# Patent

## Title
Protein having prolyl oligopeptidase activity, nucleic acid encoding same and method for producing and using same

## Abstract

Proteins isolated from Coprinus clastophyllus having prolyl oligopeptidase activity, nucleic acids encoding the protein and methods for producing and using the protein, wherein SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:9 and SEQ ID NO:10 must be contained therein to at least 60% similarity. The proteins and nucleic acids have improved heat stability and perform more favorably in vivo having optimum activity conditions around 40 degrees centigrade and around pH 7, and can therefore be used in medicaments for the treatment of celiac disease caused by proline abundant gluten or other applications.

## Background
The present invention is a divisional application claiming the benefit of U.S. patent application Ser. No. 12/081,984 filed on Apr. 24, 2008, now U.S. Pat. No. 7,741,094.


BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention relates to a protein isolated from Coprinus clastophyllus, especially to a protein isolated from Coprinus clastophyllus and having prolyl oligopeptidase activity, the isolated gene sequence thereof, method for producing and use of the same.
2. Description of the Prior Art
Prolyl oligopeptidase (EC 3.4.21.26), also known as prolyl endopeptidase or post-proline cleaving enzyme, cleaves proline containing polypeptides at the carboxyl side of a proline residue (Polgár, Methods Enzymol. 244:188-200; Polgár, Cell. Mol. Life Sci. 59:349-362).
Prolyl oligopeptidase is widely researched in recently in several application fields. Prolyl oligopeptidase degrades peptides involving memory and learning and thus considered to be connected with amnesia and conditions of degradative memory, including Parkinson's disease. Inhibitants for prolyl oligopeptidase are currently being researched to find therapies thereof (Yoshimoto et al., J. Pharmacobio-Dyn. 10:730-735; Atack et al., Nat. Prod. Res. 19:13-22; Marighetto et al., Learn Mem. 7:159-169; Lee et al., Planta Med. 70:1228-1230; Sorensen et al., Nahrung 48(1):53-56; Atta-ur-Rahman et al., Nat. Prod. Res. 19:13-22; Jarho et al., J. Med. Chem. 48:47772-4782). Researches in other application fields include: using prolyl oligopeptidase as a treatment for celiac disease caused by proline abundant gluten (Piper et al., J. Pharmacol. Exp. Ther. 311:213-219; Marti et al., J. Pharmacol. Exp. Ther. 312:19-26; Matysiak-Budnik et al., Gastroenterol. 129(3):786-796; Pyle et al., Clin. Gastroenterol. Hepatol. 3(7):687-94; Gass et al., Biotechnol. Bioeng. 92(6):674-84); purification and recovery of exogenously expressed peptides (Xiu et al., Biotechnol. Appl. Biochem. 36(Pt2):111-117); and development of a cancer-treating prodrug being less toxic to cells and will be converted by prolyl oligopeptidase to a functional drug (Heinis et al., Biochemistry 43:6293-6303).
Prolyl oligopeptidases found in animals, plants and microbes generally display relatively low activities. Some know prolyl oligopeptidases found in microbes include those originate from: Flavobacterium meningosepticum (having an activity of 0.30 U/ml according to Yoshimoto et al., J. Biol. Chem. 255:4786-4792); lactobacillus casei (having an activity of 0.15 U/g according to 6. Habibi-Najafi et al., J. Dairy Sci. 77:385-392); Propionibacterium freudenreichii (having an activity of 4.3 mU/ml according to Tobiassen et al., J. Dairy Sci. 79:2129-2136); a fermented broth of Agaricus bisporus (having an activity of 0.15 U/ml according to Abdus Sattar et al., J. Biochem. 107:256-261); and Xanthomonas spp. (having an activity of 0.15 U/ml according to Szwajcer-Dey et al., J. Baceteriol. 174:2454-2459).
Enzymatic activity of prolyl oligopeptidase may be increased by genetic engineering methods, specifically, cloning a prolyl oligopeptidase gene into host cells such as E. coli (Escherichia coli) followed by exogenous large-scale expression. Prolyl oligopeptidase originally from Shingomonas capsulata exhibited 7-fold higher activity of 0.2 U/ml in E. coli (Yoshimoto et al., Japanese patent JP10066570). A Flavobacterium meningosepticum prolyl oligopeptidase gene encoded protein expressed in E. coli exhibits maximal activity of 0.7 U/ml (Diefenthal et al., Appl. Microbiol. Biotechnol. 40:90-97). A Flavobacterium meningosepticum prolyl oligopeptidase reconstructed by Uchiyama in E. coli exhibits maximal activity of 8.1 U/ml, which further demonstrates specific activity as high as 124 U/mg after purification (Uchiyama et al., J. Biochem. 128:441-447). An Aeromonas hydrophila prolyl oligopeptidase expressed in E. coli exhibits activity of 1.48 U/ml which is 100 fold higher than expressed in original Aeromonas hydrophila strain and exhibits specific activity up to 8.8 U/mg after purification (Kanatani et al., J. Biochem. 113:790-796). An Aeromonas punctata prolyl oligopeptidase expressed in E. coli has 112 fold higher activity than that expressed in original strain and exhibits specific activity up to 67 U/mg after purification (Li et al., Wei Sheng Wu Xue Bao. 2000 40(3):277-283).
In addition, a Pyrococcus furious prolyl oligopeptidase gene encoded protein expressed in E. coli exhibits specific activity of 232 U′/mg (the activity units being alternatively defined and calculated as 1 U′ being equal to 0.1 OD410 per minute by Harwood et al., J. Bacterol. 179:3613-3618 and different from that in aforementioned literatures) and 4 U/mg (Harwood and Schreier et al., Methods Enzymol. 330:445-454) after purification.
Aforementioned examples demonstrate that purified prolyl oligopeptidases expressed in E. coli have higher activity. However, prolyl oligopeptidases of different origins have preferences for interaction conditions. Optimum conditions enable a prolyl oligopeptidase to display full activity; otherwise, only partial activity may be attained. A highly active prolyl oligopeptidase has more potential for use if its optimum conditions are similar to practical conditions where it is applied. When evaluating the potential of a prolyl oligopeptidase in such aspect, optimum temperature and optimum pH are considered. Furthermore, ranges of optimum conditions are defined by retained activity under optimum generic environmental conditions. For example, heat stability is determined by measuring the ratio of retained activity after heating to full activity.
