advantage to generate an array of monoclonal or polyclonal antibodies specific for various epitopes of the protein, thereby providing even greater sensitivity for detection of the protein. In a preferred embodiment, fragments of CAR that distinguish CAR from serum SAAs are utilized for generating epitope-specific antibodies.

[0108] Polyclonal or monoclonal antibodies immunologically specific for CAR may be used in a variety of assays designed to detect and quantitative the proteins. Such assays include, but are not limited to, (1) immunoprecipitation followed by protein quantification; (2) immunoblot analysis (e.g., dot blot, Western blot) (3) radioimmune assays, (4) nephelometry, turbidometric or immunochromatographic (lateral flow) assays, and (5) enzyme-coupled assays, including ELISA and a variety of qualitative rapid tests (e.g., dip-stick and similar tests).

[0109] Polyclonal or monoclonal antibodies that immunospecifically interact with CAR can be utilized for identifying and purifying such proteins. For example, antibodies may be utilized for affinity separation of proteins with which they immunospecifically interact. Antibodies may also be used to immunoprecipitate proteins from a sample containing a mixture of proteins and other biological molecules.

[0110] 2. Nucleic Acids

[0111] CAR-encoding nucleic acids may be used for a variety of purposes in accordance with the present invention. The DNA, RNA, or fragments thereof may be used as probes to detect the presence of and/or expression of the genes. Methods in which CAR-encoding nucleic acids may be utilized as probes for such assays include, but are not limited to: (1) in situ hybridization; (2) Southern hybridization (3) northern hybridization; and (4) assorted amplification reactions such as polymerase chain reactions (PCR) and reverse transcriptase-PCR (RT-PCR).

[0112] The exemplified CAR-encoding nucleic acids of the invention (e.g., cow, sheep, horse) may also be utilized as probes to identify related genes from other species, including s. As is well known in the art and described above, hybridization stringencies may be adjusted to allow hybridization of nucleic acid probes with complementary sequences of varying degrees of homology.

[0113] In addition to the aforementioned uses of CAR-encoding nucleic acids, they are expected to be of utility in the creation of transgenic cells, tissues and organisms.

[0114] The present invention provides novel purified and isolated nucleic acid sequences encoding CAR protein. In presently preferred forms, the DNA sequences comprise cDNA sequences encoding the novel CAR, or its conservatively modified variants, which are expressed in Nocardia cells. In a more preferred embodiment the nucleic acid sequence comprises at least about 80% identity to (SEQ ID NO: 1) or 80% identity of the encoded amino acid sequence. Specifically, the sequence isolated is depicted in (SEQ ID NO: 1). Alternate DNA forms such as genomic DNA, and DNA prepared by partial or total chemical synthesis from nucleotides as well as DNA with deletions or mutations, is also within the contemplated scope of the invention.

[0115] Association of DNA sequences provided by the invention with homologous or heterologous species expression control DNA sequences such as promoters, operators, regulators, and the like, allows in vivo and in vitro transcription to make mRNA which, in turn, is susceptible to translation to provide the proteins of the invention, and related poly- and oligo-peptides in large quantities. In a presently preferred DNA expression system of the invention CAR encoding DNA is operatively linked to a regulatory promoter DNA sequence allowing for in vitro transcription and translation of the protein.

[0116] Incorporation of DNA sequences into prokaryotic and eucaryotic host cells by standard transformation and transfection processes, potentially involving suitable viral and circular DNA plasmid vectors, is also within the contemplation of the invention and is expected to provide useful proteins in quantities heretofore unavailable from natural sources.

[0117] Most of the techniques which are used to transform cells, construct vectors, extract messenger RNA, prepare cDNA libraries, and the like are widely practiced in the art, and most practitioners are familiar with the standard resource materials which describe specific conditions and procedures. However, for convenience, the following paragraphs may serve as a guideline.

Hosts and Control Sequences

[0118] Both prokaryotic and eucaryotic systems may be used to express CAR encoding sequences; prokaryotic hosts are, of course, the most convenient for cloning procedures. Prokaryotes most frequently are represented by various strains of E. coli; however, other microbial strains may also be used. Plasmid vectors which contain replication sites, selectable markers and control sequences derived from a species compatible with the host are used; for example, E. coli is typically transformed using derivatives of pBR322, a plasmid derived from an E. coli species by Bolivar, et al, Gene (1977) 2:95. pBR322 contains genes for ampicillin and tetracycline resistance, and thus provides multiple selectable markers which can be either retained or destroyed in constructing the desired vector. Commonly used prokaryotic control sequences which are defined herein to include promoters for transcription initiation, optionally with an operator, along with ribosome binding site sequences, include such commonly used promoters as the beta-lactamase (penicillinase) and lactose (lac) promoter systems (Chang, et al, Nature (1977) 198:1056) and the tryptophan (trp) promoter system (Goeddel, et al, Nucleic Acids Res (1980) 8:4057) and the lambda derived P_L promoter and N-gene ribosome binding site (Shimatake, et al, Nature (1981) 292:128).

[0119] In addition to bacteria, eucaryotic microbes, such as yeast, may also be used as hosts. Laboratory strains of Saccharomyces cerevisiae, Baker's yeast, are most used although a number of other strains or species are commonly available. Vectors employing, for example, the 2μ origin of replication of Broach, J. R., Meth Enz (1983) 101:307, or other yeast compatible origins of replication (see, for example, Stinchcomb, et al, Nature (1979) 282:39, Tschumper, G., et al, Gene (1980) 10:157 and Clarke, L, et al, Meth Enx (1983) 101:300) may be used. Control sequences for yeast vectors include promoters for the synthesis of glycolytic enzymes (Hess, et al, J Adv Enzyme Reg (1968) 7:149; Holland, et al, Biochemistry (1978) 17:4900). Additional promoters known in the art include the promoter for 3-phosphoglycerate kinase (Hitzeman, et al J Biol Chem (1980) 255:2073). Other promoters, which have the additional advantage of transcription controlled by growth conditions and/or genetic background are the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, the alpha factor system and enzymes responsible for maltose and galactose utilization. It is also believed terminator sequences are desirable at the 3′ end of the coding sequences. Such terminators are found in the 3′ untranslated region following the coding sequences in yeast-derived genes.

