Biological method for producing cis-5-hydroxy-L-pipecolic acid
A method for producing cis-5-hydroxy-L-pipecolic acid is described. A gene recombinant microorganism enabling direct production of cis-5-hydroxy-L-pipecolic acid can be used in the method. Also described is a gene recombinant microorganism. In particular, it is described that a gene recombinant microorganism having DNAs encoding proteins involved in the biosynthesis of L-pipecolic acid and a DNA encoding a protein having the L-pipecolic acid cis-5-hydroxylase activity is cultured in a medium, and cis-5-hydroxy-L-pipecolic acid is collected from the medium.
1. A method for producing cis-5-hydroxy-L-pipecolic acid or a pharmacologically acceptable salt thereof, or a solvate thereof, which comprises a step of producing cis-5-hydroxy-L-pipecolic acid by using L-pipecolic acid as a substrate with a microorganism transformed with a heterologous polynucleotide selected from the group consisting of(A)to (F) in an expressible state:
(A) a polynucleotide having the nucleotide sequence of SEQ ID NO: 2,
(B) a polynucleotide hybridizable with a polynucleotide comprising the nucleotide sequence complementary to the nucleotide sequence of SEQ ID NO: 2 under stringent conditions, and encoding a protein having an activity of catalyzing a reaction of generating cis-5-hydroxy-L-pipecolic acid by using L-pipecolic acid as a substrate, wherein the stringent conditions comprise performing hybridization at 50° C. in the presence of a saline sodium citrate (SSC) solution of 2-fold concentration and 50% formamide followed by washing at 65° C. with an SSC solution of 0.1-fold concentration;
(C) a polynucleotide showing an identity of 90% or higher to the nucleotide sequence of SEQ ID NO: 2, and encoding a protein having the activity of catalyzing the reaction of generating cis-5-hydroxy-L-pipecolic acid by using L-pipecolic acid as a substrate, wherein the polynucleotide comprises a partial sequence encoding an aspartyl/asparaginyl beta-hydroxylase region and a partial sequence encoding an L-proline 3-hydroxylase C-terminal region;
(D) a polynucleotide encoding a protein having the amino acid sequence of SEQ ID NO: 25;
(E) a polynucleotide encoding a protein having the amino acid sequence of SEQ ID NO: 25 including substitution, deletion, insertion, and/or addition of 30 or less amino acid residues, and having the activity of catalyzing the reaction of generating cis-5-hydroxy-L-pipecolic acid by using L-pipecolic acid as a substrate, wherein the polynucleotide comprises a partial sequence encoding an aspartyl/asparaginyl beta-hydroxylase region and a partial sequence encoding an L-proline 3-hydroxylase C-terminal region; and
(F) a polynucleotide encoding a protein consisting of an amino acid sequence showing an identity of 90% or higher to the amino acid sequence of SEQ ID NO: 25, and having the activity of catalyzing the reaction of generating cis-5-hydroxy-L-pipecolic acid by using L-pipecolic acid as a substrate, wherein the polynucleotide comprises a partial sequence encoding an aspartyl/asparaginyl beta-hydroxylase region and a partial sequence encoding an L-proline 3-hydroxylase C-terminal region.
2. The production method according to claim 1 , wherein the microorganism further comprises a polynucleotide encoding a protein having an activity of catalyzing a reaction of generating L-aminoadipate-delta-semialdehyde by using L-lysine as a substrate, and a polynucleotide encoding a protein having an activity of catalyzing a reaction of generating L-pipecolic acid by using delta-1-piperideine-6-carboxylic acid as a substrate, each in an expressible state; and
the method further comprises a step of generating L-aminoadipate-delta-semialdehyde by using L-lysine as a substrate, and then converting L-aminoadipate-delta-semialdehyde into delta-1-piperideine-6-carboxylic acid; and
a step of generating L-pipecolic acid by using delta-1-piperideine-6-carboxylic acid as a substrate.
3. The production method according to claim 2 , wherein the polynucleotide encoding a protein having the activity of catalyzing the reaction of generating L-aminoadipate-delta-semialdehyde by using L-lysine as a substrate is derived from Flavobacterium lutescens.
4. The production method according to claim 2 , wherein the microorganism is Escherichia coli , and comprises an endogenous polynucleotide encoding a protein having the activity of catalyzing the reaction of generating L-pipecolic acid by using delta-1-piperideine-6-carboxylic acid as a substrate.
5. A method for producing cis-5-hydroxy-L-pipecolic acid or a pharmacologically acceptable salt thereof, or a solvate thereof, which comprises a step of allowing a protein selected from the group consisting of (d) to (f) to act on L-pipecolic acid to generate cis-5-hydroxy-L-pipecolic acid:
(d) a protein comprising the amino acid sequence of SEQ ID NO: 25;
(e) a protein comprising the amino acid sequence of SEQ ID NO: 25 including a substitution, deletion, insertion, and/or addition of 30 or less amino acid residues, and having an activity of catalyzing a reaction of generating cis-5-hydroxy-L-pipecolic acid by using L-pipecolic acid as a substrate, wherein the protein comprises a partial sequence encoding an aspartyl/asparaginyl beta-hydroxylase region and a partial sequence encoding an L-proline 3-hydroxylase C-terminal region; and
(f) a protein consisting of an amino acid sequence showing an identity of 90% or more to the amino acid sequence of SEQ ID NO: 25, and having the activity of catalyzing the reaction of generating cis-5-hydroxy-L-pipecolic acid by using L-pipecolic acid as a substrate, wherein the protein comprises a partial sequence of an aspartyl/asparaginyl beta-hydroxylase region and a partial sequence of an L-proline 3-hydroxylase C-terminal region.
