# Patent

## Title
Methods for modulating thermostability and acid tolerance of microbes

## Abstract

The present invention relates to a method for modulating thermostability or acid tolerance of a microbe by mutating a nucleic acid molecule encoding a homoserine o-succinyltransferase (MetA) to obtain a nucleic acid molecule encoding a mutant MetA and transforming a microbial cell with the nucleic acid molecule encoding a mutant MetA. The microbe, a bacteria expressing the mutant MetA of the present invention represents a growth rate improved in a vigorous environment such as higher-temperatures and/or lower pH conditions.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This application claims under 35 U.S.C. §119(a) the benefit of Korean Application No. 10-2008-0126505 filed Dec. 12, 2008, the entire contents of which are incorporated herein by reference.
SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jul. 5, 2012, is named 84821_30151_SequenceListing.txt and is 40,456 bytes in size.
TECHNICAL FIELD
The present invention relates to a method for modulating (i.e., enhancing or decreasing) the thermostability or acid tolerance of a microbe, and a homoserine o-succinyltransferase (MetA) mutant having an enhanced/decreased thermostability or acid tolerance.
BACKGROUND ART
Growth of Escherichia coli, a mesophilic bacterium, is limited at elevated temperatures (13, 14). Quite unexpectedly, earlier investigations showed that E. coli did not grow at temperatures above 44° C. because of the instability of a single protein, homoserine o-succinyltransferase (MetA) (13, 14, 15, 16). MetA (EC 2.1.3.46), the first enzyme in methionine biosynthesis (FIG. 1), catalyzes the transfer of succinate from succinyl-CoA to L-homoserine (3, 22). Recent findings report that MetAE.coli tends to unfold even at 25° C. in vitro; unfolding becomes maximal at 44° C. and is followed by massive aggregation (5). In vivo, the soluble fraction of cytoplasmic proteins lacks MetAE.coli at temperatures higher than 44° C. (5). MetA from Salmonella enterica is as sensitive to elevated temperature as to weak organic acids including benzoate, propionate and acetate (11). Moreover, hydrogen peroxide increases its sensitivity to both heat and acid and may oxidatively damage the destabilized MetA (11). Price-Carter and coworkers (11) suggested that an excess of MetAS.enterica synthesized at elevated temperatures and/or in the presence of weak organic acids leads to the accumulation of insoluble aggregates that are toxic to the cells and inhibit bacterial growth.
In view of all the foregoing data and the fact that MetA occupies the control point in methionine biosynthesis, it has been proposed that MetA plays a central role in the control of bacterial growth (2). MetA's high sensitivity to many stress factors suggests that it may serve as a sort of metabolic fuse, detecting unfavorable growth conditions (11). In this connection, it is notable that methionine relieves the inhibitory effect of high-temperature and acetic acid on E. coli growth (7, 12, 13, 14).
However, an attempt to enhance thermostability of E. coli by modifying an enzyme (particularly, MetA) responsible for the synthesis of methionine has not been reported yet. The reason is as follows: (a) it is problematic to enhance thermostability of the enzyme per se by modifying the enzyme of mesophilic bacteria; and (b) it is quite difficult to expect whether its modification enhances the growth rate of bacteria at a high-temperature.
For example, US Pat. Appln. Pub. No. 20050233308 discloses a method for enhancing thermostability of an enzyme by substituting Arg, Thr and Ala residues for Lys, Ser and Ser residues of the protein, respectively. However, this specification predicts only amino acid residues implicated in thermostability of enzymes through orthologs study of mesophilic bacteria (Corynebacterium glutamicum) and thermophilic bacteria (Corynebacterium efficiens) with no practical experiments. In other words, this patent document provide no practical data on enhancing thermostability of enzymes per se via protein modification or evolution, and did not disclose that its modification or evolution permits to enhance the growth rate of bacteria at higher temperatures. Furthermore, this patent never discloses MetA which is a target enzyme of the present invention.
US Pat. Appln. Pub. No. 20020137094 discloses a method for predicting amino acid residues pivotal in protein thermostability via a multiple alignment of protein sequences. This patent document also provides no practical data on enhancing thermostability of enzymes per se via protein modification or evolution, and never discloses that its modification or evolution contributes to enhancing the growth rate of bacteria at higher temperatures.
In these connections, it would be a quite interesting to widen the optimum growth temperatures of E. coli by increasing the stability of the MetA enzyme, which is one of aims of the present invention.
The above information disclosed in this Background Art section is only for enhancement of understanding of the background of the invention and therefore it may contain information that does not form the prior art that is already known in this country to a person of ordinary skill in the art.
Throughout this application, various publications and patents are referred and citations are provided in parentheses. The disclosures of these publications and patents in their entities are hereby incorporated by references into this application in order to fully describe this invention and the state of the art to which this invention pertains.
SUMMARY OF THE DISCLOSURE
The present inventors have made intensive researches to develop novel methods for greatly enhancing/decreasing a growth of E. coli at mild/higher temperatures and/or under an acid condition. As results, we have discovered that the growth of bacteria at mild/high-temperatures and/or under an acid condition could be enhanced/decreased by substitution mutations of the wild-type homoserine o-succinyltransferase (MetA).
Accordingly, it is an object of this invention to provide a method for modulating thermostability or acid tolerance of a homoserine o-succinyltransferase (MetA).
It is another object of this invention to provide a method for modulating thermostability or acid tolerance of a microbe.
It is still another object of this invention to provide a homoserine o-succinyltransferase (MetA) having an modulating thermostability or acid tolerance.
It is still another object of this invention to provide a nucleic acid molecule encoding the mutant homoserine o-succinyltransferase (MetA).
It is further still another object of this invention to provide a recombinant vector comprising the mutant nucleic acid molecule.
It is further still another object of this invention to provide a host cell transformed with the mutant nucleic acid molecule.
Other objects and advantages of the present invention will become apparent from the following detailed description together with the appended claims and drawings.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 schematically represents biosynthesis of L-methionine and S-adenosyl-L-methionine in E. coli. Abbreviations: 5′-methyl-THPTG—5′-methyltetrahydropteroyl-tri-L-glutamate; THPTG—tetrahydropteroyl-tri-L-glutamate.
FIG. 2 shows the effect of methionine supplementation on the growth of E. coli strain W3110 at different temperatures. The strain was grown in M9 glucose minimal medium supplemented with (open circles) or without (closed circles) L-methionine in the temperature gradient incubator over the temperature range 30-49° C. Columns indicate the ratio of specific growth rates between methionine-enriched (50 μg ml−1) and methionine-deficient media.
FIG. 3 represents the selection of the thermostable MetAE.coli-333 from the library of metAE.coli mutants. Cultures of 23 strains E. coli JW3973 harboring the plasmid pMetA with mutated metAE.colis and non-mutated control were flask-cultivated in M9 glucose medium at 44° C. The optical density was measured at 600 nm every 1 hr. Symbols: pMetA-control, ●; pMetA-333, ▾; pMetA-334, ∘. The growth curves of other metAE.coli mutants are similar to control strain.
FIG. 4 shows thermostability of E. coli metA mutants. Samples were taken from logarithmically growing cultures at 30° C. in M9 glucose medium, adjusted to equal density, serially diluted in M9 medium (no glucose). Aliquots (5 μl) were spotted on M9 glucose plates. Cells were incubated for 24 hrs at the indicated temperatures.
FIG. 5 represents the effect of different temperatures (A) and methionine supplementation (B) on growth of E. coli metA mutants. Non-mutated and mutated metAs were integrated into the chromosome of the E. coli strain JW3973 instead of the kanamycin resistance gene. The strains were grown in M9 glucose medium in the temperature gradient incubator over the temperature range 30-47° C. for 12 hrs. Methionine was added to a final concentration of 50 μg ml−1. Symbols (A): WE, ●; 333, ∘; WG, ▾; D267, Δ; T229, ▪. Symbols (B): WE, ●; 333, ∘; WE+methionine, ▾; 333+methionine, Δ.
FIG. 6 shows influence of acetic acid on the growth of thermostable E. coli mutants. The strains were cultivated in 100 μl M9 glucose medium at 30° C. in the BioScreen C incubator for 49 hrs with 15 min intervals of shaking in the presence of 30 mM acetic acid (open symbols) or without it (solid symbols). Symbols: WE, circles; 333, triangles; D267, squares; T229, diamonds.
FIG. 7 represents the densitometric analysis of MetAs in heat (A, B) or acetic acid stressed (C, D) cultures. The strains WE (white columns), 333 (gray columns), D267 (dark gray columns), and T229 (black columns) were grown in M9 glucose medium to exponential phase (approx. OD600=0.6) at 30° C. and were then shifted to 45° C. for 40 min or incubated in the presence of 30 mM acetic acid for 3 hrs at 30° C. Soluble (A, C) and aggregated (B, D) fractions of MetAs were purified from 25 ml cultures as described in Materials and Methods. Three μg of total protein were loaded on 12% SDS-PAGE followed by Western blotting using rabbit anti-MetA serum. MetAs were quantified by densitometry using LabWorks software and normalized to the total amount of protein. MetAs from the unstressed cultures were equaled to 1 (plain columns). An average of two independent experiments is presented.
FIG. 8 is thermograms of his-tagged MetAs obtained by differential scanning microcalorimetry. All the proteins were scanned as described in Materials and Methods. The Tm indicated above the corresponding curve is the midpoint of the unfolding transition in differential scanning microcalorimetry; it was determined from three independent experiments.
FIG. 9 represents temperature dependence (A) and acetic acid tolerance (B) of his-tagged MetAs. The activities of non-mutated MetAE coli and MetAGeo, and mutated MetAE coli proteins were measured by monitoring the decrease in absorbance at 232 nm caused by hydrolysis of the thioester bond of succinyl-CoA, the substrate for MetA, over the temperature range 40-58° C. (A), and at 25° C. in the presence of acetic acid (B). An average of three independent measurements is presented for each point. Symbols: MetAE coli, ●; MetAE coli-333, ∘; MetAGeo, ▾; MetAE coli-D267, ∇; MetAE coli-T229, ▪.
FIG. 10 shows a phylogeny tree (A) and multiple alignment (B) of MetA amino acid sequences from E. coli and thermophilic bacteria. Abbreviations: Geobacillus—Geobacillus kaustophilus HTA426 (YP_147640.1), Clostridium—Clostridium thermocellum ATCC 27405 (YP_001038259.1), Thermotoga—Thermotoga maritima ATCC 43589 (NP_228689.1), Streptococcus—Streptococcus thermophilus ATCC 51836 (YP_141582.1), Methylococcus—Methylococcus capsulatus str. Bath (YP_114313.1). Symbols: *, matched amino acids; *, similar amino acids; , very similar amino acids.
FIG. 11 shows a phylogeny tree (A) and multiple alignment (B) of MetA amino acid sequences from E. coli and mesophilic bacteria. Abbreviations: Citrobacter—Citrobacter koseri ATCC BAA-895 (YP_001455419.1), Salmonella—Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 (YP_153079.1), Escherichia—Escherichia coli (CAG29901), Klebsiella—Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (YP_001338016.1). Symbols: *, matched amino acids; *, similar amino acids; , very similar amino acids.



