# Patent

## Title
Practical method for enzymatically synthesizing cyclic di-GMP

## Abstract

A practical method for enzymatically synthesizing c-di-GMP with excellent productivity is provided. A diguanylate cyclase having physical and chemical characteristics (A) to (F): (A) catalytic action on reaction “2 GTP→c-di-GMP”; (B) a molecular weight of 19800±2000; (C) an optimum pH of 7.3 to 9.4; (D) an optimum temperature of 35 to 60° C.; (E) thermal stability as the remaining activity of 90% or higher after heated for 60 minutes under conditions of 50° C. and pH7.8; and (F) the presence of GGDEF (SEQ ID NO:26) domain and the lack of amino acid sequence KXXD (SEQ ID NO:23) in the i-site.

## Background
TECHNICAL FIELD
The present invention relates to a novel enzyme with diguanylate cyclase activity and a practical method for synthesizing cyclic di-GMP using the enzyme.
BACKGROUND ART
Cyclic di-GMP (hereinafter, sometimes called “c-di-GMP”) is a bacterial signal molecule involved in biofilm formation, motility, virulence factor expression, and the like of bacteria, and the physiological activity, the signaling mechanism, and the like thereof receive attention in recent years. For example, c-di-GMP was found to have immunostimulatory action and is used as an adjuvant, an active ingredient of an allergy-regulating drug, and the like, thereby being recently expected to be promising as a pharmaceutical.
C-di-GMP has been only limitedly available and very expensive. Because of this, in order to produce c-di-GMP efficiently, chemical synthesis and enzymatic synthesis have been conventionally studied and, among these, enzymatic synthesis has been considered to be practical as the production method.
C-di-GMP can be synthesized from two GTP molecules by a two-step enzymatic reaction via the catalytic action of a diguanylate cyclase (hereinafter, sometimes called “DGC”). DGCs derived from various living organisms have “GGDEF (SEQ ID NO:26) domain”, which is responsible for the activity and is well conserved among biological species. GGDEF (SEQ ID NO:26) domain has a region called an i-site that is known to be involved in product inhibition in a c-di-GMP synthesis reaction. Various living organisms have a gene that has GGDEF (SEQ ID NO:26) domain and is supposed to have DGC activity. The GGDEF (SEQ ID NO:26) domains have high homology with each other, while the regions other than the GGDEF (SEQ ID NO:26) domains vary to a great extent among the genes and assume different structures.
As a known, conventional method for enzymatically synthesizing c-di-GMP, a one-pot synthesis of c-di-GMP is disclosed where a mutant DGC that is derived from Caulobacter crescentus and results from expression in Escherichia coli or the like in a large amount in the form of an inclusion body is used along with a guanylate kinase and a nucleoside diphosphate kinase (Patent Document 1). With its c-di-GMP production process requiring a step of purifying an inclusion body from an Escherichia coli cell and a step of refolding the resultant DGC in the form of an inclusion body for reactivation, the method in Patent Document 1 has too many complicated treatment processes for large-scale industrial synthesis, thereby having many problems.
As another known method, use of a DGC derived from thermophilic bacterium Thermotoga maritima is known (Patent Document 2 and Non-patent Document 1). It is described that synthesis in this method used a modified enzyme obtained by exclusively expressing GGDEF (SEQ ID NO:26) domain, which is the minimum functional region, of a DGC derived from T. maritima and, into the i-site, introducing amino acid mutation so as to remove product inhibition.
The inventors of the present invention reported development of a c-di-GMP synthesis system where a DGC derived from Geobacillus stearothermophilus (hereinafter, sometimes called “GsDGC”) is used (Non-patent Document 2). Non-patent Document 2 describes a combined use of polyphosphate:AMP phosphotransferase derived from Acinetobacter johnsonii and a polyphosphate-dependent nucleoside diphosphate kinase derived from Pseudomonas aeruginosa in the enzymatic reaction system to develop a system for supplying GTP from GMP provided by polyphosphoric acid serving as a donor. The synthesis system in Non-patent Document 2 does not need frequent GTP addition that is necessary in the synthesis system in Patent Document 2 and Non-patent Document 1 due to substrate inhibition caused by GTP, and is therefore an excellent synthesis system. As GTP is expensive, the synthesis system in Non-patent Document 2 has cost advantage as well.
PRIOR ART DOCUMENT
Patent Document


    Patent Literature 1: International Publication No. WO 2010/066666
    Patent Literature 2: International Publication No. WO 2010/101526


Non Patent Document


    Non Patent Literature 1: Analytical Biochemistry, Vol. 389 p. 138-142 (2009)
    Non Patent Literature 2: Abstracts of Presentations at the Annual Meeting of the Japan Society for Bioscience, Biotechnology, and Agrochemistry (2011, Kyoto), p. 119


SUMMARY
Technical Problem
In the method for c-di-GMP production with the use of GsDGC in Non-patent Document 2, however, enzyme activity is not high enough and therefore a significant amount of culture medium for bacterial cells for GsDGC is required relative to the amount of the reaction mixture. In addition, the method has further disadvantages including the necessity of enzyme purification at the time of reaction and complicated procedure and therefore is nowhere near a realistic method for enzymatic synthesis in an industrial scale yet.
As explained in examples below, the inventors of the present invention also attempted gene manipulation described in Patent Document 2 and Non-patent Document 1 by using an enzyme derived from G. stearothermophilus. Specifically, GGDEF (SEQ ID NO:26) domain of a DGC derived from G. stearothermophilus was exclusively expressed and, into the i-site, amino acid mutation was introduced. This, again, did not give adequate enzyme activity.
The present invention is devised based on the circumstances described above, and an object thereof is to provide a practical method for enzymatically synthesizing c-di-GMP.
Solution to Problem
The inventors of the present invention have conducted intensive research. As a result, they have prepared a novel modified enzyme with specific activity, productivity, and thermal stability remarkably enhanced compared to conventional modified enzymes and have established a system for enzymatically synthesizing c-di-GMP with high efficiency. Thus, the present invention has now been completed.
Specifically, as described in examples below, after the minimum functional region of GsDGC was exclusively expressed and mutation was introduced into the i-site thereof, the resultant modified enzyme (hereinafter, sometimes called “tiGs3466”) was subjected to mutagenesis to replace 54th residue asparagine with glycine. The enzyme thus obtained had characteristics that specific activity and enzymatic productivity were remarkably enhanced and thermal stability was extremely high compared to conventional DGCs. The inventors of the present invention found that industrial-scale synthesis of c-di-GMP became more practical and completed the present invention.
The present invention provides:

    
    
        a diguanylate cyclase with physical and chemical characteristics of:
        (A) catalytic action on reaction “2 GTP c-di-GMP”;
        (B) a molecular weight of 19800±2000;
        (C) an optimum pH of 7.3 to 9.4;
        (D) an optimum temperature of 35 to 60° C.;
        (E) thermal stability as the remaining activity of 90% or higher after heated for 60 minutes under conditions of 50° C. and pH7.8; and
        (F) the presence of GGDEF (SEQ ID NO:26) domain and the lack of amino acid sequence KXXD (SEQ ID NO:23) in the i-site.
    
