Evolution of protein-protein interaction networks in yeast

<div><p>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 null 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.</p></div

Enriched GO terms in <i>S</i>. <i>kudriavzevii</i> cluster 113.

<p>Enriched GO terms in <i>S</i>. <i>kudriavzevii</i> cluster 113.</p

Enriched GO terms for proteins with higher than expected γ not identified when analyzing positively selected protein sequences.

<p>Enriched GO terms for proteins with higher than expected γ not identified when analyzing positively selected protein sequences.</p

An overview of the computational process used to infer PPI networks for each of the 5 yeast species, and to generate the simulated null model.

<p>Molecular evolutionary parameters were inferred under the M0 model in PAML, and were used to generate simulated datasets using INDELible. PIPE was used to infer PPI networks for both the real and simulated datasets.</p

Proteins which experience a lower or higher number of changes in PPIs in the real data compared to the simulated interactomes.

<p>Proteins which experience a lower (A) or higher (B) number of changes in inferred PPIs in the real data in comparison to the simulated interactomes. Each protein’s real γ is plotted in red and the range of γ observed in the null model are plotted in black.</p

Significant protein clusters and GO term enrichment analysis results found in each of the four non-<i>cerevisaie</i> species.

<p>Significant protein clusters and GO term enrichment analysis results found in each of the four non-<i>cerevisaie</i> species.</p

Enriched GO terms for proteins with lower than expected γ not identified when analyzing slowly evolving protein sequences.

<p>Enriched GO terms for proteins with lower than expected γ not identified when analyzing slowly evolving protein sequences.</p

Summary of the enriched GO Terms of the proteins participating in conserved PPIs.

<p>Summary of the enriched GO Terms of the proteins participating in conserved PPIs.</p

Distribution of the change in protein-protein interaction across the phylogeny.

<p>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.</p

Phosphatase Complex Pph3/Psy2 Is Involved in Regulation of Efficient Non-Homologous End-Joining Pathway in the Yeast <i>Saccharomyces cerevisiae</i>

<div><p>One of the main mechanisms for double stranded DNA break (DSB) repair is through the non-homologous end-joining (NHEJ) pathway. Using plasmid and chromosomal repair assays, we showed that deletion mutant strains for interacting proteins Pph3p and Psy2p had reduced efficiencies in NHEJ. We further observed that this activity of Pph3p and Psy2p appeared linked to cell cycle Rad53p and Chk1p checkpoint proteins. Pph3/Psy2 is a phosphatase complex, which regulates recovery from the Rad53p DNA damage checkpoint. Overexpression of Chk1p checkpoint protein in a parallel pathway to Rad53p compensated for the deletion of <i>PPH3</i> or <i>PSY2</i> in a chromosomal repair assay. Double mutant strains <i>Δpph3/Δchk1</i> and <i>Δpsy2/Δchk1</i> showed additional reductions in the efficiency of plasmid repair, compared to both single deletions which is in agreement with the activity of Pph3p and Psy2p in a parallel pathway to Chk1p. Genetic interaction analyses also supported a role for Pph3p and Psy2p in DNA damage repair, the NHEJ pathway, as well as cell cycle progression. Collectively, we report that the activity of Pph3p and Psy2p further connects NHEJ repair to cell cycle progression.</p></div