Each of the aforementioned prolyl oligopeptidases have corresponding optimum conditions. The optimum conditions for Aeromonas hydrophila prolyl oligopeptidase are 30° C. and pH 8.0. When preheated at 42° C. for 30 minutes, 50% activity is retained. The activity of an Aeromonas punctata prolyl oligopeptidase reaches optimum activity at 34° C. and pH 8.4. The optimum pH and temperature for Flavobacterium meningosepticum prolyl oligopeptidase are 7.0 and 40° C.; and its activity will be reduced to 50% when heated to 42° C. for 15 minutes (Yoshimoto et al., J. Biol. Chem. 255:4786-4792). When heated at 60° C. for 1 hour, the activity of a Flavobacterium meningosepticum prolyl oligopeptidase mutated with error-prone PCR mutagenesis drop to 50% under conditions of pH7.0 and 30° C. (Uchiyama et al., J. Biochem. 128:441-447). Of all prolyl oligopeptidases expressed in E. coli, Flavobacterium meningosepticum prolyl oligopeptidase exhibits the highest specific activity and showed the best heat stability after mutagenesis with error-prone PCR. However, since Flavobacterium meningosepticum is a pathogen, safety concerns arise for use, despite other prolyl oligopeptidases exhibiting lower heat-stability.
Nevertheless, to find and isolate a prolyl oligopeptidase corresponding to human usage from various organisms requires much research and experimentation for those generally skilled in the art of the present invention. This difficulty was compounded when the prolyl oligopeptidase found in the first screening of Aspergillus niger was later authenticated to be another serine protease. Though certain basidiomycete was known to have prolyl oligopeptidase, there are no filamentous fungi known to have prolyl oligopeptidase so far. As a result, no prolyl oligopeptidase of fungal original has been expressed in E. coli in large scale.
To overcome the shortcomings of available prolyl oligopeptidases, the present invention provides a protein having prolyl oligopeptidase activity, a nucleic acid encoding thereof and methods for producing and using the same to mitigate or obviate the aforementioned problems.
SUMMARY OF THE INVENTION
The present invention relates to proteins isolated from Coprinus clastophyllus having prolyl oligopeptidase activity, nucleic acids encoding the protein and methods for producing and using the protein.
One aspect of the present invention is to provide an isolated protein selected from the group consisting of:
(a) a protein comprising the amino acid sequence of SEQ ID NO:6 or SEQ ID NO:10;
(b) a protein encoded by a nucleic acid of the sequence of SEQ ID NO:5 or SEQ ID NO:9;
(c) a protein comprising the function of protein (a) or protein (b), and comprising an amino acid sequence having a similarity greater than 60% to the amino acid sequence of protein (a) or protein (b);
(d) a protein comprising the function of protein (c), and encoded by a nucleic acid of a sequence having a similarity greater than 60% to the sequence of SEQ ID NO:5 or SEQ ID NO:9;
(e) a protein encoded by a nucleic acid being able to hybrid to a nucleic acid of the sequence of SEQ ID NO:5 or SEQ ID NO:9 under a highly-strict condition comprising acts of allowing interaction at 50° C. for 16 hours; washing with a solution having 2×SSC and 0.1% SDS at room temperature for 5 minutes; repeating the preceding act once; allowing interaction in a solution having 0.5×SSC and 0.1% SDS at 65° C. for 15 minutes; and repeating the preceding act once.
Another aspect of the present invention is to provide isolated nucleic acids selected from the group consisting of:
(a) a nucleic acid encoding the aforementioned protein;
(b) a nucleic acid of the sequence of SEQ ID NO:5 or SEQ ID NO:9;
(c) a nucleic acid encoding a protein as that encoded by nucleic acid (b), and of a sequence having a similarity greater than 60% to nucleic acid (b);
(d) a nucleic acid being able to hybrid to a nucleic acid of the sequence of each of nucleic acid (a)-(c) under a highly-strict condition comprising acts of allowing interaction at 50° C. for 16 hours; washing with a solution having 2×SSC and 0.1% SDS at room temperature for 5 minutes; repeating the preceding act once; allowing interaction in a solution having 0.5×SSC and 0.1% SDS at 65° C. for 15 minutes; and repeating the preceding act once;
(e) a nucleic acid encoding a protein comprising a amino acid sequence identical to the amino acid sequence of the protein encoded by each of nucleic acids (a)-(d); and
(f) a nucleic acid of the complementary sequence of each of nucleic acid (a)-(e).
The present invention also relates to nucleic acid probes, chimeric genes, nucleic acid constructs, vectors, transformants, pharmaceutical compositions, composition for use with a proline containing prodrug, as well as use of the aforementioned protein.
Another aspect of the present invention provides methods for producing a protein having prolyl oligopeptidase activity comprising (a) providing the aforementioned transformant; (b) culturing the transformant in a condition allowing expression of a protein having prolyl oligopeptidase activity; and (c) purifying and acquiring the protein.
Other objectives, advantages and novel features of the invention will become more apparent from the following detailed description when taken in conjunction with the accompanying drawings.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a line graph of prolyl oligopeptidase activities of proteins pProHN14 and pProHN17 versus pH values wherein solid circles represent the pProHN14 protein and solid triangles represent the pProHN17 protein;
FIG. 2 is a bar chart of the prolyl oligopeptidase activities of proteins pProHN14 and pProHN17 versus temperature at pH 7.0 wherein black bars represent the pProHN14 protein and white bars represent the pProHN17 protein;
FIG. 3 is a bar chart of the prolyl oligopeptidase activities of proteins pProHN14 and pProHN17 versus temperature at pH 8.0 wherein black bars represent the pProHN14 protein and white bars represent the pProHN17 protein;
FIG. 4 is a broken line graph of heat stabilities of recombinant prolyl oligopeptidase wherein solid lines represent the pProHN14 protein, dotted lines represent the pProHN17 protein and shapes represent a temperature of preheated treatment, respectively being: circles representing 30° C., squares representing 37° C., triangles representing 45° C. and diamonds representing 55° C.



