# Patent

## Title
Alanine 2,3-aminomutases and related polynucleotides

## Abstract

The present invention is directed to polypeptides that have enhanced alanine 2,3-aminomutase (AAM) activity and/or thermostability relative to the wild-type enzymes that have incidental AAM activity as a result of cross reactivity with alanine. In addition, the present invention is directed to a polynucleotides that encodes for the AAM polypeptides of the present invention, to nucleic acid sequences comprising the polynucleotides, to expression vectors comprising the polynucleotides operatively linked to a promoter, to host cells transformed to express the AAM polypeptides, and to a method for producing the AAM polypeptides of the present invention.

## Background
This application is a 371 application of PCT/US2005/038552, filed Oct. 25, 2005, which claims the benefit of U.S. Ser. No. 60/622,206, filed Oct. 25, 2004.


FIELD OF THE INVENTION
The present invention is related to the field of enzymology, and particularly to the field of alanine 2,3-aminomutase (AAM) enzymology. More specifically, the present invention is directed to alanine 2,3-aminomutase polypeptides having improved enzymatic activity (i.e., high substrate turnover) and stability, and to polynucleotides sequences encoding for the improved alanine 2,3-aminomutase polypeptides. The present invention is useful because the alanine 2,3-aminomutase polypeptides can be coupled to other enzymes to produce synthetic organic chemicals, such as pantothenic acid or 3-hydroxypropionic acid in high yields.
BACKGROUND OF THE INVENTION
Organic chemicals such as organic acids, esters, and polyols can be used to synthesize plastic materials and other products. To meet the increasing demand for organic chemicals, more efficient and cost-effective production methods are being developed which utilize raw materials based on carbohydrates rather than hydrocarbons. For example, certain bacteria have been used to produce large quantities of lactic acid used in the production of polylactic acid.
3-hydroxypropionic acid (3-HP) is an organic acid. Several chemical synthesis routes have been described to produce 3-HP, and biocatalytic routes have also been disclosed (WO 01/16346 to Suthers et al.). 3-HP has utility for specialty synthesis and can be converted to commercially important intermediates by known methods in the chemical industry, e.g., acrylic acid by dehydration, malonic acid by oxidation, esters by esterification reactions with alcohols, and 1,3-propanediol by reduction.
The compound 3-HP can be produced biocatalytically from PEP or pyruvate, through a key beta-alanine intermediate (FIG. 1). Beta-alanine can be synthesized in cells from carnosine, beta-alanyl arginine, beta-alanyl lysine, uracil via 5,6-dihydrouracil and N-carbamoyl-beta-alanine, N-acetyl-beta-alanine, anserine, or aspartate. However, these routes are commercially unviable because they require rare precursors or starting compounds that are more valuable than 3-HP. Therefore, production of 3-HP using biocatalytic routes would be more efficient if alpha-alanine could be converted to beta-alanine directly (FIG. 1). Unfortunately, a naturally occurring enzyme that inter-converts alpha-alanine to beta-alanine has not yet been identified. It would be advantageous if enzymatic activities that carry out the conversion of alpha-alanine to beta-alanine were identified, such as an alanine 2,3-aminomutase. Accordingly, it is one object of the present invention to identify enzymes with improved alanine 2-3-aminomutase activity.
Lysine 2,3-aminomutase (KAM), which catalyzes the anaerobic interconversion of lysine to beta-lysine, was first described by Barker in Clostridium SB4 (now C. subterminale) catalyzing the first step in the fermentation of lysine. KAM has been purified from C. subterminale, the gene cloned and expressed in E. coli. See e.g., U.S. Pat. No. 6,248,874, which issued on Jun. 19, 2001 to Frey et al., the whole of which is hereby incorporated herein by reference. The specific activity of purified KAM from C. subterminale SB4 cells has been reported as 3040 units/mg (Lieder et. al., Biochemistry 37:2578 (1998)), where a unit is defined as μmoles lysine/min. The corresponding purified recombinantly produced KAM had equivalent enzyme activity (34.5±1.6 μmoles lysine/min/mg protein). See U.S. Patent Application Publication No. 2003/0113882 A1, which published on Jun. 19, 2003 to Frey et al., the whole of which is incorporated herein by reference.
Based upon the sequence of the KAM from C. subterminale, KAM genes have been annotated in the genomes of other organisms. However, in most cases, the enzymatic activities of the polypeptides encoded by these genes have not been confirmed. Exceptions are the B. subtilis gene (Chen, D., Ruzicka, F. J., and Frey, P. A. (2000) Biochem. J. 348:539-549)), and the Porphyromonas gingivalis and F. nucleatum genes. The B. subtilis KAM, encoded by the yodO gene, is more resistant to O2 than the C. subterminale KAM, but it is markedly less active. As reported by Frey, the B. subtilis KAM has a specific activity of only 0.62 U/mg.
C. subterminale SB4 KAM has been reported to have some cross-reactivity with L-alanine, converting it into beta-alanine. See U.S. Patent Application Publication No. 2003/0113882 A1. WO 03/062173 and WO 02/42418 disclose the first reports of AAM activity based upon modification of kam genes. In these applications, the synthetic aam genes had AAM activity as detected by the complementation of a ΔpanD E. coli strain. However, because alanine is not the natural substrate for this enzyme, the activity for this conversion is substantially less than the activity for conversion of lysine—its natural substrate. The AAM activity of a variant of B. subtilis KAM that also had AAM activity at approximately 0.001 U/mg. It is an object of the present invention to provide polynucleotides encoding a polypeptide having substantially enhanced AAM activity over that found in the wild-type enzymes.
SUMMARY OF THE INVENTION
The present invention has multiple aspects. In one aspect, the present invention is directed to polypeptides that catalyze the reaction of FIG. 1. In one embodiment of this first aspect, the present invention is directed to a polypeptide having alanine 2,3-aminomutase (AAM) activity, preferably as measured by the assay of Example 8, and,

    (a) having a polypeptide selected from the group consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48 and 51;
    (b) having an amino acid sequence which has at least 98% homology, with the amino acid sequence selected from the group consisting of SEQ ID NO: 2, 22, 28, 32, and 36;
    (c) having an amino acid sequence which has at least 99% homology, with the amino acid sequence selected from the group consisting of SEQ ID NO: 4, 6, 8, 12, 16, 24, 26, 30, 34 and 40;
    (d) being a polypeptide encoded by a nucleic acid sequence which hybridizes under high stringency conditions with either (i) the nucleotide sequence of SEQ ID NO: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 41, 43, 45, 47 or 49; (ii) a subsequence of (i) of at least 100 nucleotides, or (iii) a complementary strand of (i) or (ii) (J. Sambrook, E. F. Fritsch, and T. Maniatis, 1989, Molecular Cloning, A Laboratory Manual, 2d edition, Cold Spring Harbor, N.Y.); or
    (e) being a variant of the polypeptide of (c) comprising a substitution, deletion, and/or insertion of one to six amino acids therefrom and having AAM activity from about 1 to about 30 μM β-alanine produced/hour 1 cell OD at pH 7.0-7.6, 25° C.


Collectively, the polypeptides of (b) and (c) above are referred to herein as “homologous polypeptides.” For purposes of the present invention, the degree of homology between two amino acid sequences is expressed as “percent homology,” “percent identity,” “% identity,” “percent identical,” and “% identical” are used interchangeably herein to refer to the percent amino acid sequence identity that is obtained by ClustalW analysis (version W 1.8 available from European Bioinformatics Institute, Cambridge, UK), counting the number of identical matches in the alignment and dividing such number of identical matches by the length of the reference sequence, and using the following default ClustalW parameters to achieve slow/accurate pairwise optimal alignments—Gap Open Penalty: 10; Gap Extension Penalty: 0.10; Protein weight matrix: Gonnet series; DNA weight matrix: IUB; Toggle Slow/Fast pairwise alignments=SLOW or FULL Alignment.
In one embodiment, the present invention is also directed to an AAM polypeptide as described herein in isolated and purified form.
In another embodiment, the present invention is directed to an AAM polypeptide as described herein in lyophilized form.
In yet another embodiment, the present invention is directed to a composition comprising an AAM polypeptide as described herein and a suitable carrier, typically a buffer solution, more typically an aqueous buffer solution having a pH between 6.0 and 8.0. The composition may also be in a lyophilized form.
The novel AAM polypeptides of the present invention have significantly enhanced AAM activity relative to the wild-type KAM polypeptides from which they are ultimately derived. By significantly enhanced AAM activity is meant that the AAM polypeptide of the present invention has an AAM activity within the range of about 1 to about 32 M β-alanine produced/hour 1 cell OD (units), preferably from about 10 to about 32 units, more preferably from about 20 to about 32 units; most preferably from about 25 to about 32 units.
Preferred AAM polypeptides of the present invention have an amino acid sequences of SEQ ID NOs: 2, 6, 12, 16, 20, 24, 28, 30, 32, 34, 38, 44, 46 or 48; more preferably they have an amino acid sequence of SEQ ID NOs: 6, 12, 28, 34, 46 or 48; most preferably, they have an amino acid sequence of SEQ ID NOs: 28 or 34.
One of the grandparent molecules is the KAM of Bacillus subtilis, which had no detectible AAM activity. The DNA encoding this grandparent molecule was modified as described in WO 03/062173, entitled “Alanine 2,3-aminomutase,” to produce a polypeptide having a detectible alanine 2,3-aminomutase activity.
In the present application, the applicants utilized as one parent molecule a polynucleotide sequence of SEQ ID NO: 58, which encoded the 471 residue polypeptide of SEQ ID NO: 59 and which exhibited an AAM activity of approximately 0.001 U/mg (units/mg of cell mass). The molecule of SEQ ID NO: 59 differs from the wild-type B. subtilis KAM, which had no detectible AAM activity, by having the following four (4) amino acid substitutions: L103M, M136V, Y140H and D339H.
In yet another embodiment, the present invention is directed to a polypeptide having from about 1 to about 32 units of AAM activity and typically varying from the polypeptide of SEQ ID NO: 59 by 1-7 amino acid residues, more typically by 1-6 amino acid residues, even more typically by 1-5 amino acid residues, and most typically by 1-4 amino acid residues.
In its second aspect, the present invention is directed to a polynucleotide sequence that encodes for the correspondingly referenced AAM polypeptide. Given the degeneracy of the genetic code, the present invention is also directed to any polynucleotide that encodes for the above referenced AAM polypeptides of the present invention. In another preferred embodiment, the present invention is directed to certain specific polynucleotides of SEQ ID NOS: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47 and 49 that encode for the novel AAM polypeptides of SEQ ID NOS: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48 and 51, respectively. Preferred polynucleotides encode for a polypeptide of SEQ ID NO: 2, 6, 12, 16, 20, 24, 28, 30, 32, 34, 38, 44, 46 or 48; more preferably they encode a polypeptide of SEQ ID NO: 6, 12, 28, 34, 46 or 48; most preferably, they have a polypeptide of sequence of SEQ ID NO: 28 or 34.
In a third aspect, the present invention is directed to a nucleic acid construct, a vector, or a host cell comprising a polynucleotide sequence encoding an AAM polypeptide of the present invention operatively linked to a promoter.
In a fourth aspect, the present invention is directed to a method of making an AAM polypeptide of the present invention comprising (a) cultivating a host cell transformed with a nucleic acid sequence encoding an AAM polypeptide of the present invention under conditions suitable for production of the polypeptide; and (b) providing glucose to the cultivated host cells under conditions suitable for the production of β-alanine. The β-alanine may be optionally recovered from the cells.
In a fifth aspect, the present invention is directed to a method of producing b-alanine comprising (a) cultivating a host cell transformed with a nucleic acid sequence encoding an AAM polypeptide of the present invention under conditions suitable for production of the polypeptide; and (b) providing glucose to the cultivated host cells under conditions suitable for the production of b-alamine. The b-alanine may be optionally recovered from the cells.



