# Patent

## Title
Process for production of cis-4-hydroxy-L-proline

## Abstract

Development of a method of economically and efficiently producing cis-4-hydroxy-L-proline. The present invention provides L-proline cis-4-hydroxylase. This enzyme may be derived from Lotus corniculatus rhizobia, Mesorhizobium loti or Medicago sativa rhizobia, Sinorhizobium meliloti. The present invention provides a method of producing cis-4-hydroxy-L-proline from L-proline by using this enzyme. The present invention provides a recombinant vector containing a polynucleotide encoding the enzyme and a transformant containing the vector.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This patent application is a continuation of U.S. patent application Ser. No. 12/992,417, filed Nov. 12, 2010, now U.S. Pat. No. 8,541,209, which is the U.S. national phase of International Patent Application No. PCT/JP2009/058808, filed May 12, 2009, which claims the benefit of Japanese Patent Application No. 2008-125213, filed May 12, 2008.


INCORPORATION BY REFERENCE OF MATERIAL ELECTRONICALLY SUBMITTED
Incorporated by reference in its entirety herein is a computer-readable nucleotide/amino acid sequence listing submitted concurrently herewith and identified as follows: 8,462 bytes ASCII (Text) file named “714058SequenceListing.txt,” created Aug. 19, 2013.
TECHNICAL FIELD
The present invention relates to L-proline cis-4-hydroxylase enzyme, a production method of cis-4-hydroxy-L-proline using the enzyme, a recombinant vector containing a polynucleotide encoding the aforementioned enzyme, and a transformant containing the recombinant vector.
BACKGROUND ART
Hydroxy-L-proline is one kind of modified amino acids having a structure wherein a hydroxyl group is introduced into L-proline. It has 4 kinds of isomers due to the difference in the site into which the hydroxyl group is introduced (the 3-position or the 4-position carbon atom), and the difference in the spatial configuration of the hydroxyl group (trans configuration or cis configuration). Among the isomers of hydroxyproline, cis-4-hydroxy-L-proline is a substance useful as a starting material of a synthetic intermediate for pharmaceutical products such as carbapenem antibiotic, N-acetylhydroxyproline utilized as an anti-inflammatory agent and the like.
As a production method of cis-4-hydroxy-L-proline, a method of organic synthesis of a cis-4-hydroxy-L-proline derivative from a trans-4-hydroxy-L-proline derivative has been proposed (patent document 1). However, it has a problem in that a trans-4-hydroxy-L-proline derivative, which is the synthesis starting material, itself is expensive. While methods of producing cis-4-hydroxy-L-proline from L-proline by using microorganisms such as the genus Helicoceras and the like have also been proposed (patent documents 2 and 3), the production amount is extremely as low as 0.65 g/L, and is not practical.

    patent document 1: JP-A-2005-112761
    patent document 2: JP-B-3005085
    patent document 3: JP-B-3005086


