WO1997040192A1

WO1997040192A1 - Novel protein - traf6

Info

Publication number: WO1997040192A1
Application number: PCT/US1997/006451
Authority: WO
Inventors: David V. Goeddel; Jessie Xiong
Original assignee: Tularik, Inc.
Priority date: 1996-04-19
Filing date: 1997-04-19
Publication date: 1997-10-30
Also published as: US5710013A; EP0895545A1; EP0895545A4; CA2250425A1; US5767244A; JP2000509272A; AU706887B2; AU2675197A

Abstract

The invention provides methods and compositions relating to a novel tumor necrosis factor receptor associated factor number six (TRAF6) polypeptide, which transcriptionally activates Nuclear Factor λB. The invention provides isolated TRAF6 hybridization probes and primers capable of hybridizing with the disclosed TRAF6 gene, nucleic acids encoding the subject TRAF6 polypeptides, methods of making the subject TRAF6 polypeptides, and methods of using the subject compositions in diagnosis and drug screening.

Description

NOVEL PROTEIN - TRAF6

INTRODUCTION field of the Invention

The field of this invention is a class of human proteins involved in transcription and irnmuno-regulation.

Background

Nuclear factor KB (NF-KB) is a homo- or heterodimer of members of the Rel family of transcriptional activators that is involved in the inducible expression of a wide variety of important cellular genes including numerous cytokines, cytokine receptors, major histocompatibility antigens, serum amyloid A protein, etc. as well as many viral genes including genes of HTV, SV40, cytomegalovirus, etc.

Several tumor necrosis factor receptor-associated factor (TRAF) proteins have been identified and shown to be involved in the signaling of various cellular responses including cytotoxicity, anti-viral activity, irnmuno-regulatory activities and the transcriptional regulation of a number of genes.

Accordingly, the ability to exogenously modulate the activity of NF-κB and/or TRAF proteins would yield therapeutic application for numerous clinical indications. In addition, components of such pathways would provide valuable target reagents for automated, cost- effective, high throughput drug screening assays and hence would have immediate application in domestic and intemational pharmaceutical and biotechnology drug development programs. The present invention provides novel TRAF proteins which regulate NF-κB expression, their use in drug screens, and nucleic acids encoding the same.

Relevant Literature Rothe et al. (1994) Cell 78, 681-692 report that NF-κB expression can be mediated by the 75-80 kDa TNF receptor (TNF-R2), that a short region of the 78 amino acids at the C- terminus of the cytoplasmic domain of TNF-R2 is required for signaling NF-κB activation, and that this region binds to closely related putative effectors, TRAF1 and TRAF2, see also, Hsu et al. (1995) Cell 81, 495 and Rothe et al, pending US patent application Serial No: 08/446,915. A third distinct TRAF, TRAF3, has been reported by Huet al. (1994) J. Biol Chem 269, 30069; Cheng et al. (1995) Science 267, 1494-1498; Mosialos et al. (1995) Cell 80, 389; and Sato et al (1995) FEBS Letters, 358, 113. Rothe et al. (1995) Science 269, 1424-1427 report TRAF2- (but not TRAF1- or 3-) mediated activation of NF-κB by TNF-R2 and CD40.

SUMMARY OF THE INVENTION

The invention provides methods and compositions relating to a novel tumor necrosis factor receptor associated factor number six (TRAF6) protein and gene. The subject TRAF6 proteins are encoded by cDNAs which hybridizes with SEQ LD NO:01 under high stringency conditions; specifically bind a natural intracellular TRAF6 binding target and comprise the amino sequence of SEQ LD NO: 2 or fragment thereof sufficient to specifically bind a natural intracellular TRAF6 binding target.

The invention also provides isolated TRAF6 hybridization probes and primers capable of hybridizing with the disclosed TRAF6 cDNA, nucleic acids encoding the subject TRAF6 proteins, methods of making the subject TRAF6 proteins, and methods of using the subject compositions in diagnosis (e.g. genetic hybridization screens for TRAF6 gene mutations), and in the biopharmaceutical industry (e.g. reagents for screening chemical libraries for lead compounds for a pharmacological agent useful in the diagnosis or treatment of disease associated with immune regulation).

BRIEF DESCRIPΗON OF THE FIGURES

Figure 1 shows the effect of coexpression of a TRAF 6 deletion mutant on NF-κB-dependent reporter gene activation by TRAF6.

Figure 2 shows NF-κB-dependent reporter gene activation by TRAF proteins.

DETAILED DESCRIPTION OF THE INVENTION

The nucleotide sequence of a natural cDNA encoding human TRAF6 is shown as SEQ LD NO: 1 and the full conceptual translate shown as SEQ LD NO:2. The TRAF6 proteins of the invention include incomplete translates of SEQ LD NO:l and deletion mutants of SEQ LD NO: 2, which translates and deletions mutants have TRAFό-specific activity. The nucleotide sequence of a natural cDNA encoding a human TRAF6 polypeptide is shown as SEQ ID NO: 1 , and the full conceptual translate is shown as SEQ LD NO:2. The TRAF6 polypeptides of the invention include incomplete translates of SEQ LD NO:l and deletion mutants of SEQ LD NO:2, which translates and deletion mutants have TRAF6- specific amino acid sequence and binding specificity or function. Hence, the TRAF6 polypeptides of the invention include polypeptides comprising SEQ LD NO:2 and TRAF6 domains thereof. Such TRAF6 domains have at least 10, preferably at least about 12, more preferably at least about 14 consecutive residues of SEQ LD NO:2 and provide TRAF6 specific activity or function, such as specifically binding TRAF6, TRAF2 and/or TRAF3 distinguishably from TRAF 1-5.

