For proteins, it's all in the order

The assembly of proteins into complexes underlies a wide variety of biological processes. By combining mass spectrometry experiments with large-scale analyses of protein structure, protein interaction and genome sequence data, we found that protein complexes have experienced evolutionary selection to assemble via well-defined, ordered pathways.

HFSP Long-Term Fellow Joseph Marsh and colleagues
authored on Thu, 11 April 2013

Most proteins interact with other proteins and assemble into protein complexes, thus facilitating their diverse biological functions. How important is the order in which different proteins come together during assembly of a multiprotein complex? If assembly order is crucial for biological function, then we would expect it to be conserved in evolution. Therefore, in this study we set out to assess the biological importance of protein complex assembly order by taking advantage of a unique evolutionary phenomenon: gene fusion.

Gene fusion occurs when two previously separate genes become joined together into one larger gene. If an evolutionary gene fusion event occurs between two genes encoding two different proteins that assemble into the same complex, this will have the effect of either conserving or disrupting the existing assembly pathway of that complex (see Figure). By searching the fully sequenced genomes of a large number of organisms for evolutionary gene fusion events, we sought to test whether there has been any significant selection for assembly-conserving fusions.

We first used nanoelectrospray mass spectrometry to experimentally characterize the assembly pathways for several protein complexes where fusion is known to occur between subunits. Remarkably, by comparing the assembly of these complexes to their three-dimensional X-ray crystal structures, we found that we could predict the assembly pathways with very high accuracy using a simple model based upon the sizes of the interfaces between proteins. This allowed us to move far beyond the limited number of cases that could be characterized experimentally and predict assembly pathways on a large scale for thousands of protein complexes. With this data, we could then perform a detailed assessment of the impact of fusion on assembly.


Figure: Evolutionary gene fusion events that covalently link the subunits of protein complexes can either conserve (A-B fusion) or disrupt (A-C and B-C fusions) the existing order of assembly. We observe considerable evolutionary enrichment of those fusion events that conserve assembly pathways, thus demonstrating the biological importance of assembly order.

Our major finding is summarized in the figure above. We observed a very strong tendency for evolutionary gene fusion events to occur in such a way that they preserve existing protein complex assembly pathways. We also found an enrichment in fusion events that simplify assembly by maximally reducing the number of unique interfaces within a complex, which was further supported by analysis of high-throughput protein-protein interaction data. Thus this work shows that protein complexes have experienced evolutionary selection to assembly via ordered pathways, demonstrating the biological importance of assembly order and showing for the first time that evolution acts at the level of protein assembly. Furthermore, our method for predicting protein assembly pathways on a large scale will also open the doors to further work on the relationship between assembly and protein structure, function and evolution. Finally, our ability to predict the intermediate steps of assembly could potentially provide insight into the various human diseases known to be associated with protein misassembly.


Protein Complexes Are under Evolutionary Selection to Assemble via Ordered Pathways. Joseph A. Marsh, Helena Hernández, Zoe Hall, Sebastian E. Ahnert, Tina Perica, Carol V. Robinson and Sarah A. Teichmann (2013). Cell 153:461-470

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