DISCLOSURE OF THE INVENTION
Problems to be Solved by the Invention
There is a need to develop a method of economically and efficiently producing industrially useful cis-4-hydroxy-L-proline.
Means of Solving the Problems
The present invention provides L-proline cis-4-hydroxylase. The L-proline cis-4-hydroxylase of the present invention may be selected from the group consisting of ((1) a protein consisting of the amino acid sequence of SEQ ID NO: 1 or 2, (2) a protein consisting of an amino acid sequence wherein one or several amino acids is/are deleted from, substituted in or added to the amino acid sequence of SEQ ID NO: 1 or 2, which has L-proline cis-4-hydroxylase activity, (3) a protein consisting of an amino acid sequence having homology of not less than 80% with the amino acid sequence of SEQ ID NO: 1 or 2, which has L-proline cis-4-hydroxylase activity, (4) a protein consisting of an amino acid sequence encoded by a polynucleotide consisting of a nucleotide sequence having homology of not less than 80% with the nucleotide sequence of SEQ ID NO: 3 or 4, which has L-proline cis-4-hydroxylase activity, (5) a protein consisting of an amino acid sequence encoded by a polynucleotide that hybridizes with a polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 3 or 4 under stringent conditions, which has L-proline cis-4-hydroxylase activity, and (6) a fusion protein of any of the proteins of the aforementioned (1) to (5) and a tag peptide for specific binding attached thereto.
The present invention provides a production method of cis-4-hydroxy-L-proline. The production method of the cis-4-hydroxy-L-proline of the present invention includes a step of providing the L-proline cis-4-hydroxylase of the present invention and L-proline, and
(2) a step of reacting the aforementioned L-proline cis-4-hydroxylase with the aforementioned L-proline to give cis-4-hydroxyproline.
The present invention provides a recombinant vector containing polynucleotide encoding the L-proline cis-4-hydroxylase of the present invention.
The present invention provides a transformant containing the recombinant vector of the present invention.
In the present specification, the “protein”, “peptide”, “oligopeptide” and “polypeptide” are compounds wherein two or more amino acids are connected by peptide bond(s). The “protein”, “peptide”, “oligopeptide” and “polypeptide” may be modified by an alkyl group including methyl group, a phosphate group, a sugar chain, and/or an ester bond or other covalent bond. In addition, the “protein”, “peptide”, “oligopeptide” and “polypeptide” may be bound or associated with a metal ion, coenzyme, allosteric ligand, other atom, ion or atomic group, or other “protein”, “peptide”, “oligopeptide” or “polypeptide”, or biopolymer such as sugar, lipid, nucleic acid and the like, or polystyrene, polyethylene, polyvinyl, polyester or other synthetic polymer, via a covalent bond or noncovalent bond.
When amino acid is indicated in the present specification, it may be shown by a compound name such as L-asparagine, L-glutamine and the like, or by conventionally-used 3 letters such as Asn, Gln and the like. When a compound name is used, a prefix (L- or D-) showing the steric configuration relating to a carbon of the amino acid is used therefor. When the conventional 3 letters are used, the 3 letters represent an L form of amino acid unless otherwise specified. In the present specification, amino acid is a compound bound with an amino group and a carboxyl group via at least one carbon atom, and is any compound capable of polymerizing by peptide bond. While the amino acid in the present specification includes 20 kinds of L-amino acids used for the translation of protein synthesized from messenger RNA in ribosome in vivo and D-amino acids which are stereoisomers thereof, it is not limited thereto and may include any natural or unnatural amino acid.
In the present specification, isomers of hydroxyproline (hereinafter to be referred to as “Hyp”) may be indicated as trans-3-Hyp, cis-3-Hyp, trans-4-Hyp and cis-4-Hyp depending on the difference in the site where a hydroxyl group is introduced (carbon atom at the 3-position or the 4-position), and the difference in the spatial configuration of a hydroxyl group (trans configuration or cis configuration).
The structure of cis-4-hydroxy-L-proline (cis-4-Hyp) is represented by chemical formula I.