    


A DGC with such properties is verified in examples below to be remarkably enhanced in specific activity and enzymatic productivity and have extremely high thermal stability compared to conventional DGCs. This allows industrial-scale synthesis of c-di-GMP to be more practical. Here, GGDEF (SEQ ID NO:26) domain refers to the minimum functional region of a diguanylate cyclase. The i-site refers to a region in GGDEF (SEQ ID NO:26) domain to control product inhibition. The i-site contains a characteristic motif shown under amino acid sequence KXXD (SEQ ID NO:23). X in KXXD (SEQ ID NO:23) denotes any amino acid residue.
The present invention also provides a DGC having one or more amino acid sequences selected from the group consisting of (G) the amino acid sequence shown under SEQ ID NO:6, (H) an amino acid sequence having identity of 90% or higher with the amino acid sequence shown under SEQ ID NO:6, having 54th residue glycine in the amino acid sequence shown under SEQ ID N0:6 conserved, and with the lack of amino acid sequence KXXD (SEQ ID NO:23) in the i-site, (I) an amino acid sequence equivalent to the amino acid sequence shown under SEQ ID NO:6 including deletion, substitution, insertion, or addition of one or several amino acids, having 54th residue glycine in the amino acid sequence shown under SEQ ID NO:6 conserved, and with the lack of amino acid sequence KXXD (SEQ ID NO:23) in the i-site, and (J) an amino acid sequence coded by the base sequence of a nucleic acid that hybridizes, under stringent conditions, with a nucleic acid having a base sequence complementary to a base sequence coding for the amino acid sequence shown under SEQ ID NO:6, having 54th residue glycine in the amino acid sequence shown under SEQ ID NO:6 conserved, and with the lack of amino acid sequence KXXD (SEQ ID NO:23) in the i-site.
The present invention also provides a fusion enzyme resulting from fusion of a dimerizable protein to the N-terminus of the DGC. The present invention also provides a protein fragment of the DGC or of the fusion enzyme, with diguanylate cyclase activity.
The present invention also provides a polynucleotide or an expression vector coding for the DGC, the protein fragment of the fusion enzyme, or the protein fragment. The present invention also provides a transformant resulting from transformation with the polynucleotide or the expression vector.
The present invention also provides a method for producing c-di-GMP from two GTP molecules using an enzyme, wherein the enzyme is a diguanylate cyclase or a fusion enzyme containing a diguanylate cyclase obtained by culturing a transformant resulting from transformation of a host microorganism with the expression vector.
Effects of the Invention
The enzyme of the present invention is remarkably enhanced in specific activity, enzymatic productivity, and thermal stability compared to conventionally known DGCs. Therefore, a method with the use of the enzyme allows extremely efficient synthesis of c-di-GMP compared to conventional enzymatic synthesis. In the synthesis, a crude enzyme solution derived from bacterial cells can be used as it is and the required usage of the enzyme solution is small. Thus, the enzyme of the present invention and a method for c-di-GMP synthesis with the use of the enzyme are extremely useful as a practical method for producing c-di-GMP.



BRIEF DESCRIPTION OF DRAWINGS
FIG. 1 is a conceptual view of the procedure for preparing various plasmids in examples.
FIG. 2 is a schematic view of reaction steps in a c-di-GMP synthesis system in which a GTP supply system is used.
FIG. 3 shows how c-di-GMP synthesis proceeds when modified enzymes used in examples are in a purified state. The abscissa indicates reaction time, and the ordinate indicates the concentration of c-di-GMP in a culture medium.
FIG. 4 shows how c-di-GMP synthesis proceeds when modified enzymes used in examples are in a crude state. The abscissa indicates reaction time, and the ordinate indicates the concentration of c-di-GMP in a culture medium.
FIG. 5 is a graph showing the DGC activity of tiGs3466G at a pH ranging from 6.5 to 10.0.
FIG. 6 is a graph showing the DGC activity of various modified enzymes in examples at a pH ranging from 6.5 to 10.0.
FIG. 7 is a graph showing the DGC activity of tiGs3466G at 30 to 60° C.
FIG. 8 is a graph showing the DGC activity of various modified enzymes in examples at 30 to 60° C.