TRAFό-specific activity or function may be determined by convenient in vitro, cell- based, or in vivo assays: e.g. in vitro binding assays, cell culture assays, in ariimals (e.g. gene therapy, transgenics, etc.), etc. Binding assays encompass any assay where the molecular interaction of a TRAF6 polypeptide with a binding target is evaluated. The binding target may be a natural intracellular binding target such as TRAF6 (dimerization) or other TRAF6 regulator protein that directly modulates TRAF6 activity or its localization; or non-natural binding target such a specific immune protein such as an antibody, or a TRAF6 specific agent such as those identified in screening assays such as described below. TRAF6-binding specificity may assayed by binding equilibrium constants (usually at least about 10⁷M ', preferably at least about 10⁸ M^"1, more preferably at least about IO⁹ M^"1), by the ability of the subject polypeptide to function as negative mutants in TRAF6-expressing cells, to elicit TRAF6 specific antibody in a heterologous host (e.g a rodent or rabbit), etc. In any event, the TRAF6 binding specificity of the subject TRAF6 polypeptides necessarily distinguishes TRAF1-5.

The claimed TRAF6 polypeptides are isolated or pure: an "isolated" polypeptide is unaccompanied by at least some of the material with which it is associated in its natural state, preferably constituting at least about 0.5%, and more preferably at least about 5% by weight of the total polypeptide in a given sample and a pure polypeptide constitutes at least about 90%, and preferably at least about 99% by weight of the total polypeptide in a given sample. The TRAF6 polypeptides and polypeptide domains may be synthesized, produced by recombinant technology, or purified from mammalian, preferably human cells. A wide variety of molecular and biochemical methods are available for biochemical synthesis, molecular expression and purification of the subject compositions, see e.g. Molecular

Cloning, A Laboratory Manual (Sambrook, et al. Cold Spring Harbor Laboratory), Current Protocols in Molecular Biology (Eds. Ausubel, et al, Greene Publ. Assoc, Wiley- Interscience, NY) or that are otherwise known in the art.

The invention provides natural and non-natural TRAFό-specific binding agents, methods of identifying and making such agents, and their use in diagnosis, therapy and pharmaceutical development. For example, TRAF6-specific agents are useful in a variety of diagnostic and therapeutic applications, especially where disease or disease prognosis is associated with improper utilization of a pathway involving TRAF6, e.g. NF-κB activation. Novel TRAF6-specific binding agents include TRAFό-specific receptors, such as somatically recombined polypeptide receptors like specific antibodies or T-cell antigen receptors (see, e.g Harlow and Lane (1988) Antibodies, A Laboratory Manual, Cold Spring Harbor Laboratory) and other natural intracellular binding agents identified with assays such as one-, two- and three-hybrid screens, non-natural intracellular binding agents identified in screens of chemical libraries such as described below, etc. For diagnostic uses, the binding agents are frequently labeled, such as with fluorescent, radioactive, chemiluminescent, or other easily detectable molecules, either conjugated directly to the binding agent or conjugated to a probe specific for the binding agent. Agents of particular interest modulate TRAF6 function, e.g. TRAF6-dependent signal transduction; for example, isolated cells, whole tissues, or individuals may be treated with a TRAF6 binding agent to activate, inhibit, or alter TRAF6-dependent intracellular signalling processes. The amino acid sequences of the disclosed TRAF6 polypeptides are used to back- translate TRAF6 polypeptide-encoding nucleic acids optimized for selected expression systems (Holler et al. (1993) Gene 136, 323-328; Martin et al. (1995) Gene 154, 150-166) or used to generate degenerate oligonucleotide primers and probes for use in the isolation of natural TRAF6-encoding nucleic acid sequences ("GCG" software, Genetics Computer Group, Inc, Madison WI). TRAFό-encoding nucleic acids used in TRAF6-expression vectors and incorporated into recombinant host cells, e.g. for expression and screening, transgenic animals, e.g. for functional studies such as the efficacy of candidate drugs for disease associated with TRAF6-modulated signal transduction, etc.