BRIEF DESCRIPTION OF SEVERAL VIEWS OF THE DRAWINGS
FIG. 1 shows the reversible reaction between alpha-alanine (i.e., L-alanine or 2-aminopropionic acid) and beta-alanine (3-aminopropionic acid) that is catalyzed by alanine 2,3-aminomutase.
FIG. 2 is a pathway for 3-hydroxypropionate (3-HP) synthesis from alpha-alanine, via beta-alanine as an intermediate.
FIG. 3 is a 4036 bp expression vector (pCK110900-I Bla) of the present invention comprising a P15A origin of replication (P15A ori), a lacI repressor, a CAP binding site, a lac promoter (lac), a T7 ribosomal binding site (T7g10 RBS), and a chloramphenicol resistance gene (camR).
FIGS. 4A-4J in combination provide an alignment chart of the amino acid sequences of four parental polypeptides that were used to produce the AAM of the present invention. The parental polypeptides were non-naturally occurring and derived in part from the KAM of Clostrisium stricklandii (SEQ ID NO: 53), Porphyromonas gingivalis (SEQ ID NO: 55), Fusobacterium nucleatuim (SEQ ID NO: 57), and Bacillus subtilis (SEQ ID NO: 59), respectively. The sequences of two wild-type KAM are disclosed in SEQ ID NOS: 60 (P GI2529467_G_AAB81159.1_) and 61 (P_GI2634361_EMB_CAB13860.1_). A consensus sequence is also provided as SEQ ID NO: 62).



The foregoing summary, as well as the following detailed description of certain embodiments of the present invention, will be better understood when read in conjunction with the appended drawings. For the purpose of illustrating the invention, there is shown in the drawings, certain embodiments. It should be understood, however, that the present invention is not limited to the arrangements and instrumentality shown in the attached drawings.
DETAILED DESCRIPTION OF THE INVENTION
The present invention has multiple aspects. In one aspect, the present invention is directed to a polypeptide having alanine 2,3-aminomutase (AAM) activity, preferably as measured by the assay of Example 8, and

    (a) having a polypeptide selected from the group consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48 and 51:
    (b) having an amino acid sequence which has at least 98% homology, with the amino acid sequence selected from the group consisting of SEQ ID NO: 2, 22, 28, 32, and 36;
    (c) having an amino acid sequence which has at least 99% homology, with the amino acid sequence selected from the group consisting of SEQ ID NO: 4, 6, 8, 12, 16, 24, 26, 30, 34 and 40;
    (d) being a polypeptide encoded by a nucleic acid sequence which hybridizes under high stringency conditions with either (i) the nucleotide sequence of SEQ ID NO: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 41, 43, 45, 47 or 49; (ii) a subsequence of (i) of at least 100 nucleotides, or (iii) a complementary strand of (i) or (ii) (J. Sambrook, E. F. Fritsch, and T. Maniatis, 1989, Molecular Cloning, A Laboratory Manual, 2d edition, Cold Spring Harbor, N.Y.); or
    (e) being a variant of the polypeptide of (d) comprising a substitution, deletion, and/or insertion of one to six amino acids therefrom and having AAM activity from about 1 to about 30 μM β-alanine produced/hour 1 cell OD at pH 7.0-7.6, 25° C.


Collectively, the polypeptides of (b) and (c) above are referred to herein as “homologous polypeptides.” For purposes of the present invention, the degree of homology between two amino acid sequences is expressed as “percent homology,” “percent identity,” “% identity,” “percent identical,” and “% identical” are used interchangeably herein to refer to the percent amino acid sequence identity that is obtained by ClustalW analysis (version W 1.8 available from European Bioinformatics Institute, Cambridge, UK), counting the number of identical matches in the alignment and dividing such number of identical matches by the length of the reference sequence, and using the following default ClustalW parameters to achieve slow/accurate pairwise optimal alignments—Gap Open Penalty: 10; Gap Extension Penalty: 0.10; Protein weight matrix: Gonnet series; DNA weight matrix: IUB; Toggle Slow/Fast pairwise alignments=SLOW or FULL Alignment.
AAM polypeptides are sensitive to oxygen and are preferably maintained and used in an oxygen deficient environment. If the AAM polypeptide becomes inactivated due to exposure to oxygen, it can be activated by anaerobic incubation with a sulfhydryl compound for one hour at 37° C. in accordance with the method described in Chirpich, et al., Journal Biol. Chem., 245(7): 1778-1789 (1970), which is incorporated herein by reference in its entirety. AAM polypeptides of the present invention are preferably utilized in whole cell form (i.e., as a whole cell transformed with an AAM polynucleotide that is used under conditions such that the encoded AAM polypeptide is expressed in the cell) or alternatively, both isolated and utilized under anoxic conditions. AAM polypeptides of the present invention may be isolated, and optionally purified, under anaerobic conditions (e.g., under a nitrogen atmosphere) in accordance with the method described in Petrovich, et al., Journal Biol. Chem., 266(12):7656-7660 (1991), which describes the isolation and purification of lysine-2,3-aminomutase and which is incorporated herein by reference in its entirety. As used herein, the term “anoxic” refers to oxygen deficient. The AAM polypeptides in whole cell form or as isolated enzymes may be lyophilized. In yet another embodiment, the present invention is directed to a composition comprising an AAM polypeptide as described herein (e.g., in whole cell form or as an isolated polypeptide) and a suitable carrier, typically a buffer, more typically an aqueous buffer solution having a pH from about 6.0 to about 8.0. It is also within the scope of the present invention that the aqueous buffered composition be lyophilized to provide a composition in a lyophilized form, wherein the composition is reconstituted by the addition of an aqueous based composition.
In one embodiment, the present invention is also directed to an AAM polypeptide as described herein in isolated and purified form.
In another embodiment, the present invention is directed to an AAM polypeptide as described herein in lyophilized form. Lyophilization is performed using standard lyophilization equipment. Typically, a solution containing the polypeptide is dispensed in an appropriate sized vial, frozen and placed under reduced pressure to cause the water to evaporate, leaving the lyophilized (freeze-dried) polypeptide behind. Prior to use, the lyophilized polypeptide is reconstituted with distilled water or an appropriate buffer solution.
In yet another embodiment, the present invention is directed to a composition comprising an AAM polypeptide as described herein and a suitable carrier, typically a buffer solution, more typically an aqueous buffer solution having a pH between 6.0 and 8.0. The composition may also be in a lyophilized form.
The novel AAM polypeptides of the present invention have significantly enhanced AAM activity relative to the wild-type KAM polypeptides from which they are ultimately derived. By significantly enhanced AAM activity is meant that the AAM polypeptide of the present invention has an AAM activity within the range of about 1 to about 32 μM β-alanine produced/hour 1 cell OD (units), preferably from about 10 to about 32 units, more preferably from about 20 to about 32 units; most preferably from about 25 to about 32 units.
Table 1 provides a chart showing the AAM activities of the various AAM polypeptides of the present invention, identified by their clone number and SEQ ID NO. In Table 1, the OD600nm is reported at harvest after 5 hours (t=5) of incubation. Table 1 also reports the total μM of β-alanine produced after 5 hours per 1 cell OD. Finally, the last column of Table 1 reports the rate of β-alanine (μM) produced/hr/1 cell OD.












TABLE 1










Rate of




Harvest
uM β-alanine
β-alanine (uM)