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
Definitions
Identity: The term “identity” is defined herein as the invariant extent between two nucleic acid sequences or that between two amino acid sequences. In the context of the present invention, “identity” refers to the “Identity” score when comparing two sequences (nucleic acid or amino acid) with Gap program (Genetics Computer Group, Version 11.1), wherein gap creation penalty=8 and gap extension penaly=2.
Similarity: The term “similarity” is defined herein as the extent of relatedness between two nucleic acid sequences or that between two amino acid sequences. The similarity between two sequences can be obtained from, the ratio of identity or conservation between the two sequences, or both. In the context of the present invention, “similarity” refers to the “Similarity” score when comparing two sequences (nucleic acid or amino acid) with Gap program (Genetics Computer Group, Version 11.1), wherein gap creation penalty=8 and gap extension penaly=2.
Chimeric gene: The term “chimeric gene” is defined herein as a gene formed by a recombinant nucleic acid carrying nucleic acids of different origins. For example, a chimeric gene may be formed by a recombinant nucleic acid carrying nucleic acids of different genes, or recombined nucleic acids of different gene fragments.
Control sequence: The term “control sequence” is defined herein as a nucleic acid sequence defining the on or off states of a gene and controlling the expression of the nucleic acid thereof.
Vector: The term “vector” is defined herein as a vehicle transferring a nucleic acid molecule into a host cell, which may be a plasmid, a phage or a virus. Such vectors include but are not limited to expression vectors that routinely accept nucleic acid molecules with recombinant nucleic acid sequences and induce the expression of the nucleic acid sequence after transferring the nucleic acid molecules into a host cell. Corresponding vectors for a host cell are determined by the vector-cell compatibility. Furthermore, the aforementioned plasmid may be a linear or a closed circular nucleic acid molecule.
DETAILED DESCRIPTION OF THE INVENTION
Prolyl oligopeptidase is researched for having valuable potentials such as to degrade peptides involving memory and learning, to be used as a treatment for celiac disease caused by proline abundant gluten, to purify or recover exogenously expressed peptides and may be used as a helping agent for cancer-treating prodrugs.
In the present invention, proteins with prolyl oligopeptidase activity and gene sequences thereof are described. Data relevant to the producing of said protein and substantial practical acts are also provided. The protein provides high enzymatic activity and a range of optimum conditions suitable for various applications.
In another aspect of the present invention, the isolated prolyl oligopeptidase gene from Coprinus clastophyllus is demonstrated being used in pharmaceutical applications with methods disclosed herein.
The aforementioned protein with prolyl oligopeptidase activity can be used as a treatment for celiac disease caused by proline abundant gluten, as a helping agent for cancer-treating prodrugs or for purifying and recovering exogenously expressed peptides.
The nucleic acids, vectors and transformants relevant to the aforementioned protein and methods are also disclosed.
It will be understood by those skilled in the art that various modifications, such as minor variations of concentrations or activities of produced prolyl oligopeptidases may be made to the present invention without departing from the spirit and scope of the invention. Furthermore, the present invention is not limited to the examples described herein but may also encompasses any and all embodiments within the scope of the present invention. It is also to be understood by those skilled in the art that alternatively available biological methods and techniques may be applied without departing from the scope of the invention.
Proteins
The present invention relates to isolated proteins having prolyl oligopeptidase activity. Prolyl oligopeptidase cDNAs are cloned from previously isolated Coprinus clastophyllus strain (deposition number: BCRC 36074; Bioresource Collection and Research Centre, Food Industry Research and Development Institute, Taiwan) having heat-stable prolyl oligopeptidase (extrocellular activity 0.03 U/ml). To further raise the prolyl oligopeptidase activity, E. coli was used as a host cell to hold the cloned prolyl oligopeptidase cDNA for large-scale expression in order to obtain functional amounts of the protein.
As defined herein, 1 U of prolyl oligopeptidase activity is the capability to produce 1 μmole of p-nitroaniline per minute. In a preferred aspect, the intracellular prolyl oligopeptidase activity of the protein is 7.2 U/ml, in another preferred aspect, 7.7 U/ml. The protein may be purified. The specific activity of the purified protein may be 55.0 U/mg to 70.0 U/mg. In a more preferred aspect, the specific activity of the purified protein may be 56.1 U/mg to 70.0 U/mg. In another preferred aspect, the specific activity of the purified protein may be 56.1 U/mg or 66.8 U/mg.
The optimum pH value for the protein may be pH 6 to pH 8. In a preferred aspect, the optimum pH value for the protein may be pH 6 to pH 7 and in a most preferred aspect, the optimum pH value for the protein may be pH 7. The optimum temperature for the protein at pH 7 may be 45° C. The optimum temperature for the protein at pH 8 may be 37° C.
In a preferred aspect, the protein contains an amino acid sequence having a similarity greater than 60% to the sequence of SEQ ID NO:6 or SEQ ID NO:10 or is encoded by a nucleic acid of a sequence having a similarity greater than 60% to the sequence of SEQ ID NO:5 or SEQ ID NO:9. In another preferred aspect, the similarities of the amino acid sequence or the nucleic acid sequence are greater than 70%. In a more preferred aspect, the similarities of the amino acid sequence or the nucleic acid sequence are greater than 80%. In an even more preferred aspect, the similarities of the amino acid sequence or the nucleic acid sequence are greater than 90%. In a most preferred aspect, the similarities of the amino acid sequence or the nucleic acid sequence are greater than 95%. It is understood by those skilled in the art that there may be variations between the aforementioned proteins in accordance with the present invention without abolishing the prolyl oligopeptidase activities thereof. Thus, it is also understood by a person skilled in the art that varying proteins having the aforementioned prolyl oligopeptidase activity are also covered within the scope of the present invention. In another most preferred aspect, the protein has an amino acid sequence comprising SEQ ID NO:6 or SEQ ID NO:10 or is encoded by a nucleic acid containing the sequence of SEQ ID NO:5 or SEQ ID NO:9.
In another preferred aspect, the protein has the function of the aforementioned protein and is encoded by a nucleic acid of a sequence having a similarity greater than 60% to the sequence of SEQ ID NO:5 or SEQ ID NO:9.
In another preferred aspect, the protein has the function of the aforementioned protein and is encoded by a nucleic acid wherein the nucleic acid hybrids to another nucleic acid of the sequence of SEQ ID NO:5 or SEQ ID NO:9 under highly-strict conditions comprising acts of allowing interaction at 50° C. for 16 hours; washing with a solution having 2×SSC and 0.1% SDS at room temperature for 5 minutes; washing with a solution having 2×SSC and 0.1% SDS at room temperature for 5 minutes; allowing interaction in a solution having 0.5×SSC and 0.1% SDS at 65° C. for 15 minutes; allowing interaction in a solution having 0.5×SSC and 0.1% SDS at 65° C. for 15 minutes.
