Patent Grant
9822387
This application is the National Phase of PCT/JP2012/069247, filed Jul. 27, 2012, which claims priority to Japanese Application No. 2011-167808, filed Jul. 29, 2011, the disclosures of which are hereby incorporated by reference in their entirety.
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jul. 30, 2014, is named 096949-0115_SL.txt and is 135,247 bytes in size.
The present invention relates to an acetyl-CoA producing microorganism and a method of producing a substance using the acetyl-CoA producing microorganism.
Acetyl-CoA is one of significantly important intermediates in metabolic pathways of microorganisms. Various metabolites are produced via acetyl-CoA. Well-known examples of such substances produced via acetyl-CoA include amino acids such as L-glutamic acid, L-glutamine, L-proline, L-arginine, L-leucine, and L-isoleucine; organic acids such as acetic acid, propionic acid, butyric acid, caproic acid, citric acid, 3-hydroxybutyric acid, 3-hydroxyisobutyric acid, 3-aminoisobutyric acid, 2-hydroxyisobutyric acid, methacrylic acid, and poly-3-hydroxybutyric acid; alcohols such as isopropyl alcohol, ethanol, and butanol; acetone; and polyglutamic acids.
In most microorganisms, acetyl-CoA is produced using a sugar such as glucose as a carbon source. The sugar is first converted into pyruvate via a metabolic pathway called the glycolytic pathway, such as the Embden-Meyerhof pathway, Entner-Doudoroff pathway, or the pentose phosphate pathway. Subsequently, the pyruvate is converted into acetyl-CoA by actions of decarboxylase, pyruvate formate-lyase, and the like. In this process, carbon dioxide and formate are generated as byproducts, and some of the carbons derived from the sugar will lost. Therefore, several studies have been carried out with the aim of achieving re-fixation of carbon dioxide in order to increase the yield of acetyl-CoA.
In microorganisms, there are several known pathways for fixing carbon dioxide as a carbon source (Appl. Environ. Microbiol. 77(6), 1925-1936, 2011). Specific examples of the pathways include the Calvin-Benson cycle, the reductive TCA cycle, the Wood-Ljungdahl pathway, the 3-hydroxypropionate cycle, and the 4-hydroxybutyrate cycle. The Calvin-Benson cycle is a CO2 fixation pathway existing in plants and photosynthetic bacteria, and containing about 12 kinds of enzymes. In the Calvin-Benson cycle, CO2 is fixed by ribulose-1,5-bisphosphate carboxylase (RubisCO) and, ultimately, glyceraldehyde 3-phosphate is produced. The reductive TCA cycle is found in microaerophilic bacteria and anaerobic bacteria including green sulfur bacteria, and contains 11 kinds of enzymes. This cycle is characterized by CO2 fixation enzymes (i.e., acetyl-CoA carboxylase, 2-oxoglutarate synthase) that requires ferredoxin as a coenzyme. In the reductive TCA cycle, pyruvate is produced from CO2 by the reverse reaction of the usual TCA cycle. The Wood-Ljungdahl pathway is found in anaerobic microorganisms such as acetic acid-producing bacteria, and contains 9 kinds of enzymes. In the Wood-Ljungdahl pathway, CO2 and formate on a coenzyme are reduced by formate dehydrogenase, CO dehydrogenase, etc., and, ultimately converted into acetyl-CoA. The 3-hydroxypropionate cycle is found in Chloroflexus bacteria and the like, and contains 13 kinds of enzymes. In the 3-hydroxypropionate cycle, CO2 is fixed by the action of acetyl-CoA (propionyl-CoA) carboxylase and acetyl-CoA is produced via malonyl-CoA and the like. The 4-hydroxybutyrate cycle exists in archaeabacteria and the like. In the 4-hydroxybutyrate cycle, CO2 is fixed by the actions of pyruvate synthase, acetyl-CoA (propionyl-CoA) carboxylase, and phosphoenolpyruvate carboxylase, whereby acetyl-CoA is produced via 4-hydroxybutyryl CoA and the like.
In order to produce a useful substance, several approaches have been reported as ideas to introduce a carbon dioxide fixation pathway to a useful-compound-producing microorganism. For example, International Publication (WO) 2009/094485 and WO 2010/071697 disclose approaches to producing acetyl-CoA from carbon dioxide, by using a microorganism to which a pathway similar to the Wood-Ljungdahl pathway of acetic acid bacteria was introduced. As an example of CO2 fixation for producing a useful compound, WO 2009/046929 discloses an approach to producing lactic acid from carbon dioxide by using a microorganism to which hydrogenase and tetrahydrofolate lyase were introduced. WO 2011/099006 proposes a cycle in which CO2 is fixed via a carbon dioxide fixation reaction onto acetyl-CoA or a malonyl-CoA reduction reaction. German Patent No. 102007059248 proposes production of acetyl-CoA by a pathway similar to the 4-hydroxybutyrate cycle.
However, known carbon dioxide fixation cycles are not necessarily efficient from the viewpoints of CO2 fixation and production of useful chemical products derived from acetyl-CoA. For example, the Calvin-Benson cycle is most famous as a carbon dioxide fixation cycle found in nature, but RubisCO involved in carbon dioxide fixation has a low reaction rate and causes side reactions such as oxidative degradation. Therefore, RubisCO is inefficient as an enzyme (Journal of Bioscience and Bioengineering 94(6) 497-505, 2002). In the Wood-Ljungdahl pathway and the pathways described in WO 2009/094485, WO 2010/071697, WO 2009/046929 and the like, a pathway for reducing CO2 into CO or formate is included. However, the reduction reaction hardly occurs under ordinal conditions, and the enzyme catalyzing this kind of strong reduction reaction often only acts under a reductive environment. Therefore, it is difficult to introduce this kind of pathway into microorganisms other than strictly anaerobic microorganisms. In the reductive TCA cycle, a reduction reaction by pyruvate synthase or 2-oxoglutarate synthase requires a strong reduction power from ferredoxin as an electron acceptor, and it is difficult to carry out the reaction. The 4-hydroxybutyrate cycle, 3-hydroxypropionate cycle, and the pathways described in WO 2011/099006, WO 2009/046929, and the like utilize the reduction reaction for carboxylic acid or a (thio)ester thereof, such as reduction of succinyl-CoA or reduction of malonyl-CoA. However, it is generally difficult to carry out this kind of reaction as an enzymatic reaction, and it is desirable to avoid them as fermentation pathways where possible (Atsumi et al., Nature, 451, (3), 86-89, 2008; Yim et al., Nat. Chem. Biol., 7, 445-452, 2011). The 4-hydroxybutyrate cycle proceeds via a dehydration reaction such as dehydration of 4-hydroxybutyryl CoA or dehydration of 3-hydroxypropionate, but this cycle has a disadvantage in that this kind of dehydration reaction often competes with the reverse reaction (hydration) in water. In the 4-hydroxybutyrate cycle, the 3-hydroxypropionate cycle, and the reductive TCA cycle, the acetyl-CoA produced is converted into other substances within the cycle by the action of malonyl-CoA synthase or pyruvate synthase. Therefore, these cycles are not necessarily efficient from the viewpoint of acetyl-CoA production.
When attempting to produce a certain substance by introducing this kind of cycle to a microorganism, it is necessary to consider the number of enzymes involved in the cycle and the number of enzymatic activities to be additionally imparted. That is, when the number of enzymes involved in the cycle or the number of enzymatic activities to be additionally imparted increases, regulation becomes more difficult and the burden on the microorganism increases. For example, in order to introduce the Wood-Ljungdahl pathway to Escherichia coli, it is required to introduce at least 9 kinds of genes. It would practically be a very difficult task to construct a substance-producing pathway and also introduce and regulate so many genes. It would clearly be advantageous to construct a cycle including a small number of enzymes by imparting a smaller number of enzymes, in terms of constructing the cycle and in terms of combination with another substance production pathway.
Accordingly, in order to fix CO2 and convert it into acetyl-CoA, it would be ideal for (A) each enzyme involved in the pathway to have a sufficiently high activity; (B) the cycle to not include an enzyme that consumes acetyl-CoA; and (C) the cycle to have a simple configuration and a small number of newly imparted enzymes. However, none of the cycles for producing acetyl-CoA from CO2 reported so far satisfies all of the conditions (A) to (C), and, therefore, the possibility of realizing such cycles is low. In fact, as regards the proposals concerning the existing carbon dioxide fixation cycles, there have been almost no actual examples of converting CO2 into acetyl-CoA or a substance derived from acetyl-CoA for use in fermentation by imparting an enzymatic activity to an industrially-usable microorganism.
The present invention provides a microorganism useful for efficient production of acetyl-CoA using carbon dioxide, and a method of producing acetyl-CoA or a useful metabolite derived from acetyl-CoA using the microorganism.
The aspect of the invention is as follows.
[1] An acetyl-CoA producing microorganism including an acetyl-CoA production cycle obtained by imparting at least one type of enzymatic activity selected from the group consisting of malate thiokinase, malyl-CoA lyase, glyoxylate carboligase, 2-hydroxy-3-oxopropionate reductase, and hydroxypyruvate reductase, to a microorganism that does not have any of:
(a) a carbon dioxide fixation cycle having an enzymatic reaction from malonyl-CoA to malonate semialdehyde or 3-hydroxypropionate;
(b) a carbon dioxide fixation cycle having an enzymatic reaction from acetyl-CoA and CO2 to pyruvate;
(c) a carbon dioxide fixation cycle having an enzymatic reaction from crotonyl-CoA and CO2 to ethylmalonyl-CoA or glutaconyl-CoA;
(d) a carbon dioxide fixation cycle having an enzymatic reaction from CO2 to formate; or
(e) at least one selected from the group consisting of malate thiokinase and malyl-CoA lyase,
wherein none of (a), (b), (c), or (d) is imparted to the microorganism, or the microorganism exhibits none of the functions of (a), (b), (c), and (d) even though at least one of (a), (b), (c), or (d) is imparted.
[2] The acetyl-CoA producing microorganism according to [1], including an acetyl-CoA production cycle wherein phosphoenolpyruvate or pyruvate is converted to oxaloacetate, and then to 2-hydroxy-3-oxopropionate due to actions of malate thiokinase, malyl-CoA lyase, glyoxylate carboligase, and then to phosphoenol pyruvate again via 2-phosphoglycerate.
[3] The acetyl-CoA producing microorganism according to [1] or [2], comprising an acetyl-CoA production cycle comprising:
(f) at least one selected from the group consisting of:
(g) malate dehydrogenase;
(h) malate thiokinase;
(i) malyl-CoA lyase;
(j) glyoxylate carboligase;
(k) at least one selected from the group consisting of:
(l) at least one selected from the group consisting of:
(m) enolase.
[4] The acetyl-CoA producing microorganism according to any one of [1] to [3], wherein the microorganism is a microorganism belonging to Enterobacteriaceae or a microorganism belonging to coryneform bacteria.
[5] The acetyl-CoA producing microorganism according to any one of [1] to [4], wherein the microorganism is Escherichia bacteria or Pantoea bacteria belonging to Enterobacteriaceae, or the microorganism is Corynebacterium bacteria belonging to coryneform bacteria.
[6] The acetyl-CoA producing microorganism according to any one of [1] to [5], wherein the microorganism is an Escherichia bacterium in which an activity of lactate dehydrogenase possessed by the Escherichia bacterium is inactivated or reduced.
[7] The acetyl-CoA producing microorganism according to any one of [1] to [6], wherein the microorganism is an Escherichia bacterium in which an activity of at least one enzyme selected from the group consisting of isocitrate lyase and malate synthase possessed by the Escherichia bacterium is inactivated or reduced.
[8] The acetyl-CoA producing microorganism according to any one of [1] to [7], wherein the microorganism is an Escherichia bacterium in which a thiolase activity, a CoA transferase activity, and an acetoacetate decarboxylase activity are imparted or enhanced.
[9] The acetyl-CoA producing microorganism according to any one of [1] to [8], wherein the microorganism is an Escherichia bacterium in which a thiolase activity, a CoA transferase activity, an acetoacetate decarboxylase activity, and an isopropyl alcohol dehydrogenase activity are imparted or enhanced.
[10] The acetyl-CoA producing microorganism according to any one of [1] to [5], wherein the microorganism is a Pantoea bacterium in which activities of fumarate hydratase A and fumarate hydratase C possessed by the Pantoea bacterium are inactivated or reduced.
[11] The acetyl-CoA producing microorganism according to any one of [1] to [5] or [10], wherein the microorganism is a Pantoea bacterium in which an activity of malate synthase possessed by the Pantoea bacterium is inactivated or reduced.
[12] The acetyl-CoA producing microorganism according to any one of [1] to [11], wherein the malate thiokinase used is a malate thiokinase obtained by modifying mtkB derived from Methylobacterium extorquens so as to alter an amino acid corresponding to the 144th amino acid to isoleucine, asparagine, aspartic acid, lysine, arginine, histidine, glutamine, or proline, and/or so as to alter the 244th amino acid to glutamic acid, alanine, leucine, isoleucine, methionine, asparagine, tyrosine, lysine, or arginine.
[13] A method of producing acetyl-CoA, comprising producing acetyl-CoA from a carbon source material using the acetyl-CoA producing microorganism according to any one of [1] to [12].
[14] A method of producing acetone, comprising producing acetone from a carbon source material using the acetyl-CoA producing microorganism according to [9] or [12].
[15] A method of producing isopropyl alcohol, comprising producing isopropyl alcohol from a carbon source material using the acetyl-CoA producing microorganism according to [9] or [12].
[16] A method of producing glutamate, comprising producing glutamate from a carbon source material using the acetyl-CoA producing microorganism according to [5], [10], [11], or [12].
The invention provides a microorganism useful for efficient conversion of carbon dioxide into acetyl-CoA, and a method of producing acetyl-CoA or a useful metabolite using the microorganism.
The acetyl-CoA producing microorganism of the invention is an acetyl-CoA producing microorganism including an acetyl-CoA production cycle obtained by imparting at least one type of enzymatic activity selected from the group consisting of malate thiokinase, malyl-CoA lyase, glyoxylate carboligase, 2-hydroxy-3-oxopropionate reductase, and hydroxypyruvate reductase, to a microorganism that does not have any of the following (a), (b), (c), (d), or (e), in which none of (a), (b), (c), or (d) is imparted to the microorganism, or the microorganism exhibits none of the functions of (a), (b), (c), and (d) even though at least one of (a), (b), (c), or (d) is imparted.
(a) a carbon dioxide fixation cycle having an enzymatic reaction from malonyl-CoA to malonate semialdehyde or 3-hydroxypropionate;
(b) a carbon dioxide fixation cycle having an enzymatic reaction from acetyl-CoA and CO2 to pyruvate;
(c) a carbon dioxide fixation cycle having an enzymatic reaction from crotonyl-CoA and CO2 to ethylmalonyl-CoA or glutaconyl-CoA;
(d) a carbon dioxide fixation cycle having an enzymatic reaction from CO2 to formate; or
(e) at least one selected from the group consisting of malate thiokinase and malyl-CoA lyase.
According to the invention, by imparting a predetermined enzymatic activity, there can be constructed a carbon dioxide fixation cycle that fixes CO2 generated during carbohydrate metabolism or CO2 supplied from outside, and provided an acetyl-CoA producing microorganism having an acetyl-CoA production cycle in which CO2 is efficiently converted to acetyl-CoA.
That is, as a result of various studies on conversion of CO2 to acetyl-CoA, it was found that CO2 was converted to acetyl-CoA by imparting at least one type of enzymatic activity selected from the group consisting of malate thiokinase, malyl-CoA lyase, glyoxylate carboligase, 2-hydroxy-3-oxopropionate reductase, and hydroxypyruvate reductase, to a microorganism that does not have any of:
(a) a carbon dioxide fixation cycle having an enzymatic reaction from malonyl-CoA to malonate semialdehyde or 3-hydroxypropionate;
(b) a carbon dioxide fixation cycle having an enzymatic reaction from acetyl-CoA and CO2 to pyruvate;
(c) a carbon dioxide fixation cycle having an enzymatic reaction from crotonyl-CoA and CO2 to ethylmalonyl-CoA or glutaconyl-CoA;
(d) a carbon dioxide fixation cycle having an enzymatic reaction from CO2 to formate; or
(e) at least one selected from the group consisting of malate thiokinase and malyl-CoA lyase,
in which none of (a), (b), (c), or (d) is imparted to the microorganism, or the microorganism exhibits none of the functions of (a), (b), (c), and (d) even though at least one of (a), (b), (c), or (d) is imparted.
Furthermore, by using the acetyl-CoA producing microorganism that converts CO2 into acetyl-CoA, or by additionally imparting a predetermined enzymatic activity to the microorganism, substances including acetyl-CoA and useful metabolites derived from acetyl-CoA such as isopropyl alcohol, ethanol, acetone, citric acid, itaconic acid, acetic acid, butyric acid, (poly-)3-hydroxybutyric acid, 3-hydroxyisobutyric acid, 3-aminoisobutyric acid, 2-hydroxyisobutyric acid, methacrylic acid, (poly)glutamic acid, glutamic acid, arginine, ornithine, citrulline, leucine, isoleucine, or proline, are efficiently produced.
The invention proposes the simplest and practical acetyl-CoA production cycle which fixes CO2 and converts it into acetyl-CoA (
Preferable embodiments of the acetyl-CoA production cycle according to the invention include the acetyl-CoA production cycle shown in
The cycle involves 8 to 10 types of enzymes, that is,
at least one selected from the group consisting of:
malate dehydrogenase;
malate thiokinase;
malyl-CoA lyase;
glyoxylate carboligase;
at least one selected from the group consisting of:
at least one selected from the group consisting of:
enolase.
(Phosphoenol)pyruvate carboxylase or phosphoenolpyruvate carboxykinase is involved in carbon dioxide fixation. (Phosphoenol)pyruvate carboxylase is a carbon dioxide-fixing enzyme having a high activity. For example, RubisCO used in photosynthesis in plants or the like is known to have a specific activity of about 3 U/mg to 20 U/mg (J. Biol. Chem. 274(8) 5078-82 (1999), Anal. Biochem. 153(1) 97-101, 1986). On the other hand, (phosphoenol)pyruvate carboxylase is reported to have a specific activity of 30 U/mg in Escherichia coli, or as high as 100 U/mg to 150 U/mg (J. Biol. Chem. 247, 5785-5792 (1972); Biosci. Biotechnol. Biochem. 59, 140-142 (1995); Biochim Biophys Acta. 1475(3):191-206, 2000). In terms of malate thiokinase (mtk) that synthesizes malyl-CoA, the present study revealed that malate thiokinase according to the invention has a higher activity compared to that of the conventionally known enzymes (J. Biol. Chem. 248(21) 7295-303, 1973). The cycle of
Another advantage of the cycle of
In the cycle of
In a case in which phosphoenolpyruvate is used as the starting substance, the balanced equation for the cycle of
In a case in which pyruvate is used as the starting substance, the balanced equation is: “pyruvate+2CoA+CO2+3NAD(P)H+4ATP→2acetyl-CoA+3NAD(P)++4ADP”.
That is, the cycle of
Among fermentation pathways that produce acetyl-CoA as an intermediate, balanced equations of pathways that consume oxygen during fermentation are listed in Table 1. It is assumed that, in these fermentation pathways, a reduced coenzyme such as NADH is produced during the pathway and the reduced coenzyme is reconverted into the oxidized form by the action of oxygen. Therefore, if it is possible to consume the produced reduced coenzyme by the cycle of
Here, the reduced coenzyme refers to a coenzyme in the reduced state and involved in an oxidation-reduction reaction, and examples thereof include NADH, NADPH, FADH2, FMNH2, and a reduced quinone coenzyme. The reduced coenzyme is preferably NADH or NADPH, more preferably NADH. The oxidized coenzyme refers to the oxidized form of a reduced coenzyme, and examples thereof include NAD+, NADP+, FAD, FMN, and an oxidized quinone coenzyme. The oxidized coenzyme is preferably NAD+ or NADP+, more preferably NAD+.
As shown in Table 1, fermentation in which oxygen is present on the left side of the fermentation equation often requires a large amount oxygen. In such cases, extensive aeration and/or vigorous stirring may be required, which results in increases in equipment costs and electric power costs. Therefore, by introducing the cycle of
In order to supply the reduction power to the cycle according to the invention, the reduction power may be provided by adding a substance that can generate a reduction power, or imparting energies from outside. Specific examples thereof include using a substance that has a higher reduction degree (e.g., hydrogen, sulfite, alcohols, or paraffin) as a substrate; supplying reduction energies directly by electric culture; and supplying a reduction power by a photochemical reaction in an organism. Other than the fermentation shown in Table 1, as long as the reduction power can be supplied from outside, it is possible to drive the intended carbon dioxide fixation pathway even in fermentation in which a reduced coenzyme is not produced.
The aspects of the present invention are described below.
The “CO2 fixation” in the invention refers to conversion of CO2 generated in carbohydrate metabolism or CO2 supplied from outside into an organic compound. The CO2 may be HCO3−. Here, “CO2 fixation” may also be referred to as “carbon dioxide fixation”.
The term “process” in the present specification encompasses an independent process, as well as a process that attains an intended effect of the process although it cannot be clearly distinguished from another process. In the present specification, a numerical range indicated using “to” means a range including numerical values given before and after “to” as a minimum value and a maximum value, respectively.
In the invention, in the reference to the amount of each ingredient in the composition, when the composition includes plural substances corresponding to each ingredient, the amount of the each ingredient means the total amount of the plural substances unless otherwise specified.
As used herein, the term “inactivation” refers to a condition in which the activity of the enzyme (here, a factor that exhibit no enzymatic activity by themselves are also included in the scope of “enzyme”, unless specifically indicated to be excluded) as measured by any existing measurement system is not higher than 1/10 of the activity in the microorganism before inactivation, assuming that the activity in the microorganism before inactivation is 100.
The “reduction” of an enzymatic activity in the invention means a condition in which the activity of the enzyme is significantly reduced by a genetic recombination technique for a gene encoding the enzyme compared to those before such treatment.
The “enhancement” of an “activity” in the invention broadly means that the an enzymatic activity in microorganisms becomes higher after enhancement compared to the enzymatic activity before enhancement.
Methods for the enhancement are not particularly restricted as long as the activity of an enzyme possessed by microorganisms is enhanced. Examples thereof include enhancement by an enzyme gene introduced from outside the cell, enhancement by augmented expression of an enzyme gene inside the cell, and any combination thereof.
Specific examples of enhancement by an enzyme gene introduced from outside the cell include: introducing a gene encoding an active enzyme having a higher activity than the enzyme of host from outside the cell of the host microorganism by the genetic recombination technique, thereby adding the enzymatic activity of the introduced enzyme gene; substituting the introduced enzymatic activity for an intrinsic enzymatic activity that the host originally possesses; increasing the copy number of an enzyme gene of the host or an enzyme gene introduced from outside the cell to two or more; and any combination thereof.
Specific examples of enhancement by augmented expression of an enzyme gene in the microorganism include: introducing a base sequence that enhances the expression of an enzyme gene from the outside of the host microorganism into inside the microorganism; substitute another promoter for the promoter of an enzyme gene that the host microorganism possesses on its genome, thereby enhancing the expression of the enzyme gene; and any combination thereof.
The “imparting” of an “activity” in the invention broadly means the provision of the activity of an intended enzyme by introducing, from the outside, a gene encoding the enzyme into an organism that does not possess a gene encoding the intended enzyme. The method of imparting an activity is not particularly limited as long as the activity of an intended enzyme can be imparted to a microorganism, and examples thereof include transformation with a plasmid harboring an enzyme gene, introduction of an enzyme gene into the genome, and any combination thereof.
The promoter to be used for “enhancing” or “imparting” of an “activity” is not particularly limited as long as the promoter allows the gene expression, and examples thereof include constitutive promoters and inducible promoters.
Whether or not the microorganism has the intended enzyme gene can be determined, with reference to, for example, the gene information of respective strains registered in KEGG (Kyoto Encyclopedia of Genes and Genomes; http://www.genome.jp/kegg/) or NCBI (National Center for Biotechnology Information; http://www.ncbi.nlm.nih.gov/gene/). In the invention, only the gene information of respective strains registered in KEGG or NCBI is used.
In the invention, the enzymatic activity may be imparted by introducing, from the outside, a gene encoding the enzyme into the cell using the genetic recombination technique. In this case, the enzyme gene to be introduced may be either homologous or heterologous to the host cell.
Methods for preparation of a genomic DNA necessary to introduce a gene from outside the cell into the cell, cleavage and ligation of DNA, transformation, PCR (Polymerase Chain Reaction), the design and synthesis of oligonucleotides to be used as primers, etc. may be carried out by usual methods well known to those skilled in the art. These methods are described in Sambrook, J., et al., “Molecular Cloning A Laboratory Manual, Second Edition”, Cold Spring Harbor Laboratory Press (1989), etc.
The expression “by the genetic recombination technique” in the invention encompasses any alternation to the base sequence caused by the insertion of another DNA into the base sequence of a native gene, substitution or deletion of a certain site of a gene, or any combinations thereof. For example, the alternation may result from a mutation.
In the invention, the microorganism in which the activity of a factor or enzyme is inactivated refers to a microorganism in which the native activity is impaired by a certain method applied from outside the cell to inside the cell. Such microorganism can be generated by, for example, disrupting a gene encoding the protein or enzyme (gene disruption).
Examples of the gene disruption in the invention include introduction of a mutation to the base sequence of a gene, insertion of another DNA into the base sequence, or deletion of a certain part of a gene, which are carried out with a view to preventing the function of the gene from being performed. As a result of the gene disruption, for example, the gene becomes unable to be transcribed into mRNA, and the structural gene ceases to be translated. Alternatively, due to incompleteness of transcribed mRNA, the amino acid sequence of the translated structural protein is mutated or deleted, and, therefore, the intrinsic functions of the structural protein becomes unable to be realized.
The gene disruption variant may be prepared using any method as long as a disruption variant in which the target enzyme or protein is not expressed can be obtained. Various methods for gene disruption have been reported (natural breeding, addition of a mutagen, UV irradiation, radiation irradiation, random mutagenesis, transposons, site-directed gene disruption). In view of disrupting only a specific gene, gene disruption by homologous recombination is preferable. Methods of gene disruption by homologous recombination are described in J. Bacteriol., 161, 1219-1221 (1985), J. Bacteriol., 177, 1511-1519 (1995), Proc. Natl. Acad. Sci. U.S.A, 97, 6640-6645 (2000), and the like, and those skilled in the art may easily perform homologous recombination using these methods or applying these methods.
The “host” in the invention means a microorganism in a state that the effect of the invention can be exerted as a result of the introduction of one or more genes from outside the microorganism.
More specifically, the “host” in the invention means a microorganism that can be made to possess the ability to produce acetyl-CoA from a carbon source material by using a certain means, regardless of whether or not the microorganism intrinsically has the innate ability to produce acetyl-CoA from a carbon source material.
The “host” in the invention may have a pathway for producing a useful metabolite. The “useful metabolite” in the invention is used as a generic name for major metabolites in the metabolic pathways of microorganisms, such as alcohols, amino acids, organic acids, and terpenes. The microorganism may be any microorganism as long as it can be made to possess the ability to produce a useful metabolite by using any means, regardless of whether or not the microorganism intrinsically has the innate ability to produce the useful metabolite.
The “useful metabolite derived from acetyl-CoA” in the invention refers to any of various metabolites produced via acetyl-CoA in metabolic pathways. Examples thereof include alcohols such as isopropyl alcohol, ethanol, or butanol; amino acids such as L-glutamic acid, L-glutamine, L-arginine, L-ornithine, L-citrulline, L-isoleucine, or L-proline; organic acids such as 3-hydroxybutyric acid, poly-3-hydroxybutyric acid, polyglutamic acid, 3-hydroxyisobutyric acid, 3-aminoisobutyric acid, 2-hydroxyisobutyric acid, methacrylic acid, citric acid, acetic acid, propionic acid, butyric acid, caproic acid, or mevalonic acid; and terpenes such as isoprene, squalene, steroid, or carotenoid. Other examples thereof include acetone. The microorganism may be any microorganism as long as it can be made to possess the ability to produce a useful metabolite derived from acetyl-CoA by using a certain means, regardless of whether or not the microorganism intrinsically has the innate ability to produce the useful metabolite derived from acetyl-CoA.
The “production of acetyl-CoA” in the invention refers to conversion of any substance into acetyl-CoA in a metabolic pathway. Since acetyl-CoA is a metabolic intermediate and quickly converted into various substances in metabolic pathways, the apparent amount of acetyl-CoA does not necessarily increase. However, the effect can be confirmed indirectly by detection of a CO2-derived label in a substance derived from acetyl-CoA, by an increase in the yield of a substance derived from acetyl-CoA relative to sugar consumption, or the like. Since various factors (e.g., the quantity of a coenzyme, the quantity of a substrate, or a change in metabolism caused by a feedback inhibition) are involved in conversion, the production amount of acetyl-CoA is not always proportional to the amount of each of the substances derived from acetyl-CoA. However, in a case in which a pathway to produce a specific substance from acetyl-CoA is enhanced or a case in which such pathway is intrinsically enhanced (for example, in the case of an isopropyl alcohol-producing microorganism or a glutamate-producing microorganism described below), the efficiency of conversion from acetyl-CoA is hardly affected by external factors, and, therefore, the production efficiency of the specific substance can be regarded as an index of the production efficiency of acetyl-CoA.