OD600 nm
produced at
produced/hr



Seq. ID No.
t = 5
t = 5/1 cell OD
1 Cell OD





















34
1.0
159.7
31.9



10
3.7
31.7
6.3



38
4.0
54.9
11.0



20
3.0
73.4
14.7



14
3.7
33.5
7.7



22
2.2
4.8
1.0



42
5.0
17.5
3.5



26
3.7
23.9
4.8



18
4.7
19.3
3.9



44
2.9
64.4
12.9



51
3.7
35.0
7.0



36
3.0
29.8
6.0



48
1.1
110.1
22.0



12
4.7
17.8
3.6



4
3.7
22.4
4.5



16
1.0
136.0
19.4



24
1.4
94.7
18.9



46
1.7
107.6
20.7



28
1.5
148.0
29.2



40
1.4
14.6
2.9



32
1.6
93.2
13.6



2
1.5
87.5
17.5



30
2.7
72.6
14.3



6
1.7
125.7
23.0










Preferred AAM polypeptides of the present invention have an amino acid sequences of SEQ ID NOs: 2, 6, 12, 16, 20, 24, 28, 30, 32, 34, 38, 44, 46 or 48; more preferably they have an amino acid sequence of SEQ ID NOs: 6, 12, 28, 34, 46 or 48; most preferably, they have an amino acid sequence of SEQ ID NOs: 28 or 34.
The ultimate grandparent molecule is the KAM of Bacillus subtilis, which had no detectible AAM activity. The DNA encoding this grandparent molecule was modified as described in WO 03/062173, entitled “Alanine 2,3-aminomutase,” to produce a polypeptide having a detectible alanine 2,3-aminomutase activity.
In the present application, the applicants utilized as one parent molecule a polynucleotide of SEQ ID NO: 58, which encoded the 471 residue polypeptide of SEQ ID NO: 59 and which exhibited an AAM activity of approximately 0.001 U/mg (units/mg of cell mass). The molecule of SEQ ID NO: 59 differs from the wild-type B. subtilis KAM (SEQ ID NO: 60), which had no detectible AAM activity, by having the following four (4) amino acid substitutions: L103M, M136V, Y140H and D339H.
Other grandparent molecules utilized as starting materials in the present invention were the DNA sequences from other microorganisms (e.g., Porphyromonas gingivalis, Fusobacterium nucleatum, and Clostridium sticklandii) that encoded a KAM polypeptide. These DNA sequences were modified using standard techniques to introduce point substitutions that ultimately produced a KAM polypeptide that also had a detectible cross-reactivity with α-alanine. One such parent molecule that was derived from Porphyromonas gingivalis is the polynucleotide of SEQ ID NO: 54 which encodes the 416 residue polypeptide of SEQ ID NO: 55. The parental polypeptide of SEQ ID NO: 55 differs from the wild-type Porphyromonas gingivalis KAM by having the following seven (7) amino acid substitutions: N19Y, E30K, L53P, H85Q, I192V, D331G, and M342T. Another such parent molecule that was derived from F. nucleatum is the polynucleotide of SEQ ID NO: 56 which encodes the 425 residue polypeptide of SEQ ID NO: 57.
Yet another parent polynucleotide was derived by modification of the polynucleotide in C. stricklandii that encodes KAM. The resulting parental polynucleotide, which has a detectable cross-reactivity with α-alanine, is the polynucleotide of SEQ ID NO: 52 which encodes the 416 residue polypeptide of SEQ ID NO: 53.
The above described parental polypeptides of SEQ ID NOs: 53, 55, 57 and 58 are compared in the alignment chart of FIG. 4. From the alignment chart, it can be seen that the KAMs from P. gingivalis, C. stricklandii, and F. nucleatum are truncated at the N-terminus and at the C-terminus relative to the KAM from B. subtilis, while between the four species, about 40% of the residue positions in the central portion of the KAM polypeptide are conserved. Based upon the truncated species in the alignment chart of FIG. 4, it can be inferred that the first 8 amino acid residues at the N-terminus of SEQ ID NO: 58 and the last 40 residues at the C-terminus of SEQ ID NO: 58 are not necessary for KAM activity, or the AAM activity that is derived therefrom. In FIG. 4, there is also provided a consensus sequence.
The AAM polypeptide molecules of the present invention with their enhanced AAM activity were made by applying directed evolution techniques to the above-described parental molecules. These techniques are described in further detail herein.
In yet another aspect, the present invention is directed to AAM polypeptides that have enhanced activity in coupled reactions.
In another embodiment, the present invention is directed to an AAM a polypeptide encoded by a nucleic acid sequence which hybridizes under high stringency conditions with either (i) the nucleotide sequence of SEQ ID NO: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 41, 43, 45, 47 or 49; (ii) a subsequence of (i) of at least 100 nucleotides, or (iii) a complementary strand of (i) or (ii) (J. Sambrook, E. F. Fritsch, and T. Maniatis, 1989, Molecular Cloning, A Laboratory Manual, 2d edition, Cold Spring Harbor, N.Y.). For polynucleotides of at least 100 nucleotides in length, low to very high stringency conditions are defined as prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 μg/ml sheared and denatured salmon sperm DNA, and either 25% formamide for low stringencies, 35% formamide for medium and medium-high stringencies, or 50% formamide for high and very high stringencies, following standard Southern blotting procedures.
For polynucleotides of at least 100 nucleotides in length, the carrier material is finally washed three times each for 15 minutes using 2×SSC, 0.2% SDS at least at 50° C. (low stringency), at least at 55° C. (medium stringency), at least at 60° C. (medium-high stringency), at least at 65° C. (high stringency), and at least at 70° C. (very high stringency).
In another embodiment, the present invention is directed to a variant of the polypeptide of (d) comprising a substitution, deletion, and/or insertion of one to six amino acids there-from and having AAM activity from about 1 to about 30 μM β-alanine produced/hour 1 cell OD at pH 7.0-7.6, 25° C., such as determined by the method of Example 8. Preferably, amino acid changes are of a minor nature, that is conservative amino acid substitutions that do not significantly affect the folding and/or activity of the protein; small deletions, typically of one to six amino acids; small amino- or carboxyl-terminal extensions; a small linker peptide; or a small extension that facilitates purification by changing net charge or another function, such as a poly-histidine tract, an antigenic epitope or a binding domain.
Examples of conservative substitutions are within the group of basic amino acids (arginine, lysine and histidine), acidic amino acids (glutamic acid and aspartic acid), polar amino acids (glutamine and asparagine), hydrophobic amino acids (leucine, isoleucine and valine), aromatic amino acids (phenylalanine, tryptophan and tyrosine), and small amino acids (glycine, alanine, serine, threonine, proline, cysteine and methionine). Amino acid substitutions, which do not generally alter the specific activity are known in the art and are described, for example, by H. Neurath and R. L. Hill, 1979, In, The Proteins, Academic Press, New York. The most commonly occurring exchanges are Ala/Ser, Val/Ile, Asp/Glu, Thr/Ser, Ala/Gly, Ala/Thr, Ser/Asn, Ala/Val, Ser/Gly, Tyr/Phe, Ala/Pro, Lys/Arg, Asp/Asn, Leu/Ile, Leu/Val, Ala/Glu, and Asp/Gly as well as these in reverse.
In another embodiment, the present invention is directed to a fragment of (a), (b) or (c), as described above in the first paragraph of the Detailed Description, that has from about 1 to about 30 μM β-alanine produced/hour 1 cell OD at pH 7.0-7.6, 25° C., such as determined by the method of Example 8. By the term “fragment” is meant that the polypeptide has a deletion of 1 to 8 amino acid residues from the N-terminus or 1-40 residues from the C-terminus, or both. Preferably, the deletion is 1 to 20 residues from the C-terminus, more preferably, the deletion is 1 to 10 residues from the C-terminus.
Polynucleotides
In its second aspect, the present invention is directed to a polynucleotide sequence that encodes for an AAM polypeptide of the present invention. Given the degeneracy of the genetic code, the present invention is also directed to any polynucleotide that encodes for the above referenced AAM polypeptides of the present invention. In its second aspect, the present invention is directed to a polynucleotide sequence that encodes for the correspondingly referenced AAM polypeptide. Given the degeneracy of the genetic code, the present invention is also directed to any polynucleotide that encodes for the above referenced AAM polypeptides of the present invention. In a preferred embodiment, the present invention is directed to certain specific polynucleotides of SEQ ID NOS: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47 and 49 that encode for the novel AAM polypeptides of SEQ ID NOS: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48 and 51, respectively. Preferred polynucleotides encode for a polypeptide of SEQ ID NO: 2, 6, 12, 16, 20, 24, 28, 30, 32, 34, 38, 44, 46 or 48; more preferably they encode a polypeptide of SEQ ID NO: 6, 12, 28, 34, 46 or 48; most preferably, they have a polypeptide of sequence of SEQ ID NO: 28 or 34.
To make the improved AAM polypeptides of the present invention, one starts with one or more wild-type polynucleotides that encode a KAM polypeptide. The term “wild-type” polynucleotide means that the nucleic acid fragment does not comprise any mutations from the form isolated from nature. The term “wild-type” protein means that the protein will be active at a level of activity found in nature and typically will comprise the amino acid sequence as found in nature. Thus, the term “wild type” or “grand-parent sequence” indicates a starting or reference sequence prior to a manipulation of the invention.
Suitable sources of wild-type KAM as a starting material to be improved is readily identified by screening genomic libraries for the KAM activity. A particularly suitable source of KAM is the yodO gene of Bacillus sp. bacteria as found in nature. Using the published KAM gene sequences for B. subtilis (e.g. WO 03 0623173 A2), primers for amplification of the genes from their respective gene libraries were created using conventional techniques. One such technique for isolating the KAM of B. subtilis is disclosed in Chen et al., “A novel lysine 2,3-aminomutase encoded by the yodO gene of Bacillus subtilis: characterization on observation of organic radical intermediates,” Biochem J. 348:539-549 (2000), which is incorporated herein by reference.
The starting polynucleotides of SEQ ID NOs: 52, 54, 56 and 58 were obtained using the techniques discloses in WO 03 0623173 A2 which is incorporated herein by reference for the disclosure of those techniques as recited in the examples therein. Specifically, WO 03 0623173 A2 discloses a B. subtilis wild-type lysine 2,3-aminomutase (KAM), and a mutated form thereof, which encodes an alanine 2,3-aminomutase (AAM). In addition, WO 03 0623173 A2 also discloses a P. gingivalis wild-type lysine 2,3-aminomutase (KAM) and a mutated form thereof, which encodes an alanine 2,3-aminomutase (AAM).
Beginning with the polynucleotide of SEQ ID NO: 58, a non-naturally occurring and mutated and/or evolved enzyme, having unknown AAM activity is generated using any one of the well-known mutagenesis or directed evolution methods. See, e.g., Ling, et al., “Approaches to DNA mutagenesis: an overview,” Anal. Biochem., 254(2):157-78 (1997); Dale, et al., “Oligonucleotide-directed random mutagenesis using the phosphorothioate method,” Methods Mol. Biol., 57:369-74 (1996); Smith, “In vitro mutagenesis,” Ann. Rev. Genet., 19:423-462 (1985); Botstein, et al., “Strategies and applications of in vitro mutagenesis,” Science, 229:1193-1201 (1985); Carter, “Site-directed mutagenesis,” Biochem. J., 237:1-7 (1986); Kramer, et al., “Point Mismatch Repair,” Cell, 38:879-887 (1984); Wells, et al., “Cassette mutagenesis: an efficient method for generation of multiple mutations at defined sites,” Gene, 34:315-323 (1985); Minshull, et al., “Protein evolution by molecular breeding,” Current Opinion in Chemical Biology, 3:284-290 (1999); Christians, et al., “Directed evolution of thymidine kinase for AZT phosphorylation using DNA family shuffling,” Nature Biotechnology, 17:259-264 (1999); Crameri, et al., “DNA shuffling of a family of genes from diverse species accelerates directed evolution,” Nature, 391:288-291; Crameri, et al., “Molecular evolution of an arsenate detoxification pathway by DNA shuffling,” Nature Biotechnology, 15:436-438 (1997); Zhang, et al., “Directed evolution of an effective fucosidase from a galactosidase by DNA shuffling and screening,” Proceedings of the National Academy of Sciences, U.S.A., 94:454-4509; Crameri, et al., “Improved green fluorescent protein by molecular evolution using DNA shuffling,” Nature Biotechnology<14:315-319 (1996); Stemmer, “Rapid evolution of a protein in vitro by DNA shuffling,” Nature, 370:389-391 (1994); Stemmer, “DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution,” Proceedings of the National Academy of Sciences, U.S.A., 91:10747-10751 (1994); WO 95/22625; WO 97/0078; WO 97/35966; WO 98/27230; WO 00/42651; WO 01/75767 and U.S. Pat. No. 6,537,746 which issued to Arnold, et al. on Mar. 25, 2003 and is entitled “Method for creating polynucleotide and polypeptide sequences.”
Any of these methods can be applied to generate AAM polynucleotides. To maximize any diversity, several of the above-described techniques can be used sequentially. Typically, a library of shuffled polynucleotides is created by one mutagenic or evolutionary technique and their expression products are screened to find the polypeptides having the highest AAM activity. Then, a second mutagenic or evolutionary technique is applied to polynucleotides encoding the most active polypeptides to create a second library, which in turn is screened for AAM activity by the same technique. The process of mutating and screening can be repeated as many times as needed, including the insertion of point mutations, to arrive at a polynucleotide that encodes a polypeptide with the desired activity, thermostability, or cofactor preference.
Alternatively, polynucleotides and oligonucleotides of the invention can be prepared by standard solid-phase methods, according to known synthetic methods. Typically, fragments of up to about 100 bases are individually synthesized, then joined (e.g., by enzymatic or chemical litigation methods, or polymerase mediated methods) to form essentially any desired continuous sequence. For example, polynucleotides and oligonucleotides of the invention can be prepared by chemical synthesis using, e.g., the classical phosphoramidite method described by Beaucage et al. (1981) Tetrahedron Letters 22:1859-69, or the method described by Matthles et al. (1984) EMBO J. 3:801-05, e.g., as it is typically practiced in automated synthetic methods. According to the phosphoramidite method, oligonucleotides are synthesized, e.g., in an automatic DNA synthesizer, purified, annealed, ligated and cloned in appropriate vectors.