DESCRIPTION OF EMBODIMENTS
The embodiments of the present invention will be described in detail. An overlapping explanation of the same content is omitted, as needed, to avoid complexity caused by repetition.
(1) Novel DGC
An embodiment of the present invention is a novel DGC. The DGC may have physical and chemical characteristics (A) to (F): (A) catalytic action on reaction “2 GTP c-di-GMP”; (B) a molecular weight of 19800±2000; (C) an optimum pH of 7.3 to 9.4; (D) an optimum temperature of 35 to 60° C.; (E) thermal stability as the remaining activity of 90% or higher after heated for 60 minutes under conditions of 50° C. and pH7.8; and (F) the presence of GGDEF (SEQ ID NO:26) domain and the lack of amino acid sequence KXXD (SEQ ID NO:23) in the i-site. A DGC having characteristics (A) to (F) is verified in examples to have remarkably high specific activity and enzymatic productivity and also have extremely high thermal stability compared to tiGs3466 (a DGC having the amino acid sequence shown under SEQ ID N0:4). Therefore, use of a DGC having such physical and chemical characteristics can make industrial-scale synthesis of c-di-GMP more practical.
A DGC according to an embodiment of the present invention may have the amino acid sequence shown under SEQ ID NO:6. However, the amino acid sequence is not limited to the exact amino acid sequence shown under SEQ ID N0:6 provided that it has mutation of 54th residue asparagine in tiGs3466 to glycine and maintains DGC activity, and may be an amino acid sequence equivalent to the amino acid sequence shown under SEQ ID NO:6 including deletion, substitution, modification, or addition of one or several amino acids. Alternatively, the DGC may be an enzyme having identity of 90% or higher with the amino acid sequence shown under SEQ ID N0:6 provided that it has mutation of 54th residue asparagine in tiGs3466 to glycine and maintains DGC activity. Alternatively, the DGC may be an enzyme having an amino acid sequence coded by the base sequence of a nucleic acid that hybridizes, under stringent conditions, with a nucleic acid having a base sequence complementary to a base sequence coding for the amino acid sequence shown under SEQ ID NO:6 provided that it has mutation of 54th residue asparagine in tiGs3466 to glycine and maintains DGC activity.
A DGC according to an embodiment of the present invention may have mutation in the i-site. Specifically, the amino acid sequence thereof may be lacking in amino acid sequence KXXD (SEQ ID NO:23), for example. As the position of an i-site is well known to those skilled in the art, the sequence of a DGC in question may be compared to the sequence of a DGC derived from Geobacillus stearothermophilus, for example, so as to locate the i-site of the DGC in question at the region corresponding to KEGD of the DGC derived from Geobacillus stearothermophilus. A DGC according to an embodiment of the present invention may have GGDEF (SEQ ID NO:26) domain. As the sequence of GGDEF (SEQ ID NO:26) domain is well conserved among living organisms, GGDEF (SEQ ID NO:26) domain can be located, as needed, by a search (or comparison) based on the base sequences, the amino acid sequences, and/or the like known for GGDEF (SEQ ID NO:26) domain.
A DGC according to an embodiment of the present invention may be a fusion enzyme comprised of the DGC and a dimerizable protein. For example, it is verified in examples below that a DGC to which a dimerizable inorganic pyrophosphatase is fused is improved in efficiency of c-di-GMP production. The dimerizable protein can be selected by those skilled in the art, and examples thereof include inorganic pyrophosphatases (yPPAs).
A DGC according to an embodiment of the present invention can be obtained by the following method, for example.
(2) Preparation of tiGs3466
(2-1) Cloning of Minimum Functional Region of GsDGC
A gene coding for the minimum functional region of GsDGC (hereinafter, sometimes called “tGs3466 gene”) is obtained from Geobacillus stearothermophilus to use for preparing a recombinant vector. Cloning is performed, for example, by expression in microorganisms such as Escherichia coli by a known cloning method using a genome DNA derived from Geobacillus stearothermophilus as a template and DNA fragments of primers (a) and (b) shown in examples below as PCR primers.
(2-2) Mutagenesis; Introduction of Amino Acid Substitution into i-Site
The method for mutagenesis in an i-site that is responsible for product inhibition only has to follow the method in Patent Document 2, for example. Specifically, mutation to be introduced is not limited provided that it does not cause the loss of the DGC activity of tGs3466 and adequately reduces product inhibition, and example thereof include mutation of 74th residue lysine to alanine and mutation of 77th residue aspartic acid to glutamic acid in the amino acid sequence of tGs3466. In this way, tiGs3466 can be prepared.
(3) Modification of Enzyme
(3-1) Amino Acid Mutagenesis
A DGC according to an embodiment of the present invention is characterized by being obtained by mutagenesis of 54th residue asparagine in the amino acid sequence of tiGs3466 to glycine. The method for mutagenesis only has to follow a known method (Nucleic Acids Res. 2004 Aug. 10; 32(14); e115, for example). A DGC with mutation may be sometimes called a mutant DGC.
(3-2) Preparation of Fusion Enzyme
A DGC according to an embodiment of the present invention can be expressed as a fusion enzyme comprised of tiGs3466 into which the mutation above has been introduced and a dimerizable protein. Fusion of an enzyme can be carried out by a known method. For example, a gene coding for a modified tiGs3466 enzyme into which mutation of 54th residue asparagine in the amino acid sequence of tiGs3466 to glycine has been introduced and a gene coding for a dimerizable protein are cloned separately, and therefrom genes are cleaved out with certain restriction enzymes and are then fused together to give a fusion enzyme gene, which is incorporated into a plasmid for expression in Escherichia coli or the like. The dimerizable protein may have any mutation provided that it is still dimerizable.
(4) Synthesis of c-di-GMP Using Modified Enzyme
A DGC according to an embodiment of the present invention that is used for synthesizing c-di-GMP can be in the form of a purified enzyme or a crude enzyme solution resulting from expression, in a microorganism such as Escherichia coli, of the modified tiGs3466 enzyme into which mutation of 54th residue asparagine in the amino acid sequence of tiGs3466 to glycine has been introduced or an enzyme obtained by fusion of the modified tiGs3466 and a dimerizable protein.
Specifically, treated bacterial cells can be exemplified as the crude enzyme solution and enzymes derived from the treated bacterial cells can be exemplified as the purified enzyme. Bacterial cells can be prepared via culture by a conventional procedure in a medium in which the bacteria can grow, followed by centrifugation or the like to collect the bacterial cells. Bacterial cells of Escherichia coli, as a specific example, can be prepared by inoculating a medium such as a broth medium, an LB medium (1% tryptone, 0.5% yeast extract, 1% common salt), and a 2xYT medium (1.6% tryptone, 1% yeast extract, 0.5% common salt) with starter cells, followed by culture at 30 to 50° C. for about 1 to 100 hours with optional stirring and centrifugation of the culture medium so as to collect the bacterial cells.
Examples of the crude enzyme solution include supernatant obtained by centrifugation of bacterial cells disrupted by a common method such as mechanical disruption (with a Waring blender, a French Press, a homogenizer, a mortar, or the like), freeze-thawing, autolysis, drying (by lyophilization, air drying, or the like), enzyme treatment (with lysozyme or the like), sonication, and chemical treatment (with an acid, an alkali, or the like).
Examples of the purified enzyme include a fraction with desired enzyme activity obtained from the treated bacterial cells by an ordinary enzyme purification means (salting-out treatment, isoelectric precipitation treatment, precipitation treatment with an organic solvent, dialysis treatment, various chromatography treatment, or the like).
To the c-di-GMP synthesis system, GTP as a raw material and a DGC according to an embodiment of the present invention as an enzyme are supplied. Preferably, the amount of GTP ranges from 1 to 200 mM and preferably from 10 to 100 mM and the amount of DGC ranges from 0.001 to 50 units/mL, but these ranges are not limitative. To the reaction system, a metal salt such as a magnesium salt and a manganese salt may further be added. Specific examples of the metal salt include magnesium chloride and manganese chloride. The reaction in such a reaction system can be allowed to proceed at not lower than 15° C., preferably at 30 to 50° C., for 0.5 to 100 hours with optional stirring so as to synthesize c-di-GMP.
The raw material GTP causes substrate inhibition in the c-di-GMP synthesis system, and therefore the reaction system can be combined with a GTP supply system comprised of AMP phosphotransferase (PAP) and a polyphosphate-dependent nucleoside 5′-diphosphate kinase (PNDK).
That is, c-di-GMP can be synthesized by allowing the reaction to proceed in the synthesis system that uses not GTP but GMP as a raw material and adopts, as a GTP supply system, addition of polyphosphoric acid ranging, for example, from 1 to 1000 mM and preferably from 30 to 300 mM in terms of inorganic phosphoric acid, PAP ranging, for example, from 0.001 to 50 units/mL, and PNDK ranging, for example, from 0.001 to 50 units/mL thereto, preferably at 30 to 50° C. for 0.5 to 100 hours with optional stirring.
In each reaction above, pyrophosphoric acid resulting from the reaction can cause product inhibition, and therefore an inorganic pyrophosphatase (yPPA) can be added at an amount not lower than 0.001 units/mL and preferably 0.001 to 10 units/mL
After the reaction, c-di-GMP produced into the reaction mixture can be isolated and purified by ordinary chromatography treatment with active carbon, an ion exchange resin, or the like.
(5) Other DGCs
A DGC according to an embodiment of the present invention is a DGC having the amino acid sequence shown under SEQ ID NO:10. A DGC with such a composition is higher in DGC activity than tiGs3466G (a DGC having the amino acid sequence shown under SEQ ID NO:6) is. The amino acid sequence shown under SEQ ID NO:10 may be replaced by an amino acid sequence having identity of 90% or higher with the amino acid sequence shown under SEQ ID NO:10, having 352nd residue glycine in the amino acid sequence shown under SEQ ID NO:10 conserved, and with the lack of amino acid sequence KXXD (SEQ ID NO:23) in the i-site. Alternatively, the amino acid sequence shown under SEQ ID NO:10 may be replaced by an amino acid sequence equivalent to the amino acid sequence shown under SEQ ID NO:10 including deletion, substitution, insertion, or addition of one or several amino acids, having 352nd residue glycine in the amino acid sequence shown under SEQ ID NO:10 conserved, and with the lack of amino acid sequence KXXD (SEQ ID NO:23) in the i-site. Alternatively, the amino acid sequence shown under SEQ ID NO:10 may be replaced by an amino acid sequence coded by the base sequence of a nucleic acid that hybridizes, under stringent conditions, with a nucleic acid having a base sequence complementary to a base sequence coding for the amino acid sequence shown under SEQ ID NO:10, having 352nd residue glycine in the amino acid sequence shown under SEQ ID NO:10 conserved, and with the lack of amino acid sequence KXXD (SEQ ID NO:23) in the i-site.
In a DGC according to an embodiment of the present invention, an amino acid therein corresponding to 291st residue asparagine in a DGC derived from Geobacillus stearothermophilus may be substituted by a glycine residue. Such an amino acid corresponding to 291st residue asparagine may be located, for example, by comparing the sequence of the DGC in question with the sequence of the DGC derived from Geobacillus stearothermophilus and then select an amino acid residue corresponding to 291st residue asparagine of the DGC derived from Geobacillus stearothermophilus. The DGC derived from Geobacillus stearothermophilus may be a DGC having the amino acid sequence shown under SEQ ID NO:25, for example.
A DGC according to an embodiment of the present invention may be a fusion enzyme resulting from fusion of a DGC and a protein or a peptide. The protein for fusion is preferably a dimerizable protein. The protein for fusion may be an enzyme that hydrolyzes pyrophosphoric acid. It is verified in examples below, for example, that a DGC to which a dimerizable inorganic pyrophosphatase is fused is remarkably improved in efficiency of c-di-GMP production. A DGC according to an embodiment of the present invention may be a protein fragment provided that it maintains DGC activity.
The DGC activity of a DGC according to an embodiment of the present invention is significantly higher than that of a conventional DGC or tiGs3466, by a factor of 1.2, 1.5, 1.8, 2.0, 3.0, 5.0, or 10.0, even higher, or between any two of these. The term “significantly” includes, for example, the case where Student's t-test (one-sided test or two-sided test) gives a statistically significant difference and p<0.05 is satisfied.
