# Patent

## Title
DNA encoding polypeptide involved in biosynthesis of herboxidiene

## Abstract

The nucleotide sequence of a DNA involved in the biosynthesis of herboxidiene was determined. Utilizing this DNA, herboxidiene and analogues thereof can be efficiently produced.

## Background
TECHNICAL FIELD
The present invention relates to a polypeptide involved in the biosynthesis of herboxidiene, a DNA encoding the polypeptide, and a variant thereof. In addition, the present invention also relates to a transformant retaining a part or the entire of the DNA and the variant thereof, and a method for producing herboxidiene or an analogue thereof, using the transformant. Moreover, the present invention also relates to an analogue of herboxidiene.
BACKGROUND ART
Substances important as physiologically active substances have been found in various metabolites produced by actinomycetes. In particular, many compounds structurally having polyketide as a core structure (hereinafter referred to as polyketide compounds) have been found. For example, the following various compounds having a biological activity have been known: erythromycin, josamycin, tylosin, midecamycin and mycinamicin known as antibacterial substances; nystatin and amphotericin known as antifungal substances; milbemycin and avermectin known as insecticidal substances; tacrolimus and rapamycin known as immunosuppressive substances; and daunomycin, adriamycin, and aclacinomycin known as antitumor substances.
As one type of such compounds, there are a group of polyketide compounds having an excellent antitumor activity, named as herboxidiene. Herboxidiene is a compound represented by the formula (I) as shown below, which has been first discovered from a culture product of an actinomycete strain, Streptomyces chromofuscus A7847 (see Non Patent Literature 1). Thereafter, 5 or more types of analogues, including herboxidiene as a typical example, have been discovered from several actinomycete strains (see patent Literatures 1 and 2).




On the other hand, many facts have been known about the biosynthetic mechanism of such polyketide compounds. It has been said that the aforementioned variety of polyketide compounds share the same biosynthetic mechanism, and that the mechanism is extremely similar to the biosynthesis of fatty acid. That is to say, polyketide compounds are biosynthesized by steps of continuously condensing lower fatty acid such as acetic acid or propionic acid, and then subjecting the carbonyl group at position β of the extended acyl group to ketone reduction, dehydration, or enoyl reduction, according to the same method as fatty acid synthesis. It has been said that various repetitive steps of synthesizing these many polyketide compounds are regulated by the multifunctional enzyme complexes of polymers having different active sites (domains) necessary for individual reaction catalytic activities. A general reaction mode of polyketide biosynthesis is summarized, for example, in Non Patent Literatures 2 and 3.
It has been revealed that a DNA sequence encoding polyketide synthase generally encodes all activities necessary for the synthesis of polyketide skeletons, and that the DNA sequence is constituted with repeating units comprising a condensation step and a modification step after the condensation, namely, with modules. Each module participates in a specificity of a specific carboxylic acid constitutional unit contained in each condensation step and in a modification function after specific condensation. For example, Non Patent Literature 4 describes a gene encoding polyketide synthase involved in the biosynthesis of pikromycin by Streptomyces venezuelae ATCC15439. Patent Literature 3 describes the structure of a gene encoding erythromycin polyketide synthase of Saccharopolyspora erythraea. This gene is constituted with 6 modules, and each module conducts a single condensation step. That is, the precise sequence of acyl side chain elongation and the modification of the elongating chain are determined by gene information existing in each module.
Moreover, after the synthesis of polyketide skeletons by polyketide synthase, such variety of polyketide compounds are often modified by an enzyme catalyzing modification reactions such as hydroxylation, epoxidation or methylation (hereinafter referred to as a modifying enzyme, at times), so that they are converted to final metabolites. It has been revealed that a group of genes involved in these productions; namely, enzymes necessary for the biosynthesis of such final metabolites, and genes encoding regulatory factors necessary for the regulation of the productions (hereinafter, this gene group involved in biosynthesis may be generically referred to as solely “a biosynthetic gene”, at times), are generally disposed in the genome of producing bacteria or in a DNA region on a plasmid, while forming a cluster.
If the information of the nucleotide sequence of a gene encoding polyketide synthase is determined, it becomes possible to modify a domain based on the obtained information, so as to change the size of a carbon chain and the functional group of the carbon at position β during a condensation process. For example, Non Patent Literature 5 describes that a novel derivative of erythromycin can be produced by selectively inactivating a specific domain in the polyketide synthase gene of erythromycin. Moreover, by replacing the domain of each module with another one, it becomes possible to produce a predictable, novel compound. For example, Non Patent Literature 6 describes that a variety of novel compounds can be produced by replacing several domains in the polyketide synthase gene of erythromycin with other domains.
Furthermore, if the nucleotide sequence of a biosynthetic gene cluster comprising a gene encoding a modifying enzyme (hereinafter referred to as a modifying enzyme gene, at times) is determined, it becomes possible to selectively modify the modifying enzyme gene based on the obtained information, so as to produce a predictable, novel compound. For example, Non Patent Literature 7 describes that a novel derivative, 6-deoxyerythronolide B, can be produced by deleting a hydroxylase gene eryF, existing in the neighborhood of the polyketide synthase gene of erythromycin.
Further, there is a case in which unnecessary by-products can be reduced and a single ingredient of interest can be produced by activating the expression of a modifying enzyme gene. In order to activate gene expression, there have been generally known methods, such as the activation of transcription by the substitution of a promoter, an increase in the number of gene copies using a multicopy vector, and the improvement of an enzyme activity by the introduction of a mutation into a gene. Moreover, there is a case in which productivity can be enhanced by activating or inactivating a regulatory gene by the same above methods.
Furthermore, there is also a case in which, using a different strain, a polyketide compound of interest can be produced by obtaining a gene encoding such biosynthetic gene cluster, and then by introducing the obtained gene into the different strain according to an adequate method. As a different strain used herein, microorganisms, and particularly, Escherichia coli that can be cultured in a short time, can be advantageously used. For example, Non Patent Literature 8 describes that a 6-deoxyerythronolide B of interest as an erythromycin precursor can be efficiently produced by incorporating a polyketide synthase gene into Escherichia coli. 
Still further, Patent Literature 4 describes: a polypeptide involved in the biosynthesis of a macrolide compound, pladienolide, that is one type of polyketide compound; a DNA encoding the polypeptide and a variant thereof; a transformant retaining a part or the entire of the DNA or the variant thereof; and a method for producing the macrolide compound, pladienolide, using the transformant.
CITATION LIST
Patent Literature


    [Patent Literature 1] Japanese Patent Application Laid-Open Publication No. 6-22770
    [Patent Literature 2] Japanese Patent Application Laid-Open Publication No. 9-235283
    [Patent Literature 3] International Publication WO1993/13663, pamphlet
    [Patent Literature 4] International Publication WO2006/9276, pamphlet


Non Patent Literature


    [Non Patent Literature 1] J. Antibiot., 45 (1992) 914-921
    [Non Patent Literature 2] Ann. Rev. Gen., 24 (1990) 37-66
    [Non Patent Literature 3] Ann. Rev. Microbiol., 47 (1993) 874-912
    [Non Patent Literature 4] Proc. Natl. Acad. Sci. USA 95 (1998) 12111-12116
    [Non Patent Literature 5] Proc. Natl. Acad. Sci. USA 90 (1993) 7119-7123
    [Non Patent Literature 6] Proc. Natl. Acad. Sci. USA 96 (1999) 1846-1851
    [Non Patent Literature 7] Science 252 (1991) 114-116
    [Non Patent Literature 8] Science 291 (2001) 1790-1792


SUMMARY OF THE INVENTION
Technical Problem
It is an object of the present invention to provide a polypeptide involved in the biosynthesis of herboxidiene, a DNA encoding the polypeptide, and a variant thereof. It is another object of the present invention to provide a transformant retaining a part or the entire of the DNA or the variant thereof, and a method for producing herboxidiene or an analogue thereof using the transformant. It is yet another object of the present invention to provide a herboxidiene analogue.
Solution to Problem
In order to solve the aforementioned problems, the present inventors have attempted to obtain a DNA of interest from Streptomyces sp. Mer-16208 (hereinafter referred to as Mer-16208, at times), which is a bacterium that produces herboxidiene and analogues thereof, according to a colony hybridization method, using a probe that had been prepared based on a sequence reportedly generally conserved in the keto synthase domain of polyketide synthase. However, a large number of cosmids were selected, and thus, the DNA of interest could not be promptly identified.
Hence, the inventors have focused on the fact that a modifying enzyme gene is highly likely to exist in the neighborhood of the polyketide synthase gene, and they have produced several primers based on the sequence of a pladienolide 18,19-epoxidase gene, pldD, existing in the neighborhood of a similar polyketide biosynthetic gene possessed by a known actinomycete Streptomyces platensis Mer-11107, and have then obtained a gene, hbdD, having a high identity to pldD, from the chromosomal DNA of Mer-16208. Using this gene as a probe, several cosmids comprising a DNA of interest were selected from a large number of cosmids obtained based on the sequence of a polyketide synthase domain, and finally, a nucleotide sequence (SEQ ID NO: 1) of approximately 65 kb comprising a DNA involved in the synthesis of herboxidiene was determined.
As a result of the analysis of the DNA of SEQ ID NO: 1, it became clear that seven open reading frames, hbdAI (nucleotides 8919-28295), hbdAII (nucleotides 28326-49892), hbdAIII (nucleotides 49892-55981), hbdD (nucleotides 56115-57545), hbdF (nucleotides 57575-58435), hbdE (nucleotides 58533-59798) and hbdR (nucleotides 6681-7706), are comprised in the DNA, and that such seven open reading frames are involved in the biosynthetic pathway of herboxidiene shown in FIG. 1. Specifically, hbdAI, hbdAII and hbdAIII are the polyketide synthase genes of herboxidiene; hbdD is the 14,15-epoxidase gene of herboxidiene; hbdF is the 17-O-methyl transferase gene of herboxidiene; hbdE is the 18-hydroxylase gene of herboxidiene; and hbdR is the transcription factor gene of herboxidiene. Moreover, Mer-16208 strains, in which these genes were disrupted, were produced, and herboxidiene and analogues thereof produced by each of the produced strains were then analyzed, so that the function of each gene was confirmed. Furthermore, the antitumor activities of the herboxidiene analogues were also confirmed.
Specifically, the present invention relates to the following [1] to [22].
[1] An isolated pure DNA comprising at least one region encoding a polypeptide involved in the biosynthesis of herboxidiene.
[2] The DNA according to [1] above, which comprises all regions encoding the polypeptide involved in the biosynthesis of herboxidiene.
[3] The DNA according to [1] or [2] above, wherein the polypeptide involved in the biosynthesis of herboxidiene is at least one selected from polyketide synthase, 18-hydroxylase, 14,15-epoxidase, 17-O-methyl transferase, and a transcription factor.
[4] The DNA according to any one of [1] to [3] above, which is derived from a microorganism belonging to genus Streptomyces. 
[5] The DNA according to [1] above, which comprises at least one nucleotide sequence selected from the nucleotide sequences defined in the following (1) to (4):
(1) the nucleotide sequence defined in any one of the following (a) to (h):
(a) a nucleotide sequence consisting of contiguous nucleotides 6681 to 7706 of SEQ ID NO: 1;
(b) a nucleotide sequence consisting of contiguous nucleotides 8919 to 28295 of SEQ ID NO: 1;
(c) a nucleotide sequence consisting of contiguous nucleotides 28326 to 49892 of SEQ ID NO: 1;
(d) a nucleotide sequence consisting of contiguous nucleotides 49892 to 55981 of SEQ ID NO: 1;
(e) a nucleotide sequence consisting of contiguous nucleotides 56115 to 57545 of SEQ ID NO: 1;
(f) a nucleotide sequence consisting of contiguous nucleotides 57575 to 58435 of SEQ ID NO: 1;
(g) a nucleotide sequence consisting of contiguous nucleotides 58533 to 59798 of SEQ ID NO: 1; and
(h) a nucleotide sequence consisting of contiguous nucleotides 1 to 65360 of SEQ ID NO: 1,
(2) the nucleotide sequence of a DNA hybridizable under stringent conditions with a DNA comprising a sequence complementary to any one of the nucleotide sequences defined in (1) above,
(3) a nucleotide sequence having an identity of 85% or more to any one of the nucleotide sequences defined in (1) above, and
(4) a nucleotide sequence not hybridizable under stringent conditions with a DNA comprising a sequence complementary to the nucleotide sequences defined in (1) above due to the degeneration of the genetic code, but encoding an amino acid sequence identical to that of the nucleotide sequence defined in any one of (1) to (3) above.

[6] The DNA according to [1] above, which comprises at least one nucleotide sequence selected from the nucleotide sequences defined in the following (a) to (h):

(a) a nucleotide sequence consisting of contiguous nucleotides 6681 to 7706 of SEQ ID NO: 1;

(b) a nucleotide sequence consisting of contiguous nucleotides 8919 to 28295 of SEQ ID NO: 1;

(c) a nucleotide sequence consisting of contiguous nucleotides 28326 to 49892 of SEQ ID NO: 1;

(d) a nucleotide sequence consisting of contiguous nucleotides 49892 to 55981 of SEQ ID NO: 1;

(e) a nucleotide sequence consisting of contiguous nucleotides 56115 to 57545 of SEQ ID NO: 1;

(f) a nucleotide sequence consisting of contiguous nucleotides 57575 to 58435 of SEQ ID NO: 1;

(g) a nucleotide sequence consisting of contiguous nucleotides 58533 to 59798 of SEQ ID NO: 1; and

(h) a nucleotide sequence consisting of contiguous nucleotides 1 to 65360 of SEQ ID NO: 1.

[7] A polypeptide encoded by the DNA according to any one of [1] to [6] above.

[8] The polypeptide according to [7] above, having a polyketide synthase activity

[9] The polypeptide according to [8] above, having the amino acid sequence shown in SEQ ID NO: 2, 3 or 4, or a partial sequence thereof

[10] The polypeptide according to [7] above, having a 14,15-epoxidase activity

[11] The polypeptide according to [10] above, having the amino acid sequence shown in SEQ ID NO: 5 or a partial sequence thereof.

[12] The polypeptide according to [7] above, having a 17-O-methyl transferase activity.

[13] The polypeptide according to [12] above, having the amino acid sequence shown in SEQ ID NO: 6 or a partial sequence thereof.

[14] The polypeptide according to [7] above, having a 18-hydroxylase activity.

[15] The polypeptide according to [14] above, having the amino acid sequence shown in SEQ ID NO: 7 or a partial sequence thereof.

[16] The polypeptide according to [7] above, having a transcription factor activity.

[17] The polypeptide according to [16] above, having the amino acid sequence shown in SEQ ID NO: 8 or a partial sequence thereof.

[18] An autonomously or integratively replicating recombinant plasmid, carrying the DNA according to any one of [1] to [6] above.

[19] A transformant retaining the DNA according to any one of [1] to [6] above.

[20] A method for producing herboxidiene or an analogue thereof, comprising culturing the transformant according to [19] above in a medium and then collecting herboxidiene or an analogue thereof from the culture medium.

[21] A compound represented by the following formula (1):





[22] A compound represented by the following formula (2):





In the present specification, “DNA hybridizable under stringent conditions” means a DNA, which is obtained, for example, by using a DNA having the nucleotide sequence defined by any one of the above described items (a) to (h) as a probe, and applying a colony hybridization method, a plaque hybridization method, a Southern hybridization method or the like. Specifically, it is a DNA having a certain level or more of identity to the nucleotide sequence of the DNA used as a probe, and it is a DNA having an identity of, for example, 85% or more, preferably 90% or more, more preferably 93% or more, further preferably 95% or more, and most preferably 98% or more to the aforementioned nucleotide sequence. Conditions for hybridization may be selected, as appropriate, depending on the type of a DNA to be obtained, according to the descriptions of Sambrook et al., Molecular Cloning. A Laboratory Manual. 2nd ed., Cold Spring Harbor Laboratory Press (hereinafter abbreviated as Sambrook et al.). For example, when a DNA having an identity of 85% or more is obtained, there may be used conditions, in which hybridization is carried out at 56° C. to 59° C. in the presence of 0.5 M NaCl and 50% formamide, and the filter is then washed at 56° C. to 59° C. using a 0.1 to 2×SSC solution (wherein the composition of a 1×SSC solution consists of 150 mM sodium chloride and 15 mM sodium citrate). Moreover, when a DNA having an identity of 90% or more is obtained, there may be used conditions, in which hybridization is carried out at 61° C. to 64° C. in the presence of 0.5 M NaCl and 50% formamide, and the filter is then washed at 61° C. to 64° C. using a 0.1 to 2×SSC solution (wherein the composition of a 1×SSC solution consists of 150 mM sodium chloride and 15 mM sodium citrate).
“A variant of DNA” means a DNA modified by a deletion, conversion, addition, insertion or the like of a constitutional nucleotide(s), or a derivative thereof. “Identity” means the percentage of nucleotides shared by two sequences, when the two sequences are aligned in an optimal manner. That is to say, such identity can be calculated by the expression: identity=(the number of matched positions/the total number of positions)×100, and it can be calculated using a commercially available algorism. In addition, such algorism is integrated into the NBLAST and XBLAST programs described in Altschul et al., J. Mol. Biol. 215 (1990) 403-410. “Analogue” means a compound having a main skeleton characterized for its chemical structure, which is identical to that of a certain compound, but having a different modification or different structure of a side chain.
“A partial sequence of the amino acid sequence” may be an amino acid sequence having a domain essential for exhibiting a predetermined activity. Further, such partial sequence may comprise an amino acid sequence comprising a deletion, substitution, addition or insertion of one or multiple amino acid residues with respect to a certain amino acid sequence, and exhibiting a predetermined activity.
Advantages Effects of Invention
According to the present invention, it is possible to isolate a DNA encoding a polypeptide involved in the biosynthesis of herboxidiene and to determine the nucleotide sequence thereof. Further, it is also possible to produce a plasmid carrying the DNA and a transformant transformed with the plasmid, and to efficiently produce herboxidiene and analogues thereof, using the transformant. Still further, by modifying or changing the obtained DNA sequence, the type of carboxylic acid incorporated, a modification reaction after condensation, a modification reaction after skeleton formation, and all the combinations thereof are modified, and thereby, it becomes possible to produce a novel or specific herboxidiene analogue.