DETAILED DESCRIPTION OF EMBODIMENTS
In one aspect of this invention, there is provided a method for modulating (enhancing/decreasing) thermostability or acid tolerance of a microbe, comprising the steps of: (a) conferring a substitution mutation to a homoserine o-succinyltransferase (MetA)-encoding nucleotide sequence; and (b) transforming the MetA-encoding nucleotide sequence into a cell of the microbe.
In another aspect of this invention, there is provided a method for modulating thermostability or acid tolerance of a cell, comprising transforming the cell with a homoserine o-succinyltransferase (MetA)-encoding nucleotide sequence comprising the substitution of: (a) Thr for Ser at position 61; (b) Val for Glu at position 213; (c) Thr for Ile at position 229; (d) Asp for Asn at position 267; (e) Lys for Asn at position 271; (f) Lys for Gln at position 96; (g) Val for Leu at position 110; (h) Leu for Ile at position 124; (i) Leu for Arg at position 160; U) Thr for Ala at position 195; (k) Glu for Ala at position 200; (l) Gly for Asp at position 218; (m) Tyr for Ile at position 229; (n) Tyr for Phe at position 247; or (o) a combination thereof.
The present inventors have made intensive researches to develop novel methods for greatly enhancing/decreasing a growth of a microbe, preferably bacteria and more preferably E. coli at mild/higher temperatures and/or under an acid condition. As results, we have discovered that the growth of bacteria at mild/high-temperatures and/or under an acid condition could be improved/decreased by substitution mutations of the wild-type homoserine o-succinyltransferase (MetA).
The method of the present invention permits to enhance/decrease thermostabiltiy or acid tolerance of MetA through MetA mutation, and mutated MetA gene is transformed into cells, improving/decreasing a cell growth at mild/higher and/or under acid conditions.
The present invention is a first invention to improve/decrease thermostability and/or add tolerance of a microbe by modifying MetA.
The method of this invention may be expressed as “a method for enhancing/decreasing thermostability and/or acid tolerance of a microbe”, or “a method for improving/decreasing a growth rate of a microbe at a mild/high-temperature and/or under an acid condition”.
According to the method of this invention, a substitution for enhancing/decreasing thermostability and/or acid tolerance of a microbe may be carried out in several positions of MetA.
Preferably, the substitution of MetA includes the substitution of: (a) Thr for Ser at position 61; (b) Val for Glu at position 213; (c) Thr for Ile at position 229; (d) Asp for Asn at position 267; (e) Lys for Asn at position 271; (f) Lys for Gln at position 96; (g) Val for Leu at position 110; (h) Leu for Ile at position 124; (i) Leu for Arg at position 160; (j) Thr for Ala at position 195; (k) Glu for Ala at position 200; (l) Gly for Asp at position 218; (m) Tyr for Ile at position 229; (n) Tyr for Phe at position 247; or (o) a combination thereof.
According to a more preferable embodiment, the substitution mutation induces the enhancement of the thermostability or acid tolerance of the microbe and comprises the substitution of: (a) Thr for Ser at position 61; (b) Val for Glu at position 213; (c) Thr for Ile at position 229; (d) Asp for Asn at position 267; (e) Lys for Asn at position 271; (f) Lys for Gln at position 96; (g) Val for Leu at position 110; (h) Leu for Ile at position 124; (k) Glu for Ala at position 200; (m) Tyr for Ile at position 229; (n) Tyr for Phe at position 247; or (o) a combination thereof.
According to a more preferable embodiment, the substitution mutation induces the decrease of the thermostability or acid tolerance of the microbe and comprises the substitution of: (i) Leu for Arg at position 160; (j) Thr for Ala at position 195; (l) Gly for Asp at position 218; or (o) a combination thereof.
The position of an amino acid residue referred as an amino acid sequence of MetA in this specification is described according to the amino acid sequence of MetAE. coli (SEQ ID NO:2).
According to a preferable embodiment, the substitution of (a) Thr for Ser at 61 position is the substitution of Thr for Ser at position 4 in the Leu-Ser-Asn-Ser-Pro-Leu-Gln-Val amino acid sequence (SEQ ID NO:46) of MetA; the substitution of (b) Val for Glu at position 213 is the substitution of Val for Glu at position 4 in the Ile-Leu-Ala-Glu-Thr-Glu-Xaa1-Gly (Xaa1 represents Asp (SEQ ID NO:47) or Glu (SEQ ID NO:48)) amino acid sequence of MetA; the substitution of (c) Thr for Ile at position 229 is the substitution of Thr for Ile at position 4 in the Asp-Lys-Arg-Ile-Ala-Phe-Val-Thr amino acid sequence (SEQ ID NO:49) of MetA; the substitution of (d) Asp for Asn at position 267 is the substitution of Asp for Asn in the Tyr-Phe-Pro-Xaa1-Asn-Asp-Pro-Gln (Xaa1 represents Lys (SEQ ID NO:50), His (SEQ ID NO:51) or Gln (SEQ ID NO:52)) amino acid sequence of MetA; the substitution of (e) Lys for Asn at position 271 is the substitution of Lys for Asn at position 4 in the Asp-Pro-Gln-Asn-Xaa1-Pro-Arg-Ala (Xaa1 represents Lys (SEQ ID NO:53), Ile (SEQ ID NO:54) or Thr (SEQ ID NO:55)); the substitution of (f) Lys for Gln at 96 position is the substitution of Lys for Gln at position 4 in the Xaa1-Xaa2-Ile-Gln-Asp-Gln-Asn-Phe (Xaa1 and Xaa2 independently represent Glu or Asp) amino acid sequence (SEQ ID NO:56) of MetA; the substitution of (g) Val for Leu at 110 position is the substitution of Val for Leu at position 4 in the Gly-Ala-Pro-Leu-Gly-Leu-Val-Glu amino acid sequence (SEQ ID NO:57) of MetA; the substitution of (h) Leu for Ile at 124 position is the substitution of Leu for Ile at position 4 in the Trp-Pro-Gln-Ile-Xaa1-Gln-Val-Leu (Xaa1 represents Lys (SEQ ID NO:58) or Arg (SEQ ID NO:59)) amino acid sequence of MetA; the substitution of (i) Leu for Arg at 160 position is the substitution of Leu for Arg at position 4 in the Lys-Gln-Thr-Arg-Xaa1-Xaa2-Lys-Xaa3 (Xaa1 represents Ile, Thr or Ala; Xaa2 represents Asp or Glu; Xaa3 represents Leu or Ile) amino acid sequence (SEQ ID NO:60) of MetA; the substitution of (j) Thr for Ala at 195 position is the substitution of Thr for Ala at position 4 in the Ser-Arg-Tyr-Ala-Asp-Phe-Pro-Xaa1 (Xaa1 represents Arg (SEQ ID NO:61) or Gly (SEQ ID NO:62)) amino acid sequence of MetA; the substitution of (k) Glu for Ala at 200 position is the substitution of Glu for Ala at position 4 in the Phe-Pro-Ala-Ala-Leu-Ile-Arg-Asp amino acid sequence (SEQ ID NO:63) of MetA; the substitution of (l) Gly for Asp at 218 position is the substitution of Gly for Asp at position 4 in the Glu-Xaa1-Gly-Asp-Ala-Tyr-Leu-Phe (Xaa1 represents Asp (SEQ ID NO:64) or Glu (SEQ ID NO:65)) amino acid sequence of MetA; the substitution of (m) Tyr for Ile at 229 position is the substitution of Tyr for Ile at position 4 in the Asp-Lys-Arg-Ile-Ala-Phe-Val-Thr amino acid sequence (SEQ ID NO:66) of MetA; the substitution of (n) Tyr for Phe at 247 position is the substitution of Tyr for Phe at position 4 in the Ala-Xaa1-Glu-Phe-Phe-Arg-Asp-Val (Xaa1 represents Ser (SEQ ID NO:67), Gln (SEQ ID NO:68) or Gly (SEQ ID NO:69)) amino acid sequence of MetA; or (o) a combination thereof.
According to a more preferable embodiment, the substitution comprises the substitution of: (c) Thr for Ile at position 229; (d) Asp for Asn at position 267; (e) Lys for Gln at position 96; (h) Leu for Ile at position 124; (i) Leu for Arg at position 160; (m) Tyr for Ile at position 229; or (o) a combination thereof.
A substitution mutation of a particular amino acid in MetA may be carried out according to various methods known to those ordinarily skilled in the art. For example, the substitution mutation may be performed by a method including a PCR mutagenesis, a transposon mutagenesis, a site-directed mutagenesis, an insertional mutagenesis and a cassette mutagenesis, and preferably a site-directed mutagenesis which may be carried out using PCR (Sambrook et al., Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press (2001)). The site-directed mutagenesis using PCR utilizes the primer having a sequence in which a base at a specific site is substituted.
The procedure to transform a mutated MetA-encoding sequence into a cell may be carried out according to various methods known to those ordinarily skilled in the art. For example, the transformation may be performed using a CaCl2 method (Cohen, S. N. et al., Proc. Natl. Acac. Sci. USA, 9: 2110-2114 (1973)), a Hanahan method (Cohen, S. N. et al., Proc. Natl. Acac. Sci. USA, 9: 2110-2114 (1973); and Hanahan, D., J. Mol. Biol., 166: 557-580 (1983)) and an electroporation method (Dower, W. J. et al., Nucleic. Acids Res., 16: 6127-6145 (1988)).
According to a preferable embodiment, the MetA of the present invention is derived from a mesophilic bacterium. The term “mesophilic bacterium” used in the present invention refers to a bacterium having the most high growth rate at a mild temperature, typically 15-40° C. Preferably, the mesophilic bacterium includes Escherichia, Pseudomonas, Xanthomonas, Serratia, Lactobacillus, Bacillus, Citrobacter, Salmonella or Klebsiella, more preferably Escherichia coli, Pseudomonas aeruginosa, Xanthomonas rinicola, Serratia marcescens, Lactobacillus lactis, Bacillus subtilis, Citrobacter freundii, Salmonella enterica or Klebsiella pneumonia, and most preferably Escherichia coli. 
According to a preferable embodiment, the cell transformed with MetA-encoding nucleotide sequence is the mesophilic bacterium, more preferably Escherichia, Pseudomonas, Xanthomonas, Serratia, Lactobacillus, Bacillus, Citrobacter; Salmonella or Klebsiella, much more preferably Escherichia coli, Pseudomonas aeruginosa, Xanthomonas rinicola, Serratia marcescens, Lactobacillus lactis, Bacillus subtilis, Citrobacter freundii, Salmonella enterica or Klebsiella pneumoniae, and most preferably Escherichia coli. 
According to the method of the present invention, thermostability and/or acid tolerance of MetA is remarkably increased/decreased, resulting in enhancing/decreasing thermostability and/or acid tolerance of a transformed cell containing MetA.
The term “thermostabiltiy” used herein in conjunction with microbes means that microbes have a potential to grow at higher temperatures (generally 20-60° C., preferably 30-50° C., more preferably 30-48° C. and most preferably 30-44° C.). The term “thermostabiltiy” used herein in conjunction with MetA is intended to mean the stability of the enzyme to thermal influence. All enzyme proteins are destabilized and eventually degraded with increasing temperature, each enzyme protein having a certain temperature range wherein the protein is stable and retains its enzymatic activity. Increased thermostability means that the enzyme protein may retain its enzymatic activity and/or exhibit a higher relative activity at increased temperatures.
The term “acid tolerance” used herein in conjunction with microbes means that microbes have a potential to grow under acid conditions (i.e., at low pH conditions). The term “acid tolerance” used herein in conjunction with MetA is intended to mean the stability of the enzyme to lower pH influence.
The present invention enables bioprocesses to be effectively carried out using microbes at high-temperatures and/or under acid conditions.
