Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

A physical and functional map of the human TNF-α/NF-κB signal transduction pathway

An Erratum to this article was published on 01 May 2004

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

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Purification of cellular NF-κB/IκB complexes.
Figure 2: Connectivity map of the TNF-α/NF-κB signal transduction pathway.
Figure 3: Functional validation of candidate modulators of the TNF-α/NF-κB pathway.
Figure 4: TRAF7 is phosphorylated and ubiquitinated in a MEKK3-dependent manner.
Figure 5: MEKK3 and TRAF7 synergize to activate NF-κB, p38 and JNK pathways.

Similar content being viewed by others

References

  1. Gavin, A.C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147 (2002).

    Article  CAS  Google Scholar 

  2. Ghosh, S. & Karin, M. Missing pieces in the NF-κB puzzle. Cell 109 (Suppl.), S81–S96 (2002).

    Article  CAS  Google Scholar 

  3. 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).

    Article  CAS  Google Scholar 

  4. 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).

    Article  CAS  Google Scholar 

  5. Senftleben, U. et al. Activation by IKKα of a second, evolutionary conserved, NF-κB signaling pathway. Science 293, 1495–1499 (2001).

    Article  CAS  Google Scholar 

  6. Rigaut, G. et al. A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol. 17, 1030–1032 (1999).

    Article  CAS  Google Scholar 

  7. Chen, C.Y. et al. AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. Cell 107, 451–464 (2001).

    Article  CAS  Google Scholar 

  8. Kemmeren, P. et al. Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol. Cell 9, 1133–1143 (2002).

    Article  CAS  Google Scholar 

  9. von Mering, C. et al. Comparative assessment of large-scale data sets of protein–protein interactions. Nature 417, 399–403 (2002).

    Article  CAS  Google Scholar 

  10. Saccani, S., Pantano, S. & Natoli, G. Modulation of NF-κB activity by exchange of dimers. Mol. Cell 11, 1563–1574 (2003).

    Article  CAS  Google Scholar 

  11. Fenwick, C. et al. A subclass of Ras proteins that regulate the degradation of IκB. Science 287, 869–873 (2000).

    Article  CAS  Google Scholar 

  12. Dixit, V. & Mak, T.W. NF-κB signaling. Many roads lead to Madrid. Cell 111, 615–619 (2002).

    Article  CAS  Google Scholar 

  13. 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).

    Article  CAS  Google Scholar 

  14. 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).

    Article  CAS  Google Scholar 

  15. 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).

    Article  CAS  Google Scholar 

  16. Heusch, M., Lin, L., Geleziunas, R. & Greene, W.C. The generation of NFκB2 p52: mechanism and efficiency. Oncogene 18, 6201–6208 (1999).

    Article  CAS  Google Scholar 

  17. Kinzler, K.W. et al. Identification of a gene located at chromosome 5q21 that is mutated in colorectal cancers. Science 251, 1366–1370 (1991).

    Article  CAS  Google Scholar 

  18. 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).

    Article  CAS  Google Scholar 

  19. 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).

    Article  CAS  Google Scholar 

  20. 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).

    Article  CAS  Google Scholar 

  21. 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).

    Article  CAS  Google Scholar 

  22. Yang, J. et al. The essential role of MEKK3 in TNF-induced NF-κB activation. Nature Immunol. 2, 620–624 (2001).

    Article  CAS  Google Scholar 

  23. Humbert, P., Russell, S. & Richardson, H. Dlg, Scribble and Lgl in cell polarity, cell proliferation and cancer. BioEssays 25, 542–553 (2003).

    Article  CAS  Google Scholar 

  24. Wang, C. et al. TAK1 is a ubiquitin-dependent kinase of MKK and IKK. Nature 412, 346–351 (2001).

    Article  CAS  Google Scholar 

  25. Shevchenko, A., Wilm, M., Vorm, O. & Mann, M. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 68, 850–858 (1996).

    Article  CAS  Google Scholar 

Download references

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

Authors

Corresponding authors

Correspondence to Tewis Bouwmeester or Giulio Superti-Furga.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

Reprints 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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ncb1086

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing