# Patent

## Title
Phosphodiesterase and genes thereof

## Abstract

The present invention is to provide a novel phosphodiesterase and a gene thereof, specifically, Type 11 phosphodiesterase (PDE11) and a gene thereof, more specifically, a phosphodiesterase selected from (A) a protein having an amino acid sequenced shown by SEQ.ID.NO: 2, SEQ.ID.NO: 4, SEQ.ID.NO: 6 or SEQ.ID.NO: 39, and (B) a protein having an amino acid sequence shown by SEQ.ID.NO: 2, SEQ.ID.NO: 4, SEQ.ID.NO: 6 or SEQ.ID.NO: 39 in which one or several amino acids are deleted, substituted or added, and having an activity of hydrolyzing a cyclic nucleotide, and a gene thereof, and a method of characterizing, identifying and selecting a phosphodiesterase inhibitor by using the same.

## Background
TECHNICAL FIELD
The present invention relates to a novel phosphodiesterase and its gene.
BACKGROUND ART
Cyclic nucleotide such as cAMP, cGMP, etc. are involved in regulations of many in vivo functions as the second messenger in the intracellular signal transduction (Kukovetz et al., Naunyn Schmiedeberg's Arch. Pharmacol., Vol. 310, pp. 129-138, 1979; Schram et al., Science, Vol. 225, pp. 1350-1356, 1984; Ignarro et al., Annu. Rev. Pharmacol. Toxicol., Vol. 25, pp. 171-191, 1985; Martin et al., J. Pharmacol. Exp., Vol. 237, pp. 539-547, 1986).
Intracellular concentrations of the cAMP and cGMP, changing in response to an extracellular signal, are regulated by a balance between adenylcyclase and guanylcyclase involved in a synthesis thereof, and phosphodiesterase (PDE) involved in a hydrolysis of cyclic nucleotides.
Until recently, many phosphodiesterases have been found from tissues of mammals which hydrolyze cyclic nucleotides, and they have been classified into plural types, according to homology of amino acid sequence, biochemical properties, characterization by an inhibitor, etc. (Beavo, Physiol. Rev., Vol 75, pp. 725-748, 1995).
For example, PDE1 is Ca2+/calmodulin dependent PDE and hydrolyses both cAMP and cGMP. PDE2 is activated by cGMP and hydrolyses both cAMP and cGMP. PDE classified as PDE3 is inhibited by cGMP. PDE4 specifically recognizes cAMP as a substrate, and is Rolipram-sensitive. PDE5 specifically recognizes cGMP as a substrate. PDE6 is a photoreceptor cGMP-PDE. PDE7 specifically recognizes cAMP as a substrate, and is not sensitive to Rolipram.
Further recently, existences of 3 kinds of novel types of PDE have been reported. One is called PDE8, specifically recognizing cAMP as a substrate, and another is called PDE9, specifically recognizing cGMP as a substrate (Soderling et al., Proc. Natl. Acad. Sci. USA, Vol. 95, pp. 8991-8996, 1998; Fisher et al., Biochem. Biophys. Res. Commun., Vol. 246, pp. 570-577, 1998; Soderling et al., J. Biol. Chem., Vol. 273, pp. 15553-15558, 1998; Fisher et al., J. Biol. Chem., Vol. 273, pp. 15559-15564, 1998; Hayashi et al., Biochem. Biophys. Res. Commun., Vol. 250, pp. 751-756, 1998). These two PDEs are reported to be insensitive to IBMX (3-isobutyl-1-methylxanthine). Still another one is called PDE10, recognizing both cAMP and cGMP as a substrate. However, it has been reported to show stronger affinity toward cAMP (Fujishige et al., J. Biol. Chem., Vol. 274, pp. 18438-18445, 1999; Kotera et al., Biochem. Biophys. Res. Commun., Vol., 261, pp. 551-557, 1999).
Also, PDE is an important target compound for research and development in a pharmaceutical field, and research on its inhibitor has been earnestly carried out. Among the known pharmaceuticals, there have been found those having an inhibitory action on PDE, and also, it has been found that a specific PDE inhibitor can serve as a useful therapeutic agent.
For example, Milrinone and Zaprinast as a cardiac are inhibitors of PDE3 and PDE5, respectively (Harrison et al., Mol. Pharmacol., Vol. 29, pp. 506-514, 1986; Gillespie et al., Mol. Pharmacol., Vol. 36, pp. 773-781, 1989). Also, Rolipram whose antidepressant activity has been reported is a PDE4 inhibitor (Schneider et al., Eur. J. Pharmacol., Vol. 127, pp. 105-115, 1986). PDE4 inhibitor has been also developed and tested as an anti-inflammatory agent or an antasthmatic agent.
On top of that, IBMX is known as a non-selective type inhibitor acting on many types of PDEs. Vinpocetine is known to be a PDE1 inhibitor, EHNA [erythro-9-(2-hydroxy-3-nonyl)adenine] is known to be a PDE2 inhibitor, Dipyridamole is known to be an inhibitor of PDE5 and PDE6. Also, SCH51866 ((+)-cis-5-methyl-2-[4-(trifluoromethyl)benzyl]-3,4,5,6a,7,8,9,9a-octahydrocyclopent[4,5]imidazo-[2,1-b]purin-4-one; U.S. Pat. No. 5,939,419) is known to be an inhibitor of PDE1 and PDE5, and E4021 (sodium 1-[6-chloro-4-(3,4-methylenedioxybenzyl)aminoquinazolin-2-yl]pyperidine-4-carboxylate; CAS Registration No. 150452-19-0) is known to be an inhibitor of PDE5.
For development of an excellent pharmaceutical with a high therapeutic effect and less side effect, it is expected to choose an inhibitor having a high selectivity toward a certain type of PDE as a target.
Moreover, it has been sought to find a novel type of PDE, being a different molecular species from the known ones, for studying a complex mechanism of intracellular signal transduction, and also, for a possibility to become a target molecule of a new therapeutic agent.
An object of the present invention is to provide a novel type of phosphodiesterase [Type 11 phosphodiesterase (PDE11)] and its gene. Also, it is to provide a novel method for characterizing, identifying or selecting a phosphodiesterase inhibitor. Further, other objects than the above will be clear from the following descriptions.
DISCLOSURE OF THE INVENTION