Nucleic Acids
The present invention also relates to isolated nucleic acids of sequences encoding the aforementioned proteins. In a preferred aspect, the nucleic acid is a nucleic acid of a sequence having a similarity greater than 60% to the sequences of SEQ ID NO:5 or SEQ ID NO:9 and encodes a protein having the prolyl oligopeptidase activity as that of the aforementioned protein. In another preferred aspect of the present invention, the similarity of the sequence of the nucleic acid with the sequences of SEQ ID NO:5 or SEQ ID NO:9 is greater than 70%; in an more preferred aspect the similarity is greater than 80%; in a even more preferred aspect the similarity is greater than 90%; in a most preferred aspect the similarity is greater than 95%. In another most preferred aspect, the sequence of the nucleic acid comprises SEQ ID NO:5 or SEQ ID NO:9.
It is to be understood by those skilled in the art that there may be variations between the sequence of SEQ ID NO:5 or SEQ ID NO:9 and the sequences of aforementioned nucleic acids. Each of the nucleic acid variants encodes a protein having prolyl oligopeptidase activity expressed by the sequences of SEQ ID NO:6 or SEQ ID NO:10, or of a sequence having a considerable similarity to the sequences of SEQ ID NO:6 or SEQ ID NO:10. Thus a person with general skill in the art can easily understand that those nucleic acids are within the scope of the present invention as long as the function of the encoded protein will not be abolished by the sequence variations.
Those skilled in the art will also understand that nucleic acids encoding a protein of the same amino acid sequence of that of the proteins encoded by the aforementioned nucleic acids is within the scope of the present invention. Furthermore, nucleic acids of complementary (antisense) sequences do not depart from the spirit and scope of the present invention.
Nucleic Acid Probes
The present invention also relates to nucleic acid probes that hybrid to the aforementioned nucleic acids under highly strict conditions comprising acts of: allowing interaction at 50° C. for 16 hours; washing with a solution having 2×SSC and 0.1% SDS at room temperature for 5 minutes; washing with a solution having 2×SSC and 0.1% SDS at room temperature for 5 minutes; allowing interaction in a solution having 0.5×SSC and 0.1% SDS at 65° C. for 15 minutes; allowing interaction in a solution having 0.5×SSC and 0.1% SDS at 65° C. for 15 minutes.
Chimeric Genes
The present invention also relates to chimeric genes comprising the aforementioned nucleic acids being operably linked to a promoter allowing expression in a host cell. In an application of a research or commercial purpose, the skill necessary to operably link a nucleic acid and a promoter to achieve the purpose is well understood by those skilled in the art of the present invention.
Nucleic Acid Constructs and Vectors
The present invention also relates to nucleic acid constructs comprising the aforementioned nucleic acids being operably linked to a control sequence allowing the expression of the protein encoded by the nucleic acid in a host cell. Such nucleic acid constructs, such as recombinant plasmids, are widely applied in research or commercial fields. Building a nucleic acid construct containing a specific nucleic acid is understood and practicable to a person with general skill in the art.
The present invention also relates to vectors comprising the aforementioned nucleic acids or the aforementioned nucleic acid constructs.
Transformants
The present invention also relates to transformants being a host cell holding nucleic acids in accordance with the present invention wherein the host cell is transformed by accepting the aforementioned nucleic acids. The host cell may be an E. coli cell. For example, the host cell may be an E. coli cell of BL21(DE3) strain or DH10B strain. In another preferred aspect of the present invention, the prolyl oligopeptidase cDNA is operably linked to a promoter or a control sequence allowing expression in a host cell to form a chimeric gene or a nucleic acid construct. The chimeric gene or nucleic acid construct is able to express the cDNA in a host cell.
Compositions
The present invention also relates to compositions, such as pharmaceutical compositions. The compositions comprise the aforementioned protein in accordance with the present invention as a functional component. Prolyl oligopeptidase is known to be used as a treatment for celiac disease caused by proline abundant gluten. In addition, the range of the optimum conditions of the protein having prolyl oligopeptidase in accordance with the present invention covers conditions not covered by optimum conditions of known prolyl oligopeptidases, and is suitable for use under such conditions. As a functional component of the aforementioned composition, the protein effectively allows the purpose of the composition to be achieved. In an aspect of the present invention, the composition also comprises an excipient allowing the composition to be made as a solid matter, a semi-solid matter or a liquid matter.
The composition in accordance with the present invention may also be used with a prodrug containing proline residues. The composition for use with the proline-containing prodrug has at least one pharmaceutically acceptable excipient and the aforementioned protein. Having prolyl oligopeptidase activity, the protein is used as a functional component for converting the prodrug to a functional drug. In a preferred aspect, the composition further comprises an antibody conjugated with the aforementioned protein. The antibody is used to anchor the protein in a target tissue of an organism. When the prodrug is later administered into the circulatory system of the organism, the protein will only interact with the prodrug delivered to the target tissue. With the prolyl oligopeptidase activity of the protein, the prodrug will be converted into a functional drug in the target tissue, which significantly raises the selectivity and accuracy of the prodrug.
Use of the Aforementioned Protein
One aspect of the present invention relates to using the aforementioned protein. With the prolyl oligopeptidase activity, the protein can be used to process exogenously expressed peptides for recovering or be used in the manufacture of a purification reagent thereof.
Methods for Producing a Protein Having Prolyl Oligopeptidase Activity
The present invention also relates to methods for producing proteins having prolyl oligopeptidase activity. The method comprises providing the aforementioned transformant; culturing the transformant in a condition allowing expression of a protein having prolyl oligopeptidase activity; and purifying and obtaining the protein. The host cell includes, but is not limited to, a transformed cell of BL21(DE3) E. coli strain or DH10B E. coli strain.
EXAMPLES
The following experimental designs are illustrative, and are not intended to limit the scope of the present invention. Reasonable variations, such as those occurring to a person reasonably skilled in the art can be made herein without departing from the scope of the present invention.
Example 1
Construction of Coprinus clastophyllus cDNA Library and Cloning of Prolyl Oligopeptidase cDNA
1. Cloning of Coprinus clastophyllus Prolyl Oligopeptidase Gene Fragments and Preparation of Probes
Fungal genomic sequences were searched on NCBI web site by BLAST with the amino acid sequence of human prolyl oligopeptidase. Polymerase chain reaction (PCR) primers Pro16 and Pro17 were designed from regions of the genomes of Coprinopsis cinerea okayama7#130 and Phanerochaete chrysosporium RP-78 where high similarity to the prolyl oligopeptidase sequence was observed and have been attached, respectively as:










Pro16:




5′-tacggcggmt tcascatctc-3′
(SEQ ID NO: 1)



 



Pro17:



5′-tgccaytcyt cwccraactc-3′
(SEQ ID NO: 2)






The genomes of Coprinopsis cinerea okayama7#130 and Phanerochaete chrysosporium RP-78 are publicly available in databases maintained by the U.S. National Center for Biotechnology Information (Bethesda, Md.).
PCR was carried out using PCR primers Pro16 and Pro17 and genomic DNA of Coprinus clastophyllus as a template. 50 μl of mix solution for PCR comprises 1×PCR buffer, 0.2 mM of dNTP, 1 μM of Pro16, 1 μM of Pro17, 5 U of pfu DNA polymerase (Roach) and the template (genomic DNA of Coprinus clastophyllus). PCR was carried out with ABI 9700 thermocycler (Applied Bioscience) and the following PCR program.
PCR program:
94° C., 3 minutes [1 repeat];
94° C., 30 seconds, 64° C., 30 seconds, 72° C., 1 minute [5 repeats];
94° C., 30 seconds, 60° C., 30 seconds, 72° C., 1 minute [5 repeats];
94° C., 30 seconds, 56° C., 30 seconds, 72° C., 1 minute [35 repeats];
72° C., 7 minutes [1 repeat].
A 128 by (base pair) fragment was amplified using PCR. The amplified fragment was then cloned into a PCR®2.1-TOPO vector (Invitrogen) to obtain a plasmid referred to as ‘p128’.
Two primers Pro20 and Pro21 were designed from p128. A probe was made from the Pro20 and Pro21 primers with PCR DIG Labeling Kit (Roche) following the manual of the kit. A PCR program was used in making the probe.