[0120] It is also, of course, possible to express genes encoding polypeptides in eucaryotic host cell cultures derived from multicellular organisms. See, for example, Axel, et al, U.S. Pat. No. 4,399,216. These systems have the additional advantage of the ability to splice out introns and thus can be used directly to express genomic fragments. Useful host cell lines include VERO and HeLa cells, and Chinese hamster ovary (CHO) cells. Expression vectors for such cells ordinarily include promoters and control sequences compatible with mammalian cells such as, for example, the commonly used early and late promoters from Simian Virus 40 (SV 40) (Fiers, et al, Nature (1978) 273:113), or other viral promoters such as those derived from polyoma, Adenovirus 2, bovine papilloma virus, or avian sarcoma viruses. The controllable promoter, hMT1I (Karin, M., et al, Nature (1982) 299:797–802) may also be used. General aspects of mammalian cell host system transformations have been described by Axel (supra). It now appears, also that “enhancer” regions are important in optimizing expression; these are, generally, sequences found upstream or downstream of the promoter region in non-coding DNA regions. Origins of replication may be obtained, if needed, from viral sources. However, integration into the chromosome is a common mechanism for DNA replication in eucaryotes.

Transformations

[0121] Depending on the host cell used, transformation is done using standard techniques appropriate to such cells. The calcium treatment employing calcium chloride, as described by Cohen, S. N., Proc Natl Acad Sci (USA) 1972) 69:2110, or the rbC12 method described in Maniatis, et al, Molecular Cloning: A Laboratory Manual (1982) Cold Spring Harbor Press, p. 254 and Hanahan, D., J Mol Biol (1983) 166:557–580 may be used for prokaryotes or other cells which contain substantial cell wall barriers. For mammalian cells without such cell walls, the calcium phosphate precipitation method of Graham and van der Eb, Virology (1978) 52:546, optionally as modified by Wigler, M., et al, Cell (1979) 16:777–785 may be used. Transformations into yeast may be carried out according to the method of Beggs, J. D. Nature (1978) 275:104–109 or of Hinnen, A., et al, Proc Natl Acad Sci (USA) (1978) 75:1929.

Vector Construction

[0122] Construction of suitable vectors containing the desired coding and control sequences employs standard ligation and restriction techniques which are well understood in the art. Isolated plasmids, DNA sequences, or synthesized oligonucleotides are cleaved, tailored, and relegated in the form desired.

[0123] The DNA sequences which form the vectors are available from a number of sources. Backbone vectors and control systems are generally found on available “host” vectors which are used for the bulk of the sequences in construction. Typical sequences have been set forth above. For the pertinent coding sequence, initial construction may be, and usually is, a matter of retrieving the appropriate sequences from cDNA or genomic DNA libraries. However, once the sequence is disclosed it is possible to synthesize the entire gene sequence in vitro starting from the individual nucleoside derivatives. The entire sequence for genes or cDNA's of sizable length, e.g., 500–1000 bp may be prepared by synthesizing individual overlapping complementary oligonucleotides and filling in single stranded nonoverlapping portions using DNA polymerase in the presence of the deoxyribonucleotide triphosphates. This approach has been used successfully in the construction of several genes of known sequence. See, for example, Edge, M. D., Nature (1981) 292:756; Nambair, K. P., et al, Science (1984) 223:1299; Jay, Ernest, J Biol Chem (1984) 259:6311.

[0124] Synthetic oligonucleotides are prepared by either the phosphotriester method as described by Edge, et al, Nature (supra) and Duckworth, et al, Nucleic Acids Res (1981) 9:1691 or the phosphoramidite method as described by Beaucage, S. L., and Caruthers, M. H., Tet Letts (1981) 22:1859 and Matteucci, M. D., and Caruthers, M. H., J Am Chem Soc (1981) 103:3185 and can be prepared using commercially available automated oligonucleotide synthesizers. Kinasing of single strands prior to annealing or for labeling is achieved using an excess, e.g., approximately 10 units of polynucleotide kinase to 1 nmole substrate in the presence of 50 mM Tris, pH 7.6, 10 mM MgCl₂, 5 mM dithiothreitol, 1–2 mM ATP, 1.75y pmoles γ32P-ATP (2.9 mCi/mmole), 0.1 mM spermidine, 0.1 mM EDTA.

[0125] Once the components of the desired vectors are thus available, they can be excised and ligated using standard restriction and ligation procedures.

[0126] Site specific DNA cleavage is performed by treating with the suitable restriction enzyme (or enzymes) under conditions which are generally understood in the art, and the particulars of which are specified by the manufacturer of these commercially available restriction enzymes. See, e.g., New England Biolabs, Product Catalog. In general, about 1 μg of plasmid or DNA sequence is cleaved by one unit of enzyme in about 20 μl of buffer solution; in the examples herein, typically, an excess of restriction enzyme is used to insure complete digestion of the DNA substrate. Incubation times of about one hour to two hours at about 37° C. are workable, although variations can be tolerated. After each incubation, protein is removed by extraction with phenol/chloroform, and may be followed by ether extraction, and the nucleic acid recovered from aqueous fractions by precipitation with ethanol. If desired, size separation of the cleaved fragments may be performed by polyacrylamide gel or agarose gel electrophoresis using standard techniques. A general description of size separations is found in Methods in Enzymology (1980) 65:499–560.

[0127] Restriction cleaved fragments may be blunt ended by treating with the large fragment of E. coli DNA polymerase I (Klenow) in the presence of the four deoxynucleotide triphosphates (dNTPs) using incubation times of about 15 to 25 min at 20° to 25° C. in 50 mM Tris pH 7.6, 50 mM NaCl, 6 mM MgCl2, 6 mM DTT and 0.1–1.0 mM dNTPs. The Klenow fragment fills in at 5′ single-stranded overhangs but chews back protruding 3′ single strands, even though the four dNTPs are present. If desired, selective repair can be performed by supplying only one of the, or selected, dNTPs within the limitations dictated by the nature of the overhang. After treatment with Klenow, the mixture is extracted with phenol/chloroform and ethanol precipitated. Treatment under appropriate conditions with S1 nuclease or BAL-31 results in hydrolysis of any single-stranded portion.