The present inventors have isolated from human and rat a full-length cDNA which encodes a novel type of phosphodiesterase (also referred to as PDE11 or PDE11A.) which is a different molecular species from the known ones. Also, they have succeeded in expressing human phosphodiesterase (also referred to as PDE11 or PDE11A.) in COS cells by a genetic recombination technique and isolating the same. Moreover, they have characterized the enzymatic properties, whereby the present invention has completed.
That is, the present invention is Type 11 phosphodiesterase (PDE11) and its gene. More specifically, it is phosphodiesterase selected from the following (A) and (B), and a gene or a nucleic acid which encodes said phosphodiesterase.
(A) a protein having an amino acid sequence shown by SEQ.ID.NO: 2, SEQ.ID.NO: 4, SEQ.ID.NO: 6 or SEQ.ID.NO: 39, and
(B) a protein having an amino acid sequence shown by SEQ.ID.NO: 2, SEQ.ID.NO: 4, SEQ.ID.NO: 6 or SEQ.ID.NO: 39 in which one or several amino acids are deleted, substituted or added, which has an activity of hydrolyzing a cyclic nucleotide.
As the gene or the nucleic acid which encodes the phosphodiesterase of the present invention, there may be mentioned a gene or a nucleic acid selected from the following (a) and (b):
(a) a gene or a nucleic acid comprising a DNA having a nucleotide sequence shown by SEQ.ID.NO: 1, SEQ.ID.NO: 3, SEQ.ID.NO: 5 or SEQ.ID.NO: 38, and
(b) a gene or a nucleic acid comprising a DNA which hybridizes with a DNA having a nucleotide sequence shown by SEQ.ID.NO: 1, SEQ.ID.NO: 3, SEQ.ID.NO: 5 or SEQ.ID.NO: 38 under a stringent condition, and which encodes a protein having an activity of hydrolyzing a cyclic nucleotide.
Moreover, the present invention is a recombinant vector and a host cell containing said gene or said nucleic acid. Moreover, it is a method for characterizing, identifying or selecting a phosphodiesterase inhibitor using the same.
SEQ.ID.NO: 1 of the sequence listing mentioned below represents a nucleotide sequence of a cDNA containing an entire coding region of a human homologue (human PDE11 gene. Specifically, it is also referred to as a human PDE11A gene.) of the novel PDE gene isolated by the present inventors, and SEQ.ID.NO: 2 represents an amino acid sequence of the novel PDE (human PDE11. Specifically, it is also referred to as a human PDE11A1.) encoded by said full-length cDNA.
SEQ.ID.NO: 3 of the sequence listing mentioned below also represents a nucleotide sequence of a cDNA containing an entire coding region of a human homologue (human PDE11 gene. Specifically, it is also referred to as a human PDE11A gene.) of the novel PDE gene isolated by the present inventors, and SEQ.ID.NO: 4 represents an amino acid sequence of the novel PDE (human PDE11. Specifically, it is also referred to as a human PDE11A2.) encoded by said full-length cDNA.
SEQ.ID.NOs: 1 and 3 are nucleotide sequences of cDNAs of the two kinds of splicing variants of the human PDE11 gene, and SEQ.ID.NOs: 2 and 4 are amino acid sequences of PDE proteins of the each variant.
SEQ.ID.NO: 5 of the sequence listing mentioned below represents a nucleotide sequence of a cDNA containing an entire coding region of a rat homologue (rat PDE11 gene. Specifically, it is also referred to as a rat PDE11A gene.) of the novel PDE gene isolated by the present inventors, and SEQ.ID.NO: 6 represents an amino acid sequence of the novel PDE (rat PDE11. Specifically, it is also referred to as a rat PDE11A2.) encoded by said full-length cDNA.
SEQ.ID.NO: 38 of the sequence listing mentioned below also represents a nucleotide sequence of a cDNA containing an entire coding region of a rat homologue (rat PDE11 gene. Specifically, it is also referred to as a rat PDE11A gene.) of the novel PDE gene isolated by the present inventors, and SEQ.ID.NO: 39 represents an amino acid sequence of the novel PDE (rat PDE11. Specifically, it is also referred to as a rat PDE11A1.) encoded by said full-length cDNA
SEQ.ID.NOs: 5 and 38 are nucleotide sequences of cDNAs of the two kinds of splicing variants of the rat PDE11 gene, and SEQ.ID.NOs: 6 and 39 are amino acid sequences of PDE proteins of the each variant.
As a result of homology search carried out with respect to the nucleotide sequences shown by the above-mentioned SEQ.ID.NOs: 1, 3, 5 and 38, and amino acid sequences shown by the above-mentioned SEQ.ID.NOs: 2, 4, 6 and 39, using known DNA data bases (GenBank and EMBL) and protein data bases (NBRF and SWISS-PROT), there was found nothing that is expected to be derived from the same kinds of molecular species, except for EST (Genbank/EMBL ID No: AI025081).
Moreover, as a result from a comparison between each of the amino acid sequences of the human PDE11 shown by SEQ.ID.NO: 4 and the rat PDE11 shown by SEQ.ID.NO: 6, a homology as high as about 93% was confirmed. Also, as a result from a comparison between each of the amino acid sequences of the human PDE11 shown by SEQ.ID.NO: 2 and the rat PDE11 shown by SEQ.ID.NO: 39, a homology as high as about 94% was confirmed.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows a result of a kinetic analysis on hydrolysis of cAMP or cGMP by human PDE11A1 (Lineweaver-Burk plot).
FIG. 2 shows a result of a kinetic analysis on hydrolysis of cAMP or cGMP by human PDE11A2 (Lineweaver-Burk plot).
FIG. 3 shows a result of studies on an influence of cGMP on cAMP hydrolysis activity, and an influence of cAMP on cGMP hydrolysis activity, with respect to the human PDE11A1 and the human PDE11A2, where in relative values (%) of activity are shown, taking a cAMP hydrolysis activity without adding cGMP, or a cGMP hydrolysis activity without adding cAMP as 100%.
FIG. 4 shows kinds of organs and tissues of human for which an expression of the PDE11 gene was studied by dot blot analysis.



