23413, a novel human ubiquitin protease

Abstract

The present invention relates to a newly identified human ubiquitin protease belonging to the family of mammalian deubiquitinating enzymes. The invention also relates to polynucleotides encoding the ubiquitin protease. The invention further relates to methods using the ubiquitin protease polypeptides and polynucleotides as a target for diagnosis and treatment in ubiquitin-mediated or -related disorders. The invention further relates to drug-screening methods using the ubiquitin protease polypeptides and polynucleotides to identify agonists and antagonists for diagnosis and treatment. The invention further encompasses agonists and antagonists based on the ubiquitin protease polypeptides and polynucleotides. The invention further relates to procedures for producing the ubiquitin protease polypeptides and polynucleotides.

That which is claimed:  
     
         1 . An isolated nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of: 
 (a) a nucleotide sequence having at least 65% sequence identity to the nucleotide sequence set forth in SEQ ID NO:2, wherein said sequence identity is calculated using the GAP algorithm with a gap weight of 40 and a length weight of 4 and said nucleotide sequence encodes a polypeptide having ubiquitin protease activity; and    (b) a nucleotide sequence complementary the nucleotide sequence of (a).    
     
     
         2 . The nucleic acid molecule of  claim 1 , wherein said nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of: 
 (a) a nucleotide sequence having at least 70% sequence identity to the nucleotide sequence set forth in SEQ ID NO:2, wherein said sequence identity is calculated using the GAP algorithm with a gap weight of 40 and a length weight of 4 and said nucleotide sequence encodes a polypeptide having ubiquitin protease activity;    (b) a nucleotide sequence complementary to the nucleotide sequence of (a).    
     
     
         3 . The nucleic acid molecule of  claim 2 , wherein said nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of: 
 (a) a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence set forth in SEQ ID NO:2, wherein said sequence identity is calculated using the GAP algorithm with a gap weight of 40 and a length weight of 4 and said nucleotide sequence encodes a polypeptide having ubiquitin protease activity;    (b) a nucleotide sequence complementary to the nucleotide sequence of (a).    
     
     
         4 . The nucleic acid molecule of  claim 3 , wherein said nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of: 
 (a) a nucleotide sequence having at least 90% sequence identity to the nucleotide sequence set forth in SEQ ID NO:2, wherein said sequence identity is calculated using the GAP algorithm with a gap weight of 40 and a length weight of 4 and said nucleotide sequence encodes a polypeptide having ubiquitin protease activity;    (b) a nucleotide sequence complementary to the nucleotide sequence of (a).    
     
     
         5 . An isolated nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of: 
 (a) a nucleotide sequence encoding a polypeptide having ubiquitin protease activity, wherein said nucleotide sequence hybridizes to the complement of the nucleotide sequence shown in SEQ ID NO:2 under stringent conditions, said stringent conditions comprising hybridization in 6× sodium chloride/sodium citrate (SSC) at about 45° C., followed by one or more washes in 0.2 × SSC, 0.1% SDS at 65° C.;    (b) a nucleotide sequence encoding a polypeptide having ubiquitin protease activity, wherein said nucleotide sequence hybridizes to the cDNA insert contained in ATCC Patent Deposit No. PTA-1652 under stringent conditions, said stringent conditions comprising hybridization in 6× sodium chloride/sodium citrate (SSC) at about 45° C., followed by one or more washes in 0.2× SSC, 0.1% SDS at 65° C.; and    (c) a nucleotide sequence complementary to the nucleotide sequence of (a) or (b).    
     