In addition, essentially any nucleic acid can be custom ordered from any of a variety of commercial sources, such as The Midland Certified Reagent Company, Midland, Tex., The Great American Gene Company, Ramona, Calif., ExpressGen Inc., Chicago, Ill., Operon Technologies Inc., Alameda, Calif., all of which have internet web sites, and many others. Similarly, peptides and antibodies can be custom ordered from any of a variety of sources, such as PeptidoGenic, HTI Bio-products, Inc., BMA Biomedicals Ltd. (U.K.), Bio. Synthesis, Inc., and many others.
Polynucleotides may also be synthesized by well-known techniques as described in the technical literature. See, e.g., Carruthers et al., Cold Spring Harbor Symp. Quant. Biol. 47:411-418 (1982), and Adams et al., J. Am. Chem. Sec. 105:661 (1983). Double stranded DNA fragments may then be obtained either by synthesizing the complementary strand and annealing the strands together under appropriate conditions, or by adding the complementary strand using DNA polymerase with an appropriate primer sequence.
General texts which describe molecular biological techniques useful herein, including mutagenesis, include Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology, volume 152 Academic Press, Inc., San Diego, Calif. (“Berger”); Sambrook et al., Molecular Cloning—A Laboratory Manual (2nd Ed.), volumes 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989 (“Sambrook”); 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. (supplemented through 2000) (“Ausubel”)). Examples of techniques sufficient to direct persons of skill through in vitro amplification methods, including the polymerase chain reaction (PCR) the ligase chain reaction (LCR), Qβ-replicase amplification and other RNA polymerase mediated techniques (e.g., NASBA) are found in Berger, Sambrook, and Ausubel, as well as Mullis et al., (1987) U.S. Pat. No. 4,683,202; PCR Protocols A Guided to Methods and Applications (Innis et al., eds.) Academic Press Inc. San Diego, Calif. (1990); Arnheim & Levinson (Oct. 1, 1990) Chemical and Engineering News 36-47; The Journal Of NIH Research (1991) 3:81-94; Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173; Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87:1874; Lomell et al. (1989) J. Clin. Chem. 35:1826; Landegren et al., (1988) Science 241:1077-1080; Van Brunt (1990) Biotechnology 8:291-294; Wu and Wallace, (1989) Gene 4:560; Barringer et al. (1990) Gene 89:117, and Sooknanan and Malek (1995) Biotechnology 13:563-564. Improved methods of cloning in vitro amplified nucleic acids are described in Wallace et al., U.S. Pat. No. 5,426,039. Improved methods of amplifying large nucleic acids by PCR are summarized in Cheng et al. (1994) Nature 369:684-685 and the references therein, in which PCR amplicons of up to 40 kb are generated. One of skill will appreciate that essentially any RNA can be converted into a double stranded DNA suitable for restriction digestion, PCR expansion and sequencing using reverse transcriptase and a polymerase. See, Ausubel, Sambrook and Berger, all supra.
It will be appreciated by those skilled in the art due to the degeneracy of the genetic code, a multitude of nucleotide sequences encoding AAM polypeptides of the invention may be produced, some of which bear substantial identity to the nucleic acid sequences explicitly disclosed herein. It is also within the scope of the present invention that the polynucleotides encoding the AAM polypeptides of the present invention may be codon optimized for optimal production from the host organism selected for expression. Those having ordinary skill in the art will recognize that tables and other references providing codon preference information for a wide range of organisms are readily available. See e.g., Henaut and Danchin, “Escherichia coli and Salmonella,” Neidhardt, et al. Eds., ASM Press, Washington D.C., p. 2047-2066 (1996).
It is to be noted that expression in E. coli is different than in other organisms. For example, in the present invention, the codon (tgg) encodes Trp (W) for residue position 31 in the parent polypeptide of SEQ ID NO: 59. However, the corresponding codon for residue position 31 is “tga” in each of the progeny polynucleotides of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, and 47 encoding for the AAM polypeptides of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, and 48, respectively. One skilled in the art recognizes that the codon “tga” is usually a stop (nonsense) codon. However, in the present expression system used in the ΔpanD E. coli strain, and under the selection conditions imposed, this codon is read through by the E. coli as a sense codon and is expressed, presumably as Trp (W). Others have reported that “tga” is the weakest stop codon for E. coli and that it is often read through as a sense codon for Trp (W) in high expression. See e.g., Parker, J., “Errors and Alternatives in Reading the universal Genetic Code,” Microbiological Reviews, 53(3): 273-298 (1989); Roth, J., “UGA Nonsense Mutations in Salmonella typhimurium,” J. of Bacteriology, 102(2):467-475 (1970); and McBeath, G. and Kast, P., “UGA Read-Through Artifacts—When Popular Gene Expression Systems Need a Patch,” BioTechniques, 24:789-794 (May 1998), which are incorporated herein by reference. Hence for expression in non-E. coli systems, it would be advantageous to alter the codon (tga) at residue position 31 to “tgg” which is the universal sense codon for Trp (W).
In SEQ ID NO: 49, the codon encoding for residue 72 is “tag” which is read as a stop codon. However, two fragments are produced. The first fragment, having residues 1-71 of SEQ ID NO: 50, does not have any detectable AAM activity. The second fragment that is produced begins with residue 73 (Val) instead of the usual Met. This second fragment has 399 residues (SEQ ID NO: 51) and does have significant AAM activity (see Table 2) based upon the assay of Example 8. Thus, the first 72 residues at the N-terminus of the AAM polypeptide (based upon the consensus sequence or the parental KAM sequence from B. subtilis) are not absolutely necessary for AAM activity.
In the present case, several round No. 1 libraries were created by applying a variety of mutagenic techniques to the polynucleotides of SEQ ID NOs: 52, 54, 56 and 58.
In its third aspect, the present invention is directed to an expression vector and to a host cell comprising a polynucleotide of the present invention operatively linked to a control sequence. To obtain expression of the variant gene encoding an AAM polypeptide, the variant gene was first operatively linked to one or more heterologous regulatory sequences that control gene expression to create a nucleic acid construct, such as an expression vector or expression cassette. Thereafter, the resulting nucleic acid construct, such as an expression vector or expression cassette, was inserted into an appropriate host cell for ultimate expression of the AAM polypeptide encoded by the shuffled gene. A “nucleic acid construct” is defined herein as a nucleic acid molecule, either single- or double-stranded, which is isolated from a naturally occurring gene or which has been modified to contain segments of nucleic acid combined and juxtaposed in a manner that would not otherwise exist in nature. Thus, in one aspect, the present invention is directed to a nucleic acid construct comprising a polynucleotide encoding an AAM polypeptide of the present invention.
The term “nucleic acid construct” is synonymous with the term “expression cassette” when the nucleic acid construct contains all the control sequences required for expression of a coding sequence of the present invention. The term “coding sequence” is defined herein as a nucleic acid sequence, which directly specifies the amino acid sequence of its protein product. A coding sequence can include, but is not limited to, DNA, cDNA, and recombinant nucleic acid sequences.
An isolated polynucleotide encoding an AAM polypeptide of the present invention may be manipulated in a variety of ways to provide for expression of the polypeptide. Manipulation of the isolated polynucleotide prior to its insertion into a vector may be desirable or necessary depending on the expression vector. The techniques for modifying polynucleotides and nucleic acid sequences utilizing recombinant DNA methods are well known in the art.
The term “control sequence” is defined herein to include all components, which are necessary or advantageous for the expression of a polypeptide of the present invention. Each control sequence may be native or foreign to the nucleic acid sequence encoding the polypeptide. Such control sequences include, but are not limited to, a leader, polyadenylation sequence, propeptide sequence, promoter, signal peptide sequence, and transcription terminator. At a minimum, the control sequences include a promoter, and transcriptional and translational stop signals. The control sequences may be provided with linkers for the purpose of introducing specific restriction sites facilitating ligation of the control sequences with the coding region of the nucleic acid sequence encoding a polypeptide.
The term “operably linked” is defined herein as a configuration in which a control sequence is appropriately placed at a position relative to the coding sequence of the DNA sequence such that the control sequence directs the expression of a polypeptide.
The control sequence may be an appropriate promoter sequence. The “promoter sequence” is a relatively short nucleic acid sequence that is recognized by a host cell for expression of the longer coding region that follows. The promoter sequence contains transcriptional control sequences, which mediate the expression of the polypeptide. The promoter may be any nucleic acid sequence which shows transcriptional activity in the host cell of choice including mutant, truncated, and hybrid promoters, and may be obtained from genes encoding extracellular or intracellular polypeptides either homologous or heterologous to the host cell.
For bacterial host cells, suitable promoters for directing the transcription of the nucleic acid constructs of the present invention, include the promoters obtained from the E. coli lac operon, Streptomyces coelicolor agarase gene (dagA), Bacillus subtilis levansucrase gene (sacB), Bacillus licheniformis alpha-amylase gene (amyL), Bacillus stearothermophilus maltogenic amylase gene (amyM), Bacillus amyloliquefaciens alpha-amylase gene (amyQ), Bacillus licheniformis penicillinase gene (penP), Bacillus subtilis xylA and xylB genes, and prokaryotic beta-lactamase gene (Villa-Kamaroff et al., 1978, Proceedings of the National Academy of Sciences USA 75: 3727-3731), as well as the tac promoter (DeBoer et al., 1983, Proceedings of the National Academy of Sciences USA 80: 21-25). Further promoters are described in “Useful proteins from recombinant bacteria” in Scientific American, 1980, 242: 74-94; and in Sambrook et al., 1989, supra.
For filamentous fungal host cells, suitable promoters for directing the transcription of the nucleic acid constructs of the present invention include promoters obtained from the genes for Aspergillus oryzae TAKA amylase, Rhizomucor miehei aspartic proteinase, Aspergillus niger neutral alpha-amylase, Aspergillus niger acid stable alpha-amylase, Aspergillus niger or Aspergillus awamori glucoamylase (glaA), Rhizomucor miehei lipase, Aspergillus oryzae alkaline protease, Aspergillus oryzae triose phosphate isomerase, Aspergillus nidulans acetamidase, and Fusarium oxysporum trypsin-like protease (WO 96/00787), as well as the NA2-tpi promoter (a hybrid of the promoters from the genes for Aspergillus niger neutral alpha-amylase and Aspergillus oryzae triose phosphate isomerase), and mutant, truncated, and hybrid promoters thereof.
In a yeast host, useful promoters are obtained from the genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae galactokinase (GAL1), Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP), and Saccharomyces cerevisiae 3-phosphoglycerate kinase. Other useful promoters for yeast host cells are described by Romanos et al., 1992, Yeast 8:423-488.
The control sequence may also be a suitable transcription terminator sequence, a sequence recognized by a host cell to terminate transcription. The terminator sequence is operably linked to the 3′ terminus of the nucleic acid sequence encoding the polypeptide. Any terminator, which is functional in the host cell of choice, may be used in the present invention.
Preferred terminators for filamentous fungal host cells are obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase; Aspergillus nidulans anthranilate synthase, Aspergillus niger alpha-glucosidase, and Fusarium oxysporum trypsin-like protease.
Preferred terminators for yeast host cells are obtained from the genes for Saccharomyces cerevisiae enolase, Saccharomyces cerevisiae cytochrome C (CYC1), and Saccharomyces cerevisiae glyceraldehyde-3-phosphate dehydrogenase. Other useful terminators for yeast host cells are described by Romanos et al., 1992, supra.
The control sequence may also be a suitable leader sequence, a nontranslated region of an mRNA which is important for translation by the host cell. The leader sequence is operably linked to the 5′ terminus of the nucleic acid sequence encoding the polypeptide. Any leader sequence that is functional in the host cell of choice may be used in the present invention. Preferred leaders for filamentous fungal host cells are obtained from the genes for Aspergillus oryzae TAKA amylase and Aspergillus nidulans triose phosphate isomerase. Suitable leaders for yeast host cells are obtained from the genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae 3-phosphoglycerate kinase, Saccharomyces cerevisiae alpha-factor, and Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP).
The control sequence may also be a polyadenylation sequence, a sequence operably linked to the 3′ terminus of the nucleic acid sequence and which, when transcribed, is recognized by the host cell as a signal to add polyadenosine residues to transcribed mRNA. Any polyadenylation sequence that is functional in the host cell of choice may be used in the present invention. Preferred polyadenylation sequences for filamentous fungal host cells are obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase, Aspergillus nidulans anthranilate synthase, Fusarium oxysporum trypsin-like protease, and Aspergillus niger alpha-glucosidase. Useful polyadenylation sequences for yeast host cells are described by Guo and Sherman, 1995, Molecular Cellular Biology 15: 5983-5990.
The control sequence may also be a signal peptide coding region that codes for an amino acid sequence linked to the amino terminus of a polypeptide and directs the encoded polypeptide into the cell's secretory pathway. The 5′ end of the coding sequence of the nucleic acid sequence may inherently contain a signal peptide coding region naturally linked in translation reading frame with the segment of the coding region that encodes the secreted polypeptide. Alternatively, the 5′ end of the coding sequence may contain a signal peptide coding region that is foreign to the coding sequence. The foreign signal peptide coding region may be required where the coding sequence does not naturally contain a signal peptide coding region.