As indicated in FIGS. 10 and 11, MetA is found to be responsible for thermostability in a variety of bacteria and to have conserved sequences. In this regard, the mutagenesis approaches of the present invention for modulating thermostability or acid tolerance of bacterial cells or MetA may be applied to a large number of microbes including, preferably, Escherichia, Pseudomonas, Xanthomonas, Serratia, Lactobacillus, Bacillus, Citrobacter, Salmonella or Klebsiella, more preferably Escherichia coli, Pseudomonas aeruginosa, Xanthomonas rinicola, Serratia marcescens, Lactobacillus lactis, Bacillus subtilis, Citrobacter freundii, Salmonella enterica or Klebsiella pneumonia, and most preferably Escherichia cob:
In still another aspect of this invention, there is provided a homoserine o-succinyltransferase (MetA) having an enhanced/decreased thermostability or acid tolerance, comprising conferring a substitution mutation to MetA having the substitution of: (a) Thr for Ser at position 61; (b) Val for Glu at position 213; (c) Thr for Ile at position 229; (d) Asp for Asn at position 267; (e) Lys for Asn at position 271; (f) Lys for Gln at position 96; (g) Val for Leu at position 110; (h) Leu for Ile at position 124; (i) Leu for Arg at position 160; (j) Thr for Ala at position 195; (k) Glu for Ala at position 200; (l) Gly for Asp at position 218; (m) Tyr for Ile at position 229; (n) Tyr for Phe at position 247; or (o) a combination thereof.
According to a preferable embodiment, the substitution of (a) Thr for Ser at 61 position is the substitution of Thr for Ser at position 4 in the Leu-Ser-Asn-Ser-Pro-Leu-Gln-Val amino acid sequence (SEQ ID NO:46) of MetA; the substitution of (b) Val for Glu at position 213 is the substitution of Val for Glu at position 4 in the Ile-Leu-Ala-Glu-Thr-Glu-Xaa1-Gly (Xaa1 represents Asp (SEQ ID NO:47) or Glu (SEQ ID NO:48)) amino acid sequence of MetA; the substitution of (c) Thr for Ile at position 229 is the substitution of Thr for Ile at position 4 in the Asp-Lys-Arg-Ile-Ala-Phe-Val-Thr amino acid sequence (SEQ ID NO:49) of MetA; the substitution of (d) Asp for Asn at position 267 is the substitution of Asp for Asn in the Tyr-Phe-Pro-Xaa2-Asn-Asp-Pro-Gln (Xaa2 represents Lys (SEQ ID NO:50), His (SEQ ID NO:51) or Gln (SEQ ID NO:52)) amino acid sequence of MetA; the substitution of (e) Lys for Asn at position 271 is the substitution of Lys for Asn at position 4 in the Asp-Pro-Gln-Asn-Xaa3-Pro-Arg-Ala (Xaa3 represents Lys (SEQ ID NO:53), Ile (SEQ ID NO:54) or Thr (SEQ ID NO:55)); the substitution of (f) Lys for Gln at 96 position is the substitution of Lys for Gln at position 4 in the Xaa1-Xaa2-Ile-Gln-Asp-Gln-Asn-Phe (Xaa1 and Xaa2 independently represent Glu or Asp) amino acid sequence (SEQ ID NO:56) of MetA; the substitution of (g) Val for Leu at 110 position is the substitution of Val for Leu at position 4 in the Gly-Ala-Pro-Leu-Gly-Leu-Val-Glu amino acid sequence (SEQ ID NO:57) of MetA; the substitution of (h) Leu for Ile at 124 position is the substitution of Leu for Ile at position 4 in the Trp-Pro-Gln-Ile-Xaa1-Gln-Val-Leu (Xaa1 represents Lys (SEQ ID NO:58) or Arg (SEQ ID NO:59)) amino acid sequence of MetA; the substitution of (i) Leu for Arg at 160 position is the substitution of Leu for Arg at position 4 in the Lys-Gln-Thr-Arg-Xaa1-Xaa2-Lys-Xaa3 (Xaa1 represents Ile, Thr or Ala; Xaa2 represents Asp or Glu; Xaa3 represents Leu or Ile) amino acid sequence (SEQ ID NO:60) of MetA; the substitution of (j) Thr for Ala at 195 position is the substitution of Thr for Ala at position 4 in the Ser-Arg-Tyr-Ala-Asp-Phe-Pro-Xaa1 (Xaa1 represents Arg (SEQ ID NO:61) or Gly (SEQ ID NO:62)) amino acid sequence of MetA; the substitution of (k) Glu for Ala at 200 position is the substitution of Glu for Ala at position 4 in the Phe-Pro-Ala-Ala-Leu-Ile-Arg-Asp amino acid sequence (SEQ ID NO:63) of MetA; the substitution of (l) Gly for Asp at 218 position is the substitution of Gly for Asp at position 4 in the Glu-Xaa1-Gly-Asp-Ala-Tyr-Leu-Phe (Xaa1 represents Asp (SEQ ID NO:64) or Glu (SEQ ID NO:65)) amino acid sequence of MetA; the substitution of (m) Tyr for Ile at 229 position is the substitution of Tyr for Ile at position 4 in the Asp-Lys-Arg-Ile-Ala-Phe-Val-Thr amino acid sequence (SEQ ID NO:66) of MetA; the substitution of (n) Tyr for Phe at 247 position is the substitution of Tyr for Phe at position 4 in the Ala-Xaa1-Glu-Phe-Phe-Arg-Asp-Val (Xaa1 represents Ser (SEQ ID NO:67), Gln (SEQ ID NO:68) or Gly (SEQ ID NO:69)) amino acid sequence of MetA; or (o) a combination thereof.
According to a more preferable embodiment, the substitution comprises the substitution of: (c) Thr for Ile at position 229; (d) Asp for Asn at position 267; (e) Lys for Gln at position 96; (h) Leu for Ile at position 124; (i) Leu for Arg at position 160; (m) Tyr for Ile at position 229; or (o) a combination thereof.
An illustrative example of the amino add sequence of mutated MetA protein in the present invention is described in SEQ ID NO:2.
In still another aspect of this invention, there is provided a nucleic acid molecule encoding the mutated homoserine o-succinyltransferase (MetA).
The term “nucleic acid molecule” as used herein refers to a comprehensive DNA (gDNA and cDNA) and RNA molecule, and a nucleotide as a basic unit in the nucleic acid includes not only natural nucleotides but also analogues which a sugar or base are modified (Scheit, Nucleotide Analogs, John Wiley, New York (1980); Uhlman and Peyman, Chemical Reviews, 90:543-584 (1990)).
An illustrative example of the mutated nucleic acid molecule in the present invention includes the nucleotide sequence as set forth in SEQ ID NO:1.
In further still another aspect of this invention, there is provided a recombinant vector containing the nucleic acid molecule encoding the mutated homoserine o-succinyltransferase (MetA).
The vector system of this invention may be constructed by various methods known to those skilled in the art which are disclosed in Sambrook et al., Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press (2001), which is herein incorporated by reference.
Typically, the vector of this invention may be constructed as cloning or expression vector. The vector of the present invention may be constructed to utilize a prokaryotic or eukaryotic cell as a host. It is preferable to utilize a prokaryotic cell as a host in the senses that the nucleic acid molecule of the present invention is derived from the prokaryotic cell and the culture is convenient. The vector of this invention may be typically constructed as cloning or expression vector.
For example, the present vector which is expression vector and utilizes a prokaryotic cell as a host commonly includes a strong promoter (e.g., tac promoter, lac promoter, lacUV5 promoter, lpp promoter, pLλ promoter, pRλ promoter, rac5 promoter, amp promoter, recA promoter, SP6 promoter, trp promoter and T7 promoter, etc.) for transcription, a ribosome-binding site for translation, and transcription/translation termination sequence. The promoter and operator region of E. coli tryptophan biosynthesis pathway (Yanofsky, C., J. Bacteriol., 158:1018-1024 (1984)), and pLλ promoter (Herskowitz, I. and Hagen, D., Ann. Rev. Genet., 14:399-445 (1980)) may be used as a regulatory region in E. coli utilized as a host.
Meanwhile, the vector capable of being used in the present invention may be prepared by manipulating a plasmid (example: pSC101, ColE1, pBR322, pUC8/9, pHC79, pUC19, pET, etc.), a phage (example: λgt4.λB, λ-Charon, λΔz1, M13, etc.) or a virus (example: SV40, etc.) known to those ordinarily skilled in the art.
The vector of this invention may be fused with other sequence to purify MetA expressed from the vector in a feasible manner. For example, a fusion sequence includes glutathione-S-transferase (Pharmacia, USA), maltose-binding protein (NEB, USA), FLAG (IBI, USA) and 6× His (hexahistidine; Quiagen, USA), and most preferably 6× His. Because of the additive sequences for purification, the protein expressed in the host may be purified by a chromatography in a high-throughput and easy manner.
According to a preferable embodiment, the fusion protein expressed by the vector containing the fusion sequence is purified by an affinity chromatography. For example, in a glutathione-S-transferase-fused protein, the glutathione may be used as a substrate for purification, and in a 6× His-fused protein, a Ni-NTA His-binding resin (Novagen, USA) may be used for purification. Consequently, desirable MetAs may be obtained in a high-throughput and easy manner.
On the other hand, the expression vector of this invention includes an antibiotics-resistance gene known to those ordinarily skilled in the art as a selection marker, for example resistant genes against ampicillin, gentamycin, carbenicillin, chloramphenicol, streptomycin, kanamycin, geneticin, neomycin and tetracycline.
In another aspect of this invention, there is provided a host cell transformed with the mutated nucleic acid molecule.
The host cell capable of cloning and expressing the vector of the present invention in a stable and successive manner may utilize any one of host cells known to those ordinarily skilled in the art, for example including E. coli JM109, E. coli BL21(DE3), E. coli RR1, E. coli LE392, E. coli B, E. coli X 1776, E. coli W3110, the genus Bacillus strains such as Bacillus subtilis, Bacillus thuringiensis, and Enterococcus and strains such as Salmonella typhimurium, Serratia marcescens and various Pseudomonas species.
The procedure to deliver the present vector into a cell may be carried out according to various methods known to those ordinarily skilled in the art. For example, the transformation using a prokaryotic cell as a host may be performed according to a CaCl2 method (Cohen, S. N. et al., Proc. Natl. Acac. Sci. USA, 9: 2110-2114 (1973)), a Hanahan method (Cohen, S. N. et al., Proc. Natl. Acac. Sci. USA, 9:2110-2114 (1973); and Hanahan, D., J. Mol. Biol., 166: 557-580 (1983)) and an electroporation method (Dower, W. J. et al., Nucleic. Acids Res., 16: 6127-6145 (1988)).
The vector transferred to host cells may be expressed within the host cells, obtaining massive MetA. For example, gene expression in the expression vector containing lac promoter may be induced by treating IPTG in host cells.
As described above in detail, the present invention is a first report improving a growth rate of a microbe (e.g., E. coli) at high-temperatures only by stabilizing MetA. The stabilization of MetA enables to provide a new theoretical fundament to design a microbe platform, preferably a bacteria strain (e.g., E. coli) growing at higher-temperatures, and to carry out a bioprocess in an economical cost and time.
The features and advantages of this invention are summarized as follows:
(a) The present invention is a first report to modulate (i.e., enhance/decrease) thermostability and/or acid stability of a microbe by mutation of MetA.
(b) The mutated MetA of the present invention shows stability notably enhanced at high-temperatures and/or under acid conditions or decreased at mild temperature.
(c) The microbe, particular bacteria expressing the mutated MetA of the present invention represents a growth rate improved in a vigorous environment such as higher-temperatures and/or lower acid conditions.
The present invention will now be described in further detail by examples. It would be obvious to those skilled in the art that these examples are intended to be more concretely illustrative and the scope of the present invention as set forth in the appended claims is not limited to or by the examples.
EXAMPLES
Experimental Materials and Methods
Bacterial strains and plasmids. The strains and plasmids used in this study are listed in Table 1.