     
         6 . An isolated nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of: 
 (a) a nucleotide sequence encoding a fragment of the amino acid sequence set forth in SEQ ID NO:1, wherein said fragment has ubiquitin protease activity and consists of at least 15 contiguous amino acids of the amino acid sequence set forth in SEQ ID NO:1;    (b) a nucleotide sequence encoding a fragment of the amino acid sequence encoded by the cDNA insert of the plasmid deposited with ATCC as Patent Deposit No. PTA-1652, wherein said fragment has ubiquitin protease activity and consists of at least 15 contiguous amino acids of the amino acid sequence encoded by the cDNA insert of the plasmid deposited with ATCC as Patent Deposit No. PTA-1652;    (c) a nucleotide sequence encoding a fragment of the amino acid sequence set forth in SEQ ID NO:1, wherein said fragment has ubiquitin protease activity and consists of at least 25 contiguous amino acids of the amino acid sequence set forth in SEQ ID NO:1;    (d) a nucleotide sequence encoding a fragment of the amino acid sequence encoded by the cDNA insert of the plasmid deposited with ATCC as Patent Deposit No. PTA-1652, wherein said fragment has ubiquitin protease activity and consists of at least 25 contiguous amino acids of the amino acid sequence encoded by the cDNA insert of the plasmid deposited with ATCC as Patent Deposit No. PTA-1652;    (e) a nucleotide sequence encoding a fragment of the amino acid sequence set forth in SEQ ID NO:1, wherein said fragment has ubiquitin protease activity and consists of at least 35 contiguous amino acids of the amino acid sequence set forth in SEQ ID NO:1; and    (f) a nucleotide sequence encoding a fragment of the amino acid sequence encoded by the cDNA insert of the plasmid deposited with ATCC as Patent Deposit No. PTA-1652, wherein said fragment has ubiquitin protease activity and consists of at least 35 contiguous amino acids of the amino acid sequence encoded by the cDNA insert of the plasmid deposited with ATCC as Patent Deposit No. PTA-1652;    (g) a nucleotide sequence encoding a fragment of the amino acid sequence set forth in SEQ ID NO:1, wherein said fragment has ubiquitin protease activity and consists of at least 45 contiguous amino acids of the amino acid sequence set forth in SEQ ID NO:1; and    (h) a nucleotide sequence encoding a fragment of the amino acid sequence encoded by the cDNA insert of the plasmid deposited with ATCC as Patent Deposit No. PTA-1652, wherein said fragment has ubiquitin protease activity and consists of at least 45 contiguous amino acids of the amino acid sequence encoded by the cDNA insert of the plasmid deposited with ATCC as Patent Deposit No. PTA-1652.    
     
     
         7 . A method for producing a polypeptide comprising an amino acid sequence selected from the group consisting of: 
 (a) an amino acid sequence having at least 70% sequence identity to the amino acid sequence set forth in SEQ ID NO:1 wherein said polypeptide has ubiquitin protease activity and said sequence identity is calculated by the GAP algorithm using a Blossum 62 scoring matrix with a gap weight of 12 and a length weight of 4;    (b) an amino acid sequence having at least 80% sequence identity to the amino acid sequence set forth in SEQ ID NO:1 wherein said polypeptide has ubiquitin protease activity and said sequence identity is calculated by the GAP algorithm using a Blossum 62 scoring matrix with a gap weight of 12 and a length weight of 4;    (c) an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO:1 wherein said polypeptide has ubiquitin protease activity and said sequence identity is calculated by the GAP algorithm using a Blossum 62 scoring matrix with a gap weight of 12 and a length weight of 4;    said method comprising the steps of introducing a nucleic acid molecule encoding the polypeptide into a host cell and culturing the host cell under conditions in which the polypeptide is expressed from the nucleic acid molecule.    
     
