Limits...
Evolution of protein-protein interaction networks in yeast

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.


Distribution of the change in protein-protein interaction across the                            phylogeny.                        The distribution of γ, which represents the total number of                            interaction changes (gains or losses) over the entire phylogeny. The                            majority of proteins experience relatively few changes in interaction                            across the phylogeny with a small number of proteins experiencing many                            changes.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC5382968&req=5

pone.0171920.g003: Distribution of the change in protein-protein interaction across the phylogeny. The distribution of γ, which represents the total number of interaction changes (gains or losses) over the entire phylogeny. The majority of proteins experience relatively few changes in interaction across the phylogeny with a small number of proteins experiencing many changes.

Mentions: Phylogeny-wide changes in PPI profiles were estimated for 4179 proteins with high quality alignments from the 5-species yeast dataset of Scannell et al. [18]. For each protein, we estimated γ, which represents the total number of interaction changes (gains or losses) over the entire phylogeny (S7 Table). Median γ was 3.0, with a mean and variance of 10.06 and 2,001.74, respectively. The full distribution of γ is shown in Fig 3. It is clear that the bulk of proteins are inferred to experience very few PPI changes, but the long tail of the distribution suggests a subset of proteins experiencing many changes. This leads to the exceptionally high estimate of variance.


Evolution of protein-protein interaction networks in yeast
Distribution of the change in protein-protein interaction across the                            phylogeny.                        The distribution of γ, which represents the total number of                            interaction changes (gains or losses) over the entire phylogeny. The                            majority of proteins experience relatively few changes in interaction                            across the phylogeny with a small number of proteins experiencing many                            changes.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0171920.g003: Distribution of the change in protein-protein interaction across the phylogeny. The distribution of γ, which represents the total number of interaction changes (gains or losses) over the entire phylogeny. The majority of proteins experience relatively few changes in interaction across the phylogeny with a small number of proteins experiencing many changes.
Mentions: Phylogeny-wide changes in PPI profiles were estimated for 4179 proteins with high quality alignments from the 5-species yeast dataset of Scannell et al. [18]. For each protein, we estimated γ, which represents the total number of interaction changes (gains or losses) over the entire phylogeny (S7 Table). Median γ was 3.0, with a mean and variance of 10.06 and 2,001.74, respectively. The full distribution of γ is shown in Fig 3. It is clear that the bulk of proteins are inferred to experience very few PPI changes, but the long tail of the distribution suggests a subset of proteins experiencing many changes. This leads to the exceptionally high estimate of variance.

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.