The invention also provides nucleic acid hybridization probes and replication / amplification primers having a TRAF6 cDNA specific sequence contained in SEQ LD NO: 1 and sufficient to effect specific hybridization thereto (i.e. specifically hybridize with SEQ LD NO:l in the presence of human umbilical vein endothelial cell cDNA, preferably in the presence of TRAFl-5 cDNA). Such primers or probes are at least 12, preferably at least 24, more preferably at least 36 and most preferably at least 96 bases in length. Demonstrating specific hybridization generally requires stringent conditions, for example, hybridizing in a buffer comprising 30% formamide in 5 x SSPE (0.18 M NaCI, 0.01 M NaPO₄, pH7.7, 0.001 M EDTA) buffer at a temperature of 42°C and remaining bound when subject to washing at 42°C with 0.2 x SSPE; preferably hybridizing in a buffer comprising 50% formamide in 5 x SSPE buffer at a temperature of 42°C and remaining bound when subject to washing at 42°C with 0.2 x SSPE buffer at 42°C. TRAF6 cDNA homologs can also be distinguished from other polypeptide using alignment algorithms, such as BLASTX (Altschul et al. (1990) Basic Local Alignment Search Tool, J Mol Biol 215, 403-410).

The subject nucleic acids are of synthetic/non-natural sequences and/or are isolated, i.e. unaccompanied by at least some of the material with which it is associated in its natural state, preferably constituting at least about 0.5%, preferably at least about 5% by weight of total nucleic acid present in a given fraction, and usually recombinant, meaning they comprise a non-natural sequence or a natural sequence joined to nucleotide(s) other than that which it is joined to on a natural chromosome. Nucleic acids comprising the nucleotide sequence of SEQ LD NO:l or fragments thereof, contain such sequence or fragment at a terminus, immediately flanked by a sequence other than that which it is joined to on a natural chromosome, or flanked by a native flanking region fewer than 10 kb, preferably fewer than 2 kb, which is at a terminus or is immediately flanked by a sequence other than that which it is joined to on a natural chromosome. While the nucleic acids are usually RNA or DNA, it is often advantageous to use nucleic acids comprising other bases or nucleotide analogs to provide modified stability, etc.

The subject nucleic acids find a wide variety of applications including use as translatable transcripts, hybridization probes, PCR primers, diagnostic nucleic acids, etc.; use in detecting the presence of TRAF6 genes and gene transcripts and in detecting or amplifying nucleic acids encoding additional TRAF6 homologs and structural analogs. In diagnosis, TRAF6 hybridization probes find use in identifying wild-type and mutant TRAF6 alleles in clinical and laboratory samples. Mutant alleles are used to generate allele-specific oligonucleotide (ASO) probes for high-throughput clinical diagnoses. In therapy, therapeutic TRAF6 nucleic acids are used to modulate cellular expression or intracellular concentration or availability of active TRAF6. The invention provides efficient methods of identifying agents, compounds or lead compounds for agents active at the level of a TRAF6 modulatable cellular function. Generally, these screening methods involve assaying for compounds which modulate TRAF6 interaction with a natural TRAF6 binding target. A wide variety of assays for binding agents are provided including labeled in vitro protein-protein binding assays, immunoassays, cell based assays, etc. The methods are amenable to automated, cost- effective high throughput screening of chemical libraries for lead compounds. Identified reagents find use in the pharmaceutical industries for animal and human trials; for example, the reagents may be derivatized and rescreened in in vitro and in vivo assays to optimize activity and minimize toxicity for pharmaceutical development. Target indications may include infection, genetic disease, cell growth and regulatory disfunction, such as neoplasia, inflammation, hypersensitivity, etc.

In vitro binding assays employ a mixture of components including a TRAF6 polypeptide, which may be part of a fusion product with another peptide or polypeptide, e.g. a tag for detection or anchoring, etc. The assay mixtures comprise a natural intracellular TRAF6 binding target, such as a TRAF2, TRAF3 or TRAF6 polypeptide. While native binding targets may be used, it is frequently preferred to use portions (e.g. peptides) thereof so long as the portion provides binding affinity and avidity to the subject TRAF6 polypeptide conveniently measurable in the assay. The assay mixture also comprises a candidate pharmacological agent. Candidate agents encompass numerous chemical classes, though typically they are organic compounds; preferably small organic compounds and are obtained from a wide variety of sources including libraries of synthetic or natural compounds. A variety of other reagents may also be included in the mixture. These include reagents like salts, buffers, neutral proteins, e.g. albumin, detergents, protease inhibitors, nuclease inhibitors, antimicrobial agents, etc. may be used.

The resultant mixture is incubated under conditions whereby, but for the presence of the candidate pharmacological agent, the TRAF6 polypeptide specifically binds the cellular binding target, portion or analog with a reference binding affinity. The mixture components can be added in any order that provides for the requisite bindings and incubations may be performed at any temperature which facilitates optimal binding. Incubation periods are likewise selected for optimal binding but also minimized to facilitate rapid, high-throughput screening. After incubation, the agent-biased binding between the TRAF6 polypeptide and one or more binding targets is detected by any convenient way. For cell-free binding type assays, a separation step is often used to separate bound from unbound components. Separation may be effected by precipitation (e.g. TCA precipitation, immunoprecipitation, etc.), immobilization (e.g on a solid substrate), etc., followed by washing by, for examples, membrane filtration, gel chromatography (e.g. gel filtration, affinity, etc.).

Detection may be effected in any convenient way. For cell-free binding assays, one of the components usually comprises or is coupled to a label. The label may provide for direct detection as radioactivity, luminescence, optical or electron density, etc. or indirect detection such as an epitope tag, an enzyme, etc. A variety of methods may be used to detect the label depending on the nature of the label and other assay components, e.g. through optical or electron density, radiative emissions, nonradiative energy transfers, etc. or indirectly detected with antibody conjugates, etc.

