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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.


Enrichment of essential genes in different protein-protein interaction datasets of E. coli.(A) Overlaps between sets of proteins that are involved in binary-Y2H, co-complex and literature curated binary protein-protein interaction data sets in E. coli, including the number of essential proteins that are involved in interactions (brackets). (B) Enrichment of essential bacterial proteins as a function of their number of interactions in E. coli and S. cerevisiae. Notably, we observed that binary-Y2H interactions failed to show an ascending trend compared to literature curated binary and co-complex interactions in both organisms.
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f1: Enrichment of essential genes in different protein-protein interaction datasets of E. coli.(A) Overlaps between sets of proteins that are involved in binary-Y2H, co-complex and literature curated binary protein-protein interaction data sets in E. coli, including the number of essential proteins that are involved in interactions (brackets). (B) Enrichment of essential bacterial proteins as a function of their number of interactions in E. coli and S. cerevisiae. Notably, we observed that binary-Y2H interactions failed to show an ascending trend compared to literature curated binary and co-complex interactions in both organisms.

Mentions: The importance of a protein in a protein-protein interaction network is frequently considered a function of its number of interaction partners. For instance, the so-called centrality-lethality rule326 suggests that central proteins with many interactions are more likely to be essential than poorly connected proteins. While highly connected proteins are more often essential in S. cerevisiae they are also involved in an increasing number of protein complexes27, suggesting that their essentiality is a consequence of their involvement in essential complexes282930. To determine essentiality-specific characteristics we utilized a set of 712 essential proteins in E. coli from the DEG database18. While the overlaps between the sets of proteins that are involved in our different protein-protein interaction networks of E. coli are considerable, we surprisingly found an enrichment when we focused on the corresponding sets of essential interacting genes (Fig. 1A). In Fig. 1B we determined the enrichment of essential proteins in groups of increasingly interacting proteins in different interaction data sets of E. coli. To compare with yeast specific data we used a set of 2,930 binary-Y2H interactions3, 9,420 co-complex interactions1314 and 3,624 literature curated binary interactions17. Similarly to yeast3 we observed that essential proteins were no more essential than any other proteins in binary-Y2H protein-protein interactions in E. coli.


Protein-protein Interaction Networks of E. coli and S. cerevisiae are similar
Enrichment of essential genes in different protein-protein interaction datasets of E. coli.(A) Overlaps between sets of proteins that are involved in binary-Y2H, co-complex and literature curated binary protein-protein interaction data sets in E. coli, including the number of essential proteins that are involved in interactions (brackets). (B) Enrichment of essential bacterial proteins as a function of their number of interactions in E. coli and S. cerevisiae. Notably, we observed that binary-Y2H interactions failed to show an ascending trend compared to literature curated binary and co-complex interactions in both organisms.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Enrichment of essential genes in different protein-protein interaction datasets of E. coli.(A) Overlaps between sets of proteins that are involved in binary-Y2H, co-complex and literature curated binary protein-protein interaction data sets in E. coli, including the number of essential proteins that are involved in interactions (brackets). (B) Enrichment of essential bacterial proteins as a function of their number of interactions in E. coli and S. cerevisiae. Notably, we observed that binary-Y2H interactions failed to show an ascending trend compared to literature curated binary and co-complex interactions in both organisms.
Mentions: The importance of a protein in a protein-protein interaction network is frequently considered a function of its number of interaction partners. For instance, the so-called centrality-lethality rule326 suggests that central proteins with many interactions are more likely to be essential than poorly connected proteins. While highly connected proteins are more often essential in S. cerevisiae they are also involved in an increasing number of protein complexes27, suggesting that their essentiality is a consequence of their involvement in essential complexes282930. To determine essentiality-specific characteristics we utilized a set of 712 essential proteins in E. coli from the DEG database18. While the overlaps between the sets of proteins that are involved in our different protein-protein interaction networks of E. coli are considerable, we surprisingly found an enrichment when we focused on the corresponding sets of essential interacting genes (Fig. 1A). In Fig. 1B we determined the enrichment of essential proteins in groups of increasingly interacting proteins in different interaction data sets of E. coli. To compare with yeast specific data we used a set of 2,930 binary-Y2H interactions3, 9,420 co-complex interactions1314 and 3,624 literature curated binary interactions17. Similarly to yeast3 we observed that essential proteins were no more essential than any other proteins in binary-Y2H protein-protein interactions in E. coli.

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.