The acetyl-CoA producing microorganism according to the invention includes an acetyl-CoA production cycle obtained by imparting at least one type of enzymatic activity selected from the group consisting of malate thiokinase, malyl-CoA lyase, glyoxylate carboligase, 2-hydroxy-3-oxopropionate reductase, and hydroxypyruvate reductase, to a microorganism that does not have any of:
(a) a carbon dioxide fixation cycle having an enzymatic reaction from malonyl-CoA to malonate semialdehyde or 3-hydroxypropionate;
(b) a carbon dioxide fixation cycle having an enzymatic reaction from acetyl-CoA and CO2 to pyruvate;
(c) a carbon dioxide fixation cycle having an enzymatic reaction from crotonyl-CoA and CO2 to ethylmalonyl-CoA or glutaconyl-CoA;
(d) a carbon dioxide fixation cycle having an enzymatic reaction from CO2 to formate; or
(e) at least one selected from the group consisting of malate thiokinase and malyl-CoA lyase, in which none of (a), (b), (c), or (d) is imparted to the microorganism, or the microorganism exhibits none of the functions of (a), (b), (c), and (d) even though at least one of (a), (b), (c), or (d) is imparted.
In view of the production efficiency of acetyl-CoA, the acetyl-CoA producing microorganism is preferably imparted with the enzymatic activities of malate thiokinase and malyl-CoA lyase, more preferably imparted with the enzymatic activities of malate thiokinase, malyl-CoA lyase, and glyoxylate carboligase, still more preferably imparted with the enzymatic activities of malate thiokinase, malyl-CoA lyase, glyoxylate carboligase, and 2-hydroxy-3-oxopropionate reductase, and/or hydroxypyruvate reductase.
The expression “does not (naturally) have” herein means that the host microorganism does not intrinsically possess an attribute in nature.
Here, the “carbon dioxide fixation cycle having an enzymatic reaction from malonyl-CoA to malonate semialdehyde or 3-hydroxypropionate” refers to the following cycles (1) to (7):
(1) the cycle shown in FIG. 1 of WO 2011/099006, in which acetyl-CoA is converted into malonyl-CoA, 3-hydroxypropionate, propionyl-CoA, malate, and malyl-CoA, which are again converted into acetyl-CoA;
(2) the cycle shown in FIG. 4A of WO 2011/099006, in which acetyl-CoA is converted into malonyl-CoA, malonate semialdehyde, β-alanine, malate, and malyl-CoA, which are again converted into acetyl-CoA;
(3) the cycle shown in FIG. 4B, 16, or 18 of WO 2011/099006, in which acetyl-CoA is converted into malonyl-CoA, hydroxypropionate, (R)-lactate or (S)-lactate, malate, and malyl-CoA, which are again converted into acetyl-CoA;
(4) the cycle shown in FIG. 8 of WO 2011/099006, in which acetyl-CoA is converted into malonyl-CoA, malonate semialdehyde or hydroxypropionate, pyruvate, malate, and malyl-CoA, which are again converted into acetyl-CoA;
(5) the cycle shown in FIG. 9A, 9B, or 9C of WO 2011/099006, in which acetyl-CoA is converted into malonyl-CoA, hydroxypropionate, 2-ketoglutarate, malate, and malyl-CoA, which are again converted into acetyl-CoA;
(6) the cycle shown in FIG. 9D or 9F of WO 2011/099006, in which acetyl-CoA is converted into malonyl-CoA, hydroxypropionate, methylmalonyl-CoA, malate, and malyl-CoA, which are again converted into acetyl-CoA; and
(7) the cycle shown in FIG. 17 of WO 2011/099006, in which acetyl-CoA is converted into malonyl-CoA, malonate semialdehyde or hydroxypropionate, methylmalonyl-CoA, pyruvate, oxaloacetate, malate, and malyl-CoA, which are again converted into acetyl-CoA.
All of carbon dioxide fixation cycles (1) to (7) described above have an enzymatic reaction from malonyl-CoA to malonate semialdehyde or from malonyl-CoA to 3-hydroxypropionate. This kind of reaction is catalyzed by malonate semialdehyde dehydrogenase or malonyl-CoA reductase (WO 2011/099006). It is thought that the reduction reaction of carboxylic acid or a (thio)ester thereof, such as reduction of succinyl-CoA or reduction of malonyl-CoA, is generally difficult to carry out as enzymatic reactions and should be avoided them as fermentation pathways where possible (Atsumi et al., Nature, 451, (3), 86-89, 2008; Yim et al., Nat. Chem. Biol., 7, 445-452, 2011).
The “carbon dioxide fixation cycle having an enzymatic reaction from acetyl-CoA and CO2 to pyruvate” in the present specification refers to the following cycles (8) to (10):
(8) the cycle shown in FIG. 1 of WO 2011/099006, in which acetyl-CoA is converted into pyruvate, phosphoenolpyruvate, oxaloacetate, malate, and malyl-CoA, which are again converted into acetyl-CoA;
(9) the cycle shown in FIG. 7C, 7D or 7E of WO 2011/099006, in which acetyl-CoA is converted into pyruvate, malate, and malyl-CoA, which are again converted into acetyl-CoA; and
(10) the cycle shown in FIG. 9M of WO 2011/099006, in which acetyl-CoA is converted into pyruvate, 2-ketoglutarate, malate, and malyl-CoA, which are again converted into acetyl-CoA.
All of carbon dioxide fixation cycles (8) to (10) have an enzyme reaction converting acetyl-CoA and CO2 into pyruvate. This reaction is catalyzed by pyruvate synthase (WO 2011/099006). The synthetic reaction of pyruvate by pyruvate synthase requires a strong reduction power from ferredoxin and proceeds slowly, and proceeds only under strictly anaerobic conditions because the reaction is sensitive to oxygen.
The “carbon dioxide fixation cycle having an enzymatic reaction from crotonyl-CoA and CO2 to ethylmalonyl-CoA or glutaconyl-CoA” in the present specification refers to the cycle shown in FIG. 9H or 9J of WO 2011/099006, in which acetyl-CoA is converted into crotonyl-CoA, ethylmalonyl-CoA or glutaconyl-CoA, oxaloacetate, malate, and malyl-CoA, which are again converted into acetyl-CoA.
The conversion of crotonyl-CoA and CO2 to ethylmalonyl-CoA or glutaconyl-CoA is catalyzed by crotonyl-CoA carboxylase-reductase or methylcrotonyl-CoA carboxylase. Since the Km value of crotonyl-CoA carboxylase-reductase for carbonates is high (14 mM; PNAS 104(25) 10631-10636, 2007), sufficient activity at low substrate concentration cannot be expected. Crotonyl-CoA, which is a substrate of crotonyl-CoA carboxylase-reductase, is produced from 3-hydroxybutyryl-CoA by a dehydration reaction. In general, an enzyme involved in a dehydration reaction predominantly catalyzes the reverse reaction (i.e., hydration reaction) in an aqueous environment. Therefore, a sufficiently high production rate of crotonyl-CoA cannot be expected. Further, the reported specific activity of methylcrotonyl-CoA carboxylase is not so high (0.2 U/mg to 0.6 U/mg; Arch Biochem Biophys. 310(1) 64-75, 1994), and a sufficiently high production rate of crotonyl-CoA as a substrate cannot be expected for the same reason.
The “carbon dioxide fixation cycle having an enzymatic reaction from CO2 to formate” in the present specification refers to the cycle shown in FIG. 5, 6, 13 or 14 of WO 2009/046929, that is, a cycle having a pathway in which the reaction proceeds from CO2 via formate and serine, and oxaloacetate is converted into malate, malyl-CoA, and glycerate, which are again converted into oxaloacetate.
The enzymatic reaction from CO2 to formate requires a strong reduction power, proceeds slowly, and proceeds only under strictly anaerobic conditions because the reaction is sensitive to oxygen.
In the present specification, “exhibits none of the functions” of the carbon dioxide fixation cycle “even though imparted” means that the carbon dioxide fixation cycle does not exhibit function even when the activity of the intended enzyme is imparted by introducing a gene encoding the enzyme having the activity is introduced to a microorganism that does not possess the gene encoding the intended enzyme. The fact that “the carbon dioxide fixation cycle does not function” can be confirmed indirectly, for example, by no detection of a label derived from CO2 in a metabolite in the cycle or a substance derived from the metabolite in a test using a labeled CO2, or by no increase in the yield of a substance derived from a metabolite in the cycle relative to sugar consumption.
The acetyl-CoA production cycle to be constructed in the acetyl-CoA producing microorganism includes malate thiokinase, malyl-CoA lyase, hydroxypyruvate reductase, glyoxylate carboligase, or 2-hydroxy-3-oxopropionate reductase. An example of the acetyl-CoA production cycle is shown in
In the acetyl-CoA production cycle of
The enzymatic activity to be imparted to the acetyl-CoA producing microorganism is not particularly limited as long as the acetyl-CoA production cycle can be functionally constructed thereby, and may be appropriately selected within the scope described in the present specification depending on the host microorganism.
In a microorganism in which a closed cycle cannot be formed with any of the pathways in
Pantoea bacteria such as Pantoea ananatis does not possess malate thiokinase, malyl-CoA lyase, and glyoxylate carboligase, so that at least malate thiokinase, malyl-CoA lyase, and glyoxylate carboligase need to be imparted.
Among coryneform bacteria, for example, Corynebacterium glutamicum does not possess malate thiokinase, malyl-CoA lyase, glyoxylate carboligase, 2-hydroxy-3-oxopropionate reductase, and hydroxypyruvate reductase, so that at least malate thiokinase, malyl-CoA lyase, glyoxylate carboligase, and 2-hydroxy-3-oxopropionate reductase, and/or hydroxypyruvate reductase need to be imparted.
The enzyme that consumes acetyl-CoA as described above refers to an enzyme that uses acetyl-CoA as a substrate and catalyzes the conversion of acetyl-CoA into another substance. Examples thereof include acetyl-CoA carboxylase, which is classified as enzyme code number: 6.4.1.2 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.) and catalyzes a reaction of converting acetyl-CoA into malonyl-CoA; and pyruvate synthase, which is classified as enzyme code number: 1.2.7.1 and catalyzes a reaction of converting acetyl-CoA into pyruvate.
The cycle including an enzyme that consumes acetyl-CoA as described above refers to a closed cycle in which acetyl-CoA is converted, via the cycle, into acetyl-CoA again by the action of an enzyme that consumes acetyl-CoA. In a case in which a substance produced by the conversion reaction of an enzyme that consumes acetyl-CoA is further converted into another product without being converted into acetyl-CoA again (for example, in a case in which the substance is converted via an isopropyl alcohol-producing pathway into the end-product, isopropyl alcohol), the cycle is not closed, and, therefore, the cycle is excluded from the “cycle including an enzyme that consumes acetyl-CoA”.
The closed cycle refers to a pathway starting from an arbitrary substance in the cycle, in which the substance is converted via the cycle into another substance and, ultimately, converted into the same substance as the initial substance.
Malate thiokinase is a generic name for enzymes which are classified as enzyme code number: 6.2.1.9 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of binding of malate to CoA and converting malate into malyl-CoA. In this reaction, one molecule of ATP is consumed, and one molecule of ADP and one molecule of phosphate are produced. Malate thiokinase has a large subunit of approximately 400 amino acids and a small subunit of 300 amino acids. In the gene, the large subunit is usually followed by the small subunit. Here, for convenience, the large subunit is referred to as mtkB, and the small subunit is referred to as mtkA. It is reported that the specific activity of the purified malate thiokinase is, for example, 2.5 U/mg (Anal Biochem. 227(2), 363-367, 1995).
Malate thiokinase is mainly found in an assimilation pathway for C1 carbon sources such as methane (J. Bacteriol. 176(23), 7398-7404, 1994) and a 3-hydroxypropionate pathway (Arch. Microbiol., 151, 252-256, 1989), and is characterized in that malyl-CoA lyase is present in its vicinity in the genome. Such enzyme may be suitably used. An example of evaluation of the activity of a purified malate thiokinase is known in malate thiokinase derived from Methylobacterium extorquens, but there are only a few examples of comparing an activity with an actual sequence. The only example of evaluating an activity together with a sequence is known in an enzyme derived from Methylobacterium extorquens AM1 (GenBank Accession Numbers AAA62654 and AAA62655) (J. Bacteriol. 176(23), 7398-7404, 1994). In this literature, the gene for malate thiokinase was cloned, and the cloned gene was introduced into the same Methylobacterium extorquens strain for evaluating the activity. However, when the present inventors actually synthesized the sequence and evaluated, no activity could be detected. In view of this, the sequence of AAA62655 was compared with the sequence of malate thiokinase derived from Methylobacterium extorquens newly acquired in the invention (SEQ ID NO: 70). As a result, it was found that AAA62655 has a large deletion (36 amino acids) at the carboxy terminus, and is abnormally short compared to sequences of other malate thiokinases (e.g., in
This invention is, in actual fact, a first reported example in which malate thiokinase is actually cloned and expressed by a microorganism of another species, and the activity is correlated with the sequence.
Examples of malate thiokinase include those derived from Methylobacterium such as Methylobacterium extorquens (SEQ ID NOs:70 and 71), those derived from Hyphomicrobium such as Hyphomicrobium methylovorum or Hyphomicrobium denitrificans, those derived from Rhizobium such as Rhizobium sp. NGR234, those derived from Granulibacter such as Granulibacter bethesdensis (SEQ ID NOs:107 and 108), those derived from Nitrosomonas such as Nitrosomonas europaea, those derived from Methylococcus such as Methylococcus capsulatus, and those derived from Gammaproteobacteria.
In view of the production efficiency of useful substances produced via acetyl-CoA, specific examples of the preferable amino acid sequence include the amino acid sequences derived from Hyphomicrobium (SEQ ID NOs:73, 74, 110, and 111), amino acid sequences derived from Rhizobium (SEQ ID NOs:75 and 76), amino acid sequences derived from Nitrosomonas (SEQ ID NOs:113 and 114), amino acid sequences derived from Methylococcus (SEQ ID NOs:116 and 117), and amino acid sequences derived from Gammaproteobacteria (e.g., SEQ ID NOs:118 and 119).
The malate thiokinase derived from Hyphomicrobium (SEQ ID NOs:73, 74, 110, and 111), malate thiokinase derived from Rhizobium (SEQ ID NOs:75 and 76) and malate thiokinase derived from Nitrosomonas (SEQ ID NOs:113 and 114) share 65% to 80% sequence homology with one another. The malate thiokinase derived from Methylococcus (SEQ ID NOs:116 and 117) has 70% to 80% sequence homology with the malate thiokinase derived from Gammaproteobacteria (e.g., SEQ ID NOs:118 and 119).
Malate thiokinases having at least 70% amino acid sequence homology with each of the amino sequences of malate thiokinase derived from Hyphomicrobium, malate thiokinase derived from Rhizobium, malate thiokinase derived from Nitrosomonas, malate thiokinase derived from Methylococcus, and malate thiokinase derived from Gammaproteobacteria disclosed here, and having the malate thiokinase activity may be suitably used for the production of acetyl-CoA or the production of a useful product derived from acetyl-CoA according to the invention.
The alignment result of malate thiokinases shown in Examples is shown in
Regarding amino acids, malate thiokinase derived from Methylobacterium extorquens (indicated by Me in
The first group includes the sites at which Rhizobium sp., Hyphomicrobium methylovorum, Hyphomicrobium denitrificans, Nitrosomonas europaea, Methylococcus capsulatus, and Gammaproteobacteria, which have high enzymatic activities, have different sequences from that of Methylobacterium extorquens, and is indicated by the symbol “.” in
The first group in MtkBs (
The first group in MtkAs (
Malate thiokinases having one or more of these amino acid sequences are more preferable in view of the enzymatic activity.
The second group includes common sequences characteristic to all of Rhizobium sp., Hyphomicrobium methylovorum, Hyphomicrobium denitrificans, Nitrosomonas europaea, Methylococcus capsulatus, and Gammaproteobacteria, and is indicated by the symbol “+” in
The second group in MtkBs (
The second group in MtkAs (
The region having no homology, that is, the region other than these characteristic common sequences and the common sequences conserved among all sequences, may have a mutation. Malate thiokinases having any of these amino acid sequences are more preferable, in view of the enzymatic activity.
The third group includes common sequences characteristic to Rhizobium sp., Hyphomicrobium methylovorum, Hyphomicrobium denitrificans, and Nitrosomonas europaea, and is indicated by the symbol “#” in
The third group in MtkBs (
The third group in MtkAs (
The region having no homology, that is, the region other than these characteristic common sequences and the common sequences conserved among all sequences, may have a mutation. Malate thiokinases having any of these amino acid sequences are more preferable in view of the enzymatic activity.
The fourth group includes common sequences characteristic to Methylococcus capsulatus and Gammaproteobacteria, and is indicated by the symbol “*” in
The fourth group in MtkBs (
The fourth group in MtkAs (
The region having no homology, that is, the region other than these characteristic common sequences and the common sequences conserved among all sequences, may have a mutation.
Malate thiokinases having any of these amino acid sequences are most preferable in view of the enzymatic activity.
As a gene of malate thiokinase (mtk), a DNA having the base sequence of a gene encoding malate thiokinase obtained from each of the above-mentioned enzyme origin organisms, or a synthetic DNA sequence that is synthesized based on a known base sequence of the gene, may be used.
Preferable examples thereof include a DNA having the base sequence of a gene derived from Methylobacterium such as Methylobacterium extorquens (SEQ ID NOs: 67 and 68), Hyphomicrobium such as Hyphomicrobium methylovorum or Hyphomicrobium denitrificans, Rhizobium such as Rhizobium sp. NGR234, Granulibacter such as Granulibacter bethesdensis, Nitrosomonas such as Nitrosomonas europaea, Methylococcus such as Methylococcus capsulatus, or Gammaproteobacteria.
In view of the production efficiency of acetyl-CoA, a DNA having the base sequence of a gene derived from Hyphomicrobium (SEQ ID NOs: 61, 62, 86, and 87), Rhizobium (e.g., SEQ ID NO: 63), Granulibacter (SEQ ID NOs: 81 and 82), Nitrosomonas (SEQ ID NOs: 91 and 92), Methylococcus (SEQ ID NOs: 96 and 97), or Gammaproteobacteria (SEQ ID NOs: 102 and 103) is preferable.
In particular, the base sequence of a gene derived from Hyphomicrobium (SEQ ID NOs: 61, 62, 86, and 87), Rhizobium of which codon usage is optimized (e.g., SEQ ID NO: 63), Nitrosomonas (SEQ ID NOs: 91 and 92), Methylococcus (SEQ ID NOs: 96 and 97), or Gammaproteobacteria (SEQ ID NOs: 102 and 103) is preferable.
Malyl-CoA lyase is an enzyme which is classified as enzyme code number: 4.1.3.24 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyzes a reaction of producing glyoxylate and acetyl-CoA from malyl-CoA. Examples of malyl-CoA lyase include those derived from Methylobacterium such as Methylobacterium extorquens, Hyphomicrobium such as Hyphomicrobium methylovorum or Hyphomicrobium denitrificans, Chloroflexus such as Chloroflexus aurantiacus, Nitrosomonas such as Nitrosomonas europaea, or Methylococcus such as Methylococcus capsulatus.
In view of the production efficiency of acetyl-CoA, specific examples of the preferable amino acid sequences include an amino acid sequence derived from Methylobacterium (SEQ ID NO: 69), Hyphomicrobium (SEQ ID NO: 72 and 109), Nitrosomonas (SEQ ID NO: 112), or Methylococcus (SEQ ID NO: 115).
It is reported that the specific activity of purified malyl-CoA lyase in Methylobacterium extorquens is, for example, 28.1 U/mg (Biochem. J. 139, 399-405, 1974).
As a gene of malyl-CoA lyase (mcl), a DNA having the base sequence of a gene encoding malyl-CoA lyase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Methylobacterium such as Methylobacterium extorquens, Hyphomicrobium such as Hyphomicrobium methylovorum or Hyphomicrobium denitrificans, or Chloroflexus such as Chloroflexus aurantiacus. In view of the production efficiency of acetyl-CoA, more preferable examples thereof include a DNA having the base sequence of a gene derived from Methylobacterium and a gene having the base sequence of a gene derived from Hyphomicrobium.
Specific examples of the preferable base sequence of the gene derived from Methylobacterium include the base sequence of a gene derived from Methylobacterium extorquens (SEQ ID NO: 66). Specific examples of the preferable base sequence of a gene derived from Hyphomicrobium include the base sequence of a gene derived from Hyphomicrobium methylovorum (SEQ ID NO: 60) or Hyphomicrobium denitrificans (SEQ ID NO: 85). Specific examples of the preferable base sequence of a gene derived from Nitrosomonas include the base sequence of a gene derived from Nitrosomonas europaea (SEQ ID NO: 90). Specific examples of the preferable base sequence of the gene derived from Methylococcus include the base sequence of a gene derived from Methylococcus capsulatus (SEQ ID NO: 95).
Acetyl-CoA carboxylase is a general name for enzymes which are classified as enzyme code number: 6.4.1.2 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting acetyl-CoA and CO2 into malonyl-CoA.
Malonate semialdehyde dehydrogenase is classified as enzyme code number: 1.2.1.18 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting malonyl-CoA into malonate semialdehyde.
Malonyl-CoA reductase is a generic name for enzymes that catalyze a reaction of converting malonyl-CoA into malonate semialdehyde or 3-hydroxypropionate.
Crotonyl-CoA carboxylase-reductase is a generic name for enzymes which are classified as enzyme code number: 1.3.1.85 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze the conversion of crotonyl-CoA into ethylmalonyl-CoA.
Methylcrotonyl-CoA carboxylase is a generic name for enzymes which are classified as enzyme code number: 6.4.1.4 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting crotonyl-CoA into glutaconyl-CoA.
Pyruvate synthase is a generic name for enzymes which are classified as enzyme code number: 1.2.7.1 based on the report of the enzyme commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting acetyl-CoA into pyruvate.
It is preferable that, in the acetyl-CoA producing microorganism, the activity of at least one enzyme selected from the group consisting of lactate dehydrogenase, malate synthase, and fumarate hydratase is inactivated or reduced. As a result, acetyl-CoA can be produced more efficiently.
Among the above-mentioned lactate dehydrogenase, malate synthase, and fumarate hydratase, each of which is the target enzyme whose activity may be inactivated or reduced, malate synthase catalyzes a reaction of converting acetyl-CoA and glyoxylate into malate. This reaction is the reverse reaction of a reaction catalyzed by malate thiokinase and malyl-CoA lyase. Therefore, it is preferable to inactivate or reduce the activity of malate synthase, since the reaction of converting acetyl-CoA and glyoxylate into malate again can be blocked or reduced and the yield of acetyl-CoA is improved.
Among lactate dehydrogenase, malate synthase, and fumarate hydratase, the activity of which may be inactivated or reduced, it is preferable to inactivate fumarate hydratase in view of the production efficiency of acetyl-CoA. Inactivating fumarate hydratase prevents a conversion of malate into other substances including fumarate and a reduction in the amount of malate, and hence improves the yield of acetyl-CoA.
Lactate dehydrogenase (ldhA) is a generic name for enzymes which are classified as enzyme code number: 1.1.1.28 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting pyruvate into lactate, or converting lactate into pyruvate.
Isocitrate lyase (aceA) is classified under enzyme code number: 4.1.3.1 based on the Report of the Commission on Enzymes, International Union of Biochemistry (I.U.B.), and is a generic name for enzymes that catalyze a reaction of converting isocitrate into succinate and glyoxylate.
Malate synthase (aceB and glcB) is a generic name for enzymes which are classified as enzyme code number: 2.3.3.9 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting acetyl-CoA and glyoxylate into malate and CoA. Depending on the microorganisms, plural isomers of malate synthase is encoded in the genome. Most Escherichia coli strains possess two genes named aceB and glcB, respectively, and both are described in the present specification. Each of Pantoea ananatis and Corynebacterium glutamicum possesses a single type of gene corresponding to aceB or glcB, and the gene is collectively described as aceB in the present specification, for convenience.
Fumarate hydratase (fum) is a generic name for enzymes which are classified as enzyme code number: 4.2.1.2 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting malate into fumarate. Depending on the microorganisms, plural isomers of fumarate hydratase in encoded in the genome. For example, Escherichia coli has three types of fumarate hydratase, fumA, fumB, and fumC. Pantoea ananatis has fumA and fumC, and Corynebacterium glutamicum has fumC.
Phosphoenolpyruvate carboxylase is a generic name for enzymes which are classified as enzyme code number: 4.1.1.31 based on the report of the enzyme commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting phosphoenolpyruvate and carbon dioxide into oxaloacetate and phosphate. Examples of phosphoenolpyruvate carboxylase include those derived from Corynebacterium bacteria such as Corynebacterium glutamicum, Escherichia bacteria such as Escherichia coli, Pantoea bacteria such as Pantoea ananatis, Hyphomicrobium bacteria such as Hyphomicrobium methylovorum, Starkeya bacteria such as Starkeya novella, Rhodopseudomonas bacteria such as Rhodopseudomonas sp., or Streptomyces bacteria such as Streptomyces coelicolor.
As a gene of phosphoenolpyruvate carboxylase (ppc), a DNA having the base sequence of a gene encoding phosphoenolpyruvate carboxylase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Corynebacterium bacteria such as Corynebacterium glutamicum, Escherichia bacteria such as Escherichia coli, Pantoea bacteria such as Pantoea ananatis, Hyphomicrobium bacteria such as Hyphomicrobium methylovorum, Starkeya bacteria such as Starkeya novella, Rhodopseudomonas bacteria such as Rhodopseudomonas sp., or Streptomyces bacteria such as Streptomyces coelicolor.
Phosphoenolpyruvate carboxykinase is a generic name for enzymes which are classified as enzyme code number: 4.1.1.32, enzyme code number: 4.1.1.38, or enzyme code number: 4.1.1.49 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting phosphoenolpyruvate and carbon dioxide into oxaloacetate. Among the enzyme code numbers, the enzymes classified as enzyme code number: 4.1.1.32 are involved in a reaction of converting GDP into GTP; the enzymes classified as enzyme code number: 4.1.1.38 are involved in a reaction of converting phosphate into pyrophosphate; and the enzymes classified as enzyme code number: 4.1.1.49 are involved in a reaction of converting ADP into ATP. Examples of phosphoenolpyruvate carboxykinase include those derived from Actinobacillus bacteria such as Actinobacillus succinogenes, Mycobacterium bacteria such as Mycobacterium smegmatis, or Trypanosoma bacteria such as Trypanosoma brucei.
As a gene of phosphoenolpyruvate carboxykinase (pck), a DNA having the base sequence of a gene encoding phosphoenolpyruvate carboxykinase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Actinobacillus such as Actinobacillus succinogenes, Mycobacterium bacteria such as Mycobacterium smegmatis, or Trypanosoma bacteria such as Trypanosoma brucei.
Pyruvate carboxylase is a generic name for enzymes which are classified as enzyme code number: 6.4.1.1 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting pyruvate and carbon dioxide into oxaloacetate. The reaction consumes ATP, and produces ADP and phosphate. Examples of pyruvate carboxylase include those derived from Corynebacterium bacteria such as Corynebacterium glutamicum or Mycobacterium bacteria such as Mycobacterium smegmatis.
As a gene of pyruvate carboxylase (pyc), a DNA having the base sequence of a gene encoding phosphoenolpyruvate carboxylase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Corynebacterium bacteria such as Corynebacterium glutamicum, or Mycobacterium bacteria such as Mycobacterium smegmatis.
Malate dehydrogenase is a generic name for enzymes which are classified as enzyme code number: 1.1.1.37 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which use NADH as a coenzyme and catalyze a reaction of producing malate from oxaloacetate. Examples of malate dehydrogenase include those derived from Corynebacterium bacteria such as Corynebacterium glutamicum, or Escherichia bacteria such as Escherichia coli.
As a gene of malate dehydrogenase (mdh), a DNA having the base sequence of a gene encoding malate dehydrogenase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Corynebacterium bacteria such as Corynebacterium glutamicum, Escherichia bacteria such as Escherichia coli, or Pantoea bacteria such as Pantoea ananatis.
Glyoxylate carboligase is a generic name for enzymes which are classified as enzyme code number: 4.1.1.47 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting two molecules of glyoxylate into one molecule of 2-hydroxy-3-oxopropionate. This reaction is accompanied by decarboxylation of one molecule of carbon dioxide. Examples of glyoxylate carboligase include those derived from Escherichia bacteria such as Escherichia coli, or Rhodococcus bacteria such as Rhodococcus jostii.
As a gene of glyoxylate carboligase (gcl), a DNA having the base sequence of a gene encoding glyoxylate carboligase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Rhodococcus bacteria such as Rhodococcus jostii, or Escherichia bacteria such as Escherichia coli.
2-hydroxy-3-oxopropionate reductase is a generic name for enzymes which are classified as enzyme code number: 1.1.1.60 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which use NADH as a coenzyme and catalyze a reaction of converting 2-hydroxy-3-oxopropionate into glycerate. Examples of 2-hydroxy-3-oxopropionate reductase include those derived from Escherichia bacteria such as Escherichia coli.
As a gene of 2-hydroxy-3-oxopropionate reductase (glxR), a DNA having the base sequence of a gene encoding 2-hydroxy-3-oxopropionate reductase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Escherichia bacteria such as Escherichia coli.