The L-proline cis-4-hydroxylase of the present invention is produced by expressing a DNA consisting of a nucleotide sequence encoding the amino acid sequence thereof in a nonliving expression system or an expression system using a host organism and an expression vector. The aforementioned host organism includes procaryotes such as Escherichia coli, Bacillus subtilis and the like, and eucaryotes such as yeast, fungi, plant, animal and the like. The expression system using a host organism and an expression vector of the present invention may be a part of an organism such as cell and tissue, or a whole individual organism. The enzyme protein of the present invention may be used, as long as it has L-proline cis-4-hydroxylase activity, for the production method of cis-4-Hyp of the present invention in admixture with other components derived from a nonliving expression system or expression system using a host organism and an expression vector. When the enzyme protein of the present invention is expressed in the aforementioned expression system using a host organism and an expression vector, the host organism that expresses the aforementioned enzyme protein, for example, the transformant of the present invention, which is used for the production of cis-4-Hyp of the present invention, may be in a living state. In this case, the cis-4-Hyp of the present invention can be produced by a resting microbial cell reaction system or a fermentation method. Alternatively, the aforementioned enzyme protein may be purified for use in the production method of the cis-4-Hyp of the present invention.
The amino acid sequence of SEQ ID NO: 1 and the nucleotide sequence of SEQ ID NO: 3 are the amino acid sequence of BAB52605 protein derived from Lotus corniculatus rhizobia, Mesorhizobium loti MAFF303099, and the nucleotide sequence of a gene encoding the BAB52605 protein, respectively. The BAB52605 protein has an ability to convert L-proline to cis-4-Hyp. The amino acid sequence of SEQ ID NO: 1 is deposited under Accession No. BAB52605 in the database GenBank. The nucleotide sequence of SEQ ID NO: 3 is deposited under Accession No. BA000012 in the database GenBank. While the BAB52605 protein was annotated as L-proline 3-hydroxylase in GenBank, the protein actually has L-proline cis-4-hydroxylase activity that produces cis-4-Hyp from proline, and does not show L-proline 3-hydroxylase activity, as shown in the Examples of the present invention.
The amino acid sequence of SEQ ID NO: 2 and the nucleotide sequence of SEQ ID NO: 4 are the amino acid sequence of CAC47686 protein derived from Medicago sativa rhizobia, Sinorhizobium meliloti 1021, and the nucleotide sequence of the gene encoding the CAC47686 protein. The CAC47686 protein has an ability to convert L-proline to cis-4-Hyp. The amino acid sequence of SEQ ID NO: 2 is deposited under Accession No. CAC47686 in the database GenBank/EMBL. The amino acid sequence of SEQ ID NO: 4 is deposited under Accession No. AL591792 in the database GenBank.
In the present specification, the homology of the nucleotide sequence is represented by the percentage obtained by aligning the nucleotide sequence of the present invention and that of a comparison object such that the nucleotide sequences match with each other most, and dividing the number of nucleotides in the matched parts of the nucleotide sequence by the total number of the nucleotides of the nucleotide sequence of the present invention. Similarly, the homology of the amino acid sequence in the present specification is represented by the percentage obtained by aligning the amino acid sequence of the present invention and that of a comparison object such that the highest number of amino acid residues match between the amino acid sequences, and dividing the number of the matched amino acid residues by the total number of the amino acid residues of the amino acid sequence of the present invention. The homology of the nucleotide sequence and amino acid sequence of the present is invention can be calculated by using an alignment program CLUSTALW well known to those of ordinary skill in the art.
In the present specification, the “stringent conditions” mean to perform Southern blotting method explained in Sambrook, J. and Russell, D. W., Molecular Cloning A Laboratory Manual 3rd Edition, Cold Spring Harbor Laboratory Press (2001) under the following experiment conditions. A polynucleotide consisting of the nucleotide sequence of the comparison object is subjected to agarose electrophoresis to allow formation of a band, and immobilized on a nitrocellulose filter or other solid phase by capillary phenomenon or electrophoresis, and prewashed with a solution of 6×SSC and 0.2% SDS. A polynucleotide comprising the nucleotide sequence of the present invention is labeled with a labeling substance such as radioisotope and the like to give a probe and a hybridization reaction of the probe with the aforementioned comparison object polynucleotide immobilized on the solid phase is performed overnight in a solution of 6×SSC and 0.2% SDS at 65° C. Thereafter, the aforementioned solid phase is washed twice each with a solution of 1×SSC and 0.1% SDS at 65° C. for 30 min and washed twice each with a solution of 0.2×SSC and 0.1% SDS at 65° C. for 30 min. Finally, the amount of the probe remaining on the aforementioned solid phase is determined by quantifying the aforementioned labeling substance. In the present specification, hybridization under the “stringent conditions” means that the amount of a probe remaining on a solid phase on which a polynucleotide consisting of the nucleotide sequence of a comparison object is immobilized is at least 25%, preferably at least 50%, more preferably at least 75%, of the amount of a probe remaining on a solid phase for a positive control experiment, on which a polynucleotide consisting of the nucleotide sequence of the present invention is immobilized.
The protein of the present invention may be selected from the group consisting of (1) a protein consisting of the amino acid sequence of SEQ ID NO: 1 or 2, (2) a protein consisting of an amino acid sequence wherein one or several amino acids is/are deleted from, substituted in or added to the amino acid sequence of SEQ ID NO: 1 or 2 SEQ ID NO: 1 or 2, which has L-proline cis-4-hydroxylase activity, (3) a protein consisting of an amino acid sequence having homology of not less than 80% with the amino acid sequence of SEQ ID NO: 1 or 2, which has L-proline cis-4-hydroxylase activity, (4) a protein consisting of an amino acid sequence encoded by a polynucleotide consisting of a nucleotide sequence having homology of not less than 80% with the nucleotide sequence of SEQ ID NO: 3 or 4, which has L-proline cis-4-hydroxylase activity, (5) a protein consisting of an amino acid sequence encoded by a polynucleotide that hybridizes with a polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 3 or 4 under stringent conditions, which has L-proline cis-4-hydroxylase activity, and (6) a fusion protein of any of the proteins of the aforementioned (1) to (5) and a tag peptide for specific binding attached thereto.
The fusion protein of the present invention consists of a tag peptide for specific binding and any of the proteins of the aforementioned (1) to (5), wherein the peptide is attached to the amino terminal or carboxyl terminal of said protein.
The tag peptide for specific binding of the present invention is a polypeptide that specifically binds to other proteins, polysaccharides, glycolipids, nucleic acids, derivatives of these, resins and the like, to facilitate detection, separation or purification of expressed protein when any of the proteins of the aforementioned (1) to (5) is prepared. A ligand bound to the tag for specific binding may also be immobilized on a solid support or dissolved in a free form in an aqueous solution. Thus, since the fusion protein of the present invention specifically binds to a ligand immobilized on a solid support, other components in the expression system can be removed by washing. Thereafter, the aforementioned fusion protein can be separated from the solid support and collected by adding a ligand in a free form or changing pH, ion intensity and other conditions. The tag for specific binding of the present invention includes, but is not limited to, His tag, myc tag, HA tag, intein tag, MBP, GST and polypeptides analogous thereto. The tag for specific binding of the present invention may have any amino acid sequence as long as the fusion protein retains N-terminal amidase activity.
The L-proline cis-4-hydroxylase activity of the protein of the present invention may be evaluated by quantifying cis-4-Hyp produced by reacting the is protein of the present invention with L-proline in a reaction solution of the protein of the present invention, L-proline, 2-oxoglutaric acid, divalent ferric ion and L-ascorbic acid.
The cis-4-Hyp may be quantified by using an analytical instrument well known to those of ordinary skill in the art, such as LC/MS and the like.
Step (2) of the production method of the present invention may be performed using a reaction solution of a buffer component for pH control in addition to the composition of the present invention and L-proline. HEPES is preferably used as the aforementioned buffer component, and pH may be adjusted to 7.0-7.5. Preferably, the aforementioned reaction solution may further contain 2-oxoglutaric acid involved as an electron donor in a hydroxide reaction by the protein of the present invention. The aforementioned reaction solution may further contain divalent ferric ion, L-ascorbic acid and the like.
To allow the composition of the present invention to react with L-proline in step (2) of the production method of the present invention, the reaction solution is incubated for a predetermined reaction time at a predetermined reaction temperature. In the production method of the present invention, the concentration of the composition of the present invention, L-proline, divalent ferric ion, 2-oxoglutaric acid and the like in the reaction solution, reaction solution volume, reaction time, reaction temperature or other reaction conditions may be determined by those of ordinary skill in the art in consideration of the relationship between the desired production amounts and yield of cis-4-Hyp, time, cost, facility and the like necessary for the production, and other conditions.
The cis-4-Hyp obtained by the production method of the present invention may be collected by a combination of operations well known to those of ordinary skill in the art, such as centrifugation, column chromatography, freeze-drying and the like. In addition, the cis-4-Hyp obtained by the production method of the present invention may be evaluated for the production amounts or purity by using analysis techniques well known to those of ordinary skill in the art, such as LC/MS.
In the present specification, the “recombinant vector” is a vector incorporating a polynucleotide encoding a protein having a desired function, which is used to afford expression of the protein having the desired function in the host organism.
In the present specification, the “vector” is a genetic factor used to afford replication and expression of a protein having a desired function in a host organism by incorporating a polynucleotide encoding the protein having the desired function therein and transducing same to the host organism. Examples thereof include, but are not limited to, plasmid, virus, phage, cosmid and the like. Preferably, the aforementioned vector may be a plasmid. More preferably, the aforementioned vector may be a pET-21d(+) plasmid.
The recombinant vector of the present invention may be produced by ligating a polynucleotide encoding the protein of the present invention and any vector according to a genetic engineering method well known to those of ordinary skill in the art who use restriction enzymes, DNA ligases and the like.
In the present specification, the “transformant” is an organism into which a recombinant vector incorporating a polynucleotide encoding a protein having a desired function has been transduced, and which has become capable of showing desired property relating to the protein having the desired function.
In the present specification, the “host organism” is an organism into which a recombinant vector incorporating a polynucleotide encoding a protein having a desired function is transduced for production of a transformant. The aforementioned host organism includes procaryotes such as Escherichia coli, Bacillus subtilis and the like, and eucaryotes such as yeast, fungi, plant, animal and the like. The aforementioned host organism may be Escherichia coli. 
The transformant of the present invention is produced by transducing the recombinant vector of the present invention into any appropriate host organism. The recombinant vector may be transduced according to various methods well known to those of ordinary skill in the art, such as electroporation method forming a pore in the cellular membrane by electric stimulation, a heat shock method to be performed along with a calcium ion treatment and the like.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 Maps of recombinant plasmids.
FIG. 2 A conceptual diagram showing the procedures of quenching reaction in a hydroxide reaction test and derivatization of amino acid.
FIG. 3 Graphs showing the results of HPLC analyses of standard samples of L-proline and 4 kinds of isomers of Hyp.
FIG. 4 Graphs showing the results of HPLC analyses of a standard reaction solution from reaction with a cell-free extract containing BAB52605 protein, a Pro-free reaction solution (negative control) and a 2-OG-free reaction solution (negative control).
FIG. 5 Graphs showing the results of HPLC analyses of a standard reaction solution from reaction with a cell-free extract containing CAC47686 protein, a Pro-free reaction solution (negative control) and a 2-OG-free reaction solution (negative control).
FIG. 6 A graph showing the results of HPLC analysis of a nonexpressing reaction solution (negative control).
FIG. 7 A conceptual diagram showing procedures for preparation of an MS analysis sample.
FIG. 8 Graphs showing the results of MS analyses of standard reaction solutions from reaction with cell-free extracts containing BAB52605 protein and CAC47686 protein.
FIG. 9 Graphs showing fragmentation patterns obtained by MS/MS/MS analyses of reaction products in standard reaction solutions from reaction with cell-free extracts containing BAB52605 protein and CAC47686 protein, and a standard sample of cis-4-Hyp.