BRIEF DESCRIPTION OF DRAWINGS
FIG. 1 is a view showing the biosynthetic pathway of herboxidiene in Mer-16208; and
FIG. 2 is a view showing the correlation between each ORF of a DNA involved in the biosynthesis of herboxidiene in Mer-16208 and a cosmid.



DESCRIPTION OF EMBODIMENTS
The embodiments of the present invention will be described in detail below.
In the present invention, a DNA partly or entirely encoding a polypeptide involved in the biosynthesis of herboxidiene can be isolated from cultured cells of microorganisms having an ability to produce herboxidiene, and the nucleotide sequence thereof can be determined. As such microorganisms, any microorganisms can be used regardless of species and the type of a strain, as long as they have an ability to produce herboxidiene. Preferred microorganisms include Streptomyces sp. Mer-16208 separated from the soil. The present cell strain was deposited as an international deposition with Patent Microorganisms Depositary, National Institute of Technology and Evaluation, an Independent Administrative Institution, 2-5-8, Kazusa Kamatari, Kisarazu-shi, Chiba-ken, Japan, under accession No. NITE BP-716 on Mar. 9, 2009.
The present inventors have attempted to obtain the DNA of the present invention from the above described microorganisms according to the colony hybridization method described in Sambrook et al. First, the genomic DNA of Mer-16208 which had been partially digested with a suitable restriction enzyme such as Sau3AI, was ligated to a cosmid vector capable of replicating in Escherichia coli, which had been digested with a restriction enzyme such as BamHI, and the thus obtained recombinant DNA was then incorporated into Escherichia coli, so as to obtain a transformed strain. On the other hand, using the DNA obtained from Mer-16208 as a template, and also using primers that had been designed with reference to the sequence information reportedly generally conserved in the keto synthase domain of polyketide synthase and the sequence information of the keto synthase domain of a pikromycin-producing bacterium (see Non Patent Literature 3), PCR was carried out, so that the amplified DNA was obtained. Using the DNA as a probe, the previously prepared transformed strain was screened. As a result, a large number of positive clones (cosmids) were obtained, and thus, a transformed strain having a DNA of interest could not be immediately identified.
Hence, the present inventors have focused on the fact that a modifying enzyme gene is highly likely to exist in the neighborhood of the polyketide synthase gene. The inventors have produced several primers based on the sequence of a pladienolide 18,19-epoxidase gene, pldD (which had been registered in accession No. AB435553 of Genbank) existing in the neighborhood of a similar polyketide biosynthetic gene possessed by a known actinomycete Streptomyces sp. Mer-11107 (which had been deposited as an international deposition with the International Patent Organism Depositary (IPOD), the National Institute of Advanced Industrial Science and Technology, an Independent Administrative Institution, Tsukuba Central 6, Higashi 1-1-1, Tsukuba-shi, Ibaraki-ken, Japan, under accession No. FERM BP-7812 on Nov. 27, 2001), and as a result, the inventors have obtained a gene, hbdD, having a high identity to pldD, from the chromosomal DNA of Mer-16208. Using this gene as a probe, several cosmids comprising a DNA of interest were selected from a large number of cosmids obtained based on the sequence of a polyketide synthase domain.
Since a part of the DNA involved in the biosynthesis of herboxidiene has been clarified, Southern hybridization was carried out using, as a probe, the gene hbdD that was likely to encode a 14,15-epoxidase involved in the biosynthesis of herboxidiene. Cosmids comprising a cluster of herboxidiene biosynthetic genes adjacent to hbdD were selected and aligned.
Next, the nucleotide sequence of a DNA fragment inserted into each cosmid was determined. First, after the isolation of each cosmid, it was cleaved into fragments with a size of approximately 1 kb for subcloning. Subsequently, the nucleotide sequence of each of the obtained subclones was determined, and an approximately 65-kb nucleotide sequence comprising the DNA involved in the synthesis of herboxidiene was then determined (see SEQ ID NO: 1).
The DNA shown in SEQ ID NO: 1 comprised seven open reading frames (ORF), hbdAI (nucleotides 8919-28295), hbdAII (nucleotides 28326-49892), hbdAIII (nucleotides 49892-55981), hbdD (nucleotides 56115-57545), hbdF (nucleotides 57575-58435), hbdE (nucleotides 58533-59798) and hbdR (nucleotides 6681-7706). In addition, the amino acid sequences of polypeptides encoded by these sequences are as shown in SEQ ID NO: 2 to 8, respectively.
Among the thus obtained DNAs involved in the biosynthesis of herboxidiene of Mer-16208, hbdAI, hbdAII, and hbdAIII had several open reading frames each comprising one or more repeating units called modules, as with the already clarified other polyketide biosynthetic genes. As described later, each module encoded all or several domains selected from an acyl carrier protein (ACP) involved in the condensation reaction in polyketide synthesis, β-ketoacyl-ACP synthase (KS), acyl transferase (AT), ketoacyl reductase (KR) involved in a β-carbonyl group modification reaction, dehydratase (DH), and enoyl reductase (ER). A thioesterase (TE) domain that cleaves a polyketide chain from polyketide synthase exists in the last module.
The biosynthetic pathway of herboxidiene in Mer-16208 is shown in FIG. 1. Since a loading module (Module L) differs from other modules and the cysteine in the active center thereof is substituted with a glutamine, it is found that HbdAI is involved in the first reaction. In addition, it is also found that since module 8 has a thioesterase (TE) domain, HbdAIII is involved in the final reaction of polyketide. Thus, after the formation of the basic skeleton of polyketide, it is modified with a group of enzymes (HbdD, HbdF and HbdE) that are encoded by hbdD, hbdF and hbdE, so that herboxidiene seems to be biosynthesized. Moreover, hbdR has a high identity to a gene, lad, encoding a transcription factor, and thus, the hbdR seems to encode the transcription factor of the DNA involved in the biosynthesis of herboxidiene.
The thus clarified modules of the DNA involved in the biosynthesis of herboxidiene and the corresponding domains are as follows.
ORF hbdAI (nucleotides 8919-28295 of SEQ ID NO: 1) encodes a loading module, module 1, module 2 and module 3. The corresponding polypeptide is represented by the amino acid sequence shown in SEQ ID NO: 2.
Loading module (nucleotides 8919-12023)
KS0: nucleotides 8955-10217
AT0: nucleotides 10305-11360
ACP0: nucleotides 11790-11972
Module 1 (nucleotides 12024-16451)
KS1: nucleotides 12024-13262
AT1: nucleotides 13356-14441
KR1: nucleotides 15324-16196
ACP1: nucleotides 16218-16400
Module 2 (nucleotides 16452-21734)
KS2: nucleotides 16452-17711
AT2: nucleotides 17796-18860
DH2: nucleotides 19038-19739
KR2: nucleotides 20622-21461
ACP2: nucleotides 21483-21665
Module 3 (nucleotides 21735-28295)
KS3: nucleotides 21735-22991
AT3: nucleotides 23253-24305
DH3: nucleotides 24474-25169
ER3: nucleotides 26016-26936
KR3: nucleotides 26964-27812
ACP3: nucleotides 27834-28016
In addition, the amino acid sequence of the corresponding polypeptide is as follows.
KS0: amino acids 13-433
AT0: amino acids 463-814
ACP0: amino acids 958-1018
KS1: amino acids 1036-2511
AT1: amino acids 1480-1841
KR1: amino acids 2136-2426
ACP1: amino acids 2434-2494
KS2: amino acids 2512-2931
AT2: amino acids 2960-3314
DH2: amino acids 3374-3607
KR2: amino acids 3902-4181
ACP2: amino acids 4189-4249
KS3: amino acids 4273-4691
AT3: amino acids 4779-5129
DH3: amino acids 5186-5417
ER3: amino acids 5700-6006
KR3: amino acids 6016-6298
ACP3: amino acids 6306-6366
ORF hbdAII (nucleotides 28326-49892 of SEQ ID NO: 1) encodes module 4, module 5, module 6 and module 7, and the corresponding polypeptide is represented by the amino acid sequence shown in SEQ ID NO: 3.
Module 4 (nucleotides 28326-33644)
KS4: nucleotides 28419-29681
AT4: nucleotides 29751-30851
DH4: nucleotides 31017-31718
KR4: nucleotides 32526-33371
ACP4: nucleotides 33393-33575
Module 5 (nucleotides 33645-38873)
KS5: nucleotides 33645-34895
AT5: nucleotides 34974-36047
DH5: nucleotides 36231-36938
KR5: nucleotides 37722-38606
ACP5: nucleotides 38628-38810
Module 6 (nucleotides 38874-43532)
KS6: nucleotides 38874-40133
AT6: nucleotides 40203-41267
KR6: nucleotides 42405-43247
ACP6: nucleotides 43269-43451
Module 7 (nucleotides 43533-49892)
KS7: nucleotides 43533-44792
AT7: nucleotides 44865-45962
DH7: nucleotides 46137-46847
ER7: nucleotides 47724-48641
KR7: nucleotides 48669-49520
ACP7: nucleotides 49542-49724
Moreover, the amino acid sequence of the corresponding polypeptide is as follows.
KS4: amino acids 32-452
AT4: amino acids 476-842
DH4: amino acids 898-1131
KR4: amino acids 1401-1682
ACP4: amino acids 1690-1750
KS5: amino acids 1774-2190
AT5: amino acids 2217-2574
DH5: amino acids 2636-2871
KR5: amino acids 3133-3427
ACP5 amino acids 3435-3495
KS6: amino acids 3517-3936
AT6: amino acids 3960-4314
KR6: amino acids 4694-4974
ACP6: amino acids 4982-5042
KS7: amino acids 5070-5489
AT7: amino acids 55145879
DH7: amino acids 5938-6174
ER7: amino acids 6467-6772
KR7: amino acids 6782-7065
ACP7: amino acids 7073-7133
ORF hbdAIII (nucleotides 49892-55981 of SEQ ID NO: 1) encodes module 8, and the corresponding polypeptide is represented by the amino acid sequence shown in SEQ ID NO: 4.
Module 8 (nucleotides 49892-55981)
KS8: nucleotides 49892-51271
AT8: nucleotides 51341-52420
DH8: nucleotides 52589-53278
KR8: nucleotides 54083-54940
ACP8: nucleotides 54962-55144
TE8: nucleotides 55163-55981
Furthermore, the amino acid sequence of the corresponding polypeptide is as follows.
KS8: amino acids 41-460
AT8: amino acids 484-843
DH8: amino acids 900-1129
KR8: amino acids 1398-1683
ACP8: amino acids 1691-1751
TE8: amino acids 1758-2030
ORF hbdD (nucleotides 56115-57545 of SEQ ID NO: 1) encodes 14,15-epoxidase involved in the biosynthesis of herboxidiene, and the corresponding polypeptide is represented by the amino acid sequence shown in SEQ ID NO: 5. ORF hbdF (nucleotides 57575-58435 of SEQ ID NO: 1) encodes 17-O-methyl transferase involved in the biosynthesis of herboxidiene, and the corresponding polypeptide is represented by the amino acid sequence shown in SEQ ID NO: 6. ORF hbdE (nucleotides 58533-59798 of SEQ ID NO: 1) encodes 18-hydroxylase involved in the biosynthesis of herboxidiene, and the corresponding polypeptide is represented by the amino acid sequence shown in SEQ ID NO: 7. ORF hbdR (nucleotides 6681-7706 of SEQ ID NO: 1) encodes a transcription factor involved in the biosynthesis of herboxidiene, and the corresponding polypeptide is represented by the amino acid sequence shown in SEQ ID NO: 8.
Thus, if a nucleotide sequence is once determined, the DNA involved in the biosynthesis of herboxidiene of the present invention can be obtained by a known method based on the information of the determined nucleotide sequence.
For example, the DNA having the nucleotide sequence shown in SEQ ID NO: 1 is digested with a suitable restriction enzyme, and the digested DNA is then separated and recovered by the method described in Sambrook et al., so as to prepare an oligonucleotide used as a probe or a primer. When the obtained oligonucleotide is used as a probe, the obtained DNA fragment is preferably labeled with digoxigenin or the like. DIG Labeling & Detection Kit (Roche Diagnostics) or the like is preferably used for such labeling with digoxigenin.
Subsequently, a library is produced from a cell body of microorganisms having an ability to produce herboxidiene according to the genome cloning method or cDNA cloning method described in Sambrook et al., etc. Clones (colonies) to be hybridized with the previously prepared probe are selected from the obtained library, and plasmids are then extracted from the selected clones according to the method described in Sambrook et al. A DNA of interest involved in the biosynthesis of herboxidiene can be obtained from the obtained plasmids.
In this case, when the extracted plasmids comprise only a partial fragment of the DNA involved in the biosynthesis of herboxidiene, the extracted plasmids are digested with a suitable restriction enzyme such as BamHI, so that the restriction map of these plasmids is produced according to the conventional method. Thereafter, restriction fragments existing in common in several clones are discovered from the restriction map, and the cloned segments are connected with one another at overlapped portions, so as to obtain a DNA comprising the entire DNA involved in the biosynthesis of herboxidiene.
Otherwise, the DNA involved in the biosynthesis of herboxidiene can also be obtained by directly performing a PCR using the above-mentioned library and primer, so as to directly amplify the DNA of interest.
The nucleotide sequence of the DNA encoding a polypeptide involved in the biosynthesis of herboxidiene can be determined by analyzing by a commonly used nucleotide sequence analysis method such as a dideoxy method [Proc. Natl. Acad. Sci. USA, 74, 5463 (1977)], or using a nucleotide sequence analyzer such as a 373A DNA sequencer (manufactured by PerkinElmer). Specifically, a double-stranded plasmid DNA is directly used as a template in a cycle sequence reaction, in which various sequence-specific oligonucleotide primers are used, or, alternatively, a DNA fragment is segmented, and the DNA fragments are introduced into bacteriophage M13, randomly, using a library or a plasmid vector in which the fragments are partially overlapped, so as to produce an overlapping library, hr which a deletion has been successively introduced from the terminal portion of the DNA fragment. Subsequently, the sequence of each recombinant DNA fragment can be determined using an oligonucleotide primer specific to the vector sequence.
Moreover, based on the determined nucleotide sequence of the DNA, a DNA of interest can be prepared by performing a chemical synthesis using a DNA synthesizer such as DNA Synthesizer Type 8905 (manufactured by PerSeptive Biosystems). The arrangement, edition and analysis of the obtained nucleotide sequence data can be carried out using the existing software such as GenetyxTM manufactured by Genetyx Corporation.
Furthermore, the polypeptide of the present invention can be produced by expressing the DNA of the present invention in host cells, applying the methods described, for example, in Sambrook et al. and Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, Inc. A site, into which the DNA of the present invention or a variant thereof is to be incorporated, may be either on the plasmid or on the chromosome of a host microorganism. Such plasmid may comprise an autonomous replicating sequence, a promoter sequence, a terminator sequence, a drug resistance gene, etc. as well as the aforementioned DNA or a variant thereof. Further, the plasmid may be an integration-type plasmid having a sequence homologous to a given region of the genome of a host to be used.
Thus, a host and a plasmid-vector system for expressing a polypeptide encoded by the DNA of the present invention are not particularly limited, as long as the DNA is stably retained and expressed therein. For example, if actinomycetes originally having an ability to produce herboxidiene or an analogue strain thereof is used as a host, an autonomous replicating vector pIJ6021 [Gene 166, 133-137 (1995)], a chromosome-integration-type vector KC515 [The bacteria, vol. 9, Antibiotic-producing Streptomyces (ed: Queener, S. E. and Day, L. E.). p. 119-158. Academic Press, Orlando, Fgla], and the like can be used.
As a method for isolating and purifying a polypeptide produced by the transformant of the present invention, a conventional enzyme isolation purification method can be applied. For example, when the polypeptide of the present invention is expressed in cells in a dissolved state, after completion of a culture, the cells are recovered by centrifugation, and are then suspended in an aqueous buffer. Thereafter, the cells are disrupted using a sonicator, a French press, a homogenizer, a Dyno mill, etc., so as to obtain a cell-free extract. A purified sample can be obtained by applying a conventional enzyme isolation purification method to a supernatant obtained by centrifuging the obtained cell-free extract.
Moreover, based on the information of the amino acid sequence of the previously obtained polypeptide, a chemical synthesis method such as a fluorenylmethyloxycarbonyl method (Fmoc method) or a t-butoxycarbonyl method (t-Boc method) is applied, so as to produce the polypeptide of the present invention.
Furthermore, a transformant containing the previously obtained herboxidiene biosynthetic gene is cultured in a medium, so that herboxidiene or an analogue thereof is generated and accumulated in the culture. Thereafter, the herboxidiene or the analogue thereof can be produced by collecting it from the culture. Culture conditions are not particularly limited, and the culture is carried out under conventional host culture conditions.
Further, the size of the carbon chain of a basic polyketide skeleton and the functional group of a β-carbon during a condensation process can be changed by modifying modules, based on the nucleotide sequence information of the DNA involved in the biosynthesis of herboxidiene. Still further, by selectively inactivating a modifying enzyme after the formation of polyketide, the specific component of a predictable herboxidiene analogue can be preferentially produced. For example, by deleting the hbdE of Mer-16208 that is a strain mainly producing herboxidiene, a strain that mainly produces the 18-deoxy product of herboxidiene can be obtained. As a method for deleting such hbdE, a method of conducting a substitution or conversion by homologous recombination according to the conventional method described in Sambrook et al. may be applied.
Using the thus obtained strain capable of preferentially producing a specific herboxidiene analogue, the specific herboxidiene analogue can be produced in accordance with the method for producing herboxidiene.
EXAMPLES
The present invention will be specifically described in the following examples. However, the present invention is not limited at all by these examples. In addition, in the following descriptions, the concentration is indicated as % by weight, unless otherwise specified.
Example 1
Identification of Nucleotide Sequences of hbdD and Peripheral Region Thereof
(1): Culture of Mer-16208 and Obtainment of Genomic DNA
The hypha of Mer-16208 was inoculated into 50 ml of Tryptic Soy Broth (hereinafter referred to as TSB, at times), and it was then subjected to a shaking culture at 28° C. for 3 days. Thereafter, the obtained culture media was centrifuged at 3000 rpm for 10 minutes to collect a cell body. A chromosomal DNA was prepared from the cell body, using Blood & Cell Culture kit (QIAGEN).
(2): Cloning of Partial Sequence of DNA Encoding Protein (HbdD) Possibly Having 14,15-Epoxidation Activity
With reference to the sequence of pldD, a pladienolide 18,19-epoxidase gene, possessed by an actinomycete Streptomyces sp. Mer-11107 that produces pladienolide as a secondary metabolite having an epoxy portion similar to that of herboxidiene, the following primers (PLDDF and PLDDR) were designed and produced (see SEQ ID NOS: 9 and 10 in the sequence listing).