Hydroxypyruvate isomerase is a generic name for enzymes which are classified as enzyme code number: 5.3.1.22 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of isomerizing 2-hydroxy-3-oxopropionate to hydroxypyruvate. Examples of hydroxypyruvate isomerase include those derived from Corynebacterium bacteria such as Corynebacterium glutamicum, Escherichia bacteria such as Escherichia coli, or Pantoea bacteria such as Pantoea ananatis.
As a gene of hydroxypyruvate isomerase (hyi), a DNA having the base sequence of a gene encoding hydroxypyruvate isomerase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Corynebacterium bacteria such as Corynebacterium glutamicum, Escherichia bacteria such as Escherichia coli, or Pantoea bacteria such as Pantoea ananatis.
Hydroxypyruvate reductase is a generic name for enzymes which are classified as enzyme code number: 1.1.1.81 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which use NADH or NADPH as a coenzyme and catalyze a reaction of converting hydroxypyruvate into glycerate.
Examples of hydroxypyruvate reductase include those derived from Escherichia bacteria such as Escherichia coli, or Pantoea bacteria such as Pantoea ananatis.
As a gene for hydroxypyruvate reductase (ycdW), a DNA having the base sequence of a gene encoding hydroxypyruvate reductase obtained from any of the above-listed enzyme origin organisms, or a synthetic DNA sequence synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Escherichia bacteria such as Escherichia coli, or Pantoea bacteria such as Pantoea ananatis.
Glycerate 3-kinase is a generic name for enzymes which are classified as enzyme code number: 2.7.1.31 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting glycerate into 3-phosphoglycerate. In this reaction, one molecule of ATP is consumed, and one molecule of ADP and one molecule of phosphate are produced. Examples of the glycerate 3-kinase include those derived from Corynebacterium bacteria such as Corynebacterium glutamicum, or Escherichia bacteria such as Escherichia coli.
As a gene of glycerate 3-kinase (glxK) according to the invention, a DNA having the base sequence of a gene encoding glycerate 3-kinase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Corynebacterium bacteria such as Corynebacterium glutamicum, Escherichia bacteria such as Escherichia coli, or Pantoea bacteria such as Pantoea ananatis.
Glycerate 2-kinase is a generic name for enzymes which are classified as enzyme code number: 2.7.1.165 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting glycerate into 2-phosphoglycerate. In this reaction, one molecule of ATP is consumed, and one molecule of ADP and one molecule of phosphate are produced. Examples of glycerate 2-kinase include those derived from Corynebacterium bacteria such as Corynebacterium glutamicum, or Escherichia bacteria such as Escherichia coli.
As a gene of glycerate 2-kinase (garK) according to the invention, a DNA having the base sequence of a gene encoding glycerate 2-kinase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Corynebacterium bacteria such as Corynebacterium glutamicum, Escherichia bacteria such as Escherichia coli, or Pantoea bacteria such as Pantoea ananatis.
Phosphoglycerate mutase is a generic name for enzymes which are classified as enzyme code number: 5.4.2.1 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting 3-phosphoglycerate into 2-phosphoglycerate. Examples of the phosphoglycerate mutase include those derived from Corynebacterium bacteria such as Corynebacterium glutamicum, Escherichia bacteria such as Escherichia coli, or Pantoea bacteria such as Pantoea ananatis.
As a gene of phosphoglycerate mutase (gpm), a DNA having the base sequence of a gene encoding phosphoglycerate mutase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Corynebacterium bacteria such as Corynebacterium glutamicum, Escherichia bacteria such as Escherichia coli, or Pantoea bacteria such as Pantoea ananatis.
Enolase is a generic name for enzymes which are classified as enzyme code number: 4.2.1.11 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting 2-phosphoglycerate into phosphoenolpyruvate. Examples of enolase include those derived from Corynebacterium bacteria such as Corynebacterium glutamicum, Escherichia bacteria such as Escherichia coli, or Pantoea bacteria such as Pantoea ananatis.
As a gene of enolase (eno), a DNA having the base sequence of a gene encoding enolase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Corynebacterium bacteria such as Corynebacterium glutamicum, Escherichia bacteria such as Escherichia coli, or Pantoea bacteria such as Pantoea ananatis.
Pyruvate kinase is a generic name for enzymes which are classified as enzyme code number: 2.7.1.40 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of converting phosphoenolpyruvate and ADP into pyruvate and ATP. Examples of pyruvate kinase include those derived from Corynebacterium bacteria such as Corynebacterium glutamicum, Escherichia bacteria such as Escherichia coli, or Pantoea bacteria such as Pantoea ananatis.
As a gene of pyruvate kinase (pyk), a DNA having the base sequence of a gene encoding pyruvate kinase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Corynebacterium bacteria such as Corynebacterium glutamicum, Escherichia bacteria such as Escherichia coli, or Pantoea bacteria such as Pantoea ananatis.
Acetyl-CoA producing microorganism may be a microorganism having, in addition to the pathway for converting acetyl-CoA into a useful metabolite, a pathway that produces another metabolite by using acetyl-CoA as a raw material, or may be a microorganism whose enzymatic activity involved in a pathway that produces another metabolite is enhanced. As a result, the useful metabolites derived from acetyl-CoA can be produced from a carbon source material and carbon dioxide, and the productivity of the useful metabolite derived from acetyl-CoA can be increased.
The microorganism used in the invention is not particularly limited as long as the microorganism does not have any of:
(a) a carbon dioxide fixation cycle having an enzymatic reaction from malonyl-CoA to malonate semialdehyde or 3-hydroxypropionate;
(b) a carbon dioxide fixation cycle having an enzymatic reaction from acetyl-CoA and CO2 to pyruvate;
(c) a carbon dioxide fixation cycle having an enzymatic reaction from crotonyl-CoA and CO2 to ethylmalonyl-CoA or glutaconyl-CoA;
(d) a carbon dioxide fixation cycle having an enzymatic reaction from CO2 to formate; or
(e) at least one selected from the group consisting of malate thiokinase and malyl-CoA lyase.
Examples of the microorganism include microorganisms belonging to Enterobacteriaceae and microorganisms belonging to coryneform bacteria. Specific examples of the microorganism include microorganisms belonging to Enterobacteriaceae such as Escherichia bacteria and Pantoea bacteria; microorganisms belonging to coryneform bacteria such as Corynebacterium bacteria and Brevibacterium bacteria; filamentous fungi; and actinomycetes.
Specific examples of the microorganisms belonging to Enterobacteriaceae include bacteria belonging to Enterobacter, Erwinia, Escherichia, Klebsiella, Pantoea, Providencia, Salmonella, Serratia, Shigella, Morganella, or Erwinia. Among these, microorganisms belonging to Escherichia and microorganisms belonging to Pantoea are preferable from the viewpoint of efficient production of useful metabolites.
Examples of the Corynebacterium bacteria include Corynebacterium glutamicum.
The Escherichia bacteria are not particularly limited, and examples thereof include Escherichia coli. Specific examples of the Escherichia coli include Escherichia coli W3110 (ATCC 27325) and Escherichia coli MG1655 (ATCC 47076), derived from the prototype wild-type strain K12, and Escherichia coli B (ATCC 11303) derived from the prototype wild-type strain B.
Both Escherichia bacteria and Pantoea bacteria belong to Enterobacteriaceae, and are closely related to each other (J. Gen. Appl. Microbiol. 43(6) 355-361 (1997); International Journal of Systematic Bacteriology, p 1061-1067, 1997).
In recent years, some bacteria belonging to Enterobacter have been reclassified into Pantoea agglomerans, Pantoea dispersa, or the like (International Journal of Systematic Bacteriology, July 39(3) 337-345, 1989).
Further, some bacteria belonging to Erwinia have been reclassified into Pantoea ananas or Pantoea stewartii (International Journal of Systematic Bacteriology, 43(1), 162-173, 1993).
Examples of the Enterobacter bacteria include Enterobacter agglomerans and Enterobacter aerogenes. More specifically, strains exemplified in European Patent Laid-open No. 952221 may be used. Examples of representative strains of Enterobacter include the Enterobacter agglomerans ATCC 12287.
Examples of representative strains of the Pantoea bacteria include Pantoea ananatis, Pantoea stewartii, Pantoea agglomerans, and Pantoea citrea. Specific examples of the strains include the following.
Pantoea ananatis AJ13355 (FERM BP-6614) (European Patent Laid-open No. 0952221)
Pantoea ananatis AJ13356 (FERM BP-6615) (European Patent Laid-open No. 0952221)
Although these strains are described as Enterobacter agglomerans in European Patent Laid-open No. 0952221, the strains were reclassified into Pantoea ananatis as described above based on base sequence analysis of 16S rRNA and the like.
The “coryneform bacteria” in the invention refers to the microorganisms belonging to Corynebacterium, Brevibacterium, or Microbacterium, as defined in Bergey's Manual of Determinative Bacteriology, 8, 599 (1974).
Examples of the coryneform bacteria further include microorganisms which had been classified into Brevibacterium but was reclassified later into Corynebacterium (Int. J. Syst. Bacteriol., 41, 255, 1991), and related bacteria such as microorganisms belonging to Brevibacterium. Examples of the coryneform bacteria are listed below.
That is, examples thereof include Corynebacterium acetoacidophilum, Corynebacterium acetoglutamicum, Corynebacterium alkanolyticum, Corynebacterium callunae, Corynebacterium glutamicum, Corynebacterium lilium, Corynebacterium melassecola, Corynebacterium thermoaminogenes, Corynebacterium herculis, Brevibacterium divaricatum, Brevibacterium flavum, Brevibacterium immariophilum, Brevibacterium lactofermentum, Brevibacterium roseum, Brevibacterium saccharolyticum, Brevibacterium thiogenitalis, Corynebacterium ammoniagenes, Brevibacterium album, Brevibacterium cerinum, and Microbacterium ammoniaphilum.
Specific examples thereof include the following strains.
Corynebacterium acetoacidophilum ATCC 13870, Corynebacterium acetoglutamicum ATCC 15806, Corynebacterium alkanolyticum ATCC 21511, Corynebacterium callunae ATCC 15991, Corynebacterium glutamicum ATCC 13020, ATCC 13032 and ATCC 13060, Corynebacterium lilium ATCC 15990, Corynebacterium melassecola ATCC 17965, Corynebacterium thermoaminogenes AJ 12340 (FERM BP-1539), Corynebacterium herculis ATCC13868, Brevibacterium divaricatum ATCC 14020, Brevibacterium flavum ATCC 13826, ATCC 14067, and AJ 12418 (FERM BP-2205), Brevibacterium immariophilum ATCC 14068, Brevibacterium lactofermentum (Corynebacterium glutamicum) ATCC 13869, Brevibacterium roseum ATCC 13825, Brevibacterium saccharolyticum ATCC 14066, Brevibacterium thiogenitalis ATCC 19240, Corynebacterium ammoniagenes ATCC 6871 and ATCC 6872, Brevibacterium album ATCC 15111, Brevibacterium cerinum ATCC 15112, and Microbacterium ammoniaphilum ATCC 15354.
In a case in which the Escherichia bacterium is used as the microorganism, preferable examples of the acetyl-CoA producing microorganism in the invention include an acetyl-CoA producing Escherichia bacterium in which the thiolase activity, the CoA transferase activity, and the acetoacetate decarboxylase activity are imparted or enhanced.
In a case in which the Escherichia bacterium is used as the microorganism, preferable examples of the acetyl-CoA producing microorganism in the invention further include an acetyl-CoA producing Escherichia bacterium in which the thiolase activity, the CoA transferase activity, the acetoacetate decarboxylase activity, and the isopropyl alcohol dehydrogenase activity are imparted or enhanced.
Thiolase is a generic name for enzymes which are classified as enzyme code number: 2.3.1.9 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of producing acetoacetyl-CoA from acetyl-CoA.
Examples of thiolase include those derived from Clostridium bacteria such as Clostridium acetobutylicum or Clostridium beijerinckii, Escherichia bacteria such as Escherichia coli, Halobacterium sp., Zoogloea bacteria such as Zoogloea ramigera, Rhizobium sp., Bradyrhizobium bacteria such as Bradyrhizobium japonicum, Candida such as Candida tropicalis, Caulobacter bacteria such as Caulobacter crescentus, Streptomyces bacteria such as Streptomyces collinus, or Enterococcus bacteria such as Enterococcus faecalis.
As a gene of thiolase, a DNA having the base sequence of a gene encoding thiolase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Clostridium bacteria such as Clostridium acetobutylicum or Clostridium beijerinckii; Escherichia bacteria such as Escherichia coli, Halobacterium sp., Zoogloea bacteria such as Zoogloea ramigera, Rhizobium sp., Bradyrhizobium bacteria such as Bradyrhizobium japonicum, Candida such as Candida tropicalis, Caulobacter bacteria such as Caulobacter crescentus, Streptomyces bacteria such as Streptomyces collinus, or Enterococcus bacteria such as Enterococcus faecalis. More preferable examples thereof include a DNA having the base sequence of a gene derived from a prokaryote such as Clostridium bacteria or Escherichia bacteria, and a DNA having the base sequence of a gene derived from Clostridium acetobutylicum or Escherichia coli is particularly preferable.
Acetoacetate decarboxylase is a generic name for enzymes which are classified as enzyme code number: 4.1.1.4 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of producing acetone from acetoacetate.
Examples of acetoacetate decarboxylase include those derived from Clostridium bacteria such as Clostridium acetobutylicum or Clostridium beijerinckii; or Bacillus bacteria such as Bacillus polymyxa.
As a gene of acetoacetate decarboxylase, a DNA having the base sequence of a gene encoding acetoacetate decarboxylase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Clostridium bacteria or Bacillus bacteria. Specific examples thereof include a DNA having the base sequence of a gene derived from Clostridium acetobutylicum or Bacillus polymyxa. The DNA is more preferably a DNA having the base sequence of a gene derived from Clostridium acetobutylicum.
As a gene of acetoacetate decarboxylase, a DNA having the base sequence of a gene encoding acetoacetate decarboxylase obtained from any of the above-listed enzyme origin organisms may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Clostridium bacteria or Bacillus bacteria. Specific examples thereof include a DNA having the base sequence of a gene derived from Clostridium acetobutylicum or Bacillus polymyxa. The DNA is more preferably a DNA having the base sequence of a gene derived from Clostridium acetobutylicum.
Isopropyl alcohol dehydrogenase is a generic name for enzymes which are classified as enzyme code number: 1.1.1.80 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of producing isopropyl alcohol from acetone.
Examples of isopropyl alcohol dehydrogenase include those derived from Clostridium bacteria such as Clostridium beijerinckii.
As a gene of isopropyl alcohol dehydrogenase, a DNA having the base sequence of a gene encoding isopropyl alcohol dehydrogenase obtained from any of the above-listed enzyme origin organisms may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Clostridium bacteria, such as Clostridium beijerinckii.
CoA transferase is a generic name for enzymes which are classified as enzyme code number: 2.8.3.8 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of producing acetoacetate from acetoacetyl-CoA.
Examples of CoA transferase include those derived from Clostridium bacteria such as Clostridium acetobutylicum or Clostridium beijerinckii; Roseburia bacteria such as Roseburia intestinalis; Faecalibacterium bacteria such as Faecalibacterium prausnitzii; Coprococcus bacteria; trypanosomes such as Trypanosoma brucei; or Escherichia bacteria such as Escherichia coli.
As a gene of CoA transferase, a DNA having the base sequence of a gene encoding CoA transferase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Clostridium bacteria such as Clostridium acetobutylicum, Roseburia bacteria such as Roseburia intestinalis, Faecalibacterium bacteria such as Faecalibacterium prausnitzii, Coprococcus bacteria, trypanosomes such as Trypanosoma brucei, or Escherichia bacteria such as Escherichia coli. More preferred examples thereof include a DNA having the base sequence of a gene derived from Clostridium bacteria or Escherichia bacteria, and a DNA having the base sequence of a gene derived from Clostridium acetobutylicum or Escherichia coli is still more preferable.
From the viewpoint of the enzymatic activity, it is preferable that each of the four kinds of enzymes is an enzyme derived from at least one selected from the group consisting of Clostridium bacteria, Bacillus bacteria, and Escherichia bacteria. In particular, a case in which that acetoacetate decarboxylase and isopropyl alcohol dehydrogenase are derived from Clostridium bacteria, and in which the CoA transferase activity and the thiolase activity are derived from Escherichia bacteria, is more preferable.
In particular, from the viewpoint of the enzymatic activity, it is preferable that each of the four kinds of enzymes are derived from any of Clostridium acetobutylicum, Clostridium beijerinckii, or Escherichia coli. It is more preferable that acetoacetate decarboxylase is an enzyme derived from Clostridium acetobutylicum, and that each of CoA transferase and thiolase is derived from Clostridium acetobutylicum or Escherichia coli, and that isopropyl alcohol dehydrogenase is derived from Clostridium beijerinckii. Regarding the four kinds of enzymes, it is preferable that the acetoacetate decarboxylase activity is derived from Clostridium acetobutylicum, and that the isopropyl alcohol dehydrogenase activity is derived from Clostridium beijerinckii, and that the CoA transferase activity and the thiolase activity are derived from Escherichia coli, from the viewpoint of the enzymatic activity.
The CoA transferase genes (atoD and atoA) and the thiolase gene (atoB) derived from Escherichia coli form an operon on the genome of Escherichia coli in the order of atoD, atoA, and atoB (Journal of Bacteriology Vol. 169 pp 42-52 Lauren Sallus Jenkins et al.). Therefore, the expression of the CoA transferase genes and the thiolase gene can be simultaneously controlled by modifying the atoD promoter.
In view of above, when the CoA transferase activity and the thiolase activity are those obtained from the genomic genes of the host Escherichia coli, it is preferable to enhance the expression of both enzyme genes by, for example, replacing the promoter responsible for the expression of both enzyme genes by another promoter, from the viewpoint of obtaining sufficient isopropyl alcohol production ability. Examples of the promoter to be used in order to enhance the expression of the CoA transferase activity and the thiolase activity include the above-described Escherichia coli-derived GAPDH promoter.
Examples of the acetyl-CoA producing microorganism that produces another metabolite by using acetyl-CoA as a raw material include a microorganism obtained by imparting or enhancing, or inactivating or reducing, any of the above-described enzymatic activities, using Escherichia coli having an isopropyl alcohol production system (hereinafter referred to as “isopropyl alcohol-producing Escherichia coli”) as a host.
The isopropyl alcohol-producing Escherichia coli may be any Escherichia coli as long as the respective genes for imparting the isopropyl alcohol-producing ability can be introduced or modified.
The Escherichia coli is more preferably Escherichia coli to which the isopropyl alcohol production ability has been imparted in advance. By using such Escherichia coli, isopropyl alcohol can be efficiently produced.
An example of the isopropyl alcohol-producing Escherichia coli is an isopropyl alcohol-producing Escherichia coli to which the acetoacetate decarboxylase activity, the isopropyl alcohol dehydrogenase activity, the CoA transferase activity, and the thiolase activity have been imparted so as to be capable of producing isopropyl alcohol from a plant-derived raw material, and which is described in, for example, WO 2009/008377. Other examples of the isopropyl alcohol-producing Escherichia coli include microorganisms described in WO 2009/094485, WO 2009/094485, WO 2009/046929, or WO 2009/046929.
The isopropyl alcohol-producing Escherichia coli is Escherichia coli having an isopropyl alcohol production system, and has an isopropyl alcohol production ability that is introduced by a genetic recombination technique. The isopropyl alcohol production system may be any system that causes Escherichia coli of interest to produce isopropyl alcohol.
In the isopropyl alcohol-producing Escherichia coli according to the invention, preferably, four enzymatic activities—an acetoacetate decarboxylase activity, an isopropyl alcohol dehydrogenase activity, a CoA transferase activity, and the above-mentioned thiolase activity—are imparted from outside the cell.
In the invention, examples of the isopropyl alcohol-producing Escherichia coli having an isopropyl alcohol production system include a pIPA/B variant and a pIaaa/B variant described in WO 2009/008377. Examples of the isopropyl alcohol-producing Escherichia coli further include a variant in which, from among the enzymes involved in the production of isopropyl alcohol, the CoA transferase activity and the thiolase activity are enhanced by enhancing the expression of the respective genes on the genome of the Escherichia coli, and in which the isopropyl alcohol dehydrogenase activity and the acetoacetate decarboxylase activity are enhanced by enhancing the expression of the respective genes using a plasmid or plasmids (sometimes referred to as “pIa/B::atoDAB variant”).
In the invention, the isopropyl alcohol-producing Escherichia coli may be an isopropyl alcohol-producing Escherichia coli including an isopropyl alcohol production system, in which the activity of transcriptional repressor GntR is inactivated, and the isopropyl alcohol-producing Escherichia coli includes a group of auxiliary enzymes having an enzymatic activity pattern with which isopropyl alcohol production ability achieved by the inactivation of the GntR activity is maintained or enhanced. Consequently, production of isopropyl alcohol can be further increased.
The term “a group of auxiliary enzymes” in the invention refers to one enzyme or two or more enzymes, which affect(s) isopropyl alcohol production ability. Further, the activity of enzymes included in the group of auxiliary enzymes is inactivated, activated, or enhanced. The phrase the “enzymatic activity pattern of the group of auxiliary enzymes” as used herein refers to the enzymatic activity pattern of the enzymes that is capable of maintaining or increasing the improved isopropyl alcohol production amount achieved by inactivation of the GntR activity alone, and encompasses one enzyme of a combination of two or more of enzymes.
Examples of preferable enzymatic activity patterns of the group of auxiliary enzymes include the following patterns:
(1) maintenance of the wild-type activities of glucose-6-phosphate isomerase (Pgi), glucose-6-phosphate-1-dehydrogenase (Zwf), and the phosphogluconate dehydrogenase (Gnd);
(2) inactivation of glucose-6-phosphate isomerase (Pgi) activity, and enhancement of glucose-6-phosphate-1-dehydrogenase (Zwf) activity; and
(3) inactivation of glucose-6-phosphate isomerase (Pgi) activity, enhancement of glucose-6-phosphate-1-dehydrogenase (Zwf) activity, and inactivation of phosphogluconate dehydrogenase (Gnd) activity.
Among these, the enzymatic activity pattern of the group of auxiliary enzymes described in item (3) above is more preferable from the viewpoint of the isopropyl alcohol production ability.
The group of auxiliary enzymes and the enzymatic activity pattern thereof are not limited to those described above. Any group of auxiliary enzymes and enzymatic activity pattern thereof which include inactivation of the GntR activity, and with which the amount of isopropyl alcohol production in an isopropyl alcohol-producing Escherichia coli can be increased, are within the scope of the invention. The group of auxiliary enzymes is not necessarily constituted by plural enzymes, and may be constituted by one enzyme.
GntR refers to a transcription factor that negatively regulates an operon involved in gluconate metabolism via the Entner-Doudoroff pathway. GntR is a generic name for GntR transcriptional repressors that suppress the functions of two group of genes (GntI and GntII), which are responsible for the uptake and metabolism of gluconic acid.
Glucose-6-phosphate isomerase (Pgi) is a generic name for enzymes which are classified as enzyme code number: 5.3.1.9 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of producing D-fructose-6-phosphate from D-glucose-6-phosphate.
Glucose-6-phosphate-1-dehydrogenase (Zwf) is classified as enzyme code number: 1.1.1.49 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.) and which catalyzes a reaction to producing D-glucono-1,5-lactone-6-phosphate from D-glucose-6-phosphate.
Examples of glucose-6-phosphate-1-dehydrogenase include those derived from Deinococcus bacteria such as Deinococcus radiophilus; Aspergillus fungi such as Aspergillus niger or Aspergillus aculeatus; Acetobacter bacteria such as Acetobacter hansenii; Thermotoga bacteria such as Thermotoga maritima; Cryptococcus fungi such as Cryptococcus neoformans; Dictyostelium fungi such as Dictyostelium discoideum; Pseudomonas such as Pseudomonas fluorescens or Pseudomonas aeruginosa; Saccharomyces such as Saccharomyces cerevisiae; Bacillus bacteria such as Bacillus megaterium; or Escherichia bacteria such as Escherichia coli.
As a gene of glucose-6-phosphate-1-dehydrogenase (Zwf), a DNA having the base sequence of gene encoding thiolase obtained from any of the above-listed enzyme origin organisms, or a synthesized DNA sequence that is synthesized based on a known base sequence of the gene, may be used. Preferable examples thereof include a DNA having the base sequence of a gene derived from Deinococcus bacteria such as Deinococcus radiophilus, Aspergillus fungi such as Aspergillus niger or Aspergillus aculeatus; Acetobacter bacteria such as Acetobacter hansenii, Thermotoga bacteria such as Thermotoga maritima, Cryptococcus fungi such as Cryptococcus neoformans, Dictyostelium fungi such as Dictyostelium discoideum, Pseudomonas such as Pseudomonas fluorescens or Pseudomonas aeruginosa, Saccharomyces such as Saccharomyces cerevisiae, Bacillus bacteria such as Bacillus megaterium, or Escherichia bacteria such as Escherichia coli. More preferable examples thereof include a DNA having the base sequence of a gene derived from a prokaryote such as Deinococcus bacteria, Aspergillus fungi, Acetobacter bacteria, Thermotoga bacteria, Pseudomonas, Bacillus bacteria, or Escherichia bacteria. The DNA is more preferably a DNA having the base sequence of a gene derived from Escherichia coli.
Phosphogluconate dehydrogenase (Gnd) is a generic name for enzymes which are classified as enzyme code number: 1.1.1.44 based on the report of the Enzyme Commission of International Union of Biochemistry (I.U.B.), and which catalyze a reaction of producing D-ribulose-5-phosphate and CO2 from 6-phospho-D-gluconate.
Each of the activities of these enzymes in the invention may be an activity introduced from outside the cell into the cell, or an activity obtained by of overexpression of the enzyme gene that the host bacterium possesses on its genome via enhancement of the promoter activity for the enzyme gene or replacement of the promoter with another promoter.
The Escherichia coli having enhanced enzymatic activity in the invention refers to Escherichia coli in which the enzymatic activity is enhanced by a certain method. This kind of Escherichia coli can be constructed by introducing a gene encoding the enzyme or protein from outside the cell into the cell using a plasmid by the gene recombination technology as described above; or by overexpressing the enzyme gene that the host bacterium possesses on its genome via enhancement of the promoter activity for the enzyme gene or replacing the promoter with another promoter; or the combination of these methods.
The gene promoter applicable to the isopropyl alcohol-producing Escherichia coli may be any promoter capable of controlling the expression of any of the genes described above. The gene promoter is preferably a potent promoter that constitutively works in the microorganism, and which is not susceptible to repression of expression even in the presence of glucose. Specific examples thereof include the promoter of glyceraldehyde-3-phosphate dehydrogenase (hereinafter sometimes referred to as “GAPDH”) or the promoter of serine hydroxymethyltransferase.
The promoter in the isopropyl alcohol-producing Escherichia coli means a regain to which an RNA polymerase having a sigma factor binds to start transcription. For example, a GAPDH promoter derived from Escherichia coli is described at Base Nos. 397 to 440 in the base sequence information of GenBank accession number X02662.
In the isopropyl alcohol-producing Escherichia coli, lactate dehydrogenase (LdhA) may be disrupted. The disruption of lactate dehydrogenase suppresses lactate production even under culture conditions in which oxygen supply is restricted, as a result of which isopropyl alcohol can be efficiently produced. The “conditions in which oxygen supply is restricted” generally means conditions: 0.02 vvm to 2.0 vvm (vvm: aeration volume [mL]/liquid volume [mL]/time [min]) at an agitation speed of 200 to 600 rpm, when air alone is used as the gas.
The lactate dehydrogenase (LdhA) refers to an enzyme that produces D-lactate and NAD from pyruvate and NADH.
The acetyl-CoA producing microorganism for producing acetone may be one having only thiolase activity, CoA transferase activity, and acetoacetate decarboxylase activity among activity in the isopropyl alcohol production system. That is, when producing acetone by using the acetyl-CoA producing microorganism, the microorganism having no isopropyl alcohol dehydrogenase activity may be used.
Other examples of the pathway for producing another metabolite by using acetyl-CoA as a raw material include a pathway that produces glutamate from acetyl-CoA. Preferable example of the microorganism having a pathway that produces another metabolite or the microorganism whose enzymatic activity involved in a pathway that produces another metabolite is enhanced include a microorganism obtained by imparting or enhancing or inactivating the enzymatic activities in the above-described pathway that produces glutamate from acetyl-CoA or reducing an enzymatic activity that inhibits the production of glutamate from acetyl-CoA by using a microorganism having a pathway that efficiently produces a glutamate (hereinafter sometimes referred to as “glutamate-producing microorganism”) or by using a glutamate-producing microorganism as a host.
Examples of the glutamate-producing microorganism include the above-mentioned microorganisms having an ability to produce L-amino acids.
Specific examples of the glutamate-producing microorganism include, but not limited thereto, Enterobacteriaceae bacteria such as Escherichia bacteria or Pantoea bacteria, and coryneform bacteria such as Corynebacterium glutamicum.
The glutamate-producing microorganism may be any microorganism that allows the introduction or modification of a gene for imparting the glutamate production ability. It is more preferable that the glutamate-producing microorganism is a Pantoea bacterium or coryneform bacterium to which glutamate production ability has been imparted in advance. By using this kind of microorganism, glutamate can be more efficiently produced.
