Sci. STKE, 15 January 2002
Proteomics Protein Complexes Galore
Two papers in Nature this week greatly extend our knowledge of protein-protein interactions and provide a basis for identifying these interactions on the scale of a species' proteome. Whereas yeast two-hybrid assays can determine whether two overexpressed proteins of interest interact in vivo but might not reflect biologically relevant interactions, these new studies utilize tagged proteins expressed in endogenous amounts that capture clusters of interacting proteins. The results from these new studies indicate that physiologically relevant clusters of proteins can be obtained and that their constituent proteins identified by mass spectrometry. In addition to confirming some previously known protein-protein interactions revealed by yeast two hybrid assays, Gavin et al. and Ho et al. have reported new interactions between previously characterized proteins thought to exist in different pathways, and have assigned functions to proteins whose roles have remained unknown. Additionally, Gavin et al. found that yeast protein clusters and clusters from human cells contained the same orthologous proteins. In cases where existing in complexes were highly predictive for their human counterpart proteins in similar complexes. Kumar and Snyder state, in their accompanying News & Views, that much exciting data can be generated from studies such as these, but warn that "there is still much to be learned before we have a comprehensive knowledge of [signaling] pathways". A protocol by Pandey et al., published at STKE, utilizes mass spectrometry to identify proteins in complexes in a way similar to that used by Gavin et al. and Ho et al.
A.-C. Gavin, M. Bösche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J. M. Rick, A.-M. Michon, C.-M. Cruciat, M. Remor, C. Höfert, M. Schelder, M. Brajenovic, H. Ruffner, A. Merino, K. Klein, M. Hudak, D. Dickson, T. Rudi, V. Gnau, A. Bauch, S. Bastuck, B. Huhse, C. Leutwein, M.-A. Heurtier, R. R. Copley, A. Edelmann, E. Querfurth, V. Rybin, G. Drewes, M. Raida, T. Bouwmeester, P. Bork, B. Seraphin, B. Kuster, G. Neubauer, G. Superti-Furga, Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002). [Online Journal]
Y. Ho, A. Gruhler, A. Heilbut, G. D. Bader, L. Moore, S.-L. Adams, A. Millar, P. Taylor, K. Bennett, K. Boutilier, L. Yang, C. Wolting, I. Donaldson, S. Schandorff, J. Shewnarane, M. Vo, J. Taggart, M. Goudreault, B. Muskat, C. Alfarano, D. Dewar, Z. Lin, K. Michalickova, A. R. Willems, H. Sassi, P. A. Nielsen, K. J. Rasmussen, J. R. Andersen, L. E. Johansen, L. H. Hansen, H. Jespersen, A. Podtelejnikov, E. Nielsen, J. Crawford, V. Poulsen, B. D. Sørensen, J. Matthiesen, R. C. Hendrickson, F. Gleeson, T. Pawson, M. F. Moran, D. Durocher, M. Mann, C. W. V. Hogue, D. Figeys, M. Tyers, Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183 (2002). [Online Journal]
A. Kumar, M. Snyder, Proteomics: Protein complexes take the bait. Nature 415, 123-124 (2002). [Online Journal]
A. Pandey, J. S. Andersen, M. Mann, Use of Mass Spectrometry to Study Signaling Pathways. Science's STKE (2000), http://stke.sciencemag.org/cgi/content/full/OC_sigtrans;2000/37/pl1. [Abstract] [Full Text]
Citation: Protein Complexes Galore. Sci. STKE 2002, tw24 (2002).
Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882