Proteomics: Getting from TNF-alpha to NF-kappaB - Cell Signaling Update

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Proteomics: Getting from TNF- to NF-B

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The TNF- alpha /NF kappa B signaling pathway has been mapped using a large-scale functional proteomics approach to show hundreds of molecular associations and 80 novel interactors.

Following the completion of the Human Genome Project, biomedical research is turning towards proteomics to decipher the vast array of molecular interactions that occur within the cell. Large-scale interaction maps have already been generated in yeast and Drosophila, and now Bouwmeester et al. present the first large-scale interaction map of a signaling module in humans: the tumor necrosis factor- alpha /nuclear factor- kappa B (TNF- alpha /NF- kappa B) pathway. They identified several hundred molecular associations and 80 novel interactors, 10 of which were demonstrated to modulate NF- kappa B signaling.

The pro-inflammatory cytokine TNF- alpha is one of the most studied activators of the transcription factor family NF- kappa B. The authors used stably expressed tagged versions of 32 known or potential TNF- alpha /NF- kappa B pathway components as bait for tandem affinity purification (TAP), isolating a set of 680 complex-forming non-redundant proteins. 70% of all previously reported interactions in this pathway were represented by this data set. Using statistical analysis based on specificity and consistency, the authors filtered this network to 131 high-confidence interactors, 80 of which were previously not implicated in NF kappa B signaling. Not only did these results re-affirm pre-established pathway relationships, but new interactors were seen to cluster around known components – potentially providing insight into the mechanism of action for NF- kappa B transcription factor specificity, inhibitor specificity and precursor processing.

A diverse group of 28 of the new interactors were subjected to RNAi based loss-of-function assays. 10 of these 28 components showed a modulatory role in TNF- alpha /NF- kappa B signaling. Among this set of proteins was a new member of the TRAF family of adapter proteins, termed TRAF7, which was shown to play an important role in regulating signaling via the MAP kinase/ERK kinase kinase 3 (MEKK3) to the transcription factors NF- kappa B and activator protein 1 (AP-1).

This systems approach of large-scale pathway mapping and functional analysis could be universally applied to signal cascades throughout the cell, opening avenues to a more comprehensive understanding of signal transduction.

Brenda Riley, Assistant Editor
Assistant Editor, Signaling Gateway

References

Bouwmeester, T Bauch, A Ruffner, H Angrand, P -O Bergamini, G Croughton, K Cruciat, C Eberhard, D Gagneur, J Ghidelli, S Hopf, C Huhse, B Mangano, R Michon, A -M Schirle, M Schlegl, J Schwab, M Stein, M A Bauer, A Casari, G Drewes, G Gavin, A -C Jackson, D B Joberty, G Neubauer, G Rick, J Kuster, B Superti-Furga, G A physical and functional map of the human TNF-/NF-B signal transduction pathway. Nature Cell Biology 6 87–89 2004, 10.1038/ncb1086 | PubMed |