PLDDF:
5′-CCGATCGAGGACGGACGCTGG-3′



 



PLDDR:
5′-GGCGGCCACCGACATGCCGTGCCCGTA-3′






Subsequently, using these two types of primers (PLDDF and PLDDR), and also using the chromosomal DNA of Mer-16208 obtained in the above section (1) as a template, PCR was carried out. In the PCR, Takara LA Taq (Takara Bio Inc.) and a PCR amplifier (T Gradient by Biometra GmbH) were used, and a three-staged reaction consisting of a denaturation at 98° C. for 20 seconds, an annealing at 50° C. for 2 minutes, and an elongation at 68° C. for 2 minutes was repeated 35 times. As a result, a DNA fragment with a size of approximately 290 bp (hereinafter referred to as DNA fragment-A1) was amplified. It was highly likely that this DNA fragment-A1 was a portion of a DNA encoding a protein having a epoxidation activity. The DNA fragment-A1 amplified by the PCR was recovered from the reaction mixture, using Wizard SV Gel and PCR Clean-Up System (Promega).
Subsequently, in order to obtain the DNA fragment-A1 in an amount sufficient for analyzing the nucleotide sequence of the thus obtained DNA fragment-A1, the DNA fragment-A1 was ligated to a plasmid vector pT7Blue T (Novagen), using DNA Ligation kit ver. 2 (Takara Bio Inc.), and Escherichia coli JM109 was then transformed with the ligated product. Thereafter, the transformed Escherichia coli was selected using an L-Broth agar medium (1.0% Bactotrypton, 0.5% yeast extract, 0.5% NaCl, and 1.5% agar) containing ampicillin (50 μg/mL), X-gal (5-bromo-4-chloro-3-indolyl-β-D-galactoside; 40 μg/mL), and IPTG (isopropyl-(3-D-thiogalactopyranoside; 100 μM). The thus separated, transformed Escherichia coli colony was cultured in an L-Broth liquid medium (1% Bactotrypton, 0.5% yeast extract and 0.5% NaCl) containing ampicillin (50 μg/mL). Thereafter, a plasmid DNA was separated and purified from the cell body of the proliferated transformed Escherichia coli, using a plasmid purification kit (Labo Pass Mini, Hokkaido System Science Co., Ltd.), so as to obtain a certain amount of the DNA fragment-A1.
(3): Analysis of Nucleotide Sequence of Cloned DNA Fragment-A1
The nucleotide sequence of the DNA fragment-A 1 obtained in the above section (2) was analyzed by a dye terminator cycle sequencing method using a DNA nucleotide sequence analyzer (ABI PRISM (registered trademark) 310 Genetic Analyzer; Applied Biosystems). As a result of the analysis of the nucleotide sequence, the DNA fragment-A1 amplified by the PCR was measured to be approximately 290 bp by electrophoresis. As a result of the sequencing of the nucleotide sequence, the size of the DNA fragment-A1 was found to be exactly 288 bp (see nucleotides 56832-57119 of SEQ ID NO: 1). At both ends of the above described, cloned 288-bp DNA sequence, DNA sequences corresponding to the two types of primers used in the above described PCR were found. Thus, it became clear that the DNA fragment-A1 had been specifically amplified by these two types of primers (PLDDF and PLDDR) in the above described PCR.
(4): Analysis of Peripheral Region of DNA Fragment-A1
As described above, the partial sequence of the DNA encoding the protein (HbdD) possibly having a 14,15-epoxidation activity derived from Mer-16208 had been determined. Hence, the nucleotide sequence of a peripheral region ranging from the upstream region to downstream region of the cloned fragment was amplified by an inverse PCR method, and cloning, and sequence analysis were then carried out. Specifically, the chromosomal DNA of Mer-16208 (see the section (1)) was digested with a restriction enzyme SalI in an H buffer (50 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 1 mM dithiothreitol, and 100 mM NaCl). The obtained restriction enzyme-digested DNA fragment was self-cyclized using DNA Ligation Kit ver. 2 (Takara Bio Inc.).
On the other band, the following primers (HbdDin-1F and HbdDin-1R) were designed and produced from the nucleotide sequence of the DNA fragment-A1 (see SEQ ID NOS: 11 and 12 in the sequence listing).










HbdDin-1F:
5′-GCCCTCGGGGACGCGCTGGCCGCGTTCAAC-3′



 



HbdDin-1R:
5′-CTGCGCGGGCCTCAGGCCCGTCAGGGTGAC-3′






Subsequently, using these two types of primers (HbdDin-1F and HbdDin-1R), and also using the above self-cyclized chromosomal DNA of Mer-16208 as a template, a PCR was carried out. In the PCR, Takara LA Taq (Takara Bio Inc.) and a PCR amplifier (T Gradient by Biometra GmbH) were used, and a two-staged reaction consisting of a denaturation at 98° C. for 20 seconds, and annealing and elongation at 68° C. for 7 minutes, was repeated 30 times.
As a result, DNA fragments each having a size of approximately 2.5 kbp (DNA fragment-B1) were amplified. It was highly likely that these DNA fragments-B1 were a DNA encoding a protein having a 14,15-epoxidation activity and a DNA having a DNA sequence comprising the upstream and downstream regions thereof.
The DNA fragments-B1 were recovered from the PCR amplification reaction mixture, using Wizard SV Gel and PCR Clean-Up System (Promega). Thereafter, in order to obtain the DNA fragments-B1 in amounts sufficient for analyzing the nucleotide sequences of the thus obtained DNA fragments, in the same manner as that described in the above section (2), a certain amount of each DNA fragment was obtained using a plasmid vector pT7Blue T (Novagen), DNA Ligation kit ver. 2 (Takata Bio Inc.), Escherichia coli JM109, and a plasmid purification kit (Labo Pass Mini, Hokkaido System Science Co., Ltd.)
(5): Analysis of Nucleotide Sequence of DNA Fragment-B1 (with Size of Approximately 2.5 kbp)
The nucleotide sequence of the DNA fragment-B1 obtained in the above section (4) was analyzed by a dye terminator cycle sequencing method using a DNA nucleotide sequence analyzer (ABI PRISM (registered trademark) 310 Genetic Analyzer; Applied Biosystems). Thus, the nucleotide sequence was analyzed, and as a result, the information of the 2712-bp nucleotide sequence of the DNA fragment-B1 was obtained (see nucleotides 56703-59414 of SEQ ID NO: 1).
As a result of searching the open reading frame (ORF) in this 2712-bp sequence, it was found that 3 types of proteins were encoded. As a result of searching the amino acid sequences of the proteins using BLAST search, it was found that a partial sequence of an ORF (hbdD) encoding a protein having a high identity to an epoxidase was present in nucleotides 56703-57545 of SEQ ID NO: 1. The protein HbdD encoded by the hbdD had the highest identity to the amino acid sequence of the protein PldD having a high identity to the pladienolide 18,19-epoxidase of Streptomyces sp. Mer-11107 (57% identity). This result suggested that the hbdD was highly likely to be a gene encoding the 14,15-epoxidase involved in the biosynthesis of herboxidiene. Herein, “identity of amino acid sequences” means the percentage of polypeptides shared by two sequences, when the two sequences are aligned in an optimal manner. That is to say, such identity can be calculated by the expression: identity=(the number of matched positions/the total number of positions)×100, and it can be calculated using a commercially available algorism. In addition, such algorism is integrated into the PBLAST program described in Altschul et al., J. Mol. Biol. 215 (1990) 403-410.
Moreover, in a region immediately downstream of the hbdD (nucleotides 57575-58435 of SEQ ID NO: 1), an ORF (hbdF) encoding a protein having a high identity to a methyl transferase existed. The protein HbdF encoded by the hbdF consisted of 287 amino acids, and it had the highest identity to the amino acid sequence of the methyl transferase MitM of Streptomyces lavendulae (61% identity). This result suggested that the hbdF was highly likely to be a gene encoding the 17-O-methyl transferase involved in the biosynthesis of herboxidiene.
Furthermore, in a region immediately downstream of the hbdF (nucleotides 58533-59414 of SEQ ID NO: 1), a partial sequence of an ORF (hbdE) encoding a protein having a high identity to a cytochrome P-450 hydroxylase existed. The protein HbdE encoded by the hbdE had the highest identity to the amino acid sequence of the cytochrome P-450 hydroxylase PikC of Streptomyces venezuelae (60% identity). This result suggested that the hbdE was highly likely to be a gene encoding the 18-hydroxylase involved in the biosynthesis of herboxidiene.
Example 2
Obtainment of Cosmid Clone Comprising Biosynthetic Gene Cluster Sequence Adjacent to hbdD, E and F
(1): Preparation of Genomic Library of Mer-16208
160 μl of sterilized purified water, 200 μl of genomic DNA solution of Mer-16208 (1 mg/ml), 40 μl of 10×M buffer [100 mM Tris-HCl (pH 7.5), 100 mM MgCl2, 10 mM dithiothreitol, and 500 mM NaCl], and 1 μl of restriction enzyme Sau3AI (1 unit/μl) were mixed. The obtained mixture was incubated at 37° C. for 6 minutes. Thereafter, the reaction mixture was extracted with 400 μl of phenol-chloroform mixed solution (phenol:chloroform:isoamyl alcohol=25:24:1, volume ratio), and the aqueous phase was then recovered. It was further extracted with 400 μl of chloroform, and the aqueous phase was recovered again. Thereafter, 50 μl of 3 M sodium acetate (pH 6.0) and 1 ml of ethanol were added to this solution, and the obtained mixture was then left at −80° C. for 30 minutes. The resultant was centrifuged, and the precipitated DNA was then recovered. The recovered DNA was washed with 70% ethanol, and was then dissolved in 50 μl of sterilized purified water. Thereafter, 10 μl of 10×BAP buffer [500 mM Tris-HCl (pH 9.0) and 10 mM MgCl2] and 2 μl of calf intestional alkaline phosphatase (Takara Shuzo Co., Ltd.) were added to the above obtained solution, and the obtained mixture was then incubated at 37° C. for 1 hour. This reaction mixture was extracted with 100 μl of phenol-chloroform mixed solution (phenol:chloroform:isoamyl alcohol=25:24:1, volume ratio), and the aqueous phase was recovered. It was further extracted with 100 μl of chloroform, and the aqueous phase was recovered again. Thereafter, 10 μl of 3 M sodium acetate (pH 6.0) and 300 μl of ethanol were added to this solution, and the obtained mixture was then left at −80° C. for 30 minutes. The resultant was centrifuged, and the precipitated DNA was then recovered. The recovered DNA was washed with 70% ethanol, and was then dissolved in 20 μl of TE buffer [10 mM Tris-HCl (pH 8.0) and 1 mM EDTA].
On the other hand, 10 μg of SuperCos cosmid vector (Stratagene) was digested with a restriction enzyme XbaI in accordance with the manual provided by Stratagene, and the DNA terminus was then dephosphorylated by calf intestional alkaline phosphatase (Takara Shuzo Co., Ltd.). It was further digested with a restriction enzyme BamHI, followed by purification, and the resultant was then dissolved in 10 μl of TE buffer.
2.5 μl of solution of the Sau3AI partial digest of the aforementioned Mer-16208 genomic DNA was added to 1 μl of the obtained cosmid DNA solution. Further, 1.5 μl of sterilized purified water, 5 μl of Solution II of DNA Ligation Kit (Takara Shuzo Co., Ltd.), and 10 μl of Solution I thereof were successively added to the solution. The mixture was incubated at 23° C. for 14 hours. Thereafter, 4 μl of the reaction mixture was packaged into a lambda phage, using Gigapack III XL Kit (Stratagene). A transduction test was carried out on the obtained packaging solution (total amount: 500 μl), and its ability to form colonies was examined. As a result, the colony formation ability was found to be 192 cfu (colony forming unit)/μl.
(2) Preparation of Probe Containing hbdD, E and F
Based on the information of the 2712-bp nucleotide sequence containing the partial sequences of hbdD, hbdF and hbdE, obtained in Example 1(5), two types of primers, HbdDin-3F and hbdEin-1R, consisting of the following sequences, were synthesized (see SEQ ID NOS: 13 and 14 in the sequence listing).