BEST MODE FOR CARRYING OUT THE INVENTION
As the protein of the present invention, there are mentioned those having an amino acid sequence shown by SEQ.ID.NO: 2, 4, 6 or 39. There are also mentioned those having an amino acid sequence shown by SEQ.ID.NO: 2, 4, 6 or 39, in which one or several amino acids are deleted, substituted or added.
Deletion, substitution and addition of the amino acids are admitted as long as the activity of hydrolyzing cyclic nucleotides is not lost, and normally, it is from 1 to about 420, preferably, from 1 to about 310, and more preferably, from 1 to about 165, further more preferably, from 1 to about 80, and still further preferably, from 1 to about 40.
As a region responsible for the activity of hydrolyzing cyclic nucleotides in PDE11 (PDE11A), that is, as a catalytic region of PDE11 (PDE11A), there are exemplified a region corresponding to from the 640th to the 881st amino acid residues of the amino acid sequence shown by SEQ.ID.NO: 2 of the below mentioned sequence listing, a region corresponding to from the 390th to the 631st amino acid residues of the amino acid sequence shown by SEQ.ID.NO: 4, etc.
In order not to loose the activity of PDE11 (PDE11A) for hydrolyzing cyclic nucleotides, it is expected that more amino acid sequences are conserved in a region responsible for the activity of the PDE11 (PDE11A), that is, in a catalytic region of the PDE11 (PDE11A) than in other regions.
Deletion, substitution or addition of the amino acids in the catalytic region of the PDE11 (PDE11A) is, normally from 1 to about 20, preferably from 1 to about 10, more preferably from 1 to about 5. Such a catalytic region of a protein has a homology with a catalytic region existing in the amino acid sequence shown in SEQ.ID.NO: 2 or 4, normally by about 90% or more, preferably about 95% or more, more preferably about 97% or more.
On the other hand, deletion, substitution or addition of the amino acids in a non-catalytic region of PDE11 (PDE11A) is normally from 1 to about 400, preferably from 1 to about 300, more preferably from 1 to about 160, further preferably from 1 to about 80, yet further preferably from 1 to about 40.
These proteins include an artificially modified mutant protein, a protein derived from other living species, etc., as well as naturally occurring mutant proteins.
As the gene or the nucleic acid of the present invention, there are mentioned those comprising a DNA having a nucleotide sequence shown by SEQ.ID.NO: 1, 3, 5 or 38. Also, there are mentioned those comprising a DNA which hybridizes with a DNA having a nucleotide sequence shown by SEQ.ID.NO: 1, 3, 5 or 38, under a stringent condition. There is no limitation for such a hybridizable DNA as long as it encodes a protein having an activity of hydrolyzing cyclic nucleotide. Such a DNA has a homology with a nucleotide sequence shown by SEQ.ID.NO: 1, 3, 5 or 38, by normally about 70% or more, preferably about 80% or more, more preferably about 90% or more. Such a gene or a nucleic acid includes an artificially modified mutant gene, a homologous gene derived from a different living species, etc., as well as a naturally occurring mutant gene.
In the present invention, hybridization under a stringent condition means carrying out hybridization, in case of a normal stringent conditions, in a hybridization solution of a salt concentration of 6×SSC or an equivalent thereof, at a temperature condition of 50 ̃70° C. for 16 hours, optionally carrying out preliminary washing with a solution of a salt concentration of 6×SSC or an equivalent thereof, and washing in a solution of a salt concentration of 1×SSC or an equivalent thereof. Also, in case of a condition with a higher stringency (highly stringent condition), the above-mentioned washing is carried out in a solution of a salt concentration of 0.1×SSC or an equivalent thereof.
The gene or the nucleic acid of the present invention can be isolated by screening tissues or cells of mammals as a genetic source. As mammals, human as well as non-human animals such as dog, cow, horse, goat, sheep, ape, pig, rabbit, rat and mouse, etc. are mentioned. Among them, it is desirable to use one of human for a use in research and development of a therapeutic agent for human beings.
The gene or the nucleic acid of the present invention can be obtained by utilizing information on a sequence disclosed in the present specification (SEQ.ID.NO: 1, 3, 5 or 38 of the below mentioned sequence listing). For example, primers and probes are designed based on the information on the disclosed nucleotide sequence, and using the same, it can be chosen and obtained from the DNA library by suitably combining PCR (polymerase chain reaction) method, colony hybridization method and plaque hybridization method.
For example, cDNA is synthesized from mRNA prepared from cells or tissues of mammals, and using this as a template, cDNA fragment is obtained by PCR method. Using the obtained cDNA as a probe, cDNA library is screened by colony hybridization method or plaque hybridization method to obtain a full-length cDNA. Also, genomic DNA can be isolated by screening genomic DNA library. Further, by screening DNA library of other mammals, homologous genes from other living species can be isolated.
DNA library such as cDNA library, genomic DNA library, etc. can be prepared according to a method described in, for example, “Molecular Cloning” (written by Sambrook, J., Fritsch, E. F. and Maniatis, T., published by Cold Spring Harbor Laboratory Press in 1989). Alternatively, commercially available libraries can be used if they are available.
By determining a nucleotide sequence of the obtained cDNA, a coding region of the protein as a genetic product can be determined, thereby obtaining an amino acid sequence of this protein.
PDE of the present invention can be produced by overexpression by an usual recombinant DNA technique. Also, it can be produced in a form of a fusion protein with other protein or a peptide.
For example, a DNA coding PDE is inserted into a vector so that it is linked downstream of an appropriate promoter, thereby constructing an expression vector. Subsequently, the obtained expression vector is introduced in a host cell.
As an expression system (host-vector system), for example, expression systems such as bacteria, yeasts, insect cells and mammalian cells can be mentioned. Among these, for obtaining a functionally well preserved protein, insect cells (Spodoptera frugiperda SF9, SF21, etc.) and mammalian cells (monkey COS-7 cells, Chinese hamster CHO cells, human HeLa cells, etc.) are preferably used as a host.
As a vector, in case of the mammalian cell system, retrovirus type vector, papilloma virus vector, vaccinia virus vector, SV40 type vector, etc. can be used, and in case of the insect cell system, baculovirus vector, etc. can be used.
As a promoter, in case of the mammalian cell system, SV40 promoter, LTR promoter, elongation 1α promoter, etc., and in case of the insect cell system, polyhedrin promoter, etc, can be used.
As a DNA coding PDE, a cDNA corresponding to a naturally existing mRNA (for example, those comprising a nucleotide sequence shown by SEQ.ID.NO: 1, 3, 5 or 38) can be used, however, it is not limited to this. Alternatively, a DNA corresponding to an amino acid sequence of a desired protein is designed and used. In this case, 1 to 6 kinds are known for a codon coding each of an amino acid, and codons to be used may be chosen randomly. However, for example, by considering a codon usage (frequency) of a host to be used for expression, a sequence with a higher expression frequency can be designed. A DNA comprising the designed nucleotide sequence can be obtained by means of DNA chemical synthesis, fragmentation of the above cDNA and linking, partial modification of the nucleotide sequence, etc. Artificial and partial modification of the nucleotide sequence or an introduction of a mutation can be carried out by site specific mutagenesis (Proceedings of National Academy of Sciences, Vol. 81, pp. 5662 to 5666, 1984), etc., using a primer comprising a synthetic oligonucleotide coding a desired modification.
PDE of the present invention can be isolated and purified from a cultured product of the cells into which the expression vector is introduced, optionally combining known purification methods (salting out by inorganic salts, fractional precipitation, ion-exchange resin column chromatography, affinity column chromatography, gel filtration, etc.).
A nucleic acid (oligonucleotide or polynucleotide) which hybridizes with the gene or the nucleic acid of the present invention under a stringent condition can be used as a probe for detecting the gene of the present invention. Also, it can be used, for example, as an anti-sense oligonucleotide, a ribozyme, or a decoy for modifying an expression of a gene. As such a nucleic acid, for example, a nucleotide comprising a partial sequence of successive 14 bases or more, usually, in the nucleotide sequence shown by SEQ.ID.NO: 1, 3, 5 or 38, or a complementary sequence thereof can be used.
