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Protein-protein Interaction Networks of E. coli and S. cerevisiae are similar

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ABSTRACT

Only recently novel high-throughput binary interaction data in E. coli became available that allowed us to compare experimentally obtained protein-protein interaction networks of prokaryotes and eukaryotes (i.e. E. coli and S. cerevisiae). Utilizing binary-Y2H, co-complex and binary literature curated interaction sets in both organisms we found that characteristics of interaction sets that were determined with the same experimental methods were strikingly similar. While essentiality is frequently considered a question of a protein's increasing number of interactions, we found that binary-Y2H interactions failed to show such a trend in both organisms. Furthermore, essential genes are enriched in protein complexes in both organisms. In turn, binary-Y2H interactions hold more bottleneck interactions than co-complex interactions while both binary-Y2H and co-complex interactions are strongly enriched among co-regulated proteins and transcription factors. We discuss if such similarities are a consequence of the underlying methodology or rather reflect truly different biological patterns.

No MeSH data available.


Essential genes in the protein-protein interaction networks of E. coli.(A) The Venn diagram shows overlaps between the binary-Y2H, co-complex and literature curated binary interaction networks in E. coli, as well as interactions between essential genes in these sets (brackets). (B) We grouped E. coli proteins that were placed a given distance away from essential proteins in the underlying interaction networks. The fraction of essential proteins is largest in the immediate vicinity of other essential proteins. Error bars indicate 95% confidence interval. (C) Observed and expected sizes of the largest connected component between essential genes in E. coli. As a  model we randomly sampled essential genes 10,000 times, indicating that the size of the largest component in co-complex and literature curated binary interaction sets was significantly larger than randomly expected (P < 10−4).
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f2: Essential genes in the protein-protein interaction networks of E. coli.(A) The Venn diagram shows overlaps between the binary-Y2H, co-complex and literature curated binary interaction networks in E. coli, as well as interactions between essential genes in these sets (brackets). (B) We grouped E. coli proteins that were placed a given distance away from essential proteins in the underlying interaction networks. The fraction of essential proteins is largest in the immediate vicinity of other essential proteins. Error bars indicate 95% confidence interval. (C) Observed and expected sizes of the largest connected component between essential genes in E. coli. As a model we randomly sampled essential genes 10,000 times, indicating that the size of the largest component in co-complex and literature curated binary interaction sets was significantly larger than randomly expected (P < 10−4).

Mentions: In Fig. 2A, we determined the overlaps of protein-protein interactions in the given data sets, including interactions between essential proteins. While the overlap between interactions in the different sets is limited, interactions between essential proteins appear to further deplete overlaps. Starting from essential proteins, we determined groups of proteins that are a given number of interactions away in the underlying network. In each bin we calculated the fraction of essential proteins, indicating that essential proteins generally accumulated in the immediate vicinity of other essential proteins in all interaction sets of E. coli (Fig. 2B). Notably, enrichments of essential proteins in the network vicinity of each other was strongest in co-complex, followed by literature-curated binary and binary-Y2H interactions, an observation that matches results obtained with corresponding interaction data sets in S. cerevisiae3.


Protein-protein Interaction Networks of E. coli and S. cerevisiae are similar
Essential genes in the protein-protein interaction networks of E. coli.(A) The Venn diagram shows overlaps between the binary-Y2H, co-complex and literature curated binary interaction networks in E. coli, as well as interactions between essential genes in these sets (brackets). (B) We grouped E. coli proteins that were placed a given distance away from essential proteins in the underlying interaction networks. The fraction of essential proteins is largest in the immediate vicinity of other essential proteins. Error bars indicate 95% confidence interval. (C) Observed and expected sizes of the largest connected component between essential genes in E. coli. As a  model we randomly sampled essential genes 10,000 times, indicating that the size of the largest component in co-complex and literature curated binary interaction sets was significantly larger than randomly expected (P < 10−4).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5384207&req=5

f2: Essential genes in the protein-protein interaction networks of E. coli.(A) The Venn diagram shows overlaps between the binary-Y2H, co-complex and literature curated binary interaction networks in E. coli, as well as interactions between essential genes in these sets (brackets). (B) We grouped E. coli proteins that were placed a given distance away from essential proteins in the underlying interaction networks. The fraction of essential proteins is largest in the immediate vicinity of other essential proteins. Error bars indicate 95% confidence interval. (C) Observed and expected sizes of the largest connected component between essential genes in E. coli. As a model we randomly sampled essential genes 10,000 times, indicating that the size of the largest component in co-complex and literature curated binary interaction sets was significantly larger than randomly expected (P < 10−4).
Mentions: In Fig. 2A, we determined the overlaps of protein-protein interactions in the given data sets, including interactions between essential proteins. While the overlap between interactions in the different sets is limited, interactions between essential proteins appear to further deplete overlaps. Starting from essential proteins, we determined groups of proteins that are a given number of interactions away in the underlying network. In each bin we calculated the fraction of essential proteins, indicating that essential proteins generally accumulated in the immediate vicinity of other essential proteins in all interaction sets of E. coli (Fig. 2B). Notably, enrichments of essential proteins in the network vicinity of each other was strongest in co-complex, followed by literature-curated binary and binary-Y2H interactions, an observation that matches results obtained with corresponding interaction data sets in S. cerevisiae3.

View Article: PubMed Central - PubMed

ABSTRACT

Only recently novel high-throughput binary interaction data in E. coli became available that allowed us to compare experimentally obtained protein-protein interaction networks of prokaryotes and eukaryotes (i.e. E. coli and S. cerevisiae). Utilizing binary-Y2H, co-complex and binary literature curated interaction sets in both organisms we found that characteristics of interaction sets that were determined with the same experimental methods were strikingly similar. While essentiality is frequently considered a question of a protein's increasing number of interactions, we found that binary-Y2H interactions failed to show such a trend in both organisms. Furthermore, essential genes are enriched in protein complexes in both organisms. In turn, binary-Y2H interactions hold more bottleneck interactions than co-complex interactions while both binary-Y2H and co-complex interactions are strongly enriched among co-regulated proteins and transcription factors. We discuss if such similarities are a consequence of the underlying methodology or rather reflect truly different biological patterns.

No MeSH data available.