After heat treatment under conditions of pH7.8 and 50° C. for 60 minutes, the remaining activity of a DGC according to an embodiment of the present invention may be, for example, 80, 90, or 100%, even higher, or between any two of these. The same applies to the case where heat treatment lasts for 10 or 30 minutes. The remaining activity of a DGC according to an embodiment of the present invention after heat treatment is significantly higher than that of a conventional DGC or tiGs3466. The DGC activity may be, for example, 1.5, 2.0, 5.0, 10.0, 20.0, or 30.0 times higher, even higher, or between any two of these.
The molecular weight of a DGC according to an embodiment of the present invention may be 19800±2000, specifically 17800, 18300, 18800, 19300, 19800, 20300, 20800, 21300, or 21800, for example, or between any two of these. The molecular weight of a DGC according to an embodiment of the present invention may be about 19800. The molecular weight may be a value (Da) measured by SDS-polyacrylamide gel electrophoresis.
The optimum pH may be 7.3, 7.70, 7.85, 8.0, 8.5, 9.05, 9.15, or 9.4 or between any two of these. The optimum pH may be about 8.0 to about 8.5. The optimum pH may be a pH at which, with the activity at pH8.0 being 100, the relative activity is 60, 70, 80, or 90% thereof or higher. With the activity of a DGC according to an embodiment of the present invention at pH8.0 being 100, the relative activity at pH9.5 may be not higher than 55% thereof.
The optimum temperature may be 35, 40, 45, 50, 55, or 60° C. or between any two of these. The optimum temperature may be about 55° C. The optimum temperature may be a temperature at which, with the activity at 55° C. being 100, the relative activity is 60, 70, 80, or 90% thereof or higher.
An embodiment of the present invention is a c-di-GMP material containing a DGC according to an embodiment of the present invention. The c-di-GMP material may contain an aqueous solution or a sol, for example, at a pH within the range of the optimum pH of a DGC according to an embodiment of the present invention. The c-di-GMP material can be combined with an inorganic pyrophosphatase for use as a kit for c-di-GMP production.
An embodiment of the present invention is a polynucleotide coding for a DGC according to an embodiment of the present invention. An embodiment of the present invention is a vector harboring the polynucleotide. An embodiment of the present invention is a transformant resulting from transformation with the polynucleotide or the vector. By using the polynucleotide, the vector, or the transformant, a DGC according to an embodiment of the present invention can be produced. The transformant includes a cell or a living organism.
An embodiment of the present invention is a method for producing c-di-GMP with the use of a GTP supply system comprised of PAP and PNDK. In this production method, a DGC according to an embodiment of the present invention, GMP, polyphosphoric acid, PAP, and PNDK are used. This production method can prevent a decrease in production efficiency caused by substrate inhibition. To the reaction solution, yPPA, magnesium chloride, and/or manganese chloride may be added.
In the present specification, the term “amino acid” collectively refers to organic compounds having an amino group and a carboxy group and includes, but is not particularly limited to, Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, and Val, for example. When a DGC according to an embodiment of the present invention has a specific amino acid sequence, any amino acid in the amino acid sequence may be chemically modified, and in such a case, the DGC according to an embodiment of the present invention is still regarded as having that specific amino acid sequence. As chemical modification that an amino acid of a protein generally receives in a living organism, N-terminus modification (acetylation and myristoylation, for example), C-terminus modification (amidation and addition of glycosylphosphatidylinositol, for example), and side chain modification (phosphorylation and glycosylation, for example) are known, for example.
In the present specification, the term “polynucleotide” encompasses a plurality of nucleotides, bases, or equivalents thereof that are bonded to each other. The nucleotides and the bases include DNA bases and RNA bases. The equivalents include, for example, DNA bases and RNA bases that have chemical modification such as methylation, and nucleotide analogs. The nucleotide analogs include non-natural nucleotides. The term “DNA strand” refers to two or more DNA bases or equivalents thereof being linked to each other. The term “RNA strand” refers to two or more RNA bases or equivalents thereof being linked to each other. The term “base sequence” refers to a sequence of a nucleotide or an equivalent thereof constituting a polynucleotide. The base sequence is generally expressed with A (adenine), G (guanine), C (cytosine), and T (thymine) T can be read as U (uracil) according to the situation, and vice versa. When a polynucleotide has a specific base sequence comprised of A, G, C, T, or U, any base in the base sequence may be replaced by its equivalent, and in such a case, the polynucleotide is still regarded as having that specific base sequence. The polynucleotide can be synthesized by a DNA/RNA synthesizer or be purchased from a contractor (Invitrogen Limited, Takara Bio Inc., for example) engaged in the contract synthesis of DNA bases and/or RNA bases.
As the “vector” in the present specification, an Escherichia coli plasmid (pBR322, pUC12, pET-Blue-2, for example), a Bacillus subtilis plasmid (pUB110, pTP5, for example), a yeast plasmid (pSH19, pSH15, for example), an animal cell expression plasmid (pA1-11, pcDNAI/Neo, for example), a bacteriophage such as a λ phage, a vector derived from a virus such as adenoviruses, retroviruses, and baculoviruses, or the like can be used. Such a vector may harbor a component essential for protein expression, such as a promoter, a replication origin, and an antibacterial resistance gene. The vector may be an expression vector.
In the present specification, when a DGC includes deletion, substitution, insertion, or addition of one or several amino acids, the term “several” may indicate 15, 10, 8, 6, 4, or 2 or a number smaller than any of these. The number is preferably as small as possible because the smaller the number indicated by the term “several” is, the closer the properties of the DGC are to those of a DGC that includes no deletion nor the like in its amino acid sequence. It is generally known that a polypeptide in which one or several amino acid residues are deleted, added, inserted, or substituted with another amino acid or other amino acids maintains the biological activity (Mark et al., Proc Natl Acad Sci USA. 1984 September; 81(18):5662-5666, Zoller et al., Nucleic Acids Res. 1982 Oct. 25; 10(20):6487-6500, Wang et al., Science. 1984 Jun. 29; 224(4656):1431-1433).
In the present specification, when one or several amino acids in a DGC are substituted with other amino acids, the substitution preferably conserves the characteristics of the amino acid side chain Examples of amino acids with side chains sharing characteristics include hydrophobic amino acids (A, I, L, M, F, P, W, Y, V), hydrophilic amino acids (R, D, N, C, E, Q, G, H, K, S, T), amino acids having an aliphatic side chain (G, A, V, L, I, P), amino acids having a hydroxy-containing side chain (5, T, Y), amino acids having a sulfur-containing side chain (C, M), amino acids having a carboxylic acid- and amide-containing side chain (D, N, E, Q), amino acids having a base-containing side chain (R, K, H), and amino acids having an aromatic-containing side chain (H, F, Y, W) (each letter in parentheses is a one-letter code of an amino acid). Substitution between amino acids within each group is collectively called “conservative substitution”.
In the present specification, “90% or higher” as identity between the amino acid sequences of DGCs may be 90, 95, 98, 99, or 100%, for example, higher than any of these, or between any two of these. The numerical value is preferably as large as possible because the larger the numerical value that “90% or higher” refers to is, the closer the properties of one of the DGCs are to those of the other DGC.
In the present specification, the term “identity” generally refers to the proportion of the same amino acid alignments between two or among a plurality of amino acid sequences determined by calculation by a method known in the technical field. Prior to determining the proportion by calculation, the amino acid sequences to be compared are properly aligned and, when necessary to maximize the proportion of identity, space is inserted into the amino acid sequences. The method for proper alignment, the method for determining the proportion by calculation, the method for comparison, and related computer programs are conventionally well known in the technical field (BLAST and GENETYX, for example). In the present specification, “homology” can be expressed by numerical values determined by BLAST in NCBI (http://www.ncbi.nlm nih gov/) unless otherwise indicated. In comparison between or among amino acid sequences by BLAST, Blastp can be used as the Algorithm by default, and the results are converted into numerical values as Positives or Identities. Alternatively, “identity” is the proportion of the same base alignments determined by calculation between two or among a plurality of base sequences in the same manner as above by a method known in the technical field. Blastn can be used as the Algorithm in BLAST by default.
In the present specification, “stringent conditions” can be, for example, the following conditions: (1) washing at low ionic strength at a high temperature (at 50° C. in 0.015-M sodium chloride/0.0015-M sodium citrate/0.1% sodium dodecyl sulfate, for example), (2) using a denaturant such as formamide in hybridization (at 42° C. in 50% (v/v) formamide, 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50-mM sodium phosphate buffer at pH6.5, 750-mM sodium chloride, and 75-mM sodium citrate, for example), or (3) overnight incubation in a solution containing 20% formamide, 5×SSC, 50-mM sodium phosphate (pH7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20-mg/ml modified, sheared salmon sperm DNA at 37° C., followed by washing the filter at about 37 to 50° C. with 1×SSC. The concentration of formamide may be 50% or higher. Duration of washing may be 5, 15, 30, 60, or 120 minutes, or longer. Stringency of the hybridization reaction is possibly affected by a plurality of factors such as a temperature and a salt concentration, and for the details thereof, Ausubel et al., Current Protocols in Molecular Biology, Wiley Interscience Publishers (1995) can be referred to.
The embodiments of the present invention are described above. These are examples of the present invention, and various other configurations can be adopted. The configurations described in the embodiments can be adopted in combination.
EXAMPLES
The present invention will be described more specifically by examples. Obviously, the present invention is not limited to these examples. In examples, the methods for DNA preparation, cleavage with restriction enzymes, DNA linkage with T4 DNA ligase, and transformation of Escherichia coli followed “Molecular Cloning, A Laboratory Manual, Second Edition” (Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989)). The amount of nucleotide in a reaction mixture was determined by HPLC. FIG. 1 is a conceptual view of the procedure for preparing various plasmids in examples.
Example 1
Introduction of Site-Specific Mutation into tiGs3466
(1) Identification and Cloning of c-di-GMP Synthase Gene
The DGC gene of Geobacillus stearothermophilus was not yet identified and was therefore first searched for by using the genome DNA sequence information of Geobacillus kaustophilus (Accession No BA000043) that had its genome DNA sequence known. The genome DNA sequence of Geobacillus kaustophilus was searched by tBLASTn program for a DNA region coding for an open reading frame (hereinafter, abbreviated as ORF) that was similar to the amino acid sequence of GGDEF (SEQ ID NO:26) domain in PleD derived from Caulobacter crescentus having activity to synthesize c-di-GMP. The results gave an unidentified DNA sequence expected to be DGC gene. The information of the unidentified DNA sequence was used in an attempt to clone a gene homolog thereof (hereinafter, sometimes called “Gs3466 gene”) in Geobacillus stearothermophilus strain TH6-2. The strain TH6-2 was internationally deposited as FERM BP-10466 on Dec. 7, 2005 with the International Patent Organism Depositary at National Institute of Advanced Industrial Science and Technology.
Using the chromosome DNA derived from Geobacillus stearothermophilus strain TH6-2 as a template and (a) and (b) as primers, PCR was performed to amplify a gene coding for a DGC including deletion of an amino acid residue at the N-terminal region:









(a) 



(SEQ ID NO: 11)



AACCATGGGACTCCGAGCACGACCGATTAT



 



(b) 



(SEQ ID NO: 12)



AAACTCGAGCCCGCATTGGGCTGATAC.






The resultant DNA fragment was cleaved with restriction enzymes NcoI and XhoI, while plasmid pET-Blue-2 (obtained from Novagen) was also digested with restriction enzymes NcoI and XhoI. Then, the resultant two DNA fragments were linked with T4 DNA ligase, followed by transformation of Escherichia coli strain JM109. From the resultant ampicillin-resistant transformant, plasmid pET-tGs3466 was isolated.
Plasmid pET-tGs3466 was a plasmid harboring a DNA fragment containing a gene (hereinafter, sometimes called tGs3466 gene) coding for the 239th to 408th amino acid residues of Gs3466. Analysis of the base sequence of the gene thus cloned revealed that tGs3466 gene had the DNA base sequence shown under SEQ ID NO:1. Translation of the DNA base sequence into an amino acid sequence revealed that tGs3466 had the amino acid sequence shown under SEQ ID NO:2. The amino acid sequence of tGs3466 had 34% homology with the amino acid sequence of GGDEF (SEQ ID NO:26) domain of a DGC (PleD) derived from Caulobacter crescentus. 
A DGC has a site called an i-site that is a c-di-GMP-binding site and is responsible for causing product inhibition. In order to avoid product inhibition, site-specific mutation was introduced into the i-site of pET-tGs3466. Introduction of site-specific mutation was carried out according to a known method (Nucleic Acids Res. 2004 Aug. 10; 32(14):e115) using the following primers (c) and (d) in mutagenesis:









(c) 



(SEQ ID NO: 13)



GTTTCTCGCAGAGGGCGAATTCTTGTTCCGCAGCGG



 



(d) 



(SEQ ID NO: 14)



CGCCCTCTGCGAGAAACTGTTTCAAGGTTGAG.






As a result, plasmid pET-tiGs3466 was isolated. Plasmid pET-tiGs3466 was a plasmid harboring a DNA fragment that was the 239th to 408th amino acid residues of Gs3466 and contained a gene (hereinafter, sometimes called “tiGs3466 gene”) coding for a protein including mutation at the 311th and 314th amino acid residues of Gs3466 corresponding to the i-site. Analysis of the base sequence of the gene thus cloned revealed that tiGs3466 gene had the DNA base sequence shown under SEQ ID NO:3. Translation of the DNA base sequence into an amino acid sequence revealed that tiGs3466 had the amino acid sequence shown under SEQ ID NO:4. The full-length DNA base sequence of Gs3466 gene was found to be the base sequence shown under SEQ ID NO:24, and translation thereof into an amino acid sequence revealed that Gs3466 had the amino acid sequence shown under SEQ ID NO:25.
(2) Introduction of Site-Specific Mutation into tiGs3466
PCR was performed with the following primers (q) and (r) to introduce mutation into 54th residue asparagine of tiGs3466:









(q) 



(SEQ ID NO: 15)



CACGTATGGCCATGCCGTCGGCGACGA



 



(r) 



(SEQ ID NO: 16)



CGGCATGGCCATACGTGTCGTTGATCGTTTTAAA.






The DNA resulting from the amplification reaction was purified and was then treated with restriction enzyme DpnI. The resultant DNA was used to transform Escherichia coli strain JM109, and from the resultant ampicillin-resistant transformant, plasmid pET-tiGs3466G was isolated.
Plasmid pET-tiGs3466G was a plasmid harboring a DNA fragment that contained a gene (hereinafter, sometimes called “tiGs3466G gene”) coding for a protein that included mutation of 54th residue asparagine in the amino acid sequence of tiGs3466 to glycine. Analysis of the base sequences of the both genes thus cloned revealed that tiGs3466G gene had the DNA base sequence shown under SEQ ID NO:5. Translation of the DNA base sequence into an amino acid sequence revealed that tiGs3466G had the amino acid sequence shown under SEQ ID NO:6. Plasmid pET-tiGs3466G was used to transform Escherichia coli Tuner (DE3) pLacI, and a transformant was obtained.
Subsequently, the DGC activity (unit) of a crude enzyme solution was measured and calculated by a method shown below. To a 50-mM Tris-hydrochloride buffer (pH8.0) containing 10-mM magnesium chloride, 1-mM manganese chloride, and 2-mM GTP, 0.6 mg/mL of a purified enzyme solution resulting from purification of the transformant was added, and the temperature was maintained at 37° C. so as to carry out a reaction, which was then stopped by heat treatment at 100° C. for 30 seconds. The amount of nucleotide in the reaction mixture was determined by HPLC, and the activity of the enzyme to produce 1 mole of pppGpG and c-di-GMP at 37° C. in 1 minute was defined as 1 unit. Here, the purified enzyme was obtained by purification by the same method as in Example 2 (3) below.
The results of measuring DGC activity using tiGs3466 and tiGs3466G are shown in Table 1.









TABLE 1







specific activity



(units/mg)



















tiGs3466
0.017



tiGs3466G
0.056










tiGs3466G, which was a single amino acid mutant of tiGs3466, was proved to have specific activity 3.3 times as high as unmodified tiGs3466.
The thermal stability of both of the enzymes was also evaluated. Each enzyme was subjected to heat treatment at pH7.8 at 50° C. and was sampled 0, 10, 30, and 60 minutes into the treatment for measuring the activity. With the activity at 0 minute into the heat treatment being defined as 100(%), the remaining activity is shown in Table 2.










TABLE 2









Remaining activity (%)













0 min
10 min
30 min
60 min

















tiGs3466
100.0
37.5
11.9
3.3



tiGs3466G
100.0
101.0
107.1
102.3










The results proved that, compared to unmodified tiGs3466 that rapidly lost its activity due to heat treatment, tiGs3466G had high thermal stability, which was very preferable for a c-di-GMP synthase.
Example 2
Development of Fusion tiGs3466
(1) Cloning of Fusion tiGs3466
Cloning of a fusion product of tiGs3466 and a dimer-forming protein (dimerizable protein) started with cloning of tiGs3466. For cloning, PCR was performed using primers (e) and (f) below and plasmid pET-tiGs3466 in Example 1 as a template:







(e)


(SEQ ID NO: 17)


AAGAGCTCGGTGGCGGTGGCTCGGGCGGTGGTGGGTCGGACCACTTCGA


 


AAAAATGGC


 


(f) 


(SEQ ID NO: 18)


AAACTCGAGCCCGCATTGGGCTGATAC.






