Commentary: On large protein complexes and the essentiality of hubs

August 2, 2008

In 2001, Jeong and coworkers published a paper in Nature in which they showed that the central proteins in interaction networks, that is the proteins with the highest connectivity, are enriched for essential proteins. This publication has been highly influential as evidenced by the numerous subsequent publications on the importance of “hub” proteins. Several hypothesis have been published that try to explain why hubs are essential, for example that certain protein interactions are essential and that a protein with many interactions is thus more likely to be involved in at least one essential interaction (He and Zhang, 2006).

Yesterday, Zotenko and coworkers published a paper in PLoS Computational Biology in which they take a closer look at the cause of this phenomenon:

Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality.

The centrality-lethality rule, which notes that high-degree nodes in a protein interaction network tend to correspond to proteins that are essential, suggests that the topological prominence of a protein in a protein interaction network may be a good predictor of its biological importance. Even though the correlation between degree and essentiality was confirmed by many independent studies, the reason for this correlation remains illusive. Several hypotheses about putative connections between essentiality of hubs and the topology of protein-protein interaction networks have been proposed, but as we demonstrate, these explanations are not supported by the properties of protein interaction networks. To identify the main topological determinant of essentiality and to provide a biological explanation for the connection between the network topology and essentiality, we performed a rigorous analysis of six variants of the genomewide protein interaction network for Saccharomyces cerevisiae obtained using different techniques. We demonstrated that the majority of hubs are essential due to their involvement in Essential Complex Biological Modules, a group of densely connected proteins with shared biological function that are enriched in essential proteins. Moreover, we rejected two previously proposed explanations for the centrality-lethality rule, one relating the essentiality of hubs to their role in the overall network connectivity and another relying on the recently published essential protein interactions model.

What Zotenko et al. show is, in other words, that essential hubs tend to be highly connected with each other and hence form large “Essential Complex Biological Modules”. Table 7 in their paper lists the Gene Ontology terms associated with these modules; among the recurring themes are “rRNA metabolic process”, “mRNA metabolic process”, “RNA splicing”, “ribosome biogenesis and assembly”, and “proteolysis”. These Gene Ontology terms obviously correspond to well known protein complexes, namely the RNA polymerases, the spliceosome, the ribosome, and the proteoasome. The analysis of Zotenko et al. thus suggests that the much debated correlation between centrality and essentiality is simply a consequence of the fact that many of the large protein complexes in a eukaryotic cell are essential, which is hardly surprising considering that they have been conserved through more than two billion years of evolution (Brocks et al., 1999).

Edit: For more views on the results of Zotenko et al. see the discussion on FriendFeed.

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One Response to “Commentary: On large protein complexes and the essentiality of hubs”

  1. mywordpressname Says:

    This recent paper from Serano might also be of interest,

    Evolvability and hieracrchy in rewired bacterial gene networks    
    Isalan et al. Nature 452:840                                                    

    It was discussed at the Molecular Evolution club at your workplace last month. They seem to have a pretty cool platform for studying network topology.

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