Alternatively, the foreign signal peptide coding region may simply replace the natural signal peptide coding region in order to enhance secretion of the polypeptide. However, any signal peptide coding region that directs the expressed polypeptide into the secretory pathway of a host cell of choice may be used in the present invention.
Effective signal peptide coding regions for bacterial host cells are the signal peptide coding regions obtained from the genes for Bacillus NCIB 11837 maltogenic amylase, Bacillus stearothermophilus alpha-amylase, Bacillus licheniformis subtilisin, Bacillus licheniformis beta-lactamase, Bacillus stearothermophilus neutral proteases (nprT, nprS, nprM), and Bacillus subtilis prsA. Further signal peptides are described by Simonen and Palva, 1993, Microbiological Reviews 57: 109-137.
Effective signal peptide coding regions for filamentous fungal host cells are the signal peptide coding regions obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger neutral amylase, Aspergillus niger glucoamylase, Rhizomucor miehei aspartic proteinase, Humicola insolens cellulase, and Humicola lanuginosa lipase.
Useful signal peptides for yeast host cells are obtained from the genes for Saccharomyces cerevisiae alpha-factor and Saccharomyces cerevisiae invertase. Other useful signal peptide coding regions are described by Romanos et al., 1992, supra.
The control sequence may also be a propeptide coding region that codes for an amino acid sequence positioned at the amino terminus of a polypeptide. The resultant polypeptide is known as a proenzyme or propolypeptide (or a zymogen in some cases). A propolypeptide is generally inactive and can be converted to a mature active polypeptide by catalytic or autocatalytic cleavage of the propeptide from the propolypeptide. The propeptide coding region may be obtained from the genes for Bacillus subtilis alkaline protease (aprE), Bacillus subtilis neutral protease (nprT), Saccharomyces cerevisiae alpha-factor, Rhizomucor miehei aspartic proteinase, and Myceliophthora thermophila lactase (WO 95/33836).
Where both signal peptide and propeptide regions are present at the amino terminus of a polypeptide, the propeptide region is positioned next to the amino terminus of a polypeptide and the signal peptide region is positioned next to the amino terminus of the propeptide region.
It may also be desirable to add regulatory sequences, which allow the regulation of the expression of the polypeptide relative to the growth of the host cell. Examples of regulatory systems are those which cause the expression of the gene to be turned on or off in response to a chemical or physical stimulus, including the presence of a regulatory compound. In prokaryotic host cells, suitable regulatory sequences include the lac, tac, and trp operator systems. In yeast host cells, suitable regulatory systems include the ADH2 system or GAL1 system. In filamentous fungi, suitable regulatory sequences include the TAKA alpha-amylase promoter, Aspergillus niger glucoamylase promoter, and Aspergillus oryzae glucoamylase promoter.
Other examples of regulatory sequences are those which allow for gene amplification. In eukaryotic systems, these include the dihydrofolate reductase gene, which is amplified in the presence of methotrexate, and the metallothionein genes, which are amplified with heavy metals. In these cases, the nucleic acid sequence encoding the AAM polypeptide of the present invention would be operably linked with the regulatory sequence.
Expression Vectors
In another aspect, the present invention is also directed to a recombinant expression vector comprising a polynucleotide of the present invention (which encodes an AAM polypeptide of the present invention), and one or more expression regulating regions. An expression regulating region includes a promoter, a terminator, a replication origin, etc., depending on the type of hosts into which they are to be introduced. The various nucleic acid and control sequences described above may be joined together to produce a recombinant expression vector which may include one or more convenient restriction sites to allow for insertion or substitution of the nucleic acid sequence encoding the polypeptide at such sites. Alternatively, the nucleic acid sequence of the present invention may be expressed by inserting the nucleic acid sequence or a nucleic acid construct comprising the sequence into an appropriate vector for expression. In creating the expression vector, the coding sequence is located in the vector so that the coding sequence is operably linked with the appropriate control sequences for expression.
The recombinant expression vector may be any sector (e.g., a plasmid or virus), which can be conveniently subjected to recombinant DNA procedures and can bring about the expression of the polynucleotide sequence. The choice of the vector will typically depend on the compatibility of the vector with the host cell into which the vector is to be introduced. The vectors may be linear or closed circular plasmids.
The expression vector may be an autonomously replicating vector, i.e., a vector that, exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g., a plasmid, an extrachromosomal element, a minichromosome, or an artificial chromosome. The vector may contain any means for assuring self-replication. Alternatively, the vector may be one which, when introduced into the host cell, is integrated into the genome and replicated together with the chromosome(s) into which it has been integrated. Furthermore, a single vector or plasmid or two or more vectors or plasmids which together contain the total DNA to be introduced into the genome of the host cell, or a transposon may be used.
The expression vector of the present invention preferably contains one or more selectable markers, which permit easy selection of transformed cells. A selectable marker is a gene the product of which provides for biocide or viral resistance, resistance to heavy metals, prototrophy to auxotrophs, and the like. Examples of bacterial selectable markers are the dal genes from Bacillus subtilis or Bacillus licheniformis, or markers, which confer antibiotic resistance such as ampicillin, kanamycin, chloramphenicol (Example 1) or tetracycline resistance. Suitable markers for yeast host cells are ADE2, HIS3, LEU2, LYS2, MET3, TRP1, and URA3.
Selectable markers for use in a filamentous fungal host cell include, but are not limited to, amdS (acetamidase), argB (ornithine carbamoyltransferase), bar (phosphinothricin acetyltransferase), hph (hygromycin phosphotransferase), niaD (nitrate reductase), pyrG (orotidine-5′-phosphate decarboxylase), (sulfate adenyltransferase), and trpC (anthranilate synthase), as well as equivalents thereof. Preferred for use in an Aspergillus cell are the amdS and pyrG genes of Aspergillus nidulans or Aspergillus oryzae and the bar gene of Streptomyces hygroscopicus. 
The vectors of the present invention preferably contain an element(s) that permits integration of the vector into the host cell's genome or autonomous replication of the vector in the cell independent of the genome. For integration into the host cell genome, the vector may rely on the nucleic acid sequence encoding the polypeptide or any other element of the vector for integration of the vector into the genome by homologous or nonhomologous recombination.
Alternatively, the vector may contain additional nucleic acid sequences for directing integration by homologous recombination into the genome of the host cell. The additional nucleic acid sequences enable the vector to be integrated into the host cell genome at a precise location(s) in the chromosome(s). To increase the likelihood of integration at a precise location, the integrational elements should preferably contain a sufficient number of nucleic acids, such as 100 to 10,000 base pairs, preferably 400 to 10,000 base pairs, and most preferably 800 to 10,000 base pairs, which are highly homologous with the corresponding target sequence to enhance the probability of homologous recombination. The integrational elements may be any sequence that is homologous with the target sequence in the genome of the host cell. Furthermore, the integrational elements may be non-encoding or encoding nucleic acid sequences. On the other hand, the vector may be integrated into the genome of the host cell by non-homologous recombination.
For autonomous replication, the vector may further comprise an origin of replication enabling the vector to replicate autonomously in the host cell in question. Examples of bacterial origins of replication are P15A, pSC101, pMB1 and ColE1. Origins of replication of plasmids pBR322 (which has a pMB1 origin of replication) pUC19 (which has a ColE1 origin of replication), pACYC177 and pACYC184 (which have a P15A origin of replication), permit replication in E. coli; origins of replication for plasmids pUB110, pE194, pTA1060, or pAM.beta.1 permit replication in Bacillus. Examples of origins of replication for use in a yeast host cell are the 2 micron origin of replication, ARS1, ARS4, the combination of ARS1 and CEN3, and the combination of ARS4 and CEN6. The origin of replication may be one having a mutation which makes its functioning temperature-sensitive in the host cell (see, e.g., Ehrlich, 1978, Proceedings of the National Academy of Sciences USA 75: 1433).
More than one copy of a nucleic acid sequence of the present invention may be inserted into the host cell to increase production of the gene product. An increase in the copy number of the nucleic acid sequence can be obtained by integrating at least one additional copy of the sequence into the host cell genome or by including an amplifiable selectable marker gene with the nucleic acid sequence where cells containing amplified copies of the selectable marker gene, and thereby additional copies of the nucleic acid sequence, can be selected for by cultivating the cells in the presence of the appropriate selectable agent
The procedures used to ligate the elements described above to construct the recombinant nucleic acid construct and expression vectors of the present invention are well known to one skilled in the art (see, e.g., J. Sambrook, E. F. Fritsch, and T. Maniatis, 1989, Molecular Cloning, A Laboratory Manual, 2d edition, Cold Spring Harbor, N.Y.).
Many of the expression vectors for use in the present invention are commercially available. Suitable commercial expression vectors include p3xFLAGTMTM expression vectors from Sigma-Aldrich Chemicals, St. Louis Mo., which includes a CMV promoter and hGH polyadenylation site for expression in mammalian host cells and a pBR322 origin of replication and ampicillin resistance markers for amplification in E. coli. Other suitable expression vectors are pBluescriptII SK(−) and pBK-CMV, which are commercially available from Stratagene, LaJolla Calif., and plasmids that are derived front pBR322 (Gibco BRL), pUC (Gibco BRL), pREP4, pCEP4 (Invitrogene) or pPoly (Lathe et al., 1987, Gene 57, 193-201).
Example 6 herein discloses the use of the expression vector pCK110900-I Bla, as shown in the vector map of FIG. 3.
Host Cells
Host cells for use in expressing the expression vectors of the present invention include but are not limited to, bacterial cells, such as E. coli, Streptomyces and Salmonella typhimurium cells; fungal cells, such as yeast cells (e.g., Saccharomyces cerevisiae or Pichia pastoris (ATCC Accession No. 201178)); insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, 293, and Bowes melanoma cells; and plant cells. Appropriate culture mediums and conditions for the above-described host cells are well known in the art.
By way of example, Escherichia coli W3110 was transformed by an expression vector for expressing the shuffled genes of the present invention. The expression vector was created by operatively linking a variant gene of the present invention to the lac promoter under control of the lacI repressor gene. The expression vector also contained the P15A origin of replication and the chloroamphenicol resistance gene. The transformed Escherichia coli W3110 was cultured under appropriate culture medium containing chloramphenicol such that only transformed E coli cells that expressed the expression vector survived. See e.g., Example 1.
Purification
Once the AAM polypeptides were expressed by the variant genes in E. coli, the polypeptides were purified from the cells and or the culture medium using any one or more of the well known techniques for protein purification, including lysozyme treatment, sonication, filtration, salting, ultra-centrifugation, affinity chromatography, and the like under strict anoxic conditions. Suitable solutions for high efficiency extraction of proteins from bacteria, such as E. coli, are commercially available under the trade name CelLytic BTM from Sigma-Aldrich of St. Louis Mo. A suitable process for purifying AAM polypeptides sufficiently from cell lysate for applications in a chemical process is disclosed in the references: Chirpich, T. P. et al., J. Biol. Chem., 1970, 245, 1778-1789; and Petrovich, R. M. et al., J. Biol. Chem., 1991, 266, 7656-7660, both of which are incorporated herein by reference.
Screening
After several rounds of directed evolution were performed, the resulting libraries of exemplary AAM polypeptides were screened. Screening for transformed cells that express a polypeptide having AAM activity is, in general, a two-step process. First, one physically separates the cells and then determines which cells do and do not possess a desired property. Selection is a form of screening in which identification and physical separation are achieved simultaneously by expression of a selection marker, which, in some genetic circumstances, allows cells expressing the marker to survive while other cells die (or vice versa). Exemplary screening markers include luciferase, β-galactosidase, and green fluorescent protein. Selection markers include drug and toxin resistance genes, such as resistance to chloramphenicol, ampicillin and the like. Although spontaneous selection can and does occur in the course of natural evolution, in the present methods selection is performed by man.
The AAM polynucleotides generated by the mutagenesis or directed evolution method are screened in accordance with the protocol described in Example 8 to identify those having enhanced activity that are suitable for inclusion as an improved AAM polypeptide of the present invention. In the process of Example 8, the screening of clones from the expression libraries for enhanced AAM activity was performed by measuring the conversion of α-alanine to β-alanine using liquid chromatography and mass spectrometry. Based upon the screening results, the AAM polypeptides of the present invention axe listed in Table 2 below along with their residue changes and enhanced AAM activity relative to one parental AAM polypeptide, i.e., the polypeptide of SEQ ID NO: 59.