Examples of a method of imparting the glutamate production ability to a microorganism include modifying the microorganism such that expression of a gene encoding an enzyme involved in L-glutamate biosynthesis is increased and/or is overexpressed. Examples of the enzyme involved in L-glutamate biosynthetic include glutamate dehydrogenase, glutamine synthetase, glutamate synthase, isocitrate dehydrogenase, aconitate hydratase, citrate synthase, phosphoenolpyruvate carboxylase, pyruvate carboxylase, pyruvate dehydrogenase, pyruvate kinase, phosphoenolpyruvate synthase, enolase, phosphoglyceromutase, phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase, triose-phosphate isomerase, fructose-bisphosphate aldolase, phosphofructokinase, and glucose-phosphate isomerase. Among these enzymes, it is preferable that one or more of citrate synthase, phosphoenolpyruvate carboxylase, and glutamate dehydrogenase has an increased activity, and it is more preferable that 4 all of the three enzymes have enhanced activities.
Examples of the glutamate-producing microorganism include a glutamate-producing microorganism described in Japanese Patent Application Laid-Open (JP-A) No. 2005-278643.
The L-glutamate-producing microorganism to be used may be a microorganism having an ability to accumulate L-glutamate in an amount exceeding the saturation concentration of L-glutamate in a liquid medium when the microorganism was cultured under acidic conditions (hereinafter referred to as “L-glutamate-accumulating ability under acidic conditions”). For example, a variant having increased resistance to L-glutamate in a low-pH environment may be obtained by a method described in European Patent Laid-open No. 1078989, whereby the ability to accumulate L-glutamate in an amount exceeding the saturation concentration is imparted.
Specific examples of the microorganism having an intrinsic L-glutamate-accumulating ability under acidic conditions include Pantoea ananatis AJ13356 (FERM BP-6615) and AJ13601 (FERM BP-7207) (see European Patent Laid-open No. 0952221). Pantoea ananatis AJ13356 was deposited with National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology, Ministry of International Trade and Industry (present name: International Patent Organism Depositary, National Institute of Technology and Evaluation (IPOD, NITE); address: Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan) under accession No. FERM P-16645 on Feb. 19, 1998, and then transferred to an international depository authority under the Budapest Treaty under accession No. FERM BP-6615 on Jan. 11, 1999. This strain was identified as Enterobacter agglomerans and deposited as Enterobacter agglomerans AJ13355 when first isolated, but, according to recent base sequence analysis of 16S rRNA and the like, the strain was reclassified as Pantoea ananatis (see Examples below). Similarly, AJ13356 and AJ13601 mentioned below induced from AJ13355 were deposited to the above depositary as Enterobacter agglomerans, but these strains are described as Pantoea ananatis in the present specification. AJ13601 was deposited with National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology, Ministry of International Trade and Industry (present name: International Patent Organism Depositary, National Institute of Technology and Evaluation (IPOD, NITE) under accession No. FERM P-17156 on Aug. 18, 1999, and then transferred to an international depository authority under the Budapest Treaty under accession No. FERM BP-7207 on Jul. 6, 2000.
Other examples of the method of imparting or enhancing the L-glutamate production ability include a method of imparting resistance to an organic acid analogue or a respiratory inhibitor, and a method of imparting sensitivity to a cell wall synthesis inhibitor. Specific examples of the method include imparting resistance to monofluoroacetic acid (JP-A No. S50-113209), imparting resistance to adenine or resistance to thymine (JP-A No. S57-065198), weakening urease (JP-A No. S52-038088), imparting resistance to malonic acid (JP-A No. S52-038088), imparting resistance to benzopyrone or naphthoquinones (JP-A No. S56-001889), imparting resistance to HOQNO (JP-A No. S56-140895 A), imparting resistance to α-ketomalonic acid (JP-A No. S57-002689 A), imparting resistance to guanidine (JP-A No. S56-035981), and method of imparting resistance to penicillin (JP-A No. H04-088994).
Specific examples of the resistant microorganisms include the following strains.
Brevibacterium flavum AJ3949 (FERM BP-2632; see JP-A No. S50-113209)
Corynebacterium glutamicum AJ11628 (FERM P-5736; see JP-A No. S57-065198)
Brevibacterium flavum AJ11355 (FERM P-5007; see JP-A No. S56-001889)
Corynebacterium glutamicum AJ11368 (FERM P-5020; see JP-A S56-001889)
Brevibacterium flavum AJ11217 (FERM P-4318; see JP-A No. S57-002689)
Corynebacterium glutamicum AJ11218 (FERM P-4319; see JP-A No. S57-002689)
Brevibacterium flavum AJ11564 (FERM P-5472; see JP-A No. S56-140895)
Brevibacterium flavum AJ11439 (FERM P-5136; see JP-A No. S56-035981)
Corynebacterium glutamicum H7684 (FERM BP-3004; see JP-A No. H04-088994)
Brevibacterium lactofermentum AJ11426 (FERM P-5123; see JP-A No. S56-048890)
Corynebacterium glutamicum AJ11440 (FERM P-5137; see JP-A No. S56-048890)
Brevibacterium lactofermentum AJ11796 (FERM P-6402; see JP-A No. S58-158192)
Preferable examples of the microorganism having an L-glutamine production ability include a microorganism in which the glutamate dehydrogenase activity is enhanced, a microorganism in which the glutamine synthetase (glnA) activity is enhanced, and a microorganism in which the glutaminase gene is disrupted (European Patent Laid-open Nos. 1229121 and 1424398). Enhancement of the glutamine synthetase activity can also be achieved by disrupting glutamine adenylyl transferase (glnF) or disrupting the PII regulation protein (glnB). Other preferable examples of the L-glutamine-producing microorganism include a variant belonging to genus Escherichia, and the variant harbors a mutant glutamine synthetase in which the tyrosine residue at position 397 in glutamine synthetase is replaced by another amino acid residue (U.S. Patent Published Application No. 2003-0148474).
Another method of imparting or enhancing the L-glutamine production ability include imparting resistance to 6-diazo-5-oxo-norleucine (JP-A No. H03-232497), imparting resistance to a purine analogue and resistance to methionine sulfoxide (JP-A No. S61-202694), and imparting resistance to α-ketomaleic acid (JP-A No. S56-151495). Specific examples of coryneform bacteria having the L-glutamine production ability include the following microorganisms.
Brevibacterium flavum AJ11573 (FERM P-5492; JP-A No. S56-161495)
Brevibacterium flavum AJ11576 (FERM BP-10381; JP-A No. S56-161495)
Preferable examples of microorganisms that produce proline, leucine, isoleucine, valine, arginine, citrulline, ornithine, and/or polyglutamic acid include a microorganism described in JP-A No. 2010-41920. Microorganisms that produce acetic acid, (poly)3-hydroxybutyric acid, itaconic acid, citric acid, and/or butyric acid are described in Fermentation Handbook (Kyoritsu Shuppan Co., Ltd.).
Examples of microorganisms that produce 4-aminobutyric acid include a microorganism in which glutamate decarboxylase is introduced to a glutamate-producing microorganism, such as those described in JP-A No. 2011-167097.
Examples of microorganisms that produce 4-hydroxybutyric acid include a microorganism in which glutamate decarboxylase, transaminase, and/or aldehyde dehydrogenase are introduced to a glutamate-producing microorganism, such as those described in JP-A No. 2009-171960.
Examples of microorganisms that produce 3-hydroxyisobutyric acid include a microorganism to which a pathway described in WO 2009/135074 or WO 2008/145737 was introduced.
Examples of microorganisms that produce 2-hydroxyisobutyric acid include a microorganism to which a pathway described in WO 2009/135074 or WO 2009/156214 was introduced.
Examples of microorganisms that produce 3-aminoisobutyric acid or methacrylic acid include a microorganism to which a pathway described in WO 2009/135074 was introduced.
The microorganism in the invention is a microorganism that is constructed to have the acetyl-CoA production cycle of
Examples of the microorganisms intrinsically having Mtk and mcl include methanotrophic microorganisms such as Methylobacterium extorquens. Since vector systems suitable for methanotrophic microorganisms or techniques for modification of genomic genes of methanotrophic microorganisms have not been developed, genetic manipulation of microorganisms is more difficult than industrial microorganisms such as Escherichia coli and Corynebacterium. Further, these microorganisms grow slowly in many cases and therefore are not suitable for producing useful metabolites.
The method of producing acetyl-CoA, acetone, isopropyl alcohol, or glutamate according to the invention includes producing acetyl-CoA, acetone, isopropyl alcohol, or glutamate as the product of interest from a carbon source material using the above-described acetyl-CoA producing microorganism. That is, the method of producing acetyl-CoA includes: culturing the acetyl-CoA producing microorganism in a state in which the acetyl-CoA producing microorganism contacts with a carbon source material (hereinafter, culture process), and collecting the product of interest (acetyl-CoA, acetone, isopropyl alcohol, or glutamate) obtained by the contact (hereinafter, collection process).
According to the method of producing acetyl-CoA, since the acetyl-CoA producing microorganism is cultured in a state in which the acetyl-CoA producing microorganism contacts with a carbon source material, the carbon source material is assimilated by the acetyl-CoA producing microorganism, and the product of interest can be efficiently produced while carbon dioxide is fixed.
The carbon source material is not restricted as long as the material contains a carbon source that can be assimilated by the microorganism, and the material is preferably a plant-derived raw material.
In the invention, the plant-derived raw material refers to organs such as roots, stems, trunks, branches, leaves, flowers, and seeds; plant bodies containing the organs; and decomposition products of the plant organs, and further encompasses carbon sources that can be used as carbon sources by microorganisms during cultivation for among carbon sources obtained from the plant bodies, the plant organs and the decomposition products thereof.
General examples of the carbon sources in the plant-derived raw material include sugars such as starch, sucrose, glucose, fructose, xylose, and arabinose; herbaceous and ligneous plant decomposition products or cellulose hydrolysates, each of which contains the above ingredients in large amounts; and combinations thereof. The carbon source in the invention may further include vegetable oil-derived glycerin and fatty acids.
Preferable examples of the plant-derived raw material include agricultural crops such as grain, corn, rice, wheat, soybean, sugarcane, beet, cotton, and the like, and combinations thereof. The form thereof as the raw materials is not specifically limited, and may be a crude products, squeezed juice, a crushed products, or the like. Alternatively, the plant-derived raw material may be in a form that consists only of carbon source described above.
In the culture process, the contact between the acetyl-CoA producing microorganism and plant-derived raw material is generally made by culturing the acetyl-CoA producing microorganism in a culture medium containing the plant-derived raw material.
The density of contact between the plant-derived raw material and the acetyl-CoA producing microorganism may be varied depending on the activity of the acetyl-CoA producing microorganism. In general, the concentration of the plant-derived raw material in the culture medium may be such that the initial sugar concentration in terms of glucose may be set to be 20% by mass or lower relative to the total mass of the mixture. From the viewpoint of sugar tolerance of the acetyl-CoA producing microorganism, the initial sugar concentration is preferably set to be 15% by mass or lower. Other components may be added in usual addition amounts for microorganisms culture media, without particular limitation.
The content of the acetyl-CoA producing microorganism in the culture medium may be varied with the kind and the activity of the microorganism, and the amount of a preculture bacterial liquid (OD 660 nm=4 to 8) to be added when starting initially cultivation may generally set to be 0.1% by mass to 30% by mass relative to the culture liquid, and is preferably set to be 1% by mass to 10% by mass relative to the culture liquid from the viewpoint of controlling culture conditions.
The medium to be used for culture of the acetyl-CoA producing microorganism may be any usually-employed culture medium that includes a carbon source, a nitrogen source, and an inorganic ion, and further an inorganic trace element, a nucleic acid, and a vitamin, etc., required by microorganisms to produce the product of interest, without particular limitation.
Culture conditions for the culture process are not particularly restricted, and culturing may be carried out, for example, under aerobic conditions at an appropriately controlled pH and temperature within a range of pH 4 to 9, preferably pH 6 to 8, and within a range of 20° C. to 50° C., preferably 25° C. to 42° C.
The aeration volume of gas into the mixture described above is not particularly restricted. When air alone is used as the gas, the aeration volume is generally 0.02 vvm to 2.0 vvm (vvm: aeration volume [mL]/liquid volume [mL]/time [min]) at 50 to 600 rpm. From the viewpoint of suppressing physical damage to Escherichia coli, the aeration is carried out preferably at 0.1 vvm to 2.0 vvm, more preferably at 0.1 win to 1.0 vvm.
The culture process may be continued from the beginning of the culturing until the carbon source material in the mixture is exhausted, or until the activity of the acetyl-CoA producing microorganism disappears. The duration of the culture process may be varied with the number and the activity of the acetyl-CoA producing microorganism in the mixture and the amount of the carbon source material. In general, the duration may be at least one hour, and preferably at least four hours. The duration of the culture process may be unlimitedly continued by anew addition of the carbon source material or the acetyl-CoA producing microorganism, However, from the viewpoint of process efficiency, the duration may generally be set 5 days or less, preferably 72 hours or less. With regard to other conditions, conditions employed for usual cultivation may be applied as they are.
Methods of collecting the product of interest accumulated in the culture medium are not particularly restricted. For example, a method may be employed which includes removing microorganism cells from the culture medium by, for example, centrifugal separation, and thereafter separating the product of interest using a usual separation method such as distillation or membrane separation under conditions suitable for the kind of the product of interest.
The method of producing acetyl-CoA according to the invention may further include, before the culture process, a preculture process for achieving an appropriate cells number and/or appropriate activated state of the acetyl-CoA producing microorganism to be used. The preculture process may be any cultivation conducted under usually-employed conditions suitable for the type of the acetyl-CoA producing microorganism.
The acetyl-CoA producing microorganism used in the method of producing acetone is preferably the acetyl-CoA producing microorganism having the thiolase activity, the CoA transferase activity, and the acetoacetate decarboxylase activity, described above as a preferable aspect of the acetyl-CoA producing microorganism, from the viewpoint of the efficiency acetone production.
The acetyl-CoA producing microorganism used in the method of producing isopropyl alcohol is preferably the acetyl-CoA producing microorganism having the thiolase activity, the CoA transferase activity, the acetoacetate decarboxylase activity, and the isopropyl alcohol dehydrogenase activity, described above as a preferable aspect of the acetyl-CoA producing microorganism, from the viewpoint of the efficiency of isopropyl alcohol production.
The method of producing isopropyl alcohol or the method of producing acetone preferably includes a culture process in which the acetyl-CoA producing microorganism is cultured while gas is supplied into the mixture containing the acetyl-CoA producing microorganism and the carbon source material; and a collection process for collecting the product of interest, in which isopropyl alcohol or acetone produced by the culturing is separated and collected from the mixture.
According to the method of producing isopropyl alcohol or the method of producing acetone, the acetyl-CoA producing microorganism is cultured while gas is supplied into the mixture (aeration culture). In this aeration culture, isopropyl alcohol produced or acetone produced is released into the mixture, and evaporated from the mixture. As a result, the isopropyl alcohol produced or the acetone produced can be easily separated from the mixture. Further, since the isopropyl alcohol produced or the acetone produced is continuously separated from the mixture, an increase in the concentration of the isopropyl alcohol or acetone in the mixture can be suppressed. Therefore, it is not necessary to pay particular attention to the tolerance of the acetyl-CoA producing microorganism against isopropyl alcohol or acetone.
The mixture in this method may be mainly composed of a basic medium generally used fin culture of the host microorganism. With regard to culture conditions, those described above shall apply as they are.
In the collection process, isopropyl alcohol or acetone produced in the culture process and separated from the mixture is collected. The collection method may be any method capable of collecting isopropyl alcohol or acetone in the gaseous or droplet state evaporated from the mixture by usual cultivation. Examples thereof include a method of collecting into a collecting member such as a commonly-employed airtight container. In particular, the method preferably includes contacting a trap solution for trapping isopropyl alcohol or acetone with the isopropyl alcohol or acetone separated from the mixture, from the viewpoint of collecting only isopropyl alcohol or acetone with high purity.
In the method of producing isopropyl alcohol or the method of producing acetone, the isopropyl alcohol or acetone can be collected in a state in which isopropyl alcohol or acetone is dissolved in a trap solution or the mixture. Examples of the collection method include a method described in WO 2009/008377. The isopropyl alcohol or acetone collected can be confirmed using a usual detection means such as HPLC. The isopropyl alcohol collected may be further purified, if necessary. Examples of the purification method include distillation, etc.
In a case in which the isopropyl alcohol or acetone collected is in the state of aqueous solution, the method of producing isopropyl alcohol or the method of producing acetone may further include a dehydration process in addition to the collection process. The dehydration of isopropyl alcohol or acetone can be carried out by an ordinary method.
Examples of apparatuses applicable to the method of producing isopropyl alcohol or acetone in which isopropyl alcohol or acetone can be collected in the state being dissolved in the trap solution or the mixture include the production apparatus shown in FIG. 1 of WO 2009/008377.
In this production apparatus, an injection pipe for injecting a gas from outside the apparatus is connected to the culture tank that contains a culture medium including a microorganism to be used and a plant-derived raw material, thereby enabling aeration to the culture medium.
A trap tank that contains a trap solution as the trap liquid is connected to the culture tank via a connecting pipe. A gas or liquid that has moved to the trap tank contacts the trap solution, and bubbling occurs.
As a result, isopropyl alcohol or acetone, which has been produced in the culture tank by cultivation under aeration, is evaporated due to aeration, and, therefore, easily separated from the culture medium, and is trapped in the trap solution in the trap tank. As a result, isopropyl alcohol or acetone can be produced in a more purified state in a simple and continuous manner.
A method of producing glutamate according to the invention includes producing glutamate as the product of interest from a carbon source material using the above-described acetyl-CoA producing microorganism. Specifically, the method of producing glutamate includes culturing the acetyl-CoA producing microorganism in a state in which the acetyl-CoA producing microorganism contacts with a carbon source material (hereinafter, culture process), and collecting the product of interest (glutamate) obtained by the contact (hereinafter, collection process).
According to the method of producing glutamate, since the acetyl-CoA producing microorganism is cultured in a state in which the acetyl-CoA producing microorganism contacts with a carbon source material, the carbon source material is assimilated by the acetyl-CoA producing microorganism, and the product of interest can be efficiently produced while carbon dioxide is fixed.
The culture medium to be used for culture may be any usually-employed culture medium that includes a carbon source, a nitrogen source, and an inorganic salt; and an organic trace nutrient such as an amino acid or a vitamins as necessary. Either a synthetic culture medium or natural culture medium may be used. The carbon source and nitrogen source used in the culture medium may be of any types that can be utilized by the microorganisms to be cultured.
Examples of the carbon source material which may be used include sugars such as glucose, glycerol, fructose, sucrose, maltose, mannose, galactose, starch hydrolysates, and molasses; and organic acids such as acetic acid or citric acid, and alcohols such as ethanol may be used singly or in combination with other carbon sources.
Examples of the nitrogen source which may be used include ammonia, ammonium salts such as ammonium sulfate, ammonium carbonate, ammonium chloride, ammonium phosphate, or ammonium acetate, and nitric acid salts.
Examples of the organic micronutrient which may be used include amino acids, vitamins, fatty acids, and nucleic acids; and peptones, casamino acids, yeast extracts, and soybean protein hydrolysates, each of which contains the above ingredients. In a case in which an auxotrophic mutant that requires an amino acid and the like for growth is used, it is preferable to supply a nutrient to be required.
Examples of the inorganic salt which may be used include phosphoric acid salts, magnesium salts, calcium salts, iron salts, and manganese salts.
The culture is preferably carried out at a fermentation temperature of 20° C. to 45° C. at a pH of 3 to 9 under aeration. For adjusting the pH, an inorganic or organic, acidic or alkaline substance, ammonia gas, etc. may be used. L-amino acid is accumulated in the culture medium or in the cells by culturing the microorganism preferably for 10 hours to 120 hours under these conditions.
In a case in which the L-amino acid of interest is L-glutamate, the culture may be carried out such that L-glutamate produced is precipitated and accumulated in the culture medium, by using a liquid medium whose conditions are adjusted to precipitate L-glutamate. For example, the conditions to precipitate L-glutamate may be a pH of 5.0 to 4.0, preferably a pH of 4.5 to 4.0, more preferably a pH of 4.3 to 4.0, still more preferably a pH of 4.0. For achieving both increased growth under acidic conditions and efficient precipitation of L-glutamate, the pH is preferably from 5.0 to 4.0, more preferably from 4.5 to 4.0, still more preferably from 4.3 to 4.0. The culture at the above-described pH may be carried out either through the whole culture period or during a part of the culture period.
The L-amino acid may be collected from the culture liquid after completion of the culture according to a known collection method. For example, the collection may be carried out by a method in which concentration crystallization is carried out after removal of bacterial cells from a culture medium, or by ion-exchange chromatography. In a case in which the culture was carried out under conditions that allow precipitation of L-glutamate in a culture medium, the L-glutamate precipitated into the culture medium can be collected by centrifugal separation, filtration, or the like. In such cases, L-glutamate remaining dissolved in the culture medium may be crystallized, and the crystallized L-glutamate may be isolated together.
Examples of methods for producing proline, leucine, isoleucine, valine, arginine, citrulline, ornithine, acetic acid, (poly)3-hydroxybutyric acid, itaconic acid, citric acid, butyric acid, or polyglutamic acid include methods described in Fermentation Handbook (Kyoritsu Shuppan Co., Ltd.).
Examples of methods for producing 4-aminobutyric acid include a production method using a microorganism obtained by introducing glutamate decarboxylase to a glutamate-producing microorganism, and which is described, in for example, JP-A No. 2011-167097.
Examples of methods for producing 4-hydroxybutyric acid include a production method using a microorganism obtained by introducing glutamate decarboxylase, aminotransferase, and aldehyde dehydrogenase to a glutamate-producing microorganism, and which is described in, for example, JP-A No. 2009-171960.
Examples of methods for producing 3-hydroxyisobutyric acid include a production method using a microorganism to which the pathway described in, for example, WO 2009/135074 or WO 2008/145737 was introduced.
Examples of methods for producing 2-hydroxyisobutyric acid include a production method using a microorganism to which the pathway described in, for example, WO 2009/135074 or WO 2009/156214 was introduced.
Examples of methods for producing 3-aminoisobutyric acid or methacrylic acid include a production method using a microorganism to which the pathway described in, for example, WO 2009/135074 was introduced.
Hereinbelow, examples of the present invention is described in detail. However, the invention is by no means limited to these examples.
<Preparation of Escherichia coli B, atoD Genome-Enhanced Variant>
The whole sequence of the genomic DNA of Escherichia coli MG1655 is known (GenBank accession number U00096), and the base sequence of a gene encoding CoA transferase a subunit (hereinafter sometimes abbreviated to “atoD”) of Escherichia coli MG1655 has also been reported. That is, atoD is described in 2321469 to 2322131 of the Escherichia coli MG1655 genome sequence, which is described in GenBank accession number U00096.
As the base sequence of a promoter necessary for express the above-mentioned gene, the promoter sequence of glyceraldehyde-3-phosphate dehydrogenase (hereinafter sometimes referred to as “GAPDH”) derived from Escherichia coli, which is described in 397 to 440 in the base sequence information with a GenBank accession number X02662, can be used. In order to obtain the GAPDH promoter, amplification by a PCR method was carried out using the genomic DNA of Escherichia coli MG1655 as a template and using CGCTCAATTGCAATGATTGACACGATTCCG (SEQ ID NO: 1) and ACAGAATTCGCTATTTGTTAGTGAATAAAAGG (SEQ ID NO: 2) as primers and the DNA fragment obtained was digested with restriction enzymes MfeI and EcoRI, thereby obtaining a DNA fragment of about 100 bp encoding the GAPDH promoter. The obtained DNA fragment and a fragment obtained by digesting plasmid pUC19 (GenBank accession number X02514) with restriction enzyme EcoRI followed by alkaline phosphatase treatment were mixed, and the mixed fragments were ligated using a ligase. Thereafter, Escherichia coli DH5α competent cells (DNA-903, manufactured by Toyobo Co., Ltd.) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 50 μg/mL ampicillin were obtained. Ten of the colonies obtained were individually cultured at 37° C. overnight in an LB liquid medium containing 50 μg/mL ampicillin, and the plasmids were recovered, and plasmids from which the GAPDH promoter was not cut out when digested with restriction enzymes EcoRI and KpnI were selected. Further, the DNA sequence thereof was checked, and a plasmid in which the GAPDH promoter was properly inserted was named pGAP. The pGAP obtained was digested with restriction enzymes EcoRI and KpnI.
Furthermore, in order to obtain atoD, amplification by a PCR method was carried out using the genomic DNA of Escherichia coli MG1655 as a template and using CGAATTCGCTGGTGGAACATATGAAAACAAAATTGATGACATTACAAGAC (SEQ ID NO: 3) and GCGGTACCTTATTTGCTCTCCTGTGAAACG (SEQ ID NO: 4) as primers, and the DNA fragment obtained was digested with restriction enzymes EcoRI and KpnI, thereby obtaining an atoD fragment of about 690 bp. This DNA fragment was mixed with pGAP that had previously been digested with restriction enzymes EcoRI and KpnI. The mixed fragments were ligated using a ligase. Thereafter, Escherichia coli DH5α competent cells (DNA-903, manufactured by Toyobo Co., Ltd.) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 50 μg/mL ampicillin were obtained. A plasmid was recovered from the bacterial cells obtained, and it was confirmed that atoD was properly inserted. The plasmid obtained was named pGAPatoD.
Here, Escherichia coli MG1655 is available from American Type Culture Collection.
As described above, the base sequence of atoD in the genomic DNA of Escherichia coli MG1655 has also been reported. PCR was carried out using genomic DNA of Escherichia coli MG1655 as a template and using GCTCTAGATGCTGAAATCCACTAGTCTTGTC (SEQ ID NO: 5) and TACTGCAGCGTTCCAGCACCTTATCAACC (SEQ ID NO: 6) as primers, which were prepared based on the gene information of the 5′-flanking region of atoD of Escherichia coli MG1655, as a result of which a DNA fragment of about 1.1 kbp was amplified.
In addition, PCR was carried out using the expression vector pGAPatoD prepared above as a template, and using GGTCTAGAGCAATGATTGACACGATTCCG (SEQ ID NO: 7) prepared based on the sequence information of the GAPDH promoter of Escherichia coli MG1655 and a primer of SEQ ID NO:4 prepared based on the sequence information of atoD of Escherichia coli MG1655, as a result of which a DNA fragment of about 790 bp having the GAPDH promoter and atoD was obtained.
The fragments obtained from the above were digested with restriction enzymes PstI and XbaI, and XbaI and KpnI, respectively, and the resulting fragments were mixed with a fragment obtained by digesting a temperature-sensitive plasmid pTH18cs1 (GenBank accession number AB019610) [Hashimoto-Gotoh, T., Gene, 241, 185-191 (2000)] with PstI and KpnI, and the mixed fragments were ligating using a ligase. Thereafter, DH5α cells were transformed with the ligation product, and transformants that grew on an LB agar plate containing 10 μg/ml chloramphenicol at 30° C. were obtained. The colonies obtained were cultured at 30° C. overnight in an LB liquid medium containing 10 μg/ml chloramphenicol, and plasmids were recovered from the bacterial cells obtained. Escherichia coli B (ATCC 11303) was transformed with the plasmid, and was cultured at 30° C. overnight on an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which transformants were obtained. The transformants obtained were inoculated into an LB liquid medium containing 10 μg/ml chloramphenicol, and cultured at 30° C. overnight. The obtained cultured bacterial cells were applied to an LB agar plate containing 10 μg/ml chloramphenicol and cultured at 42° C., as a result of which colonies were obtained. The obtained colonies were cultured in an LB liquid medium containing no antibiotic at 30° C. for 2 hours, and the resulting culture was then applied to an LB agar plate containing no antibiotic, as a result of which colonies that grew at 42° C. were obtained.
From the colonies that appeared, 100 colonies were randomly picked up, and each individually grown on an antibiotic-free both an LB agar plate and an LB agar plate containing 10 μg/ml chloramphenicol, and chloramphenicol-sensitive clones were selected. Furthermore, a fragment of about 790 bp that contained the GAPDH promoter and atoD was amplified by PCR, from the chromosomal DNA of these clones, and a variant in which an atoD promoter region was replaced by the GAPDH promoter was selected. Then, a clone satisfying the above conditions was named Escherichia coli B, atoD genome-enhanced variant (hereinafter sometimes abbreviated to “B::atoDAB variant”).
Here, Escherichia coli B (ATCC 11303) is available from American Type Culture Collection, which is a bank of cells, microorganisms, and genes.
<Preparation of Escherichia coli B, atoD Genome-Enhanced, Pgi Gene-Deleted Variant>
The whole sequence of the genomic DNA of Escherichia coli MG1655 is known (GenBank accession number U00096), and the base sequence of a gene encoding phosphoglucose isomerase (hereinafter sometimes referred to as “pgi”) of Escherichia coli has also been reported (GenBank accession number X15196). In order to clone a region flanking the base sequence of the gene encoding pgi (1,650 bp), four types of oligonucleotide primers represented by CAGGAATTCGCTATATCTGGCTCTGCACG (SEQ ID NO: 8), CAGTCTAGAGCAATACTCTTCTGATTTTGAG (SEQ ID NO: 9), CAGTCTAGATCATCGTCGATATGTAGGCC (SEQ ID NO: 10), and GACCTGCAGATCATCCGTCAGCTGTACGC (SEQ ID NO: 11) were synthesized. The primer of SEQ ID NO: 8 has an EcoRI recognition site in the 5′-end side thereof, each of the primers of SEQ ID NOs: 9 and 10 has an XbaI recognition site in the 5′-end side thereof, and the primer of SEQ ID NO: 11 has a PstI recognition site in the 5′-end side thereof.