A difference in the binding affinity of the TRAF6 polypeptide to the target in the absence of the agent as compared with the binding affinity in the presence of the agent indicates that the agent modulates the binding of the TRAF6 polypeptide to the TRAF6 binding target. Analogously, in the cell-based assay also described below, a difference in the TRAF6-dependent chromatin degradation or instability in the presence and absence of an agent indicates the agent modulates TRAF6 function. A difference, as used herein, is statistically significant and preferably represents at least a 50%, more preferably at least a 90% difference.

The following experiments and examples are offered by way of illustration and not by way of limitation.

EXPERIMENTAL

The human TRAF6 cDNA of SEQ LD NO: 1 was cloned from human spleen cell and human umbilical vein endothelial cell cDNA libraries by high stringency hybridization: hybridization in 40% formamide, 5% Dextran sulfate, 0.5% SDS, 5x SSPE at 42 °C followed by washes in 2x SSPE, 0.1% SDS at 25°C and in O.lx SSPE, 0.1% SDS at 42°C; using TRAF oligonucleotide probes. The resultant cDNA (SEQ ID NO:l) encodes human TRAF6 (SEQ LD NO:2). In cotransfection experiments, TRAF6 was shown to activate an NF-κB-dependent reporter gene, see Fig 1.

A yeast two-hybrid system was used to identify TRAF2, TRAF3 and TRAF6 as an intracellular binding targets of the TRAF6 protein of SEQ LD NO: 2. A transfection based co-immunoprecipitation assay was also used to identify intracellular binding targets of the TRAF6 protein of SEQ LD NO: 2. Briefly, FLAG-tagged TRAF1, 2, 3, 4 and 6 were cotransfected with HA-tagged TRAF6. Lysates were immunoprecipitated with anti-HA antibody and proteinA glass beads. Western blot analysis using an anti-FLAG antibody revealed TRAF6-TRAF6 and TRAF6-TRAF3 complexes.

Deletion mutagenesis of TRAF6 indicate that residues 115-522 are sufficient to mediate activation of NF-κB, see Fig 2. In contrast, continuing the 5' deletion to the second Zn finger domain abolished activity; as did 5' deletions through all five Zn finger domains, and deletions through the C domain. Similarly, an internal delection of the Zn finger domains abolished activity.

EXAMPLES 1. Protocol for High-Throughput Human TRAF6 - TRAF6 Binding Assay. A. Reagents: - Neutralite Avidin: 20 μg/ml in PBS.

- Blocking buffer: 5% BSA, 0.5% Tween 20 in PBS; 1 hour at room temperature.

- Assay Buffer: 100 mM KCl, 20 mM HEPES pH 7.6, 0.25 mM EDTA, 1% glycerol, 0.5% NP-40, 50 mM β-mercaptoethanol, 1 mg/ml BSA, cocktail of protease inhibitors.

- ^P human TRAF6 .SEQUENCE ID NO:2. residues 1-522Ϊ lOx stock: 10⁸ - 10"⁶M unlabeled human TRAF6 supplemented with 200,000-250,000 cpm of labeled human

TRAF6 (Beckman counter). Place in the 4°C microfridge during screening.

- Protease inhibitor cocktail (T000XL- 10 mg Trypsin Inhibitor (BMB # 109894), 10 mg Aprotinin (BMB # 236624), 25 mg Benzamidine (Sigma # B-6506), 25 mg Leupeptin (BMB # 1017128), 10 mg APMSF (BMB # 917575), and 2mM NaVo₃ (Sigma # S-6508) in 10 ml of PBS.

- ΔTRAF6: 10"⁸ - 10^"5 M biotinylated truncated ΔTRAF6 (SEQUENCE LD NO:2, residues 115-522) in PBS. B. Preparation of assay plates:

- Coat with 120 μl of stock N-Avidin per well overnight at 4°C.

- Wash 2 times with 200 μl PBS.

- Block with 150 μl of blocking buffer. - Wash 2 times with 200 μl PBS.

C. Assay:

- Add 40 μl assay buffer/well.

- Add 10 μl compound or extract.

- Add 10 μl "P-human TRAF6 (20,000-25,000 cpm/0.1-10 pmoles/well =10^"9- IO^"7 M final concentration).

- Shake at 25 °C for 15 minutes.

- Incubate additional 45 minutes at 25 °C.

- Add 40 μl biotinylated truncated ΔTRAF6 (0.1-10 pmoles/40 ul in assay buffer)

- Incubate 1 hour at room temperature. - Stop the reaction by washing 4 times with 200 μl PBS.

- Add 150 μl scintillation cocktail.

- Count in Topcount.

D. Controls for all assays (located on each plate): a. Non-specific binding b. Soluble (non-biotinylated truncated ΔTRAF6) at 80% inhibition.

2. Protocol for NF-κB-Dependent Reporter Gene Assay

- 293 cells are transiently co-transfected with an E-selectin-luciferase reporter gene plasmid (Schindler et al. (1994) Mol Cell Biol 14, 5820) and TRAF6 expression vectors containing the TRAF6 coding region (see, SEQUENCE LD NO: 1 ) produced as described for TRAF1, 2 and 3 in Rothe et al (1995) Science 269, 1424.