[0128] Ligations are performed in 15–50 μl volumes under the following standard conditions and temperatures: for example, 20 mM Tris-Cl pH 7.5, 10 mM MgCl₂, 10 mM DTT, 33 μg/ml BSA, 10 mM–50 mM NaCl, and either 40 μM ATP, 0.01–0.02 (Weiss) units T4 DNA ligase at 0 C (for “sticky end” ligation) or 1 mM ATP, 0.3–0.6 (Weiss) units T4 DNA ligase at 14° C. (for “blunt end” ligation). Intermolecular “sticky end” ligations are usually performed at 33–100 μg/ml total DNA concentrations (5–100 nM total end concentration). Intermolecular blunt end ligations are performed at 1 μM total ends concentration.

[0129] In vector construction employing “vector fragments”, the vector fragment is commonly treated with bacterial alkaline phosphatase (BAP) or calf intestinal alkaline phosphatase (CIP) in order to remove the 5′ phosphate and prevent self-ligation of the vector. Digestions are conducted at pH 8 in approximately 10 mM Tris-HCl, 1 mM EDTA using about 1 unit of BAP or CIP per μg of vector at 60° for about one hour. In order to recover the nucleic acid fragments, the preparation is extracted with phenol/chloroform and ethanol precipitated. Alternatively, re-ligation can be prevented in vectors which have been double digested by additional restriction enzyme digestion and/or separation of the unwanted fragments.

[0130] For portions of vectors derived from cDNA or genomic DNA which require sequence modifications, site specific primer directed mutagenesis may be used (Zoller, M. J., and Smith, M. Nucleic Acids Res (1982) 10:6487–6500 and Adelman, J. P., et al, DNA (1983) 2:183–193). This is conducted using a primer synthetic oligonucleotide complementary to a single stranded phage DNA to be mutagenized except for limited mismatching, representing the desired mutation. Briefly, the synthetic oligonucleotide is used as a primer to direct synthesis of a strand complementary to the phage, and the resulting partially or fully double-stranded DNA is transformed into a phage-supporting host bacterium. Cultures of the transformed bacteria are plated in top agar, permitting plaque formation from single cells which harbor the phage.

[0131] Theoretically, 50% of the new plaques will contain the phage having, as a single strand, the mutated form; 50% will have the original sequence. The resulting plaques are washed after hybridization with kinased synthetic primer at a wash temperature which permits binding of an exact match, but at which the mismatches with the original strand are sufficient to prevent binding. Plaques which hybridize with the probe are then picked, cultured, and the DNA recovered.

Verification of Construction

[0132] Correct ligations for plasmid construction can be confirmed by first transforming E. coli strain MC1061 obtained from Dr. M. Casadaban (Casadaban, M., et al, J Mol Biol (1980) 138:179–207) or other suitable host with the ligation mixture. Successful transformants are selected by ampicillin, tetracycline or other antibiotic resistance by using other markers depending on the mode of plasmid construction, as is understood in the art. Plasmids from the transformants are then prepared according to the method of Clewell, D. B., et al, Proc Natl Acad Sci (USA) (1969) 62:1159, optionally following chloramphenicol amplification (Clewell, D. B., J Bacteriol (1972) 110:667). Several mini DNA preps are commonly used, e.g., Holmes, D. S., et al, Anal Biochem Acids Res (1979) 7:1513–1523. The isolated DNA is analyzed by restriction and/or sequenced by the dideoxy nucleotide method of Sanger, F., et al, Proc Natl Acad Sci (USA) (1977) 74:5463 as further described by Messing, et al, Nucleic Acids Res (1981) 9:309, o4 by the method of Maxam, et al, Methods in Enzymology (1980) 65:499.

Hosts Exemplified

[0133] Host strains used in cloning and prokaryotic expression herein are as follows:

[0134] For cloning and sequencing, and for expression of construction under control of most bacterial promoters, E. coli strains such as MC1061, DH1, RR1, C600hfl, K803, HB101, JA221, and JM101 can be used.

[0135] It can therefore be seen that the above invention accomplishes at least all of its stated objectives. All references cited herein are hereby expressly incorporated herein in their entirety by reference.

[0136] Materials and enzymes. Restriction enzymes, T4 DNA ligase and shrimp alkaline phosphatase were purchased from New England Biolabs (Beverly, Mass.); PGEM-T easy vector kit from Promega (Madison, Wis.); Escherichia coli BL21(DE3) and BL21-CodonPlus® (DE3)-RP competent cells from Stratagene (La Jolla, Calif.); Polyclonal rabbit anti-HAT antibody, pHAT10 vector and Talon® resin from Clontech (Palo Alto, Calif.); goat anti-rabbit IgG-conjugated alkaline phosphatase and Immun-Star Chemiluminescent Substrate Kit from Bio-Rad (Hercules, Calif.); Qiaprep Spin Miniprep kit and Qiaquick kit from Qiagen Inc. (Chatsworth, Calif.). All other chemicals were from Sigma (St Louis, Mo.) unless specified.

[0137] Bacterial strains, plasmids, media and growth conditions. The bacteria and plasmids used in this study are given in Table 1. Nocardia sp. NRRL 5646 (9), maintained in the University of Iowa College of Pharmacy culture collection on slants of Sabouraud-Dextrose agar or sporulation agar (ATCC no. 5 medium), was grown in Luria-Bertani (LB) medium containing 0.05% Tween 80 (vol/vol, liquid medium only). With E. coli (JM109, BL21 (DE3), or BL21-CodonPlus® (DE3)-RP) as the recombinant host for pHAT based vectors, cells were grown at 37° C. on solid or in liquid LB medium. Ampicillin (100 μg/ml) was incorporated into LB medium to select for recombinants. In addition, isopropyl-β-D-thiogalactopyranoside (IPTG, 1 mM) and/or 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-Gal, 80 μg/ml) were included for recombinant selection and identification.