TABLE 1







Bacterial strains and plasmids









Strain




or Plasmid
Relevant descriptiona
Source or reference





E. Coli




W3110
Wild-type
Laboratory stock


DH5α
F-, supE44 hsdR17 recA1 gyrA96
(17)



endA1 thi-1 relA1 deoR λ-



JW3973
F-, Δ(araD-araB)567, ΔlacZ4787(::rrnB-3),
Keio collection (JP)



LAM-, rph-1, ΔmetA780::kan, Δ(rhaD-rhaB)568,




Δ(rhaD-rhaB)568, hsdR514



WE
JW3973 carrying non-mutated metAE.coli
This study



on the chromosome, prototroph



333
JW3973 carrying mutated metAE.coli-333
This study



on the chromosome, prototroph



T61
JW3973 carrying metAE.coli with
This study



S61T substitution on the chromosome,




prototroph



V213
JW3973 carrying metAE.coli with
This study



E213V substitution on the chromosome,




prototroph



T229
JW3973 carrying metAE.coli with
This study



I229T substitution on the chromosome,




prototroph



D267
JW3973 carrying metAE.coli with
This study



N267D substitution on the chromosome,




prototroph



K271
JW3973 carrying metAE.coli with
This study



N271K substitution on the chromosome,




prototroph



WG
JW3973 carrying metAGeo on
This study



the chromosome, prototroph



K96
JW3973 carrying metAE.coli with Q96K substitution
This study



on the chromosome, prototroph



V110
JW3973 carrying metAE.coli with L110V substitution




on the chromosome, prototroph



L124
JW3973 carrying metAE.coli with I124L substitution
This study



on the chromosome, prototroph



L160
JW3973 carrying metAE.coli with R160L substitution
This study



on the chromosome, prototroph



T195
JW3973 carrying metAE.coli with A195T substitution
This study



on the chromosome, prototroph



E200
JW3973 carrying metAE.coli with A200E substitution
This study



on the chromosome, prototroph



G218
JW3973 carrying metAE.coli with D218G substitution
This study



on the chromosome, prototroph



Y229
JW3973 carrying metAE.coli with I229Y substitution
This study



on the chromosome, prototroph



Y247
JW3973 carrying metAE.coli with F247Y substitution
This study



on the chromosome, prototroph



BL21(DE3)
F-ompT hsdSB(r-Bm-B) gal dcm(DE3)
Novagen, USA


Geobacillus
Wild-type
KCTC 3397


kaustophilus




Plasmids




pACYC177
Plasmid vector, Ampr Kanr
New England Biolabs, USA


pET22b
Expression vector, Ampr
Novagen, USA


pKD46
λ Red (gam bet exo) ara C rep101(Ts) Ampr
(4)


pPmetA
pACYC17 carrying metApE.coli, Ampr
This study


pMetA
pPmetA carrying metAE.coli, Ampr
This study


pMetA-333
pPmetA carrying thermostable metAE.coli, Ampr
This study


pGeo-MetA
pPmetA carrying metAGeo, Ampr
This study





aAmpr, ampicillin resistance; Kanr, kanamycin resistance; metApE.coli, promoter of E. coli metA gene; metAE.coli, E. coli metA gene; metAGeo, G. kaustophilus metA gene.






Growth Conditions.
The E. coli strains were grown in minimal M9 medium (17) supplemented with glucose (0.2%), LB (Difco, USA) or 2×YT (17). Antibiotics were used in the following concentrations: ampicillin—100 μg ml−1, kanamycin—25 μg ml−1. L-methionine was added to the medium to a final concentration of 50 μg ml−1. The strain Geobacillus kaustophilus KCTC 3397 was cultivated aerobically in nutrient broth (Difco, USA) at 50° C.
Preparation of Plasmid DNA.
Plasmid DNA was Extracted from the Cells using a Plasmid mini prep kit (SolGent Co, Ltd., Korea). All the restriction enzymes used in this study were purchased from New England BioLabs Inc., USA.
Cloning of E. coli metA.
The natural promoter of metA was amplified from the genomic DNA of E. coli strain W3110 using the primers metA1 (CGCCTACTCGAGATCGCAACGAGTTCCTCC) (SEQ ID NO:3) and metA2 (GCCTCAAAGCTTCATATGCTGATTACCTCACTACATACGC) (SEQ ID NO:4), and was cloned into XhoI and HindIII sites of the plasmid vector pACYC177 to yield the plasmid pPmetA. The structural metA gene amplified from the genomic DNA of E. coli W3110 using the primers metA3 (CGCCTCCATATGCCGATTCGTGTGCCG) (SEQ ID NO:5) and metA4 (CGCCTCAAGCTTGGTGCCTGAGGTAAGGTGCTG) (SEQ ID NO:6) was cloned into NdeI and HindIII sites of the plasmid pPmetA to obtain the plasmid pMetA.
Cloning of metA from the Thermophilic Strain G. Kaustophilus KCTC 3397.