     
         8 . An isolated polypeptide comprising an amino acid sequence selected from the group consisting of: 
 (a) the amino acid sequence set forth in SEQ ID NO:1;    (b) the amino acid sequence encoded by the cDNA insert of the plasmid deposited with the ATCC as Patent Deposit Number PTA-1652;    (c) the amino acid sequence of a sequence variant of the amino acid sequence shown in SEQ ID NO:1, wherein said sequence variant has ubiquitin protease activity and is encoded by a nucleotide sequence having at least about 70% sequence identity to the nucleotide sequence set forth in SEQ ID NO:2;    (d) the amino acid sequence of an sequence variant of the amino acid sequence encoded by the cDNA insert of the plasmid deposited with the ATCC as Patent Deposit Number PTA-1652, wherein said sequence variant has ubiquitin protease activity and is encoded by a nucleotide sequence having at least about 70% sequence identity to the nucleotide sequence of the cDNA insert of the plasmid deposited with the ATCC as Patent Deposit Number PTA-1652;    (e) the amino acid sequence of a sequence variant of the amino acid sequence shown in SEQ ID NO:1, wherein the sequence variant has ubiquitin protease activity and is encoded by a nucleic acid molecule that hybridizes to the complement of the nucleotide sequence set forth in SEQ ID NO:2 under stringent conditions;    (f) the amino acid sequence of a sequence variant of the amino acid sequence encoded by the cDNA insert of the plasmid deposited with the ATCC as Patent Deposit Number PTA-1652, wherein the sequence variant has ubiquitin protease activity and is encoded by a nucleic acid molecule that hybridizes under stringent conditions the cDNA insert of the plasmid deposited with the ATCC as Patent Deposit Number PTA-1652;    (g) the amino acid sequence of the mature polypeptide from about amino acid 6 to the last amino acid set forth in SEQ ID NO:1;    (h) the amino acid sequence of a fragment of the amino acid sequence set forth in SEQ ID NO:1, wherein said fragment has ubiquitin protease activity and consists of at least 15 contiguous amino acids of the amino acid sequence set forth in SEQ ID NO:1; and    (i) the amino acid sequence of a fragment of the amino acid sequence encoded by the cDNA insert of the plasmid deposited with the ATCC as Patent Deposit Number PTA-1652, wherein the fragment has ubiquitin protease activity and consists of at least 15 contiguous amino acids of the amino acid sequence encoded by the cDNA insert of the plasmid deposited with the ATCC as Patent Deposit Number PTA-1652.    
     
     
         9 . An isolated antibody that selectively binds to a polypeptide of  claim 8 .  
     
     
         10 . A method for detecting the presence of at least one polypeptides of  claim 8  in a sample, said method comprising contacting said sample with an agent that specifically allows detection of the presence of the polypeptide in the sample and then detecting the presence of the polypeptide.  
     
     
         11 . The method of  claim 10 , wherein said agent is an antibody.  
     
     
         12 . The method of  claim 10 , wherein said agent is ubiquitinated protein or polyubiquitin.  
     
     
         13 . A kit comprising reagents used for the method of  claim 8 , wherein the reagents comprise an agent that specifically binds to said polypeptide.  
     
     
         14 . A method for identifying an agent that binds to any of the polypeptides in  claim 8 , said method comprising contacting the polypeptide with an agent that binds to the polypeptide and assaying the complex formed with the agent bound to the polypeptide.  
     
     
         15 . A method for identifying an agent that modulates the level or activity of any of the polypeptides in  claim 1  in a cell, the method comprising contacting the agent with a cell capable of expressing said polypeptide such that said polypeptide level or activity can be modulated in said cell by said agent and measuring said polypeptide level or activity.  
     
     
         16 . A method for identifying an agent that interacts with any of the polypeptides in  claim 8  in a cell, the method comprising contacting said agent with a cell expressing a polypeptide of  claim 8  under conditions such that said polypeptide can interact with said agent and measuring the interaction between said polypeptide and said agent.  
     
     
         17 . A method of screening a cell to identify an agent that modulates the level or activity of any of the polypeptides in  claim 8  in said cell, said method comprising contacting said agent with a cell capable of expressing said polypeptide such that said polypeptide level or activity can be modulated in said cell by said agent and measuring said polypeptide level or activity.  
     
     
         18 . A method of screening a cell to identify an agent that interacts with any of the polypeptides in  claim 8 , said method comprising contacting said agent with a cell capable of allowing an interaction between said polypeptide and said agent such that said polypeptide can interact with said agent and measuring the interaction.  
     
     
         19 . A method for modulating the activity of any of at least one polypeptide of  claim 8 , the method comprising contacting a polypeptide of  claim 8  with an agent under conditions that allow the agent to modulate the activity of the polypeptide.  
     
     
         20 . The method of  claim 19  wherein said modulation is in cells derived from tissues selected from the group consisting of breast, testes, brain, lung, kidney, liver, and colonic liver metastases.  
     
     
         21 . The method of  claim 20  wherein said cells are malignant breast, lung, and colonic liver metastatic cells.  
     
     
         22 . The method of  claim 20  wherein said modulation is in a patient having breast cancer.  
     
     
         23 . A composition containing any of the polypeptides in  claim 8  in a pharmaceutically acceptable carrier.