HbdDin-3F:
5′-CCCGCCCTTCACGGAGCGGGAGCGCGCGCT-3′



 



HbdEin-1R:
5′-GAGCAGTTCGCAGATCACCGCGATGGGCAG-3′






Using these primers, PCR was carried out under the following conditions.
(Composition of PCR Reaction Mixture)















Sterilized purified water
31 μl



2x GC buffer II
50 μl



dNTP mixed solution
16 μl



(dATP, dGTP, dTTP and dCTP; 2.5 mM each)




HbdDin-3F (100 pmol/μl)
0.5 μl



HbdEin-1R (100 pmol/μl)
0.5 μl



Mer-16208 total DNA (100 ng/μl)
 1 μl



LA Taq polymerase (5 U/μl, Takara Shuzo Co., Ltd.)
 1 μl









(Reaction Temperature Conditions)
95° C., 3 minutes
(98° C., 20 seconds; 63° C., 30 seconds; 68° C., 2 minutes) 30 cycles
68° C., 3 minutes
A 1.5-kb DNA fragment amplified as a result of this reaction was electrophoresed on 0.8% agarose gel, and the separated 1.5-kb DNA fragment was cut out. Thereafter, the DNA was recovered and purified using Wizard SV Gel and PCR Clean-Up System (Promega). The obtained 50 μl of TE solution was defined as a probe solution containing hbdD, E and F.
(3): Screening Using Probe Containing hbdD, E and F
Using the packaging solution of the genomic DNA library of Mer-16208 prepared in the above section (1), Escherichia coli XL-1 Blue MR (Stratagene) used as a host was transfected in accordance with the manual provided by Stratagene. The cell suspension obtained after the transfection operation was poured and spread onto each of 10 Petri dishes (each having an internal diameter of 90 mm and a height of 15 mm) each containing LB-50 μg/ml ampicillin-1.5% agar medium, and it was then cultured at 37° C. for 18 hours. Colonies growing in each Petri dish were transferred to a Hybond N+ filter (Amersham Biosciences), and thereafter, an alkali treatment and a neutralization treatment were carried out under conditions described in the manual included with the Hybond N+ filter. Thereafter, the resultant was dried at 80° C. for 2 hours, so that a DNA derived from the colonies was immobilized on the filter.
Using 100 ng of the 1.5-kb DNA fragment containing hbdD, E, and F prepared in the above section (2) as a probe, the genomic DNA library was screened by a colony hybridization method, employing AlkPhos Direct System (Amersham Biosciences). The hybridization was carried out in NaCl with a salt concentration of 0.5 M at 68° C. for 1 hour. Conditions for the labeling of the probe DNA, hybridization, and detection were determined in accordance with the manual included with AlkPhos Direct System. Among the examined approximately 2,200 colonies, two colonies which had strongly hybridized with the alkaline phosphatase-labeled probe were separated. Cosmids (pHb635 and pHb197) were extracted and purified from Escherichia coli clones derived from these colonies.
(4): Preparation of Probe Containing Terminal Sequence of pHb635
The terminal sequences of DNA fragments inserted into the cosmids pHb635 and pHb197 obtained in the above section (3) were analyzed by a dye terminator cycle sequencing method using a DNA nucleotide sequence analyzer (ABI PRISM (registered trademark) 310 Genetic Analyzer, Applied Biosystems). As a result, it was found that the pHb635 possessed the area ranging from a region in the midcourse of a gene encoding polyketide synthase (nucleotide 22595 of SEQ ID NO: 1) to a region in the midcourse of hbdE (nucleotide 58958 of SEQ ID NO: 1), and that the pHb197 possessed the area ranging from a region in the midcourse of hbdD (nucleotide 57359 of SEQ ID NO: 1) to a region downstream of hbdE. Hence, in order to obtain a cosmid clone containing a sequence upstream of the terminal sequence of pHb635, a probe containing the terminal sequence of pHb635 was prepared. Based on the information of a 537-bp nucleotide sequence containing the terminal sequence of pHb635 (nucleotides 22595-23131 of SEQ ID NO: 1), two types of primers, 635-1F and 635-1R, consisting of the following sequences, were synthesized (see SEQ ID NOS: 15 and 16 in the sequence listing).








635-1F:
5′-GGTCGAGGGGCACGGTACGGGGACGACGCT-3′


 


635-1R:
5′-CCCTGCACCGTGGCCGGGCCCTGCTCGGT-3′






Using these primers, PCR was carried out under the following conditions.
(Composition of PCR Reaction Mixture)















Sterilized purified water
31 μl



2x GC buffer II
50 μl



dNTP mixed solution
16 μl



(dATP, dGTP, dTTP and dCTP; 2.5 mM each)




635-1F (100 pmol/μl)
0.5 μl 



635-1R (100 pmol/μl)
0.5 μl 



pHb635 cosmid DNA (50 ng/μl)
 1 μl



LA Taq polymerase (5 u/μl, Takara Shuzo Co., Ltd.)
 1 μl









(Reaction Temperature Conditions)
95° C., 6 minutes
(98° C., 20 seconds; 65° C., 30 seconds; 68° C., 1 minute) 30 cycles
68° C., 2 minutes
A 486-bp DNA fragment amplified as a result of this reaction was electrophoresed on 0.8% agarose gel, and the separated 486-bp DNA fragment was cut out. Thereafter, a DNA was recovered and purified using Wizard SV Gel and PCR Clean-Up System (Promega). The obtained 50 μl of TE solution was defined as a probe solution containing the terminal sequence of pHb635.
(5): Screening Using Probe Containing Terminal Sequence of pHb635
Using the packaging solution of the genomic DNA library of Mer-16208 prepared in the section (1) above, Escherichia coli XL-1 Blue MR (Stratagene) used as a host was transfected in accordance with the manual provided by Stratagene. The cell suspension obtained after the transfection operation was poured and spread onto each of 10 Petri dishes (each having an internal diameter of 90 mm and a height of 15 mm) each containing LB-50 μg/ml ampicillin-1.5% agar medium, and it was then cultured at 37° C. for 18 hours. Colonies growing in each Petri dish were transferred to a Hybond N+ filter (Amersham Biosciences), and thereafter, an alkali treatment and a neutralization treatment were carried out under conditions described in the manual included with the Hybond N+ filter. Thereafter the resultant was dried at 80° C. for 2 hours, so that a DNA derived from the colonies was immobilized on the filter. Using 100 ng of the 486-bp DNA fragment containing the terminal sequence of pHb635 prepared in the above section (4) as a probe, the genomic DNA library was screened by a colony hybridization method, employing AlkPhos Direct System (Amersham Biosciences). The hybridization was carried out in NaCl with a salt concentration of 0.5 M at 70° C. for 1 hour. Conditions for the labeling of the probe DNA, hybridization, and detection were determined in accordance with the manual included with AlkPhos Direct System. Among the examined approximately 1,900 colonies, one colony which had strongly hybridized with the alkaline phosphatase-labeled probe was separated. A cosmid (pHb8221) was extracted and purified from an Escherichia coli clone derived from this colony.
Example 3
Determination of Nucleotide Sequence of Herboxidiene Biosynthetic Gene Cluster
The terminal sequence of a DNA fragment inserted into the cosmid pHb8221 obtained in the above Example 2(5) was analyzed by a dye terminator cycle sequencing method using a DNA nucleotide sequence analyzer (ABI PRISM (registered trademark) 310 Genetic Analyzer, Applied Biosystems). As a result, it was found that the pHb8221 possessed the area ranging from a region in the midcourse of a gene encoding polyketide synthase (nucleotide 37955 of SEQ ID NO: 1) to an upstream region containing the terminal sequence o pHb635. From the above results, pHb197, pHb635, and pHb8221 were selected as cosmids each containing a herboxidiene biosynthetic gene, and the nucleotide sequences of DNA fragments inserted into these cosmids were then determined.
Each cosmid was isolated using QIAGEN Large-Construct Kit (QIAGEN), and it was then sheared to a size of approximately 1 kb using HydroShear (Genomic Solutions), followed by subcloning using BKL Kit (Takara Shuzo Co., Ltd.).
The obtained subclone was analyzed by a dye terminator cycle sequencing method using a DNA nucleotide sequence analyzer (ABI PRISM (registered trademark) 310 Genetic Analyzer; Applied Biosystems). As a result, an approximately 65-kb nucleotide sequence containing the DNA involved in the synthesis of herboxidiene was determined (see SEQ ID NO: 1).
This DNA shown in SEQ ID NO: 1 comprised seven open reading frames (ORFs), hbdAI (nucleotides 8919-28295), hbdAII (nucleotides 28326-49892), hbdAIII (nucleotides 49892-55981), hbdD (nucleotides 56115-57545), hbdF (nucleotides 57575-58435), hbdE (nucleotides 58533-59798) and hbdR (nucleotides 6681-7706). In addition, the amino acid sequences of polypeptides encoded by these sequences are as shown in SEQ ID NOS: 2 to 8, respectively. Among the thus obtained DNAs involved in the biosynthesis of herboxidiene of Mer-16208, the functions of hbdAI, hbdAII and hbdAIII were analyzed based on the descriptions of Omura et al., Macrolide Antibiotics: Chemistry, Biology, and Practice, Second Edition, Academic Press. As a result, they had eleven open reading frames each comprising one or more repeating units called modules, as with the already clarified other polyketide biosynthetic genes. As described later, it was identified from the amino acid sequence conserved in each domain that each module encoded all or several domains selected from an acyl carrier protein (ACP) involved in the condensation reaction in polyketide synthesis, β-ketoacyl-ACP synthase (KS), acyl transferase (AT), ketoacyl reductase (KR) involved in a β-carbonyl group modification reaction, dehydratase (DH), and enoyl reductase (ER), and that a thioesterase (TE) domain that cleaves a polyketide chain from polyketide synthase existed in the last module (a GFDSL motif containing a pantotheine-binding serine residue in the ACP domain, a conserved active motif TVDTGCSSSLV in the KS domain, motifs GHSXG and AXHs involved in the activity of the AT domain; an NADP(H)-binding site motif GXGXXAXXXA in the KR domain; an active site motif HXXXG(D)XXXXP in the DH domain; an NADP(H)-binding site motif LXHXAXGGVG in the ER domain; and GXSXG and GDH motifs in the TE domain).
It was found that a loading module (Module L) differs from other modules and the cysteine in the active center thereof is substituted with a glutamine, and thus that HbdAI is involved in the first reaction. In addition, it was also found that since module 8 has a thioesterase (TE) domain, HbdAIII is involved in the final reaction of polyketide. Thus, it was thought that, after the formation of the basic skeleton of polyketide, it is modified with a group of enzymes (HbdD, HbdF and HbdE) that are encoded by hbdD, hbdF and hbdE, so that herboxidiene seems to be biosynthesized. Moreover, hbdR had a high identity to a gene, lacI, encoding a transcription factor, and thus, the hbdR seemed to encode the transcription factor of the DNA involved in the biosynthesis of herboxidiene.
The thus clarified modules of the DNA involved in the biosynthesis of herboxidiene and the corresponding domains were as follows.
ORF hbdAI (nucleotides 8919-28295 of SEQ ID NO: 1) encoded a loading module, module 1, module 2 and module 3. The corresponding polypeptide was represented by the amino acid sequence shown in SEQ ID NO: 2.
Loading module (nucleotides 8919-12023)
KS0: nucleotides 8955-10217
AT0: nucleotides 10305-11360
ACP0: nucleotides 11790-11972
Module 1 (nucleotides 12024-16451)
KS1: nucleotides 12024-13262
AT1: nucleotides 13356-14441
KR1: nucleotides 15324-16196
ACP1: nucleotides 16218-16400
Module 2 (nucleotides 16452-21734)
KS2: nucleotides 16452-17711
AT2: nucleotides 17796-18860
DH2: nucleotides 19038-19739
KR2: nucleotides 20622-21461
ACP2: nucleotides 21483-21665
Module 3 (nucleotides 21735-28295)
KS3: nucleotides 21735-22991
AT3: nucleotides 23253-24305
DH3: nucleotides 24474-25169
ER3: nucleotides 26016-26936
KR3: nucleotides 26964-27812
ACP3: nucleotides 27834-28016
In addition, the amino acid sequence of the corresponding polypeptide was as follows.
KS0: amino acids 13-433
AT0: amino acids 463-814
ACP0: amino acids 958-1018
KS1: amino acids 1036-2511
AT1: amino acids 1480-1841
KR1: amino acids 2136-2426
ACP1: amino acids 2434-2494
KS2: amino acids 2512-2931
AT2: amino acids 2960-3314
DH2: amino acids 3374-3607
KR2: amino acids 3902-4181
ACP2: amino acids 4189-4249
KS3: amino acids 4273-4691
AT3: amino acids 4779-5129
DH3: amino acids 5186-5417
ER3: amino acids 5700-6006
KR3: amino acids 6016-6298
ACP3: amino acids 6306-6366
ORF hbdAII (nucleotides 28326-49892 of SEQ ID NO: 1) encoded module 4, module 5, module 6 and module 7, and the corresponding polypeptide was represented by the amino acid sequence shown in SEQ ID NO: 3.
Module 4 (nucleotides 28326-33644)
KS4: nucleotides 28419-29681
AT4: nucleotides 29751-30851
DH4: nucleotides 31017-31718
KR4: nucleotides 32526-33371
ACP4: nucleotides 33393-33575
Module 5 (nucleotides 33645-38873)
KS5: nucleotides 33645-34895
AT5: nucleotides 34974-36047
DH5: nucleotides 36231-36938
KR5: nucleotides 37722-38606
ACP5: nucleotides 38628-38810
Module 6 (nucleotides 38874-43532)
KS6: nucleotides 38874-40133
AT6: nucleotides 40203-41267
KR6: nucleotides 42405-43247
ACP6: nucleotides 43269-43451
Module 7 (nucleotides 43533-49892)
KS7: nucleotides 43533-44792
AT7: nucleotides 44865-45962
DH7: nucleotides 46137-46847
ER7: nucleotides 47724-48641
KR7: nucleotides 48669-49520
ACP7: nucleotides 49542-49724
Moreover, the amino acid sequence of the corresponding polypeptide was as follows.
KS4: amino acids 32-452
AT4: amino acids 476-842
DH4: amino acids 898-1131
KR4: amino acids 1401-1682
ACP4: amino acids 1690-1750
KS5: amino acids 1774-2190
AT5: amino acids 2217-2574
DH5: amino acids 2636-2871
KR5: amino acids 3133-3427
ACP5: amino acids 3435-3495
KS6: amino acids 3517-3936
AT6: amino acids 3960-4314
KR6: amino acids 4694-4974
ACP6: amino acids 4982-5042
KS7: amino acids 5070-5489
AT7: amino acids 5514-5879
DH7: amino acids 5938-6174
ER7: amino acids 6467-6772
KR7: amino acids 6782-7065
ACP7: amino acids 7073-7133
ORF hbdAIII (nucleotides 49892-55981 of SEQ ID NO: 1) encoded module 8, and the corresponding polypeptide was represented by the amino acid sequence shown in SEQ ID NO: 4.
Module 8 (nucleotides 49892-55981)
KS8: nucleotides 49892-51271
AT8: nucleotides 51341-52420
DH8: nucleotides 52589-53278
KR8: nucleotides 54083-54940
ACP8: nucleotides 54962-55144
TE8: nucleotides 55163-55981
Furthermore, the amino acid sequence of the corresponding polypeptide was as follows.
KS8: amino acids 41-460
AT8: amino acids 484-843
DH8: amino acids 900-1129
KR8: amino acids 1398-1683
ACP8: amino acids 1691-1751
TE8: amino acids 1758-2030
Moreover, AT0, AT1, AT2, AT3, AT5 and AT6 have an amino acid sequence characteristic for an AT domain that incorporates methylmalonic acid (GHSQG, VDYASH, etc. of a motif involved in activity), and AT4, AT7 and AT8 have an amino acid sequence characteristic for an AT domain that incorporates malonic acid (GHSV(I)G, HAFHS, etc. of a motif involved in activity). From these results, it has become clear that each AT domain has appropriate substrate specificity.
As described above, the protein HbdD encoded by ORF hbdD (nucleotides 56115-57545 of SEQ ID NO: 1) had the highest identity to the amino acid sequence of the protein PldD having a high identity to the pladienolide 18,19-epoxidase of Streptomyces sp. Mer-11107 (57% identity). This result suggested that the hbdD was highly likely to be a gene encoding the 14,15-epoxidase involved in the biosynthesis of herboxidiene. The corresponding polypeptide HbdD was represented by the amino acid sequence shown in SEQ ID NO: 5.
As described above, the protein HbdF encoded by ORF hbdF (nucleotides 57575-58435 of SEQ ID NO: 1) had the highest identity to the amino acid sequence of the methyl transferase MitM of Streptomyces lavendulae (61% identity). This result suggested that the hbdF was highly likely to be a gene encoding the 17-O-methyl transferase involved in the biosynthesis of herboxidiene. The corresponding polypeptide HbdF was represented by the amino acid sequence shown in SEQ ID NO: 6.
As described above, the protein HbdE encoded by ORF hbdE (nucleotides 58533-59798 of SEQ ID NO: 1) had the highest identity to the amino acid sequence of the cytochrome P-450 hydroxylase PikC of Streptomyces venezuelae (60% identity). This result suggested that the hbdE was highly likely to be a gene encoding the 18-hydroxylase involved in the biosynthesis of herboxidiene. The corresponding polypeptide HbdE was represented by the amino acid sequence shown in SEQ ID NO: 7.
A protein HbdR encoded by ORF hbdR (nucleotides 6681-7706) had the highest identity to the amino acid sequence of the transcription factor SACE—4536 of Saccharopolyspora erythraea (57% identity). This result suggested that the hbdR was highly likely to be a gene encoding the transcription factor of the biosynthetic gene of herboxidiene. The corresponding polypeptide HbdR was represented by the amino acid sequence shown in SEQ ID NO: 8. FIG. 1 shows the biosynthetic pathway of herboxidiene in Mer-16208. In addition, FIG. 2 shows the correlation between each ORF and a cosmid.
Example 4
Construction of Herboxidiene 18-Hydroxylase Gene (hbdE)-Deficient Strain
Based on the approximately 65-kb nucleotide sequence containing the DNA involved in the biosynthesis of herboxidiene determined in Example 3 (see SEQ ID NO: 1), it became clear that herboxidiene is biosynthesized in the biosynthetic pathway shown in FIG. 1. Thus, it was considered that a strain producing only the 18-deoxy product of herboxidiene could be obtained by disrupting only the cytochrome P-450 gene hbdE thereof. Such hbdE-deficient strain was constructed by the following method.
(1) Preparation of Shuttle Vector pMKOSCPR
A shuttle vector pMKOSCPR capable of replicating in a herboxidiene-producing strain, Streptomyces sp. Mer-16208, and in Escherichia coli, was produced. Based on the nucleotide sequence of a SuperCos1 cosmid vector (Stratagene), two types of primers, NP2-SN2F and CE1-NXHR, consisting of the following sequences, were synthesized (see SEQ ID NOS: 17 and 18 in the sequence listing).