The genomic DNA of the Escherichia coli MG1655 (ATCC 700926) was prepared, and PCR was carried out using the obtained genomic DNA as a template and using a primer pair of SEQ ID NO: 8 and SEQ ID NO: 9, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “pgi-L fragment”) was amplified. In addition, PCR was carried out using a primer pair of SEQ ID NO: 10 and SEQ ID NO: 11, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “pgi-R fragment”) was amplified. These DNA fragments were separated by agarose electrophoresis, and recovered. The pgi-L fragment was digested with EcoRI and XbaI, and the pgi-R fragment was digested with XbaI and PstI. The two types of digested fragments and a fragment obtained by digesting a temperature-sensitive plasmid pTH18cs1 (GenBank accession number AB019610) with EcoRI and PstI were mixed, and allowed to react using T4 DNA ligase. Thereafter, Escherichia coli DH5α competent cells (manufactured by Toyobo Co., Ltd.) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 10 μg/ml chloramphenicol at 30° C. were obtained. Plasmid were recovered from the transformants obtained, and it was confirmed that the two fragments—the 5′-upstream flanking region fragment and 3′-downstream flanking region fragment of the gene encoding pgi—were properly inserted in pTH18cs1. The plasmid obtained was digested with XbaI, and then subjected to blunt-end treatment with T4 DNA polymerase. The resultant DNA fragment was mixed with a kanamycin-resistance gene obtained by digesting pUC4K plasmid (GenBank accession number X06404) (Pharmacia) with EcoRI and subjecting the resulting product to blunt-end treatment with T4 DNA polymerase, and the mixed fragments were ligated using T4 DNA ligase. Subsequently, Escherichia coli DH5α competent cells were transformed with the ligation product, and transformants that grew on an LB agar plate containing 10 μg/ml chloramphenicol and 50 μg/ml kanamycin at 30° C. were obtained. A plasmid was recovered from the transformants obtained, and it was confirmed that the kanamycin-resistance gene was properly inserted between the 5′-upstream flanking region fragment and 3′-downstream flanking region fragment of the gene encoding pgi. The plasmid obtained was named pTH18cs1-pgi.
Here, Escherichia coli MG1655 can be obtained from American Type Culture Collection.
The B::atoDAB variants prepared in Example 1 were transformed with the thus-obtained plasmid pTH18cs1-pgi, and was cultured at 30° C. overnight on an LB agar plate containing 10 μg/ml chloramphenicol and 50 μg/ml kanamycin, as a result of which transformants were obtained. The transformants obtained were inoculated into an LB liquid medium containing 50 μg/ml kanamycin, and cultured at 30° C. overnight. Subsequently, part of the resulting culture liquid was applied to an LB agar plate containing 50 μg/ml kanamycin, as a result of which colonies that grew at 42° C. were obtained. The colonies obtained were cultured at 30° C. for 24 hours in an LB liquid medium containing 50 μg/ml kanamycin, and was applied to an LB agar plate containing 50 μg/ml kanamycin, as a result of which colonies that grew at 42° C. were obtained.
From the colonies that appeared, 100 colonies were randomly picked up, and each individually grown on an LB agar plate containing 50 μg/ml kanamycin and an LB agar plate containing 10 μg/ml chloramphenicol, and chloramphenicol-sensitive clones that grew only on the LB agar plate containing kanamycin were selected. Furthermore, the chromosomal DNAs of these target clones were amplified by PCR, and a variant from which a fragment of about 3.3 kbp, which indicates replacement of the pgi gene by the kanamycin-resistance gene, could be amplified was selected. The variant obtained was named Escherichia coli B, atoD genome-enhanced, pgi gene-deleted variant (hereinafter sometimes abbreviated to “B::atoDABΔpgi variant”).
Here, Escherichia coli MG1655 and Escherichia coli B are available from American Type Culture Collection.
<Preparation of Escherichia coli B atoD Genome-Enhanced, Pgi Gene-Deleted, gntR Gene-Deleted Variant>
The whole sequence of the genomic DNA of Escherichia coli B is known (GenBank accession No. CP000819), and the base sequence encoding GntR is described in 3509184 to 3510179 of the genomic sequence of Escherichia coli B, which is described in GenBank accession No. CP000819. In order to clone a region flanking the base sequence of the gene encoding GntR (gntR), four types of oligonucleotide primers represented by GGAATTCGGGTCAATTTTCACCCTCTATC (SEQ ID NO: 12), GTGGGCCGTCCTGAAGGTACAAAAGAGATAGATTCTC (SEQ ID NO: 13), CTCTTTTGTACCTTCAGGACGGCCCACAAATTTGAAG (SEQ ID NO: 14), and GGAATTCCCAGCCCCGCAAGGCCGATGGC (SEQ ID NO: 15) were synthesized. Each of the primers of SEQ ID NOs: 12 and 13 has an EcoRI recognition site in the 5′-end side thereof.
The genomic DNA of Escherichia coli B (GenBank accession No. CP000819) was prepared, and PCR was carried out using the obtained genomic DNA as a template and a primer pair of SEQ ID NO: 12 and SEQ ID NO: 13, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “gntR-L fragment”) was amplified. In addition, PCR was carried out using a primer pair of SEQ ID NO: 14 and SEQ ID NO: 15, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “gntR-R fragment”) was amplified. These DNA fragments were separated by agarose electrophoresis, and recovered. PCR was carried out using the gntR-L and gntR-R fragments as templates and using a primer pair of SEQ ID NO: 12 and SEQ ID NO: 15, as a result of which a DNA fragment of about 2.0 kbp (hereinafter sometimes referred to as “gntR-LR fragment”) was amplified. This gntR-LR fragment was separated by agarose electrophoresis, recovered, digested with EcoRI, and mixed with a fragment obtained by digesting a temperature-sensitive plasmid pTH18cs1 (GenBank accession number AB019610) with EcoRI. The mixed fragments were allowed to react using T4 DNA ligase. Thereafter, Escherichia coli DH5α competent cells (manufactured by Toyobo Co., Ltd.) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 10 μg/ml chloramphenicol at 30° C. were obtained. A plasmid was recovered from the transformants obtained, and it was confirmed that the gntLR fragment was properly inserted in pTH18cs1. The plasmid obtained was named pTH18cs1-gntR.
The Escherichia coli B::atoDABΔpgi variant prepared in Example 2 was transformed with the thus-obtained plasmid pTH18cs1-gntR, and was cultured at 30° C. overnight on an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which transformants were obtained. The transformants obtained were inoculated into an LB liquid medium containing 10 μg/ml chloramphenicol, and cultured at 30° C. overnight. Subsequently, part of the culture liquid was applied to an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which colonies that grew at 42° C. were obtained. The colonies obtained were cultured at 30° C. for 24 hours in an LB liquid medium, and was applied to an LB agar plate, as a result of which colonies that grew at 42° C. were obtained.
From the colonies that appeared, 100 colonies were randomly picked up, and each individually grown on an LB agar plate and an LB agar plate containing 10 μg/ml chloramphenicol, and chloramphenicol-sensitive clones were selected. Furthermore, the chromosomal DNAs of these target clones were amplified by PCR, and a variant from which a fragment of about 2.0 kbp, which indicates deletion of the gntR gene, could be amplified was selected. The variant obtained was named Escherichia coli B, atoD genome-enhanced, pgi gene-deleted, gntR gene-deleted variant (hereinafter sometimes abbreviated to “B::atoDABΔpgiΔgntR variant”).
<Preparation of Escherichia coli B, atoD Genome-Enhanced, Pgi Gene-Deleted, gntR Gene-Deleted, Gnd Gene-Deleted Variant>
In order to clone a region flanking the base sequence of the gene encoding phosphogluconate dehydrogenase (gnd), four types of oligonucleotide primers represented by CGCCATATGAATGGCGCGGCGGGGCCGGTGG (SEQ ID NO: 16), TGGAGCTCTGTTTACTCCTGTCAGGGGG (SEQ ID NO: 17), TGGAGCTCTCTGATTTAATCAACAATAAAATTG (SEQ ID NO: 18), and CGGGATCCACCACCATAACCAAACGACGG (SEQ ID NO: 19) were synthesized. The primer of SEQ ID NO: 16 has an NdeI recognition site in the 5′-end side thereof, and each of the primers of SEQ ID NOs: 17 and 18 has a SacI recognition site in the 5′-end side thereof. Further, the primer of SEQ ID NO: 19 has a BamHI recognition site in the 5′-end side thereof.
The genomic DNA of Escherichia coli B (GenBank accession No. CP000819) was prepared, and PCR was carried out using a primer pair of SEQ ID NO: 16 and SEQ ID NO: 17, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “gnd-L fragment”) was amplified. In addition, PCR was carried out using a primer pair of SEQ ID NO: 18 and SEQ ID NO: 19, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “gnd-R fragment”) was amplified. These DNA fragments were separated by agarose electrophoresis, and recovered. The gnd-L fragment was digested with NdeI and SacI, and the gnd-R fragment was digested with SacI and BamHI. These two types of digested fragments were mixed with a fragment obtained by digesting a temperature-sensitive plasmid pTH18cs1 (GenBank accession number AB019610) with NdeI and BamHI, and the mixed fragments were allowed to react using T4 DNA ligase. Thereafter, s competent cells (manufactured by Toyobo Co., Ltd.) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 10 μg/ml chloramphenicol at 30° C. were obtained. Plasmids were recovered from the transformants obtained, and it was confirmed that the two fragments—the 5′-upstream flanking region fragment and 3′-downstream flanking region fragment of the gene encoding gnd—were properly inserted in pTH18cs1. The plasmid obtained was named pTH18cs1-gnd.
The Escherichia coli B::atoDABΔpgiΔgntR variant prepared in Example 3 was transformed with the thus-obtained plasmid pTH18cs1-gnd, and was cultured at 30° C. overnight on an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which transformants were obtained. The transformants obtained were inoculated into an LB liquid medium containing 10 μg/ml chloramphenicol, and cultured at 30° C. overnight. Next, part of this culture liquid was applied to an LB agar plate containing 10 μg/ml kanamycin, as a result of which colonies that grew at 42° C. were obtained. The colonies obtained were cultured at 30° C. for 24 hours in an LB liquid medium, and was applied to an LB agar plate, as a result of which colonies that grew at 42° C. were obtained.
From the colonies that appeared, 100 colonies were randomly picked up, and each individually grown on an LB agar plate and an LB agar plate containing 10 μg/ml chloramphenicol, and chloramphenicol-sensitive clones were selected. Furthermore, the chromosomal DNAs of these target clones were amplified by PCR, and a variant from which a fragment of about 2.0 kbp, which indicates deletion of the gnd gene, could be amplified was selected. The variant obtained was named Escherichia coli B, atoD genome-enhanced, pgi gene-deleted, gntR gene-deleted, gnd gene-deleted variant (B::atoDABΔpgiΔgntRΔgnd variant).
<Preparation of Escherichia coli B, atoD Genome-Enhanced, Pgi Gene-Deleted, gntR Gene-Deleted, Gnd Gene-Deleted, ldhA Gene-Deleted Variant>
In order to clone a region flanking the base sequence of the gene encoding D-lactate dehydrogenase (hereinafter sometimes abbreviated to “ldhA”) (990 bp), four types of oligonucleotide primers represented by GGAATTCGACCATCGCTTACGGTCAATTG (SEQ ID NO: 20), GAGCGGCAAGAAAGACTTTCTCCAGTGATMTG (SEQ ID NO: 21), GGAGAAAGTCTTTCTTGCCGCTCCCCTGCAAC (SEQ ID NO: 22), and GGAATTCTTTAGCAAATGGCTTTCTTC (SEQ ID NO: 23) were synthesized. Each of the primers of SEQ ID NOs: 20 and 23 has an EcoRI recognition site in the 5′-end side thereof.
The genomic DNA of Escherichia coli B (GenBank accession No. CP000819) was prepared, and PCR was carried out using the obtained genomic DNA as a template and a primer pair of SEQ ID NO: 20 and SEQ ID NO: 21, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “ldhA-L fragment”) was amplified. In addition, PCR was carried out using a primer pair of SEQ ID NO: 22 and SEQ ID NO: 23, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “ldhA-R fragment”) was amplified. These DNA fragments were separated by agarose electrophoresis, and recovered. PCR was carried out using the ldhA-L and ldhA-R fragments as templates and using a primer pair of SEQ ID NO: 20 and SEQ ID NO: 23, as a result of which a DNA fragment of about 2.0 kbp (hereinafter sometimes referred to as “ldhA-LR fragment”) was amplified. This ldhA-LR fragment was separated by agarose electrophoresis, recovered, digested with EcoRI, and mixed with a fragment obtained by digesting a temperature-sensitive plasmid pTH18cs1 (GenBank accession number AB019610) with EcoRI. The mixed fragments were allowed to react using T4 DNA ligase. Thereafter, Escherichia coli DH5α competent cells (manufactured by Toyobo Co., Ltd.) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 10 μg/ml chloramphenicol at 30° C. were obtained. A plasmid was recovered from the transformants obtained, and it was confirmed that the ldhA-LR fragment was properly inserted in pTH18cs1. The plasmid obtained was named pTH18cs1-ldhA.
The Escherichia coli B::atoDABΔpgiΔgntRΔgnd variant prepared in Example 4 was transformed with the thus-obtained plasmid pTH18cs1-ldhA, and was cultured at 30° C. overnight on an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which transformants were obtained. The transformants obtained were inoculated into an LB liquid medium containing 10 μg/ml chloramphenicol, and cultured at 30° C. overnight. Subsequently, part of the culture liquid was applied to an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which colonies that grew at 42° C. were obtained. The colonies obtained were cultured at 30° C. for 24 hours in an LB liquid medium, and was applied to an LB agar plate, as a result of which colonies that grew at 42° C. were obtained.
From the colonies that appeared, 100 colonies were randomly picked up, and each individually grown on an LB agar plate and an LB agar plate containing 10 μg/ml chloramphenicol, and chloramphenicol-sensitive clones were selected. Furthermore, the chromosomal DNAs of these target clones were amplified by PCR, and a variant from which a fragment of about 2.0 kbp, which indicates deletion of the ldhA gene, could be amplified was selected. The variant obtained was named Escherichia coli B, atoD genome-enhanced, pgi gene-deleted, gntR gene-deleted, gnd gene-deleted, ldhA gene-deleted variant (hereinafter sometimes abbreviated to “B::atoDABΔpgiΔgntRΔgndΔldhA variant”).
<Preparation of Escherichia coli B, atoD Genome-Enhanced, Pgi Gene-Deleted, gntR Gene-Deleted, Gnd Gene-Deleted, ldhA Gene-Deleted, aceBA Gene-Deleted Variant>
In order to clone a region flanking the base sequence of the gene encoding isocitrate lyase and the gene encoding malate synthase (hereinafter sometimes abbreviated to “aceBA”) (2936 bp), four types of oligonucleotide primers represented by GGAATTCATTCAGCTGTTGCGCATCGATTC (SEQ ID NO: 24), CGGTTGTTGTTGCCGTGCAGCTCCTCGTCATGGATC (SEQ ID NO: 25), GGAGCTGCACGGCAACAACAACCGTTGCTGACTG (SEQ ID NO: 26), and GGAATTCCAGGCAGGTATCAATAAATAAC (SEQ ID NO: 27) were synthesized. Each of the primers of SEQ ID NOs: 24 and 27 has an EcoRI recognition site in the 5′-end side thereof.
The genomic DNA of Escherichia coli B (GenBank accession No. CP000819) was prepared, and PCR was carried out using the obtained genomic DNA as a template and a primer pair of SEQ ID NO: 24 and SEQ ID NO: 25, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “aceBA-L fragment”) was amplified. In addition, PCR was carried out using a primer pair of SEQ ID NO: 26 and SEQ ID NO: 27, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “aceBA-R fragment”) was amplified. These DNA fragments were separated by agarose electrophoresis, and recovered. PCR was carried out using the aceBA-L and aceBA-R fragments as templates and using a primer pair of SEQ ID NO: 24 and SEQ ID NO: 27, as a result of which a DNA fragment of about 2.0 kbp (hereinafter sometimes referred to as “aceBA-LR fragment”) was amplified. This aceBA-LR fragment was separated by agarose electrophoresis, recovered, digested with EcoRI, and mixed with a fragment obtained by digesting a temperature-sensitive plasmid pTH18cs1 (GenBank accession number AB019610) with EcoRI. The mixed fragments were allowed to react using T4 DNA ligase. Thereafter, Escherichia coli DH5α competent cells (manufactured by Toyobo Co., Ltd.) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 10 μg/ml chloramphenicol at 30° C. were obtained. A plasmid was recovered from the transformants obtained, and it was confirmed that the aceBA-LR fragment was properly inserted in pTH18cs1. The plasmid obtained was named pTH18cs1-aceBA.
The Escherichia coli B::atoDABΔpgiΔgntRΔgndΔldhA variant prepared in Example 5 was transformed with the thus-obtained plasmid pTH18cs1-aceBA, and was cultured at 30° C. overnight on an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which transformants were obtained. The transformants obtained were inoculated into an LB liquid medium containing 10 μg/ml chloramphenicol, and cultured at 30° C. overnight. Subsequently, part of the culture liquid was applied to an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which colonies that grew at 42° C. were obtained. The colonies obtained were cultured at 30° C. for 24 hours in an LB liquid medium, and was applied to an LB agar plate, as a result of which colonies that grew at 42° C. were obtained.
From the colonies that appeared, 100 colonies were randomly picked up, and each individually grown on an LB agar plate and an LB agar plate containing 10 μg/ml chloramphenicol, and chloramphenicol-sensitive clones were selected. Furthermore, the chromosomal DNAs of these target clones were amplified by PCR, and a variant from which a fragment of about 2.0 kbp, which indicates deletion of the aceBA gene, could be amplified was selected. The variant obtained was named Escherichia coli B, atoD genome-enhanced, pgi gene-deleted, gntR gene-deleted, gnd gene-deleted, ldhA gene-deleted, aceBA gene-deleted variant (hereinafter sometimes abbreviated to “B::atoDABΔpgiΔgntRΔgndΔldhAΔaceBA variant”).
<Preparation of Escherichia coli B, atoD Genome-Enhanced, Pgi Gene-Deleted, gntR Gene-Deleted, Gnd Gene-Deleted, ldhA Gene-Deleted, aceBA Gene-Deleted, glcB Gene-Deleted Variant>
In order to clone a region flanking the base sequence of the gene encoding malate synthase G (hereinafter sometimes abbreviated to “glcB”) (723 bp), four types of oligonucleotide primers represented by GGAATTCCAGGAGAAAGGGCTGGCACGGG (SEQ ID NO: 28), CTTTTTTGACGCTATGTTTATCTCCTCGTTTTCGC (SEQ ID NO: 29), GAGATAAACATAGCGTCAAAAAAGCCCCGGC (SEQ ID NO: 30), and GGAATTCCGTCCATCATTGCTACCAGCC (SEQ ID NO: 31) were synthesized. Each of the primers of SEQ ID NOs: 28 and 31 has an EcoRI recognition site in the 5′-end side thereof.
The genomic DNA of Escherichia coli B (GenBank accession No. CP000819) was prepared, and PCR was carried out using the obtained genomic DNA as a template and a primer pair of SEQ ID NO: 28 and SEQ ID NO: 29, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “glcB-L fragment”) was amplified. In addition, PCR was carried out using a primer pair of SEQ ID NO: 30 and SEQ ID NO: 31, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “glcB-R fragment”) was amplified. These DNA fragments were separated by agarose electrophoresis, and recovered. PCR was carried out using the glcB-L and glcB-R fragments as templates and using a primer pair of SEQ ID NO: 28 and SEQ ID NO: 31, as a result of which a DNA fragment of about 2.0 kbp (hereinafter sometimes referred to as “glcB-LR fragment”) was amplified. This glcB-LR fragment was separated by agarose electrophoresis, recovered, digested with EcoRI, and mixed with a fragment obtained by digesting a temperature-sensitive plasmid pTH18cs1 (GenBank accession number AB019610) with EcoRI. The mixed fragments were allowed to react using T4 DNA ligase. Thereafter, Escherichia coli DH5α competent cells (manufactured by Toyobo Co., Ltd.) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 10 μg/ml chloramphenicol at 30° C. were obtained. A plasmid was recovered from the transformants obtained, and it was confirmed that the glcB-LR fragment was properly inserted in pTH18cs1. The plasmid obtained was named pTH18cs1-glcB.
The Escherichia coli B::atoDABΔpgiΔgntRΔgndΔldhAΔaceBA variant prepared in Example 6 was transformed with the thus-obtained plasmid pTH18cs1-glcB, and was cultured at 30° C. overnight on an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which transformants were obtained. The transformants obtained were inoculated into an LB liquid medium containing 10 μg/ml chloramphenicol, and cultured at 30° C. overnight. Subsequently, part of the culture liquid was applied to an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which colonies that grew at 42° C. were obtained. The colonies obtained were cultured at 30° C. for 24 hours in an LB liquid medium, and was applied to an LB agar plate, as a result of which colonies that grew at 42° C. were obtained.
From the colonies that appeared, 100 colonies were randomly picked up, and each individually grown on an LB agar plate and an LB agar plate containing 10 μg/ml chloramphenicol, and chloramphenicol-sensitive clones were selected. Furthermore, the chromosomal DNAs of these target clones were amplified by PCR, and a variant from which a fragment of about 2.0 kbp, which indicates deletion of the glcB gene, could be amplified was selected. The variant obtained was named Escherichia coli B, atoD genome-enhanced, pgi gene-deleted, gntR gene-deleted, gnd gene-deleted, ldhA gene-deleted, aceBA gene-deleted, glcB gene-deleted variant (hereinafter sometimes abbreviated to “B::atoDABΔpgiΔgntRΔgndΔldhAΔaceBAΔglcB variant”).
<Preparation of Escherichia coli B, atoD Genome-Enhanced, Pgi Gene-Deleted, gntR Gene-Deleted, Gnd Gene-Deleted, ldhA Gene-Deleted, aceBA Gene-Deleted, glcB Gene-Deleted, fumAC Gene-Deleted Variant>
In order to clone a region flanking the base sequence of the gene encoding fumarate hydratase A and the gene encoding fumarate hydratase C (hereinafter sometimes abbreviated to “fumAC”) (3193 bp), four types of oligonucleotide primers represented by CGCCATATGATCGCCAGCGCGCGGGATTTTTC (SEQ ID NO: 32), CGAGCTCTGTTCTCTCACTTACTGCCTGG (SEQ ID NO: 33), ATGAGCTCTCTGCAACATACAGGTGCAG (SEQ ID NO: 34), and CGGGATCCACTACGCGCACGATGGTCAAG (SEQ ID NO: 35) were synthesized. The primer of SEQ ID NO: 32 has a NdeI recognition site in the 5′-end side thereof. Each of the primers of SEQ ID NOs: 33 and 34 has a SacI recognition site in the 5′-end side thereof. The primer of SEQ ID NO: 35 has a BamHI recognition site in the 5′-end side thereof.
The genomic DNA of Escherichia coli B (GenBank accession No. CP000819) was prepared, and PCR was carried out using the obtained genomic DNA as a template and a primer pair of SEQ ID NO: 32 and SEQ ID NO: 33, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “fumA-L fragment”) was amplified. In addition, PCR was carried out using a primer pair of SEQ ID NO: 34 and SEQ ID NO: 35, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “fumC-R fragment”) was amplified. These DNA fragments were separated by agarose electrophoresis, and recovered. The fumA-L fragment was digested with NdeI and SacI, and the fumC-R fragment was digested with SacI and BamHI. These digested fragments were mixed with a fragment obtained by digesting a temperature-sensitive plasmid pTH18cs1 (GenBank accession number AB019610) with NdeI and BamHI. The mixed fragments were allowed to react using T4 DNA ligase. Thereafter, Escherichia coli DH5α competent cells (manufactured by Toyobo Co., Ltd.) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 10 μg/ml chloramphenicol at 30° C. were obtained. A plasmid was recovered from the transformants obtained, and it was confirmed that the fumA-L fragment and the fumC-R fragment were properly inserted in pTH18cs1. The plasmid obtained was named pTH18cs1-fumAC.
The Escherichia coli B::atoDABΔpgiΔgntRΔgndΔldhAΔaceBAΔglcB variant prepared in Example 7 was transformed with the thus-obtained plasmid pTH18cs1-fumAC, and was cultured at 30° C. overnight on an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which transformants were obtained. The transformants obtained were inoculated into an LB liquid medium containing 10 μg/ml chloramphenicol, and cultured at 30° C. overnight. Subsequently, part of the culture liquid was applied to an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which colonies that grew at 42° C. were obtained. The colonies obtained were cultured at 30° C. for 24 hours in an LB liquid medium, and was applied to an LB agar plate, as a result of which colonies that grew at 42° C. were obtained.
From the colonies that appeared, 100 colonies were randomly picked up, and each individually grown on an LB agar plate and an LB agar plate containing 10 μg/ml chloramphenicol, and chloramphenicol-sensitive clones were selected. Furthermore, the chromosomal DNAs of these target clones were amplified by PCR, and a variant from which a fragment of about 2.0 kbp, which indicates deletion of the fumAC gene, could be amplified was selected. The variant obtained was named Escherichia coli B, atoD genome-enhanced, pgi gene-deleted, gntR gene-deleted, gnd gene-deleted, ldhA gene-deleted, aceBA gene-deleted, glcB gene-deleted, fumAC gene-deleted variant (hereinafter sometimes abbreviated to “B::atoDABΔpgiΔgntRΔgndΔldhAΔaceBAΔglcBΔfumAC variant”).
<Preparation of Plasmid pIaz>
Acetoacetate decarboxylase of Clostridium bacteria is described in GenBank accession number M55392, and isopropyl alcohol dehydrogenase of Clostridium bacteria is described in GenBank accession number AF157307.
As the base sequence of a promoter necessary to express the above-mentioned gene group, the promoter sequence of glyceraldehyde-3-phosphate dehydrogenase (hereinafter sometimes referred to as “GAPDH”) from Escherichia coli, which is described at 397 to 440 in the base sequence information with a GenBank accession number X02662, can be used.
In order to obtain the GAPDH promoter, amplification by a PCR method was carried out using the genomic DNA of Escherichia coli MG1655 as a template and using CGAGCTACATATGCAATGATTGACACGATTCCG (SEQ ID NO: 36) and CGCGCGCATGCTATTTGTTAGTGAATAAAAGG (SEQ ID NO: 37), and the DNA fragment obtained was digested with restriction enzymes NdeI and SphI, as a result of which a DNA fragment of about 110 bp corresponding to the GAPDH promoter was obtained. The DNA fragment obtained was mixed with a fragment obtained by digesting plasmid pBR322 (GenBank accession number J01749) with restriction enzymes NdeI and SphI, and the mixed fragments were ligated using a ligase. Thereafter, Escherichia coli DH5α competent cells (Toyobo Co., Ltd., DNA-903) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 50 μg/mL ampicillin were obtained. The colonies obtained were cultured at 37° C. overnight in an LB liquid medium containing 50 μg/mL ampicillin, and plasmid pBRgapP was recovered from the bacterial cells obtained.
In order to obtain the isopropyl alcohol dehydrogenase gene, amplification by a PCR method was carried out using the genomic DNA of Clostridium beijerinckii NRRL B-593 as a template and using AATATGCATGCTGGTGGAACATATGAAAGGTTTTGCAATGCTAGG (SEQ ID NO: 38) and ACGCGTCGACTTATAATATAACTACTGCTTTAATTAAGTC (SEQ ID NO: 39), and the DNA fragment obtained was digested with restriction enzymes SphI and SalI, as a result of which an isopropyl alcohol dehydrogenase fragment of about 1.1 kbp was obtained. The DNA fragment obtained was mixed with a fragment obtained by digesting plasmid pUC119 with restriction enzymes SphI and SalI, and these fragments were ligated together using ligase. Thereafter, Escherichia coli DH5α competent cells were transformed with the ligation product, and transformants that grew on an LB agar plate containing 50 μg/mL ampicillin were obtained. The obtained colonies were cultured at 37° C. overnight in an LB liquid medium containing 50 μg/mL ampicillin, and plasmids were recovered from the obtained bacterial cells. Correct insertion of the IPAdh was confirmed, and the plasmid obtained was named pUC-I.
The fragment having IPAdh obtained by digesting plasmid pUC-I with restriction enzymes SphI and EcoRI was mixed with a fragment obtained by digesting plasmid pBRgapP with restriction enzymes SphI and EcoRI, and the mixed fragments were ligated using a ligase. Thereafter, Escherichia coli DH5α competent cells were transformed with the ligation product, and transformants that grew on an LB agar plate containing 50 μg/mL ampicillin were obtained. The colonies obtained were cultured at 37° C. overnight in an LB liquid medium containing 50 μg/mL ampicillin, and plasmids were recovered from the bacterial cells obtained, and it was confirmed that IPAdh was properly inserted. The plasmid obtained was named pGAP-I.
