PROTEINS, EXPRESSION VEHICLES COMPRISING DNA ENCODING SUCH PROTEINS AND CELLS COMPRISING SUCH EXPRESSION VEHICLES

Abstract: Proteins having chorismate mutase-prephenate dehydratase (CMPD) activity, but lacking phenylalanine sensitivity are produced by genetic engineering. The proteins contain a sequence substantially corresponding to the N-terminal 337 amino acids of Escherichia coli CMPD. Expression vectors including genes coding for those proteins and regulatory DNA enabling their expression are used to transform host microorganisms, which are cultured to produce phenylalanine.

Description: This invention relates to proteins having chorismate mutase and/or prephenate dehydratase activity, expression vehicles comprising DNA encoding such problems, and their use in the production of desired compounds such as phenylalanine. The phenylalanine synthesis pathway in microbes is known to include reactions catalyzed by a single dual-function enzyme, or two separate enzymes, having chorismate mutase and prephenate dehydratase (CMPD) activity. Generally, this activity is subject to feedback inhibition from phenylalanine. Escherichia coli has a chromosomal gene encoding CMPD activity, termed phe A. Tribe, Australian Published Application 72727/81 discloses an E. coli mutant termed NST37 said to produce chorismate mutase prephenate dehydratase substantially free from inhibition by phenylalanine. Hudson and Davidson, J. Mol. Biol. 180 :1023-1051 (1984), disclose the nucleotide sequence of E . coli phe A. Baldwin et al., Arch. Biochem. Biophys. 211 :66-85 (1981), disclose that increasing phenylalanine concentration converts dimeric CMPD to inactive tetramers and octamers. Gething and Davidson, Eur. J. Biochem. 86 :159-164 (1978), disclose that changes in the CMPD aggregation state do not induce gross secondary structural changes, and when CMPD is exposed to phenylalanine, a tryptophanyl residue moves into a more hydrophobic microenvironment. Gething and Davidson, Eur. J. Biochem. 86 :165-174 (1978), disclose that modification of CMPD cysteinyl residues with 5,5-dithiobis[nitrobenzoate] desensitizes CMPD to phenylalanine feedback inhibition. Gething and Davidson, Eur. J. Biochem. 78 :111-117 (1977), disclose that modification of the two tryptophanyl residues of CMPD, using dimethyl[2-hydroxy-5-nitrobenzyl sulphonium bromide], results in a partially active, feedback resistant enzyme. We have discovered a class of proteins possessing CMPD activity that are substantially insensitive to phenylalanine feedback inhibition. The proteins have the formula: ΓCO-Δ where Γ is an amino acid sequence having CMPD activity, substantially corresponding to the N-terminal 337 amino acid sequence of E. coli CMPD; CO is the carbonyl group of the C-terminal amino acid residue of Γ; and Δ is -OH, -O⁻, an amino acid residue other than tryptophan connected via a peptide bond to the C-terminal residue of Γ, or an amino acid sequence having an N-terminal residue other than tryptophan, connected via a peptide bond to the C-terminal residue of Γ. "Substantially corresponding" to the CMPD sequence means having sufficient homology to retain activity substantially equivalent to CMPD. For example, sequences of phe A genes of bacteria related to E. coli having such homology are included. Minor alterations in structure (e.g., the addition, deletion, or non-conservative substitution of a limited number of residues or the conservative substitution of many residues) which retain substantial activity are included within the meaning of that term. Preferably Γ comprises amino acids 1-337 of E. coli CMPD. That sequence can be determined from pKB912 or pKB702, described below, or from the following sequence published by Hudson and Davidson (1984), cited above, where the single-letter codes refer to the table given below: Also preferably, Δ is -OH or -O⁻. Alternatively, Δ is the amino acid sequence Ψ-Ω where: Ψ is either an amino acid residue other than tryptophan or an amino acid sequence whose N-terminal residue is a residue other than tryptophan; and Ω is the sequence EEMFYLDIQANLESAEMQKALKELGITRSMKVLGCYPSENVVPVDPT, or a sequence