NP2-SN2F:
5′-GGGCATATGACTAGTCTGATCAAGAGACAGGATG-3′


 


CE1-NXHR:
5′-GGGCATATGTCTAGAAGCTTGGTAACTGTCAGACCA



AGT-3′






Based on the nucleotide sequence of a conjugal gene oriT (J. Bacteriol., 169, 5320-5323, 1987) derived from Escherichia coli plasmid RP4, two types of primers, OT-SF and OT-SR, consisting of the following sequences, were synthesized (see SEQ ID NOS: 19 and 20 in the sequence listing).










OT-SF:
5′-GGGCCCGGGCTCGGTCTTGCCTTGCTCGT-3′



 



OT-SR:
5′-GGGCCCGGGGCGCTTTTCCGCTGCATAAC-3′






Based on the nucleotide sequence of a plasmid SCP2 (J. Gen. Microbiol., 126, 427-442, 1981) derived from an actinomycete Streptomyces coelicolor A3(2) (NBRC151732), two types of primers, SCPR-AF and SCPR-SR, consisting of the following sequences, were synthesized (see SEQ ID NOS: 21 and 22 in the sequence listing).










SCPR-AF: 
5′-GGGCCTAGGTCGACGGCCTCGGTCACGGCGC




T-3′



 



SCPR-SR: 
5′-CCCACTAGTCCTCGAATTCTTCGAGCAATGG




ATCCATC-3′






Using these primers, PCR was carried out under the following conditions.
(Composition of PCR Reaction Mixture)















Sterilized purified water
31.5 μl  



10x KOD buffer
5 μl



dNTP mixed solution
5 μl



(dATP, dGTP, dTTP and dCTP; 2.5 mM each)




MgSO4 solution
3 μl



Dimethyl sulfoxide
2.5 μl  



NP2-SN2F or OT-SF or SCPR-AF (50 pmol/μl)
0.5 μl  



CE1-NXHR or OT-SR or SCPR-SR (50 pmol/μl)
0.5 μl  



SuperCos1 or RP4 or SCP2 (100 ng/μl)
1 μl



KOD-plus-polymerase (1 u/μl, Toyobo Co., Ltd.)
1 μl









(Reaction Temperature Conditions)
95° C., 6 minutes
(98° C., 20 seconds; 60° C., 30 seconds; 68° C., 6 minutes) 30 cycles
68° C., 7 minutes
As a result of this reaction, a 3.2-kb DNA fragment (DNA fragment AC1) comprising an aminoglycoside resistance gene aphII (Gene, 19(3), 327-336, 1982) and an Escherichia coli plasmid replicating origin ColE1 (Gene, 33(1), 103-119, 1985) was amplified by a reaction using NP2-SN2F, CE1-NXHR and SuperCos1. A 0.8-kb DNA fragment (DNA fragment OT1) comprising the conjugal gene oriT was amplified by a reaction using OT-SF, OT-SR and RP4. A 5.8-kb DNA fragment (DNA fragment SR1) comprising the replication region of the plasmid SCP2 of Actinomycetes was amplified by a reaction using SCPR-AF, SCPR-SR and SCP2. The DNA fragments AC1, OT1 and SR1 were purified using Wizard SV Gel and PCR Clean-Up System (Promega). The DNA fragment AC1 was digested with a restriction enzyme NdeI, and it was then self-cyclized using DNA Ligation Kit ver. 2.1 (Takara Bio Inc.). The obtained cyclized DNA AC1 and the DNA fragment OT1 were each digested with a restriction enzyme SmaI, and they were then ligated to each other using DNA Ligation Kit ver. 2.1 (Takara Bio Inc.). Thus, Escherichia coli plasmid pMKO1 having an aminoglycoside resistance gene aphII and the conjugal gene oriT were obtained. In addition, the DNA fragment SR1 was digested with restriction enzymes SpeI and AvrII, and using DNA Ligation Kit ver. 2.1 (Takara Bio Inc.), the thus digested DNA fragment was then ligated to a plasmid pMKO1 that had been digested with a restriction enzyme SpeI. Hence, a shuttle vector pMKOSCPR, in which the replication region of the plasmid SCP2 of actinomycetes had been inserted into pMKO1, was constructed.
(2) Preparation of hbdE-Deficient Plasmid pMKOSCPR-EU-tsr-ED
Based on the nucleotide sequence shown in SEQ ID NO: 1, four types of primers, dEU-AHEF, dEU-NXR, dED-XF and dED-EHR, consisting of the following sequences, were synthesized (see SEQ ID NOS: 23, 24, 25 and 26 in the sequence listing).








dEU-AHEF:
5′-CCCATTAATAAGCTTGAATTCACGGGAACGGGTCC



TCAT-3′


 


dEU-NXR:
5′-CCCTCTAGACATATGGTCGTCCTCCGGGAGACG-3′


 


dED-XF:
5′-CCCTCTAGAGCCCGGAGTCAGAGGTGGT-3′


 


dED-EHR:
5′-CCCAAGCTTGAATTCGCCGATGGCGGAGCGCAT-3′






Based on the nucleotide sequence of a thiostrepton resistance gene tsr (Mol. Gen. Genet., 199(1), 26-36, 1985) derived from Streptomyces azureus NBRC12744, two types of primers, TR-AF and TR-XR, consisting of the following sequences, were synthesized (see SEQ ID NOS: 27 and 28 in the sequence listing).










TR-AF:
5′-CCCATTAATCGGCATCGCGTGGCGGGCCCGATT-3′



 



TR-XR:
5′-CGGTCTAGATTATCGGTTGGCCGCGAGATT-3′






Using these primers, PCR was carried out under the following conditions.
(Composition of PCR Reaction Mixture)













Sterilized purified water
31.5 μl  


10x KOD buffer
5 μl


dNTP mixed solution
5 μl


(dATP, dGTP, dTTP and dCTP; 2.5 mM each)



MgSO4 solution
3 μl


Dimethyl sulfoxide
2.5 μl  


dEU-AHEF or dED-XF or TR-AF (50 pmol/μl)
0.5 μl  


dEU-NXR or dED-EHR or TR-XR (50 pmol/μl)
0.5 μl  


Mer-16208 chromosomal DNA or S. azureus NBRC12744
1 μl


chromosomal DNA (100 ng/μl)



KOD-plus-polymerase (1 u/μl, Toyobo Co., Ltd.)
1 μl









(Reaction Temperature Conditions)
95° C., 6 minutes
(98° C., 20 seconds; 60° C., 30 seconds; 68° C., 3 minutes) 30 cycles
68° C., 4 minutes
As a result of this reaction, a 2.1-kb DNA fragment (DNA fragment EU1) comprising nucleotides 56477-58529 of SEQ ID NO: 1 was amplified by a reaction using dEU-AHEF, a dEU-NXR and Mer-16208 chromosomal DNA. A 2.1-kb DNA fragment (DNA fragment ED1) comprising nucleotides 59808-61863 of SEQ ID NO: 1 was amplified by a reaction using dED-XF, a dED-EHR and Mer-16208 chromosomal DNA. A 1.2-kb DNA fragment (DNA fragment TR1) comprising a thiostrepton resistance gene tsr was amplified by a reaction using TR-AF, TR-XR and S. azureus NBRC12744 chromosomal DNA. The DNA fragments EU1, ED1 and TR1 were purified using Wizard SV Gel and PCR Clean-Up System (Promega).
Total four DNA fragments, namely, the DNA fragment EU1 digested with restriction enzymes NdeI and HindIII, the DNA fragment ED1 digested with restriction enzymes XbaI and HindIII, the DNA fragment TR1 digested with restriction enzymes XbaI and NdeI, and the shuttle vector pMKOSCPR digested with a restriction enzyme HindIII were ligated to one another, using DNA Ligation Kit ver. 2.1 (Takara Bio Inc.). Thus, there was constructed an approximately 15.1-kb plasmid pMKOSCPR-EU-tsr-ED, in which an approximately 5.3-kb DNA fragment in which the thiostrepton resistance gene tsr had been inserted between the DNA fragments EU1 and ED1 was inserted into pMKOSCPR.
(3) Preparation of hbdE-Deficient Strain Using pMKOSCPR-EU-tsr-ED
Conjugal Escherichia coli S17-1 (ATCC47055) was transformed with the obtained pMKOSCPR-EU-tsr-ED by an electroporation method, so as to obtain an S17-1/pMKOSCPR-EU-tsr-ED strain. The obtained S17-1/pMKOSCPR-EU-tsr-ED strain was inoculated into 12 ml of LB medium (1% Bactotrypton, 0.5% yeast extract and 0.5% NaCl) containing 25 μg/ml kanamycin, followed by a shaking culture at 30° C. for 3 hours. Thereafter, the cells were collected, were then washed with 10 ml of LB medium twice, and were then suspended in 2 ml of LB medium. The obtained suspension was defined as a donor cell suspension.
At the same time of the preparation of the donor cell suspension, Mer-16208 was applied to an ISP4 medium (Becton, Dickinson and Company), and it was then cultured at 30° C. for 1 week. Thereafter, the spores were collected, and were then suspended in 1 ml of saline. The obtained suspension was defined as a receptor cell suspension.
500 μl of the obtained S17-1/pMKOSCPR-EU-tsr-ED strain donor cell suspension was mixed with 10 μl of Mer-16208 receptor cell suspension, and the obtained mixture was then applied to an ISP4 medium (Becton, Dickinson and Company). The mixture was cultured at 30° C. for 18 hours, and 2.5 ml of SNA (0.8% nutritive medium: Becton, Dickinson and Company, 0.4% agar) containing 2 mg/ml ribostamycin was laminated on the culture. The resultant was cultured at 30° C. for 7 days, so as to obtain a pMKOSCPR-EU-tsr-ED transformed strain resistant to ribostamycin.
The obtained pMKOSCPR-EU-tsr-ED transformed strain was inoculated into 25 ml of TSB medium that did not contain ribostamycin, and the obtained mixture was then subjected to a shaking culture at 30° C. for 2 weeks. It is to be noted that the plasmid vector pMKOSCPR had a low replication efficiency in Mer-16208, and that, if it is cultured in a medium containing no drug resistance marker (ribostamycin), Mer-16208 cannot retain the pMKOSCPR. The culture solution of the pMKOSCPR-EU-tsr-ED transformed strain was collected, and it was then washed with 10 ml of sterilized water twice and suspended in 10 ml of sterilized water. The appropriately diluted suspension was applied to a YMS agar medium (0.4% yeast extract 1% malt extract, 0.4% soluble starch, 2% agar and 10 mM calcium chloride) containing 25 μg/ml thiostrepton, and it was then cultured at 30° C. for 4 days. A single colony growing on the YMS medium containing thiostrepton was transferred to a YMS agar medium containing 25 μg/ml thiostrepton and a YMS agar medium containing 200 μg/ml ribostamycin, followed by a culture at 30° C. for 2 days.
After completion of the culture, a strain which was resistant to thiostrepton and was sensitive for ribostamycin was selected. The obtained strain was an hbdE-deficient strain, in which 1278 bp (nucleotides 58530-59807 of SEQ ID NO: 1) was deleted from the hbdE gene in the genome and a thiostrepton resistance gene was inserted into the deleted site, and this strain was defined as an Mer-16208 hbdE::tsr strain.
Example 5
Construction of Herboxidiene 17-O-methyl Transferase Gene (hbdF)-Deficient Strain
Based on the approximately 65-kb nucleotide sequence containing the DNA involved in the biosynthesis of herboxidiene determined in Example 3 (see SEQ ID NO: 1), it became clear that herboxidiene is biosynthesized in the biosynthetic pathway shown in FIG. 1. Thus, it was considered that a strain producing only the 17-demethyl product of herboxidiene could be obtained by disrupting only the methyl transferase gene hbdF thereof. Such hbdF-deficient strain was constructed by the following method.
(1) Preparation of Plasmid pMKOSCPR-FU-tsr-FD Used for Disrupting hbdF
Based on the nucleotide sequence shown in SEQ ID NO: 1, four types of primers, dFU-AHEF, dFU-NXR, dFD-XF and dFD-EHR, consisting of the following sequences, were synthesized (see SEQ ID NOS: 29, 30, 31 and 32 in the sequence listing).








dFU-AHEF:
5′-CCCATTAATAAGCTTGAATTCCTCCACGCCGAGACG



GTA-3′


 


dFU-NXR:
5′-CCCTCTAGACATATGGCTGTCCTTCCGGTCGCC-3′


 


dFD-XF:
5′-CCCTCTAGAGTGCCGCTGACCGCCCGA-3′


 


dFD-EHR:
5′-CCCAAGCTTGAATTCCGAGCGGTACGTCGCGTT-3′






Using these primers, PCR was carried out under the following conditions.
(Composition of PCR Reaction Mixture)















Sterilized purified water
31.5 μl  



10x KOD buffer
5 μl



dNTP mixed solution
5 μl



(dATP, dGTP, dTTP and dCTP; 2.5 mM each)




MgSO4 solution
3 μl



Dimethyl sulfoxide
2.5 μl  



dFU-AHEF or dFD-XF (50 pmol/μl)
0.5 μl  



dFU-NXR or dFD-EHR (50 pmol/μl)
0.5 μl  



Mer-16208 chromosomal DNA (100 ng/μl)
1 μl



KOD-plus-polymerase (1 u/μl, Toyobo Co., Ltd.)
1 μl









(Reaction Temperature Conditions)
95° C., 6 minutes
(98° C., 20 seconds; 60° C., 30 seconds; 68° C., 3 minutes) 30 cycles
68° C., 4 minutes
As a result of this reaction, a 2.1-kb DNA fragment (DNA fragment FU1) comprising nucleotides 55517-57571 of SEQ ID NO: 1 was amplified by a reaction using dFU-AHEF and dFU-NXR, and a 2.1-kb DNA fragment (DNA fragment FD1) comprising nucleotides 58445-60523 of SEQ ID NO: 1 was amplified by a reaction using dFD-XF and dFD-EHR. The DNA fragments FU1 and FD1 were purified using Wizard SV Gel and PCR Clean-Up System (Promega).
Total four DNA fragments, namely, the DNA fragment FU1 digested with restriction enzymes NdeI and HindIII, the DNA fragment FD1 digested with restriction enzymes XbaI and HindIII, the DNA fragment TR1 digested with restriction enzymes XbaI and NdeI, which was obtained in Example 4(2), and the shuttle vector pMKOSCPR digested with a restriction enzyme HindIII, which was obtained in Example 4(1), were ligated to one another, using DNA Ligation Kit ver. 2.1 (Takara Bio Inc.). Thus, there was constructed an approximately 15.1-kb plasmid pMKOSCPR-FU-tsr-FD, in which an approximately 5.3-kb DNA fragment in which the thiostrepton resistance gene tsr had been inserted between the DNA fragments FU1 and FD1 was inserted into pMKOSCPR.
(2) Preparation of hbdF-Deficient Strain Using pMKOSCPR-FU-tsr-FD
Conjugal Escherichia coli S17-1 (ATCC47055) was transformed with the obtained pMKOSCPR-FU-tsr-FD by an electroporation method, so as to obtain an S17-1/pMKOSCPR-FU-tsr-FD strain. The obtained S17-1/pMKOSCPR-FU-tsr-FD strain was inoculated into 12 ml of LB medium (1% Bactotrypton, 0.5% yeast extract and 0.5% NaCl) containing 25 μg/ml kanamycin, followed by a shaking culture at 30° C. for 3 hours. Thereafter, the cells were collected, were then washed with 10 ml of LB medium twice, and were then suspended in 2 ml of LB medium. The obtained suspension was defined as a donor cell suspension.
At the same time of the preparation of the donor cell suspension, Mer-16208 was applied to an ISP4 medium (Becton, Dickinson and Company), and it was then cultured at 30° C. for 1 week. Thereafter, the spores were collected, and were then suspended in 1 ml of saline. The obtained suspension was defined as a receptor cell suspension.
500 μl of the obtained S17-1/pMKOSCPR-FU-tsr-FD strain donor cell suspension was mixed with 10 μl of Mer-16208 receptor cell suspension, and the obtained mixture was then applied to an ISP4 medium (Becton, Dickinson and Company). The mixture was cultured at 30° C. for 18 hours, and 2.5 ml of SNA (0.8% nutritive medium: Becton, Dickinson and Company, 0.4% agar) containing 2 mg/ml ribostamycin was laminated on the culture. The resultant was cultured at 30° C. for 7 days, so as to obtain a pMKOSCPR-FU-tsr-FD transformed strain resistant to ribostamycin.
The obtained pMKOSCPR-FU-tsr-FD transformed strain was inoculated into 25 ml of TSB medium that did not contain ribostamycin, and the obtained mixture was then subjected to a shaking culture at 30° C. for 2 weeks. The culture solution of the pMKOSCPR-FU-tsr-FD transformed strain was collected, and it was then washed with 10 ml of sterilized water twice and suspended in 10 ml of sterilized water. The appropriately diluted suspension was applied to a YMS agar medium (0.4% yeast extract, 1% malt extract, 0.4% soluble starch, 2% agar and 10 mM calcium chloride) containing 25 μg/ml thiostrepton, and it was then cultured at 30° C. for 4 days. A single colony growing on the YMS medium containing thiostrepton was transferred to a YMS agar medium containing 25 μg/ml thiostrepton and a YMS agar medium containing 200 μg/ml ribostamycin, followed by a culture at 30° C. for 2 days.
After completion of the culture, a strain which was resistant to thiostrepton and was sensitive for ribostamycin was selected. The obtained strain was an hbdF-deficient strain, in which 873 bp (nucleotides 57572-58141 of SEQ ID NO: 1) was deleted from the hbdF gene in the genome and a thiostrepton resistance gene was inserted into the deleted site, and this strain was defined as an Mer-16208 hbdF::tsr strain.
Example 6
Construction of Herboxidiene 14,15-Epoxidase Gene (hbdD)-Deficient Strain
Based on the approximately 65-kb nucleotide sequence containing the DNA involved in the biosynthesis of herboxidiene determined in Example 3 (see SEQ ID NO: 1), it became clear that herboxidiene is biosynthesized in the biosynthetic pathway shown in FIG. 1. Thus, it was considered that a strain producing only the 14,15-olefin product of herboxidiene could be obtained by disrupting only the 14,15-epoxidase gene hbdD thereof. Such hbdD-deficient strain was constructed by the following method.
(1) Preparation of Plasmid pMKOSCPR-DU-tsr-DD Used for Disrupting hbdD
Based on the nucleotide sequence shown in SEQ ID NO: 1, four types of primers, dDU-AHEF, dDU-NXR, dDD-XF and dDD-EHR, consisting of the following sequences, were synthesized (see SEQ ID NOS: 33, 34, 35 and 36 in the sequence listing).