The DNA fragment resulting from PCR amplification was cleaved with restriction enzymes SacI and XhoI, and the resultant was subjected to cloning into the SacI-XhoI site of pET-Blue-2, whereby plasmid pET-linker-tiGs3466 was isolated. Plasmid pET-linker-tiGs3466 was pET-Blue-2 in which, into the SacI-XhoI-cleaved site downstream from pET promoter, tiGs3466 gene having a DNA sequence coding for 10 amino acid residues GGGGSGGGGS (SEQ ID N0:28) added to its N-terminus was inserted.
Then, as a dimerizable protein, an inorganic pyrophosphatase (yPPA) derived from Saccharomyces cerevisiae was used. Expression of tiGsDGC to which yPPA had been fused started with PCR amplification of yPPA gene using the genome DNA of Saccharomyces cerevisiae as a template and primers (g) to (j). Subsequently, following treatment with restriction enzyme NcoI-SacI, cloning was performed into the NcoI-SacI site of plasmid pET-linker-tiGs3466.









(g)



(SEQ ID NO: 19)



CATGCCATGGCCTACACTACCAGACAAA



 



(h)



(SEQ ID NO: 20)



GTTAGAAACTGTTTCCCTCATCATGGTTACATTCACAACT 



 



(i)



(SEQ ID NO: 21)



AACCATGATGAGGGAAACAGTTTCTAAC



 



(j)



(SEQ ID NO: 22)



TTGAGCTCAACAGAACCGGAGATGAAGAACC






PCR followed a conventional procedure except that, in amplification of yPPA gene, silent mutation was introduced by SOE-PCR technique (Gene. 1989 Apr. 15; 77(1):51-9) so as to remove the NcoI-cleaved site in the sequence. Specifically, a 603-bp DNA fragment obtained by PCR using primers (g) and (h) and a 261-bp DNA fragment obtained by PCR using primers (i) and (j) were used as templates to carry out PCR using primers (g) and (j), whereby a desired 864-bp DNA fragment was obtained.
As a result of cloning, plasmid pET-yPPAtiGs3466 was obtained from the transformed bacterial cell. Plasmid pET-yPPAtiGs3466 was a plasmid harboring the DNA sequence of a gene (hereinafter, sometimes called “yPPA-tiGs3466 gene”) coding for a fusion enzyme that resulted from fusion of yPPA to the N-terminus of tiGs3466 with a linker sequence interposed therebetween. An NcoI-XhoI DNA fragment having yPPA-tiGs3466 gene was inserted into pET-Blue-2 at the NcoI-XhoI-cleaved site downstream from pET promoter. Analysis of the base sequence of the fusion enzyme gene thus cloned revealed that yPPA-tiGs3466 gene had the DNA base sequence shown under SEQ ID NO:7. Translation of the DNA base sequence into an amino acid sequence revealed that yPPA-tiGs3466 had the amino acid sequence shown under SEQ ID NO:8.
(2) Preparation of DGC Enzyme Solution
Escherichia coli strain Tuner (DE3) pLacI was transformed with the plasmid harboring tiGs3466 gene and yPPA-tiGs3466 gene. The resultant strain was inoculated in 50 mL of a 2xYT medium containing 100 μg/mL of ampicillin and 0.15% glucose, followed by shake culture at 37° C. When 4×108 cells/mL was reached, the culture medium was cooled to 30° C. and IPTG was added to achieve the final concentration of 1 mM, followed by shake culture continued overnight. After the completion of culture, bacterial cells were collected by centrifugation (10,000×g, 10 minutes), followed by suspension in 5 mL of a buffer (containing 50-mM Tris-hydrochloride (pH7.8), 500-mM NaCl, and 20-mM imidazole) and then sonication to disrupt the bacterial cells. Another round of centrifugation (10,000×g, 10 minutes) was performed to remove the residue of bacterial cells. The resultant supernatant fraction was purified with an Ni-sepharose resin. The protein concentration in the purified enzyme was measured with a protein assay kit (Bio-Rad Laboratories, Inc.).
(3) Measurement of Activity of Enzyme tiGs3466 and Fusion Enzyme
The DGC activity (unit) of the crude enzyme solution was measured and calculated by the following method. To a 50-mM Tris-hydrochloride buffer (pH8.0) containing 10-mM magnesium chloride, 1-mM manganese chloride, and 2 mM-GTP, 0.6 mg/mL of the purified enzyme solution was added, and the temperature was maintained at 37° C. so as to carry out a reaction, which was then stopped by heat treatment at 100° C. for 30 seconds. The amount of nucleotide in the reaction mixture was determined by HPLC, and the activity of the enzyme to produce 1 mole of pppGpG and c-di-GMP at 37° C. in 1 minute was defined as 1 unit.
DGC relative activity when tiGs3466, the fusion enzyme (yPPA-tiGs3466), or yPPA at a weight (about 0.36 mg/mL) equivalent to the weight of yPPA in the fusion enzyme (tiGs3466+yPPA) was added to the reaction mixture is shown in Table 3.










TABLE 3








Relative



Enzyme
activity (%)



















tiGs3466
100



yPPA-tiGs3466
262



tiGs3466 + yPPA
97










Table 3 revealed that, although no enhancement in activity was observed when yPPA was added to tiGs3466, the DGC activity of the fusion enzyme with yPPA was enhanced compared to untreated tiGs3466. It was assumed that, in the fusion enzyme, dimer formation between yPPAs facilitated dimerization of tiGs3466 with another tiGs3466.
Example 3
Preparation of yPPA-tiGs3466G
In order to combine two enzyme modifications in Example 1 and Example 2 so as to prepare a fusion enzyme comprised of yPPA and tiGs3466G, cloning was performed as follows.
PCR was performed using two primers (e) and (f) and plasmid pET-tiGs3466G prepared in the earlier section as a template, followed by treatment with restriction enzymes SacI and XhoI and then cloning into the SacI-XhoI site of plasmid pET-yPPAtiGs3466. From the resultant transformant, plasmid pET-yPPAtiGs3466G was isolated. Plasmid pET-yPPAtiGs3466G was a plasmid harboring a DNA fragment containing a gene (hereinafter, sometimes called “yPPA-tiGs3466G gene”) coding for a fusion enzyme that resulted from binding of yPPA to the N-terminus of tiGs3466G with a linker sequence interposed therebetween. Analysis of the base sequences of both of the genes thus cloned revealed that yPPA-tiGs3466G gene had the DNA base sequence shown under SEQ ID NO:9. Translation of the DNA base sequence into an amino acid sequence revealed that yPPA-tiGs3466G had the amino acid sequence shown under SEQ ID NO:10. Escherichia coli Tuner (DE3) pLacI was transformed with plasmid pET-yPPAtiGs3466G to give a transformant, and the method in Example 2 (3) was followed to prepare a purified enzyme.
After the concentration of the purified enzyme was adjusted to 0.1 mg/mL, the activity of the purified enzyme was measured by the activity measurement system in Example 1. As a result, as shown in Table 4, tiGs3466G and mutant yPPA-tiGs3466G were remarkably enhanced in specific activity compared to unmodified enzyme tiGs3466. The amino acid sequence of each enzyme is shown in Table 5.