    
    
        The metAGeo from the genomic DNA was amplified using the primers Geo1 (CGCCTCCATATGCCAATCAACATTCCAAAAG) (SEQ ID NO:10) and Geo2 (CAGGGCGATTGTCGAAACACG) (SEQ ID NO:11) and cloned into an NdeI restriction site of the plasmid pPmetA. The resulting plasmid pGeo-MetA was transferred into the strain E. coli JW3973 (ΔmetA). The transformed cells were incubated on minimal M9 plates supplemented with glucose and ampicillin.
    
    


Library Construction and Selection of Thermostable metA Mutants.
The metA together with its promoter region was isolated from the pMetA plasmid, gel-purified and used as a template for error-prone PCR. Random mutagenesis was performed with a Diversify PCR Random Mutagenesis Kit (Clontech Laboratories, Inc., USA) to obtain 3, 5 and 8 nucleotide substitutions per kb. The PCR conditions were as described in the manual using the primers metA5 (GTAGTGAGGTAATCAGCATATG) (SEQ ID NO:7) and metA4 (SEQ ID NO:6). The PCR products were purified using a QIAquick PCR Purification Kit (Qiagen, USA), amplified one more time using the same primers and TaKaRa Ex Taq polymerase, digested with the restriction enzymes NdeI and HindIII and cloned into the plasmid pPmetA. The resulting DNA mixture was transferred into freshly prepared E. coli JW3973(ΔmetA) cells by electroporation. The transformed cells were incubated at 37° C. on M9 plates supplemented with glucose and ampicillin. The clones were then cultivated on solid M9 glucose medium at 44° C. to select the growing ones. The fastest-growing mutant was identified during the cultivation in liquid M9 glucose medium at 44° C.
Incorporation of metA Mutants into the E. coli Chromosome.
The metA mutants were transferred into the E. coli JW3973 (ΔmetA) chromosome using the lambda Red recombination system (4). The structural genes flanked by 50 bp nucleotide sequences up- and down-stream were synthesized using the primers metA8 (ATCTGGATGTCTAAACGTATAAGCGTATGTAGTGAGG) (SEQ ID NO:8) and metA9 (ATCGCTTAACGATCGACTATCACAGAAGATTAATCC) (SEQ ID NO:9), Vent polymerase (New England BioLabs Inc., USA) and the corresponding plasmids as templates. G. kaustophilus metA was amplified from the genomic DNA as template using the primers Geo4 (ATCTGGATGTCTAAACGTATAAGCGTATGTAGTGAGGTAATCAGGTTATGCCAATCAACATTCC) (SEQ ID NO:12) and Geo5 (ATCGCTTAACGATCGACTATCACAGAAG ATTAATCCAGCGTTGGATTCATCAGGGCGATTGTCGAAACACG) (SEQ ID NO:13). Freshly-prepared competent cells of the strain E. coli JW3973 (ΔmetA) harboring the helper plasmid pKD46 were transformed with 150 μg of PCR products by electroporation as described (4).
The transformed cells were incubated on M9 methionine deficient medium plates supplemented with glucose at 37° C. The grown colonies were checked for loss of kanamycin resistance and cultivated on nonselective LB plates at 43° C. to eliminate the plasmid pKD46. The inserted metA mutants were amplified from the chromosome and sequenced.
Site-Directed Mutagenesis of metA.
To introduce multiple direct mutations into metA a Quick Change Multi Site-Directed Mutagenesis kit (Stratagene, USA) was employed. The primers used were metT (GCCTGCTTTCAAACACACACCTTTGCAGGTCG) (SEQ ID NO:14), metD (CTATTTCCCGCACGATGATCCGCAAAATACACC) (SEQ ID NO:16), metK (GATCCGCAAAAGACACCGCGAGCGAGC) (SEQ ID NO:17), metT2 (GCCAGTAAA GATAAGCGCACTGCC TTTGTGACG) (SEQ ID NO:15) and metV (CTGGAAATTCTGGCAGTGACGGAAGAAGGG) (SEQ ID NO:18).
The other site-directed metA mutants were obtained using a KOD-Plus-Mutagenesis Kit (Toyobo Co., Ltd) according to the manufacturer's protocol. Plasmid pMetA was used as a template, and the primers are shown in the table 2. The mutants Y229 were constructed by overlap extension PCR using a QuickChange II-E Site-Directed Mutagenesis Kit (Stratagene) and primers MetY-forward (GCCAGTAAAGATAAGCGCTACGCCTTTGTGACGGG) (SEQ ID NO:35) and MetY-reverse (SEQ ID NO:36) complemented of forward primer.







TABLE 2







Sequences of the primers used in


the construction of MetA mutants









Primer
Mutation
Primer sequence





K3-forward
Q96K
AAGGATCAGAACTTTGACGGTTTG




(SEQ ID NO: 19)


 


K3-reverse
Q96K
AATATCTTCAAAGTTACAGTAGAAG




(SEQ ID NO: 20)


 


V3-forward
L110V
GGTGGGCCTGGTGGAGTTTAATG




(SEQ ID NO: 21)


 


V3-reverse
L110V
GGCGCACCAGTTACAATCAAACC




(SEQ ID NO: 22)


 


L2-forward
I124L
CAGCTCAAACAGGTGCTGGAGTG




(SEQ ID NO: 23)


 


L2-reverse
I124L
CGGCCAGTAAGCGACATCATTAAAC




(SEQ ID NO: 24)


 


L1-forward
R160L
CTCTCACCGAAAAACTCTCTGGC




(SEQ ID NO: 25)


 


L1-reverse
R160L
TTTGCTTAGGAATGCCGTAGAGG




(SEQ ID NO: 26)


 


T4-forward
A195T
CTATACTGACTTTCCGGCAGCGTTG




(SEQ ID NO: 27)


 


T4-reverse
A195T
CGCGAATGCGGTGCCAGGAATGAATC




(SEQ ID NO: 28)


 


E1-forward
A200E
CAGAGTTGATTCGTGATTACACCG




(SEQ ID NO: 29)


 


E1-reverse
A200E
CCGGAAAGTCAGCATAGCGCGAATG




(SEQ ID NO: 30)


 


G1-forward
D218G
GGTGCATATCTGTTTGCCAGTAAAG




(SEQ ID NO: 31)


 


G1-reverse
D218G
CCCTTCTTCCGTCTCTGCCAGAATTTC




(SEQ ID NO: 32)


 


Y2-forward
F247Y
GAATATTTCCGCGATGTGGAAGCC




(SEQ ID NO: 33)


 


Y2-reverse
F247Y
CTGCGCCAGCGTTTGCGCATCATATTC




(SEQ ID NO: 34)





a - The mutation sites are in bold.