-Control cells are transiently co-transfected with a CMV promoter luciferase reporter gene plasmid and/or TRAF2 expression vectors as described supra.

- The transfected cells are incubated 24 hours in the presence of the candidate compound or extract and then the cells harvested and luciferase activities determined and normalized on the basis of β-galactosidase expression, as described in Fig 3B of Rothe et al (1995) Science 269, 1424. All publications and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference. Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be readily apparent to those of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims.

SEQUENCE LISTING (1) GENERAL INFORMATION:

(i) APPLICANT: TULARIK, INC. (ii) TITLE OF INVENTION: Novel Protein - TRAF6 (iii) NUMBER OF SEQUENCES: 2

(iv) CORRESPONDENCE ADDRESS:

(A) ADDRESSEE: Science & Technology Law Group

(B) STREET: 268 Bush Street, Suite 3200

(C) CITY: San Francisco (D) STATE: California

(E) COUNTRY: USA

(F) ZIP: 94104

(v) COMPUTER READABLE FORM: (A) MEDIUM TYPE: Floppy disk

(B) COMPUTER: IBM PC compatible

(C) OPERATING SYSTEM: PC-DOS/MS-DOS

(D) SOFTWARE: Patentln Release #1.0, Version #1.30 (vi) CURRENT APPLICATION DATA:

(A) APPLICATION NUMBER:

(B) FILING DATE:

(C) CLASSIFICATION: (viii) ATTORNEY/AGENT INFORMATION:

(A) NAME: Osman, Richard Aron

(B) REGISTRATION NUMBER: 36,627

(C) REFERENCE/DOCKET NUMBER: T96-004/PCT (ix) TELECOMMUNICATION INFORMATION:

(A) TELEPHONE: (415) 343-4341

(B) TELEFAX: (415) 343-4342

(2) INFORMATION FOR SEQ ID NO:1: (I) SEQUENCE CHARACTERISTICS:

(A) LENGTH: .2248 base pairs

(B) TYPE: nucleic acid

(C) STRANDEDNESS: single

(D) TOPOLOGY: linear

(ii) MOLECULE TYPE: cDNA

(ix) FEATURE:

(A) NAME/KEY: CDS (B) LOCATION: 230..1795

(xi) SEQUENCE DESCRIPTION: SEQ ID NO:l:

GGCACGAGCC GCAGCTGGGG CTTGGCCTGC GGGCGGCCAG CGAAGGTGGC GAAGGCTCCC 60

ACTGGATCCA GAGTTTGCCG TCCAAGCAGC CTCGTCTCGG CGCGCAGTGT CTGTGTCCGT 120 P 1

CCTCTACCAG CGCCTTGGCT GAGCGGAGTC GTGCGGTTGG TGGGGGAGCC CTGCCCTCCT 180

GGTTCGGCCT CCCCGCGCAC TAGAACGAGC AAGTGATAAT CAAGTTACT ATG AGT 235

Met Ser

1

CTG CTA AAC TGT GAA AAC AGC TGT GGA TCC AGC CAG TCT GAA AGT GAC 283 Leu Leu Asn Cys Glu Asn Ser Cys Gly Ser Ser Gin Ser Glu Ser Asp 5 10 15

TGC TGT GTG GCC ATG GCC AGC TCC TGT AGC GCT GTA ACA AAA GAT GAT 331 Cys Cys Val Ala Met Ala Ser Ser Cys Ser Ala Val Thr Lys Asp Asp 20 25 30 AGT GTG GGT GGA ACT GCC AGC ACG GGG AAC CTC TCC AGC TCA TTT ATG 379 Ser Val Gly Gly Thr Ala Ser Thr Gly Asn Leu Ser Ser Ser Phe Met 35 40 45 50

GAG GAG ATC CAG GGA TAT GAT GTA GAG TTT GAC CCA CCC CTG GAA AGC 427 Glu Glu lie Gin Gly Tyr Asp Val Glu Phe Asp Pro Pro Leu Glu Ser

55 60 65

AAG TAT GAA TGC CCC ATC TGC TTG ATG GCA TTA CGA GAA GCA GTG CAA 475 Lys Tyr Glu Cys Pro lie Cys Leu Met Ala Leu Arg Glu Ala Val Gin 70 75 80

ACG CCA TGC GGC CAT AGG TTC TGC AAA GCC TGC ATC ATA AAA TCA ATA 523

Thr Pro Cys Gly His Arg Phe Cys Lys Ala Cys lie lie Lys Ser lie 85 90 95

AGG GAT GCA GGT CAC AAA TGT CCA GTT GAC AAT GAA ATA CTG CTG GAA 571

Arg Asp Ala Gly His Lys Cys Pro Val Asp Asn Glu lie Leu Leu Glu 100 105 110 AAT CAA CTA TTT CCA GAC AAT TTT GCA AAA CGT GAG ATT CTT TCT CTG 619 Asn Gin Leu Phe Pro Asp Asn Phe Ala Lys Arg Glu lie Leu Ser Leu 115 120 125 130