Using the PDE of the present invention or a protein or peptide having an immunological equivalency thereto (a synthetic peptide containing a fragment or a partial sequence of a protein) as an antigen, an antibody which recognizes the PDE of the present invention can be obtained. Immunological equivalency means, for example, ability to cross-react with an antibody against the PDE of the present invention.
A polyclonal antibody can be prepared by an ordinary method of inoculating a host animal (for example, rat, rabbit, etc.) with an antigen, and collecting immune serum. A monoclonal antibody can be prepared by an ordinary technique such as a hybridoma method. Further, a gene of a monoclonal antibody is modified to prepare a humanized monoclonal antibody.
Using the above-obtained antibody, an expression of PDE of the present invention in a cell or a tissue can be detected by an ordinary immunochemical method (enzyme immunoassay, etc.). Also, by means of an affinity chromatography using an antibody, purification of PDE of the present invention can be carried out.
The fact that PDE of the present invention has an activity of hydrolyzing a cyclic nucleotide (cAMP or cGMP) can be confirmed by a generally known method for measuring PDE activity (Thompson et al., Adv. Cyclic Nucleotide Res., Vol. 10, pp. 69-92, 1979; Yanaka et al., Eur. J. Biochem., Vol. 255, pp. 391-399, 1998).
As a substrate for an enzyme reaction, cyclic nucleotide such as cAMP, cGMP, etc. and their derivatives may be used. PDE of the present invention recognizes either of cAMP and cGMP as a substrate and hydrolyzes them.
PDE of the present invention can be used for characterization, identification or selection of phosphodiesterases inhibitors.
For example, by carrying out an enzyme reaction in a system containing PDE of the present invention, a substrate for the enzyme and a test substance (preferably a compound with a low molecular weight, etc.), an inhibitory action of the test substance on the enzyme activity (an activity of hydrolyzing a cyclic nucleotide) is determined.
Alternatively, by carrying out a binding reaction in a system containing PDE of the present invention and a test substance (preferably a compound with a low molecular weight, etc.), whether or not the test substance has a binding ability toward PDE of the present invention is determined. A test substance having a binding ability (a ligand) has a high possibility to serve as an inhibitor.
Moreover, by measuring an inhibitory action (or a binding ability) against PDE of the present invention of the test substance (preferably a compound with a low molecular weight, etc.), and by comparing an inhibitory action (or a binding ability) on other types of PDE, selectivity of the inhibitory action (or the binding ability) can be determined. Accordingly, an inhibitor having a relatively high action toward a specific type of PDE (a selective inhibitor) can be selected. Also, an identification and characterization of an inhibitor become possible.
Hereinafter, the present invention will be explained in more detail by Examples, however, the present invention is not limited to these Examples.
Incidentally, in Examples below, each operation was carried out, unless otherwise specified, according to methods described in “Molecular Cloning” (written by Sambrook, J., Fritsch, E. F. and Maniatis, T., published by Cold Spring Harbor Laboratory Press in 1989), or according to directions attached to commercially available reagents and kits when they were used.
EXAMPLES
Example 1
Isolation of cDNA of Human Novel PDE (PDE11) (I)
(1) From a comparison of amino acid sequences of catalytic regions of various known PDE molecules, a highly conserved region was chosen, and a sense primer and an anti-sense primer were designed for PCR based on the nucleotide sequence coding this region. As the sense primer, an oligonucleotide was designed comprising a sequence shown by SEQ.ID.NO: 7 of the below mentioned sequence listing, and as the anti-sense primer, an oligonucleotide comprising a sequence shown by SEQ.ID.NO: 8 was designed.
RT-PCR (reverse transcript-polymerase chain reaction) was carried out using these PCR primers to isolate a cDNA fragment from mRNA of human testis.
That is, a reverse transcript reaction was carried out using mRNA of human testis (available from Clontech), RNA PCR kit (GeneAmp RNA PCR Core kit, available from PE Biosystems) and random primer (hexamer) to obtain cDNA. Using the obtained cDNA as a template, PCR reaction was carried out using the above-designed oligonucleotides comprising nucleotide sequences shown in SEQ.ID.NOs: 7 and 8 as a sense primer and an anti-sense primer, respectively. The PCR reaction was repeated for 30 cycles in total, one cycle being carried out under conditions of at 94° C. for 30 sec., at 55° C. for 30 sec., and at 72° C. for 30 sec.
The obtained PCR product was linked to a vector plasmid pGEM-T Easy (available from Promega), and a nucleotide sequence thereof was determined. The nucleotide sequence was determined using an automatic DNA sequencer (ABI PRISM 310, available from PE Biosystems), by dideoxy method (using BigDye terminator cycle sequencing reaction kit available from PE Biosystems) (hereinafter the same as the above). The nucleotide sequence of the thus obtained cDNA fragment was found to be a novel nucleotide sequence which has never been reported, and was found to be a nucleotide sequence with a high homology with a part of a cDNA coding PDE5.
(2) From the cDNA fragment obtained in the above (1), full-length cDNA was obtained by means of RACE method (rapid amplification of cDNA ends) with a procedure described below.
First, based on the information of the nucleotide sequence of cDNA obtained in the above (1), an oligonucleotide comprising a sequence shown in SEQ.ID.NO: 9 of the below mentioned sequence listing was designed as an anti-sense primer, and using this primer and a kit for RACE for elongation of 5′ end (5′-RACE) (5′-Full RACE Core Set, available from TaKaRa Shuzo), cDNA fragment was prepared from mRNA of human testis (available from Clontech).
Further, using the prepared cDNA fragment as a template, LA PCR (long and accurate PCR) (using LA PCR Kit, available from TaKaRa Shuzo) was carried out. As the PCR primer, two kinds of oligonucleotides comprising a sequence shown in SEQ.ID.NOs: 10 and 11 of the below mentioned sequence listing for the first amplification, and for the second amplification, two kinds of oligonucleotides comprising a sequences shown in SEQ.ID.Nos: 12 and 13, were used as a sense primer and an anti-sense primer, respectively. Incidentally, each of these 4 kinds of PCR primers were designed according to the information on the nucleotide sequence of cDNA fragment obtained in the above (1).
A nucleotide sequence of the obtained PCR product was determined. Accordingly, it was found that a part of a missing 5′ end region was recovered by the above 5′-RACE, and a nucleotide sequence of the recovered 5′ end region was confirmed.
Next, by further carrying out 5′-RACE (using Marathon-Ready cDNA (human prostate), available from Clontech) using cDNA derived from human prostate as a template, a 5′ region was completely recovered. As a primer, in the first amplification, the first primer (AP1 primer) corresponding to the linker part and a primer comprising a sequence shown in SEQ.ID.NO: 14 of the below mentioned sequence listing, and in the second amplification, the second primer corresponding to the linker part (AP2 primer) and a primer comprising a sequence shown in SEQ.ID.NO: 15 were used, respectively, as a sense primer and an anti-sense primer. These two kinds of anti-sense primers were designed according to the information on the nucleotide sequence of the 5′ end region recovered by the above mentioned 5′-RACE.
Next, 3′-RACE was carried out using a kit for RACE for 3′ end elongation (3′-RACE) (SMART RACE cDNA Amplification kit, available from Clontech) and mRNA of human thyroid gland (available from Clontech) to completely recover a 3′ end region. As a PCR primer for the 3′-RACE, in the first amplification, a primer comprising a sequence shown in SEQ.ID.NO: 16 of the below mentioned sequence and the first primer (UPM primer) corresponding to the linker part, and in the second amplification, a primer comprising a sequence shown in SEQ.ID.NO: 17 and the second primer (NUP primer) corresponding to the linker part were used, respectively, as a sense primer and an anti-sense primer. These two kinds of sense primers were designed according to the information on the nucleotide sequence of cDNA obtained in the above (1).