TABLE 4








Specific activity



Enzyme
(units/mg)









tiGs3466
0.017



yPPA-tiGs3466
0.046



tiGs3466G
0.056



yPPA-tiGs3466G
0.137

















TABLE 5 







tGs3466 (SEQ ID NO: 2)


MDHFEKMAYTDFLTGIHNRAYMDQTIAKLNGSGEWIGVVVADIDNFKTINDTYNHAVGDEVI


RHFASTLKQFLKEGDFLFRSGGEEFTMFLRNRTFEESVRLVEEIREAVRHSTVLVDYMAAKR


PIAYTSSFGLYFCQAEGTMSIEKAYIYADHLLLRSKESGKNKVSAQCGLE


 


tiGs3466 (SEQ ID NO: 4)


MDHFEKMAYTDFLTGIHNRAYMDQTIAKLNGSGEWIGVVVADIDNFKTINDTYNHAVGDFVI


RHFASTLKQFLAEGEFLFRSGGEEFTMFLRNRTFEESVRLVEEIREAVRHSTVLVDYMAAKR


PIAYTSSFGLYFCQAEGTMSIEKAYIYADHLLLRSKESGKNKVSAQCGLE


 


tiGs3466G (SEQ ID NO: 6)


MDHFEKMAYTDFLTGIHNRAYMDQTIAKLNGSGEWIGVVVADIDNFKTINDTYGHAVGDEVI


RHFASTLKQFLAEGEFLFRSGGEEFTMFLRNRTFEESVRLVEEIREAVRHSTVLVDYMAAKR


PIAYTSSFGLYFCQAEGTMSIEKAYIYADHLLLRSKESGKNKVSAQCGLE


 


yPPA-tiGs3466 (SEQ ID NO: 8)


MAYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKE


ETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEI


GETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNE


WFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDT


PTYSKAASDAIPPASPKADAPIDKSIDKWFFISGSVELGGGGSGGGGSDHFEKMAYTDFLTGI


HNRAYMDQTIAKLNGSGEWIGVVVADIDNFKTINDTYNHAVGDEVIRHFASTLKQFLAEGEF


LFRSGGEEFTMFLRNRTFEESVRLVEEIREAVRHSTVLVDYMAAKRPIAYTSSFGLYFCQAEG


TMSIEKAYIYADHLLLRSKESGKNKVSAQCGLE


 


yPPA-tiGs3466G (SEQ ID NO: 10)


MAYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKE


ETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEI


GETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNE


WFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDT


PTYSKAASDAIPPASPKADAPIDKSIDKWFFISGSVELGGGGSGGGGSDHFEKMAYTDFLTGI


HNRAYMDQTIAKLNGSGEWIGVVVADIDNFKTINDTYGHAVGDEVIRHFASTLKQFLAEGEF


LFRSGGEEFTMFLRNRTFEESVRLVEEIREAVRHSTVLVDYMAAKRPIAYTSSFGLYFCQAEG


TMSIEKAYIYADHLLLRSKESGKNKVSAQCGLE









Example 4
Reaction for c-di-GMP Synthesis Using Purified Enzyme DGC
(1) Preparation of Polyphosphate:AMP Phosphotransferase (PAP) Derived from Acinetobacter johnsonii 
PAP was prepared from Acinetobacter johnsonii by a method described in a known literature (WO03/100056), and the activity was measured. The amount of ATP in the reaction mixture was determined by high-performance liquid chromatography (HPLC), and the activity of the enzyme to produce 1 mole of ADP in 1 minute was defined as 1 unit.
(2) Preparation of Polyphosphate-Dependent Nucleoside 5′-Diphosphate Kinase (PNDK) from Pseudomonas aeruginosa 
PNDK was prepared from Pseudomonas aeruginosa strain PAO1 by a method described in a known literature (WO2006/080313), and the activity was measured. The amount of ATP in the reaction mixture was determined by high-performance liquid chromatography (HPLC), and the activity of the enzyme to produce 1 mole of ATP at 37° C. in 1 minute was defined as 1 unit.
(3) Preparation of Inorganic Pyrophosphatase (yPPA)
yPPA was obtained from Roche Diagnostics. The activity was measured by a method described in a known literature (WO2006/080313), where the amount of the product was determined and the activity of inorganic pyrophosphatase to produce 2 μmol of inorganic phosphoric acid in 1 minute was defined as 1 unit.
(4) Synthesis of c-di-GMP Combined with GTP Supply System Comprised of PAP and PNDK
Synthesis of c-di-GMP was performed with the use of a GTP supply system. FIG. 2 is a schematic view of the reaction steps in this synthesis system. Specific reaction procedure was as follows.
To 200 mL of a 50-mM aqueous Tris-hydrochloride buffer (pH9.0) containing 20-mM magnesium chloride, 40-mM GMP, 1-mM manganese chloride, and polyphosphoric acid (50 mM in terms of inorganic phosphoric acid), PAP (0.5 units/mL), PNDK (1.0 units/mL), and a DGC at each unit value shown in Table 6 were added, and then reaction was initiated at 37° C. At 8 hours into the reaction, polyphosphoric acid was added at an amount equivalent to 50 mM of inorganic phosphoric acid, and the reaction was continuously allowed to proceed. When tiGs3466 and tiGs3466G were used in the synthesis reaction, an inorganic pyrophosphatase (1.0 units/mL) was further added. The results showed that the amount of c-di-GMP production at 24 hours into the reaction reached about 12.6 mM (63% in terms of 1⁄2 GMP conversion) regardless of the enzyme used (FIG. 3). The amount in Table 6 was determined based on the unit value determined in the activity measurement above.
As described above, each of the modified enzymes of the present invention revealed to have adequate DGC activity.










TABLE 6







Enzyme
Amount




















tiGs3466
0.065
units/mL



yPPA-tiGs3466
0.10
units/mL



tiGs3466G
0.065
units/mL



yPPA-tiGs3466G
0.050
units/mL










Based on the amount of purified enzyme collected per unit amount of culture medium, the amount of bacterial cells required to be cultured for synthesizing the same amount of c-di-GMP relative to the total amount of the reaction mixture was calculated, and the results are shown in Table 7.











TABLE 7









Amount of




Amount of
culture required



Amount of en-
purified enzyme
(with amount



zyme required
collected (units/
of reaction mix-



(units/mL-RM)
mL-culture)
ture being 1)



















tiGs3466
0.065
0.0047
13.9


yPPA-tiGs3466
0.10
0.016
6.2


tiGs3466G
0.065
0.019
3.4


yPPA-tiGs3466G
0.050
0.022
2.2









The results revealed that the modified enzyme of the present invention was able to remarkably reduce the amount of culture required for enzyme preparation.
Example 5
Reaction for c-di-GMP Synthesis Using Crude Enzyme DGC
(1) Measurement of Specific Activity of Enzyme
In order to omit the enzyme purification step, c-di-GMP synthesis using a crude enzyme as enzyme DGC was studied.
Bacterial cells for enzyme production cultured in the same method as above were suspended in 5 mL of a 50-mM Tris-hydrochloride buffer (pH7.8), and the resultant was subjected to sonication to disrupt the bacterial cells, followed by centrifugation to give supernatant. The supernatant was to be used as a crude enzyme solution, and the DGC enzyme activity was measured. Activity measurement was performed in the same manner as in the measurement system for purified enzyme in Example 1, with each crude enzyme solution at an amount in the following table added to the reaction system to allow the reaction to proceed.
Activity per unit amount of crude enzyme solution and activity per unit amount of protein (specific activity) were calculated and are shown in Table 8.











TABLE 8








Activity of
Specific activity



Amount of
crude enzyme
of crude enzyme



crude enzyme
solution
solution



solution
(units/ml)
(units/mg)



















tiGs3466
10%
0.018
0.001


yPPA-tiGs3466
 5%
0.190
0.012


tiGs3466G
10%
0.223
0.015


yPPA-tiGs3466G
 5%
0.262
0.043









Comparison of the activity of crude enzyme solutions of the crude enzymes showed that the modified enzyme of the present invention was significantly enhanced in specific activity compared to unmodified tiGs3466.
(2) Synthesis of c-di-GMP Using Crude Enzyme
Synthesis reaction using a crude enzyme was studied. Synthesis reaction was carried out under the same conditions as in Example 4 (4), with 1.0 unit/mL of yPPA added to the reaction of tiGs3466 or tiGs3466G. The amount of each enzyme to be added was determined as follows depending on the activity of the crude enzyme:
















yPPA-tiGs3466
0.075 units/mL



tiGs3466G
0.075 units/mL



yPPA-tiGs3466G
0.075 units/mL



tiGs3466
equivalent to 0.065 units/mL










(the amount of tiGs3466 calculated from the activity of the crude enzyme was too large to be practical and therefore, based on the amount thereof in the crude enzyme solution estimated from the amount of enzyme collected at the time of enzyme purification, the crude enzyme was added at an amount 1.4 times the amount of the reaction mixture).