[0138] Molecular biology techniques. All DNA manipulations used for this study were performed by standard protocols (33). Nocardia sp. NRRL 5646 chromosomal DNA (gDNA) was purified as described by Pelicic et al. (29) with modifications. Briefly, ampicillin (0.2 mg/ml) and glycine (1.5%, vol/vol) were added into 100 ml stationary phase cultures, two hrs before harvest by centrifugation at 4,000×g for 15 min and 4° C. Cells (1.5 g, wet weight) were resuspended in 5 ml of lysis solution I (25% sucrose in 50 mM Tris-HCl, pH 8.0 containing 50 mM EDTA and 12 mg/ml lysozyme), and incubated at 37° C. with shaking at 50 rpm for 1.5 hrs. Lysis solution II (3 ml of 100 mM Tris-HCl, pH 8.0 containing 1% SDS and 700 □g/ml proteinase K) was then added, and the sample was incubated at 55° C. for 4 hrs. Then 45 □l Rnase (500 □g/ml) was added into the lysate, and incubated with shaking at 50 rpm and 37° C. for 1 h. The lysate was then extracted with phenol-chloroform-isoamyl alcohol (25:24:1, vol/vol/vol, Invitrogen Life Technologies), and gDNA was concentrated by ethanol precipitation, yielding a total of 90 μg gDNA.

[0139] Recombinant plasmids from E. coli were purified by using a Qiaprep spin miniprep kit, and Qiaquick kits were used for PCR cleanup and gel extractions with vector constructs as instructed by the manufacturer. All PCR cloning amplification was done with either Platinum Taq DNA polymerase or Platinum Pfx DNA polymerase (Invitrogen). Restriction enzymes and DNA-modification enzymes were used according to the manufacturer's protocols. Sequencing was conducted using an Applied Biosystem 373A DNA sequencer.

[0140] PCR and cloning of PCR product. In order to obtain a portion of Nocardia car, oligonucleotides were constructed corresponding to N-terminal and internal amino acid sequences, which were determined with purified CARBOXYLIC ACID REDUCTASE (23). Forward primers (Noc-1 and Noc-2) were based on the N-terminal amino acid sequence AVDSPDERLQRRIAQL (SEQ ID NO:6), and reverse primers (Noc-3 and Noc-4) were based on the complementary strand sequence encoding the internal amino acid sequence KLSQGEFVTVAHLEAV (SEQ ID NO:7) (Table 2). Degeneracy of all four primers was minimized by taking advantage of the reported Nocardia codon preferences (10). A typical 50 μl reaction in 1×PCR buffer contained 500 ng Nocardia DNA, 5 mM⁺⁺, 500 μM of each dNTP, 0.5 μM of each primer, 1% DM50 (vol/vol) and 3.5 units of Taq DNA polymerase. The reaction mixtures were subjected to the following cycles: one cycle at 94° C. for 4 mm, thirty cycles at 94°for 45 s, 56°for 45 s, and 72° C. for 2 mm, and finally one cycle at 72° C. for 10 mm. PCR products were separated on 1% agarose gel. The desired band was excised and extracted with a Qiagen gel extraction kit. The resulting PCR product was ligated into pGEM-T by T4 ligase. The ligation mixture was mixed with E. coli JM109 cells and chilled on ice for 30 nun. Cells were transformed by heat shock, then placed immediately on ice. Transformed E. coli JM 109 cells were mixed with 800 μl SOC medium and incubated at 37° C. for 1.5 hrs on a rotary. shaker at 170 rpm. Plasmid transformants were spreadplated onto LB/X-Gal agar supplemented with 100 μg/ml ampicillin. Ampicillin resistant colonies were picked and used to inoculate 5 ml LB broth supplemented with 100 μg/ml ampicillin and incubated overnight at 37° C. on a rotary shaker operating at 170 rpm. Cultures were harvested by centrifugation and subjected to a plasmid miniprep procedure (Qiagen). The resulting recombinant plasmid was sequenced in both directions with sequencing primers (Table 2).

[0141] Inverse PCR. Inverse PCR was used to obtain the entire Nocardia asteriodes car gene sequence. To prepare the template for Inverse PCR analysis, 1 μg of Nocardia asteriodes gDNA was completely digested with 20 U SalI or Acc65I at 37° C. Digested gDNA was diluted five fold and then circularized with T4 DNA ligase. PCR primers CA-5 (Forward) and CA-7 (Reverse) were designed based on part of the Nocardia asteriodes car sequence obtained above. Inverse PCR was performed using Taq DNA polymerase for a total of 30 cycles with the following cycling pattern: melting at 94° C. for 45 s, annealing at 57° C. for 45 s, and polymerization at 72° C. for 2 min. The amplified PCR product was cloned in PGEM-T, and transformed into E. coli JM109 cells by heat shock treatment as described above. Plasmid preparations from independent clones were sequenced in both directions. The resulting sequence combined with the above part of Nocardia asteriodes car gave a 4.6 Kb sequence which contained the entire Nocardia asteriodes car gene (with Acc65I digested and then religated gDNA as the template). A sequence of 2.5 Kb upstream car was obtained with SalI digested and religated gDNA as the template for PCR.

[0142] Construction of expression vectors. To express recombinant Nocardia asteriodes car in E. coli, a DNA fragment containing Nocardia asteriodes car was generated by PCR using the primers car-F and car-R with Nocardia asteriodes gDNA as the template. For cloning purposes, those two primers incorporated a BamHI site at the 5′ end and an KpnI site at the 3′ end of the Nocardia gene insert. PCR was performed using Platinum Pfx DNA polymerase for a total of 30 cycles with the following cycling pattern: melting at 94° C. for 18 s, annealing at 59° C. for 30 s, and polymerization at 72° C. for 4 min. PCR products were sequentially digested with BamHI and KpnI was separated on a 1% agarose gel and purified using a Qiagen gel extraction kit, and then subcloned into the corresponding sites of pHAT10 to result in pHAT-305. One round of sequencing confirmed that Nocardia car had been correctly cloned into the pHAT vector by using sequence primers.

[0143] Expression of Nocardia car in E. coli. A 100 ml culture of E coli cells (BL21(DE3) or BL21-CodonPlus® (DE3)-RP) harboring pHAT-305 were grown overnight in LB medium containing 100 □g/ml ampicillin at 37° C. Overnight broth cultures were diluted 20 fold in fresh LB medium containing 100 μg/mL ampicillin, and then incubated at 170 rpm in a rotary shaker at 37° C. to an optical density at 600 nm of 0.6, followed by addition of 1 mM IPTG and further incubation for 4.5 h. The cells were harvested by centrifugation (10 min, 5,000×g), and then stored at −65° C. before use.