dDU-AHEF:
5′-CCCATTAATAAGCTTGAATTCCCGTACCGTCACCA



CGGA-3′


 


dDU-NXR:
5′-CCCTCTAGACATATGCGTGACGTTCCTTCCTCG-3′


 


dDD-XF:
5′-CCCTCTAGAGCGACCGGAAGGACAGCG-3′


 


dDD-EHR:
5′-CCCAAGCTTGAATTCGAGATGGCCCTCGTTCTT-3′






Using these primers, PCR was carried out under the following conditions.
(Composition of PCR Reaction Mixture)















Sterilized purified water
31.5 μl  



10x KOD buffer
5 μl



dNTP mixed solution
5 μl



(dATP, dGTP, dTTP and dCTP; 2.5 mM each)




MgSO4 solution
3 μl



Dimethyl sulfoxide
2.5 μl  



dDU-AHEF or dDD-XF (50 pmol/μl)
0.5 μl  



dDU-NXR or dDD-EHR (50 pmol/μl)
0.5 μl  



Mer-16208 chromosomal DNA (100 ng/μl)
1 μl



KOD-plus-polymerase (1 u/μl, Toyobo Co., Ltd.)
1 μl









(Reaction Temperature Conditions)
95° C., 6 minutes
(98° C., 20 seconds; 60° C., 30 seconds; 68° C., 3 minutes) 30 cycles
68° C., 4 minutes
As a result of this reaction, a 2.1-kb DNA fragment (DNA fragment DU1) comprising nucleotides 54058-56111 of SEQ ID NO: 1 was amplified by a reaction using dDU-AHEF and dDU-NXR, and a 2.1-kb DNA fragment (DNA fragment DD1) comprising nucleotides 57555-59606 of SEQ ID NO: 1 was amplified by a reaction using dDD-XF and dDD-EHR. The DNA fragments DU1 and DD1 were purified using Wizard SV Gel and PCR Clean-Up System (Promega).
Total four DNA fragments, namely, the DNA fragment DU1 digested with restriction enzymes NdeI and HindIII, the DNA fragment DD1 digested with restriction enzymes XbaI and HindIII, the DNA fragment TR1 digested with restriction enzymes XbaI and NdeI, which was obtained in Example 4(2), and the shuttle vector pMKOSCPR digested with a restriction enzyme HindIII, which was obtained in Example 4(1), were ligated to one another, using DNA Ligation Kit vet 2.1 (Takara Bio Inc.). Thus, there was constructed an approximately 15.1-kb plasmid pMKOSCPR-DU-tsr-DD, in which an approximately 5.3-kb DNA fragment in which the thiostrepton resistance gene tsr had been inserted between the DNA fragments DU1 and DD1 was inserted into pMKOSCPR.
(2) Preparation of hbdD-Deficient Strain Using pMKOSCPR-DU-tsr-DD
Conjugal Escherichia coli S17-1 (ATCC47055) was transformed with the obtained pMKOSCPR-DU-tsr-DD by an electroporation method, so as to obtain an S17-1/pMKOSCPR-DU-tsr-DD strain. The obtained S17-1/pMKOSCPR-DU-tsr-DD strain was inoculated into 12 ml of LB medium (1% Bactotrypton, 0.5% yeast extract and 0.5% NaCl) containing 25 μg/ml kanamycin, followed by a shaking culture at 30° C. for 3 hours. Thereafter, the cells were collected, were then washed with 10 ml of LB medium twice, and were then suspended in 2 ml of LB medium. The obtained suspension was defined as a donor cell suspension.
At the same time of the preparation of the donor cell suspension, Mer-16208 was applied to an ISP4 medium (Becton, Dickinson and Company), and it was then cultured at 30° C. for 1 week. Thereafter, the spores were collected, and were then suspended in 1 ml of saline. The obtained suspension was defined as a receptor cell suspension.
500 μl of the obtained S17-1/pMKOSCPR-DU-tsr-DD strain donor cell suspension was mixed with 10 μl of Mer-16208 receptor cell suspension, and the obtained mixture was then applied to an ISP4 medium (Becton, Dickinson and Company). The mixture was cultured at 30° C. for 18 hours, and 2.5 ml of SNA (0.8% nutritive medium: Becton, Dickinson and Company, 0.4% agar) containing 2 mg/ml ribostamycin was laminated on the culture. The resultant was cultured at 30° C. for 7 days, so as to obtain a pMKOSCPR-DU-tsr-DD transformed strain resistant to ribostamycin.
The obtained pMKOSCPR-DU-tsr-DD transformed strain was inoculated into 25 ml of TSB medium that did not contain ribostamycin, and the obtained mixture was then subjected to a shaking culture at 30° C. for 2 weeks. The culture solution of the pMKOSCPR-DU-tsr-DD transformed strain was collected, and it was then washed with 10 ml of sterilized water twice and suspended in 10 ml of sterilized water. The appropriately diluted suspension was applied to a YMS agar medium (0.4% yeast extract, 1% malt extract, 0.4% soluble starch, 2% agar and 10 mM calcium chloride) containing 25 μg/ml thiostrepton, and it was then cultured at 30° C. for 4 days. A single colony growing on the YMS medium containing thiostrepton was transferred to a YMS agar medium containing 25 μg/ml thiostrepton and a YMS agar medium containing 200 μg/ml ribostamycin, followed by a culture at 30° C. for 2 days.
After completion of the culture, a strain which was resistant to thiostrepton and was sensitive for ribostamycin was selected. The obtained strain was an hbdD-deficient strain, in which 1443 bp (nucleotides 56112-57554 of SEQ ID NO: 1) was deleted from the hbdD gene in the genome and a thiostrepton resistance gene was inserted into the deleted site, and this strain was defined as an Mer-16208 hbdD::tsr strain.
Example 7
Construction of Herboxidiene Polyketide Synthase Gene (hbdAIII)-Deficient Strain
Based on the approximately 65-kb nucleotide sequence containing the DNA involved in the biosynthesis of herboxidiene determined in Example 3 (see SEQ ID NO: 1), it became clear that herboxidiene is biosynthesized in the biosynthetic pathway shown in FIG. 1. Since a protein HbdAIII encoded by hbdAIII thereof had the highest identity to the amino acid sequence of the polyketide synthase Orf17 of Streptomyces aizunensis (54% identity), the hbdAIII was considered to be a polyketide synthase gene, which constitutes the basic skeleton of herboxidiene, together with hbdAI and hbdAII. Thus, in order to confirm that a strain that does not produce herboxidiene can be produced by disrupting the hbdAIII, a hbdAIII-deficient strain was constructed by the following method.
(1) Preparation of Plasmid pMKOSCPR-A3U-tsr-A3D Used for Disrupting hbdAIII
Based on the nucleotide sequence shown in SEQ ID NO: 1, four types of primers, dA3U-AHFE, dA3U-NXR, dA3D-XF and dA3D-EHR, consisting of the following sequences, were synthesized (see SEQ ID NOS: 37, 38, 39 and 40 in the sequence listing).








dA3U-AHEF:
5′-CCCATTAATAAGCTTGAATTCCGTCAACTTCCGCG



ATGT-3′


 


dA3U-NXR:
5′-CCCTCTAGACATATGGGTCATGACATCTCCAAG-3′


 


dA3D-XF:
5′-CCCTCTAGATACCGACGTACCCACCGA-3′


 


dA3D-EHR:
5′-CCCAAGCTTGAATTCCCATGTGCATGATCGATT-3′






Using these primers, PCR was carried out under the following conditions.
(Composition of PCR Reaction Mixture)















Sterilized purified water
31.5 μl 



10x KOD buffer
5 μl



dNTP mixed solution
5 μl



(dATP, dGTP, dTTP and dCTP; 2.5 mM each)




MgSO4 solution
3 μl



Dimethyl sulfoxide
2.5 μl  



dA3U-AHEF or dA3D-XF (50 pmol/μl)
0.5 μl  



dA3U-NXR or dA3D-EHR (50 pmol/μl)
0.5 μl  



Mer-16208 chromosomal DNA (100 ng/μl)
1 μl



KOD-plus-polymerase (1 u/μl, Toyobo Co., Ltd.)
1 μl









(Reaction Temperature Conditions)
95° C., 6 minutes
(98° C., 20 seconds; 60° C., 30 seconds; 68° C., 3 minutes) 30 cycles
68° C., 4 minutes
As a result of this reaction, a 2.1-kb DNA fragment (DNA fragment A3U1) comprising nucleotides 47816-49897 of SEQ ID NO: 1 was amplified by a reaction using dA3U-AHEF and dA3U-NXR, and a 2.0-kb DNA fragment (DNA fragment A3D1) comprising nucleotides 55991-58022 of SEQ ID NO: 1 was amplified by a reaction using dA3D-XF and dA3D-EHR. The DNA fragments A3U1 and A3D1 were purified using Wizard SV Gel and PCR Clean-Up System (Promega).
Total four DNA fragments, namely, the DNA fragment A3U1 digested with restriction enzymes NdeI and HindIII, the DNA fragment A3D1 digested with restriction enzymes XbaI and the DNA fragment TR1 digested with restriction enzymes XbaI and NdeI, which was obtained in Example 4(2), and the shuttle vector pMKOSCPR digested with a restriction enzyme HindIII, which was obtained in Example 4(1), were ligated to one another, using DNA Ligation Kit vet 2.1 (Takara Bio Inc.). Thus, there was constructed an approximately 15.1-kb plasmid pMKOSCPR-A3U-tsr-A3D, in which an approximately 5.3-kb DNA fragment in which the thiostrepton resistance gene tsr had been inserted between the DNA fragments A3U1 and A3D1 was inserted into pMKOSCPR.
(2) Preparation of hbdAIII-Deficient Strain Using pMKOSCPR-A3U-tsr-A3D
Conjugal Escherichia coli S17-1 (ATCC47055) was transformed with the obtained pMKOSCPR-A3U-tsr-A3D by an electroporation method, so as to obtain an S17-1/pMKOSCPR-A3U-Ar-A3D strain. The obtained S17-1/pMKOSCPR-A3U-tsr-A3D strain was inoculated into 12 ml of LB medium (1% Bactotrypton, 0.5% yeast extract and 0.5% NaCl) containing 25 μg/ml kanamycin, followed by a shaking culture at 30° C. for 3 hours. Thereafter, the cells were collected, were then washed with 10 ml of LB medium twice, and were then suspended in 2 ml of LB medium. The obtained suspension was defined as a donor cell suspension.
At the same time of the preparation of the donor cell suspension, Mer-16208 was applied to an ISP4 medium (Becton, Dickinson and Company), and it was then cultured at 30° C. for 1 week. Thereafter, the spores were collected, and were then suspended in 1 ml of saline. The obtained suspension was defined as a receptor cell suspension.
500 μl of the obtained S17-1/pMKOSCPR-A3U-tsr-A3D strain donor cell suspension was mixed with 10 μl of Mer-16208 receptor cell suspension, and the obtained mixture was then applied to an ISP4 medium (Becton, Dickinson and Company). The mixture was cultured at 30° C. for 18 hours, and 2.5 ml of SNA (0.8% nutritive medium: Becton, Dickinson and Company, 0.4% agar) containing 2 mg/ml ribostamycin was laminated on the culture. The resultant was cultured at 30° C. for 7 days, so as to obtain a pMKOSCPR-A3U-tsr-A3D transformed strain resistant to ribostamycin.
The obtained pMKOSCPR-A3U-tsr-A3D transformed strain was inoculated into 25 ml of TSB medium that did not contain ribostamycin, and the obtained mixture was then subjected to a shaking culture at 30° C. for 2 weeks. The culture solution of the pMKOSCPR-A3U-tsr-A3D transformed strain was collected, and it was then washed with 10 ml of sterilized water twice and suspended in 10 ml of sterilized water. The appropriately diluted suspension was applied to a YMS agar medium (0.4% yeast extract, 1% malt extract, 0.4% soluble starch, 2% agar and 10 mM calcium chloride) containing 25 μg/ml thiostrepton, and it was then cultured at 30° C. for 4 days. A single colony growing on the YMS medium containing thiostrepton was transferred to a YMS agar medium containing 25 μg/ml thiostrepton and a YMS agar medium containing 200 μg/ml ribostamycin, followed by a culture at 30° C. for 2 days.
After completion of the culture, a strain which was resistant to thiostrepton and was sensitive for ribostamycin was selected. The obtained strain was an hbdA/H-deficient strain, in which 6093 bp (nucleotides 49898-55990 of SEQ ID NO: 1) was deleted from the hbdAIII gene in the genome and a thiostrepton resistance gene was inserted into the deleted site, and this strain was defined as an Mer-16208 hbdAIII::tsr strain.
Example 8
Production of Herboxidiene Transcription Factor Gene (hbdR)-Deficient Strain
Based on the approximately 65-kb nucleotide sequence containing the DNA involved in the biosynthesis of herboxidiene determined in Example 3 (see SEQ ID NO: 1), it became clear that herboxidiene is biosynthesized in the biosynthetic pathway shown in FIG. 1. Since a protein HbdR encoded by hbdR thereof had the highest identity to the amino acid sequence of the transcription factor SACE—4536 of Saccharopolyspora erythraea (57% identity), the hbdR was considered to be a gene encoding the transcription factor of the herboxidiene biosynthetic gene. Thus, in order to confirm that a strain whose herboxidiene productivity is changed can be produced by disrupting the hbdR, a hbdR-deficient strain was constructed by the following method.
(1) Preparation of Plasmid pMKOSCPR-RU-tsr-RD Used for Disrupting hbdR
Based on the nucleotide sequence shown in SEQ ID NO: 1, four types of primers, dRU-AHEF, dRU-NXR, dRD-XF and dRD-EHR, consisting of the following sequences, were synthesized (see SEQ ID NOS: 41, 42, 43 and 44 in the sequence listing).








dRU-AHEF:
5′-CCCATTAATAAGCTTGAATTCGGTGGTGACGGACT



CGAT-3′


 


dRU-NXR:
5′-CCCTCTAGACATATGTGGCCTCCTCGGTAGACA-3′


 


dRD-XF:
5′-CCCTCTAGAGGACCCGAGCTGGGGCTA-3′


 


dRD-EHR:
5′-CCCAAGCTTGAATTCGTTGATGACGCAGTGGAC-3′






Using these primers, PCR was carried out under the following conditions.
(Composition of PCR Reaction Mixture)















Sterilized purified water
31.5 μl  



10x KOD buffer
5 μl



dNTP mixed solution
5 μl



(dATP, dGTP, dTTP and dCTP; 2.5 mM each)