coding for enzymatic activity other than CMPD activity, preferably the activity of a phenylalanine synthesis pathway enzyme. Another activity-encoding sequence suitable for Ω is the lac Zα, which can be derived from the portion of pUC19 encoding lac Zα, Yanisch-Perron et al. (1985) Gene 33:103, or it can be the following sequence RRIPGNSLAVVLQRRD WENPGVTQLNRLAAHPPFASWRNSEEARTORPSQQLRSLNGEWRLMRYFLLTHLCGISHRIWCTL STICSDAA. In one embodiment, Ψ can be arg-gly. The invention also features an expression vehicle comprising DNA encoding the above-described protein, and regulatory DNA positioned and oriented to effect its expression. For example, the protein-encoding DNA comprises a nucleotide sequence of about 1011 base pairs identical to, or encoding the same amino acids as, the first 1011 base pairs of the E. coli phe A structural gene. Also preferably, the regulatory DNA comprises a promoter (e.g., lac P) that is not subject to phenylalanine feedback regulation and specifically lacks any attenuator sequence intervening between the promoter and the protein-encoding DNA. Moreover, the promoter may control expression of an artificial operon that includes the protein-encoding DNA and DNA encoding a phenylalanine synthesis pathway enzyme other than CMPD, e.g., DNA encoding DAHP synthase. Microbial cells transformed with the expression vehicle are cultured in a fermentation broth from which phenylalanine is recovered. Finally, the invention features a method of engineering a cell to produce feedback insensitive CMPD, by isolating DNA comprising the E. coli phe A gene and converting the codon corresponding to the TGG codon for tryptophan 338 into a TGA stop codon. We have recognized that the catalytically critical segment of E. coli CMPD lies within its N-terminal 337 amino acids, that phenylalanine feedback sensitivity depends on a single amino acid, tryptophan 338, and that deletion of the entire 49 C-terminal amino acids of CMPD does not destroy catalytic activity but does substantially destroy feedback sensitivity. Similarly, substitution of other amino acid(s) for trp 338 results in a feedback insensitive enzyme. The resulting CMPD-active, phenylalanine-insensitive enzymes are useful, particularly for in vivo phenylalanine synthesis, because the penultimate two synthesis steps (chorismate→prephenate→phenylpyruvate) proceed even in the presence of phenylalanine product, thus enabling greater product yields, all other things being equal. Other features and advantages of the invention will be apparent from the following description of the preferred embodiments thereof, and from the claims. First, the drawings will be described briefly. Figure 1 is a diagrammatic representation of selected restriction enzyme cleavage sites in an E. coli chromosomal segment that includes the phe A gene and surrounding regions; Figure 2 is a diagrammatic representation of construction of a truncated phe A termed phe A′; Figure 3 is a diagrammatic representation of the construction of a lac P phe A′ fusion; Figure 4 is a diagrammatic representation of the construction of pKB692; Figure 5 is a diagrammatic representation of the construction of a phe A′ aro F fusion; Figures 6 and 7 are diagrammatic representations of the construction of pKB697 and pKB693; Figure 8 is a diagrammatic representation of the construction of pKB702; Figures 9 and 10 are diagrammatic representations of the construction of plasmids containing a lac P- phe A′ fusions; Figure 11 is a schematic representation of the construction of a phe A′- lac Z fusion and of an in-frame substitution in the phe A gene. The following three-letter and single-letter codes are used for amino acids: Ala, A -alanine Arg, R -arginine Asn, N -asparagine Asp, D -aspartic acid Cys, C -cysteine Gln, Q -glutamine Glu, E -glutamic aicd Gly, G -glycine His, H -histidine Ile, I -isoleucine Leu, L -leucine Lys, K -lysine Met, M -methionine Phe, F -phenylalanine Pro, P -proline Ser, S -serine Thr, T -threonine Trp, W -tryptophan Tyr, Y -tyrosine Val, V -valine Referring to Fig. 1, the horizontal line represents the chromosomal DNA of E . coli encoding chorismate-mutase-prephenate