In order to obtain the acetoacetate decarboxylase gene, amplification by a PCR method was carried out using the genomic DNA of Clostridium acetobutylicum ATCC 824 as a template and using ACGCGTCGACGCTGGTGGAACATATGTTAAAGGATGAAGTAATTAAACAAATTAGC (SEQ ID NO: 40) and GCTCTAGAGGTACCTTACTTAAGATAATCATATATAACTTCAGC (SEQ ID NO: 41), and the DNA fragment obtained was digested with restriction enzymes SalI and XbaI, as a result of which an acetoacetate decarboxylase fragment of about 700 bp was obtained. The DNA fragment obtained was mixed with a fragment obtained by digesting the plasmid pGAP-I prepared above with restriction enzymes SalI and XbaI, and the mixed fragments were ligated using a ligase. Thereafter, Escherichia coli DH5α competent cells were transformed with the ligation product, and transformants that grew on an LB agar plate containing 50 μg/mL ampicillin were obtained. The colonies obtained were cultured at 37° C. overnight in an LB liquid medium containing 50 μg/mL ampicillin, and plasmids were recovered from the bacterial cells obtained, and it is confirmed that adc was correctly inserted. The plasmid obtained was named pIa.
In order to obtain the glucose-6-phosphate-1-dehydrogenase gene (zwf), amplification by a PCR method was carried out using the genomic DNA of Escherichia coli B (GenBank accession No. CP000819) as a template and using GCTCTAGACGGAGAAAGTCTTATGGCGGTAACGCAAACAGCCCAGG (SEQ ID NO: 42) and CGGGATCCCGGAGAAAGTCTTATGAAGCAAACAGTTTATATCGCC (SEQ ID NO: 43), and the DNA fragment obtained was digested with restriction enzymes BamHI and XbaI, as a result of which a glucose-6-phosphate-1-dehydrogenase fragment of about 1,500 bp was obtained. The DNA fragment obtained was mixed with a fragment obtained by digesting the plasmid pIa prepared above with restriction enzymes BamHI and XbaI, and the mixed fragments were ligated using a ligase. Thereafter, Escherichia coli DH5α competent cells were transformed with the ligation product, and transformants that grew on an LB agar plate containing 50 μg/mL ampicillin were obtained. The colonies obtained was cultured at 37° C. overnight in an LB liquid medium containing 50 μg/mL ampicillin, and this plasmid was named pIaz.
<Preparation of Plasmid pMWGKC>
Amplification by a PCR method was carried out using pBRgapP as a template and using CCGCTCGAGCATATGCTGTCGCAATGATTGACACG (SEQ ID NO: 44) and GCTATTCCATATGCAGGGTTATTGTCTCATGAGC (SEQ ID NO: 45), and the DNA fragment obtained was phosphorylated using T4 Polynucleotide kinase (Takara), as a result of which a DNA fragment harboring the GAPDH promoter was obtained. Further, plasmid pMW119 (GenBank accession number AB005476) was treated with restriction enzymes NdeI, and the DNA fragment obtained was subjected to blunt-end treatment with KOD plus DNA polymerase (Takara), as a result of which a DNA fragment harboring the replication origin of pMW119 was obtained. The DNA fragment harboring the GAPDH promoter and the DNA fragment harboring the replication origin of pMW119 were mixed, and the mixed fragments were ligated using a ligase. Thereafter, Escherichia coli DH5α competent cells were transformed with the ligation product, and transformants that grew on an LB agar plate containing 50 μg/mL ampicillin were obtained. The colonies obtained were cultured at 37° C. overnight in an LB liquid medium containing 50 μg/mL ampicillin, and plasmid pMWG was recovered from the bacterial cells obtained.
In order to obtain a chloramphenicol-resistance gene, amplification by a PCR method was carried out using pTH18cs1 (GenBank accession No. AB019610) as a template and using TCGGCACGTAAGAGGTTCC (SEQ ID NO: 46) and CGGGTCGAATTTGCTTTCG (SEQ ID NO: 47), and the DNA fragment obtained was phosphorylated using T4 Polynucleotide kinase (Takara), as a result of which a DNA fragment containing a chloramphenicol-resistance gene was obtained. In addition, amplification by a PCR method was carried out using pMWG as a template and using CTAGATCTGACAGTAAGACGGGTAAGCC (SEQ ID NO: 48) and CTAGATCTCAGGGTTATTGTCTCATGAGC (SEQ ID NO: 49). The DNA fragment obtained was mixed with the DNA fragment containing the chloramphenicol-resistance gene, and the mixed fragments were ligated using a ligase. Thereafter, Escherichia coli DH5α competent cells were transformed with the ligation product, and transformants that grew on an LB agar plate containing 25 μg/mL chloramphenicol were obtained. The colonies obtained were cultured at 37° C. overnight in an LB liquid medium containing 25 μg/mL chloramphenicol, and the plasmid obtained was named pMWGC.
Amplification by a PCR method was carried out using the pMWGC gene as a template and using CCTTTGGTTAAAGGCTTTAAGATCTTCCAGTGGACAAACTATGCC (SEQ ID NO: 50) and GGCATAGTTTGTCCACTGGAAGATCTTAAAGCCTTTAACCAAAGG (SEQ ID NO: 51). Thereafter, Escherichia coli DH5α competent cells were transformed with the DNA fragment obtained, and transformants that grew on an LB agar plate containing 25 μg/mL chloramphenicol were obtained. The colonies obtained were cultured at 37° C. overnight in an LB liquid medium containing 25 μg/mL chloramphenicol, and plasmid pMWGKC was recovered from the bacterial cells obtained.
<Construction of Expression Plasmid for Malate Thiokinase Derived from Methylobacterium extorquens IAM12632>
Methylobacterium extorquens IAM 12632 was purchased from IAM Culture Collection, Institute of Molecular and Cellular Biosciences, the University of Tokyo. IAM 12632 was cultured in a medium (medium number: 352, NBRC), and chromosomal DNA was obtained therefrom using DNeasy Blood &Tissue Kit (QIAGEN).
PCR was carried out using the chromosomal DNA of Methylobacterium extorquens IAM 12632 as a template and using AAAAGGCGGAATTCACAAAAAGGATAAAACAATGGACGTTCACGAGTACCAAGC C (SEQ ID NO: 52) and CATGCCTGCAGGTCGACTCTAGAGGCGAGGTTCTTTTTCCGGACTC (SEQ ID NO: 53) as primers, as a result of which a malate thiokinase fragment was obtained. In addition, PCR was carried out using the chromosomal DNA of Methylobacterium extorquens as a template and using GGATCCTCTAGACTGGTGGAATATATGAGCTTCACCCTGATCCAGCAG (SEQ ID NO: 54) and GGCATGCAAGCTTTTACTTTCCGCCCATCGCGTC (SEQ ID NO: 55) as primers, as a result of which a malyl-CoA lyase fragment was obtained. The malate thiokinase fragment and the malyl-CoA lyase fragment of Methylobacterium extorquens were ligated to pMWGKC, and the plasmid obtained was named pMWGKC_mtk(Mex)_mcl.
pMWGKC_mtk(Mex)_mcl harbors the base sequence of the mcl gene (SEQ ID NO: 66), the base sequence of the mtkA gene (SEQ ID NO: 67), and the base sequence of the mtkB gene (SEQ ID NO: 68) derived from Methylobacterium extorquens. The amino acid sequences of mcl, mtkA, and mtkB derived from Methylobacterium extorquens are shown in SEQ ID NO: 69, SEQ ID NO: 70, and SEQ ID NO: 71, respectively.
<Construction of Expression Plasmid for Malate Thiokinase Derived from Hyphomicrobium methylovorum NBRC 14180>
Hyphomicrobium methylovorum NBRC 14180 was purchased from NBRC (Biological Resource Center, Biotechnology Field, National Institute of Technology and Evaluation). NBRC 14180 was cultured in a medium (medium number: 233, NBRC), and chromosomal DNA was obtained therefrom using DNeasy Blood &Tissue Kit (QIAGEN).
A primer (SEQ ID NO: 56) was prepared based on the DNA sequence of the N-terminal region of serine-glyoxylate aminotransferase of NBRC 14180 (GenBank Accession No. D13739).
Based on the amino acid sequence of phosphoenolpyruvate carboxylase of Hyphomicrobium denitrificans (http://www.ncbi.nlm.nih.gov/nuccore/300021538?from=3218417&to=3221272&report=gbw ithparts), sequence homology was compared using a homology search tool by NCBI (National Center for Biotechnology Information) (http://blast.ncbinlm.nih.gov/Blast.cgi?PROGRAM=blastp&BLAST_PROGRAMS=blastp& PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome).
A primer (SEQ ID NO: 57) was prepared based on an amino acid sequence having high homology.
PCR was carried out using primers of SEQ ID NO:56 and SEQ ID NO:57 obtained as described above and the chromosomal DNA obtained above as a template. The fragment obtained was ligated to a DNA prepared by digesting pUC19 with SmaI, whereby part of the phosphoenolpyruvate carboxylase gene was cloned from the serine-glyoxylate aminotransferase gene derived from Hyphomicrobium methylovorum NBRC 14180. After confirming the sequence of the clone, primers (SEQ ID NOs: 58 and 59) were prepared.
PCR was carried out using the chromosomal DNA of Hyphomicrobium methylovorum NBRC 14180 as a template and primers of SEQ ID NOs: 58 and 59 obtained as described above, and the DNA obtained was digested with EcoRI and XbaI, as a result of which a DNA fragment containing the mcl and mtk genes of Hyphomicrobium was obtained. In addition, the above-described plasmid pMWGKC_mtk(Mex)_mcl was digested, and a fragment of about 4.3 kb containing mcl was recovered. This fragment obtained was ligated to the DNA fragment containing the mcl and mtk genes of Hyphomicrobium. The obtained plasmid was named pMWGKC_mcl(Hme)_mtk(Hme)_mcl.
pMWGKC_mcl(Hme)_mtk(Hme)_mcl contains the base sequence of the mcl gene (SEQ ID NO: 60), the base sequence of the mtkA gene (SEQ ID NO: 61), and the base sequence of the mtkB gene (SEQ ID NO: 62) derived from Hyphomicrobium methylovorum. The amino acid sequences of mcl, mtkA, and mtkB derived from Hyphomicrobium methylovorum are as shown in SEQ ID NO: 72, SEQ ID NO: 73 and SEQ ID NO: 74, respectively.
<Construction of Expression Plasmid for Malate Thiokinase Derived from Rhizobium sp. NGR234>
Based on the amino acid sequence information of the malate thiokinase beta subunit (GenBank Accession No. ACP26381) and the succinyl-CoA synthetase alpha subunit (GenBank Accession No. ACP26382) of Rhizobium sp. NGR234, full length of the malate thiokinase gene was synthesized (SEQ ID NO: 63). The gene obtained was digested with NdeI and XbaI, and ligated to pMWGKC digested with NdeI and XbaI. The plasmid obtained was named pMWGKC_mtk(Rhi). Further, PCR was carried out using the chromosomal DNA of Methylobacterium extorquens as a template and primers of SEQ ID NOs: 64 and 65, and the DNA obtained was digested with XbaI and HindIII. The fragment obtained was subjected to blunt-end treatment, and ligated to a gene obtained by digesting MWGKC_mtk(Rhi) with XbaI and subjecting the resultant fragment to blunt-end treatment and phosphorylation treatment. A resulting plasmid in which the mtk gene and mcl gene were introduced in the same direction was named pMWGKC_mtk(Rhi)_mcl. The amino acid sequences of mtkA and mtkB derived from Rhizobium sp. are as shown in SEQ ID NO: 75 and SEQ ID NO: 76, respectively.
<Preparation of Malate Thiokinase and Malyl-CoA Lyase-Introduced Isopropyl Alcohol-Producing Variant>
Competent cells of the Escherichia coli B variant (atoDAB, Δpgi_gntR_gnd_ldhA_aceBA_glcB_fumAC) prepared in Example 8 were transformed with the plasmid pIaz prepared in Example 9 and each of the plasmids expressing mtk and mcl. Transformants that grew on an LB agar plate containing 25 mg/L chloramphenicol and 100 mg/L ampicillin were named as follows (see Table 2).
The variant numbers in Table 2 represent the variants prepared by introducing pIaz and each of the plasmids described in Table 2 into the Escherichia coli B variant (atoDAB, Δpgi_gntR_gnd_ldhA_aceBA_glcB_fumAC).
Rhizobium sp.
<Confirmation of Incorporation of 13C-Labeled CO2 into Isopropyl Alcohol>
100 ml of LB liquid medium was added into 500-ml Erlenmeyer flask equipped with a baffle, and was sterilized by autoclaving at 121° C. for 20 minutes. To the sterilized medium, ampicillin was added to have a final concentration of 50 μg/ml, and chloramphenicol was added to have a final concentration of 34 μg/ml. Subsequently, one platinum loop of each of the variants shown in Table 2 having a carbon dioxide fixation pathway introduced thereto were inoculated into the medium, and cultured at 30° C. and 130 rpm for about 20 hours. Only the bacterial cells were separated from the culture liquid by centrifugation (5,000 G for 15 minutes), and then the separated bacterial cells were resuspended in 10 mL of physiologic saline, thereby obtaining the respective bacterial suspensions.
In a 100-mL Erlenmeyer flask, 30 mL of M9 minimal medium containing 100 mM 13C-labeled sodium hydrogen carbonate, 50 g/L glucose, 34 μg/ml chloramphenicol, and 50 μg/ml ampicillin was prepared. 3 mL of the bacterial suspension obtained above was inoculated into this medium, and cultured at 30° C., 100 rpm for 24 hours, while the flask was tightly sealed with a silicone plug. The culture liquid obtained was filtered under reduced pressure using a hydrophilic PTFE membrane filter (H050A047A, pore size: 0.5 μm; diameter: 47 mm; manufactured by ADVANTEC) placed in a filter holder for filtration under reduced pressure (KGS-47; manufactured by ADVANTEC), thereby separating the bacterial cells from the culture supernatant.
The membrane filter to which the bacterial cells were attached was immediately immersed in 1.6 mL methanol (LC/MS grade) cooled to −20° C. and stirred, and the membrane was left to stand at −20° C. for 1 hour. Thereafter, 1.6 mL of chloroform (HPLC grade) cooled to −20° C. and 0.64 mL of pure water cooled to 4° C. were added thereto, followed by vortex-mixing for 30 seconds. Subsequently, the supernatant was collected by centrifugal separation at 4° C., thereby obtaining a methanol extract of the bacterial cells. The obtained extract was analyzed by LC-MS/MS and the molecular weight distribution of acetyl-CoA in the bacterial cells was determined. The results are shown in Table 3. The molecular weight distribution of acetyl-CoA was calculated by defining the ratios of mass spectrometry peaks at molecular weights of 808, 809, and 810 as M+0, M+1, and M+2, respectively.
Separately, from the culture supernatant obtain above, alcohols and acetone were recovered at high concentrations by distillation, and used as raw materials for measurement of the molecular weight distribution. The molecular weight distributions of isopropyl alcohol and ethanol in the culture supernatant were analyzed by GC-MS. The results are shown in Tables 4 and 5. The molecular weight distribution of isopropyl alcohol (IPA) (Table 4) was calculated by defining the ratios of mass spectrometry peaks at molecular weights of 117, 118, and 119 from the as M+0, M+1, and M+2, respectively. The molecular weight distribution of ethanol (EtOH) (Table 5) was calculated by defining the ratios of mass spectrometry peaks at molecular weights of 103, 104, and 105 as M+0, M+1, and M+2, respectively.
As shown in Table 3, the MT-1 variant and the MT-2 variant had a high ratio of acetyl-CoA into which 13C was not incorporated (M+0) and a high ratio of acetyl-CoA into which one atom of 13C was incorporated (M+1), as compared to the control strain. In particular, the ration of M+1 was high in the MT-2 variant. From this result, it was found that carbon derived from the 13C-labeled carbonate was incorporated into acetyl-CoA in the MT-1 variant and the MT-2 variant, and that the effect was especially pronounced for the MT-2 variant.
Furthermore, the MT-2 variant had a low ratio of isopropyl alcohol or ethanol into which 13C was not incorporated (M+0) and a high ratio of isopropyl alcohol or ethanol into which one atom of 13C was incorporated (M+1), as compared to the commercially available isopropyl alcohol or ethanol (Table 4 and Table 5). From this result, it was found that carbon derived from the 13C-labeled carbonate was incorporated also into isopropyl alcohol or ethanol in the MT-2 variant.
<Measurement of Glyoxylate Production Activity Using Malate as Substrate>
The variants expressing mtk and mcl described above were cultured in 2 mL of LB medium containing 25 μg/ml chloramphenicol and 100 μg/ml ampicillin. A crude enzyme solution was extracted according to the following method. That is, bacterial cells in logarithmic growth phase were collected by centrifugation, and washed with 200 mM MOPS-K buffer (pH 7.7) and then dissolved in MOPS-K buffer, followed by sonication. The supernatant obtained by centrifugal separation (12,000 rpm for 2 minutes) was used as the crude enzyme solution.
The protein concentration in the crude enzyme solution was determined based on a calibration curve generated with OD values at 595 nm measured with a UV plate reader (Molecular Devices, SpectraMax 190) using the crude enzyme solution and known concentrations of BSA for preparing the calibration curve, each of which had been reacted with Quick Start Bradford Dye Reagent (manufactured by Bio-Rad Laboratories, Inc.) and subject to color development.
The enzymatic activity in the solution was determined according to the following procedure. That is, MOPS-K buffer (pH 7.7), 3.5 mM phenylhydrazine, 10 mM MgCl2, 3 mM ATP, 0.3 mM CoA, and 10% by mass of crude enzyme solution were mixed in a microwell and the mixture was incubated at room temperature for 30 minutes. As background values, changes in OD values at 324 nm with time were measured using a UV plate reader. To the mixture, sodium (S)-L-malate solution (pH 7.5) was added to have a final concentration of 5 nm, and changes in OD values at 324 nm with time was measured. In order to generate a calibration curve for glyoxylate, glyoxylate was added to the above buffer and the mixture was left to stand for 5 minutes at room temperature and then OD values at 324 nm was measured. Regarding the value of enzymatic activity, the slope of the background values was subtracted from the slope of OD values at 324 nm after the addition of sodium (S)-L-malate, and the obtained value was converted into a glyoxylate consumption rate based on the calibration curve for glyoxylate. The enzymatic activity per protein was determined by dividing the glyoxylate consumption rate by the protein concentration (Table 6).
As shown in Table 6, it was confirmed that all of the MT-1, MT-2, and MT-3 variants have enzymatic activity. It was found that the MT-2 variant and the MT-3 variant have a higher enzymatic activity compared to the MT-1 variant. In contrast, no enzymatic activity was shown in the control.
<Number of Viable Cells and Plasmid Retention Rate in Malate Thiokinase and Malyl-CoA Lyase-Introduced Variant>
In a 100-mL Erlenmeyer flask, 30 mL of M9 minimal medium or LB medium each containing 50 g/L glucose, 30 μg/ml chloramphenicol, and 100 μg/ml ampicillin was prepared. Each of the above variants expressing mtk and mcl were inoculated into the M9 minimal medium or LB medium and cultured at 30° C., 100 rpm for 24 hours, while the flask tightly sealed with a silicone plug. The culture liquid was diluted with water, and 100 μL of the diluted culture liquid was applied to an antibiotic-free LB plate. The total number of viable cells was counted. Furthermore, the diluted culture liquid was applied to an LB plate containing 30 μg/ml chloramphenicol, and the number of bacterial cells retaining the plasmid harboring mtk (smt) and mcl was counted.
As shown in Table 7, it was found that each of the MT-2 variant and the MT-3 variant had a higher number of viable cells in the culture liquid and grew better, as compared with the MT-1 variant. The plasmids harboring mtk and mcl were stably maintained in all of the MT-1, MT-2, and MT-3 variants.
<Construction of Expression Plasmid for Malate Thiokinase Derived from Granulibacter bethesdensis BAA-1260>
The genomic DNA of Granulibacter bethesdensis BAA-1260D-5 was purchased from ATCC.
PCR was carried out using the genomic DNA of Granulibacter bethesdensis as a template and using CCCTGAGGAGGGTCCAAGAGATGGACGTCCATGAGTACCA (SEQ ID NO: 77) and GCTCTAGATCAGGCTGCCTGACGCCCA (SEQ ID NO: 78) as primers, as a result of which an mtk fragment of Granulibacter was obtained. In addition, PCR was carried out using pMWGKC_mcl(Hme)_mtk(Hme)_mcl prepared in Example 12 as a template and using GGAATTCACAAAAAGGATAAAA (SEQ ID NO: 79) and TGGTACTCATGGACGTCCATCTCTTGGACCCTCCTCAGGG (SEQ ID NO: 80) as primers, as a result of which an mcl fragment of Hyphomicrobium was obtained. PCR was carried out using the obtained mtk fragment of Granulibacter and mcl fragment of Hyphomicrobium as templates and primers of SEQ ID NO: 79 and SEQ ID NO: 78, thereby obtaining a DNA fragment containing mcl from Hyphomicrobium and the mtk fragment gene from Granulibacter. The DNA fragment obtained was digested with restriction enzymes EcoRI and XbaI, and ligated to the plasmid pMWGKC prepared in Example 10. The plasmid obtained was named pMWGKC_mcl(Hme)_mtk(Gb).
pMWGKC_mcl(Hme)_mtk(Gb) harbors the mtkA gene (SEQ ID NO: 81) and the mtkB gene (SEQ ID NO:82) derived from Granulibacter bethesdensis. The amino acid sequences of mtkA and mtkB derived from Granulibacter bethesdensis are shown in SEQ ID NO: 107 and SEQ ID NO: 108, respectively.
<Construction of Expression Plasmid for Malate Thiokinase Derived from Hyphomicrobium denitrificans DSMZ 1869>
Hyphomicrobium denitrificans DSMZ 1869 was purchased from DSMZ (Deutsche Sammlung von Mikroorganismen and Zellkulturen GmbH, Germany). DSMZ 1869 was cultured in a medium (medium number: 803, DSMZ), and chromosomal DNA was obtained therefrom using DNeasy Blood &Tissue Kit (QIAGEN).
PCR was carried out using the chromosomal DNA of Hyphomicrobium denitrificans as a template and using ACCAGGGAATTCACAAAAAGGATAAAACAATGAGCTATACCCTCTACCCAACCGTA AGC (SEQ ID NO: 83) and GCCCACTCTAGATCAGGCAACTTTTTTCTGCTTGCCGAGAACC (SEQ ID NO: 84) as primers, as a result of which an mcl-mtk fragment of Hyphomicrobium was obtained. The fragment obtained was ligated to the plasmid pMWGKC_mcl(Hme) mtk(Hme)_mcl prepared in Example 12. The plasmid obtained was named pMWGKC_mcl(Hde)_mtk(Hde)_mcl.
pMWGKC_mcl(Hde)_mtk(Hde)_mcl harbors the base sequence of the mcl gene (SEQ ID NO: 85), the base sequence of the mtkA gene (SEQ ID NO: 86), and the base sequence of the mtkB gene (SEQ ID NO: 87) derived from Hyphomicrobium denitrificans. The amino acid sequences of mcl, mtkA, and mtkB derived from Hyphomicrobium denitrificans are shown in SEQ ID NO: 109, SEQ ID NO: 110, and SEQ ID NO: 111, respectively.
<Construction of Expression Plasmid for Malate Thiokinase Derived from Nitrosomonas europaea NBRC 14298>
Nitrosomonas europaea NBRC 14298 was purchased from NBRC (Biological Resource Center, NITE). NBRC 14298 was cultured in a medium (medium number: 829, NBRC), and chromosomal DNA was obtained therefrom using DNeasy Blood &Tissue Kit (QIAGEN).
PCR was carried out using the chromosomal DNA of Nitrosomonas europaea as a template and using GCGGGGGAATTCACAAAAAGGATAAAACAATGAGTCATACCCTGTATGAACCAAA ACACC (SEQ ID NO: 88) and CAGGCGTCTAGATTAGAGTCCGGCCAGAACTTTTGCGACG (SEQ ID NO: 89) as primers, as a result of which an mtk fragment of Nitrosomonas europaea was obtained. The fragment obtained was ligated to the plasmid pMWGKC_mcl(Hme)_mtk(Hme)_mcl prepared in Example 12. The plasmid obtained was named pMWGKC_mcl(Ne)_mtk(Ne)_mcl.
pMWGKC_mcl(Ne)_mtk(Ne)_mcl harbors the base sequence of the mcl gene (SEQ ID NO: 90), the base sequence of the mtkA gene (SEQ ID NO: 91), and the base sequence of the mtkB gene (SEQ ID NO: 92) derived from Nitrosomonas europaea. The amino acid sequences of mcl, mtkA, and mtkB derived from Nitrosomonas europaea are shown in SEQ ID NO: 112, SEQ ID NO: 113, and SEQ ID NO: 114, respectively.
<Construction of Expression Plasmids for Malate Thiokinase Derived from Methylococcus capsulatus ATCC 33009>
Genomic DNA of Methylococcus capsulatus ATCC 33009D-5 was purchased from ATCC.
PCR was carried out using the chromosomal DNA of Methylococcus capsulatus as a template and using GGAATTCCATATGGCTGTTAAAAATCGTCTAC (SEQ ID NO: 93) and GCTCTAGATCAGAATCTGATTCCGTGTTC (SEQ ID NO: 94) as primers, as a result of which an mcl-mtk fragment of Methylococcus was obtained. The fragment obtained was ligated to the plasmid pMWGKC prepared in Example 10 or to the plasmid pMWGC prepared in Example 10. The plasmid obtained was named pMWGKC_mcl(Mc)_mtk(Mc) or pMWGC_mcl(Mc)_mtk(Mc).
Each of pMWGKC_mcl(Mc)_mtk(Mc) and pMWGC_mcl(Mc)_mtk(Mc) harbours the base sequence of the mcl gene (SEQ ID NO: 95), the base sequence of the mtkA gene (SEQ ID NO: 96), and the base sequence of the mtkB gene (SEQ ID NO: 97) derived from Methylococcus capsulatus. The amino acid sequences of mcl, mtkA, and mtkB derived from Methylococcus capsulatus are shown in SEQ ID NO: 115, SEQ ID NO: 116, and SEQ ID NO: 117, respectively.
<Construction of Expression Plasmid for Malate Thiokinase Derived from Uncultured Gamma Proteobacterium (GenBank: AP011641.1)>
In order to obtain mtk derived from an uncultured gamma proteobacterium, a gamma proteobacterium-derived mtk was designed based on the amino acid sequence of GenBank: AP011641.1, and the following DNA fragment (SEQ ID NO: 98) was prepared by DNA synthesis.
PCR was carried out using the prepared DNA fragment as a template and using GTTGAACGAGGAGATCGTCCATGAACATTCACGAATATCA (SEQ ID NO: 99) and GCTCTAGATTAGCCAGAAACTGCAGATCC (SEQ ID NO: 100) as primers, as a result of which an mtk fragment of the gamma proteobacterium was obtained. In addition, PCR was carried out using pMWGKC_mcl(Mc)_mtk(Mc) or pMWGC_mcl(Mc)_mtk(Mc) prepared in Example 21 as a template and using primers of SEQ ID NO: 93 and TGATATTCGTGAATGTTCATGGACGATCTCCTCGTTCAAC (SEQ ID NO: 101), thereby obtaining an mcl fragment of Methylococcus. In addition, PCR was carried out using the gamma proteobacterium mtk fragment obtained and the Methylococcus mcl fragment obtained as templates and using primers of SEQ ID NO: 93 and SEQ ID NO: 100, thereby obtaining a DNA fragment containing the mcl gene of Methylococcus and the mtk fragment gene of the gamma proteobacterium. The DNA fragment obtained was ligated to the plasmid pMWGKC prepared in Example 10. The plasmid obtained was named pMWGKC_mcl(Mc)_mtk(gamma).
pMWGKC_mcl(Mc)_mtk(gamma) harbors the mtkA gene (SEQ ID NO: 102) and the mtkB gene (SEQ ID NO: 103) derived from the uncultured gamma proteobacterium. The amino acid sequences of mtkA and mtkB derived from the uncultured gamma proteobacterium are shown in SEQ ID NO: 118 and SEQ ID NO:119, respectively.
<Preparation of Malate Thiokinase- and Malyl-CoA Lyase-Introduced, Isopropyl Alcohol-Producing, atoD Genome-Enhanced, Pgi Gene-Deleted, gntR Gene-Deleted, Gnd Gene-Deleted, ldhA Gene-Deleted, fumAC Gene-Deleted, aceBA Gene-Deleted, glcB Gene-Deleted Variant>
Competent cells of the Escherichia coli B variant (atoDAB, Δpgi_gntR_gnd_ldhA_aceBA_glcB_fumAC) prepared in Example 8 were transformed with plasmid pIaz and each of the plasmids expressing mtk and mcl prepared in Examples 18 to 22. Transformants that grew on an LB agar medium containing 25 mg/L chloramphenicol and 100 mg/L ampicillin were named as follows (see Table 8).
The variant numbers described in Table 8 represent the variants prepared by introducing pIaz and each of the plasmids described in Table 8 into the Escherichia coli B variant (atoDAB, Δpgi_gntR_gnd_ldhA_aceBA_glcB_fumAC).
<Measurement of Glyoxylate Production Activity Using Malate as Substrate>
In the same manner as in Example 16, the enzymatic activity per protein was determined (Table 9).
As shown in Table 9, it was confirmed that each of the MT-4 to MT-8 variants has enzymatic activity, and that the enzymatic activity was higher compared to the MT-1 variant. In particular, it was found that the MT-5 variant, the MT-6 variant, the MT-7 variant, and the MT-8 variant have an equivalent or higher activity compared to the MT-2 variant and the MT-3 variant shown in Example 16. In contrast, no enzymatic activity was detected in the control.