[0144] Enzyme assay. The standard reaction mixture contained 1 mM ATP, 0.15 mM NADPH, 5 mM sodium benzoate, 10 mM MgCl₂ and enzyme in 0.05 M Tris buffer (pH 7.5) containing 1 mM EDTA, 1 mM DTT and 10% glycerol (vol/vol), in a final volume of 1.4 ml. The reference cuvette contained all components except benzoate. Reactions were initiated by adding enzyme, and were monitored by recording the absorption decrease at 340 nm at 25° C. with a Shimadzu UV-2010PC scanning spectrophotometer. One unit of the enzyme was defined as the amount of enzyme that catalyzed the reduction of 1 □mol of benzoate to benzaldehyde.min⁻¹ under standard assay condition. Protein concentrations were measured by the Bradford protein microassay (4) with bovine serum albumin as the standard.

[0145] Purification of overexpressed HAT-CAR fusion protein. E. coli BL21-CodonPlus® (DE3)-RP cells (4.3 g wet weight) transformed with pHAT-305 were suspended in 26 ml of 0.05 M K₂HPO₄ (pH 7.5) buffer containing 0.3 M NaCl, 10% (vol/vol) glycerol, 0.2 mM PMSF and 3 mM β-mercaptoethanol. The cells were disrupted by passing through a French Press cell at 12,000 psi twice. The cell debris was removed by centrifugation for 60 min at 25,000×g and 4° C. The resulting supernatant (27 ml) was referred to as cell-free extract (CFE) and used for HAT-CAR purification. 24 ml of CFE was loaded on a 6 ml bed volume column of Talon resin (A cobalt complexed resin made by Clontech that specifically binds the HAT tag.) equilibrated with 0.05 M K₂HPO₄ buffer pH 7.5 containing 0.3 M NaCl, 10% (vol/vol) glycerol, at a flow rate of 0.4 ml/min. After the column was washed with 35 ml 0.05 M K₂HPO₄ buffer pH 7.5 containing 0.3 M NaCl, 10% (vol/vol) glycerol, the HAT-CAR was eluted sequentially by 16 ml of 5 mM, 7.5 mM, 10 mM, and 20 mM of Imidazole in 0.05 M K₂HPO₄ buffer pH 7.5 containing 0.3 M NaCl, 10% (vol/vol) glycerol. Active fractions were pooled and then concentrated by ultrafiltration in an Amicon concentrator (PM-10 membrane) and then diluted with 100 ml of 50 mM Tris buffer (pH 7.5) containing 1 mM EDTA, 1 mM DTT, and 10% glycerol. The resulting enzyme preparation was loaded on a DEAE Sepharose column (1.5 by 20 cm with a bed volume of 24 ml) equilibrated with 50 mM Tris buffer (pH 7.5) containing 1 mM EDTA, 1 mM DTT, and 10% glycerol. The column was washed with 30 ml of starting buffer and eluted with a 0 to 0.5 M NaCl linear gradient (total 100 ml). The active fractions (29 to 34) were combined for subsequent analysis (Table 3).

[0146] SDS-PAGE and Western blot analysis. Proteins were separated by SDS-PAGE as described by Laemmli (22). For Western blot analysis, protein samples were subjected to SDS-PAGE and then transferred to a polyvinylidene difluoride (PVDF) membrane. To identify proteins containing the HAT tag, the PVDF membrane was first incubated with 2% fat-free milk in TBS, then with a polyclonal anti-HAT antibody (diluted 1:20,000) that recognizes epitopes throughout the HAT tag, and finally with a polyclonal goat anit-rabbit IgG conjugated to alkaline phosphatase (diluted 1:20,000), which was used with the Bio-Rad Immuno-Star Chemoluminescent Substrate. Proteins containing the HAT tag were identified with Kodak BioMax MR photographic film after 2 min exposures. E. coli JM 109 carrying an expression vector coding for HAT-tagged dihydrofolate reductase (DHFR, Clontech) was used as a positive control for each Western blot analysis, and E. coli BL21-CodonPlus® (DE3)-RP carrying the pHAT10 vector was used as a negative control.

[0147] In vitro and in vivo transformations of benzoate, vanillic acid, and ferulic acid. In vitro enzyme reactions were carried out in a reaction mixture of 50 ml of 50 mM Tris-HCl buffer (pH 7.5) containing 0.1 mmol of substrate, 12.5 mg of NADPH, 55 mg ATP, 101 mg MgCl₂, 33.6 mg glucose-6-phosphate, and 3 U of glucose-6-phosphate dehydrogenase, and 1 mg purified HAT-CAR (0.1 U). Reaction mixtures were incubated at 30° C. with gentle shaking at 50 rpm for 24 h.

[0148] In vivo whole cell reactions were typically conducted with 100 ml cultures of E. coli BL21-CodonPlus® (DE3)-RP carrying pHAT-305. Cultures were induced by 1 mM IPTG for 4 hrs before receiving 1 mg/ml of benzoic acid, vanillic acid, or ferulic acid.

[0149] Samples of approximately 2 mL were removed at various time intervals, sample pH was adjusted to pH 2.0 with 6N HCl, and samples were extracted with 1 ml ethyl acetate, and centrifuged for 2 min at 1,000×g. Organic phases were removed and used to spot silica gel GF₂₅₄ TLC plates for analysis, and comparison with authentic standards of benzaldehyde, vanillin and coniferaldehyde. For metabolite isolation, reactions were stopped by adjustment of mixtures to pH 2.0 with 6N HCl, and extracted three times with half-volumes of ethyl acetate. After removal of solvent by rotary evaporation, reduction products were purified by preparative TLC for analysis and comparison with authentic standards.

[0150] Four degenerate primers (two forward, CA-1 and CA-2; and two reverse, CA-3 and CA-4) incorporating Nocardia codon preferences (10) were initially designed to identify part of Nocardia car, based on the known N-terminal amino acid sequence and internal amino acid sequences (Li and Rosazza, 1997). PCR products were cloned into a pGEM-T vector and sequenced to give a 1.6 Kb sequence.