MgSO4 solution
3 μl



Dimethyl sulfoxide
2.5 μl  



dRU-AHEF or dRD-XF (50 pmol/μl)
0.5 μl  



dRU-NXR or dRD-EHR (50 pmol/μl)
0.5 μl  



Mer-16208 chromosomal DNA (100 ng/μl)
1 μl



KOD-plus-polymerase (1 u/μl, Toyobo Co., Ltd.)
1 μl









(Reaction Temperature Conditions)
95° C., 6 minutes
(98° C., 20 seconds; 60° C., 30 seconds; 68° C., 3 minutes) 30 cycles
68° C., 4 minutes
As a result of this reaction, a 2.0-kb DNA fragment (DNA fragment RU1) comprising nucleotides 4658-6677 of SEQ ID NO: 1 was amplified by a reaction using dRU-AHEF and dRU-NXR, and a 2.0-kb DNA fragment (DNA fragment RD1) comprising nucleotides 7716-9740 of SEQ ID NO: 1 was amplified by a reaction using dRD-XF and dRD-EHR. The DNA fragments RU1 and RD1 were purified using Wizard SV Gel and PCR Clean-Up System (Promega).
Total four DNA fragments, namely, the DNA fragment RU1 digested with restriction enzymes NdeI and HindIII, the DNA fragment RD1 digested with restriction enzymes XbaI and HindIII, the DNA fragment TR1 digested with restriction enzymes XbaI and NdeI, which was obtained in Example 5(2), and the shuttle vector pMKOSCPR digested with a restriction enzyme HindIII, which was obtained in Example 5(1), were ligated to one another, using DNA Ligation Kit vet 2.1 (Takara Bio Inc.). Thus, there was constructed an approximately 15.0-kb plasmid pMKOSCPR-RU-tsr-RD, in which an approximately 5.3-kb DNA fragment in which the thiostrepton resistance gene tsr had been inserted between the DNA fragments RU1 and RD1 was inserted into pMKOSCPR.
(2) Preparation of hbdR-Deficient Strain Using pMKOSCPR-RU-tsr-RD
Conjugal Escherichia coli S17-1 (ATCC47055) was transformed with the obtained pMKOSCPR-RU-tsr-RD by an electroporation method, so as to obtain an S17-1/pMKOSCPR-RU-tsr-RD strain. The obtained 517-1/pMKOSCPR-RU-tsr-RD strain was inoculated into 12 ml of LB medium (1% Bactotrypton, 0.5% yeast extract and 0.5% NaCl) containing 25 μg/ml kanamycin, followed by a shaking culture at 30° C. for 3 hours. Thereafter, the cells were collected, were then washed with 10 ml of LB medium twice, and were then suspended in 2 ml of LB medium. The obtained suspension was defined as a donor cell suspension.
At the same time of the preparation of the donor cell suspension, Mer-16208 was applied to an ISP4 medium (Becton, Dickinson and Company), and it was then cultured at 30° C. for 1 week. Thereafter, the spores were collected, and were then suspended in 1 ml of saline. The obtained suspension was defined as a receptor cell suspension.
500 μl of the obtained S17-1/pMKOSCPR-RU-tsr-RD strain donor cell suspension was mixed with 10 μl of Mer-16208 receptor cell suspension, and the obtained mixture was then applied to an ISP4 medium (Becton, Dickinson and Company). The mixture was cultured at 30° C. for 18 hours, and 25 ml of SNA (0.8% nutritive medium: Becton, Dickinson and Company, 0.4% agar) containing 2 mg/ml ribostamycin was laminated on the culture. The resultant was cultured at 30° C. for 7 days, so as to obtain a pMKOSCPR-RU-tsr-RD transformed strain resistant to ribostamycin.
The obtained pMKOSCPR-RU-tsr-RD transformed strain was inoculated into 25 ml of TSB medium that did not contain ribostamycin, and the obtained mixture was then subjected to a shaking culture at 30° C. for 2 weeks. The culture solution of the pMKOSCPR-RU-tsr-RD transformed strain was collected, and it was then washed with 10 ml of sterilized water twice and suspended in 10 ml of sterilized water. The appropriately diluted suspension was applied to a YMS agar medium (0.4% yeast extract, 1% malt extract, 0.4% soluble starch, 2% agar and 10 mM calcium chloride) containing 25 μg/ml thiostrepton, and it was then cultured at 30° C. for 4 days. A single colony growing on the YMS medium containing thiostrepton was transferred to a YMS agar medium containing 25 μg/ml thiostrepton and a YMS agar medium containing 200 μg/ml ribostamycin, followed by a culture at 30° C. for 2 days.
After completion of the culture, a strain which was resistant to thiostrepton and was sensitive for ribostamycin was selected. The obtained strain was an hbdR-deficient strain, in which 1038 bp (nucleotides 6678-7715 of SEQ ID NO: 1) was deleted from the hbdR gene in the genome and a thiostrepton resistance gene was inserted into the deleted site, and this strain was defined as an Mer-16208 hbdR::tsr strain.
Example 9
Test Regarding Productivity of Herboxidiene and Analogue Thereof by Herboxidiene Biosynthetic Gene hbdE-Deficient Strain
250 μl of the frozen stock of the Mer-16208 hbdE::tsr strain obtained in Example 4 was inoculated into 25 ml of a seed culture medium (2% potato starch, 2% glucose, 2% soybean powder (Honen SoyPro (registered trademark); manufactured by J-OIL MILLS Inc.), 0.5% yeast extract, 0.25% NaCl, 0.32% CaCO3, 0.0005% CuSO4, 0.0005% ZnSO4.7H2O, 0.0005% MnCl2.4H2O, pH7.4), and it was then cultured at 28° C. for 3 days.
4 ml of the obtained seed culture solution was inoculated into 400 ml of a main culture medium (2% potato starch, 2% glucose, 2% soybean powder, 0.5% yeast extract, 0.25% NaCl, 0.32% CaCO3, 0.0005% CuSO4, 0.0005% ZnSO4.7H2O, 0.0005% MnCl2.4H2O, pH7.4), and it was then cultured at 28° C. for 7 days.
After completion of the culture, to 600 μl of the obtained culture solution, acetonitrile was added in an equal amount, for extraction. A supernatant obtained by centrifuging the extract was subjected to high performance liquid chromatography (HPLC) under the conditions as shown below, so as to measure the amounts of herboxidiene and analogues thereof. The measurement results are shown in Table 1.
Example 10
Test Regarding Productivity of Herboxidiene and Analogue Thereof by Herboxidiene Biosynthetic Gene hbdF-Deficient Strain
250 μl of the frozen stock of the Mer-16208 hbdF::tsr strain obtained in Example 5 was inoculated into 25 ml of a seed culture medium (2% potato starch, 2% glucose, 2% soybean powder, 0.5% yeast extract, 0.25% NaCl, 0.32% CaCO3, 0.0005% CuSO4, 0.0005% ZnSO4.7H2O, 0.0005% MnCl2.4H2O, pH7.4), and it was then cultured at 28° C. for 3 days.
1 ml of the obtained seed culture solution was inoculated into 100 ml of a main culture medium (2% potato starch, 2% glucose, 2% soybean powder, 0.5% yeast extract, 0.25% NaCl, 0.32% CaCO3, 0.0005% CuSO4, 0.0005% ZnSO4.7H2O, 0.0005% MnCl2.4H2O, pH7.4), and it was then cultured at 28° C. for 3 days.
After completion of the culture, to 600 μl of the obtained culture solution, acetonitrile was added in an equal amount, for extraction. A supernatant obtained by centrifuging the extract was subjected to HPLC under the conditions as shown below, so as to measure the amounts of herboxidiene and analogues thereof. The measurement results are shown in Table 1.
Example 11
Test Regarding Productivity of Herboxidiene and Analogue Thereof by Herboxidiene Biosynthetic Gene hbdD-Deficient Strain
250 μl of the frozen stock of the Mer-16208 hbdD::tsr strain obtained in Example 6 was inoculated into 25 ml of a seed culture medium (2% potato starch, 2% glucose, 2% soybean powder, 0.5% yeast extract, 0.25% NaCl, 0.32% CaCO3, 0.0005% CuSO4, 0.0005% ThSO4.7H2O, 0.0005% MnCl2.4H2O, pH7.4), and it was then cultured at 28° C. for 3 days.
2 ml of the obtained seed culture solution was inoculated into 200 ml of a main culture medium (2% potato starch, 2% glucose, 2% soybean powder, 0.5% yeast extract, 0.25% NaCl, 0.32% CaCO3, 0.0005% CuSO4, 0.0005% ZnSO4.7H2O, 0.0005% MnCl2.4H2O, 2% β-cyclodextrin, pH7.4), and it was then cultured at 28° C. for 3 days.
After completion of the culture, to 600 μl of the obtained culture solution, acetonitrile was added in an equal amount, for extraction. A supernatant obtained by centrifuging the extract was subjected to HPLC under the conditions as shown below, so as to measure the amounts of herboxidiene and analogues thereof. The measurement results are shown in Table 1.
Example 12
Test Regarding Productivity of Herboxidiene and Analogue Thereof by Herboxidiene Biosynthetic Gene hbdAIII-Deficient Strain
250 μl of the frozen stock of the Mer-16208 hbdAIII::tsr strain obtained in Example 7 was inoculated into 25 ml of a seed culture medium (2% potato starch, 2% glucose, 2% soybean powder, 0.5% yeast extract, 0.25% NaCl, 0.32% CaCO3, 0.0005% CuSO4, 0.0005% ZnSa4.7H2O, 0.0005% MnCl2.4H2O, pH7.4), and it was then cultured at 28° C. for 3 days.
600 μl of the obtained seed culture solution was inoculated into 60 ml of a main culture medium (2% potato starch, 2% glucose, 2% soybean powder, 0.5% yeast extract, 0.25% NaCl, 0.32% CaCO3, 0.0005% CuSO4, 0.0005% ZnSO4.7H2O, 0.0005% MnCl2.4H2O, pH7.4), and it was then cultured at 28° C. for 3 days.
After completion of the culture, to 600 μl of the obtained culture solution, acetonitrile was added in an equal amount, for extraction. A supernatant obtained by centrifuging the extract was subjected to HPLC under the conditions as shown below, so as to measure the amounts of herboxidiene and analogues thereof. The measurement results are shown in Table 1.
Example 13
Test Regarding Productivity of Herboxidiene and Analogue Thereof by Herboxidiene Biosynthetic Gene hbdR-Deficient Strain
250 μl of the frozen stock of the Mer-16208 hbdR tsr strain obtained in Example 8 was inoculated into 25 ml of a seed culture medium (2% potato starch, 2% glucose, 2% soybean powder, 0.5% yeast extract, 0.25% NaCl, 0.32% CaCO3, 0.0005% CuSO4, 0.0005% ZnSO4.7H2O, 0.0005% MnCl2.4H2O, pH7.4), and it was then cultured at 28° C. for 3 days.
600 μl of the obtained seed culture solution was inoculated into 60 ml of a main culture medium (2% potato starch, 2% glucose, 2% soybean powder, 0.5% yeast extract 0.25% NaCl, 0.32% CaCO3, 0.0005% CuSO4, 0.0005% ZnSO4.7H2O, 0.0005% MnCl2.4H2O, pH7.4), and it was then cultured at 28° C. for 3 days.
After completion of the culture, to 600 μl of the obtained culture solution, acetonitrile was added in an equal amount, for extraction. A supernatant obtained by centrifuging the extract was subjected to HPLC under the conditions as shown below, so as to measure the amounts of herboxidiene and analogues thereof. The measurement results are shown in Table 1.
Example 14
Test Regarding Productivity of Herboxidiene and Analogue Thereof by Herboxidiene-Producing Strain, Mer-16208
250 μl of the frozen stock of Mer-16208 was inoculated into 25 ml of a seed culture medium (2% potato starch, 2% glucose, 2% soybean powder, 0.5% yeast extract, 0.25% NaCl, 0.32% CaCO3, 0.0005% CuSO4, 0.0005% ZnSO4.7H2O, 0.0005% MnCl2.4H2O, pH7.4), and it was then cultured at 28° C. for 3 days.
600 μl of the obtained seed culture solution was inoculated into 60 ml of a main culture medium (2% potato starch, 2% glucose, 2% soybean powder, 0.5% yeast extract, 0.25% NaCl, 0.32% CaCO3, 0.0005% CuSO4, 0.0005% ZnSO4.7H2O, 0.0005% MnCl2.4H2O, pH7.4), and it was then cultured at 28° C. for 3 days.
After completion of the culture, to 600 μl of each of the obtained culture solutions, acetonitrile was added in an equal amount, for extraction. A supernatant obtained by centrifuging the extract was subjected to HPLC under the conditions as shown below, so as to measure the amounts of herboxidiene and analogues thereof. The measurement results are shown in Table 1.
HPLC conditions applied in Examples 9-14
Analyzer: Agilent 1100 series
Column: Unison UK-C18 (4.6 mm×50 mm, 3 μm)
Mobile phase A: water/acetonitrile/formic acid=1000/10/1
Mobile phase B: acetonitrile/water/formic acid=1000/10/1
Gradient: 30%-70% mobile phase B (0 to 4 minutes)


    
    
        70%-100% mobile phase B (4 to 4.5 minutes)
        100% mobile phase B (4.5 to 6 minutes)
        100%-30% mobile phase B (6 to 6.01 minutes)
        30% mobile phase B (6.01 to 7 minutes)

Flow rate: 2.0 mL/min

Detection: UV 254 nm

Injection volume: 10 μl

Column temperature: 30° C.

Analysis time: 7 minutes

Retention time: herboxidiene, 3.33 minutes; HX354, 4.94 minutes; HX355, 3.83 minutes; HX356, 2.78 minutes; MW392, 4.91 minutes

    
    















TABLE 1







HX356
Herboxidiene
HX355
MW392
HX354



(mg/L)
(mg/L)
(mg/L)
(mg/L)
(mg/L)





















Mer-16208
0.00
0.00
9.40
0.00
23.26


hbdE::tsr


strain


Mer-16208
90.63
0.00
5.87
0.00
0.00


hbdF::tsr


strain


Mer-16208
0.00
0.00
0.00
35.82
0.00


hbdD::tsr


strain


Mer-16208
0.00
0.00
0.00
0.00
0.00


hbdAIII::tsr


strain


Mer-16208
0.00
0.60
0.65
0.00
0.00


hbdR::tsr


strain


Mer-16208
0.00
78.64
0.65
0.00
0.00









It was confirmed that the Mer-16208 hbdAIII::tsr strain as an hbdAIII-deficient strain did not produce herboxidiene and analogues thereof. In addition, it was confirmed that the amount of herboxidiene produced by the Mer-16208 hbdR::tsr strain as an hbdR-deficient strain was significantly smaller than that produced by Mer-16208.
Example 15
Isolation and Purification of HX354 and HX355, and Confirmation of Structures Thereof
80 g of salt was added to a supernatant obtained by centrifuging 400 ml of the cell suspension obtained in Example 9, and the pH of the suspension was then adjusted to pH 2-3 by addition of 2 mol/L hydrochloric acid. Thereafter, 400 ml of ethyl acetate was added to the suspension, and the mixture was then intensively stirred and was extracted. Centrifugation was carried out. Anhydrous sodium sulfate was added to the obtained ethyl acetate layer to remove water from the ethyl acetate layer. Filtration was carried out, and the filtrate was washed with an adequate amount of ethyl acetate. Thereafter, the resultant was subjected to an evaporator, and ethyl acetate was distilled away. The obtained dry solid was dissolved in 1.5 ml of methanol, and the peaks of HX354 and HX355 were then fractionated by preparative HPLC. The solvent was distilled away from these fraction samples, so as to obtain 5 mg of HX354 and 2 mg of HX355.
(Preparative HPLC Conditions)
Preparatory device: Agilent 1100 series, preparatory autosampler
Column: Zorbax RX-C18 (9.4 mm×250 mm, 5 μm)
Mobile phase A: water
Mobile phase B: acetonitrile
Gradient: 20% mobile phase B (0 to 1 minute)


    
    
        20%-100% mobile phase B (1 to 8 minutes)
        100% mobile phase B (8 to 14 minutes)
        100%-20% mobile phase B (14 to 15 minutes)
        20% mobile phase B (15 to 18 minutes)

Flow rate: 3.0 ml/min

Detection: UV 254 nm

Injection volume: 50 μl

Column temperature: 40° C.