DESCRIPTION OF EMBODIMENTS
The present invention is explained in detail in the following by referring to Examples, which are not to be construed as limitative.
Example 1
1. Cloning, Transduction and Expression of Genes Encoding Proteins BAB52605 and CAC47686
1-1. Method
(Extraction of Microorganism Chromosomal DNA to be Used as Template for Gene Amplification)
Lotus corniculatus rhizobia, Mesorhizobium loti MAFF303099, was obtained from National Institute of Agrobiological Sciences Genebank, and Medicago sativa rhizobia, Sinorhizobium meliloti 1021 (NBRC 14782T), was obtained from National Institute of Technology and Evaluation, and chromosomal DNAs thereof were used as templates for gene amplification.
The aforementioned two kinds of microorganisms were subjected to liquid shaking culture in 5 mL of TY medium (0.5% Bacto Trypton, 0.3% Bacto Yeast extract, 0.04% CaCl2) at 28° C. for 3 days. After the culture, bacterial cells were collected by centrifugation (4° C., 5000×g, 10 min), and chromosomal DNAs were extracted from the bacterial cells according to a conventional method.
(Amplification of Object Gene)
A gene encoding the enzyme of the present invention shown in Table 1 was amplified by a polymerase chain reaction (PCR) using chromosomal DNA of each bacterial cell as a template. Expand High Fidelity PCR System (Roche) was used for the aforementioned PCR. The reaction conditions are shown in Table 2. The conditions for the cloning and expression are shown in Table 3. The sense primers and antisense primers using Lotus corniculatus rhizobia, Mesorhizobium loti MAFF303099, and Medicago sativa rhizobia, Sinorhizobium meliloti 1021, as templates are shown in SEQ ID NOs: 5 and 6, and SEQ ID NOs: 7 and 8, respectively.