dehydratase ( phe A) and its surrounding regions. The box represents the translated region of phe A. The tryptophan amino acid residue at position 338, 49 amino acids away from the carboxy terminus of the protein, is shown, and Nco I represents a restriction endonuclease cleavage site, the sequence of which contains the codon for the tryptophan residue. "P" represents the promoter of phe A, and "A" a transcription attenuator within the 5′ end of the phe A control region. The expression vector can be assembled from readily available components using techniques such as those described in Maniatis et al., Molecular Cloning , A Laboratory Manual , Cold Spring Harbor 1982. For example, the phe A gene can be derived from pKB45 [Zurawski et al. Proc. Nat'l. Acad. Sci. 75:4275-4274 (1978)], or from other plasmids such as pKB663 (deposited in E . coli YMC9, ATCC 39462, and described in our European Patent Application 85306789.0 (EP-A-0176349). The phe A gene (Fig. 1) can be truncated or altered as generally described below to yield phe A′, a gene coding for phenylalanine-insensitive CMPD. The phe A′ gene is then spliced to a suitable promoter and other regulatory DNA. For example, the phe A′ is spliced to lac P, derived from pKB663 (referenced above), or from pKB430 (referenced below). The novel operon can be constructed as generally described in SN 653,193, referenced above, using a gene encoding another phenylalanine synthesis pathway enzyme, e.g. aro F. For example, aro F can be derived from pKB45, referenced above, or from appropriate digests of pKB712 (ATCC 39856) or pKB750 (ATCC 39857) each of which is described in the above-referenced EP-A-0176349. Specifically, a truncated phe A gene (termed phe A′) which determines an active CMPD enzyme lacking the C-terminal 49 amino acids can be constructed by deleting the DNA from the Nco I site in the phe A gene (Fig. 1) through the end of the gene. This altered gene has a stop codon (TGA) in place of a naturally-occuring tryptophan codon (TGG). This deletion can be prepared repeatably from any cloned phe A gene by Nco I cleavage, filling in the resulting sticky ends with DNA polymerase, and abutting to a DNA end beginning with an A (e.g., a filled-in Eco RI end). Determination that the resulting altered enzyme is feedback resistant is accomplished by assay of either chorismate mutase or prephenate dehydratase (using the technique of Gething et al. (1976) Eur. J. Biochem. 71 :317-325) in the presence of sufficient phenylalanine to feedback inhibit wild type CMPD. Neither activity of the truncated CMPD is affected by phenylalanine at concentrations of at least 1.2mM. Moreover, the CMPD activity and phenylalanine insensitivity are retained when the truncated CMPD is expressed as a fusion with other peptides or proteins, e.g., the lac Z alpha peptide. Finally, the CMPD activity and phenylalanine insensitivity are retained when an amino acid substitution to wild-type CMPD is made at trp 338. The following examples are illustrative, and are not intended to limit the invention. Example 1 (pheA′, pKB631) Referring to Fig. 2, pKB45 (referenced above) was cleaved with Pst I and ligated into Pst I cut pBR322 (ATCC 37017) to give pKB629. This plasmid was then cleaved with Nco I and Eco RI; the sticky ends were filled in with DNA polymerase and ligated together, to give pKB631. pKB631 contains the 5′ portion of phe A in a truncated form which we have termed phe A′. Example 2 (lacP-pheA′, pKB823) Referring to Fig. 3, a phe A′ derivative of pKB663 (deposited in E. coli ATCC strain 39462) was constructed by deleting the Nco I- Eco Rl fragment of pKB663 and religating the plasmid together to yield pKB823, in which the phe A′ gene is under the control of the lac promoter. As explained below, this construction includes a weak attenuator sequence between lac P and phe A′. Examples 3 and 4 (pheA′-aroF fusions pKB684 and pKB689) Referring to Fig. 5, pKB631 (Fig. 2) was used to fuse phe A′ to aro F by cleaving both pKB631 and pKB668 (EP-A-0176349 cited above) with Eco Rl and Pvu II and ligating the appropriate fragments together, yielding pKB684. In