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Evolution of protein-protein interaction networks in yeast

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ABSTRACT

Interest in the evolution of protein-protein and genetic interaction networks has been rising in recent years, but the lack of large-scale high quality comparative datasets has acted as a barrier. Here, we carried out a comparative analysis of computationally predicted protein-protein interaction (PPI) networks from five closely related yeast species. We used the Protein-protein Interaction Prediction Engine (PIPE), which uses a database of known interactions to make sequence-based PPI predictions, to generate high quality predicted interactomes. Simulated proteomes and corresponding PPI networks were used to provide expectations for the extent and nature of PPI network evolution. We found strong evidence for conservation of PPIs, with lower than expected levels of change in PPIs for about a quarter of the proteome. Furthermore, we found that changes in predicted PPI networks are poorly predicted by sequence divergence. Our analyses identified a number of functional classes experiencing fewer PPI changes than expected, suggestive of purifying selection on PPIs. Our results demonstrate the added benefit of considering predicted PPI networks when studying the evolution of closely related organisms.

No MeSH data available.


Related in: MedlinePlus

Comparing the change in protein-protein interaction to protein degree                            and rate of sequence change across the phylogeny.                        Comparison of changes in PPIs across the phylogeny (γ) to degree                            (A) or to rate of substitution across the phylogeny (ω) (B). A                            protein’s γ is correlated with its degree in the network                            (see regression line in panel A), but not with its overall rate of                            substitution.
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pone.0171920.g004: Comparing the change in protein-protein interaction to protein degree and rate of sequence change across the phylogeny. Comparison of changes in PPIs across the phylogeny (γ) to degree (A) or to rate of substitution across the phylogeny (ω) (B). A protein’s γ is correlated with its degree in the network (see regression line in panel A), but not with its overall rate of substitution.

Mentions: A protein’s γ is correlated with its number of interactions in S. cerevisiae (i.e., its degree), such that proteins with many interactions tend to undergo more changes than proteins with few interactions (Kendall’s τ = 0.488, P < 2x10-16; Fig 4A). This correlation is expected since a protein with more PPIs has more opportunities to lose interactions than a protein with few interactions.


Evolution of protein-protein interaction networks in yeast
Comparing the change in protein-protein interaction to protein degree                            and rate of sequence change across the phylogeny.                        Comparison of changes in PPIs across the phylogeny (γ) to degree                            (A) or to rate of substitution across the phylogeny (ω) (B). A                            protein’s γ is correlated with its degree in the network                            (see regression line in panel A), but not with its overall rate of                            substitution.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5382968&req=5

pone.0171920.g004: Comparing the change in protein-protein interaction to protein degree and rate of sequence change across the phylogeny. Comparison of changes in PPIs across the phylogeny (γ) to degree (A) or to rate of substitution across the phylogeny (ω) (B). A protein’s γ is correlated with its degree in the network (see regression line in panel A), but not with its overall rate of substitution.
Mentions: A protein’s γ is correlated with its number of interactions in S. cerevisiae (i.e., its degree), such that proteins with many interactions tend to undergo more changes than proteins with few interactions (Kendall’s τ = 0.488, P < 2x10-16; Fig 4A). This correlation is expected since a protein with more PPIs has more opportunities to lose interactions than a protein with few interactions.

View Article: PubMed Central - PubMed

ABSTRACT

Interest in the evolution of protein-protein and genetic interaction networks has been rising in recent years, but the lack of large-scale high quality comparative datasets has acted as a barrier. Here, we carried out a comparative analysis of computationally predicted protein-protein interaction (PPI) networks from five closely related yeast species. We used the Protein-protein Interaction Prediction Engine (PIPE), which uses a database of known interactions to make sequence-based PPI predictions, to generate high quality predicted interactomes. Simulated proteomes and corresponding PPI networks were used to provide expectations for the extent and nature of PPI network evolution. We found strong evidence for conservation of PPIs, with lower than expected levels of change in PPIs for about a quarter of the proteome. Furthermore, we found that changes in predicted PPI networks are poorly predicted by sequence divergence. Our analyses identified a number of functional classes experiencing fewer PPI changes than expected, suggestive of purifying selection on PPIs. Our results demonstrate the added benefit of considering predicted PPI networks when studying the evolution of closely related organisms.

No MeSH data available.


Related in: MedlinePlus