Analysis time: 18 minutes

Retention time: HX354, 11.6 minutes; HX355, 10.3 minutes

    
    






Physical Values of HX354 (1)
1H-NMR (500 MHz, CD3OD) δ (ppm): 6.32 (dd, 1H, J=15, 11 Hz, H10), 5.94 (d, 1H, J=11 Hz, H9), 5.49 (dd, 1H, J=15, 9 Hz, H11), 3.79 (m, 1H, H3), 3.39 (s, 3H, H25), 3.37 (d, 1H, J=10 Hz, H7), 3.13 (m, 1H, H17), 2.64 (d, 1H, J=10 Hz, H15), 2.48 (dd, 1H, J=16, 8 Hz, H2a), 2.47 (overlap, 1H, H12), 2.41 (dd, 1H, J=16, 6 Hz, H2b), 1.91 (dd, 1H, J=13, 4 Hz, H13a), 1.88 (m, 1H, H5a), 1.74 (m, 1H, H4a), 1.71 (s, 3H, H21), 1.62 (m, 1H, H18a), 1.56 (m, 1H, H18b), 1.56 (m, 1H, H6), 1.44 (m, 1H, H16), 1.36 (m, 1H, H4b), 1.32 (m, 1H, H5b), 1.29 (s, 3H, H23), 1.19 (dd, 1H, J=13, 11 Hz, H13b), 1.07 (d, 3H, J=7, H22), 0.90 (t, 3H, J=8, H19), 0.84 (d, 3H, J=7, H24), 0.71 (d, 3H, J=7, H20)
13C-NMR (125 MHz, CD3OD) δ (ppm): 175.19 (C1), 140.76 (C11), 136.17 (C8), 129.66 (C9), 126.54 (C10), 92.19 (C7), 85.72 (C17), 75.48 (C3), 67.78 (C15), 61.85 (C14), 58.45 (C25), 48.13 (C13), 42.28 (C2), 37.52 (C16), 36.56 (C12), 33.50 (C5), 33.40 (C6), 32.81 (C4), 24.90 (C18), 22.71 (C22), 18.09 (C20), 16.84 (C23), 12.07 (C21), 11.80 (C24), 10.13 (C19)
ESI-MS: m/z=421 [M-H]−




Physical Values of HX355 (2)
1H-NMR (500 MHz, CD3OD) δ (ppm): 6.30 (dd, 1H, J=15, 11 Hz, H10), 5.91 (d, 1H, J=11 Hz, H9), 5.48 (dd, 1H, J=15, 9 Hz, H11), 3.76 (m, 1H, H3), 3.44 (m, 1H, H17), 334 (d, 1H, J=10 Hz, H7), 2.63 (d, 1H, J=9 Hz, H15), 2.46 (dd, 1H, J=16, 7 Hz, H2a), 2.46 (overlap, 1H, H12), 2.38 (dd, 1H, J=16, 6 Hz, H2b), 1.90 (dd, 1H, J=13, 5 Hz, H13a), 1.86 (m, 1H, H5a), 1.71 (m, 1H, H4a), 1.69 (s, 3H, H21), 1.53 (m, 2H, H6 and H18a), 1.44 (m, 1H, H18b), 133 (m, 2H, H4b and H16), 1.27 (s, 3H, H23), 1.27 (m, 1H, H5b), 1.17 (dd, 1H, J=13, 11 Hz, H13b), 1.04 (d, 3H, J=7, H22), 0.93 (t, 3H, J=8, H19), 0.84 (d, 3H, J=7, H24), 0.69 (d, 3H, J=7, H20)
13C-NMR (125 MHz, CD3OD) δ (ppm): 175.19 (C1), 140.73 (C11), 136.16 (C8), 129.67 (C9), 126.51 (C10), 92.20 (C7), 75.80 (C17), 75.52 (C3), 68.05 (C15), 61.74 (C14), 48.12 (C13), 42.33 (C2), 39.79 (C16), 36.49 (C12), 33.48 (C5), 33.42 (C6), 32.82 (C4), 28.83 (C18), 22.65 (C22), 18.11 (C20), 16.83 (C23), 12.11 (C21), 11.57 (C24), 10.80 (C19)
ESI-MS: m/z=407 [M-H]−
As a result, it was confirmed that the Mer-16208 hbdE::tsr strain as an hbdE-deficient strain did not produce herboxidiene, but it produced HX354 as a 18-deoxy product of herboxidiene and HX355 as a 18-deoxy, 17-O-demethyl product of herboxidiene.
Example 16
Isolation and Purification of HX356 and Confirmation of Structure Thereof
20 g of salt was added to a supernatant obtained by centrifuging 100 ml of the cell suspension obtained in Example 10, and the pH of the suspension was then adjusted to pH 2-3 by addition of 2 mol/L hydrochloric acid. Thereafter, 100 ml of ethyl acetate was added to the suspension, and the mixture was then intensively stirred and was extracted. Centrifugation was carried out Anhydrous sodium sulfate was added to the obtained ethyl acetate layer to remove water from the ethyl acetate layer. Filtration was carried out, and the filtrate was washed with an adequate amount of ethyl acetate. Thereafter, the resultant was subjected to an evaporator, and the ethyl acetate was distilled away. The obtained dry solid was dissolved in 1.5 ml of methanol, and the peak of HX356 was then fractionated by preparative HPLC. The solvent was distilled away from this fraction sample, so as to obtain 4.5 mg of HX356.
(Preparative HPLC Conditions)
Preparatory device: Agilent 1100 series, preparatory autosampler
Column: Zorbax RX-C18 (9.4 mm×250 mm, 5 μm)
Mobile phase A: water
Mobile phase B: acetonitrile
Gradient: 20% mobile phase B (0 to 1 minute)


    
    
        20%-100% mobile phase B (1 to 8 minutes)
        100% mobile phase B (8 to 14 minutes)
        100%-20% mobile phase B (14 to 15 minutes)
        20% mobile phase B (15 to 18 minutes)

Flow rate: 3.0 ml/min

Detection: UV 254 nm

Injection volume: 50 μl

Column temperature: 40° C.

Analysis time: 18 minutes

Retention time: HX356, 9.0 minutes

    
    






Physical Values of HX356 (3)
1H-NMR (500 MHz, CD3OD) δ (ppm): 6.30 (dd, 1H, J=15, 11 Hz, H10), 5.91 (d, 1H, J=11 Hz, H9), 5.48 (dd, 1H, J=15, 9 Hz, H11), 3.77 (m, 2H, H18 and H3), 3.34 (d, 1H, J=10 Hz, 1H, H7), 327 (t, 1H, J=6 Hz, H17), 2.66 (d, 1H, J=5 Hz, H15), 2.46 (overlap, 1H, H12), 2.46 (dd, 1H, J=15, 8 Hz, H2a), 2.38 (dd, 1H, J=15, 6 Hz, H2b), 1.92 (dd, 1H, J=14, 5 Hz, H13a), 1.85 (m, 1H, H5a), 1.71 (m, 1H, H4a), 1.64 (s, 3H, H21), 1.54 (m, 1H, H6), 1.46 (m, 1H, H16), 1.33 (m, 1H, H4b), 1.30 (s, 3H, H23), 1.25 (m, 1H, H5b), 1.17 (dd, 1H, J=14, 11 Hz, H13b), 1.12 (d, 3H, J=7, H19), 1.04 (d, 3H, J=7, H22), 0.87 (d, 3H, J=7, H24), 0.69 (d, 3H, J=7, H20)
13C-NMR (125 MHz, CD3OD) δ (ppm): 175.36 (C1), 140.70 (C11), 136.19 (C8), 129.66 (C9), 126.54 (C10), 92.19 (C7), 78.24 (C17), 75.55 (C3), 69.59 (C18), 67.83 (C15), 62.23 (C14), 48.09 (C13), 42.42 (C2), 37.12 (C16), 36.50 (C12), 33.48 (C5), 33.43 (C6), 32.82 (C4), 22.66 (C22), 19.63 (C19), 18.11 (C20), 16.80 (C23), 12.12 (C21), 11.90 (C24)
ESI-MS: m/z=423 [M-H]−
As a result, it was confirmed that the Mer-16208 hbdF::tsr strain as an hbdF-deficient strain did not produce herboxidiene, but it produced HX356 as a 17-O-demethyl product of herboxidiene and HX355 as a 18-deoxy, 17-O-demethyl product of herboxidiene.
Example 17
Isolation and Purification of MW392 and Confirmation of Structure Thereof
40 g of salt was added to a supernatant obtained by centrifuging 200 ml of the cell suspension obtained in Example 11, and the pH of the suspension was then adjusted to pH 2-3 by addition of 2 mol/L hydrochloric acid. Thereafter, 200 ml of ethyl acetate was added to the suspension, and the mixture was then intensively stirred and was extracted. Centrifugation was carried out. Anhydrous sodium sulfate was added to the obtained ethyl acetate layer to remove water from the ethyl acetate layer. Filtration was carried out, and the filtrate was washed with an adequate amount of ethyl acetate. Thereafter, the resultant was subjected to an evaporator, and the ethyl acetate was distilled away. The obtained dry solid was dissolved in 1.5 ml of methanol, and the peak of MW392 was then fractionated by preparative HPLC. The solvent was distilled away from this fraction sample, so as to obtain 4.5 mg of MW392.
(Preparative HPLC Conditions)
Preparatory device: Agilent 1100 series, preparatory autosampler
Column: Zorbax RX-C18 (9.4 mm×250 mm, 5 μm)
Mobile phase A: water
Mobile phase B: acetonitrile
Gradient: 20% mobile phase B (0 to 1 minute)


    
    
        20%-100% mobile phase B (1 to 8 minutes)
        100% mobile phase B (8 to 14 minutes)
        100%-20% mobile phase B (14 to 15 minutes)
        20% mobile phase B (15 to 18 minutes)

Flow rate: 3.0 ml/min

Detection: UV 254 nm

Injection volume: 50 μl

Column temperature: 40° C.

Analysis time: 18 minutes

Retention time: MW392, 11.3 minutes

    
    






Physical Values of MW392 (4)
1H-NMR (500 MHz, CD3OD) δ (ppm): 6.20 (dd, 1H, J=15, 11 Hz, H10), 5.89 (d, 1H, J=11 Hz, H9), 5.33 (dd, 1H, J=15, 8 Hz, H11), 4.93 (d, 1H, J=11 Hz, H15), 3.76 (m, 1H, H3), 3.31 (overlap, 1H, H7), 3.12 (td, 1H, J=9, 3 Hz, H17), 2.46 (dd, 1H, J=16, 8 Hz, H2a), 2.38 (overlap, 1H, H12), 2.38 (dd, 1H, J=16, 6 Hz, H2b), 2.30 (m, 1H, H16), 1.97 (dd, 2H, J=7, 4 Hz, H13ab), 1.85 (m, 1H, H5a), 1.68 (m, 1H, H4a), 1.68 (s, 3H, H21), 1.60 (s, 3H, H23), 1.52 (m, 2H, H6 and H18a), 126 (m, 3H, H4b, H5b and H18b), 0.98 (d, 31-1, J=7, H22), 0.92 (d, 3H, J=7, H24), 0.91 (t, 3H, J=7, H19), 0.68 (d, 31-1, J=7, H20)
13C-NMR (125 MHz, CD3OD) δ (ppm): 175.21 (C1), 141.67 (C11), 135.26 (C8), 133.94 (C14), 131.44 (C15), 129.82 (C9), 12531 (C10), 92.18 (C7), 78.57 (C17), 7551 (C3), 49.88 (C13), 42.29 (C2), 40.02 (C16), 36.72 (C12), 33.50 (C5), 33.46 (C6), 32.84 (C4), 28.94 (C18), 20.84 (C22), 18.04 (C20), 17.70 (C19), 16.71 (C23), 12.20 (C21), 10.65 (C24)
ESI-MS: m/z=391 [M-H]−
As a result, it was confirmed that the Mer-16208 hbdD::tsr strain as an hbdD-deficient strain did not produce herboxidiene, but it produced MW392 as a 14,15-olefin, 17-O-demethyl and 18-deoxy product of herboxidiene.
Test Example
Proliferation Inhibitory Action on WiDr Human Colon Cancer Cells
WiDr human colon cancer cells, which had been cultured in an RPMI1640 medium (manufactured by SIGMA) containing 10% fetal bovine serum, penicillin (100 units/mL) and streptomycin (100 μg/mL), were dispersed on a 96-well plate in an amount of 2×103 cells/90 μl/well. The cells were cultured in a CO2 incubator overnight. Thereafter, 10 μl of the aforementioned culture solution containing the compound HX354 or HX355 of 3-fold dilution series used in the aforementioned examples was added to the culture, and the mixture was then cultured. Three days later, 50 μl of CellTiter-Glo Luminescent Cell Viability Assay (Promega) was added to the culture, the mixture was then shaken for 2 minutes, and it was then left at rest for 15 minutes. Thereafter, luciferase luminescence was measured with a luminometer, and the measured luminescence was used as an indicator for the number of living cells
The concentrations (IC50 values) of HX354 and HX355, where the proliferation of the WiDr human colon cancer cells was inhibited by were obtained. The results are shown in the following table.









TABLE 2






Compound No.
IC50(nM)


















HX354
91



HX355
168

## Claims

1. An isolated DNA comprising a nucleotide sequence consisting of:
contiguous nucleotides 8919 to 28295 of SEQ ID NO:1;
contiguous nucleotides 28326 to 49892 of SEQ ID NO:1; or
contiguous nucleotides 49892 to 55981 of SEQ ID NO:1.

2. The isolated DNA of claim 1, wherein the nucleotide sequence consists of contiguous nucleotides 8919 to 28295 of SEQ ID NO:1.

3. The isolated DNA of claim 1, wherein the nucleotide sequence consists of contiguous nucleotides 28326 to 49892 of SEQ ID NO:1.

4. The isolated DNA of claim 1, wherein the nucleotide sequence consists of contiguous nucleotides 49892 to 55981 of SEQ ID NO:1.

5. An isolated DNA comprising a nucleotide sequence encoding a polypeptide comprising the amino acid sequence of SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4.

6. The isolated DNA of claim 5, wherein the nucleotide sequence encodes a polypeptide comprising the amino acid sequence of SEQ ID NO:2.

7. The isolated DNA of claim 5, wherein the nucleotide sequence encodes a polypeptide comprising the amino acid sequence of SEQ ID NO:3.

8. The isolated DNA of claim 5, wherein the nucleotide sequence encodes a polypeptide comprising the amino acid sequence of SEQ ID NO:4.

9. An isolated DNA comprising a nucleotide sequence encoding a polypeptide exhibiting polyketide synthase activity, wherein the nucleotide sequence hybridizes, under conditions of hybridization at 61° C. to 64° C. in the presence of 0.5 M NaCl and 50% formamide and washing at 61° C. to 64° C. using a 0.1 to 2×SSC solution, to a polynucleotide sequence fully complementary to:
contiguous nucleotides 8919 to 28295 of SEQ ID NO:1;
contiguous nucleotides 28326 to 49892 of SEQ ID NO:1; or
contiguous nucleotides 49892 to 55981 of SEQ ID NO:1.

10. The isolated DNA of claim 9, wherein the nucleotide sequence hybridizes, under conditions of hybridization at 61° C. to 64° C. in the presence of 0.5 M NaCl and 50% formamide and washing at 61° C. to 64° C. using a 0.1 to 2×SSC solution, to a polynucleotide sequence fully complementary to contiguous nucleotides 8919 to 28295 of SEQ ID NO:1.

11. The isolated DNA of claim 9, wherein the nucleotide sequence hybridizes, under conditions of hybridization at 61° C. to 64° C. in the presence of 0.5 M NaCl and 50% formamide and washing at 61° C. to 64° C. using a 0.1 to 2×SSC solution, to a polynucleotide sequence fully complementary to contiguous nucleotides 28326 to 49892 of SEQ ID NO:1.

12. The isolated DNA of claim 9, wherein the nucleotide sequence hybridizes, under conditions of hybridization at 61° C. to 64° C. in the presence of 0.5 M NaCl and 50% formamide and washing at 61° C. to 64° C. using a 0.1 to 2×SSC solution, to a polynucleotide sequence fully complementary to contiguous nucleotides 49892 to 55981 of SEQ ID NO:1.

13. An isolated DNA comprising a nucleotide sequence encoding a polypeptide exhibiting polyketide synthase activity, wherein the nucleotide sequence is at least 90% identical to a polynucleotide consisting of:
contiguous nucleotides 8919 to 28295 of SEQ ID NO:1;
contiguous nucleotides 28326 to 49892 of SEQ ID NO:1; or
contiguous nucleotides 49892 to 55981 of SEQ ID NO:1.

14. The isolated DNA of claim 13, wherein the nucleotide sequence is at least 90% identical to a polynucleotide consisting of contiguous nucleotides 8919 to 28295 of SEQ ID NO:1.

15. The isolated DNA of claim 13, wherein the nucleotide sequence is at least 90% identical to a polynucleotide consisting of contiguous nucleotides 28326 to 49892 of SEQ ID NO:1.

16. The isolated DNA of claim 13, wherein the nucleotide sequence is at least 90% identical to a polynucleotide consisting of contiguous nucleotides 49892 to 55981 of SEQ ID NO:1.

17. The isolated DNA of claim 13, wherein the nucleotide sequence is at least 95% identical to a polynucleotide consisting of contiguous nucleotides 8919 to 28295 of SEQ ID NO:1.

18. The isolated DNA of claim 13, wherein the nucleotide sequence is at least 95% identical to a polynucleotide consisting of contiguous nucleotides 28326 to 49892 of SEQ ID NO:1.

19. The isolated DNA of claim 13, wherein the nucleotide sequence is at least 95% identical to a polynucleotide consisting of contiguous nucleotides 49892 to 55981 of SEQ ID NO:1.

20. An autonomously or integratively replicating recombinant plasmid, comprising the DNA of claim 1.

21. A transformant comprising the DNA of claim 1.

22. An autonomously or integratively replicating recombinant plasmid, comprising the DNA of claim 5.

23. A transformant comprising the DNA of claim 5.

24. An autonomously or integratively replicating recombinant plasmid, comprising the DNA of claim 9.

25. A transformant comprising the DNA of claim 9.

26. An autonomously or integratively replicating recombinant plasmid, comprising the DNA of claim 13.

27. A transformant comprising the DNA of claim 13.