[0151] Gene sequence specific primers (CA-5 and CA-6) based on this identified fragment were synthesized for inverse PCR to clone the entire Nocardia car gene. The sequence derived from two inverse PCR experiments and the above-obtained sequence gave a total of 6.9 Kb of data, which included the entire Nocardia car gene and its flanking regions. The DNA sequence and the deduced amino acid sequence of Nocardia car will be deposited in the GenBank upon filing of a patent. Nocardia car consisted of 3525 bp, corresponding to 1174 amino acid residues with a calculated molecular mass of 128.3 kDa and an isoelectric point (pI) of 4.74. The N-terminal amino acid sequence of purified Nocardia CAR exactly matched the deduced amino acid sequence of the N-terminus, with Ala as the first amino acid. Met, encoded by the start codon ATG in Nocardia car, is apparently removed by posttranslational modification in the mature form of the protein produced in wild type Nocardia cells.

[0152] Comparative sequence analysis. When the Nocardia car sequence was compared by BLAST analysis with DNA sequences in the NCBI database, the BestFit analysis of two nucleotide sequences showed that the Nocardia CAR was 60% and 57% identical to the putative polyketide synthetase fadD9 of M. tuberculosis and putative acyl-CoA synthetase of M. leprae respectively. Putative proteins in M. smegmatis and M. bovis strain BCG were 61.8% and 60.3% identical to Nocardia CAR. The Clustal W program (35) was used to align CAR with these closely-related putative proteins from different species (FIG. 1).

[0153] Heterologous expression of Nocardia car. For expression of Nocardia CAR, the Nocardia car gene was successfully cloned in frame into pHAT10 to form the expression vector pHAT-305. Constructed vectors were found by complete sequencing to have a car that was 100% identical to the original Nocardia car sequence, proving that no errors were introduced by Pfx DNA polymerase cloning. Lysate from E. coli BL21(DE3) cells carrying pHAT-305 had moderate carboxylic acid reductase activity (0.003 U/mg of protein) versus that of Nocardia wild type cells (0.03 U/mg of protein) (23). However, the expression of pHAT-305 was much improved when it was transformed into E. coli CodonPlus® (DE3)-RP cells, where a crude extract specific activity of 0.009 U/mg of protein was observed. When these cultures were examined by SDS-PAGE, the Coomassie blue-stained band with an apparent molecular size of 132.4 kDa were confirmed to be the HAT-CAR by activity assay and Western blot analysis (FIG. 2). Also, the DHFR-positive control (lysate of E. coli carrying the DHFR gene cloned into the same pHAT 10 vector) and negative control (lysate of E. coli BL21-CodonPlus® (DE3)-RP cells carrying the pHAT10 vector) showed the absence of a 132.4 kDa band by SDS-PAGE and Western blot analyses.

[0154] The HAT-CAR protein from E. coli was purified to homogeneity on SDS-PAGE by Talon® resin affinity chromatography and DEAE sepharose column with a overall recovery of 85%. Western blot analysis showed that there were some HAT-tag positive smear bands with lower molecular weight than that of HAT-CAR. The purified HAT-CAR showed a specific CAR activity of 0.11 μmol·min⁻¹·mg⁻¹ protein, which was less than that of CAR purified from Nocardia cells (5.89 U/mg of protein) (23). Kinetic constants were determined by fitting experimental data with Cleland's kinetics program (9). Km values for benzoate, ATP and NADPH were determined to be 852±82 mM, 69±6.6 μM, and 57±3.6 μM, respectively. These are similar to the Km values of the natural protein. Vmax was determined to be 0.135±0.004 μmol·min⁻²¹·mg⁻¹ protein, which is lower than that of the natural protein at 0.902±0.04 μmol·min⁻¹.mg⁻¹ protein (23).

[0155] In vitro transformations showed that pure HAT-CAR could reduce various carboxylic acids to their corresponding aldehydes in reactions that were not optimized. Benzoic acid was converted to benzaldehyde (96% yield), vanillic acid to vanillin (49% yield), and ferulic acid to coniferyl aldehyde (22% yield). In vivo studies on the transformation of the same substrates showed that benzoate was quickly converted to benzyl alcohol, while vanillin and coniferyl aldehyde converted to their corresponding alcohols.

[0156] Recombinant CAR bound weakly to Talon® affinity matrix, being eluted from columns by 10 mM imidazole, rather than the 100 mM imidazole usually required for HAT-tagged proteins elution. HAT-CAR can be easily purified to near homogeneity (SDS-PAGE) with Talon® matrix chromatography. Minor impurities in enzyme preparations after the affinity step were not completely removed by DEAE sepharose column chromatography. Although trace impurities were not detected by SDS-PAGE, they were detected by Western blot analysis (FIG. 2).

[0157] These trace impurities were HAT-tag containing proteins that are likely hydrolyzed fragments of HAT-CAR cleaved by metal proteases. Metal protease inhibitors were not used to prevent protease cleavage during cell disruption because they would be incompatible with Talon® matrix chromatography.

[0158] CAR was only moderately expressed in E. coli BL21 (DE3) cells carrying pHAT-305. It was thought that low expression was mainly due to the codon bias that can cause early termination and misincorporation of amino acids since the G+C content of the sequence is 66%. In searching for new hosts to overcome the codon bias, the expression of pHAT-305 was much improved when it was carried out in E. coli CodonPlus® (DE3)-RP cells. The protein bands were clearly seen on the SDS-PAGE (FIG. 2) with the CFE enzyme preparation. Although CAR of the correct molecular mass accumulates in cells, the specific activity of the crude extract was only improved about 3 fold. The specific activity of CAR in E. coli BL21 (DE3) may be higher than in E. coli CodonPlus® (DE3)-RP cells. We have shown that approximately 50 mg pure HAT-CAR can be obtained from a 1 liter culture of E. coli CodonPlus® (DE3)-RP cells.