ATG GTG AAA TGT CCA AAT GAA GGT TGT TTG CAC AAG ATG GAA CTG AGA 667 Met Val Lys Cys Pro Asn Glu Gly Cys Leu His Lys Met Glu Leu Arg

135 140 145

CAT CTT GAG GAT CAT CAA GCA CAT TGT GAG TTT GCT CTT ATG GAT TGT 715 His Leu Glu Asp His Gin Ala His Cys Glu Phe Ala Leu Met Asp Cyε 150 155 160

CCC CAA TGC CAG CGT CCC TTC CAA AAA TTC CAT ATT AAT ATT CAC ATT 763 Pro Gin Cys Gin Arg Pro Phe Gin Lys Phe His lie Asn lie His lie 165 170 175

CTG AAG GAT TGT CCA AGG AGA CAG GTT TCT TGT GAC AAC TGT GCT GCA 811 Leu Lys Asp Cys Pro Arg Arg Gin Val Ser Cys Asp Asn Cys Ala Ala 180 185 190 TCA ATG GCA TTT GAA GAT AAA GAG ATC CAT GAC CAG AAC TGT CCT TTG 859 Ser Met Ala Phe Glu Asp Lys Glu lie His Asp Gin Asn Cys Pro Leu 195 200 205 210

GCA AAT GTC ATC TGT GAA TAC TGC AAT ACT ATA CTC ATC AGA GAA CAG 907 Ala Asn Val lie Cys Glu Tyr Cys Asn Thr lie Leu lie Arg Glu Gin 215 220 225

ATG CCT AAT CAT TAT GAT CTA GAC TGC CCT ACA GCC CCA ATT CCA TGC 955 Met Pro Asn His Tyr Asp Leu Asp Cys Pro Thr Ala Pro lie Pro Cys 230 235 240

ACA TTC AGT ACT TTT GGT TGC CAT GAA AAG ATG CAG AGG AAT CAC TTG 1003 Thr Phe Ser Thr Phe Gly Cys His Glu Lys Met Gin Arg Asn His Leu 245 250 255 GCA CGC CAC CTA CAA GAG AAC ACC CAG TCA CAC ATG AGA ATG TTG GCC 1051 Ala Arg His Leu Gin Glu Asn Thr Gin Ser His Met Arg Met Leu Ala 260 265 270

CAG GCT GTT CAT AGT TTG AGC GTT ATA CCC GAC TCT GGG TAT ATC TCA 1099 Gin Ala Val His Ser Leu Ser Val lie Pro Asp Ser Gly Tyr lie Ser 275 280 285 290

GAG GTC CGG AAT TTC CAG GAA ACT ATT CAC CAG TTA GAG GGT CGC CTT 1147 Glu Val Arg Asn Phe Gin Glu Thr lie His Gin Leu Glu Gly Arg Leu 295 300 305

GTA AGA CAA GAC CAT CAA ATC CGG GAG CTG ACT GCT AAA ATG GAA ACT 1195 Val Arg Gin Asp His Gin lie Arg Glu Leu Thr Ala Lys Met Glu Thr 310 315 320

CAG AGT ATG TAT GTA AGT GAG CTC AAA CGA ACC ATT CGA ACC CTT GAG 1243 Gin Ser Met Tyr Val Ser Glu Leu Lys Arg Thr lie Arg Thr Leu Glu 325 330 335 GAC AAA GTT GCT GAA ATC GAA GCA CAG CAG TGC AAT GGA ATT TAT ATT 1291 Asp Lys Val Ala Glu lie Glu Ala Gin Gin Cys Asn Gly lie Tyr lie 340 345 350

TGG AAG ATT GGC AAC TTT GGA ATG CAT TTG AAA TGT CAA GAA GAG GAG 1339 Trp Lys lie Gly Asn Phe Gly Met His Leu Lys Cys Gin Glu Glu Glu 355 360 365 370

AAA CCT GTT GTG ATT CAT AGC CCT GGA TTC TAC ACT GGC AAA CCC GGG 1387 Lys Pro Val Val lie His Ser Pro Gly Phe Tyr Thr Gly Lys Pro Gly 375 380 385

TAC AAA CTG TGC ATG CGC TTG CAC CTT CAG TTA CCG ACT GCT CAG CGC 1435 Tyr Lys Leu Cys Met Arg Leu His Leu Gin Leu Pro Thr Ala Gin Arg 390 395 400

TGT GCA AAC TAT ATA TCC CTT TTT GTC CAC ACA ATG CAA GGA GAA TAT 1483 Cys Ala Asn Tyr lie Ser Leu Phe Val His Thr Met Gin Gly Glu Tyr 405 410 415 GAC AGC CAC CTC CCT TGG CCC TTC CAG GGT ACA ATA CGC CTT ACA ATT 1531 Asp Ser His Leu Pro Trp Pro Phe Gin Gly Thr He Arg Leu Thr He 420 425 430

CTT GAT CAG TCT GAA GCA CCT GTA AGG CAA AAC CAC GAA GAG ATA ATG 1579 Leu Asp Gin Ser Glu Ala Pro Val Arg Gin Asn His Glu Glu He Met 435 440 445 450