In any of the above RACEs, PCR reaction was repeated for 5 cycles under conditions at 94° C. for 1 min. followed by at 94° C. for 30 sec. and at 72° C. for 3 min., 5 cycles under conditions at 94° C. for 30 sec., at 70° C. for 30 sec. and at 72° C. for 3 min., and 25 cycles under condition at 94° C. for 30 sec., at 68° C. for 30 sec. and at 72° C. for 3 min.
(3) The nucleotide sequence of the thus obtained full-length cDNA was analyzed and compared with the amino acid sequences of the known PDEs to identify an open reading frame.
Further, based on the information on the nucleotide sequence, PCR primers were designed enclosing an open reading frame, and RT-PCR was carried out as described below, using these primers and mRNA of human prostate.
That is, a reverse transcript reaction was carried out using mRNA of human prostate (available from Clontech), RNA PCR kit (GeneAmp RNA PCR Core kit, available from PE Biosystems) and a random primer (hexamer), to obtain cDNA. Using the thus obtained cDNA as a template, PCR was carried out. As a PCR primer, an oligonucleotide comprising a nucleotide sequence shown in SEQ.ID.Nos: 18 and 19 of the below mentioned sequence listing were used as a sense primer and an anti-sense primer, respectively. PCR reaction was done with one cycle being carried out under conditions of at 94° C. for 30 sec., at 55° C. for 30 sec. and at 72° C. for 5 min.
With respect to plural clones obtained from PCR, nucleotide sequences of cDNA fragments (about 3 kb) were determined, and by comparing each of them, errors made by PCR were corrected to confirm a nucleotide sequence of a full-length cDNA.
(4) The thus obtained full-length cDNA (4476 bp) was thought to be a full-length cDNA of a novel human PDE (referred to as human PDE11 or human PDE11A.) gene. The nucleotide sequence was shown in SEQ.ID.NO: 1 of the below mentioned sequence listing, and an amino acid sequence of a protein encoded thereby, that is, human PDE11 (specifically referred to as human PDE11A1.) was shown in SEQ.ID.NO: 2. A molecular weight of human PDE11 (human PDE11A1) estimated from the amino acid sequence (934 amino acid residues) was about 105 kDa.
Further, from a homology search with the known PDEs with respect to an amino acid sequence, it was assumed that a catalytic domain of the obtained human PDE11 (human PDE11A1) was a region corresponding to the 640th to the 881st amino acid residues, and that a region comprising a sequence with a high homology to a cGMP binding region reported in a literature (McAllister-Lucus, et al., J. Biol. Chem., Vol 268, pp 22863-22873, 1993) (hereinafter referred to as cGMP binding region) was a region corresponding to the 195th to the 403rd and the 379th to the 591st amino acid residues, from a homology of the sequence.
When the amino acid sequence of the human PDE11 (human PDE11A1) was compared to various known human PDEs with cGMP-binding type, homologies in the catalytic domain were 42% with PDE2A, 51% with PDE5A, 44% with PDE6A, 44% with PDE6B, and 43% with PDE10A. Further, homologies in the two cGMP-binding region were, 19 to 47% with PDE2A, PDE5A, PDE6A, PDE6B and PDE10A, respectively.
Example 2
Isolation of cDNA of Human Novel PDE (PDE11) (II)
(1) cDNA was obtained in the same manner as in the above-stated Example 1 (1).
(2) RACE was carried out to obtain a full-length cDNA from the cDNA fragment obtained in the above (1), according to the procedure described below.
First, in the same manner as in the above Example 1, a part of the 5′end region was recovered.
Next, 5′-RACE was further carried out using cDNA derived from human testis as a template (using Marathon-Ready cDNA (human testis), available from Clontech). As a primer, in the first amplification, the first primer (AP1 primer) corresponding to the linker part and a primer comprising a sequence shown in SEQ.ID.NO: 15 of the below mentioned sequence listing, and in the second amplification, the second primer corresponding to the linker part (AP2 primer) and a primer comprising a sequence shown in SEQ.ID.NO: 20 were used, respectively, as a sense primer and an anti-sense primer. These two kinds of anti-sense primers were designed according to the information on the nucleotide sequence of the 5′ end region recovered in the above.
Further, 5′-RACE was carried out again in the same manner as in the above, to completely recover the 5′ end region. As a primer, in the first amplification, AP1 primer and a primer comprising a sequence shown in SEQ.ID.NO: 21 of the below mentioned sequence listing, and in the second amplification, AP2 primer and a primer comprising a sequence shown in SEQ.ID.NO: 22 were used, respectively, as a sense primer and an anti-sense primer. These two kinds of anti-sense primers were designed according to the information on the nucleotide sequence of the 5′ end region recovered by the above mentioned 5′-RACE.
Next, 3′-RACE was carried out in the same manner as in the above Example 1, to completely recover a 3′ end region.
(3) After analyzing the nucleotide sequence of the thus obtained full-length cDNA, it was compared to an amino acid sequence of the known PDEs to identify an open reading frame.
Moreover, PCR primers enclosing the open reading frame were designed based on the information on the nucleotide sequence, and RT-PCR was carried out using these primers and mRNA of human testis as follows.
That is, a reverse transcript reaction was carried out using mRNA of human testis (available from Clontech), RNA PCR kit (GeneAmp RNA PCR Core kit, available from PE Biosystems) and random primer (hexamer) to obtain cDNA. Using the obtained cDNA as a template, PCR reaction was carried out. As PCR primers, oligonucleotides comprising nucleotide sequences shown in SEQ.ID.NOs: 23 and 19 were used as a sense primer and an anti-sense primer, respectively. PCR reaction was done with one cycle being carried out under conditions of at 95° C. for 30 sec., at 55° C. for 30 sec. and at 72° C. for 3 min.
With respect to plural clones obtained from PCR, nucleotide sequences of cDNA fragments (about 2.4 kb) were determined, and by comparing each of them, errors made by PCR were corrected to confirm a nucleotide sequence of a full-length cDNA.
(4) The thus obtained full-length cDNA (3507 bp) was thought to be a full-length cDNA of a novel human PDE (referred to as human PDE11 or human PDE11A.) gene. The nucleotide sequence was shown in SEQ.ID.NO: 3 of the below mentioned sequence listing, and an amino acid sequence of a protein encoded thereby, that is, human PDE11 (specifically referred to as human PDE11A2.) was shown in SEQ.ID.NO: 4. A molecular weight of human PDE11 (human PDE11A2) estimated from the amino acid sequence (684 amino acid residues) was about 78 kDa.
The cDNA of human PDE11 (human PDE11A2) obtained in the present Example was assumed to be a splicing variant of the cDNA of human PDE11 (human PDE11A1) obtained in Example 1. Two kinds of PDEs derived from the two kinds of splicing variants, that is, human PDE11A1 and human PDE11A2 were different in N terminals of amino acid sequences (the 1st to the 304th amino acid residues in SEQ.ID.NO: 2 and the 1st to the 54th amino acid residues in SEQ.ID.NO: 4) and in cDNA sequences corresponding thereto.
Further, from a homology search with known PDEs with respect to an amino acid sequence, it was assumed that a catalytic domain of human PDE11A2 was a region corresponding to the 390th to the 631st amino acid residues, and that cGMP binding region of human PDE11A2 was a region corresponding to the 129th to the 341st amino acid residues, from a homology of the sequence. The amino acid sequences in the catalytic domain of human PDE11A2 coincide with those in the catalytic domain of human PDE11A1. Also, the amino acid sequences in the cGMP binding region of human PDE11A2 coincide with those in one of the two cGMP binding regions existing downstream (at 3′ side) of the human PDE11A1.
Example 3
Expression and Purification of Human PDE11A1 in COS Cells
(1) Construction of a Vector Plasmid for PDE11A1 Expression
With respect to human PDE11A1 obtained in the above Exmaple 1, cDNA fragment amplified in Example 1 (3) was linked to a vector plasmid pGEM-T Easy (available from Promega) to obtain a plasmid pGEM-PDE11PF. Using this pGEM-PDE11PF as a template, PCR was carried out using oligonucleotides comprising a nucleotide sequence shown in SEQ.ID.NOs: 24 and 25 of the below mentioned sequence listing as a sense primer and an anti-sense primer, respectively. Incidentally, these PCR primers were designed based on the 319th to 684th nucleotide sequence of SEQ.ID.NO: 1 (That is, a nucleotide sequence corresponding to the 1st to the 122nd amino acid residues of SEQ.ID.NO: 2).