this construction, the phe A′ gene would be transcribed from the phe A promoter. The Stu I site on pKB684 is then converted to a Hin d III site by cutting with Stu I and ligating Hin d III linkers into the site, yielding pKB689. This process places a linker between the promoter and operon of phe A, so that a heterologous promoter can be readily inserted if desired. Examples 5, 6, and 7 ( phe A′- aro F fusion, lac P, pKB694, pKB697, pKB702) As shown in Fig. 4, the Tth lllI site in pKB663 (referenced above) near the lac P DNA was converted to a more convenient Hin d III site using Hin d III linkers, to give pKB692. Plasmid pKB694 was then constructed by treating pKB689 (Fig. 6) and pKB692 (Fig. 4) with Hin d III and Hpa I, and ligating the relevant fragments, as shown in Fig. 6. This plasmid is a varient of the phe A′- aro F operon of Examples 3, and 4,except that the phe A promoter has been supplemented by the lac promoter. The Tth lllI site on pKB694 was converted to a Hin d III site using Hin d III linkers, yielding pKB697 (Fig. 6). This was done so that a plasmid which determines tetracycline resistance could be derived from pKB697 as shown in Fig. 8, by fusing Hin d III cut pBR322 with Hin d III cut pKB697 to yield pKB702 (deposited in ATCC strain 67068). This resistance factor facilitates manipulation and selection of the plasmid. Example 8 (pheA′-aroF fusion lacking attenuator, pKB693) Wild-type phe A includes an attenuator sequence that operates to regulate transcription in the presence of sufficient phenylalanine to form a leader peptide. It has been found that in some previous phe A- aro F fusions, expressed from a foreign promoter such as the lac promoter, at least some of this attenuator sequence remains between the promoter and the phe A or phe A′ gene and appears to exert some regulatory effect on transcription, thus reducing the level of phe A or phe A′ expression. It is desirable to eliminate the attenuator sequence entirely. Specifically, pKB693, which lacks the attenuator sequence, is derived from pKB689, which includes at least some of the attenuator sequence, (Fig. 5) as shown in Figs. 6 and 7 and as described below. In Fig. 7, pKB45 and pBR322 (referenced above) are ligated with Pst I and recircularized yielding pKB628. pKB628 is cleaved at Stu I, chewed back with an exonuclease and resealed with a Kpn I linker, yielding pKB632. pKB632 is cleaved at Kpn I, chewed back further with an exonuclease, and resealed with a Kpn I linker, yielding pKB638. The Kpn I site in pKB638 is converted to a Hin d III site by a linker, yielding pKB688. In Fig. 6, pKB693 is constructed by treating pKB689 (Fig. 5) and pKB688 (Fig. 7) with Hin d III and Hpa I and ligating fragments (selected by size separation on agarose gels) together. Example 9 lacP-pheA′ lacking attenuator (pKB912) Another phe A′ construction lacking the above-described attenuator DNA is pKB912 (deposited in ATCC 67067), constructed as shown in Figs. 9 and 10. In Fig. 9, the Kpn I- Eco RI fragment of pKB750 (ATCC 39857, referenced in EP-A-0176349) includes the phe A gene without the attenuator DNA. That fragment is cloned onto pKB444 to yield pKB909. Then, as shown in Fig. 10, the Nco I- Eco RI fragment from pKB909 is deleted, yielding the lac P- phe A′ fusion of pKB912, which is deposited in ATCC 67067. As shown in Fig. 9, pKB444 is derived from pKB430 (a pBR322 derivative described in EP-A-0176349) by changing the Pvu II site of pKB430 first to Hpa I and then to Kpn I using linkers. Example 10 lacP-phe A′-aroF lacking attenuator (pKB951) A plasmid carrying the new lac P- phe A′ fusion and also carrying aro F is constructed. This plasmid, pKB951 (Fig. 10), in an analogue of pKB712 (EP-A-0176349), which has been previously used for biosynthesis of phenylalanine. pKB951 is constructed from pKB912 by converting the Tth lllI site to a Cla I site, using Cla I linkers, removing the Cla I- Hpa I fragment and ligating it to the appropriate Cla I- Hpa I fragment of pKB702 (Fig. 8). Example 11 substitution for trp 338 of pheA (pKB894) A small change in phe A (resulting in replacement of the tryptophan 338 residue in the wild