GAT GCC AAA CCA GAG CTG CTT GCT TTC CAG CGA CCC ACA ATC CCA CGG 1627 Asp Ala Lys Pro Glu Leu Leu Ala Phe Gin Arg Pro Thr He Pro Arg 455 460 465

AAC CCA AAA GGT TTT GGC TAT GTA ACT TTT ATG CAT CTG GAA GCC CTA 1675 Asn Pro Lys Gly Phe Gly Tyr Val Thr Phe Met His Leu Glu Ala Leu 470 475 480 AGA CAA AGA ACT TTC ATT AAG GAT GAC ACA TTA TTA GTG CGC TGT GAG 1723 Arg Gin Arg Thr Phe He Lys Asp Asp Thr Leu Leu Val Arg Cys Glu 485 490 495

GTC TCC ACC CGC TTT GAC ATG GGT AGC CTT CGG AGG GAG GGT TTT CAG 1771 Val Ser Thr Arg Phe Asp Met Gly Ser Leu Arg Arg Glu Gly Phe Gin 500 505 510

CCA CGA AGT ACT GAT GCA GGG GTA TAGCTTGCCC TCACTTGCTC AAAAACAACT 1825 Pro Arg Ser Thr Asp Ala Gly Val 515 520

ACCTGGAGAA AACAGTGCCT TTCCTTGCCC TGTTCTCAAT AACATGCAAA CAAACAAGCC 1885

ACGGGAAATA TGTAATATCT ACTAGTGAGT GTTGTTAGAG AGGTCACTTA CTATTTCTTC 1945

CTGTTACAAA TGATCTGAGG CAGTTTTTTC CTGGGAATCC ACACGTTCCA TGCTTTTTCA 2005

GAAATGTTAG GCCTGAAGTG CCTGTGGCAT GTTGCAGCAG CTATTTTGCC AGTTAGTATA 2065 CCTCTTTOTT GTACTTTCTT GGGCTTTTGC TCTGGTGTAT TTTATTGTCA GAAAGTCCAG 2125

ACTCAAGAGT ACTAAACTTT TAATAATAAT GGATTTTCCT TAAAACTTCA GTCTTTTTGT 2185

AGTATTATAT GTAATATATT AAAAGTGAAA ATCACTACCG CCTTGAAAAA AAAAAAAAAA 2245

AAA 2248

(2) INFORMATION FOR SEQ ID Nθ:2:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 522 amino acids

(B) TYPE: amino acid (D) TOPOLOGY: linear

(ii) MOLECULE TYPE: protein

(xi) SEQUENCE DESCRIPTION: SEQ ID NO:2: Met Ser Leu Leu Asn Cys Glu Asn Ser Cys Gly Ser Ser Gin Ser Glu 1 5 10 15 Ser Asp Cys Cys Val Ala Met Ala Ser Ser Cys Ser Ala Val Thr Lys

20 25 30

Asp Asp Ser Val Gly Gly Thr Ala Ser Thr Gly Asn Leu Ser Ser Ser 35 40 45

Phe Met Glu Glu He Gin Gly Tyr Asp Val Glu Phe Asp Pro Pro Leu

50 55 60 Glu Ser Lys Tyr Glu Cys Pro He Cys Leu Met Ala Leu Arg Glu Ala

65 70 75 80

Val Gin Thr Pro Cys Gly His Arg Phe Cys Lys Ala Cys He He Lys 85 90 95

Ser He Arg Asp Ala Gly His Lys Cys Pro Val Asp Asn Glu He Leu 100 105 110

Leu Glu Asn Gin Leu Phe Pro Asp Asn Phe Ala Lys Arg Glu He Leu 115 120 125

Ser Leu Met Val Lys Cys Pro Asn Glu Gly Cys Leu His Lys Met Glu

130 135 140 Leu Arg His Leu Glu Asp His Gin Ala His Cys Glu Phe Ala Leu Met

145 ISO 155 160

Asp Cys Pro Gin Cys Gin Arg Pro Phe Gin Lys Phe His He Asn He 165 170 175

His He Leu Lys Asp Cys Pro Arg Arg Gin Val Ser Cys Asp Asn Cys 180 185 190

Ala Ala Ser Met Ala Phe Glu Asp Lys Glu He His Asp Gin Asn Cys 195 200 205

Pro Leu Ala Asn Val He Cys Glu Tyr Cys Asn Thr He Leu He Arg 210 215 220 Glu Gin Met Pro Asn His Tyr Asp Leu Asp Cys Pro Thr Ala Pro He 225 230 235 240

Pro Cyε Thr Phe Ser Thr Phe Gly Cys His Glu Lys Met Gin Arg Asn 245 250 255

His Leu Ala Arg His Leu Gin Glu Asn Thr Gin Ser His Met Arg Met 260 265 270

Leu Ala Gin Ala Val His Ser Leu Ser Val He Pro Asp Ser Gly Tyr 275 280 285

He Ser Glu Val Arg Asn Phe Gin Glu Thr He His Gin Leu Glu Gly 290 295 300 Arg Leu Val Arg Gin Asp His Gin He Arg Glu Leu Thr Ala Lys Met 305 310 315 320 Glu Thr Gin Ser Met Tyr Val Ser Glu Leu Lys Arg Thr He Arg Thr 325 330 335