cDNA fragment amplified by PCR was linked to pGEM-T Easy (available from Promega) to obtain a plasmid pGEM-PDE11PBM, and its nucleotide sequence was confirmed.
Further, cDNA fragments obtained by treating pGEM-PDE11PF with restriction enzymes KpnI and SalI, and cDNA fragments obtained by treating pGEM-PDE11PBM with restriction enzymes BamHI and KpnI were inserted into a BamHI-XhoI site of an expression vector, pcDNA4/HisMaxC (available from Invitrogen: hereinafter referred to as pHis) to obtain a vector plasmid pHis-PDE11P for PDE11A1 expression.
(2) Transfection of COS Cells
COS-7 cells (ATCCCRL1651) were subcultured in Dulbecco's modified Eagle's medium (available from Life Technologies) to which 10% bovine fetal serum, 100 unit/ml penicillin and 100 μM/streptomycin were added, under conditions of at 37° C. and 5% of carbon dioxide.
COS-7 cells were transfected with the above pHis-PDE11 P (or vector pHis for control) Transfection was carried out using a polycationic liposome agent (LipofectAMINE PLUS: available from Life Technologies).
(3) Purification of Recombinant Human PDE11A1
After 24 hours from transfection, the cells were washed with an ice cold phosphate buffer, and homogenized by ultrasonic treatment in an ice cold homogenizing buffer (40 mM Tris-HCl, pH 7.5, 15 mM benzamidine, 5 μg/ml pepstatin A, 5 μg/ml leupeptin). The obtained homogenate was centrifuged (100000 g, 60 min.) to collect supernatant.
The above-obtained supernatant was applied to a nickel-nitrotriacetate resin (available from Qiagen) equilibrated with a buffer solution and incubated at 4° C. for 4 hours. This resin was filled in a column (0.8×5 cm) and then, the resin in the column was washed with a washing buffer (40 mM Tris-HCl, pH 7.5, 15 mM benzamidine, 200 mM sodium chloride, 5 mM imidazole, 5 μg/ml pepstatin A, 5 μg/ml leupeptin). Then, proteins were eluted with an eluting buffer (40 mM Tris-HCl, pH 7.5, 15 mM benzamidine, 200 mM sodium chloride, 200 mM imidazole, 5 μg/ml pepstatin A, 5 μg/ml leupeptin).
The obtained protein was measured with respect to hydrolysis activity (PDE activity) for cAMP and cGMP, it was found to have a hydrolysis activity for both cAMP and cGMP.
Incidentally, measurement of PDE activity was done according to a radio-labeled nucleotide method. That is, to 500 μl of a buffer for an assay [50 mM Tris-HCl, pH 8.0, 5 mM magnesium chloride, 4 mM 2-mercaptoethanol, 0.33 mg/ml bovine serum albumin (available from Sigma)], containing 1 μM of unlabeled cAMP (or cGMP) and 22 nM of [3H]-cAMP (or [3H]-cGMP) (available from Amersham Pharmacia Biotech), 8 ̃10 μl of the enzyme solution was added to start a reaction. After carrying out a reaction by keeping a temperature at 37° C. for 30 minutes, reaction was terminated by boiling the reaction mixture for 2 minutes, and 100 μl of 1 mg/ml of snake venom (Crotalus atrox snake venom) was further added thereto and the temperature was kept at 37° C. for 30 minutes. Subsequently, 500 μl of methanol was added thereto, and the reaction mixture was applied to Dowex column (1×8-400). Scintillation cocktail was added to each of the eluates, and radioactivity was measured.
Example 4
Expression and Purification of Human PDE11A2 in COS Cells
(1) Construction of a Vector Plasmid for PDE11A2 Expression
With respect to human PDE11A2 obtained in the above Example 2, cDNA fragment amplified in Example 2 (4) was linked to a vector plasmid pGEM-T Easy (available from Promega) to obtain a plasmid pGEM-PDE11TF. Using this pGEM-PDE11TF as a template, PCR was carried out using oligonucleotides comprising a nucleotide sequence shown in SEQ.ID.NOs: 26 and 27 of the below mentioned sequence listing as a sense primer and an anti-sense primer, respectively. Incidentally, these PCR primers were designed based on the 100th to 417th nucleotide sequence of SEQ.ID.NO: 3 (That is, a nucleotide sequence corresponding to the 1st to the 106th amino acid residues of SEQ.ID.NO: 4).
cDNA fragment amplified by PCR was linked to pGEM-T Easy (available from Promega) to obtain a plasmid pGEM-PDE11TBM, and its nucleotide sequence was confirmed.
Further, cDNA fragments obtained by treating pGEM-PDE11TF with restriction enzymes SacI and EcoRV, and EcoRV and SalI, cDNA fragments obtained by treating pGEM-PDE11TBM with restriction enzymes BamHI and SacI were inserted into a BamHI-XhoI site of an expression vector, pHis, to obtain a vector plasmid pHis-PDE11T for PDE11A2 expression.
(2) Transfection of COS Cells
COS-7 cells which were subcultured under the same conditions as in the above Example 3 (2) were transfected with the above-mentioned pHis-PDE11T (or vector pHis for control) in the same manner as in the above Example 3 (2).
(3) Purification of Recombinant Human PDE11A2
Purification of recombinant human PDE11A2 was carried out in the same manner as in the above Example 3 (3). Also, when its PDE activity was measured in the same manner as in the above Example 3 (3), it was found to have a hydrolysis activity for both cAMP and cGMP.
Example 5
Analysis of Enzymatic Properties of Human PDE11
Using each of the purified recombinant human PDE11A1 obtained in Example 3 and the purified recombinant human PDE11A2 obtained in Example 4, various enzymatic properties of human PDE11 were analyzed.
(1) Kinetic Analysis of Enzyme Reaction
Enzyme reactions were carried out using a substrate (cAMP or cGMP) of various concentrations, to measure PDE activity (initial reaction rate). Enzyme reaction and PDE activity measurement were done in the same manner as in the above Example 3 (3), provided that, in a reaction mixture, a concentration of unlabeled cAMP (or cGMP) was set to be 0.1 to 10 μM.
The results (Lineweaver-Burk plot) are shown in FIG. 1 for human PDE11A1 and FIG. 2 for human PDE11A2.
From the analysis, Km value of human PDE11A1 was 2.96±0.4 5 7 μM, and Vmax was 267±47.9 pmol/min/μg of protein, when cAMP was a substrate. On the other hand, Km value of human PDE11A1 was 1.43±0.109 μM and Vmax was 121±8.08 pmol/min/μg protein, when cGMP was a substrate.
Km value of human PDE11A2 was 2.99±0.488 μM and Vmax was 9.63±1.88 pmol/min/μg protein, when cAMP was a substrate. On the other hand, Km value of human PDE11A2 was 1.47±0.115 μM and Vmax was 4.02±0.214 p mol/min/μg of protein, when cGMP was a substrate.
From the above, it was found that although human PDE11 has an activity of hydrolyzing both cAMP and cGMP, it has a higher affinity for cGMP.
(2) Influence of cGMP on cAMP Hydrolysis Activity and Influence of cAMP on cGMP Hydrolysis Activity
It was studied how an addition of cGMP of various concentrations to a reaction mixture would affect cAMP hydrolysis activity. It was also studied how an addition of cAMP of various concentrations to a reaction mixture would affect cGMP hydrolysis activity.
Enzyme reaction and PDE activity measurement were done in the same manner as in the above Example 3 (3), except that in an experiment for measuring cAMP hydrolysis activity, 3.5 μM of unlabeled cAMP was added, and 0.01 ̃100 μM of cGMP (unlabeled) was added (or was not added). On the other hand, in an experiment for measuring cGMP hydrolysis activity, 1.3 μM of unlabeld cGMP was added, and 0.01 ̃100 μM of cAMP (unlabeled) was added (or was not added).
cAMP hydrolysis activity was calculated as a relative value (%) taking an activity measured without adding cGMP as 100%. Also, cGMP hydrolysis activity was calculated as a relative value (%) taking an activity measured without adding cAMP as 100%. The results are shown in FIG. 3. It is clearly confirmed in FIG. 3 that, in case of human PDE11, cAMP hydrolysis activity was lowered depending on a concentration of cGMP added, while cGMP hydrolysis activity was lowered depending on a concentration of cAMP added.
(3) Inhibition of Activity by Various Known PDE Inhibitors
Effects of various known PDE inhibitors [IBMX, Vinpocetine, EHNA, Milrinone, Rolipram, Zaprinast, Dipyridamole, SCH51866, and E4021] on a cAMP and cGMP hydrolysis activity (PDE activity) of human PDE11 were studied as follows.
Enzyme reaction was carried out using cAMP or cGMP as a substrate, and various kinds of known PDE inhibitors were added in the reaction mixture to measure a hydrolysis activity. Enzyme reaction and measurement of PDE activity was done in the same manner as in the above Example 3 (3), except that, in the reaction mixture, in case of adding unlabeled cAMP, a concentration was 3.5 μM, and in case of adding unlabeled cGMP, a concentration was 1.3 μM, and various kinds of known PDE inhibitors were added in an amount of 0 ̃100 μM.
Inhibitory actions of various PDE inhibitors on an activity of human PDE11 expressed in terms of IC 50 are shown in Table 1 for human PDE11A1 and Table 2 for human PDE11A2, respectively.