29 ± 0
23 ± 0
<Preparation of atoD Genome-Enhanced, aceB Gene-Deleted Variant>
In order to clone a region flanking the base sequence of the gene encoding malate synthase (hereinafter sometimes abbreviated to “aceB”) (1602 bp), four types of oligonucleotide primers represented by GGAATTCATTCAGCTGTTGCGCATCGATTC (SEQ ID NO: 24), GTTATGTGGTGGTCGTGCAGCTCCTCGTCATGG (SEQ ID NO: 104), GAGCTGCACGACCACCACATAACTATGGAG (SEQ ID NO: 105), and GGAATTCCAGTTGAACGACGGCGAGCAG (SEQ ID NO: 106) were synthesized. Each of these primers has an EcoRI recognition site in the 5′-end side thereof.
The genomic DNA of the Escherichia coli B (accession No. CP000819) was prepared, and PCR was carried out using the obtained genomic DNA as a template and using a primer pair of SEQ ID NO: 24 and SEQ ID NO: 106, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “aceB-L fragment”) was amplified. In addition, PCR was carried out using a primer pair of SEQ ID NO: 105 and SEQ ID NO: 106, as a result of which a DNA fragment of about 1.0 kb (hereinafter sometimes referred to as “aceB-R fragment”) was amplified. These DNA fragments were separated by agarose electrophoresis, and recovered. PCR was carried out using the aceB-L and aceB-R fragments as templates and using a primer pair of SEQ ID NO: 24 and SEQ ID NO: 108, as a result of which a DNA fragment of about 2.0 kbp (hereinafter sometimes referred to as “aceB-LR fragment”) was amplified. The aceB-LR fragment was separated by agarose electrophoresis, and recovered, digested with EcoRI, and mixed with a fragment obtained by digesting a temperature-sensitive plasmid pTH18cs1 (GenBank accession number AB019610) with EcoRI and dephosphorylating the same. The mixed fragments were allowed to react using T4 DNA ligase. Thereafter, Escherichia coli DH5α competent cells (manufactured by Toyobo Co., Ltd.) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 10 μg/ml chloramphenicol at 30° C. were obtained. A plasmid was recovered from the transformants obtained, and it was confirmed that the aceB-LR fragment was properly inserted in pTH18cs1. The plasmid obtained was named pTH18cs1-aceB.
The Escherichia coli B::atoDAB variant prepared in Example 1 was transformed with the thus-obtained plasmid pTH18cs1-aceB, and was cultured at 30° C. overnight on an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which transformants were obtained. The transformants obtained were inoculated into an LB liquid medium containing 10 μg/ml chloramphenicol, and cultured at 30° C. overnight. Subsequently, part of the culture liquid was applied to an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which colonies that grew at 42° C. were obtained. The colonies obtained were cultured at 30° C. for 24 hours in an LB liquid medium, and was applied to an LB agar plate, as a result of which colonies that grew at 42° C. were obtained.
From the colonies that appeared, 100 colonies were randomly picked up, and each individually grown on an LB agar plate and an LB agar plate containing 10 μg/ml chloramphenicol, and chloramphenicol-sensitive clones were selected. Furthermore, the chromosomal DNAs of these target clones were amplified by PCR, and a variant from which a fragment of about 2.0 kbp, which indicates deletion of the aceB gene, could be amplified was selected. The variant obtained was named atoD genome-enhanced, aceB gene-deleted variant (hereinafter sometimes abbreviated to “B::atoDABΔaceB variant”).
<Preparation of atoD Genome-Enhanced, aceB Gene-Deleted, glcB Gene-Deleted Variant>
The Escherichia coli B::atoDABΔaceB variant prepared in Example 25 was transformed with the plasmid pTH18cs1-gclB prepared in Example 7, and was cultured at 30° C. overnight on an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which transformants were obtained. The transformants obtained were inoculated into an LB liquid medium containing 10 μg/ml chloramphenicol, and cultured at 30° C. overnight. Subsequently, part of the culture liquid was applied to an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which colonies that grew at 42° C. were obtained. The colonies obtained were cultured at 30° C. for 24 hours in an LB liquid medium, and was applied to an LB agar plate, as a result of which colonies that grew at 42° C. were obtained.
From the colonies that appeared, 100 colonies were randomly picked up, and each individually grown on an LB agar plate and an LB agar plate containing 10 μg/ml chloramphenicol, and chloramphenicol-sensitive clones were selected. Furthermore, the chromosomal DNAs of these target clones were amplified by PCR, and a variant from which a fragment of about 2.0 kbp, which indicates deletion of the AglcB gene, could be amplified was selected. The variant obtained was named atoD genome-enhanced, aceB gene-deleted, glcB gene-deleted variant (hereinafter sometimes abbreviated to “B::atoDABΔaceBΔgclB variant”).
<Preparation of atoD Genome-Enhanced, ldhA Gene-Deleted Variant>
The Escherichia coli B::atoDAB variant prepared in Example 1 was transformed with the plasmid pTH18cs1-ldhA prepared in Example 5, and was cultured at 30° C. overnight on an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which transformants were obtained. The transformants obtained were inoculated into an LB liquid medium containing 10 μg/ml chloramphenicol, and cultured at 30° C. overnight. Subsequently, part of the culture liquid was applied to an LB agar plate containing 10 μg/ml chloramphenicol, as a result of which colonies that grew at 42° C. were obtained. The colonies obtained were cultured at 30° C. for 24 hours in an LB liquid medium, and was applied to an LB agar plate, as a result of which colonies that grew at 42° C. were obtained.
From the colonies that appeared, 100 colonies were randomly picked up, and each individually grown on an LB agar plate and an LB agar plate containing 10 μg/ml chloramphenicol, and chloramphenicol-sensitive clones were selected. Furthermore, the chromosomal DNAs of these target clones were amplified by PCR, and a variant from which a fragment of about 2.0 kbp, which indicates deletion of the ldhA gene, could be amplified was selected. The variant obtained was named atoD genome-enhanced, ldhA gene-deleted variant (hereinafter sometimes abbreviated to “B::atoDABΔldhA variant”).
<Preparation of pBRgapP, pMWGC_mcl(Mc)_mtk(Mc)/B Variant and pBRgapP, pMWGC/B Variant>
Competent cells of Escherichia coli B was transformed with the plasmid pBRgapP prepared in Example 2, and the plasmid pMWGC_mcl(Mc)_mtk(Mc) prepared in Example 21 or the plasmid pMWGC prepared in Example 21, and applied to an LB agar plate containing 25 mg/L chloramphenicol and 100 mg/L ampicillin. As a result, transformants that grew on the medium were obtained.
<Preparation of pIa, pMWGC_mcl(Mc)_mtk(Mc)/B::atoDAB Variant, and pIa, pMWGC/B::atoDAB Variant>
Competent cells of the Escherichia coli B variant (B::atoDAB) prepared in Example 1 were transformed with the plasmid pIa prepared in Example 9, and the plasmid pMWGC_mcl(Mc)_mtk(Mc) prepared in Example 21 or the plasmid pMWGC prepared in Example 21, and applied to an LB agar plate containing 25 mg/L chloramphenicol and 100 mg/L ampicillin. As a result, transformants grew on the medium were obtained.
<Preparation of pIa, pMWGC_mcl(Mc)_mtk(Mc)/B::atoDABΔaceB Variant, and pIa, pMWGC/B::atoDABΔaceB Variant>
Competent cells of the Escherichia coli B variant (B::atoDABΔaceB) prepared in Example 25 were transformed with the plasmid pIa prepared in Example 9, and the plasmid pMWGC_mcl(Mc)_mtk(Mc) prepared in Example 21 or the plasmid pMWGC prepared in Example 21, and applied on an LB agar medium containing 25 mg/L chloramphenicol and 100 mg/L ampicillin, and transformants grown on the medium were obtained.
<Preparation of pIa, pMWGC_mcl(Mc)_mtk(Mc)/B::atoDABΔaceBΔglcB Variant, and pIa, pMWGC/B::atoDABΔaceBΔglcB Variant>
Competent cells of the Escherichia coli B variant (B::atoDABΔaceBΔglcB) prepared in Example 26 were transformed with the plasmid pIa prepared in Example 9, and the plasmid pMWGC_mcl(Mc)_mtk(Mc) prepared in Example 21 or the plasmid pMWGC prepared in Example 21, and applied on an LB agar medium containing 25 mg/L chloramphenicol and 100 mg/L ampicillin. As a result, transformants grew on the medium were obtained.
<Preparation of pIa, pMWGC_mcl(Mc)_mtk(Mc)/B::atoDABΔldhA Variant, and pIa, pMWGC/B::atoDABΔldhA Variant>
Competent cells of the Escherichia coli B variant (B::atoDABΔldhA) prepared in Example 27 were transformed with the plasmid pIa prepared in Example 9, and the plasmid pMWGC_mcl(Mc)_mtk(Mc) prepared in Example 21 or the plasmid pMWGC prepared in Example 21, and applied on an LB agar medium containing 25 mg/L chloramphenicol and 100 mg/L ampicillin. As a result, transformants grew on the medium were obtained.
<Production of Isopropyl Alcohol>
In this example, isopropyl alcohol was produced using a production apparatus shown in FIG. 1 of WO 2009/008377. The culture tank used was a tank having a capacity of 3 L and made of glass. Into the trap tanks, water as a trap solution (trap water) in an amount of 9 L per tank was injected, and the two trap tanks were connected to for use.
A list of variants used in the evaluation of isopropyl alcohol production is shown in Table 10.
As preculture, each of the variants to be evaluated was individually inoculated into an Erlenmeyer flask having a capacity of 500 mL and containing 50 mL of a Miller's LB broth (Difco 244620) that contains 25 mg/L chloramphenicol and 100 mg/L ampicillin, and cultured overnight at a culture temperature of 30° C. while stirring at 120 rpm. Thereafter, 45 mL of the preculture was transferred to a culture tank (culture device BMS-PI manufactured by ABLE corporation) having a capacity of 3 L and containing 900 g of the medium having the following composition, and was cultured. The culture was carried out at an aeration volume of 0.45 L/min, a stirring rate of 490 rpm, a culture temperature of 30° C., and a pH of 7.0 (adjusted with NH3 aqueous solution) under atmospheric pressure. To the culture, a 50 wt/wt % glucose aqueous solution was added at a flow rate of 20 g/L/hour during the period from the initiation of the cultivation to 8 hours after the initiation of the cultivation. Thereafter, a 50 wt/wt % glucose aqueous solution was added at a flow rate of 20 g/L/hour, as appropriate, such that the amount of glucose left in the culture tank was minimized. The bacterial culture liquid was sampled several times during the period from the initiation of the cultivation to 30 hours after the initiation of the cultivation, and, after the bacterial cells were removed by centrifugal operation, the amounts of isopropyl alcohol, acetone, and major byproducts accumulated in the culture supernatants and trap waters obtained were measured by HPLC according to an ordinary method. Each of the measurement values is a sum of the amounts in the culture liquid and the two trap tanks after the cultivation. The results are shown in Table 11, and the byproducts are shown in Table 12.
<Composition of Culture Medium>
Corn steep liquor (manufactured by Nihon Shokuhin Kako Co., Ltd.), 50 g/L
Fe2SO4.7H2O: 0.1 g/L
K2HPO4: 2 g/L,
KH2PO4: 2 g/L
MgSO4.7H2O: 2 g/L
(NH4)2SO4: 2 g/L
ADEKANOL LG126 (ADEKA Corporation): 0.1 g/L
(Blance: water)
As a result of the evaluation, the amount of isopropyl alcohol produced by the control strain (vec/atoDAB) was 33.2 g/30 h, and the amount produced by the mtk-introduced variant (mtk_mcl/atoDAB) was 34.6 g/30 h. The amount of acetone produced was 6.0 g/30 h in the control strain (vec/atoDAB), and 8.8 g/30 h in the mtk-introduced variant (mtk_mcl/atoDAB). From these results, it was found that the production amounts of isopropyl alcohol and acetone are increased by the introduction of mtk and mcl. The yield of isopropyl alcohol relative to sugar consumption at 30 hours after the initiation of the cultivation was 15.8% in the control strain (vec/atoDAB), and 16.5% in the mtk+mcl-introduced variant (mtk_mcl/atoDAB). The yield of isopropyl alcohol and acetone relative to sugar consumption at 30 hours after the initiation of the cultivation was 18.6% in the control strain (vec/atoDAB), and 20.7% in the mtk+mcl-introduced variant (mtk_mcl/atoDAB). From these results, it was shown that the conversion efficiencies of sugar into isopropyl alcohol or acetone were increased by the introduction of the mtk+mcl pathway.
Regarding atoDABΔldhA, the production amounts of isopropyl alcohol and acetone and the yields of isopropyl alcohol and acetone relative to sugar consumption were improved in the mtk+mcl-introduced variant similarly to the case of atoDAB. Regarding atoDABΔldhA, atoDABΔaceB, and atoDABΔaceBΔglcB, the yields relative to sugar consumption were increased in the mtk+mcl-introduced variant, as compared with that of the control strain (vec) of each variant. Therefore, it is thought that the production of acetyl-CoA and the useful substances derived from acetyl-CoA were efficiently increased by mtk+mcl.
Table 12 shows the byproducts. Compared with the control strain (vec/B), it was found that the amounts of ethanol, pyruvate, and succinate were reduced in the mtk+mcl-introduced variant (mtk_mcl/B) at 30 hours after the initiation of the cultivation, and the total amount of byproducts was also unexpectedly reduced in the mtk+mcl-introduced variant. Similarly, regarding atoDAB, atoDABΔaceB, atoDABΔaceBΔglcB, and atoDABΔldhA, the amounts of ethanol, pyruvate, and succinate and the total amount of byproducts were reduced in the mtk+mcl-introduced variants as compared with the respective control strains. From these results, it was found that mtk+mcl produced similar effects with or without atoDAB.
Regarding atoDABΔaceB and atoDABΔaceBΔglcB, the yield of IPA and the yield of IPA and acetone relative to sugar consumption were almost the same as those in the atoDAB variant. However, the total amount of byproducts was reduced in both the vec-introduced variants and the mtk-introduced variants. Unexpectedly, the amounts of lactate and succinate accumulated were significantly decreased in the mtk+mcl-introduced variants. Therefore, atoDABΔaceB and atoDABΔaceBΔglcB are industrially preferable, since a smaller amount of byproducts allow a significant reduction in the purification load when isopropyl alcohol or acetone is collected from a culture liquid.
Regarding atoDABΔldhA, it was shown that the production amounts of alcohol and acetone and the yields of alcohol and acetone relative to sugar consumption were improved in the mtk+mcl introduced variant similarly to the case of atoDAB. Regarding all of the above variants, the yields relative to sugar consumption were improved in the mtk+mcl-introduced variants as compared with the control strain (vec). Therefore, it is thought that acetyl-CoA and the useful substances derived from acetyl-CoA were efficiently increased.
Regarding atoDABΔldhA, the total amount of byproducts was reduced, and the amount of pyruvate accumulated was significantly reduced in the mtk+mcl-introduced variant. Furthermore, the yields of isopropyl alcohol and acetone relative to sugar consumption were increased in the mtk+mcl-introduced atoDABΔldhA variant, indicating that isopropyl alcohol and acetone were efficiently produced by both the glucose and mtk+mcl pathways. The amount of byproducts in atoDABΔldhA was reduced similarly to the cases of atoDABΔaceB and atoDABΔaceBΔglcB. In addition, the yields of isopropyl alcohol and acetone relative to sugar consumption was improved in atoDABΔldhA when mtk+mcl was introduced. These results indicate that, in the industrial production of isopropyl alcohol and/or acetone, disruption of ldhA is preferable in view of reducing the purification load during collection of isopropyl alcohol and/or acetone and in view of increasing their yields.
The isopropyl alcohol production pathway and acetone production pathway have not been introduced into the B variants. Since the amount of acetate was significantly increased in the B variants, it is thought that acetyl-CoA was mainly converted into acetate. Further, it is assumed that the increased acetyl-CoA was converted into acetate and ethanol in the mtk+mcl-introduced variant (mtk_mcl/B). These results indicate that the amount of acetyl-CoA was increased by the effect of mtk+mcl even in the B variants.
<Construction of Plasmid pGAPS>
In order to obtain a spectinomycin-resistance gene, amplification by a PCR method was carried out using plasmid pIC156 (Steinmetz et. Al., Gene, 1994, 142(1): 79-83) as a template and CCGCGGTACCGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGG (SEQ ID NO: 120) and CTTTTGTTTATAAGTGGGTAAACCGTGAATATCGTGTTCTTTTCAC (SEQ ID NO: 121), and the DNA fragment obtained was phosphorylated using T4 Polynucleotide kinase (Toyobo), as a result of which a DNA fragment containing a spectinomycin-resistance gene was obtained. In addition, the plasmid pGAP was treated with PvuI, and the DNA fragment obtained was subjected to blunt-end treatment with Toyobo BLUNTING HIGH, and ligated to the above-described DNA fragment containing the spectinomycin-resistance gene. Thereafter, Escherichia coli DH5α competent cells were transformed with the ligation product, and transformants that grew on an LB agar plate containing 120 μg/mL spectinomycin were obtained. The colonies obtained were cultured overnight in an LB liquid medium containing 120 μg/mL spectinomycin, and the plasmid obtained was named pGAPS.
<Preparation of Plasmid pGAPS_gcl>
Chromosomal DNA was obtained from Escherichia coli MG1655 using DNeasy Blood &Tissue Kit (QIAGEN). Based on the operon containing glyoxylate carboligase (gcl, NCBI-GI: 945394), two types of primers represented by AAGAACTCTAGAACAAAAAGGATAAAACAATGGCAAAAATGAGAGCCGTTGACG CGGCAATG (SEQ ID NO: 122) and GACCAGCTGCAGTCAGGCCAGTTTATGGTTAGCCATTAATTCCAGC (SEQ ID NO: 123) were prepared.
Further, two types of primers represented by ACACAACTGCAGACAAAAAGGATAAAACAATGAAGATTGTCATTGCGCCAGACTC TTTTAAAGAGAGCT (SEQ ID NO: 124) and GCCCCCAAGCTTTCAGTTTTTAATTCCCTGACCTATTTTAATGGCGCAGG (SEQ ID NO: 125) were prepared.
Amplification by PCR was carried out the chromosomal DNA of Escherichia coli MG1655 as a template and using primers of SEQ ID NOs: 122 and 123 obtained as described above, as a result of which a DNA fragment of about 3 kb was obtained. In addition, amplification by PCR was carried out using the chromosomal DNA of Escherichia coli MG1655 as a template and using primers of SEQ ID NOs:124 and 125 obtained as described above, as a result of which a DNA fragment of about 1.1 kb was obtained. These DNAs obtained were digested with PstI, and these fragments were ligated together. Amplification by PCR was carried out using the ligated DNA as a template and using AAGAACTCTAGAACAAAAAGGATAAAACAATGGCAAAAATGAGAGCCGTTGACG CGGCAATG (SEQ ID NO: 126) and GCCCCCAAGCTTTCAGTTTTTAATTCCCTGACCTATTTTAATGGCGCAGG (SEQ ID NO: 127) as primers, as a result of which a DNA fragment was obtained. The DNA fragment obtained was digested with restriction enzymes XbaI and HindIII, and ligated to a plasmid pGAPS that had been digested with restriction enzymes XbaI and HindIII. Thereafter, Escherichia coli DH5α was transformed with the ligation product, and cultured on an LB agar plate containing spectinomycin, and a plasmid was recovered from transformants obtained.
The plasmid was digested with restriction enzymes ClaI and HindIII, and a DNA fragment of about 4 kb harboring pGAPS and the gcl gene was recovered. The DNA fragment was subjected to blunt-end treatment and self-ligation. Escherichia coli DH5α was transformed with the ligation product, and cultured on an LB agar plate containing 120 μg/mL spectinomycin. Bacterial cells that grew on the plate were cultured in an LB liquid medium containing 120 μg/mL spectinomycin, as a result of which transformants were obtained. A plasmid was recovered from the transformants obtained, as a result of which plasmid pGAPS_gcl was obtained.
<Obtaining Pantoea ananatis PA Variant>
Plasmid RSFCPG was recovered from Pantoea ananatis AJ13601 (patent deposited strain BP-7207). The plasmid RSFCPG is a tetracycline resistance plasmid having the enzymes glutamate dehydrogenase, citrate synthase, and phosphoenolpyruvate carboxylase that catalyze the reaction of L-glutamate biosynthesis (JP-A No. 2001-333769). Pantoea ananatis AJ417 (patent deposited strain BP-8646) was transformed with RSFCPG using the CaCl2 method (Molecular Cloning, 3rd edition, Cold Spring Harbor press, 2001), and cultured in an LB liquid medium containing 10 μg/mL tetracycline, as a result of which Pantoea ananatis AJ417/RSFCPG (hereinafter sometimes abbreviated to “PA variant”) was obtained.
<Preparation of Pantoea ananatis aceB Gene-Deleted Variant>
The whole sequence of the genomic DNA of Pantoea ananatis AJ13355 (patent deposited strain BP-6614) is known (GenBank accession number AP012032), and the base sequence of the gene encoding malate synthase of Pantoea ananatis (hereinafter sometimes referred to as “PAaceB”) has also been reported (GenBank accession number NC_017531). In order to clone a region flanking the base sequence of the gene encoding aceB (1,599 bp), four types of oligonucleotide primers represented by GACTCTAGAGGATCCCCGGGATGACAGACTCGGTTATCAACAGTGAATTACTTTTC AG (SEQ ID NO: 128), GACGGGACGGCGGCTTTGTTGGCTTCCGCGTTATGAAAAAAGTAGAGAGC (SEQ ID NO: 129), TTGAGACACAACGTGGCTTTCCCAGCAAGGACAGCGCGCGCAATGAATG (SEQ ID NO: 130), and ATGACCATGATTACGAATTCTCAGGGAAGCAGGCGGTAGCCTGGCAGAGTCAG (SEQ ID NO: 131) were synthesized.
Further, in order to clone a kanamycin-resistance gene, two types of oligonucleotide primers represented by TTTTTCATAACGCGGAAGCCAACAAAGCCGCCGTCCCGTCAAGTCAGC (SEQ ID NO: 132) and CGCGCGCTGTCCTTGCTGGGAAAGCCACGTTGTGTCTCAAAATCTCTGATGTTACA TTGC (SEQ ID NO: 133) were synthesized.
The genomic DNA of Pantoea ananatis AJ417 was prepared, and amplification by PCR was carried out using the obtained genomic DNA as a template and a primer pair of SEQ ID NO: 128 and SEQ ID NO: 129, as a result of which a DNA fragment containing a sequence flanking the aceB gene (hereinafter sometimes referred to as “PAaceB-L fragment”) was obtained. In addition, amplification by PCR was carried out using a primer pair of SEQ ID NO:130 and SEQ ID NO: 131, as a result of which a DNA fragment containing a sequence flanking the aceB gene (hereinafter sometimes referred to as “PAaceB-R fragment”) was obtained. Further, amplification by PCR was carried out using plasmid pUC4K having a kanamycin-resistance gene and using a primer pair of SEQ ID NO: 132 and SEQ ID NO: 133, as a result of which a DNA fragment containing the kanamycin resistance gene (hereinafter sometimes referred to as “KanR fragment”) was amplified. Plasmid pUC18 was treated with EcoRI and XmaI, thereby preparing a pUC18 fragment. These PAaceB-L fragment, PAaceB-R fragment, KanR fragment, and pUC18 fragment were recovered, and the fragments were mixed together and treated using In-fusion HD cloning kit (Invitrogen). Escherichia coli DH5α competent cells (NEB5α; New England Biolabs) were transformed with the reaction product, and cultured on an LB plate containing 30 μg/mL kanamycin. A plasmid was recovered from a transformants obtained, and it was confirmed by DNA sequencing that the pUC 18 vector was constructed such that the sequence of “the 5′-flanking sequence of aceB_kanamycin-resistance gene_the 3′-flanking sequence of aceB” was included. PCR was carried out using this plasmid as a template and using GCCGCCGAATTCCCGAAAAGTGCCACCTGACGTCTAAGAAACC (SEQ ID NO: 134) and ATGACCATGATTACGAATTCTCAGGGAAGCAGGCGGTAGCCTGGCAGAGTCAG (SEQ ID NO: 135). The amplification product was purified and digested with EcoRI, followed by self-ligation of the resulting fragment using DNA ligase (Takara), as a result of which a plasmid having no replication origin was obtained. Pantoea ananatis AJ417 was transformed with the plasmid obtained, and cultured on an LB plate containing 30 μg/mL kanamycin. The colonies obtained were subjected to genomic PCR and DNA sequencing, and it was confirmed that the aceB gene was properly deleted. The bacteria obtained were transformed with RSFCPG using the CaCl2 method, and cultured in LB medium containing 10 μg/mL tetracycline. The variant obtained was named the Pantoea ananatis AJ417 aceB gene-deleted variant (hereinafter sometimes abbreviated to “PAΔaceB variant”).
<Preparation of Pantoea ananatis fumA Gene-Deleted Variant>
The genomic DNA of Bacillus subtilis subsp. subtilis str. 168 (ATCC 23857) was prepared, and amplification by a PCR method was carried out using the obtained genomic DNA as a template and using AGTCTAGAGATCCTTTTTAACCCATCAC (SEQ ID NO: 136) and AGTCTAGAAGTCGATAAACAGCAATATT (SEQ ID NO: 137) as primers. The DNA fragment obtained was digested with restriction enzyme XbaI, thereby obtaining a DNA fragment of about 2.0 kbp containing the sacB gene. The DNA fragment obtained was mixed with a DNA fragment prepared by digesting plasmid pHSG298 (Takara) with restriction enzyme XbaI and subjecting the resulting product to alkaline phosphatase treatment, and the mixed fragments were ligated using a ligase. Escherichia coli DH5α competent cells (Toyobo Co., Ltd., DNA-903) were transformed with the resulting ligation product, and transformants that grew on an LB agar plate containing 25 μg/mL kanamycin were obtained. A plasmid was recovered from the bacterial cells obtained, as a result of which the plasmid pHSG-sacB, in which the DNA fragment containing the sacB gene was inserted in pHSG298, was obtained.
The whole sequence of the plasmid pEA320, originally found in Pantoea ananatis AJ13355, is known (NCBI Reference Sequence NC_017533.1), and the base sequence of the gene encoding fumarate hydratase class I (hereinafter sometimes referred to as “fumA”) has also been reported. In order to clone a region flanking the base sequence of the gene encoding fumA (1,647 bp), four types of oligonucleotide primers represented by GCAACGTTGGCTCTCATCT (SEQ ID NO: 138), CGGGATCCAAACACGCGGCGGAAAACA (SEQ ID NO: 139), CGGGATCCGTTAACGCAGGCTGAC (SEQ ID NO: 140), and GCTGCTGGCGTACTGGTTC (SEQ ID NO: 141) were synthesized.
The genomic DNA of Pantoea ananatis AJ417 was prepared, and PCR was carried out using the obtained genomic DNA as a template and using a primer pair of SEQ ID NO:138 and SEQ ID NO:139, as a result of which a DNA fragment of about 0.7 kb (hereinafter sometimes referred to as “fumA-L fragment”) was amplified. In addition, PCR was carried out using a primer pair of SEQ ID NO:140 and SEQ ID NO:141, as a result of which a DNA fragment of about 0.9 kb was amplified (hereinafter sometimes referred to as “fumA-R fragment”) was amplified.
These DNA fragments were separated by agarose electrophoresis and recovered, and each of the fumA-L fragment and the fumA-R fragment was digested with BamHI. The resulting fragments were ligated using a ligase, and the 5′-ends of the ligated product was phosphorylated using T4 polynucleotide kinase. The DNA fragment obtained was mixed with a DNA fragment prepared by digesting the above-described pHSG-sacB with BamHI and further subjecting the resulting product to blunt-end treatment with T4 DNA polymerase and alkaline phosphatase treatment, and the mixed fragments were ligated using a ligase. Thereafter, Escherichia coli DH5α competent cells (manufactured by Toyobo Co., Ltd.) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 25 μg/ml kanamycin at 30° C. were obtained. A plasmid was recovered from an obtained transformants, and it was confirmed that the two fragments—the 5′-upstream flanking region fragment and 3′-downstream flanking region fragment of the gene encoding fumA—were properly inserted in pHSG-sacB. The plasmid obtained was named psacB-PAfumA.
The plasmid psacB-PAfumA is replicable in Pantoea ananatis. Therefore, in order to obtain a plasmid for deleting fumA gene that lacks a replication origin and would not be replicated in Pantoea ananatis, amplification by PCR was carried out using psacB-PAfumA as a template and a primer pair of CITIACACTTTATGCTTCC (SEQ ID NO: 142) and TTGAGCTCGAGAGGTCTGCCTCGTGA (SEQ ID NO: 143) having a SacI recognition site in the 5′-end side thereof, as a result of which a DNA fragment of about 5 kb was obtained. The DNA fragment obtained was digested with SacI and allowed to ligate using a ligase, as a result of which plasmid pPAfumA was obtained. The obtained pPAfumA harbors the fumA-L fragment, the fumA-R fragment, the sacB gene, and the kanamycin-resistance gene, but no replication origin. Pantoea ananatis AJ417 was transformed with pPAfumA by electroporation, and applied to an LB agar plate containing 40 μg/ml kanamycin. The single-crossover clone that grew on the above medium were cultured overnight in an LB liquid medium, and part of the culture liquid was applied to an LB agar medium containing 10% (w/v) sucrose.