Leu Glu Asp Lys Val Ala Glu He Glu Ala Gin Gin Cys Asn Gly He 340 345 350

Tyr He Trp Lys He Gly Asn Phe Gly Met His Leu Lys Cys Gin Glu 355 360 365 Glu Glu Lys Pro Val Val He His Ser Pro Gly Phe Tyr Thr Gly Lys 370 375 380

Pro Gly Tyr Lys Leu Cys Met Arg Leu His Leu Gin Leu Pro Thr Al:_- 385 390 395 400

Gin Arg Cys Ala Asn Tyr He Ser Leu Phe Val His Thr Met Gin Gly 405 410 415

Glu Tyr Asp Ser His Leu Pro Trp Pro Phe Gin Gly Thr He Arg Leu 420 425 430

Thr He Leu Asp Gin Ser Glu Ala Pro Val Arg Gin Asn His Glu Glu 435 440 445 He Met Asp Ala Lys Pro Glu Leu Leu Ala Phe Gin Arg Pro Thr He 450 455 460

Pro Arg Asn Pro Lys Gly Phe Gly Tyr Val Thr Phe Met His Leu Glu 465 470 475 480

Ala Leu Arg Gin Arg Thr Phe He Lys Asp Asp Thr Leu Leu Val Arg 485 490 495

Cys Glu Val Ser Thr Arg Phe Asp Met Gly Ser Leu Arg Arg Glu Gly 500 505 510

Phe Gin Pro Arg Ser Thr Asp Ala Gly Val 515 520

Claims

WHAT TS CLAIMED IS:

1. An isolated tumor necrosis factor receptor associated factor number six (TRAF6) polypeptide wherein said polypeptide comprises the amino acid sequence of SEQ ID NO:2 or a deletion mutant of SEQ ID NO:2 sufficient to specifically bind a natural intracellular TRAF6 binding target.

2. An isolated tumor necrosis factor receptor associated factor number six (TRAF6) polypeptide according to claim 1, wherein said polypeptide comprises SEQ ED NO:2, residues 1-114.

3. An isolated tumor necrosis factor receptor associated factor number six (TRAF6) polypeptide according to claim 1, wherein said polypeptide comprises SEQ ED NO:2, residues 115-522.

4. An isolated nucleic acid encoding a tumor necrosis factor receptor associated factor number six (TRAF6) polypeptide according to claim 1.

5. A recombinant nucleic acid comprising an open reading frame encoding a tumor necrosis factor receptor associated factor number six (TRAF6) polypeptide according to claim 1 , said open reading frame joined directly to a nucleotide other than that which said open reading frame is joined to on a natural chromosome.

6. An isolated hybridization probe or primer comprising a portion of SEQ ED NO: 1 sufficient to specifically hybridize with a nucleic acid having the sequence defined by SEQ ED NO: 1 in the presence of human umbilical vein endothelial cell cDNA.

7. A method of making an isolated tumor necrosis factor receptor associated factor number six (TRAF6) polypeptide, comprising steps: introducing a nucleic acid according to claim 5 into a host cell, growing said host cell under conditions whereby said nucleic acid is expressed as a transcript and said transcript is expressed as a translation product comprising said polypeptide, and isolating said translation product.

8. A method of screening for an agent which modulates the binding of a tumor necrosis factor receptor associated factor number six (TRAF6) polypeptide to a natural intracellular TRAF6 binding target, said method comprising the steps of: incubating a mixture comprising: an isolated TRAF6 polypeptide according to claim 1, a natural intracellular binding target of said polypeptide, wherein said binding target is capable of specifically binding said polypeptide, and a candidate agent; under conditions whereby, but for the presence of said agent, said polypeptide specifically binds said binding target at a reference affinity; detecting the binding affinity of said polypeptide to said binding target to determine an agent-biased affinity, wherein a difference between the agent-biased affinity and the reference affinity indicates that said agent modulates the binding of said polypeptide to said binding target.

9. A method according to claim 8, wherein said binding target comprises a tumor necrosis factor receptor associated factor or fragment thereof sufficient to specifically bind said TRAF6 polypeptide.

10. A method of identifying an agent which modulates the transcription of a tumor necrosis factor receptor associated factor number six (TRAF6) polypeptide-inducible gene, said method comprising the steps of: contacting a cell comprising a reporter gene operatively linked to an NF-κB inducible promoter, and a TRAF6 gene comprising a nucleic acid according to claims 5, wherein said TRAF6 gene is expressed as a TRAF6 polypeptide, with a candidate agent; incubating said cell under conditions whereby, but for the presence of said agent, said TRAF6 polypeptide specifically induces said promoter at a reference induction; detecting the induction of said promoter by said TRAF6 polypeptide by measuring the expression of said reporter gene to determine an agent-biased induction, wherein a difference between said agent-biased induction and said reference affinity indicates that said agent modulates the transcription of a TRAF6 polypeptide-inducible gene.