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Non-uniform survival rate of heterodimerization links in the evolution of the yeast protein-protein interaction network.

ABSTRACT: Protein-protein interaction networks (PINs) are scale-free networks with a small-world property. In a small-world network, the average cluster coefficient () is much higher than in a random network, but the average shortest path length () is similar between the two networks. To understand the evolutionary mechanisms shaping the structure of PINs, simulation studies using various network growth models have been performed. It has been reported that the heterodimerization (HD) model, in which a new link is added between duplicated nodes with a uniform probability, could reproduce scale-freeness and a high . In this paper, however, we show that the HD model is unsatisfactory, because (i) to reproduce the high in the yeast PIN, a much larger number (n(HI)) of HD links (links between duplicated nodes) are required than the estimated number of n(HI) in the yeast PIN and (ii) the spatial distribution of triangles in the yeast PIN is highly skewed but the HD model cannot reproduce the skewed distribution. To resolve these discrepancies, we here propose a new model named the non-uniform heterodimerization (NHD) model. In this model, an HD link is preferentially attached between duplicated nodes when they share many common neighbors. Simulation studies demonstrated that the NHD model can successfully reproduce the high , the low n(HI), and the skewed distribution of triangles in the yeast PIN. These results suggest that the survival rate of HD links is not uniform in the evolution of PINs, and that an HD link between high-degree nodes tends to be evolutionarily conservative. The non-uniform survival rate of HD links can be explained by assuming a low mutation rate for a high-degree node, and thus this model appears to be biologically plausible.

SUBMITTER: Hase T

PROVIDER: S-EPMC2253498 | biostudies-literature | 2008 Feb

REPOSITORIES: biostudies-literature

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Non-uniform survival rate of heterodimerization links in the evolution of the yeast protein-protein interaction network.

Hase Takeshi T Niimura Yoshihito Y Kaminuma Tsuguchika T Tanaka Hiroshi H

PloS one 20080227 2

Protein-protein interaction networks (PINs) are scale-free networks with a small-world property. In a small-world network, the average cluster coefficient (<C>) is much higher than in a random network, but the average shortest path length (<L>) is similar between the two networks. To understand the evolutionary mechanisms shaping the structure of PINs, simulation studies using various network growth models have been performed. It has been reported that the heterodimerization (HD) model, in which ...[more]

PMID: 18301745

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Project description:BackgroundThe recently emerged protein interaction network paradigm can provide novel and important insights into the innerworkings of a cell. Yet, the heavy burden of both false positive and false negative protein-protein interaction data casts doubt on the broader usefulness of these interaction sets. Approaches focusing on one-protein-at-a-time have been powerfully employed to demonstrate the high degree of conservation of proteins participating in numerous interactions; here, we expand his 'node' focused paradigm to investigate the relative persistence of 'link' based evolutionary signals in a protein interaction network of S. cerevisiae and point out the value of this relatively untapped source of information.ResultsThe trend for highly connected proteins to be preferably conserved in evolution is stable, even in the context of tremendous noise in the underlying protein interactions as well as in the assignment of orthology among five higher eukaryotes. We find that local clustering around interactions correlates with preferred evolutionary conservation of the participating proteins; furthermore the correlation between high local clustering and evolutionary conservation is accompanied by a stable elevated degree of coexpression of the interacting proteins. We use this conserved interaction data, combined with P. falciparum/Yeast orthologs, as proof-of-principle that high-order network topology can be used comparatively to deduce local network structure in non-model organisms.ConclusionHigh local clustering is a criterion for the reliability of an interaction and coincides with preferred evolutionary conservation and significant coexpression. These strong and stable correlations indicate that evolutionary units go beyond a single protein to include the interactions among them. In particular, the stability of these signals in the face of extreme noise suggests that empirical protein interaction data can be integrated with orthologous clustering around these protein interactions to reliably infer local network structures in non-model organisms.

Dataset Information

Non-uniform survival rate of heterodimerization links in the evolution of the yeast protein-protein interaction network.

Publications

Non-uniform survival rate of heterodimerization links in the evolution of the yeast protein-protein interaction network.

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