TABLE 1







Proline hydroxylase used for experiment















Putative protein

Amino


Microorganism to

GenBank
function
Number
acid


be gene source
Strain name
Protein No.
published
of bases
residue





Mesorhizobium
MAFF303099
BAR52605.1
L-proline 3-
843
280


loti


hydroxylase


Sinorhizobium
NBRC 14782T
CAC47686.1
PUTATIVE L-
843
280


meliloti


PROLINE 3-





HYDROXYLASE





PROTEIN
















TABLE 2







PCR conditions









Temperature (° C.)
Time (sec)
Cycle












94
180
1


94
15
25


50
10


72
50


72
420
1
















TABLE 3 







Cloning and expression condition














BAB52605.1
CAC47686. 1


No
Item

(Mesorhizobium loti)
(Sinorhizobium meliloti)












1
Host
Escherichia coli Rosetta2 (DE3)



Vector
pET-21d (+)


 











2
Primer
Sense
5′- TGAATATACCATGGCAAC
5′-TGAATATACCATGGGCAC





GCGGATATTGGGTGTGGTC-3′
CCATTTCTTGGGCAAGG-3′





(SEQ ID NO: 5)
(SEQ ID NO: 7)




Anti-
5′-ATGAATTCAAGCTTATAAGTC
5′-ATGAATTCAAGCTTGTATGTC




sense
ATGACCTCGCCAGCAGCAC-3′
ATCACCTCGCCACGTTC-3′





(SEQ ID NO: 6)
(SEQ ID NO: 8)


 










3
Restriction
5′ side
Nco I



enzyme
3′ side
Hind III



recognition





sequence




 


4
Culture
Pre-
inoculation of single colony to LB medium (5 ml) + Amp



method
culture
100 μg/ml + Cm 34 μg/ml



(expression)

                    ↓





culture at 37° C., 200 rpm, 16 hr




Main
addition of pre-culture medium (1 ml) to LB medium




culture
(100 ml) + Amp 100 μg/ml + Cm 34 μg/ml, and culture at





37° C., 200 rpm to reach O.D.650 = 0.5





                        ↓





addition of IPTG (final concentration 0.1 mM) and culture





at 25° C., 100 rpm, 9 hr









(Obtainment of Recombinant Plasmid)