6. The production method according to claim 5 , which further comprises:
a step of allowing a protein having an activity of catalyzing a reaction of generating L-aminoadipate-delta-semialdehyde by using L-lysine as a substrate to act on L-lysine to generate L-aminoadipate-delta-semialdehyde, and then converting L-aminoadipate-delta-semialdehyde into delta-1-piperideine-6-carboxylic acid; and
a step of allowing a protein having an activity of catalyzing a reaction of generating L-pipecolic acid by using delta-1-piperideine-6-carboxylic acid as a substrate to act on the obtained delta-1-piperideine-6-carboxylic acid to generate L-pipecolic acid.
7. The production method according to claim 1 , wherein the polynucleotide is selected from the group consisting of (A)-(D) and (F).
8. The method according to claim 1 , wherein the polynucleotide is selected from the group consisting of a polynucleotide having the nucleotide sequence of SEQ ID NO: 2; a polynucleotide having the nucleotide sequence of SEQ ID NO: 23; a polynucleotide encoding a protein having the amino acid sequence of SEQ ID NO: 25; and a polynucleotide encoding a protein having the amino acid sequence of SEQ ID NO: 26.
9. The production method according to claim 5 , wherein the protein is selected from the group consisting of (d) and (f).
10. The production method according to claim 5 , wherein the protein is a protein consisting of an amino acid sequence showing an identity of 95% or more to the amino acid sequence of SEQ ID NO: 25, and having the activity of catalyzing the reaction of generating cis-5-hydroxy-L-pipecolic acid by using L-pipecolic acid as a substrate, wherein the protein comprises a partial sequence of an aspartyl/asparaginyl beta-hydroxylase region and a partial sequence of an L-proline 3-hydroxylase C-terminal region.
11. The production method according to claim 5 , wherein the protein is selected from the group consisting of a protein comprising the amino acid sequence of SEQ ID NO: 25 and a protein comprising the amino acid sequence of SEQ ID NO: 26.
12. A method for producing cis-5-hydroxy-L-pipecolic acid or a pharmacologically acceptable salt thereof, or a solvate thereof, which comprises a step of producing cis-5-hydroxy-L-pipecolic acid by using L-pipecolic acid as a substrate with a microorganism transformed with a heterologous polynucleotide selected from the group consisting of (A)-(D) and (F) in a expressible state:
(A) a polynucleotide having the nucleotide sequence of SEQ ID NO: 2,
(B) a polynucleotide hybridizable with a polynucleotide comprising the nucleotide sequence complementary to the nucleotide sequence of SEQ ID NO: 2 under stringent conditions, and encoding a protein having an activity of catalyzing a reaction of generating cis-5-hydroxy-L-pipecolic acid by using L-pipecolic acid as a substrate, wherein the stringent conditions comprise performing hybridization at 50° C. in the presence of a saline sodium citrate (SSC) solution of 2-fold concentration and 50% formamide followed by washing at 65° C. with an SSC solution of 0.1-fold concentration;
(C) a polynucleotide showing an identity of 95% or higher to the nucleotide sequence of SEQ ID NO: 2, and encoding a protein having the activity of catalyzing the reaction of generating cis-5-hydroxy-L-pipecolic acid by using L-pipecolic acid as a substrate, wherein the polynucleotide comprises a sequence encoding an aspartyl/asparaginyl beta-hydroxylase region comprising residues 26-174 of SEQ ID NO: 25 and a sequence encoding an L-proline 3-hydroxylase C-terminal region comprising residues 190-274 of SEQ ID NO: 25;
(D) a polynucleotide encoding a protein having the amino acid sequence of SEQ ID NO: 25;
(F) a polynucleotide encoding a protein consisting of an amino acid sequence showing an identity of 95% or higher to the amino acid sequence of SEQ ID NO: 25, and having the activity of catalyzing the reaction of generating cis-5-hydroxy-L-pipecolic acid by using L-pipecolic acid as a substrate, wherein the polynucleotide comprises a sequence encoding an aspartyl/asparaginyl beta-hydroxylase region comprising residues 26-174 of SEQ ID NO: 25 and a sequence encoding an L-proline 3-hydroxylase C-terminal region comprising residues 190-274 of SEQ ID NO: 25.
13. The production method according to claim 12 , wherein the microorganism further comprises a polynucleotide encoding a protein having an activity of catalyzing a reaction of generating L-aminoadipate-delta-semialdehyde by using L-lysine as a substrate, and a polynucleotide encoding a protein having an activity of catalyzing a reaction of generating L-pipecolic acid by using delta-1-piperideine-6-carboxylic acid as a substrate, each in an expressible state; and
the method further comprises a step of generating L-aminoadipate-delta-semialdehyde by using L-lysine as a substrate, and then converting L-aminoadipate-delta-semialdehyde into delta-1-piperideine-6-carboxylic acid; and
a step of generating L-pipecolic acid by using delta-1-piperideine-6-carboxylic acid as a substrate.
14. The production method according to claim 12 , wherein the polynucleotide encoding a protein having the activity of catalyzing the reaction of generating L-aminoadipate-delta-semialdehyde by using L-lysine as a substrate is derived from Flavobacterium lutescens.
15. The production method according to claim 12 , wherein the microorganism is Escherichia coli , and comprises an endogenous polynucleotide encoding a protein having the activity of catalyzing the reaction of generating L-pipecolic acid by using delta-1-piperideine-6-carboxylic acid as a substrate.