Abstract
Signal transduction pathways are modular composites of functionally interdependent sets of proteins that act in a coordinated fashion to transform environmental information into a phenotypic response. The pro-inflammatory cytokine tumour necrosis factor (TNF)-α triggers a signalling cascade, converging on the activation of the transcription factor NF-κB, which forms the basis for numerous physiological and pathological processes. Here we report the mapping of a protein interaction network around 32 known and candidate TNF-α/NF-κB pathway components by using an integrated approach comprising tandem affinity purification, liquid-chromatography tandem mass spectrometry, network analysis and directed functional perturbation studies using RNA interference. We identified 221 molecular associations and 80 previously unknown interactors, including 10 new functional modulators of the pathway. This systems approach provides significant insight into the logic of the TNF-α/NF-κB pathway and is generally applicable to other pathways relevant to human disease.
This is a preview of subscription content, access via your institution
Access options
Subscription info for Japanese customers
We have a dedicated website for our Japanese customers. Please go to natureasia.com to subscribe to this journal.
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Gavin, A.C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147 (2002).
Ghosh, S. & Karin, M. Missing pieces in the NF-κB puzzle. Cell 109 (Suppl.), S81–S96 (2002).
Ghosh, S., May, M.J. & Kopp, E.B. NF-κB and Rel proteins: evolutionarily conserved mediators of immune responses. Annu. Rev. Immunol. 16, 225–260 (1998).
Xiao, G., Harhaj, E.W. & Sun, S.C. NF-κB-inducing kinase regulates the processing of NF-κB2 p100. Mol. Cell 7, 401–409 (2001).
Senftleben, U. et al. Activation by IKKα of a second, evolutionary conserved, NF-κB signaling pathway. Science 293, 1495–1499 (2001).
Rigaut, G. et al. A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol. 17, 1030–1032 (1999).
Chen, C.Y. et al. AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. Cell 107, 451–464 (2001).
Kemmeren, P. et al. Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol. Cell 9, 1133–1143 (2002).
von Mering, C. et al. Comparative assessment of large-scale data sets of protein–protein interactions. Nature 417, 399–403 (2002).
Saccani, S., Pantano, S. & Natoli, G. Modulation of NF-κB activity by exchange of dimers. Mol. Cell 11, 1563–1574 (2003).
Fenwick, C. et al. A subclass of Ras proteins that regulate the degradation of IκB. Science 287, 869–873 (2000).
Dixit, V. & Mak, T.W. NF-κB signaling. Many roads lead to Madrid. Cell 111, 615–619 (2002).
Mordmuller, B., Krappmann, D., Esen, M., Wegener, E. & Scheidereit, C. Lymphotoxin and lipopolysaccharide induce NF-κB–p52 generation by a co-translational mechanism. EMBO Rep. 4, 82–87 (2003).
Fong, A., Zhang, M., Neely, J. & Sun, S.C. S9, a 19 S proteasome subunit interacting with ubiquitinated NF-κB2/p100. J. Biol. Chem. 277, 40697–40702 (2002).
Fong, A. & Sun, S.C. Genetic evidence for the essential role of beta-transducin repeat-containing protein in the inducible processing of NF-κB2/p100. J. Biol. Chem. 277, 22111–22114 (2002).
Heusch, M., Lin, L., Geleziunas, R. & Greene, W.C. The generation of NFκB2 p52: mechanism and efficiency. Oncogene 18, 6201–6208 (1999).
Kinzler, K.W. et al. Identification of a gene located at chromosome 5q21 that is mutated in colorectal cancers. Science 251, 1366–1370 (1991).
Matsumine, A. et al. MCC, a cytoplasmic protein that blocks cell cycle progression from the G0/G1 to S phase. J. Biol. Chem. 271, 10341–10346 (1996).
Lee, C.M., Onesime, D., Reddy, C.D., Dhanasekaran, N. & Reddy, E.P. JLP: A scaffolding protein that tethers JNK/p38MAPK signaling modules and transcription factors. Proc. Natl Acad. Sci. USA 99, 14189–14194 (2002).
Nair, S.C. et al. Molecular cloning of human FKBP51 and comparisons of immunophilin interactions with Hsp90 and progesterone receptor. Mol. Cell. Biol. 17, 594–603 (1997).
Chen, G., Cao, P. & Goeddel, D.V. TNF-induced recruitment and activation of the IKK complex require Cdc37 and Hsp90. Mol. Cell 9, 401–410 (2002).
Yang, J. et al. The essential role of MEKK3 in TNF-induced NF-κB activation. Nature Immunol. 2, 620–624 (2001).
Humbert, P., Russell, S. & Richardson, H. Dlg, Scribble and Lgl in cell polarity, cell proliferation and cancer. BioEssays 25, 542–553 (2003).
Wang, C. et al. TAK1 is a ubiquitin-dependent kinase of MKK and IKK. Nature 412, 346–351 (2001).
Shevchenko, A., Wilm, M., Vorm, O. & Mann, M. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 68, 850–858 (1996).
Acknowledgements
We thank all our colleagues at Cellzome, in particular, G. Stark and M. Boesche with their teams, and C. Gaessler, P. Voelkel, E. M. Lorenz and H. Wilkinson for technical expertise. We thank A. Rowley and D. Brown for continuous support, M. Pasparakis and A. Nebreda for input throughout this project, and F. Weisbrodt for graphical support.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Rights and permissions
About this article
Cite this article
Bouwmeester, T., Bauch, A., Ruffner, H. et al. A physical and functional map of the human TNF-α/NF-κB signal transduction pathway. Nat Cell Biol 6, 97–105 (2004). https://doi.org/10.1038/ncb1086
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/ncb1086