[0159] Comparing relative protein expression and differing specific activities of CARBOXYLIC ACID REDUCTASE in these two different hosts, we speculate that two forms of the enzyme may exist in E. coli cells: one active, while the other is an inactive variant. It is possible that the conversion of an inactive form of the enzyme (pre-CARBOXYLIC ACID REDUCTASE) to the catalytically active form of the enzyme (CARBOXYLIC ACID REDUCTASE) may occur by posttranslational modification. One such modification that has precedence in the type of reaction catalyzed by carboxylic acid reductase would be phosphopantetheinylation (12). In this type of model, inactive pre-carboxylic acid reductase would be converted to active carboxylic acid reductase by attachment of phosphopantetheine prosthetic group possibly attached to Ser688 to function as a Swinging arm. In the active enzyme, carboxylic acid reductase, the SH of the phosphopantetheine prosthetic group would react with acyl-AMP to form an acyl-S-pantotheine-carboxylic acid reductase intermediate. The C-terminal reductase domain finishes the catalytic cycle by delivering hydride from NADPH to the acyl-S-pantotheine carboxylic acid reductase intermediate freeing an aldehyde product. α-Aminoadipate reductase is well studied, and motifs responsible for adenylation of α-aminoadipate, reduction, NADPH binding and attachment of a phosphopantetheinyl group used in the reaction have been identified (5, 18). While traditional blast analysis does not reveal the expected common motifs in the N-terminal portion of car, they do appear in the C-terminal portion. A P-pantotheine attachment site, domain J, is clearly present in carboxylic acid reductase (LGGxSxxA) (SEQ ID NO:8), as are the reduction domain (GYxxSKW) (SEQ ID NO:9) and the NADP binding domain (GxxGxLG) (SEQ ID NO: 10). These motifs are fully conserved in the Mycobactrium carboxylic acid reductase homologs (FIG. 1). Whether benzoate induction (23) increases the expression of carboxylic acid reductase, or catalyzes the conversion of inactive form enzyme to active form by a posttranslational modification remains to be established.

[0160] Biotransformation reactions using IPTG-induced whole growing cells of E. coli CodonPlus® (DE3)-RP cells carrying pHAT-305 were simple to conduct, and they smoothly converted carboxylic acids to aldehydes—and subsequently to alcohols. With whole cells, expensive cofactors are not needed (25), and the relatively slow reduction of aldehyde products formed by CAR to alcohols by an endogenous E. coli alcohol dehydrogenase similar to that in Nocardia (25) may be obviated by judicious biochemical engineering approaches with the recombinant organism.

[0161] The unique car sequence car for the carboxylic acid reductase enzyme, CAR, may be used to produce recombinant cultures such as E. coli for direct use in whole cell biocatalytic conversions of an enormous number of synthetic or natural carboxylic acids (23, 32) including aromatic, aliphatic, alicyclic and others. Alternatively, this gene sequence, or homologs of this gene sequence may be incorporated into the genomes of multiply recombinant strains through pathway engineering to be used as a part of a biosynthetic or biodegradative pathway leading to useful compounds.

[0162]

TABLE 1
Strains and plasmids used in this study
Strains or		Reference
plasmids	Relevant properties	or source
Nocardia sp.	Wild type	8
NRRL 5646
E. coli JM 109	RecA, recombinant vector host strain	Promega
E. coil BL21	Inducible T7 RNA polymerase, Ampr	Stratagene
(DE3)
E. coil BL21-	having argU and proL tRNA genes	Stratagene
CodonPlus ®
(DE3)-RP
pGEM-T easy	T/A PCR cloning vector, Ampr	Promega
pHAT10	Cloning vector for addition of HAT-tag	Clontech
	to the N-terminus, Ampr
pHAT-305	pHAT-10 with car insert	This study
pHAT-DHFR	Positive control expression vector with	Clontech
	dihydrofolate reductase gene tagged with
	HAT at the N-terminus

[0163]

TABLE 2
Oligonucleotides used in this study
GTSGATTCACCSGATGAG	This study 11
CCSGATGARCGSCTACAG	This Study 12
TGSGCSACSGTSACGAAC	This Study 13
SACGAAYTCSCCCTGSGAC	This Study 14
GGTCGGGATCAATCTCAACTACATG	This Study 15
CTTCAGCTGCTCTGACGGATATCAG	This Study 16
CCTGCTCATCTTCTGCAAACAACTG	This Study 17
CGCGGATCCGCAGTGGATTCACCGG	This Study 18
ATGAGC
CGGGGTACCCCTGATATCCGTCAGA	This Study 19
GCAGCTG
Sequencing
primers
TAATACGACTCACTATAGGG	Sigma-Genosys 20
CATACGATTTAGGTGACACTATAG	Sigma-Genosys 21
CAGGAAACAGCTATGACC	Sigma-Genosys 22
CTCGACCTGGCCGATATCCAC	This Study 23
GAGGACGGCTTCTACAAGAC	This Study 24
GACGCGCACTTCACCGACCTG	This Study 25
GTCGACCTGATCGTCCATCC	This Study 26
ACCTACGACGTGCTCAATC	This Study 27
CGTACGACGATGGCATCTC	This Study 28
GTGGATATCGGCCAGGTCGAG	This Study 29
GGTGGCAGGATGGAATCGG	This Study 30
CGTCGATTCGCGATTCCCTG	This Study 31
aRestriction cleavage sites are underlined; R = A or G, Y = C or T, S = G or C.

[0164]

TABLE 3
Purification of recombinant HAT-CAR from Nocardia.
	Total	Total	Specific
Step	protein	activity	activity	Yield
Purification	(mg)	(U)1	(U/mg)	(%)
Crude extract	600	5.21	0.009	100	1
Talon Matrix	69.1	4.57	0.066	87.7	7.62
DEAE Sepharose	49	4.43	0.09	85	10
1One unit of the enzyme is defined as the amount of the enzyme that catalyzed the reduction of 1 μmol of benzoate to benzaldehyde per min at 25° C.

Homology

[0165] In conducting BLAST analysis the database proteins most similar to CAR are proteins of unknown function in mycobacteria. The most similar known enzymes are Alpha aminoadipate reducatase and peptide synthetases, but it is unlikely that Car is either of these. Nonetheless, it is likely that the mechanism of benzoate reduction is similar to alpha-aminoadipate reduction. Piperideine-6-carboxylate dehydrogenase has no sequence similarity to CAR, and its mechanism is unlikely to be related to that of Car.

[0166] CAR shows very unique catalytic properties. It is very tolerant, taking carboxylic acids with different structures, as long as they are hydrophobic. In addition, when CAR was tested with alpha amino acids, none of them were reduced. If the alpha amino group is protected with a hydrophobic group, such as Boc, all were reduced with good efficiencies. Therefore, CAR is most likely different from alpha-amino adipate reductase despite the similar motifs.