TABLE 2







Rate of




β-alanine (uM)



Residue changes relative to
produced/hr


Seq. ID No.
parent SEQ ID NO: 59
1 Cell OD

















34
I177L, I227M, G308R, I408L,
31.9



F416S, D447G


10
I298V, G308R, F416S, D447G
6.3


38
D125N, I177L, T210S,
11.0


20
K2E, I3O7L,
14.7


14
K13E, L17R, L197P, I200T,
7.7



M281V, F310S, F416S, D447G


22
Y72H, L118P, R145L, I220V,
1.0



F240L, S250P, R311C, F416S,



D447G


42
K19R, T99S, G308R, F416S,
3.5



D447G


26
N80K, G308R, E319G, R325G,
4.8



Q350R


18
Q32R, S74P, S113T, L118P,
3.9



G308R, F416S, D447G


44
D79E, G308R, S329P, F393S,
12.9



F414S, D445G, L453S,


51 (fragment)
A73V, G308R, Y331N, F416S,
7.0



D447G


36
D79E, S93P, N132D, M281I,
6.0



G308R, Y331N, F416S, D447G


48
K2E, M76I, D79E, T131A,
22.0



L203P, G308R, Y331C, F416S,



D447G


12
R38G, C134G, C141R, L203P,
3.6



I280T, G308R, F416S, D447G


4
2KE, I220V, N237D, G308R,
4.5



D360G, K361R, F416S, D447G


16
K13E, L17R, L197P, I200T,
19.4



M281V, G308R, F310S, F416S,



D447G


24
E23D, L43S, D124G, Y137H,
18.9



K156E, G308R, D411G, F416S,



D447G


46
W18R, M76I, D79E, V90A,
20.7



M152T, I163T, S178P, V215G,



G308R, V354A, F416S, D447G


28
E22G, Y71C, S74P, H108R,
29.2



D187G, I244V, G308R, E396G,



F416S, D447G, F454S


40
Y137H, G308R, D411G, F416S,
2.9



D422V, D447G


32
H35R, D79E, K98T, T99S,
13.6



N132S, S135P, E204G, K230R,



G308R, F416S, D447G


2
W235R, S250P, C254R, D276G,
17.5



G308R, Y380C, I381T, F416S,



K440E, D447G


30
Q32R, N67S, H140R, G308R,
14.3



F416S, D447G


6
E24G, M96I, E109G, G308R,
23.0



F416S, D447G


8
G308R, S329P, F416S, D447G,
14.7



L455S









In Table 2 above, it is seen that the AAM polypeptides of the present invention have from 2 to 11 residue differences than their parent polypeptide of SEQ ID NO: 59, and very significant AAM activity as evidenced by the production of β-alanine in the assay of Example 8. In comparison, β-alanine was not detected for SEQ ID NO: 59 under the assay conditions used to test the AAM variants. However, some β-alanine production for parental SEQ ID NO: 59 was detected in a qualitative growth based complementation assay.
Referring to Table 2 above, two preferred residue changes for the AMM polypeptides of the present invention relative to the parental sequence of SEQ ID NO: 59 are G308R and F416S. In those AAM polypeptides of the present invention that are at least 447 residues long, an additional preferred residue change is D447G relative to the parental sequence of SEQ ID NO: 59. Additional suitable residue changes are G308K, F416M and D447L, A, I or V. Thus, in one aspect, the present invention is directed to an AAM polypeptide having at least 5 amino acid residue changes, typically 5-11 residue changes, relative to SEQ ID NO: 59 or a truncated fragment thereof as taught herein, the residue changes including from 1 to 3 residue changes selected from the group consisting of G308R, G308K, F416S, F416M, D447G, D447L, D447A, D447I and D447V.
Based upon the AAM activity in Table 2, an especially preferred AAM polypeptide of the present invention is a polypeptide having 95% sequence homology with the polypeptide of SEQ ID NO: 34, more preferably 98% homology, most preferably 99% homology.
The parental polypeptides of SEQ ID NOs: 53, 55 and 57 demonstrate that the residues 1-8 at the N-terminus and residues 434-473 at the C-terminus are not necessary for KAM or AAM activity. Likewise, the polypeptide fragment of SEQ ID NO: 51, which is a 399 residue expression product, discloses that the first 72 amino acids at the N-terminus relative to the parental clone of SEQ ID NO: 59 are not necessary for AAM activity. (See Table 2) Thus, it is also within the scope of the present invention that the polypeptides described herein include fragments thereof that lack from 1 to 72 residues from their N-terminus relative to the parental sequence of SEQ ID NO: 59, typically from 1 to 40 residues, more typically from 1-20 residues, most typically from 1 to 11 residues. It is also within the scope of the present invention that the above described N-terminal truncation be utilized in combination with a C-terminal truncation as described elsewhere herein.
Only a very few (≦0.5%) of the mutations to the parental B. subtilis KAM (SEQ ID NO: 59) backbone were found to be beneficial. Specifically, for every 1000 clones screened, there occurred only 3-5 single point or double point mutations that were beneficial. In fact, some of the mutations were found to be detrimental.
The first of the following two sets of sequences provides the sequence of the wild type B. subtilis lysine 2,3-aminomutase (KAM) polypeptides of the prior art, as deposited (GI—2529467_GB_AAB81159.1_). This sequence (SEQ ID NO: 60) was not used as a parent sequence but is provided only for purposes of comparison.









M K N K W Y K P K R H W K E I E L W K D V P E E K W N D W L W Q L T H T
(SEQ ID NO: 60)



 


V R T L D D L K K V I N L T E D E E E G V R I S T K T I P L N I T P Y Y A S L


 


M D P D N P R C P V R M Q S V P L S E E M H K T K Y D L E D P L H E D E D


 


S R V P G L T H R Y P D R V L F L V T N Q C S M Y C R Y C T R R R F S G Q I


 


G M G V P K K Q L D A A I A Y I R E T P E I R D C L I S G G D G L L I N D Q I


 


L E Y I L K E L R S I P H L E V I R I G T R A P V V F P Q R I T D H L C E I L K


 


K Y H P V W L N T H F N T S I E M T E E S V E A C E K L V N A G V P V G N


 


Q A V V L A G I N D S V P I M K K L M H D L V K I R V R P Y Y I Y Q C D L S


 


E G I G H F R A P V S K G L E I I E G L R G H T S G Y A V P T F V V D A P G G


 


G G K I A L Q P N Y V L S Q S P D K V I L R N F E G V I T S Y P E P E N Y I P


 


N Q A D A Y F E S V F P E T A D K K E P I G L S A I F A D K E V S F T P E N V


 


D R I K R R E A Y I A N P E H E T L K D R R E R R D Q L K E K K F L A Q Q K


 


K Q K E T E C G G D S S






The second sequence in the set indicates the diversity of the AAM polypeptides of the present invention relative to the known wild-type B. subtilis KAM sequence by designating with the letter “S” followed by the residue number those residues in the Applicants' AAM polypeptides that differ from those of wild-type B. subtilis KAM sequence:









M X2 N K W Y K P K R H W X13 E I E X17 W X19 D V P X23 X24 K W N D W L W
(SEQ ID NO: 65)



 


X32 L T X35 T V X38 T L D D X43 K K V I N L T E D E E E G V R I S T K T I P L


 


X67 I T P X71 X72 X73 X74 L M D P X79 X80 P R C P V R M Q S V P L X93 E E X96 H


 


X98 X99 K Y D L E D P L X108 X109 D E D S X114 V P G X115 T H R Y P X124 R V L F


 


L V T X132 Q X134 X135 X136 X137 C R X140 X141 T R R X145 F S G Q I G M G V P


 


X156 K Q L D A A I A Y I R E T P E I R D C L I S G G D G L L I N X187 Q I L E Y I


 


L K E X197 R S X200 P H X203 X204 V I R I G T R A P V V F P Q R I T D H X224 C E I


 


L K X230 X231 H P V X235 L X237 T H X240 N T S I E M T E E X250 V E A X254 E K L


 


V N A G V P V G N Q A V V L A G I N X276 S V P X280 X281 K K L M H D L V K I


 


R V R P Y Y I Y Q C D L S E G X307 X308 H X310 X311 A P V S K G L X319 I I E G L


 


R G H T X329 G X331 A V P T F V V X339 A P G G G G K I A L X350 P N Y V L S Q


 


S P X360 K V I L R N F E G V I T S Y P E P E N X380 X381 P N Q A D A Y F E S V


 


X393 P X395 T A D K K E P I G L S A X408 F A X411 K E V S X416 T P E N V X422 R I


 


K R R E A Y I A N P E H E T L X400 D R R E X445 R X447 Q L K E K K X454 X455 A


 


Q Q K K Q K E T E C G G D S S






The diversity of changes at various residue positions for the AAM polypeptides of the present invention are shown to the right of the arrow in Table 2 below and relative amino acid residues of wild-type KAM of B. subtilis (GI—2529467_GB_AAB81159.1_) (SEQ ID NO: 60) which are shown to the left of the arrow:










TABLE 3









X2:
K→E



X13:
K→E



X17:
L→R



X19:
K→R



X23:
E→D, G



X24:
E→G



X32:
Q→R



X35:
H→R



X38:
R→G



X43:
L→S



X67:
N→S



X71:
Y→C



X72:
Y→H, W



X73:
A→V



X74:
S→P



X79:
D→G



X80:
N→K



X93:
S→P



X96:
M→I



X98:
K→T



X99:
T→S



X108:
H→R



X109:
E→G



X114:
R→P



X118:
L→P



X124:
D→N



X132:
N→D, S



X134:
C→G



X135:
S→P



X136:
M→V



X137:
Y→H



X140:
Y→H



X141:
C→R



X145:
R→L



X156:
K→E



X187:
D→G



X197:
L→P



X200:
I→T



X203:
L→P



X204:
E→G



X224:
L→P



X230:
K→R



X231:
Y→H



X235:
W→R



X237:
N→D



X240:
F→L



X250:
S→P



X254:
C→Y, R



X276:
D→G



X280:
I→T



X281:
M→I, V



X307:
I→L



X308:
G→R



X310:
F→S



X311:
R→C



X319:
E→G



X329:
S→P



X331:
Y→N



X339:
D→H



X350:
Q→R



X360:
D→G



X361:
K→R



X380:
Y→C



X381:
I→T



X393:
F→S



X395:
E→G



X408:
I→L



X411:
D→G



X416:
F→S



X422:
D→V



X440:
K→E



X445:
R→K



X447:
D→G



X454:
F→S



X455:
L→S










In a fourth aspect, the present invention is directed to a method of making an AAM a nucleic polypeptide of the present invention comprising (a) cultivating a host cell transformed with a nucleic acid sequence encoding an AAM polypeptide of the present invention under conditions suitable for production of the polypeptide; and (b) providing glucose to the cultivated host cells under conditions suitable for the production of β-alanine. The β-alanine may be optionally recovered from the cells.
EXAMPLE 1
Transformation Protocol for aam Libraries/ΔpanD Strain
A mutant E. coli strain—ΔpanD, derived from BW25113 which is described in Datsenko, K. A. and Wanner, B. L., Proc. Natl. Acad. Sci. USA 97:6640-6645 (2000) was used as the host strain for screening of the aam gene libraries. The protocol used to make the deletion is detailed in Example 4 of Cargill patent application WO 03/062173.
Chemical competent E. coli ΔpanD was removed from −80° C. frozen storage and thawed. Thereafter, it was kept on ice until used. An aliquot (100 μl per transformation) was transferred into a sterile 1.5 ml centrifuge tube. A KCM (5×) salt solution was added until the concentration in the aliquot was 1×. KCM consists of 700 mM KCl; 10 mM morpholinopropanesulphonic acid (MOPS) adjusted to pH 5.8. 1-5 μl of the ligation mixture was added to the cells. The cells containing the ligation mixture were first incubated on ice for 30 minutes. The cells were heat shocked at 42° C. for 1 min, and subsequently incubated on ice for 2 minutes. 500 μl of SOC (Maniatis, T., Fritsch, E. F., and Sambrook J. (1982) Molecular Cloning: A Laboratory Manual, 1st Ed., pp. A.2 and A.3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.) was added to the cells, and the cells were incubated at 37° C. for 1 hour with agitation. The cells were then centrifuged at 5000 rpm for 3 minutes, and the SOC was removed. The cell pellet was re-suspended in 500 μl of M9 selection medium ((Maniatis, T., Fritsch, E. F., and Sambrook, J. (1982) Molecular Cloning: A Laboratory Manual, 1st Ed., pp. A.2 and A.3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.) and incubated at 30-C for 2-4 hours with agitation. The cells were then plated onto M9 minimal agar medium supplemented with 1% mannose, 20 μM iron citrate, 5.0 g/l α-alanine, 0.1 mM isopropyl-β-D-thiogalactoside (IPTG) (Sigma Chemical Corp., St. Louis, Mo.), 50 mM MOPS, 25 mM bicarbonate, and 30 μg/ml chloramphenicol. The plated cells were incubated at 30° C. for 3 days or until colonies were of sufficient size to be picked using the Q-BOTTM robot colony picker (Genetix USA, Inc, Boston Mass.).
In Round 2 of the transformation, the above procedure was followed except that the incubation temperature of the last two incubations in the procedure was increased to 37° C., and M9 minimal selection medium was not supplemented with α-alanine (0 g/L α-alanine).
A. Alternate Transformation Protocol for aam Libraries/ΔpanD KIfldA Strain
A mutant E. coli strain ΔpanD, derived from BW25113 which is described in Datsenko, K. A. and Wanner, B. L., Proc. Natl. Acad. Sci. USA 97:6640-6645 (2000) is used as the host strain for screening of the aam gene libraries. The protocol used to make the deletion is detailed in Example 4 of International patent publication WO 03/062173. Optimally, a strain additionally having an increased expression of the flavodoxin (fldA) gene was used as the host strain for screening of the aam gene libraries, since increased flavodoxin enhances aminomutase activity when produced in E. coli. See U.S. Ser. No. 60/726,925, by Cargill, Inc. (Liao, et al), filed Oct. 14, 2005, entitled “Increasing the Activity of Radical S-Adenosyl Methionine (SAM) Enzymes” describes the production of β-alanine from cells that express AAM and overexpress flavodoxin at Examples 1-4, and these example are incorporated herein by reference. This same application, U.S. Ser. No. 60/726,925, by Cargill, Inc. (Liao, et al.) filed Oct. 14, 2005, describes in Example 4 (incorporated herein) the construction of a strain of E. coli in which an artificial Plac/ara hybrid was placed immediately upstream of the fldA gene. Strains carrying the artificial promoter before the fldA gene are designated KifldA, where KI refers to “knock-in”.
Competent cells of E. coli ΔpanD KIfldA are prepared either chemically or electrochemically using standard protocols. Competent E. coli ΔpanD KIfldA was removed from −80° C. frozen storage and thawed. Thereafter, it was kept on ice until used. An aliquot (100 μl per transformation) was transferred into a sterile 1.5 ml centrifuge tube. A KCM (5×) salt solution was added until the concentration in the aliquot was 1×. KCM consists of 700 mM KCl; 10 mM morpholinopropanesulphonic acid (MOPS) adjusted to pH 5.8. 1-5 μl of the ligation mixture was added to the cells. The cells containing the ligation mixture were first incubated on ice for 30 minutes. The cells were heat shocked at 42° C. for 1 min, and subsequently incubated on ice for 2 minutes. 50001 of SOC (Maniatis, T., Fritsch, E. F., and Sambrook, J. (1982) Molecular Cloning: A Laboratory Manual, 1st Ed., pp. A.2 and A.3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.) was added to the cells, and the cells were incubated at 37° C. for 1 hour with agitation. The cells were then centrifuged at 5000 rpm for 3 minutes, and the SOC was removed. Pellets were subsequently resuspended in a medium appropriate for either the complementation assay (Example 3) or the biotransformation assay (Example 4).
EXAMPLE 2
Cloning of aam Genes into pCK110900 Series Vectors
The strategy employed for cloning the alanine aminomutase genes into an inducible expression system involved the isolation of the aam gene by PCR and cloning of the PCR fragment into the SfiI restriction sites downstream from a mutant lac promoter/operator system. Initially, PCR primers were designed to contain a nucleotide sequence that is specific to the 5′ and 3′ ends of the aam gene, as well as the Shine-Delgarno sequence of the ribosome-binding site, and the unique SfiI restriction sites. The gene was then amplified from a template, purified and digested with the restriction endonuclease SfiI. The restricted PCR fragment was purified using the QIAquick PCR purification kit (Qiagen), and cloned into the SfiI sites of the expression vector pCK110900-I Bla of FIG. 3 under the control of a lac promoter and lacI repressor gene. The expression vector also contained the P15a origin of replication and the chloramphenicol resistance gene. Shuffled aam gene libraries were cloned by the same method. Several clones were found that expressed an active alanine 2,3-aminomutase (as per the method of Example 8) and the synthetic genes were sequenced. A polynucleotide sequence designated BSAAM (SEQ ID NO: 58)—was used as a starting material for all further mutations and shuffling. BSAAM (SEQ ID NO: 58) has approximately 99.2% nucleotide identity with the wild-type Bacillus subtilis lysine aminomutase (GenBank Accession No. H10329).
EXAMPLE 3
Screening Via the Tier 2a Growth Assay
Tier 2a Growth Assay
The growth assay identifies variants capable of generating the essential metabolite AcetylCoA via β-alanine produced by AAM variants in the E. coli ΔpanD host strain. Growth is therefore a function of CoA production, and indirectly of AAM activity.
A. Procedure
AAM active clones from the tier 1 complementation assay were picked with a QBOTTM robot colony picker (Genetix USA, Inc., Boston Mass.) and inoculated into a 96-well master plate. The inoculums were grown in the 96 well master plate on a buffered minimal selection media. (Na2HPO. 7H2O 12.8 g/L; KH2PO4 3 g/L; NaCl 0.5 g/L; NH4Cl 1 g/L; MgSO4 2 mM; CaCl2 0.04 mM; mannose 2%; IPTG 1 mM; ferric citrate 20 uM; chloramphenicol 30 μg/ml; MOPS pH 7, 50 mM; and sodium bicarbonate pH 9, 25 mM) (hereinafter “MSM”) to which was added 0.1 uM β-alanine and 0.5 g/L α-alanine. Plates were covered using AirPoreTM microporous tape (Qiagen, Inc.) and incubated at 25° C., 250 rpm, 85% humidity until cultures reached saturation, at which time glycerol was added to the cultures to a final concentration of 20-30%, and the plates stored at −80° C.
Samples from a frozen master plate were arrayed into an “inoculum” plate containing buffered minimal selection media (MSM), as described above, further containing 0.5 g/L α-alanine. The inoculum plates were covered with AirPoreTM microporous tape (Qiagen, Inc.) and incubated at 25° C., 250 rpm, 85% humidity until cultures reached saturation.
15 μl from the inoculum plate was inoculated into a 96-well “assay” plate containing 185 μl of fresh MSM with 0.5 g/L α-alanine. The assay plates were covered with AirPoreTM microporous tape (Qiagen, Inc.) and a lid, and incubated at 25° C., 85% humidity, 250 rpm. Measurements of OD at 600 nm were made at discrete times for a period of approximately ( ̃) 40 hours.
B. Data Analysis
Since library variants exhibit unique growth profiles, it was preferable to calculate and compare growth rates (slopes) at three (3) different growth phases (early, mid and late) to identify all potentially improved variants. Clones that exhibit three (3) standard deviations above the plate average in any of the three (3) phases were designated as potentially improved variants and were retested in tier 2b for comparative ranking.
EXAMPLE 4
Screening Via the Tier 2b Growth Assay
The stringency of the growth screen is increased in Tier 2b by excluding α-alanine (the substrate for AAM) from the medium. Under these conditions, the cell relies on internal/cellular pools of α-alanine to serve as a substrate for AAM, and subsequently, for cell growth. AAM variants capable of utilizing low, intracellular pools of α-alanine might represent low KM variants.
A. Procedure
Samples from a frozen master plate were arrayed into an “inoculum” plate containing buffered minimal selection media (MSM), as described above, further containing 0.5 g/L α-alanine. The inoculum plates were covered using AirPoreTM microporous tape and incubated at 25° C., 250 rpm, 85% humidity until cultures reached growth saturation.
A TECANTM Robotic Sample Processor (Columbus, Ohio) was used to remove 10 μl of inoculum from each Tier 2a variant from the inoculum plates and seed it in replicates of 8 into each of the following:

    96-well Assay plate containing 190 μl of fresh MSM, 0.5 g/L α-alanine.
    96-well Assay plate containing 190 μl of fresh MSM, containing no α-alanine.
    The Assay plates were covered with AirPoreTM microporous tape and a lid and grown at 25° C., 85% humidity, 250-rpm. Samples were collected at time points for approximately 3-4 days and the OD600nm was measured for each sample.