TABLE 1









IC50 value (μM) for human




PDE11A1 activity












Effect on cAMP
Effect on cGMP



Inhibitor
hydrolysis activity
hydrolysis activity







IBMX
65 ± 13
81 ± 16



Vinpocetine
>100
>100



EHNA
>100
>100



Milrinone
>100
>100



Rolipram
>100
>100



Zaprinast
 26 ± 6.8
 33 ± 5.3



Dipyridamole
0.82 ± 0.28
0.72 ± 0.08



SCH51866
 22 ± 1.8
 25 ± 5.8



E4021
 1.8 ± 0.33
 1.8 ± 0.25




















TABLE 2









IC50 value (μM) for human




PDE11A2 activity












Effect on cAMP
Effect on cGMP



Inhibitor
hydrolysis activity
hydrolysis activity







IBMX
 30 ± 3.9
 38 ± 3.5



Vinpocetine
 49 ± 9.2
 68 ± 4.0



EHNA
>100
>100



Milrinone
>100
>100



Rolipram
>100
>100



Zaprinast
 18 ± 1.0
 11 ± 3.6



Dipyridamole
0.36 ± 0.11
0.34 ± 0.09



SCH51866
 11 ± 4.8
8.6 ± 2.7



E4021
0.88 ± 0.13
0.66 ± 0.19










Example 6
Expressions of PDE11 in Various Tissues of Human
Various kinds of human tissues were examined whether or not PDE11 gene was expressed as follows.
Using mRNAs of various human tissues (Human Multiple Tissue Expression Array: available from Clontech), dot blot analysis was done with respect to mRNAs of tissues and organs as shown in FIG. 4. As a probe, a DNA fragment obtained in the above Examples 1 and 2 coding a part of human PDE11A (a nucleotide sequence of the fragment corresponds to the 1237th to the 1801st nucleotide sequence of the human PDE11A1 cDNA shown in SEQ.ID.NO: 1, and also corresponds to the 268th to the 832nd nucleotide sequence of the human PDE11A2 cDNA shown in SEQ.ID.NO: 3.) was used by labeling with 32P. In addition, an amount of mRNA was controlled to make signal for probes constant, when cDNA of human ubiquitin and major histocompatibility complex class Ic were taken as probes.
Hybridization was carried out under conditions described below. That is, a nylon membrane was placed in a hybridization solution containing a probe labeled with 32P (50% formamide, 4×SSC, 0.5% SDS, 5×Denhardt's solution, 100 g/ml salmon sperm DNA) at 42° C. for 20 hours for hybridization to proceed. Subsequently, the membrane was washed with washing solution A (0.5×SSC, 0.1% SDS) at room temperature for 3 min and further washed with washing solution B (0.2×SSC, 0.1% SDS) at 60° C. for 30 min. for twice. Subsequently, autoradiography was carried out at −80° C. for 3 days.
The result of dot blotting, as shown in FIG. 4, strong expressions of PDE11 mRNA were detected in prostate and testis. Also, slightly weak expressions were detected in salivary gland, pituitary gland, thyroid gland and liver (order of intensity of expression was in order of the description).
Further, with respect to mRNA of human testis and human prostate, Northern blot analysis was done using the same probe as the above and under the same conditions.
As a result of Northern blotting analysis, a band of about 3 kb was detected in testis, and in prostate, bands of about 2 kb, about 6 kb and about 10 kb were observed.
Example 7
Isolation of cDNA of Novel Rat PDE (PDE11) (I)
(1) Based on the information on the nucleotide sequence of the cDNA of human PDE11A obtained in the above Examples 1 and 2, PCR primers were designed, and RT-PCR was carried out using these to isolate cDNA of PDE11 from mRNA of rat testis.
That is, reverse transcript reaction was carried out using mRNA of rat testis (available from Wako Junyaku), RNA PCR kit (available from PE Biosystems, GeneAmp RNA PCR Core kit) and random primer (hexamer) to obtain cDNA. Using the obtained cDNA as a-template, PCR was carried out. As PCR primers, oligonucleotides comprising nucleotide sequences shown in SEQ.ID.NOs: 28 and 29 of the below mentioned sequence listing were used as a sense primer and an anti-sense primer, respectively. The PCR reaction was repeated for 30 cycles in total, one cycle being carried out under conditions of at 95° C. for 30 sec., at 54° C. for 30 sec., and at 72° C. for 2 min.
A nucleotide sequence of the cDNA fragment amplified by PCR was determined.
(2) In order to obtain full-length cDNA from the cDNA fragment obtained in the above (1), 5′-RACE and 3′-RACE were done using mRNA of rat testis (available from Wako Junyaku) according to the below described procedures. For RACE, a kit for RACE (available from Clontech, SMART RACE cDNA Amplification kit) was used.
First, 5′-RACE was done to recover a part of 5′ end region. As primers, in the first amplification, the first primer (UPM primer) corresponding to the linker part and a primer comprising a sequence shown in SEQ.ID.NO: 30 of the below mentioned sequence listing, and in the second amplification, the second primer corresponding to the linker part (NUP primer) and a primer comprising a sequence shown in SEQ.ID.NO: 31 were used, respectively, as a sense primer and an anti-sense primer. These two kinds of anti-sense primers were designed according to the information on the nucleotide sequence of the cDNA obtained in the above (1).
5′-RACE was further carried out to completely recover the 5′ end region. As primers, in the first amplification, the UPM primer and a primer comprising a sequence shown in SEQ.ID.NO: 32 of the below mentioned sequence listing, and in the second amplification, the NUP primer and a primer comprising a sequence shown in SEQ.ID.NO: 33 were used, respectively, as a sense primer and an anti-sense primer. These two kinds of anti-sense primers were designed according to the information on the nucleotide sequence of the above-recovered 5′ end region.
Next, 3′-RACE was done to completely recover a 3′ end region. As primers, in the first amplification, a primer comprising a sequence shown in SEQ.ID.NO: 34 of the below mentioned sequence listing and the UPM primer, and in the second amplification, a primer comprising a sequence shown in SEQ.ID.NO: 35 and the NUP primer were used, respectively, as a sense primer and an anti-sense primer. These two kinds of anti-sense primers were designed according to the information on the nucleotide sequence of the cDNA fragment obtained in the above (1).