[0167] CAR is most homologous to a set of proteins of similar large size, thus far found only among the mycobacteria. The best hit is with the Mycobacterium tuberculosis protein identified as a ‘putative substrate-CoA ligase’ (in Mtb CDC1551) or ‘putative acyl CoA ligase’ (FadD9; Rv2590, in Mtb H37Rv). These proteins give a score of 1336, E value of 0, and are 60% identical and 75% positive. The next best hit is with a ‘putative acyl-CoA synthetase’ from Mycobacterium leprae. Another strong hit is also obtained with the Mycobacterium smegmatis database.

[0168] A conserved domain search shows that the protein consists of two main domains, plus a small third domain. The N-terminal portion has homology with a variety of acyl-CoA synthetases and AMP-binding proteins, polyketide synthase, and peptide synthetase modules. Between the N-terminal and C-terminal regions is a short section similar to phosphopantetheine attachment sites (aa 650–725). The C-terminal portion has homology with a variety of dehydrogenases and NAD(P)-dependent enzymes. The 740 N-terminal amino acids and the 482 C-terminal amino acids were blasted giving a bit of overlap. Tables 1 and 2 describe most of the best blast hits. Most protein homologues listed do not have known functions. It appears that the N-terminal and C-terminal Blast hits of CAR with Streptomyces are not with the same proteins, but this is not yet clear, since the S. coelicolor database is not yet fully annotated. The closest hits to known proteins are with alpha-aminoadipate reductase and a non-ribosomal peptide synthetase (for both N-terminal and C-terminal portions). These hits with known proteins are not very strong.

[0169] alpha-Aminoadipate semialdehyde is in chemical equilibrium with 1-piperideine-6-carboxylate. It is of interest that there is some similarity in structure between the 1-piperideine-6-carboxylate and benzoic acid. This might suggest some evolutionary relationship between the benzoate reductase and the aminoadipate enzyme. However, given the low level of identity, it is unlikely that the benzoate reductase is actually an alpha-aminoadipate semialdehyde dehydrogenase. Furthermore, the Mycobacterium homologues would not be Aar because these organisms make lysine via the diaminopimelic acid path rather than the aminoadipate path.

[0170] Bacterial means for converting piperideine-6-carboxylate (a-aminoadipate semialdehyde) into a-aminoadipate exists in Nocardia, Streptomyces, Flavobacterium and Pseudomonas, by use of 1-piperideine-6-carboxylate dehydrogenase.

[0171] The gene for this enzyme has been identified in Flavobacterium and Streptomyces clavuligerus, and it has good homology with AldB (Rv3293 in M. tuberculosis). However, it has no homology with Car, despite the similarity of the piperideine-6-carboxylate dehydrogenase with the Car reaction. This makes sense, since this reaction does not involve ATP and NAD is used instead of NADP.

[0172] Alpha-Aminoadipate reductase has been well studied. Motifs responsible for adenylation of alpha-aminoadipate, reduction, NADP(H) binding, and attachment of the P-pantetheinyl group used in the reaction have been identified. Given the similar overall sizes of Aar proteins and Car, and at least weak blast hits with both the N-terminal and C-terminal portions of the Car sequence, it might be reasonable to postulate a great similarity in mechanism between the two enzymes. However, traditional blast analysis does not reveal the expected common motifs in the N-terminal portion of car, although they appear in the C-terminal portion. Nonetheless, when the motifs are searched for “visually”, many of them are found, as shown in FIG. 3. FIG. 4, FIG. 5, and FIG. 6 show the locations of these motifs within Car, the M. tuberculosis homologue FadD9, and a yeast Aar. “Adenylation domain” motifs C, D, F, H and I are found in Car, although A, B, E, and G are not. The P-pantetheine attachment site, domain J, is clearly present, as are the reduction (R) domain and the NADP-binding domain.

[0173]

TABLE 1
Comparison of amino acid sequence of N-terminal 740 aa
of Car to database sequences using Blast analysis
	Sequence	Sequence	Blast
Organism	ID	function	score	E value	% ID	% Positive
M. tuberculosis	FadD9	Putative acyl-CoA synthetase	764	0	57	72
M. bovis BCG	2.885331	Not annotated	“2074”	2.4 × 10−213	57	72
M. leprae	ML0484	Putative acyl-CoA ligase	769	0	54	70
M. smegmatis	3.09264	Not annotated	“3528”	0	61	75
S. coelicolor	SCO2561	Putative fatty acid-CoA ligase	251	3.5 × 10−29	29	50
S. coelicolor	SCO4383	Putative 4-coumarate: CoA ligase	221	6.8 × 10−18	28	42
Drosophila	CG3961-PA	Hypothetical protein	211	4 × 10−53	31	49
Mus	AAH31544	Similar to fatty acid Co-A ligase	202	2 × 10−50	27	46
T. fusca	Scaf 1	Not annotated	121	3 × 10−28	25	41
Stigmatella	MxaA	Non-ribosomal peptide synthetase	39	7 × 10−5	26	41
aurantica		(in myxalamid biosynthesis)
Schizosaccharomyces	P40976	□-Aminoadipate reductase	25	0.14	23	43
pombe
Candida albicans	AAC02241	□-Aminoadipate reductase	25	0.18	22	40
Bold letters indicate genes known to make a particular enzyme.

[0174]

TABLE 2
Comparison of amino acid sequence of C-terminal 482 aa
of Car to database sequences using Blast analysis
	Sequence	Sequence		E value
Organism	ID	function	Blast	score	% ID	% Positive
M. tuberculosis	FadD9	Putative acyl-CoA synthetase	583	10−165	61	74
M. bovis BCG	2.887365	Not annotated	“1531”	3 × 10−155	60	74
M. leprae	ML0484	Putative acyl-CoA ligase	555	1 × 10−157	58	74
M. smegmatis	3.11301	Not annotated	“1597”	4.8 × 10−164	62	77
S. coelicolor	SCO6273	Putative polyketide synthase	323	1.6 × 10−27	35	51
S. coelicolor	SCO1273	Putative reductase	248	4.7 × 10−28	39	52
Stigmatella	MxaA	Non-ribosomal peptide synthetase	148	2 × 10−34	33	46
aurantica		(in myxalamid biosynthesis)
Schizosaccharomyces	P40976	□-Aminoadipate reductase	116	9 × 10−25	27	46
pombe
Pichia farinosa	CAB97252	□-Aminoadipate reductase	108	2 × 10−22	25	42
T. fusca		No Hits
Bold letters indicate genes known to make a particular enzyme.