type enzyme by an arginine-glycine dipeptide) substantially removes sensitivity to feedback inhibition. The above noted alteration is made by cleavage of phe A with Nco I, treatment of the linearized DNA with mung bean nuclease, and reclosure of the DNA with addition of an Xho I linker, as shown in Fig. 11, in the conversion of pKB685 (derived from pKB663 by deletion of the Ban I- Bam HI fragment shown in Fig. 3) to pKB894. Although this procedure is not ordinarily expected to cause the specific change referred to above, sequence analysis showed that an extra nucleotide was serendipitously removed (most likely by the mung bean nuclease treatment), yielding the observed result. One skilled in the art will recognize that there are other ways to obtain this construction, for example, by synthesizing an appropriate DNA fragment. Example 12 pheA′-lacZ fusions phe A′ is fused to a portion of the lac Z gene, yielding a phe A′- lac Z alpha peptide fusion (Fig. 11). The resulting fusion retains CMPD activity. The fusion is formed by cloning a lac P- phe A′ gene fragment from pKB894 to the lacZ gene in pUC9, which is commercially available and is referenced in Yanisch et al., cited above. The lac Z portion of the fusion has the sequence: RRIPGNSLAVVLQRRDWENPGVTQLNRLAAHPPFAS WRNSEEARTORPSQQLRSLNGEWRLMRYFLLTHLCGISHRIWCTLSTICSDAA. pKB894 is cut with Tth lllI, rendered blunt with DNA polymerase I and cut with Xho I. pUC9 is cut with Hin d III, rendered blunt with DNA polymerase I and cut with Sal I. The Xho I and Sal I ends are joined as are the blunt ends, to yield pKB906. Plasmids pKB912 and pKB702 in E . coli K12 strain MM294 have been deposited in the ATCC and assigned numbers 67067 and 67068 respectively. Phenylalanine Production In order to produce phenylalanine, one of the above-described expression vectors is transformed by standard techniques into an appropriate microorganism so that the phenylalanine insensitive CMPD is produced in the microorganism. The vectors of the invention generally enable increased phenylalanine production in host organisms. Those skilled in the art will be able to select appropriate microorganisms and, if necessary, to make appropriate modifications to the vectors to adapt them to particular hosts, E. coli is generally a suitable organism particularly for the above-described specific vectors pKB702 and pKB912. Those skilled in the art will recognize that other desirable traits may be incorporated into the host organism by engineering to enhance production of the desired product. The transformed organisms are cultured in a suitable medium, and phenylalanine is recovered. Those skilled in the art of growing bacterial cells will appreciate that a wide range of growth media will be suitable for practicing the invention, including media recipes disclosed in Miller, Experiments in Molecular Genetics , Cold Spring Harbor 1972, and the following recipe for minimal salts medium (15 g/l glucose, 0.3 g/l MgSO₄ · 7H₂O, 14.7 mg/l Cacl₂ · 2H₂O, 0.5 g/l NaCl, 5 g/l (NH₂)₂SO₄, 5 mg/l Vitamin B₁, 1.5 g/l KH₂PO₄, 7.5 mg/l FeSO₄· 7H₂O, 1 g/l Na citrate, and 10 ml of micronutrient solution per litre broth. Micronutrient solution has the following composition: 0.015 g/l Na₂MoO₄ · 2H₂O, 0.25 g/l H₃BO₃, 0.07 g/l CoCl₂ · 6H₂O, 0.025 g/l CuSO₄ · 5H₂O, 0.16 g/l MnCl₂ · 4H₂O, and 0.03 g/l ZnSO₄ · 7H₂O). Those skilled in the art will recognize that other sequences having CMPD can be engineered. For example, starting with a phe A′ sequence such as appears in pKB702 or pKB912, standard engineering techniques can be used to derive other sequences, e.g., by truncating and substituting for residues in the phe A′ sequence, and testing the resulting engineered sequence for CMPD activity. Such modified phe A′ sequences may be greater or less than 337 residues, and they are included within the scope of this invention. For example, the E. coli phe A-encoded sequence, altered only by deletion of trp 338, should retain CMPD activity and substantially lack phenylalanine feedback sensitivity. Other expression vectors having other regulatory DNA can be used, and other expression systems can be used.