Cultivation of E. coli Strains in a Temperature Gradient Incubator.
Growth of E. coli strains in M9 glucose medium at different temperatures was studied using a temperature gradient incubator (TVS126MA, Adventec MSF Inc., USA). A single colony of each strain was cultivated in 5 ml M9 medium overnight at 30° C. The overnight cultures were diluted to OD600 of 0.05 in 300 ml fresh M9 medium, dispensed into 15 ml tubes and incubated at 30-47° C. for 12 h with shaking. Growth was measured by monitoring the optical density at 600 nm every 5 min.
Purification of Aggregated and Soluble Proteins.
The metA chromosomal mutants of E. coli were grown in 75 ml M9 glucose medium in the flasks at 30° C. to mid-exponential phase (approx. OD600 of 0.6). Twenty five ml of each culture were shifted to 45° C. for 40 min or treated with 30 mM acetic acid for 3 h at 30° C. The remaining 25 ml was used as a control. Aggregated and soluble protein fractions were purified as described previously (5, 19).
SDS-PAGE and Immunoblotting.
Gel electrophoresis was performed using 12% SDS-PAGE. After electrophoresis, the proteins were electroblotted on to nitrocellulose membranes (Bio-Rad, USA). MetA protein was detected using a rabbit anti-MetA serum raised against a synthetic oligopeptide consisting of 74-94 amino acids (2) of MetA (Peptron Inc., Korea) as primary antibody, and horseradish peroxidase-conjugated anti-rabbit IgG (Pierce, USA) as secondary antibody. The immunoblots were developed using a SuperSignal West Pico Chemiluminescent Substrate kit (Pierce, USA), scanned with Image Reader Fujufilm LAS-3000 and analyzed using LabWorks software.
Cloning, Expression and Protein Purification.
The wild-type and mutated metAs were cloned into NdeI/HindIII restriction sites of the plasmid pET22b in frame with a C-terminal 6×-histidine tag. The plasmid DNA was purified from ampicillin-resistant clones and sequenced to verify that the correct genes had been cloned. The resulting plasmids were transformed into competent E. coli BL21 (DE3) cells. A single colony of the strain E. coli BL21 (DE3) harboring the corresponding plasmid was cultivated overnight at 30° C. in 15 ml LB medium with ampicillin. Half a liter of 2×YT medium containing ampicillin was inoculated with an overnight culture, incubated at 30° C. to an OD600 of 0.6, induced with IPTG (1 mM final concentration) and then cooled to 22° C. After 4 hrs induction, the cells were harvested by centrifugation and the pellets were resuspended in ice-cold buffer (50 mM Tris-HCl, 300 mM NaCl, 10 mM MgCl2, 5 mM imidazole, pH 7.5) in the ratio 3 ml buffer/1 g of wet cells. The cells were lysed by incubation with 0.5 mg/ml lysozyme, 1 mM PMSF and DNase I for 30 min with stirring at 4° C., followed by sonication for 10×20 s with 20 s intervals using a Branson Sonifier (model 450). The cell debris was removed by centrifugation at 12000×g for 40 min. The proteins were purified from the supernatants using Ni-NTA agarose (Qiagen, USA). Two milliliters of agarose slurry was incubated with 6 ml supernatant overnight at 4° C. with rocking. The unbound proteins were removed by gravity filtration and the agarose was washed with 4 ml buffer (50 mM Tris-HCl, 300 mM NaCl, 100 mM imidazole, pH 7.5). The proteins were released from the agarose by elution with 6 ml buffer (50 mM Tris-HCl, 300 mM NaCl, 250 mM imidazole, pH 7.5) and the eluate was dialyzed against two changes of dialysis buffer (21, 50 mM K-phosphate buffer, 150 mM NaCl, pH 7.6) then against 50 mM K-phosphate buffer (pH 7.6) containing 150 mM NaCl and 50% glycerol for 6 h. The presence of pure protein in all the samples was confirmed by SDS-PAGE.
Measurement of Enzyme Activity.
Reaction rates were determined by monitoring the decrease in absorbance at 232 nm caused by hydrolysis of the thioester bond of succinyl-CoA (3) in a ND1000 UV/Vis Spectrophotometer (Nanodrop Technologies, USA). The assay solutions containing 50 mM K-phosphate buffer (pH 7.5), 200 μM succinyl-CoA, 5 mM L-homoserine, 1 μM of protein in a final volume of 20 μl were incubated for 30 min at 40, 45, 50, 55 and 58° C., or at 25° C. in the presence of acetic acid. L-homoserine was omitted from the control tubes. The reaction was started by adding the enzyme. The consumption of succinyl-CoA in the reaction was calculated as the difference between values obtained in the presence and absence of L-homoserine. Three independent measurements were performed for each point.
Differential Scanning Calorimetry.
The thermal stabilities of the MetAs were measured calorimetrically over the temperature interval 15-90° C. at a scan rate of 90° C./h. A VP-DSC calorimeter (MicroCal Inc., USA) was employed using 10 μM protein in 50 mM K-phosphate buffer (pH 7.5). Three scans were obtained from independent protein preparations.
Results
L-Methionine Stimulates E. coli Growth.
To confirm the stimulatory effect of methionine on E. coli growth at elevated temperatures, strain W3110 was cultivated in M9 glucose medium in the temperature range 30-49° C. with or without L-methionine (50 μg ml−1) in the temperature gradient incubator. Methionine accelerated E. coli growth at temperatures over 30° C. (FIG. 2). E. coli strain W3110 grew very slowly without methionine at 45° C. and completely ceased to grow at 46° C. or over (FIG. 2), confirming previous findings (16). Supplementation of the culture medium with methionine allowed growth at 45° C. and 46° C., but no growth was detected over 47° C. (FIG. 2). Expectedly, the methionine effect was more prominent at higher growth temperatures: the specific growth rate was increased two-fold at 44° C. and 10-fold at 45° C. (FIG. 2).
MetA from the Thermophilic Strain Geobacillus kaustophilus Accelerates E. coli Growth at Elevated Temperature.
We checked whether MetA from the thermophilic strain would simply improve E. coli growth at higher temperature. As a thermostable gene we used metA from the strain G. kaustophilus KCTC 3397. This is an aerobic gram-positive endospore-forming bacterium which can grow at 37-75° C. with an optimum 55-65° C. (21). The metAGeo was cloned under the E. coli metAp on the pPmetA plasmid. The resulting plasmid, pGeo-metA, compensated the growth of the metA-null mutant on M9 medium. However, the specific growth rate of E. coli strain JW3973 (pGeo-MetA) was 20% less than that of E. coli JW3973 (pMetA) at 37° C. We integrated metAGeo into the E. coli chromosome to yield the strain WG. The metAGeo stimulated E. coli growth on solid M9 medium at 44° C. (FIG. 4).
Directed Evolution of MetA Results in Thermotolerant E. coli Strains.
As methionine and thermostable MetAGeo relieve the impairment of E. coli growth at higher temperatures, we tried to obtain a more thermostable MetAE coli by monitoring the enhancement of growth of E. coli cells carrying mutant metAE coli at higher temperatures. We supposed that thermostable MetAE coli might accelerate the E. coli growth not only at elevated but at mild temperatures in contrast to MetAGeo lowering the specific growth rate of E. coli at 37° C. Random mutagenesis of metAE.coli was performed with error-prone PCR as described in Materials and Methods. We constructed a library of mutated metAs into the pPmetA plasmid that completely restored growth of the metA null mutant E. coli JW3973 on M9 glucose medium. The library, consisting of 490 clones, was incubated on M9 minimal plates at 44° C. to select the growing clones. Twenty-three selected clones were then cultivated in liquid M9 glucose medium at 44° C. to identify the most rapidly-growing one. One prospective clone, which grew faster than the others at the elevated temperature, was designated strain 333 (FIG. 3). Sequencing showed the presence of five amino acid substitutions—S61T, E213V, I229T, N267D and N271K—in MetAE.coli-333. To determine which amino acid residue is responsible for the improved thermostability, single amino acid substitutions corresponding to those found in MetAE.coli-333 were introduced into the wild-type enzyme by site-directed mutagenesis. We integrated all the mutated metAE. coli genes into the E. coli JW3973(ΔmetA) chromosome to yield strains 333, T61, V213, T229, D267 and K271. To study the thermostabilities of these metA mutants, we cultivated them on solid M9 glucose plates at 44° C. In FIG. 4, the left panel shows that the control strain WE, which harbors non-mutated metA on the chromosome, weakly grew at 44° C., in contrast to the mutants 333 and WG. Among the single mutants only two strains, T229 and D267, grew better than the control strain at the elevated temperature (FIG. 4). All the strains grew normally at 37° C. (FIG. 4, right panel) except the WG, which grew more slowly than the others.
Thermotolerant E. coli metA Mutants Grow Faster at Elevated Temperatures.
To study the growth of thermostable mutants at different temperatures we cultivated them in a temperature gradient incubator. The results presented in FIG. 5A show that the strains 333 grew 5-12% faster than the non-mutated strain WE over the temperature range 30-42° C. However, the difference in specific growth rate between the thermostable strain 333 and the control strain WE increased to 30% at 43° C. and to 64% at 44° C. (FIG. 5A). The single-mutated metA strains T229 and D267 grew 48 and 31% faster at 44° C., and 18 and 10% faster at 43° C., respectively. In the temperature range 39-41° C. the difference in specific growth rate between single-site mutants and control strain decreased to 4-12% and fell to zero over the range 30-38° C. (FIG. 5A). No growth was detected at 45° C. or over for any strains tested.
The foreign metAGeo lowered host strain growth in liquid M9 medium at mild temperatures, 30-42° C., by approximately 10% (FIG. 5A). At 43° C. the specific growth rate of WG was the same as for the control strain WE, and at 44° C. it grew 20% faster than the control strain (FIG. 5A).
We also cultivated the other single-site mutants at different temperatures. Two of them, V213 and K271, had lower specific growth rates than wild type at 44° C. (64% and 22% of control strain) (data not shown), but grew 15-20% faster than the non-mutated strain at 36-41° C. (data not shown). The single-site mutant T61 grew as the wild-type at elevated temperatures, but its specific growth rate at 36-41° C. was similar to the mutants V213 and K271 (data not shown). Apparently, the multiple metA mutant 333 combined the abilities of the thermosensitive mutants to accelerate the growth at mild temperatures and of the thermostable mutants to grow faster at higher temperatures.
In order to ascertain the influence of methionine on growth of the thermostable E. coli 333 strain, we cultivated these strains with or without methionine at different temperatures using the non-mutated WE strain as a control (FIG. 5B). Despite the presence of the thermostable MetAE.coli-333, this mutant could not attain the specific growth rate obtained in the presence of methionine. However, although the non-mutated strain grew 1.6 and 2 times slower in methionine-deficient medium at 43 and 44° C., respectively, the thermostable variant decreased this difference to 1.4-fold at both temperatures. This is apparently because another thermolabile protein is present in the methionine biosynthesis pathway. Previous investigations have shown that MetE, which catalyzes the final step in methionine biosynthesis, is also sensitive to elevated temperature (9).
Thermostable metA Mutants are Tolerant to Acetic Acid.
Since it is known that weak organic acids can destabilize MetAS.enterica (11), we supposed that thermostable metA mutants might also be resistant to acetic acid. The strains 333, D267, T229 and WE were cultivated in M9 glucose medium supplemented with 30 mM acetic acid at 30° C. in the BioScreen C incubator (Labsystems, Finland). As shown in FIG. 6, the wild-type strain reached stationary phase 29 h after the beginning of cultivation. In contrast, the thermostable E. coli strains 333 and T229 grew intensively for a further 11 h and achieved a 1.4 times greater cell density than the control strain. Another mutant, D267, grew slower than other thermostable strains, and its cell density was only 16% more than control.
Thermostable MetA Enzymes are Less Susceptible to Aggregation In Vivo Under Heat or Acetic Acid Stress Conditions.
To determine the effect of elevated temperature or acetic acid treatment on thermostable MetAE coli proteins in vivo, the mutant and control strains were heated from 30° C. to 45° C. for 40 min or incubated with 30 mM acetic acid for 3 h at 30° C., and the relative amount of MetAE coli was evaluated by immunoblotting. Biran and coworkers (2) showed that E. coli cells contain no soluble MetAE coli at temperatures above 44° C. Surprisingly, we found wild-type MetAE coli protein in the soluble fraction after the heat stress; its level was about 35% of that in an unstressed culture (FIG. 7A). Perhaps part of the unfolded MetAE coli protein partitioned into the soluble fraction. The relative amounts of the soluble thermostable MetAE coli-333 and MetAE coli-D267 proteins were 58% and 67% (FIG. 7A). In contrast, soluble MetAE coli-T229 protein at 45° C. was only 29% of that in the unheated control (FIG. 7A). The relative content of insoluble non-mutated MetAE coli protein increased 44 times after heating (FIG. 7B). The insoluble fractions of all the mutants tested were only 13-19 times more abundant after high-temperature treatment than in unheated cultures (FIG. 7B). The data obtained in this experiment confirmed that the MetAE coli-333 and MetAE coli-D267 mutants are more resistant in forming aggregates after a heat challenge. For MetAE coli-T229, we assume that resistance to aggregation is greater because of a more stable protein secondary structure.
Acetic acid challenge of exponentially growing cultures produced a relative level of soluble MetAE coli 1.5-3 times higher in all the mutants tested than in the wild-type strain (FIG. 7C). The insoluble MetAE coli content was approximately 15 times greater in the wild-type strain, 8-9 times in the D267 and 333 strains, and 2.6 times in the T229 strain (FIG. 7D). These results confirm that the mutated MetAE coli proteins are more resistant in forming aggregates than the wild-type protein when challenged with acetic acid.
Thermostable MetA Enzymes have Increased Transition Midpoints.
Differential scanning calorimetry (DSC) was used to compare the transition midpoint (Tm) of mutated and wild-type MetA proteins. Tm is an indicator of thermostability, and proteins with higher Tm are less susceptible to unfolding and denaturation. Non-mutated and mutated MetAs containing a C-terminal 6×-histidine tag were purified as described in Materials and Methods. As shown in FIG. 8, the wild-type 6-his-tagged MetAE.coli had a Tm at 47.075±0082° C., while MetAE coli-333 had a higher Tm (48.76±0.026° C.) (FIG. 8). The highest Tm (67.68±0.055° C.) was found for MetAGeo (FIG. 8). Although the single-site mutated proteins MetAE.coli-D267 and MetAE.coli-T229 stimulated E. coli growth at elevated temperatures, they had Tm values very close to that of wild-type MetAE.coli (47.36±0.014° C. and 46.99±0.063° C., respectively). Maybe these mutant enzymes are not more stable than wild type but more resistant in forming aggregates after heat challenge. This possibility will be investigated in a near future.
Mutated MetA Enzymes have Enhanced Activities at Elevated Temperatures and in the Presence of Acetic Acid.
The activities of the 6×-histidine tagged MetA enzymes purified as described in Materials and Methods were measured at temperatures between 40 and 58° C. by monitoring the change in absorbance at 232 nm due to hydrolysis of the succinyl-CoA thioester bond. The data obtained for the thermostable MetA proteins are presented in the top panel of FIG. 9. MetAE.coli-333 was approximately 2.5 times more active than the non-mutated protein at 40-55° C. but completely lost its activity at 58° C. In contrast to MetAE coli-333, MetAGeo, MetAE.coli-D267 and MetAE.coli-T229 displayed the lower activities at 40-45° C. but at 50° C. and higher the temperature profiles of all thermostable MetAs were similar. Surprisingly, the catalytic activity of MetAGeo, gradually decreased at elevating temperatures, perhaps because of the thermal instability of succinyl-CoA.
We tested the catalytic activity of the mutated MetAs in the presence of acetic acid at 25° C. Acetic acid in a final concentration of 10 mM lowered the pH of reaction buffer from 7.5 to 7.0; 20 mM-to pH 6.6; 30 mM-to pH 6.2; 40 mM-to pH 5.8; 50 mM-to pH 5.4. FIG. 9B shows that the activity of wild-type MetAE.coli decreased sharply when the acetic acid concentration raised over 30 mM (pH 6.2), and was not detectable at 50 mM (pH 5.4). Our findings confirmed the earlier investigations that the wild-type MetAE.coli activity significantly dropped over pH range of 6.0-6.5 (3). Acetic acid also inhibited the activity of MetAE.coli-333 starting from 30 mM, but somewhat less severely than the wild-type enzyme. Moreover, MetAE.coli-333 remained active in 50 mM acetic acid (FIG. 9B). Two other enzymes, MetAE.coli-D267 and MetAE.coli-T229, had unchanged catalytic activities at all the acetic acid concentrations tested (FIG. 9B). Interestingly, MetAGeo was almost inactive at 25° C. (FIG. 9B).
Consequently, we compared the catalytic activities of the wild-type MetAE.coli, and thermostable MetAE coli mutant enzymes at 25 and 40° C. (FIGS. 9A and B). The wild-type enzyme activity was 80% lower at 40° C. In contrast, MetAE.coli-333 was 50% less active at 40° C., while MetAGeo was 3.5 times more active at the elevated temperature (FIGS. 9A and B). These results of wild-type enzymes are consistent with previous findings; the activity of MetAE.coli decreased by 70% at 37° C. and 42° C. (14).
Single-Mutated MetAs′ Stimulates E. Coli Growth at Elevated Temperature.
In order to extend the mutation study of the MetAE.coli, we performed the multiple alignment of MetA amino acid sequences from E. coli and thermophilic bacteria (FIG. 10). As a result, we found eight amino acid residues presented in all the thermophilic MetAs′ but not in MetAE.coli (FIG. 10). To determine which amino acid residue might increase the MetAE.coli thermostability, single amino acid substitutions—Q96K, L110V, I124L, R160L, A195T, A200E, D218G and F247Y—were introduced into wild-type enzyme by site-directed mutagenesis. We integrated all of the mutated metAE.coli genes into E. coli JW3973 (ΔmetA) chromosome to yield strains K96, V110, L124, L160, T195, E200, G218 and Y247. To study the thermostability of these single-site metAE.coli mutants, we cultivated them in liquid M9 glucose medium at 44° C. The results presented in Table 3 show that five mutants K96, V110, L124, E200, and Y247 grew faster at elevated temperature in contrast to control strain WE. The cultivation of five thermostable metA mutants at mild temperatures 32 and 37° C. did not reveal any differences between them and nonmutated WE strain (Table 3). What is surprising is that other three single-site metA mutations did not maintain the E. coli growth at elevated temperature but significantly decreased the specific grow rate at 37° C. at 50%-G218, at 32%-L160, at 17%-T195 (Table 3). All the thermosensitive mutants also grew slower at 32° C. than the control strain (Table 3).
Earlier, we obtained the thermostable T229 mutant harboring 1229T substitution. Using the program, we determined that the replacement of isoleucine with tyrosine might additionally increase the MetAE.coli protein stability. The single-site mutant Y229 also revealed an accelerated growth at 44° C. (Table 3) but not higher than another mutant T229 (data not shown).