The object DNA amplified by PCR was used as insert DNA, and each insert DNA (1 μg) and a vector, pET-21d(+) (1 μg), were cleaved by a reaction using restriction enzymes NcoI and HindIII at 37° C. for 16 hr. The cleavage products were purified by GFX PCR Purification Kit (GE Healthcare), and each insert DNA and vector were ligated by a reaction using DNA Ligation Kit <Mighty Mix> (Takara) at 16° C. for 3 hr. The ligation product was transduced by a heat shock method into Escherichia coli JM 109 treated with calcium chloride. Escherichia coli JM 109 carrying each recombinant plasmid was cultured in an LB-A agar medium (1% Bacto Trypton, 0.5% Bacto Yeast extract, 1% NaCl, 1.5% Bacto Agar, 100 μg/mL ampicillin) at 37° C. for 16 hr, and then cultured in an LB-A liquid medium (1% Bacto Trypton, 0.5% Bacto Yeast extract, 1% NaCl, 100 μg/mL ampicillin, 5 mL) at 37° C. for 16 hr, after which the plasmid was extracted using QlAprep Spin Miniprep Kit (QIAGEN). The internal base sequence of the extracted plasmid was analyzed by a DNA Sequencer to confirm insertion of desired DNA. The plasmid maps of the produced recombinant plasmids are shown in FIG. 1.
(Expression of Object Gene)
The recombinant plasmids confirmed of insertion of DNA encoding each of BAB52605 protein and CAC47686 protein (to be referred to as pEBAB52605 and pECAC47686, respectively) were transduced by a heat shock method into Escherichia coli Rosetta 2 (DE3) treated with calcium chloride, and expressed by the procedures shown in Table 3. That is, the aforementioned Escherichia coli was cultured in an LB-AC agar medium (1% Bacto Trypton, 0.5% Bacto Yeast extract, 1% NaCl, 1.5% Bacto Agar, 100 μg/mL ampicillin, 34 μg/mL chloramphenicol) at 37° C. overnight. The single colony grown was inoculated in an LB-AC liquid medium (1% Bacto Trypton, 0.5% Bacto Yeast extract, 1% NaCl, 100 μg/mL ampicillin, 34 μg/mL chloramphenicol, 5 mL), and cultured with shaking at 37° C. and 200 rpm for 16 hr. Thereafter, the aforementioned liquid medium (1 mL) was added to a fresh LB-AC liquid medium (100 mL), and cultured with shaking at 37° C. and 200 rpm. At the time point when O.D.660=0.5 was reached, isopropyl-β-d-thiogalactopyranoside (IPTG) was added to a final concentration of 0.1 mM, the mixture was cultured at 25° C. and 100 rpm to induce gene expression. After 9 hr, the cultured cells were collected by centrifugation (4° C., 5000×g, 10 min), and suspended in 20 mM HEPES NaOH buffer (pH 7.5, 5 mL). The aforementioned suspension was disrupted by ultrasonication (3 min), centrifuged (4° C., 20000×g, 30 min), and the supernatant (cell-free extract) was collected.
1-2. Results
By the aforementioned extraction and amplification operation, genes encoding BAB52605 protein and CAC47686 protein were successfully cloned. By the aforementioned recombinant operation and the like, recombinant plasmids containing the aforementioned genes could be produced. The plasmid maps of the obtained recombinant plasmids are shown in FIG. 1. By the transduction operation of the aforementioned recombinant plasmids, transformants having the recombinant plasmids could be produced. By the expression operation of the aforementioned genes by the aforementioned transformants, cell-free extracts containing BAB52605 protein and CAC47686 protein could be respectively obtained. The obtained cell-free extracts were used for the following experiments.
Example 2
2. Hydroxylation Reaction of L-proline with BAB52605 Protein and CAC47686 Protein
2-1. Method
Hydroxylation reaction of L-proline with a cell-free extract containing BAB52605 protein or CAC47686 protein obtained in Example 1 was performed. A reaction solution of the composition shown in Table 4 (hereinafter to be is referred to as “standard reaction solution”) was prepared, and the reaction was performed with stirring at 30° C. and 170 rpm for 30 min. In addition, as a negative control, a reaction solution obtained by excluding L-proline from the standard reaction solution (hereinafter to be referred to as “Pro-free reaction solution”), a reaction solution free of 2-oxoglutaric acid (2-OG) (hereinafter to be referred to as “2-OG-free reaction solution”), and a reaction solution containing, instead of the cell-free extracts containing BAB52605 protein and CAC47686 protein, a cell-free extract of Escherichia coli Rosetta 2 (DE3) free of a vector expressing the aforementioned proteins (hereinafter to be referred to as “nonexpressing reaction solution”) were prepared, and the reaction was performed with stirring at 30° C. and 170 rpm for 30 min in the same manner as with the standard reaction solution. After the reaction, according to the procedures shown in FIG. 2, the reaction was quenched and whole amino acids contained in the reaction solution was derivatized using a Marfey's reagent (1-fluoro-2,4-dinitrophenyl-5-L-leucinamide). Thereafter, the reaction solution was filtered with a 0.45 μm filter, and subjected to high performance liquid chromatography (HPLC) analysis. Various conditions of HPLC analysis are shown in Tables 5A and 5B. In addition, for molecular weight measurement of the resultant products, mass spectrometry (MS analysis) of the standard reaction solutions after reaction with a cell-free extract containing BAB52605 protein or CAC47686 protein was performed. According to the procedures shown in FIG. 7, the substance in the reaction solution was purified using an ion exchange column (Waters Oasis HLB 6 cc Extraction Cartridge), dried to solidness under reduced pressure and dissolved in methanol to give an MS analysis sample. The conditions of MS analysis are shown in Table 6.