Pro20:




5′-tacggcggat tcagcatctc-3′
(SEQ ID NO: 3)



 



Pro21:



5′-tgccactcct caccaaactc-3′
(SEQ ID NO: 4)






PCR program:
94° C., 3 minutes [1 repeat];
94° C., 30 seconds, 58° C., 30 seconds, 72° C., 40 seconds [35 repeats];
72° C., 7 minutes [1 repeat].
2. Cultivation of Strains
Coprinus clastophyllus was cultured in YMA plate (Difco, No. 0712) at 25° C. for 18 days and then transferred to medium N at 25° C. and shaken at 200 rpm for 7 days. Medium N was adjusted to pH6 and comprised 2% glucose (Merck), 0.3% soybean flour, 1% Tryptone, 0.3% KH2PO4 (Merck) and 0.1% MgSO4 (Merck).
3. Building Coprinus clastophyllus cDNA Library
1.2 g of dehydrated mycelium was taken on day 7 of the aforementioned Coprinus clastophyllus cultivation and total RNA was extracted with TRIZOL (Invitrogen) according to the operation process provided therewith.
325 μg of Coprinus clastophyllus total RNA was obtained wherein the ratio of OD260/OD280 was 2.05. The amount of total RNA to be extracted may be up to 500 μg.
An mRNA isolation kit, such as PolyATtract® mRNA Isolation Systems Kit provided by Promega, was used to extract mRNA from the total RNA according to the operation process provided with the kit. 6 μg of mRNA (with polyA) was obtained, wherein the ratio of OD260/OD280 was 2.01. The aforementioned PolyATtract® mRNA Isolation Systems Kit primarily comprises 50 μl Biotinylated Oligo(dT) Probe (50 pmol/μl), 2.8 ml 20×SSC Solution (2×1.4 ml), 9 ml Streptavidin MagneSphere® Paramagnetic Particles (15×0.6 ml), 50 ml Nuclease-Free Water (2×25 ml), 1 each MagneSphere® Magnetic Separation Stand for 1.5 ml. The forementioned mRNA extraction was carried out with magnetic separation technology (MagneSphere® technology). Other mRNA isolation kits being able to extract mRNA from total RNA may also be employed.
ZAP-cDNA® Gigapack® III Gold Cloning Kit (Stratagen) was used according to operation process provided therewith. DNA fragments having lengths within 0.75-3 kb were collected as cDNAs with the ZAP-cDNA® Gigapack® III Gold Cloning Kit. 8×105 plasmid-carrying plaques were screened as a collection of strains defining a Coprinus clastophyllus cDNA library.
Different plasmids were respectively carried by the strains in the Coprinus clastophyllus cDNA library. Each plasmid comprised at least one vector and at least one cDNA. Each of the at least one vector comprised multiple restriction sites. The multiple restriction sites at least include EcoRI and HindIII sites. In addition, the sequences of regions flanking the two ends of the cDNA respectively correspond to T3 primer and T7 primer.
4. Plaque Selection
Plaque hybridization was carried out according to the following operation process of ZAP-cDNA® Gigapack® III Gold Cloning Kit to obtain multiple plaques formed with helper phage. A plaque lift was made with nitrocellulose membrane.
The plaque lift was first prehybridized in a Southern-blot hybridization solution such as the FastHyb solution (Biochain) at 50° C. for 2 hours and then undergones hybridization in a probe-containing FastHyb solution at 50° C. for 16 hours.
The plaque lift was then washed as follows:
(1) washing with a solution having 2×SSC and 0.1% SDS at room temperature for 5 minutes;
(2) repeating act (1) washing with a solution having 2×SSC and 0.1% SDS at room temperature for 5 minutes once;
(3) allowing interaction in a solution having 0.5×SSC and 0.1% SDS at 65° C. for 15 minutes; and
(4) repeating act (3) allowing interaction in a solution having 0.5×SSC and 0.1% SDS at 65° C. for 15 minutes once.
The DIG antibodies conjugated with the probes were then detected after washing the plaque lift. The detection was visualized on X-ray films with autoradio development signals to identify plaques.
5. Obtaining Transformant
With the aforementioned process, 93 significant signals were identified. A secondary selection was carried out using ZAP-cDNA® Gigapack® III Gold Cloning Kit according to its operation process to further screen a pure single plaque. T3 primer and T7 primer were used to obtain PCR products from the plaques. PCR products having first 11 largest molecular weight were amplified from 11 plaques. The 11 plaques were selected and processed with in vivo excision.
The plasmid obtained from the 11 plaques were confirmed with EcoRI and HindIII restriction enzymes and then analyzed with gel electrophoresis. 4 longest plasmids, 49-1, 71-1, 76-3 and 91-1, were picked for producing transformants.
6. Sequencing
The lateral region of cDNA carried by aforementioned plasmids were first sequenced using available primers such as T3 and T7. Primers were further designed from sequences of lateral regions to sequence nested regions to complete the full length of the cDNA.
7. Obtaining and Confirming Coprinus clastophyllus Prolyl Oligopeptidase cDNA
The nucleic acid sequence of Coprinus clastophyllus prolyl oligopeptidase cDNA (SEQ ID NO:5) shows that the full length is 2508 nt (nucleotides) and a 2217 nt long ORF (open reading frame) (SEQ ID NO:6) starts at 65th nt of the cDNA. The ORF encodes a 83.9 kD protein having 739 amino acids and prolyl oligopeptidase activity.
With reference to Table 1, the amino acid sequence of Coprinus clastophyllus prolyl oligopeptidase was aligned with amino acid sequences of prolyl oligopeptidases from other species using the GAP utility of GCG software (Accelrys). A highest identity (45.8%) to Xenopus tropicalis and a secondary highest identity (44.7%) to ustilago maydis were observed. Though Coprinus clastophyllus and Cryptococcus neoformans belong to the same genus, identities in a range between 40%-43.9% for human, mouse, pig, blue-green algae, Arabidopsis thaliana or bovine were higher than the identities in a range between 31.6%-32% to Cryptococcus neoformans.