TABLE 3







Effect of single amino acid substitutions in metA gene on


the E. coli growth at different temperatures.








Name of
Specific growth rate μ, h−1a











mutant
Mutation
at 32° C.
at 37° C.
at 44° C.





WE
Wild-type
0.43 ± 0.007
0.59 ± 0.01
No growth


K96
Q96K
0.48 ± 0.007▴
0.58 ± 0.007
0.52 ± 0.007▴


V110
L110V
ND
0.55 ± 0.008
0.19 ± 0.07▴


L124
I124L
0.46 ± 0.007
 0.6 ± 0.06
0.51 ± 0.02▴


L160
R160L
0.37 ± 0.014▾
 0.4 ± 0.03▾
No growth


T195
A195T
0.37 ± 0.007▾
0.49 ± 0.007▾
No growth


E200
A200E
ND
0.56 ± 0.014
0.37 ± 0.09▴


G218
D218G
0.36 ± 0.004▾
0.29 ± 0.03▾
No growth


Y229
I229Y
0.45 ± 0.014
0.61 ± 0.024
0.31 ± 0.1▴


Y247
F247Y
ND
 0.6 ± 0.007
 0.1 ± 0.03▴





The growth experiments were performed by flask cultivation in minimal M9 medium. A single colony of each strain was cultivated in 5 ml M9 medium overnight at 30° C. The overnight cultures were diluted to OD600 of 0.1 in 25 ml fresh M9 medium and incubated at 32, 37 or 44° C. with shaking. Growth was measured by monitoring the optical density at 600 nm every 1 h.


aSpecific growth rate was calculated as In (X/X0) where X0 and X are OD600 values in zero time point and 1 h afterward for an exponentially growing culture.


Symbols:


▾decrease of specific growth rate is ≧10% of control strain;


▴increase of specific growth rate is ≧10% of control strains;


ND—not determined.