Subsequently, among the clones obtained with the above medium, kanamycin-sensitive clones that grew on the sucrose-containing medium were selected. Furthermore, the chromosomal DNAs of these clones were amplified by PCR using a primer pair of SEQ ID NO: 138 and SEQ ID NO: 141, and a variant from which a fragment of about 1.5 kbp, which indicates deletion of the fumA gene, could be amplified was selected. The variant obtained was named Pantoea ananatis AJ417 fumA gene-deleted variant (hereinafter sometimes abbreviated to “PAΔfumA variant”).
<Preparation of Pantoea ananatis fumA Gene-Deled, fumC Gene-Deleted Variant>
In order to clone a region flanking the base sequence of the gene encoding fumarate hydratase class II (hereinafter sometimes referred to as “fumC”) (1,398 bp), four types of oligonucleotide primers represented by TCGCCATGATGCTGCTGTG (SEQ ID NO: 144), CGGGATCCGACTTAGCGTCATCGGTTG (SEQ ID NO: 145), CGGGATCCGATGAAGATTGCTAACGACG (SEQ ID NO: 146), and TGATGCCGACAATATTACGC (SEQ ID NO: 147) were synthesized.
The genomic DNA of the Pantoea ananatis AJ417 was prepared, and PCR was carried out using the obtained genomic DNA as a template and using a primer pair of SEQ ID NO: 144 and SEQ ID NO: 145, as a result of which a DNA fragment of about 0.8 kb (hereinafter sometimes referred to as “fumC-L fragment”) was amplified. In addition, PCR was carrying out using a primer pair of SEQ ID NO: 146 and SEQ ID NO: 147, as a result of which a DNA fragment of about 0.7 kb (hereinafter sometimes referred to as “fumC-R fragment”) was amplified.
These DNA fragments were separated by agarose electrophoresis, and recovered. Each of the fumC-L fragment and the fumC-R fragment was digested with BamHI, and these fragments were allowed to ligate using a ligase, followed by phosphorylation treatment of the 5′-ends using T4 polynucleotide kinase. The resulting DNA fragment was mixed with a DNA fragment prepared by digesting pHSG-sacB prepared in Example 38 with BamHI and further subjecting the resulting product to blunt-end treatment with T4 DNA polymerase and alkaline phosphatase treatment, and the mixed fragments were ligated using a ligase. Thereafter, Escherichia coli DH5α competent cells (manufactured by Toyobo Co., Ltd.) were transformed with the resulting ligation product, and transformants growing on an LB agar plate containing 25 μg/mL kanamycin at 30° C. were obtained. A plasmid was recovered from transformants obtained, and it was confirmed that the two fragments—the 5′-upstream flanking region fragment and 3′-downstream flanking region fragment of the gene encoding fumC—were properly inserted in pHSG-sacB. The plasmid obtained was named psacB-PAfumC.
Plasmid pPAfumC for deleting the fumC gene that lacks a replication origin and would not be replicated in Pantoea ananatis was obtained in the same manner as in Example 38, except that the plasmid psacB-PAfumC was used instead of psacB-PAfumA. Furthermore, kanamycin-sensitive clones that grew on a sucrose-containing medium were selected in the same manner as in Example 38, except that the plasmid pPAfumC was used instead of pPAfumA and that the PAΔfumA variant was used instead of the Pantoea ananatis AJ417. The chromosomal DNAs of these clones were amplified by PCR using a primer pair of SEQ ID NO: 138 and SEQ ID NO: 141, and a variant from which a fragment of about 1.5 kbp, which indicates deletion of the fumC gene, could be amplified was selected. The variant obtained was transformed with RSFCPG by the CaCl2 method, and cultured in LB medium containing 10 μg/mL tetracycline. The variant obtained was named Pantoea ananatis, fumA gene-deleted, fumC gene-deleted variant (hereinafter sometimes abbreviated to “PAΔfumAC variant”).
<Construction of Pantoea ananatis Variants for Evaluation>
Each of the Pantoea ananatis PA variant prepared in Example 36, the PAΔaceB variant prepared in Example 37, and the PAΔfumAC variant prepared in Example 39, was transformed with pGAPS prepared in Example 34, pGAPS_gcl prepared in Example 35, pMWGKC prepared in Example 10, and/or pMWGKC_mcl(Mc)_mtk(Mc) in Example 21 by the CaCl2 method or electroporation, and was applied to an LB agar plate containing 30 μg/mL chloramphenicol, 120 μg/mL spectinomycin, and 15 μg/mL tetracycline. The colony that grew on the plate was used as the variant for evaluation. The obtained variants are summarized in Table 13.
<Confirmation of Incorporation of 13C-Labeled CO2 into Glutamate in Pantoea Variants>
Each of the target Pantoea variants was pre-cultured in an LB medium containing 30 μg/mL chloramphenicol, 120 μg/mL spectinomycin, and 15 μg/mL tetracycline at 30° C., 220 rpm. The bacterial cells were collected from the preculture by centrifugal separation (5,000 rpm for 5 minutes). 2 mL of minimal medium for Pantoea (17 g/L Na2HPO4.12H2O, 3 g/L KH2PO4, 0.5 g/L NaCl, 1 g/L NH4Cl, 10 mM MgSO4, 10 μM CaCl2, 50 mg/L L-lysine, 50 mg/L L-Methionine, pH 6.0) containing 100 mM sodium hydrogen carbonate (13C-labeled), 20 g/L glucose, 30 μg/mL chloramphenicol, 120 μg/mL spectinomycin, and 15 μg/mL tetracycline was prepared, and the bacterial cells obtained were added thereto such that the OD was adjusted to within the range of 1 to 5. After tightly sealing the culture vessel, the bacterial cells were cultured at 30° C., 220 rpm for 1 day. The culture liquid was periodically sampled, and the bacterial cells were removed by centrifugal separation (12,000 rpm for 3 minutes). The supernatant obtained was filtered through a hydrophilic PTFE membrane filter (Millipore Corporation, MSGVN2B50), thereby obtaining a culture sample. The variants used as culture samples are summarized in Table 13.
For measuring the 13C content of glutamate in each culture sample, 500 μL of MTBSTFA with 1% TBDMSCl (manufactured by Sigma-Aldrich Co., 375934) and 500 μL of dry DMF were added to an appropriate amount of the sample, which was dried by, for example, freeze-drying or vacuum drying. The mixture obtained was heated at 80° C. for 2 hours, and then separated by centrifugation (14,000 rpm for 5 minutes). The supernatant obtained was analyzed by GC-MS (Agilent 7890A and 5975c). Respective areas of the mass spectrum peaks at molecular weights of 432, 433, and 434, each of which was assumed to correspond to a structure in which one t-butyl group was removed from a glutamate derivative, were measured. Here, it is assumed that the molecular weight of 432 corresponds to a structure in which all atoms are formed from most abundant isotopes, that the molecular weight of 433 corresponds to a structure containing one neutron, and that the molecular weight of 434 corresponds to a structure containing two neutrons. The peaks at molecular weights of 432, 433, and 434 were defined as [M+0], [M+1], and [M+2], respectively. The value of [M+1]/[M+0] was plotted on the x-axis and the value of [M+2]/[M+0] was plotted on the y-axis. The analysis results are shown in Table 4.
In general glutamate fermentation, 13C derived from NaH13CO3 is incorporated via oxaloacetate into glutamate only at the C1- or C5-position. Therefore, the above-mentioned values will be positioned on a reference line. The reference line was determined according to the following equations.
x=(x0−x0×α+α)/(1−α).
y=(y0−y0×α+x0×α)/(1−α).
α represents the ratio of the 13C isotope in the CO2-derived carbon (at the C1-position or C5-position) in glutamate [≈13C/(13C+12C)]. x and y represent the coordinates of an arbitrary point on the reference line. x0 and y0 represent the values of x and y, assuming that the isotope ratio of 12C in the CO2-derived carbon (at one of the 1-position and 5-position of glutamate) in glutamate is 100% and that the isotope ratios of other atoms are the same as their natural isotope ratios (that is, the values of x and y, if α=0). x0 and y0 were set to 0.358527 and 0.16822084314, respectively. By solving the above equations, the reference line is expressed in the following equation.
y=x0·x+y0−x02
In the intrinsic glutamate production pathway, 13C derived from NaH13CO3-derived is fixed by a carbon dioxide fixation enzyme such as phosphoenolpyruvate carboxylase (ppc), pyruvate carboxylase (pyc), or phosphoenolpyruvate carboxykinase (pck), and incorporated via oxaloacetate into glutamate either at the C1-position or C5-position. Although values of [M+1] and [M+2] vary depending on the ratios of 12CO2 and 13CO2 incorporated by ppc, the values are always plotted on the reference line in a case in which the incorporation occurs at a single position. On the other hand, in a case in which the intended carbon dioxide fixation pathway functions, 13C is incorporated into glutamate via both oxaloacetate and acetyl-CoA. In this case, there is a possibility that 13C is incorporated into glutamate both at the C1-position and the C5-position, as a result of which the [M+2] value should be increased to give a value plotted above the reference line.
As shown in
<Production of Glutamate by Pantoea Variants>
The amount of glutamate and the amounts of byproducts in the culture liquid in Example 41 were measured. The amount of glutamate in the culture sample was measured using a HPLC (2695, Waters) equipped with an NN-814 column (Showa Denko K.K.) and a UV/Vis detector (2489, Waters). The amounts of glucose and other products in the filtrate were measured using a HPLC (2695, Waters) equipped with an ULTRON PS-80H column (Shinwa Chemical Industries Ltd.) and an RI detector (2414, Waters). The results are shown in Tables 14 and 15.
The mtk+mcl+gcl-induced variant (PA/mtk_mcl/gcl) showed an improved yield relative to sugar consumption, as compared with the control strain (PA/vec) and the mtk+mcl-induced variant (PA/mtk_mcl). In the case of disruption of the aceB gene or the fumAC gene (PAΔaceB/mtk_mcl/gcl, PAΔfumAC/mtk_mcl/gcl), the yield relative to sugar consumption was further increased.
Regarding the amounts of byproducts, when compared to the control strain (PA/vec), it was found that, unexpectedly, the amounts of succinate and 2,3-butanediol (2,3-BDO) were reduced and the total amount of byproducts were reduced in the mtk+mcl+gcl-introduced variant (PA/mtk_mcl/gcl). Further, when compared to the aceB gene-non-disrupted variant (PA/mtk_mcl/gcl), it was revealed that, unexpectedly, the amounts of succinate and acetate were reduced, and also the total amount of byproducts was remarkably reduced in the aceB gene-disrupted variant (PAΔaceB/mtk_mcl/gcl). In the fumAC gene-disrupted variant (PAΔfumAC/mtk_mcl/gcl), the amount of succinate was remarkably decreased compared to the fumAC gene-non-disrupted variant (PA/mtk_mcl/gcl), but the amount of acetate was increased and the total amount of byproducts was reduced. These variants are industrially preferable, since a smaller amount of byproducts allow a significant reduction in the purification load when glutamate is collected from a culture liquid.
The above effect of decreasing byproducts was similarly observed in the PA variant having no RSFCPG.
<Preparation of Plasmid pCASET>
Amplification by a PCR method was carried out using pHSG298 (Takara) as a template and using CGCCTCGAGTGACTCATACCAGGCCTG (SEQ ID NO: 148) and CGCCTCGAGGCAACACCTTCTTCACGAG (SEQ ID NO: 149) as primers, and the DNA fragment obtained was digested with restriction enzyme XhoI and allowed to ligate using a ligase. Thereafter, Escherichia coli DH5α competent cells (Toyobo Co., Ltd., DNA-903) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 25 μg/mL kanamycin were obtained. Plasmids were recovered from the bacterial cells obtained, and a plasmid in which a recognition site of XhoI is inserted in pHSG298 was named pHSG298-XhoI.
In order to obtain the tac promoter, amplification by a PCR method was carried out using pKK223-3 (Pharmacia) as a template and using ATCATCCAGCTGTCAGGCAGCCATCGGAAG (SEQ ID NO: 150) and ATCCCCGGGAATTCTGTT (SEQ ID NO: 151) as primers, and the DNA fragment obtained was digested with restriction enzymes PvuII and SmaI, as a result of which a DNA fragment of about 0.2 kbp encoding the tac promoter was obtained. The obtained DNA fragment was mixed with a DNA fragment of about 2.4 kbp prepared by digesting the plasmid pHSG298-XhoI with restriction enzyme PvuII and subjecting the resulting product to alkaline phosphatase treatment, and the mixed fragments were ligated using a ligase. Thereafter, the Escherichia coli DH5α competent cells (Toyobo Co., Ltd., DNA-903) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 25 μg/mL kanamycin were obtained. A plasmid was recovered from the bacterial cells obtained, thereby obtaining a plasmid pHSGT1 in which the lac promoter of pHSG298-XhoI is replaced by the tac promoter and the tac promoter is inserted in the same direction as the original lac promoter.
In order to ligate the multi-cloning site of pHSG298 to the downstream of the tac promoter of pHSGT1, pHSG298 was digested with restriction enzymes EcoRI and ClaI, thereby obtaining a DNA fragment of about 1.0 kbp containing the multi-cloning site of pHSG298. The DNA fragment obtained was mixed with a DNA fragment of about 1.7 kbp prepared by digesting the plasmid pHSGT1 with restriction enzymes EcoRI and ClaI and subjecting the resulting product to alkaline phosphatase treatment, and the mixed fragments were ligated using a ligase. Thereafter, Escherichia coli DH5α competent cells (Toyobo Co., Ltd., DNA-903) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 25 μg/mL kanamycin were obtained. A plasmid was recovered the bacterial cells obtained, thereby obtaining a plasmid pHSGT2 in which the multi-cloning site of pHSG298 is ligated to the downstream of the tac promoter.
The following DNA fragment (SEQ ID NO:152) containing the replication origin, repA, and repB of pCASE1 (Appl Microbiol Biotechnol (2009) 81:1107-1115) isolated from Corynebacterium casei JCM 12072 was prepared by DNA synthesis. The sequence thereof is shown below.
The DNA fragment prepared was digested with restriction enzyme XhoI. The DNA fragment obtained was mixed with a DNA fragment prepared by digesting the plasmid pHSGT2 with restriction enzyme XhoI and subjecting the resulting product to alkaline phosphatase treatment, and the mixed fragments were ligated using a ligase. Thereafter, Escherichia coli DH5α competent cells (Toyobo Co., Ltd., DNA-903) were transformed with the ligation product, and transformants that grew on an LB agar plate containing 25 μg/mL kanamycin were obtained. Plasmids were recovered from the bacterial cells obtained, and a plasmid in which the DNA fragment containing the replication origin, repA, and repB of pCASE1 is inserted at the XhoI recognition site of pHSGT2 was named pCASET. In the pCASET recovered, the repA derived from pCASE1 was inserted in the opposite direction with respect to the tac promoter.
<Construction of Plasmid pCASEL>
The DNA fragment synthesized in Example 43 (SEQ ID NO: 152) containing the replication origin, repA, and repB of pCASE1 was digested with restriction enzyme XhoI. The DNA fragment obtained was mixed with a DNA fragment prepared by digesting the plasmid pHSG298-XhoI prepared in Example 43 with restriction enzyme XhoI and subjecting the resulting product to alkaline phosphatase treatment, and the mixed fragments were ligated using a ligase. Thereafter, Escherichia coli DH5α competent cells were transformed with the ligation product, and transformants that grew on an LB agar plate containing 25 μg/mL kanamycin were obtained. Plasmids were recovered from the bacterial cells obtained, and a plasmid in which the DNA fragment containing the replication origin, repA, and repB of pCASE1 is inserted at the XhoI recognition site of pHSG298-XhoI was named pCASEL. In the pCASEL recovered, the repA derived from pCASE1 was inserted in the opposite direction with respect to the lac promoter derived from pHSG298.
<Construction of Expression Plasmid for Mtk and Mcl Derived from Methylococcus capsulatus>
PCR was carried out using pMWGKC_mcl(Mc)_mtk(Mc) as a template and using a primer pair of GGAATTCACAAAAAGGATAAAACAATGGCTGTCAAGAACCGTCTAC (SEQ ID NO: 153) and CGAATTCTCAGAATCTGATTCCGTGTTCCTG (SEQ ID NO: 154), as a result of which a DNA fragment containing mcl-mtk of Methylococcus was obtained. Each of the primers of SEQ ID NOs: 153 and 154 has an EcoRI recognition site in the 5′-end side. Each of the DNA fragment obtained and plasmid pCASET were digested with EcoRI and dephosphorylated, and the resulting fragments were allowed to be ligated. Similarly, the DNA fragment obtained and plasmid pCASEL were digested. By DNA sequencing, it was confirmed that the mcl-mtk fragment was inserted in the direction appropriate for expression with the promoter of the plasmid. The plasmid obtained was named pCASET_mcl(Mc)_mtk(Mc) or pCASEL_mcl(Mc)_mtk(Mc).
<Construction of Expression Plasmids for mtk Derived from Granulibacter bethesdensis, Nitrosomonas europaea, and Hyphomicrobium methylovorum>
dam−/dcm− Competent Escherichia coli cells (New England Biolabs) were transformed with each of pMWGKC_mcl(Hme)_mtk(Gb), pMWGKC_mcl(Hme)_mtk(Hme)_mcl, and pMWGKC_mcl(Ne)_mtk(Ne), and grown on an LB medium containing 30 μg/mL chloramphenicol. A plasmid was recovered therefrom digested with restriction enzymes EcoRI and XbaI, as a result of which a DNA fragment of about 3 kb containing mtk and mcl was obtained. The DNA fragment containing mtk and mcl was ligated to a plasmid pCASEL that had been digested with restriction enzymes EcoRI and XbaI, thereby preparing vectors pCASEL_mcl(Hme)_mtk(Gb), pCASEL_mcl(Hme)_mtk(Hme), and pCASEL_mcl(Ne)_mtk(Ne) for expressing mtk and mcl in Corynebacterium. Each of these vectors has mtk of Granulibacter bethesdensis, Nitrosomonas europaea, or Hyphomicrobium methylovorum.
The plasmids for Corynebacterium prepared are summarized in Table 16.
<Measurement of mtk Activity in Corynebacterium>
Corynebacterium glutamicum ATCC 13012 was transformed with each of the plasmids prepared in Example 45 and Example 46 by electroporation. The resultant was applied to an LB agar plate containing 15 μg/mg kanamycin, and cultured at 30° C. for 1 to 4 days. The colonies obtained was cultured at 30° C. for 1 to 4 days in an LB liquid medium containing 15 μg/mg kanamycin, and bacterial cells were collected by centrifugal separation. The bacterial cells were suspended in MOPS-K buffer (pH 7.7), and suspension obtained was crushed with 0.1 mm glass beads using a Beads Shocker (MB5000, Yasui Kikai Corporation). Thereafter, the supernatant obtained by centrifugal separation (13,000 rpm for 2 minutes) was used as a mutant crude enzyme extract. The activity in the bacterial cells was measured using the extract in the same manner as in Example 16. The results are shown in Table 17.
In a case in which the pCASEL plasmid was used as the expression vector, the plasmid expressing mtk derived from Methylococcus capsulatus provided the highest value of activity. Further, when compared to Table 9, almost the same correlation was observed between mtk having high activity and mtk having low activity. The evaluation of the activities of Methylococcus capsulatus-derived mtk introduced into pCASEL and that introduced into pCASET showed a higher activity in the variant having mtk introduced into pCASET.
<Construction of Expression Plasmid for mtk, mcl, gcl, and glxR in Corynebacterium>
Rhodococcus jostii NBRC16295 was purchased from NBRC (Biological Resource Center, Biotechnology Field, National Institute of Technology and Evaluation). NBRC16295 was cultured in a medium (medium number: 802, NBRC), and genomic DNA was obtained therefrom using DNeasy Blood &Tissue Kit (QIAGEN). PCR was carried out using this genomic DNA as a template and using CGAGCTCAAGCTTACAAAAAGGATAAAACAATGAGCACCATTGCATTCATCGG (SEQ ID NO: 155) and CGGGATCCCTAGTCCAGCAGCATGAGAG (SEQ ID NO: 156) as primers, as a result of which a glxR-gcl fragment of Rhodococcus (SEQ ID NO: 157) was obtained. The fragment obtained was digested with SacI and BamHI, and the resultant was ligated to a fragment obtained by digesting pCASET_mcl(Mc)_mtk(Mc) with SacI and BamHI. The plasmid obtained was named pCASET_mcl(Mc)_mtk(Mc)_glxR(Rj)_gcl(Rj).
<Construction of Corynebacterium glutamicum Variant for Evaluation of Glutamate Production and Incorporation of 13C>
Corynebacterium glutamicum DSM1412 (hereinafter sometimes referred to as “CG strain”) was transformed with each of the plasmids constructed in Examples 43, 45, and 48 by electroporation, and applied to an LB agar plate containing 15 μg/mL kanamycin. The colony that grew on the plate was used as the variant for evaluation. The obtained variants are summarized in Table 18.
<Confirmation of Introduction of 13C-labeled CO2 into Glutamate in Corynebacterium Variants>
Each of the microorganism variants to be analyzed was cultured in 2 mL of LB liquid medium containing 15 μg/mL kanamycin at 30° C. and 280 rpm until sufficient growth was achieved. In a 100-mL Erlenmeyer flask equipped with stirrer blades, 10 mL of minimal medium [30 g/L (NH4)2SO4, 3 g/L Na2HPO4, 6 g/L KH2PO4, 2 g/L NaCl, 84 mg/L CaCl2, 3.9 mg/L FeCl3, 0.9 mg/L ZnSO4.7H2O, 0.3 mg/L CuCl2.H2O, 5.56 mg/L MnSO4.5H2O, 0.1 mg/L (NH4)6Mo7O24.4H2O, 0.3 mg/L Na2B4O7.10H2O, 0.4 g/L MgSO4.7H2O, 40 mg/L FeSO4.7H2O, 500 μg/L Vitamine B1.HCl, 0.1 g/L EDTA, 10 μg/L Biotin] for Corynebacterium containing 20 g/L glucose and 15 μg/mL kanamycin was prepared. 1 mL of culture in the LB liquid medium above was added thereto, and the mixture was cultured for 1 to 4 days until sufficient growth was achieved, whereby a preculture was obtained. From the preculture, bacterial cells were collected by centrifugal separation (5,000 rpm for 5 minutes).
2 mL of the minimal medium for Corynebacterium (the final concentration of Biotin was changed to 2 μg/L) containing 100 mM sodium hydrogen carbonate (13C-labeled), 20 g/L glucose, 1.5% (w/v) Tween 60 (manufactured by Sigma-Aldrich Co.), and 15 μg/mL kanamycin was prepared, and the bacterial cells from preculture were added thereto such that the OD was adjusted to within the range of 1 to 5. After tightly sealing the culture vessel, the bacterial cells were cultured at 30° C. and 150 rpm for 1 to 2 days. The culture liquid was periodically sampled, and the bacterial cells were removed by centrifugal separation (Millipore Corporation, 12,000 rpm for 3 minutes). The supernatant obtained was filtered through a hydrophilic PTFE membrane filter (Millipore Corporation, MSGVN2B50), thereby obtaining a culture sample. The 13C content of the culture sample was analyzed in the same manner as in Example 41. That is, respective areas of the peaks at molecular weights of 432, 433, and 434 in GC-MS analysis were defined as [M], [M+1], and [M+2], respectively, and the value of [M+1]/[M] was plotted on the x-axis and the value of [M+2]/[M] was plotted on the y-axis. The reference line was obtained by a calculation according to the method described in Example 41.
Based on
<Test for Production of Glutamate in Corynebacterium Variants>
The amount of glutamate and the amounts of byproducts in the culture liquid in Example 50 were measured. In the same manner as in Example 42, glutamate, glucose, and other organic compounds in the culture liquid were analyzed. The results are shown in Tables 19 and 20.
The mtk+mcl+gcl+glxR-introduced variant (CG/mtk_mcl_gcl_glxR) showed an improved yield relative to sugar consumption, as compared with the control strain (CG/vec) and the variant (CG/mtk_mcl) in which only mtk+mcl was introduced.
Regarding the amounts of byproducts, as compared with the control strain (CG/vec), it was found that, unexpectedly, the amount of lactate was mainly reduced and the total amount of byproducts were reduced in the mtk+mcl+gcl+glxR-introduced variant (CG/mtk_mcl_gcl_glxR). In the variant (CG/mtk_mcl) in which only mtk+mcl was introduced, the amounts of byproducts were almost the same as those in the control strain.
<Enhancement of Activity by Introduction of Mutations into Malate Thiokinase Gene Derived from Methylobacterium extorquens>
PCR was carried out using pMWGKC_mtk(Mex)_mcl as a template and each of the primer pairs shown in Table 21. The template was digested with restriction enzyme DpnI. Thereafter, Escherichia coli DH5α competent cells were transformed with the obtained product, and transformants that grew on an LB agar plate containing 10 μg/mL chloramphenicol were obtained. The colonies obtained were cultured at 30° C. overnight in an LB liquid medium containing 10 μg/mL chloramphenicol. A plasmid was recovered from a part of the culture liquid, and the DNA sequence thereof was checked. A plasmid in which the intended mutation was properly introduced was used as the mutant sample. This sample was pre-cultured in an LB liquid medium containing 10 μg/mL chloramphenicol, and then inoculated into 3 mL of LB liquid medium containing 10 μg/mL chloramphenicol and cultured at 30° C. and 280 rpm overnight. Two milliliters of the culture was separated by centrifugation at 10,000 rpm for 5 minutes to remove the supernatant, and 2 mL of 10 mM phosphate buffer (pH 7.0) was added thereto, followed by washing the cells. The washing operation was repeated once, and the cells were suspended in 500 μL of 10 mM phosphate buffer (pH 7.0). The suspension obtained was crushed with 0.1 mm glass beads using a Beads Shocker (MB5000, Yasui Kikai Corporation), and the supernatant obtained by centrifugal separation (13,000 rpm for 2 minutes) was used as a mutant crude enzyme extract.
The activity of each mutant crude enzyme extract was evaluated in accordance with the method described in Example 16. The results are shown in Table 21. As a result, the Q244E mutation in mtkB and the L144I mutation in mtkB improved the activity value compared to the non-mutated mtkB. In addition, the activity was improved by introducing another amino acid into the Q244 position of mtkB, when the introduced amino acid was A, L, I, M, N, Y, K, or R. Further, the activity was improved by introducing a mutation into the L144 position of mtkB, when the introduced amino acid was N, D, K, R, H, Q, or P.
According to the invention, CO2 can be converted into acetyl-CoA. Further, according to the invention, substances derived from acetyl-CoA such as isopropyl alcohol, acetone, and glutamic acid can be efficiently produced.
The disclosure of Japanese Patent Application No. 2011-167808 filed on Jul. 29, 2011 is incorporated herein by reference in its entirety.
All publications, patent applications, and technical standards mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent application, or technical standard was specifically and individually indicated to be incorporated by reference.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2011-167808 | Jul 2011 | JP | national |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/JP2012/069247 | 7/27/2012 | WO | 00 | 1/28/2014 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2013/018734 | 2/7/2013 | WO | A |
| Number | Date | Country |
|---|---|---|
| 102007047206 | Apr 2009 | DE |
| 1020070 59 248 | Jun 2009 | DE |
| WO-2009046929 | Apr 2009 | WO |
| WO-2009094485 | Jul 2009 | WO |
| WO-2010071697 | Jun 2010 | WO |
| WO-2011099006 | Aug 2011 | WO |
| Entry |
|---|
| Erb et al. The Apparent Malate Synthase Activity of Rhodobacter sphaeroides Is Due to Two Paralogous Enzymes, (3S)-Malyl-Coenzyme A (CoA)/β-Methylmalyl-CoA Lyase and (3S)-Malyl-CoA Thioesterase. J. Bacteriol. Mar. 2010 vol. 192 No. 5 1249-1258. |
| Chistoserdova et al. Genetics of the Serine Cycle in Methylobacterium extorquens AM1: Identification, Sequence, and Mutation of Three New Genes Involved in C1 Assimilation, orf4, mtkA, and mtkB. Journal of Bacteriology, Dec. 1994, p. 7398-7404. |
| Friedmann et al. Properties of Succinyl-Coenzyme A:L-Malate Coenzyme A Transferase and Its Role in the Autotrophic 3-Hydroxypropionate Cycle of Chloroflexus aurantiacus. Journal of Bacteriology, Apr. 2006, p. 2646-2655. |
| Extended European Search Report issued in Application No. 12819719.1 dated Jan. 29, 2015. |
| Berg, I. A., Ecological aspects of the distribution of different autotrophic CO2 fixation pathways, Applied and Environmental Microbiology, Mar. 2011, vol. 77 No. 6, pp. 1925-1936. |
| International Search Report dated Oct. 9, 2012 received in International Application No. PCT/JP2012/069247. |
| Chinese Office Action issued in Chinese Patent Application No. 201280036982.9 dated Apr. 19, 2016. |
| Tobias J. Erb et al., “The Apparent Malate Synthase Activity of Rhodobacter sphaeroides Is Due to Two Paralogous Enzymes, (3S)-Malyl-Coenzyme A (CoA)/β-Methylmalyl-CoA Lyase and (3S)-Malyl-CoA Thioesterase”, Journal of Bacterilogy, Mar. 2010, vol. 192, No. 5, pp. 1249-1258. |
| Number | Date | Country | |
|---|---|---|---|
| 20140363847 A1 | Dec 2014 | US |