TABLE 4





Reaction composition



















L-Proline
5.0
mM



2-Oxoglutarate
10
mM



L-Ascorbate
1.0
mM



FeSO4
0.5
mM



HEPES
100
mM



Cell-free extract
1.0
mg







Total volume 1 ml 30° C., 30 min, shake













TABLE 5





HPLC analysis conditions







(a) Setting











Apparatus
Hitachi high performance liquid chromatograph L-2000


used
series


Analytical
XDB-C18 (5 μm), 4.6 mm × 150 mm (Agilent)


column


Column
40° C.


temperature


Detector
UV 340 nm









Eluent
A
50 mM KH2PO4/CH3OH/CH3CN = 90/5/5



B
50 mM KH2PO4/CH3OH/CH3CN = 60/5/35



C
CH3CN/THF/H2O = 60/20/20










(b) Pump program











Time (min)
A (%)
B (%)
C (%)
Flow rate (ml/min)





 0.0
100
0
0
1.0


54.0
55
45
0


54.1
0
0
100


60.0
0
0
100


60.1
100
0
0


75.0
100
0
0
















TABLE 6







MS analysis conditions











Apparatus used
LCQ Deca (Thermo Quest)
ESI positive







Setting
Sheath Gas Flow Rate
20 arb




Aux Gas Flow Rate
20 arb




Spray Voltage
5 kV




Capillary Temp
200° C.




Capillary Vortage
17 V




Tube Lens offset
5 V










2-2. Results

FIG. 3 shows the results of HPLC analysis of standard samples of L-proline and 4 kinds of isomers of Hyp. Since any isomer of Hyp was detected as a separated single peak, the peak substance was identified based on the retention time.
FIG. 4 shows the results of the HPLC analysis of standard reaction solutions obtained by a reaction with a cell-free extract containing BAB52605 protein, a Pro-free reaction solution (negative control) and a 2-OG-free reaction solution (negative control). While the standard reaction solutions showed a decrease in the peak of L-proline and emergence of peak of cis-4-Hyp, the 2-OG-free reaction solution showed a peak of L-proline alone, and the Pro-free reaction solution showed no peak.
FIG. 5 shows the results of the HPLC analysis of standard reaction solutions obtained by a reaction with a cell-free extract containing CAC47686 protein, a Pro-free reaction solution (negative control) and a 2-OG-free reaction solution (negative control). Like the results of FIG. 4 using BAB52605 protein, while the standard reaction solutions showed a decrease in the peak of Pro and emergence of peak of cis-4-Hyp, the 2-OG-free reaction solution showed a peak of Pro alone, and the Pro-free reaction solution showed no peak. (Since the small peak in 33 min observed with the 2-OG-free reaction solution was also observed with the Pro-free reaction solution, the peak is considered to be derived from a substance originally contained in the reaction solution, which is not a substrate or a resultant product.)
FIG. 6 shows the results of the HPLC analysis of nonexpressing reaction solution (negative control). The nonexpressing reaction solution showed only a peak of L-proline.
FIG. 8 shows the results of the MS analysis of standard reaction solutions obtained by a reaction with a cell-free extract containing BAB52605 protein (upper panel) or CAC47686 protein (lower panel). In respective analysis results, protonated ion (m/z=426.1) and sodium added ion (m/z=448.1) corresponding to cis-4-Hyp derivatives were detected.
FIG. 9 shows fragmentation patterns obtained by MS/MS/MS analyses of is reaction products in standard reaction solutions from reaction with cell-free extracts containing BAB52605 protein (upper panel) and CAC47686 protein (middle panel), and a standard sample of cis-4-Hyp (lower panel). In respective analysis results, a common fragmentation pattern was observed, which confirms that the fragmentation patterns of MS/MS/MS analyses of the reaction products from cell-free extracts containing the aforementioned proteins are the same as the pattern of the cis-4-Hyp standard sample.
From these results, since cis-4-Hyp is produced in the presence of BAB52605 or CAC47686 protein and L-proline, it has been confirmed that the aforementioned proteins are all hydroxygenases that regioselectively and sterically selectively hydroxylate L-proline and produce cis-4-Hyp. The putative protein function disclosed in the databases such as Entrez Protein and the like is “L-proline 3-hydroxylase” for BAB52605 protein and “PUTATIVE L-PROLINE 3-HYDROXYLASE PROTEIN” for CAC47686 protein. However, the results of this experiment confirm that the function of the both proteins mentioned above is L-proline cis-4-hydroxylase and L-proline 3-hydroxylase activity is absent. Moreover, since cis-4-Hyp is produced in the presence of 2-OG in reactions catalyzed by BAB52605 or CAC47686 protein, both the aforementioned proteins were confirmed to be 2-OG dependent dioxygenases that add an oxygen atom between the carbon atom at the 4-position of Pro and a hydrogen atom bonded thereto in the presence of 2-OG.