The results proved that, as shown in FIG. 4, c-di-GMP could be synthesized at a concentration as high as 10 mM using crude enzyme yPPA-tiGs3466G. The results also proved that c-di-GMP could be synthesized using the crude enzyme solution of tiGs3466G.
Example 6
Physical and Chemical Characteristics of DGC
(1) Molecular Weight
As to tiGs3466G, after the purified enzyme was prepared, the molecular weight was determined by SDS-polyacrylamide gel electrophoresis. The results showed that the molecular weight was about 19800. The molecular weights of tiGs3466, yPPA-tiGs3466, and yPPA-tiGs3466G were also measured in the same manner to be about 19800 for tiGs3466 and about 52800 for yPPA-tiGs3466 and yPPA-tiGs3466G.
(2) Optimum pH
As to tiGs3466G, after the purified enzyme was prepared, DGC activity was measured in the same measurement system as in Example 1 with the pH of the reaction mixture adjusted to 6.5 to 10.0. As buffers, an MES buffer, a Tris buffer, and a Glycine buffer were used. The results showed that the activity of tiGs3466G was highest at pH8.0 to 8.5. With the activity at pH8.0 being 100, the relative activity was determined, and the results are shown in Table 9 and FIG. 5. The activity of tiGs3466G at a pH ranging from 7.3 to 9.4 was not lower than 60% of the activity at pH8.0. From this, the optimum pH for tiGs3466G was evaluated to be a pH ranging from 7.3 to 9.4.










TABLE 9








Relative



pH
activity




















tiGs3466G
6.5
15




7
54




7.4
63




7.8
89




8
100




8.5
101




9
97




9.5
51




10
37










As to tiGs3466, yPPA-tiGs3466, and yPPA-tiGs3466G, activity at a pH ranging from 6.5 to 10.0 was measured in the same procedure as above. The results are shown in Table 10 and FIG. 6.










TABLE 10








Relative



pH
activity




















tiGs3466
6.5
0




7
36




7.4
48




7.8
94




8
100




8.5
100




9
94




9.5
83




10
44



yPPA-tiGs3466
6.5
17




7
53




7.4
59




7.8
85




8
100




8.5
104




9
81




9.5
78




10
64



yPPA-tiGs3466G
6.5
16




7
60




7
58




7.4
64




7.8
102




8
100




8.5
122




9
83




9.5
72




10
50










(3) Optimum Temperature
As to tiGs3466G, after the purified enzyme was prepared, DGC activity was measured in the same measurement system as in Example 1 with the temperature of the reaction mixture adjusted to 30 to 60° C. The results showed that the activity of tiGs3466G was highest at about 55° C. With the activity at 37° C. being 100, the relative activity was determined, and the results are shown in Table 11 and FIG. 7. The activity of tiGs3466G at 35 to 60° C. was not lower than 60% of the activity at 55° C. From this, the optimum temperature for tiGs3466G was evaluated to be 35 to 60° C.










TABLE 11







Temperature
Relative



(° C.)
Activity




















tiGs3466G
30
77




37
100




45
124




50
133




55
148




60
141










As to tiGs3466, yPPA-tiGs3466, and yPPA-tiGs3466G, the activity at a temperature of the reaction mixture of 30 to 60° C. was measured in the same procedure as above. The results are shown in Table 12 and FIG. 8.










TABLE 12







Temperature
Relative



(° C.)
Activity




















tiGs3466
37
100




45
132




50
151




55
175




60
151



yPPA-tiGs3466
30
67




37
100




45
145




50
179




55
191




60
177



yPPA-tiGs3466G
30
73




37
100




45
165




50
183




55
196




60
187










Thus, the enzyme in the example with mutation of 54th residue asparagine in the amino acid sequence to glycine was remarkably enhanced in specific activity and enzymatic productivity and, in addition to this, when fused with yPPA, gave a fusion enzyme that was even more enhanced in activity. Therefore, the enzymes in the examples can significantly reduce the amount of enzyme solution required to be cultured in the step of c-di-GMP production and even eliminate the necessity for a column that is essential for purification, so that it is proved that c-di-GMP synthesis is made more practical than in conventional methods.
The present invention has been described by examples. These examples are merely exemplification, and those skilled in the art understand that various modifications can be made and these modifications are also within the scope of the present invention.

## Claims

1. A method for producing c-di-GMP from two GTP molecules using an enzyme, wherein the enzyme is a diguanylate cyclase having a molecular weight of 19,800±2,000 Da and comprising an amino acid sequence selected from the group consisting of:
(A) the amino acid sequence of SEQ ID NO:6; and
(B) an amino acid sequence having at least 90% identity to the amino acid sequence of SEQ ID NO:6, wherein glycine at position 54 in the amino acid of SEQ ID NO:6 is conserved and the amino acid sequence comprises a GGDEF (SEQ ID NO:26) domain or GGEEF (positions 83-87 of SEQ ID NO:6) domain comprising i-site, but lacks the amino acid sequence KXXD (SEQ ID NO: 23) in the i-site;
the method comprising contacting two GTP molecules with said enzyme.

2. The method according to claim 1, wherein said enzyme is comprised within a fusion enzyme comprising said diguanylate cyclase and a dimerizable protein fused to the N-terminus of said diguanylate cyclase.

3. The method according to claim 2, wherein the diguanylate cyclase comprises an amino acid sequence having at least 98% identity to the amino acid sequence of SEQ ID NO:6, wherein glycine at position 54 in the amino acid of SEQ ID NO:6 is conserved and the amino acid sequence comprises a GGDEF (SEQ ID NO:26) domain or GGEEF (position 83-87 of SEQ ID NO:6) domain comprising i-site, but lacks the amino acid sequence KXXD (SEQ ID NO: 23) in the i-site, and is encoded by a modified diguanylate cyclase gene of a bacterium of the genus Geobacillus.

4. The method according to claim 2, wherein the dimerizable protein is an inorganic pyrophosphatase.

5. The method according to claim 1, wherein the diguanylate cyclase comprises the amino acid sequence of SEQ ID NO:6.

6. The method according to claim 1, wherein the diguanylate cyclase comprises an amino acid sequence having at least 98% identity to the amino acid sequence of SEQ ID NO:6, wherein glycine at position 54 in the amino acid of SEQ ID NO:6 is conserved and the amino acid sequence comprises a GGDEF (SEQ ID NO:26) domain or GGEEF (positions 83-87 of SEQ ID NO:6) domain comprising i-site, but lacks the amino acid sequence KXXD (SEQ ID NO: 23) in the i-site, and is encoded by a modified diguanylate cyclase gene of a bacterium of the genus Geobacillus.

7. The method according to claim 1, wherein the diguanylate cyclase comprises an amino acid sequence having at least 90% identity to the amino acid sequence of SEQ ID NO:6, wherein glycine at position 54 of the amino acid sequence of SEQ ID NO:6 is conserved and the amino acid sequence comprises a GGDEF (SEQ ID NO:26) domain or GGEEF (positions 83-87 of SEQ ID NO:6) domain comprising i-site, but lacks the amino acid sequence KXXD (SEQ ID NO: 23) in the i-site.

8. The method according to claim 7, wherein said diguanylate cyclase comprises an amino acid sequence having at least 95% identity to the amino acid sequence of SEQ ID NO:6, wherein glycine at position 54 of the amino acid sequence of SEQ ID NO:6 is conserved and the amino acid sequence comprises a GGDEF (SEQ ID NO:26) domain or GGEEF (position 83-87 of SEQ ID NO:6) domain comprising i-site, but the amino acid sequence lacks the amino acid sequence KXXD (SEQ ID NO: 23) in the i-site.

9. The method according to claim 1, wherein the amino acid sequence GGEEF (positions 83-87 of SEQ ID NO: 6) at positions 83-87 of the amino acid sequence of SEQ ID NO:6 is conserved.

10. The method according to claim 1, wherein the diguanylate cyclase has the following physical and chemical characteristics:
(A) catalytic action on the reaction “2 GTP→c-di-GMP”;
(B) an optimum pH of 7.3 to 9.4 for catalytic activity;
(C) an optimum temperature of 35 to 60° C. for catalytic activity; and
(D) thermal stability as shown by activity of 90% or higher remaining after heating for 60 minutes at 50° C., pH7.8.