B. Tier 2b Data Analysis
Variants were ranked by the following 3 criteria:

    i) Growth ratio equal to a final culture OD600 on medium without α-alanine/final culture OD600nm on medium containing α-alanine;
    ii) Final culture OD600; and
    iii) Initial growth rates (in phase 1, from approximately 0-20 hour)

Clones with final culture OD600nm>0.7 were retained.

Clones were then ranked based on the growth ratio of criteria (i). Any clones with a OD600nm>0.7 were retained. However, clones that did not meet the above two criteria, but had a very good initial growth rate (iii) were also selected for further evaluation.



EXAMPLE 5
Screening Via Tier 2c-PCR Analysis
The PCR screen identifies variants that contain the correct size gene in the expression vector prior to further screening for function. It excludes unstable gene variants that may have undergone deletions/truncations during the screening process.
A. Procedure
Potentially improved variants from frozen master plates were inoculated into a 96-microwell plate containing LB media with 1% glucose and 30 μg/mL chloramphenicol. Cultures were grown at 25° C., 250 rpm, 85% humidity in plates covered with AirPoreTM microporous tape (Qiagen, Inc.) until cultures reached saturation, approximately 2 days. 10 μL of the culture was transferred to a PCR plate and boiled at 99° C. for 10 minutes to disrupt the cells. Thereafter, 90 μL of the following PCR Master Mix was added to the disrupted cells:

PCR Master Mix:















10
μL
10X Taq Polymerase Buffer (QIAGEN, Valencia CA)


4
μL
25 mM MgCl2


2
μL
10 mM dNTPs


1.25
μL
20 μM primer - Bforward (specific for BsAAM gene)


1.25
μL
20 μM primer - Breverse (specific for BsAAM gene)


1
μL
5 U/μL Taq polymerase (QIAGEN)


70.5
μL
Sterile water


90
μL
Total volume









The Bacillus specific primers used in the PCR reaction are as follows:









B-forward:









SEQ ID NO: 63









5′ccagcctggccataaggagatatacatatgaaaaacaaatggtataaa



c 3′


 


B-reverse:








SEQ ID NO: 64









5′atggtgatggtgatggtggccagtttggccttatgaagaatcccctcc



gc 3′






The amplification reaction was run for 30 cycles. The first cycle was run at 94° C. for 1 minute. Thereafter, the extension procedure was performed for 29 cycles: 94.0° C. for 1 minute; 55.0° C. for 30 seconds; and 72.0° C. for 1 minute. The final extension was performed at 72.0° C. for 5 minutes. The products of the PCR reactions were analyzed by gel-electrophoresis on a 0.8% agarose gel.

EXAMPLE 6
Growth of AAM Variants for β-Alanine Production (50 ml Scale)
Cell Selection Method for Identifying AAM Activity.
To identify genes encoding polypeptides that can perform the alanine 2,3-aminomutase reaction, an efficient screen or selection for the desired activity is needed. Therefore, a selection method was developed by recognizing that E. coli uses beta-alanine for the synthesis of pantothenic acid, which in turn is a component of coenzyme A (CoA) and of acyl carrier protein (ACP). CoA and ACP are the predominant acyl group carriers in living organisms, and are essential for growth.
In E. coli, the primary route to beta-alanine is from aspartate in a reaction catalyzed by aspartate decarboxylase (E.C. 4.1.1.11), which is encoded by the panD gene. A functional deletion mutation of panD (shown as ΔpanD) results in beta-alanine auxotrophy and growth inhibition, which can be alleviated by the exogenous addition of pantothenate or beta-alanine, or by the production of beta-alanine from another source.
Strain description: E. coli ΔpanD host (derived from BW25113, described in Datsenko, K. A. and Wanner, B. L., Proc. Natl. Acad. Sci. USA 97:6640-6645 (2000)), transformed with pCK110900-I Bla vector (low promoter strength resulting from mutated lac promoter sequence). The inoculum culture was grown in buffered minimal selection medium (MSM): M9 salts, pH 7.0-7.4, 50 mM MOPs, pH 7.0, 25 mM sodium bicarbonate, pH 9.0, 1 mM isopropyl-β-D-thiogalactoside (IPTG), 30 μg/ml chloramphenicol, 0.1 g/L alanine, 5 uM pyridoxine HCl, and 20 uM ferric citrate. A 1:20 dilution of inoculum was used to inoculate 50 ml of MSM medium described above. Cultures were incubated at 25° C., 250 rpm for approximately 3 days or until the culture reaches OD600nm ̃1. Then, α-alanine was added to the medium to a final concentration of 300 mM, and pantothenate was added to about 300 uM. Incubation of the supplemented medium continued at 25° C., 250 rpm. Samples were removed from the medium for analysis at time points from t=0 through t=5 hours following the addition of α-alanine.
EXAMPLE 7
Method for Extracting Cells for β-Alanine Detection
Cells from the cultures of Example 6 were harvested by centrifugation of the cultures. The supernatant (spent media) was decanted and saved for further analysis (below). The cell pellets were washed with water. Pellets may be stored at −80° C. for future extraction. The 50 ml cell pellets (OD  ̃4.0) were re-suspended completely in a test tube in 0.9 ml water. The extraction volume for each sample was adjusted to this proportion according to the harvest OD600. An equal volume of methanol (−20° C.) and 200 μL of micro-glass beads was added and the mixture vortexed vigorously. Tubes containing the mixtures were placed on dry ice/EtOH, or in a −80° C. freezer, for about 30 min. The frozen contents in the tube were thawed at room temperature and vortexed vigorously again, and centrifuged at maximum speed for about 10 minutes. The supernatants were filtered using 0.2-0.45 micron filter plates, or syringe filters.
The spent medium was filtered using a 0.2-0.45 micron filter plate or syringe filter. The filtered spent medium was diluted 1:10 in −20° C. methanol/water (final methanol concentration 50%).
The β-alanine content of cell extract and spent media was analyzed by LC/MS/MS (Example 8).
For spent medium sample, the first minute was diverted to waste. The β-alanine peak arrived at approximately 2.0 minutes.
The assay can be scaled to 2 ml, if only the spent media is analyzed.
EXAMPLE 8
Assay for β-alanine (LC/MS/MS)
β-alanine was determined using a combination of liquid chromatography and mass spectrometry. Suitable analytes were the cell extracts and spent media as prepared in Example 7.
The liquid chromatography (LC) phase was performed using an ASTEC CHIROBIOTICTM 4.6 cm×50 mm chiral LC column (Advanced Separation Technologies, Inc., Whippany, N.J. USA). The mobile phase consisted of two solutions: A: 0.25% aqueous acetic acid; and B: 0.25% (v/v) acetic acid in methanol. The elution was isocratic @ 0.6 ml/minute.
The mass spectrometer (MS) analysis was performed on a Micromass Ultima Triple Quad mass spectrometer, using the following tune parameters: Capillary: 3.5 kV; cone: 20 V; hex 1: 15 V; aperture: 1.0V; source temp: 100° C.; desolvation temp: 350° C.; cone gas: 40 L/hr; desolvation gas: 500 L/h; low mass resolution (Q1): 12; high mass resolution (Q1): 12; ion energy (Q1): 0.1; collision cell entrance: −5; collision energy: 14; exit: 1; low mass resolution (Q2): 15 high mass resolution (Q2): 15; ion energy (Q2): 3.0; multiplier: 650 V.
MS Method










Alanine transitions










Analyte
Parent Ion (m/z)
Daughter Ion (m/z)
Dwell Time (sec)













α-alanine
90
44.7
0.1


β-alanine
90
30.7
0.1


α-lysine
147
84.5
0.1


β-lysine
147
70.5
0.1





The inter-channel delay was 0.1 seconds.

## Claims

1. A polypeptide having alanine 2,3-aminomutase (AAM) activity and having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence selected from the group consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, and 51;
(b) an amino acid sequence which has at least 95% homology with the amino acid sequence of SEQ ID NO: 34, wherein the amino acid sequence of the AAM polypeptide comprises an amino acid residue selected from the group consisting of L at position 177, M at position 227, R at position 308, L at position 408, S at position 416, and G at position 447; and
(c) an amino acid sequence encoded by a nucleic sequence which hybridizes under high stringency conditions with the complement of the nucleotide sequence of SEQ ID NO: 33, wherein the encoded amino acid sequence comprises an amino acid residue selected from the group consisting of L at position 177, M at position 227, R at position 308, L at position 408, S at position 416, and G at position 447, wherein the amino acid positions refer to the corresponding positions in SEQ ID NO:34, and
wherein the high stringency conditions are hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 μg/ml sheared and denatured salmon sperm DNA and 50% formamide, and washing three times each for 15 minutes using 2× SSC, 0.2% SDS at a temperature of at least 65° C.

2. The polypeptide of claim 1, wherein the polypeptide has an amino acid sequence encoded by a nucleic acid sequence which hybridizes under high stringency conditions with the complement of the nucleotide sequence of SEQ ID NO: 33, wherein the encoded amino acid sequence comprises an amino acid residue selected from the group consisting of L at position 177, M at position 227, R at position 308, L at position 408, S at position 416, and G at position 447, wherein the amino acid positions refer to the corresponding positions in SEQ ID NO: 34, and
wherein the high stringency conditions are hybridization at 42° C. in 5× SSPE, 0.3% SDS, 200 μg/ml sheared and denatured salmon sperm DNA and 50% formamide, and washing three times each for 15 minutes using 2× SSC, 0.2% SDS at a temperature of at least 65° C.

3. The polypeptide of claim 1 having the amino acid sequence of SEQ ID NO: 34.

4. An AAM polypeptide of claim 1 in lyophilized form.

5. A composition comprising a polypeptide of claim 1 in a buffered medium

6. A method of making an AAM polypeptide comprising (a) cultivating a host cell comprising a nucleic acid construct comprising a nucleic acid sequence encoding the AAM polypeptide of claim 1 under conditions suitable for production of the polypeptide; and (b) recovering the AAM polypeptide.

7. The polypeptide of claim 1 having an amino acid sequence which has at least 95% homology with the amino acid sequence of SEQ ID NO: 34, wherein the amino acid sequence of the AAM polypeptide comprises an amino acid residue selected from the group consisting of L at position 177, M at position 227, R at position 308, L at position 408, S at position 416, and G at position 447.

8. The polypeptide of claim 7 wherein the amino acid sequence comprises an amino acid residue selected from the group consisting of R at position 308 and S at position 416.

9. The polypeptide of claim 8 wherein the amino acid sequence comprises R at position 308 and S at position 416.

10. The polypeptide of claim 7 having an amino acid sequence which has at least 98% homology with the amino acid sequence of SEQ ID NO: 34.

11. The polypeptide of claim 10 having an amino acid sequence which has at least 99% homology with the amino acid sequence of SEQ ID NO: 34.

12. A polynucleotide encoding an AAM polypeptide of claim 1.

13. A host cell transformed to express a polynucleotide of claim 12.

14. A polynucleotide encoding a polypeptide having AAM activity, said polynucleotide having the sequence of SEQ ID NO: 33.

15. An expression vector comprising a polynucleotide of claim 12 or 14 operatively linked to a promoter.

16. A polynucleotide encoding the AAM polypeptide of claim 7.

17. An expression vector comprising the polynucleotide of claim 16.

18. A host cell transformed to express the polynucleotide of claim 16.

19. A method of making an AAM polypeptide comprising (a) cultivating a host cell comprising a nucleic acid construct comprising a nucleic acid sequence encoding the AAM polypeptide of claim 7 under conditions suitable for production of the polypeptide; and (b) recovering the AAM polypeptide.