TABLE 1







Similarities and identities of prolyl oligopeptidase amino acid


sequences between Coprinus clastophyllus and other species









Species
Similarity (%)
Identity (%)





Xenopus tropicalis
54.6
45.8


Ustilago maydis
54.2
44.6


Anabaena variabilis
55.1
43.9


Human
54.6
43.8


Human-2
54.5
43.7


Mouse
53.7
43.5


Rat
53.5
43.5


Pig
54.0
43.2


Nostoc sp.
54.9
43.2


Oryza sativa
53.2
43.2


Arabidopsis thaliana
52.6
43.2


Bovine
53.2
43.0


Deinococcus radiodurans
49.6
39.9


Aeromonas punctata
50.8
39.2


Aeromonas hydrophila
49.9
38.6


Novosphingobium capsulatum
47.2
37.7


Flavobacterium meningosepticum
47.4
37.6


Pyrococcus horikoshii
45.2
34.9


Pyrococcus abyssi
46.6
34.6


Pyrococcus furiosus
44.9
33.2


Cryptococcus neoformans
44.5
32.0


Cryptococcus neoformans-2
42.2
31.6


Pseudomonas entomophila
36.0
28.5


Neisseria menigitidis
34.9
27.1









It is observed that various proteins of amino acid sequences having similarity lower than 60% to the amino acid sequence of SEQ ID NO:6 encoded by nucleic acid SEQ ID NO:5. Variations of amino acid sequences do not necessarily alter the prolyl oligopeptidase activities. Thus it will be understood by a person skilled in the art that proteins having the aforementioned prolyloligopeptidase activities as in the present invention may also have similarities greater than 60% therewith. These varying proteins are also covered within the scope of the present invention.
Example 2
Expression of Coprinus clastophyllus Prolyl Oligopeptidase cDNA in E. coli 
Primers Pro31 and Pro32 were designed to generate a stop codon in an amplified full-length prolyl oligopeptidase cDNA using PCR with pfu DNA polymerase.










Pro 31:




5′-atggtgacca aaacctgggt-3′
(SEQ ID NO: 7)



 



Pro 32:



5′-ctagagtgta gctttatctt tc-3′
(SEQ ID NO: 8)