(3) After analyzing the nucleotide sequence of the thus obtained full-length cDNA, it was compared to an amino acid sequence of the known PDE to identify an open reading frame.
Further, PCR primers enclosing the open reading frame were designed based on the information on the nucleotide sequence, and RT-PCR was carried out using these primers and mRNA of rat testis as follows.
That is, a reverse transcription reaction was carried out using mRNA of rat testis (available from Wako Junyaku), RNA PCR kit (GeneAmp RNA PCR Core kit, available from PE Biosystems) and a polydT-tailed primer to obtain cDNA. Using the obtained cDNA as a template, PCR reaction was carried out. As a PCR primer, oligonucleotides comprising nucleotide sequences shown in SEQ.ID.NOs: 36 and 37 were used as a sense primer and an anti-sense primer, respectively. PCR reaction was repeated for 30 cycles in total, one cycle being carried out under conditions of at 95° C. for 30 sec., at 57° C. for 30 sec. and at 72° C. for 3 min.
With respect to plural clones obtained from PCR, nucleotide sequences of cDNA fragments (about 2.3 kb) were determined, and by comparing each of them, errors made by PCR were corrected to confirm a nucleotide sequence of a full-length cDNA.
(4) The thus obtained full-length cDNA (3492 bp) was thought to be a full-length cDNA of a novel rat PDE (referred to as rat PDE11 or rat PDE11A.) gene. The nucleotide sequence was shown in SEQ.ID.NO: 5 of the below mentioned sequence listing, and an amino acid sequence of a protein encoded thereby, that is, rat PDE11 (specifically referred to as rat PDE11A2.) was shown in SEQ.ID.NO: 6. A molecular weight of rat PDE11 (rat PDE11A2) estimated from the amino acid sequence (685 amino acid residues) was about 78 kDa.
When the amino acid sequence of rat PDE11 (rat PDE11A2) was compared to the amino acid sequence of human PDE11A2 obtained in Example 2, a homology as high as about 93% was confirmed.
Example 8
Isolation of cDNA of Novel Rat PDE (PDE11) (II)
(1) 5′-RACE was carried out using cDNA derived from rat liver (available from Clontech, Marathon-Ready cDNA (rat liver) was used). As primers, in the first amplification, the first primer (AP1 primer) corresponding to the linker part and a primer comprising a sequence shown in SEQ.ID.NO: 32 of the below mentioned sequence listing, and in the second amplification, the second primer corresponding to the linker part (AP2 primer) and a primer comprising a sequence shown in SEQ.ID.NO: 33 were used, respectively, as a sense primer and an anti-sense primer. These two kinds of anti-sense primers were designed according to the information on the nucleotide sequence of the cDNA of the rat PDE11 (rat PDE11A2) obtained in the above Example 7.
5′-RACE was further carried out using the cDNA of rat liver (available from Clontech, Marathon-Ready cDNA (rat liver) was used) to completely recover the 5′ end region. As primers, in the first amplification, the AP1 primer and a primer comprising a sequence shown in SEQ.ID.NO: 40 of the below mentioned sequence listing, and in the second amplification, the AP2 primer and a primer comprising a sequence shown in SEQ.ID.NO: 41 were used, respectively, as a sense primer and an anti-sense primer. These two kinds of anti-sense primers were designed according to the information on the nucleotide sequence of the 5′ end region recovered in the above 5′-RACE.
(2) After analyzing the nucleotide sequence of the thus obtained full-length cDNA, it was compared to an amino acid sequence of the known PDE to identify an open reading frame.
Further, PCR primers enclosing the open reading frame were designed based on the information on the nucleotide sequence, and RT-PCR was carried out using these primers and mRNA derived from rat liver as follows.
That is, a reverse transcript reaction was carried out using mRNA of rat liver (available from Clontech), RNA PCR kit (GeneAmp RNA PCR Core kit, available from PE Biosystems) and random primer (hexamer) to obtain cDNA. Using the obtained cDNA as a template, PCR reaction was carried out. As PCR primers, oligonucleotides comprising nucleotide sequences shown in SEQ.ID.NOs: 42 and 37 were used as a sense primer and an anti-sense primer, respectively. PCR reaction was repeated for 30 cycles in total, one cycle being carried out under conditions of at 95° C. for 30 sec., at 57° C. for 30 sec. and at 72° C. for 4 min.
With respect to plural clones obtained from PCR, nucleotide sequences of cDNA fragments (about 3.0 kb) were determined, and by comparing each of them, errors made by PCR were corrected to determine a nucleotide sequence of a full-length cDNA.
(3) The thus obtained full-length cDNA (4170 bp) was thought to be a full-length cDNA of a novel rat PDE (rat PDE11A) gene. The nucleotide sequence was shown in SEQ.ID.NO: 38 of the below mentioned sequence listing, and an amino acid sequence of a protein encoded thereby, that is, rat PDE11 (specifically referred to as rat PDE11A1.) was shown in SEQ.ID.NO: 39. A molecular weight of rat PDE11 (rat PDE11A1) estimated from the amino acid sequence (935 amino acid residues) was about 105 kDa.
When the amino acid sequence of rat PDE11 (rat PDE11A1) was compared to the amino acid sequence of human PDE11A1 obtained in Example 1, a homology of as high as about 94% was confirmed.
INDUSTRIAL APPLICABILITY
The novel PDE of the present invention and the gene thereof are useful for study of a complex mechanism of intracellular signal transduction. Also, it can possibly serve as a target compound of a therapeutic agent for novel disease.
Additionally, a method for characterizing, identifying and selecting an inhibitor, using the novel PDE of the present invention and the gene thereof is useful for development of an inhibitor with a high selectivity and an excellent pharmaceutical with a high therapeutic effect and less side effect.

## Claims

1. An isolated protein having the amino acid sequence shown by SEQ ID NO:2.

2. The protein according to claim 1, wherein said protein is a human protein.

3. The protein according to claim 1, wherein said protein is a recombinant protein.