Claims: A protein characterized by chorismate mutase/prephenate dehydratase (CMPD) activity that is substantially insensitive to phenylalanine feedback inhibition, said protein comprising the sequence ΓCOΔ where Γ is an amino acid sequence substantially corresponding to the N-terminal 337 amino acid residues of Escherichia coli CMPD, CO is the carbonyl group of C-terminal residue of Γ, and Δ is -OH, -O⁻, an amino acid residue other than tryptophan or an amino acid sequence whose N-terminus is an amino acid other than tryptophan, connected via a peptide bond to the C-terminal residue. The protein of claim 1, wherein Γ comprises the sequence: The protein of claim 1, wherein Γ comprises amino acids 1-337 of E. coli CMPD. The protein of claim 1 or 2, wherein Δ is -OH or -O⁻. The protein of claim 1 or 2, wherein Δ is an amino acid sequence Ψ-Ω, where Ψ is an amino acid residue other than tryptophan, or a pair of amino acid residues that does not contain a tryptophanyl residue; and Ω is a) EEMFYLDIQANLESAEMQKALKELGEITRSMKVLGCYPSENVVPVDPT, or b) a sequence encoding enzymatic activity other than CMPD. The protein of claim 5, wherein Ω comprises a phenylalanine synthesis pathway enzyme activity or lac Zα activity. The protein of claim 5, wherein Ψ is arg-gly. An engineered expression vehicle comprising DNA encoding the protein of any preceding claim, and regulatory DNA positioned and oriented to effect expression of said protein-encoding DNA. The engineered expression vehicle of claim 8 wherein the protein-encoding DNA comprises a nucleotide sequence of about 1011 base pairs functionally identical to the first 1011 base pairs of the E. coli phe A structural gene. The engineered expression vehicle of claim 9, wherein the codon immediately downstream from said nucleotide sequence is TGA. The engineered expression vehicle of claim 8, wherein said regulatory DNA comprises a promoter that is not subject to phenylalanine regulation. The engineered expression vehicle of claim 11, wherein said vehicle comprises a promoter not associated with phe A in wild type organisms, the vehicle being characterized by the absence of an attenuator between said promoter and said protein-encoding DNA. The expression vehicle of claim 11, further comprising an artificial operon, said operon comprising said protein-encoding DNA and DNA encoding an enzyme other than CMPD catalyzing a phenylalanine synthesis pathway step, said operon being expressed under the control of said promoter. The expression vehicle of claim 11, 12, or 13, wherein said promoter is the lac promoter. The expression vehicle of claim 8, wherein said vehicle is selected from pKB912 (present in ATCC strain accession number 67067) and pKB702 (present in ATCC strain accession number 67068), or functionally equivalent vehicles derived therefrom. A cell comprising the expression vehicle of any of claims 8 to 15. A method of producing phenylalanine comprising culturing the cell of claim 16 in a fermentation broth and recovering phenylalanine from said broth. A method of engineering the expression vehicle of claim 10, comprising: providing E. coli phe A gene, altering said phe A gene by converting the codon for residue 338 from TGG to TGA, and fusing said altered phe A gene into an expression vehicle.

Inventors: BACKMAN, KEITH C., BALAKRISHNAN, RAMASWAMY
Applicants: BIOTECHNICA INTERNATIONAL, INC., H.J. HEINZ COMPANY
Application year: 1988
Main classification: C12N15
IPC codes: C12N15, C12N9, C12P13