PCR program:
94° C., 3 minutes [1 repeat];
94° C., 30 seconds, 58° C., 30 seconds, 72° C., 180 seconds [35 repeats];
72° C., 3 minutes [1 repeat].
The amplified full-length prolyl oligopeptidase cDNA was ligated into an expression vector pET 151/D-TOPO (Invitrogen) comprising a T7 primer corresponding sequence and an N-terminal His-tag. A recombinant construct was obtained as a result of the ligation. The recombinant construct was then used to transform host cells. The host cells were DH10B E. coli strain cells (Invitrogen). The host cells were cultured at 37° C. in LB broth (USB) or on LB plates (USB). Multiple colonies were obtained and 3 colonies were further selected. Recombinant plasmids were obtained from the cells of the selected colonies. The recombinant plasmids were further used to transform host cells, being BL21(DE3) E. coli strain cells (Invitrogen), for expression.
The BL21(DE3) host cells were divided into 3 groups each group was respectively transformed with the recombinant plasmids obtained from the 3 colonies which were further selected. The BL21(DE3) host cells were added to shaking flasks containing LB broth and the densities of OD600 readings were within 0.4-0.6. 0.4 mM (final concentration) of IPTG was added into each flask and the cultivation lasted for another 20 hours thereafter. Coprinus clastophyllus prolyl oligopeptidase cDNAs carried by the recombinant plasmids were expressed in the BL21(DE3) host cells. The expressed proteins having prolyl oligopeptidase activities were purified according the purification methods disclosed in the manual of the pET system (Novagen). Bio-Rad Protein Assay (Bio Rad) was used to measure masses of the expressed proteins. Standard curves were plotted using BSA (bovine serum albumin) as standard to determine masses of the expressed proteins.
Example 3
Measuring Activity of Coprinus clastophyllus Prolyl Oligopeptidase
1. Selecting pProHN14 and pProHN17 and Measuring Prolyl Oligopeptidase Activities of Proteins Encoded Thereby
400 μl of 0.1 M Na-phosphate buffer, 50 μl of 10 mM Z-glycyl-L-proline-4-nitroanilide (Fluka) and 50 μl of diluted solution of the aforementioned protein having prolyl oligopeptidase activity were added into a micro centrifuge tube. The mixture was allowed to react for 5 to 60 minutes. 500 μl of 1N HCL quenching solution was added to quench the reaction. After 13000 rpm centrifugation for 5 minutes, the supernatant was obtained to measure the reading of OD410.
The amount of p-nitroaniline was determined with a stand curve of OD410 readings versus p-nitroaniline amounts. At pH 7.0 and 45° C., 1 U of prolyl oligopeptidase activity was defined as the ability to generate 1 μmole of p-nitroaniline per minute.
The reading of OD410 was than used to determine the prolyl oligopeptidase activities shown in the aforementioned 3 groups of BL21(DE3) host cells. The 2 groups having highest prolyl oligopeptidase activities were selected. The recombinant plasmids carried in the 2 groups of BL21(DE3) host cells were pProHN14 and pProHN17. The proteins respectively encoded by pProHN14 and pProHN17 showed prolyl oligopeptidase activities of 7.2 U/ml and 7.7 U/ml.
2. Sequencing pProHN14 and pProHN17
The recombinant plasmids, pProHN14 and pProHN17, were sequenced with available sequencing techniques to those skilled in the art. The sequence of pProHN17 was shown in the nucleic acid sequence of SEQ ID NO:5 as predicted.
In addition, the nucleic acid sequence of pProHN14 was shown in SEQ ID NO: 9. It was observed by comparing SEQ ID NO:5 and SEQ ID NO:9 that 4 nucleotides (CTAG) were deleted in the C-terminal of pProHN14 and frame-shift were induced. As a result, 24 amino acids (R ASSDPAANKA RKEAELAAAT AEQ) (SEQ ID NO: 11) were added to the C-terminal of the protein expressed from pProHN14. The amino acid sequence of the protein expressed from pProHN14 was shown in SEQ ID NO:10.
In an aspect of the present invention, a DNA fragment having the sequence of pProHN14 (SEQ ID NO:9), is obtained from BCRC 36074 as a PCR template, using a PCR primer having the aforementioned 4 nucleotides (CTAG) deleted. The DNA fragment has the nucleic acid sequence of SEQ ID NO:9. By expressing the DNA fragment with an expression vector, a protein having amino acid sequence of SEQ ID NO:10 is obtained. In a preferred aspect of the present invention, pET151/D-TOPO is used as the expression vector.
3. Comparison of Activities and Specific Activities of Known Prolyl Oligopeptidase and that of Proteins Encoded by pProHN14 and pProHN17
The proteins expressed from pProHN14 and pProHN17 in host cells of BL21(DE3) E. coli strain exhibit prolyl oligopeptidase activities of 7.2 U/ml and 7.7 U/ml, which is similar to the activity (8.1 U/ml) of Flavobacterium meningosepticum prolyl oligopeptidase and is superior to most known prolyl oligopeptidase.
Ni-NTA affinity column packed with Ni-NTA gel was commercially available in Invitrogen. The Ni-NTA affinity column was used to purify proteins expressed from pProHN14 and pProHN17. Purified proteins of pProHN14 and pProHN17 were observed to have specific activities of 56.1 U/mg and 66.8 U/mg, which were lower than the specific activity of Flavobacterium meningosepticum prolyl oligopeptidase but higher than most known prolyl oligopeptidase.
Example 4
Analysis Basic Properties of Proteins Encoded by pProHN14 and pProHN17
1. Optimum pH for Coprinus clastophyllus Prolyl Oligopeptidases
The aforementioned method for determining prolyl oligopeptidase activity was used to determine an optimum pH value using pH 3-8 citric acid-Na2HPO4 buffer solution or pH 9-12 glycine-NaOH buffer solution.
The proteins expressed from pProHN14 and pProHN17 demonstrated highest prolyl oligopeptidase activity at pH 7.0. With reference to FIG. 1, the protein of pProHN14 demonstrated a wider range of optimum pH. The protein of pProHN14 exhibited 90% activity while the protein of pProHN17 exhibited only 50% at pH 6.0.
2. Optimum Temperature for Coprinus clastophyllus Prolyl Oligopeptidases
Optimum temperature was determined by measuring prolyl oligopeptidase activities at 25° C., 30° C., 37° C., 45° C. or 45° C. with the aforementioned method for determining prolyl oligopeptidase activity.
With reference to FIG. 2, at pH 7.0, the proteins of pProHN14 and pProHN17 exhibited highest activity at 45° C. Thus the optimum temperature was determined to be 45° C., which is higher than the optimum temperatures of prolyl oligopeptidases known to show high activities.
With reference to FIG. 3, at pH 8.0, the proteins of pProHN14 and pProHN17 exhibited highest activity at 37° C.
3. Heat Stability Coprinus clastophyllus Prolyl Oligopeptidases
The proteins of pProHN14 and pProHN17 were preheated at 30° C., 37° C. or 45° C. for 0, 20, 40, 60 or 80 minutes or preheated at 55° C. for 0, 5, 10 15, 20, 25 or 30 minutes. The activities of preheated proteins were then measured with the aforementioned method for determining prolyl oligopeptidase activity.
With reference to FIG. 4, being preheated at 30° C. or 37° C. for 80 minutes, the protein expressed from pProHN14 was observed to retain 99% and 93% of activities. The protein expressed from pProHN17 was observed to retain 80% and 73% of activities under the same conditions.
Being preheated at 45° C. for 60 minutes, the protein of pProHN14 was observed to retain 67% of activity. The protein of pProHN17 was observed to retain 32% of activity. Thus it was apparent that the protein of pProHN14 has better heat stability than the protein of pProHN17.
Being preheated at 55° C. for 5 minutes, the proteins of pProHN14 and pProHN17 were both observed to retain only 9% activities.
Even though numerous characteristics and advantages of the present invention have been set forth in the foregoing description, together with details of the structure and features of the invention, the disclosure is illustrative only. Changes may be made in the details, especially in matters of shape, size, and arrangement of parts within the principles of the invention to the full extent indicated by the broad general meaning of the terms in which the appended claims are expressed.

## Claims

1. An isolated protein selected from the group consisting of:
(a) the amino acid sequence of SEQ ID NO: 10;
(b) the amino acid sequence encoded by SEQ ID NO:9;
(c) an amino acid sequence having at least 95% identity to SEQ ID NO: 10, wherein said amino acid sequence has prolyl oligopeptidase activity;
(d) an amino acid sequence encoded by a nucleic acid sequence having at least 95% identity to SEQ ID NO:9, wherein said amino acid sequence has prolyl oligopeptidase activity; and
(e) an amino acid sequence encoded by a nucleic acid that hybridizes to SEQ ID NO:9 under highly stringent conditions, wherein said highly stringent conditions are hybridization at 50° C. for 16 hours; washing twice with a solution having 2×SSC and 0.1% SDS at room temperature for 5 minutes; and incubation twice with a solution having 0.5×SSC and 0.1% SDS at 65° C. for 15 minutes, wherein said amino acid sequence has prolyl oligopeptidase activity.