Discussion

The unusual instability of MetA, the first enzyme in the methionine biosynthesis pathway, is the main factor limiting E. coli growth at elevated temperatures (2, 5, 13, 14, 15). MetAE.coli activity is reduced at temperatures higher than 33° C. due to the formation of aggregates (2). As addition of methionine or replacing with thermostable MetA relieved the growth inhibition at higher temperatures, directed evolution of the MetAE coli should widen the temperature range over which E. coli strains can grow. Using directed evolution, we obtained the thermotolerant enzyme MetAE.coli-333 with five the amino acid substitutions (S61T, E213V, I229T, N267D and N271K), which accelerates the growth of the host strain not only at higher temperatures but also at normal growth temperature 37° C. The higher thermostability of MetAE.coli-333 was confirmed in vivo by the differential scanning calorimetry data, and higher activity was demonstrated at elevated temperatures. MetAE.coli-333 was also classified as stable using ProtParam software (http://ca.expasy.org/): it has an instability index of 39.79, in contrast to the wild-type MetAE coli, which has an instability index of 42.26. The instability index provides an estimate of the protein stability. A protein whose instability index is smaller than 40 is predicted as stable, a value above 40 predicts that the protein may be unstable (6).
Accelerated growth of the single-site metAE.coli mutants at 44° C. allowed the identification of critical amino acid residues involved in the thermal instability of MetAE.coli. Substitution of asparagine-267 with aspartic acid was expected to increase thermostability because the MetA proteins known from thermophilic strains carry a positively charged amino acid in this position (FIG. 1). In general, this finding confirms the earlier observation that proteins from thermophiles contain more charged amino acid residues than those from mesophiles (18). The substitution of isoleucine-229 with threonine is an ‘opposite’ case: theoretically, it would not be expected to increase the thermostability of MetA because proteins from thermophilic strains usually contain lower levels of polar amino acids (18). Secondary structure prediction for MetAE.coli (see World Wide Web (www) igb.uci.edu) showed that isoleucine-229 belongs to one of the beta strands. Several beta strands connected laterally by three or more hydrogen bonds generally form a twisted, pleated sheet (20). Association among beta sheets has been implicated in the formation of protein aggregates and fibrils observed in many human diseases, notably the amyloidoses (10). We assume that the substitution of isoleucine-229 with threonine lowers the beta strand length (see World Wide Web (www) igb.uci.edu) and decreases the capacity of MetAE.coli to aggregate under stress conditions. These mutant enzymes may improve the growth of E. coli at higher temperatures not because they became more thermostable but because they became more resistant in forming aggregates after heat challenge.
Biran and coworkers (2) attempted to stabilize MetAE.coli. They showed that the amino-terminal part of the protein (first 23 amino acids) was responsible for its instability, and assumed that this sequence constituted a proteolytic site, or a binding site for proteins that might convert MetAE coli into a proteolytic substrate (2). On the basis of this investigation, we supposed that thermostable MetAE coli might carry mutations in the N-terminal region. However, the thermostable MetAE.coli-333 mutant harbored no amino acid substitutions in that region.
Quite notably, thermostable E. coli MetAs were more resistant to acetic acid in vivo than the wild-type protein. In previous investigations it has been shown that methionine relieves the inhibition of E. coli growth by acetic acid (7, 12). Extended exponential growth of the metAE. coli mutants in the presence of acetic acid might serve as additional evidence of their increased acid tolerance because mid-exponential phase cultures were found to be more acid-sensitive than stationary phase cultures (1). Price-Carter and coworkers found that MetA from Salmonella enterica was as unstable at elevated temperature as in the presence of weak organic acids including acetate, benzoate, and propionate (11). Earlier, Roe and coworkers (12) concluded that inhibition of E. coli growth by acetate treatment was due to accumulation of homocysteine, the substrate of MetE. We assume that instability in both these enzymes may affect E. coli growth under stress conditions of heat and acetic acid.
In this study, we showed that methionine stimulates E. coli growth not only at elevated temperatures (42-46° C.) but also under normal growth temperature (37° C.). The thermotolerant MetAE.coli-333 significantly increased growth rate of host strain at 44° C. but did not rescue it at 45° C. The same effect was found in the strain WG, which harbors a metA from the thermophilic bacterium G. kaustophilus. Supplementation with methionine produces additional E. coli growth at 45° and 46° C., indicating that there would be at least one more thermosensitive enzyme in the methionine biosynthesis pathway. We suppose that MetE, which catalyzes the final step in methionine biosynthesis, is a candidate because MetE has been shown to be sensitive to high-temperature (9) and oxidative stress (8).
This paper describes the first experimental demonstration that E. coli growth is accelerated under normal and stress conditions by increasing the stability of a single cytosolic enzyme, MetA. This study paves the way to obtaining a new platform E. coli strains growing at higher speed at normal growth temperature, thus potentially improving the productivity of microbial factory. More directly, being able to grow E. coli cells at higher temperatures means a reduced cooling, which is a considerable cost factor in bioprocesses.
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Having described a preferred embodiment of the present invention, it is to be understood that variants and modifications thereof falling within the spirit of the invention may become apparent to those skilled in this art, and the scope of this invention is to be determined by appended claims and their equivalents.

## Claims

1. A method for increasing or decreasing the thermostability or acid tolerance of a microbe, comprising the steps of:
mutating a nucleotide sequence which encodes Homoserine o-succinyltransferase (Met A) consisting of the amino acid sequence of SEQ ID NO:41 to obtain a nucleic acid molecule encoding a mutant MetA;
transforming a microbial host cell with the nucleic acid molecule encoding the mutant MetA; and
culturing the microbial host cell transformed with the nucleic acid molecule encoding the mutant MetA to express the mutant MetA, thereby increasing or decreasing the thermostability or acid tolerance of the transformed microbial host cell, wherein the mutant MetA comprises the substitution mutation of: (a) Thr for Ser at position 61 of SEQ ID NO:41; (b) Val for Glu at position 213 of SEQ ID NO:41; (c) Thr for Ile at position 229 of SEQ ID NO:41; (d) Asp for Asn at position 267 of SEQ ID NO:41; (e) Lys for Asn at position 271 of SEQ ID NO:41; (g) Val for Leu at position 110 of SEQ ID NO:41; (h) Leu for Ile at position 124 of SEQ ID NO:41; (i) Leu for Arg at position 160 of SEQ ID NO:41; (j) Thr for Ala at position 195 of SEQ ID NO:41; (k) Glu for Ala at position 200 of SEQ ID NO:41; (l) Gly for Asp at position 218 of SEQ ID NO:41; (m) Tyr for Ile at position 229 of SEQ ID NO:41; or (n) Tyr for Phe at position 247 of SEQ ID NO:41.

2. The method of claim 1, wherein the mutant MetA induces the increase of the thermostability or acid tolerance of the microbe and comprises the substitution of: (a) Thr for Ser at position 61 of SEQ ID NO:41; (b) Val for Glu at position 213 of SEQ ID NO:41; (c) Thr for Ile at position 229 of SEQ ID NO:41; (d) Asp for Asn at position 267 of SEQ ID NO:41; (e) Lys for Asn at position 271 of SEQ ID NO:41; (g) Val for Leu at position 110 of SEQ ID NO:41; (h) Leu for Ile at position 124 of SEQ ID NO:41; (k) Glu for Ala at position 200 of SEQ ID NO:41; (m) Tyr for Ile at position 229 of SEQ ID NO:41; or (n) Tyr for Phe at position 247 of SEQ ID NO:41.

3. The method of claim 1, wherein the mutant MetA induces the decrease of the thermostability or acid tolerance of the microbe and comprises the substitution of: (i) Leu for Arg at position 160 of SEQ ID NO:41; (j) Thr for Ala at position 195 of SEQ ID NO:41; or (l) Gly for Asp at position 218 of SEQ ID NO:41.

4. A method for increasing or decreasing the thermostability or acid tolerance of homoserine o-succinyltransferase (MetA), comprising conferring a substitution mutation to MetA consisting of the amino acid sequence of SEQ ID NO:41 to prepare a mutant MetA, wherein the mutant MetA comprises the substitution mutation of: (a) Thr for Ser at position 61 of SEQ ID NO:41; (b) Val for Glu at position 213 of SEQ ID NO:41; (c) Thr for Ile at position 229 of SEQ ID NO:41; (d) Asp for Asn at position 267 of SEQ ID NO:41; (e) Lys for Asn at position 271 of SEQ ID NO:41; (g) Val for Leu at position 110 of SEQ ID NO:41; (h) Leu for Ile at position 124 of SEQ ID NO:41; (i) Leu for Arg at position 160 of SEQ ID NO:41; (j) Thr for Ala at position 195 of SEQ ID NO:41; (k) Glu for Ala at position 200 of SEQ ID NO:41; (l) Gly for Asp at position 218 of SEQ ID NO:41; (m) Tyr for Ile at position 229 of SEQ ID NO:41; or (n) Tyr for Phe at position 247 of SEQ ID NO:41.

5. The method of claim 4, wherein the substitution mutation induces the increase of the thermostability or acid tolerance of MetA and the mutant MetA comprises the substitution of: (a) Thr for Ser at position 61 of SEQ ID NO:41; (b) Val for Glu at position 213 of SEQ ID NO:41; (c) Thr for Ile at position 229 of SEQ ID NO:41; (d) Asp for Asn at position 267 of SEQ ID NO:41; (e) Lys for Asn at position 271 of SEQ ID NO:41; (g) Val for Leu at position 110 of SEQ ID NO:41; (h) Leu for Ile at position 124 of SEQ ID NO:41; (k) Glu for Ala at position 200 of SEQ ID NO:41; (m) Tyr for Ile at position 229 of SEQ ID NO:41; or (n) Tyr for Phe at position 247 of SEQ ID NO:41.

6. The method of claim 4, wherein the substitution mutation induces the decrease of the thermostability or acid tolerance of MetA and the mutant MetA comprises the substitution of: (i) Leu for Arg at position 160 of SEQ ID NO:41; (j) Thr for Ala at position 195 of SEQ ID NO:41; or (l) Gly for Asp at position 218 of SEQ ID NO:41.

7. The method of claim 1, wherein the mutant MetA comprises the substitution of: (c) Thr for Be at position 229 of SEQ ID NO:41; (d) Asp for Asn at position 267 of SEQ ID NO:41; (h) Leu for Ile at position 124 of SEQ ID NO:41; (i) Leu for Arg at position 160 of SEQ ID NO:41; or (m) Tyr for Ile at position 229 of SEQ ID NO:41.

8. The method of claim 1, wherein the microbe is a mesophilic bacterium.

9. The method of claim 8, wherein the mesophilic bacterium is a member of a genus selected from the group consisting of Escherichia, Pseudomonas, Xanthomonas, Serratia, Lactobacillus, Bacillus, Citrobacter, Salmonella and Klebsiella.