## Claims

1. A method of producing cis-4-hydroxy-L-proline, comprising the steps of:
(A) providing a prokaryote that produces an enzyme protein selected from the group consisting of
(1) the protein consisting of SEQ ID NO: 1 or 2,
(2) a protein consisting of an amino acid sequence wherein one or several amino acids is/are deleted from, substituted in or added to the amino acid sequence of SEQ ID NO: 1 or 2, wherein the protein has L-proline cis-4-hydroxylase activity, and
(3) a protein consisting of an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions with the nucleic acid complement of SEQ ID NO: 3 or 4, wherein the protein has L-proline cis-4-hydroxylase activity and, wherein the stringent conditions comprise hybridization overnight in a solution of 6× saline-sodium citrate (SSC) and 0.2% sodium dodecyl sulfate (SDS) at 65° C., washing two times with a solution of 1×SSC and 0.1% SDS at 65° C. for 30 minutes, and washing two times with a solution of 0.2×SSC and 0.1% SDS at 65° C. for 30 minutes,
(B) contacting the prokaryote with L-proline in a reaction system to produce cis-4-hydroxy-L-proline, and
(C) recovering cis-4-hydroxy-L-proline from the reaction system.

2. The method of claim 1, wherein the protein consists of SEQ ID NO: 1 or 2.

3. The method of claim 1, wherein the protein consists of an amino acid sequence wherein one or several amino acids is/are deleted from, substituted in, or added to the amino acid sequence of SEQ ID NO: 1 or 2, wherein the protein has L-proline cis-4-hydroxylase activity.

4. The method of claim 1, wherein the protein consists of an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions with the nucleic acid complement of SEQ ID NO: 3 or 4, wherein the protein has L-proline cis-4-hydroxylase activity and, wherein the stringent conditions comprise hybridization overnight in a solution of 6×SSC and 0.2% SDS at 65° C., washing two times with a solution of 1×SSC and 0.1% SDS at 65° C. for 30 minutes, and washing two times with a solution of 0.2×SSC and 0.1% SDS at 65° C. for 30 minutes.

5. A method of producing cis-4-hydroxy-L-proline, comprising the steps of:
(A) providing a host organism that produces an enzyme protein selected from the group consisting of
(1) the protein consisting of SEQ ID NO: 1 or 2,
(2) a protein consisting of an amino acid sequence wherein one or several amino acids is/are deleted from, substituted in or added to the amino acid sequence of SEQ ID NO: 1 or 2, wherein the protein has L-proline cis-4-hydroxylase activity, and
(3) a protein consisting of an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions with the nucleic acid complement of SEQ ID NO: 3 or 4, wherein the protein has L-proline cis-4-hydroxylase activity and, wherein the stringent conditions comprise hybridization overnight in a solution of 6×SSC and 0.2% SDS at 65° C., washing two times with a solution of 1×SSC and 0.1% SDS at 65° C. for 30 minutes, and washing two times with a solution of 0.2×SSC and 0.1% SDS at 65° C. for 30 minutes,
(B) culturing the host organism in a culture medium to produce cis-4-hydroxy-L-proline, and
(C) recovering cis-4-hydroxy-L-proline from the culture medium.

6. The method of claim 5, wherein the protein consists of SEQ ID NO: 1 or 2.

7. The method of claim 5, wherein the protein consists of an amino acid sequence wherein one or several amino acids is/are deleted from, substituted in, or added to the amino acid sequence of SEQ ID NO: 1 or 2, wherein the protein has L-proline cis-4-hydroxylase activity.

8. The method of claim 5, wherein the protein consists of an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions with the nucleic acid complement of SEQ ID NO: 3 or 4, wherein the protein has L-proline cis-4-hydroxylase activity and, wherein the stringent conditions comprise hybridization overnight in a solution of 6×SSC and 0.2% SDS at 65° C., washing two times with a solution of 1×SSC and 0.1% SDS at 65° C. for 30 minutes, and washing two times with a solution of 0.2×SSC and 0.1% SDS at 65° C. for 30 minutes.

9. The method of claim 5, wherein the host organism is a prokaryote.

10. The method of claim 9, wherein the protein consists of SEQ ID NO: 1 or 2.

11. The method of claim 9, wherein the protein consists of an amino acid sequence wherein one or several amino acids is/are deleted from, substituted in, or added to the amino acid sequence of SEQ ID NO: 1 or 2, wherein the protein has L-proline cis-4-hydroxylase activity.

12. The method of claim 9, wherein the protein consists of an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions with the nucleic acid complement of SEQ ID NO: 3 or 4, wherein the protein has L-proline cis-4-hydroxylase activity and, wherein the stringent conditions comprise hybridization overnight in a solution of 6×SSC and 0.2% SDS at 65° C., washing two times with a solution of 1×SSC and 0.1% SDS at 65° C. for 30 minutes, and washing two times with a solution of 0.2×SSC and 0.1% SDS at 65° C. for 30 minutes.