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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.

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Interactions between functional classes.Significant connections between functional classes are mediated by protein-protein interactions. For each dataset and each class combination a P-value was calculated, reflecting the significance of the interaction density between classes in an interaction dataset of certain size and class coverage. Functional groups that exhibit cross-talk are highlighted (dotted lines are a guide to the eye).
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f3: Interactions between functional classes.Significant connections between functional classes are mediated by protein-protein interactions. For each dataset and each class combination a P-value was calculated, reflecting the significance of the interaction density between classes in an interaction dataset of certain size and class coverage. Functional groups that exhibit cross-talk are highlighted (dotted lines are a guide to the eye).

Mentions: We grouped E. coli and yeast proteins according to broad functional classes that were defined by clusters of orthologous groups (COGs)2425 and counted the occurrence of inter-class PPIs within the different interaction datasets8. We determined a log-odds ratio of the observed and expected frequencies of interactions between proteins of the corresponding functional classes, allowing us to calculate a P-value with a Z-test (see Materials and Methods). Fig. 3 shows that interactions mostly appeared between the same classes in binary-Y2H, co-complex and literature curated binary data. Interestingly, we found significant cross-talk between different functions that was dependent on the species and method used. For instance, both binary-Y2H and co-complex data show enriched interactions among yeast cell cycle (letter “D”) and cytoskeleton proteins (“Z”). However, co-complex and literature-curated binary interactions in yeast also point to interactions between chromatin proteins and transcription/replication proteins/RNA processing (Fig. 3). By contrast, the difference between binary-Y2H and co-complex data is much more pronounced in E. coli. Here, binary-Y2H interaction data sets detect the strongest cross-talk signal between transcription and signal transduction while co-complex data indicates a strong connection between translation/ribosomes and a number of other processes. However, given the unusually strong connection of ribosomal proteins to several other processes we suspect that this observation is the consequence of an artifact of ribosome-associated proteins (see discussion).


Protein-protein Interaction Networks of E. coli and S. cerevisiae are similar
Interactions between functional classes.Significant connections between functional classes are mediated by protein-protein interactions. For each dataset and each class combination a P-value was calculated, reflecting the significance of the interaction density between classes in an interaction dataset of certain size and class coverage. Functional groups that exhibit cross-talk are highlighted (dotted lines are a guide to the eye).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Interactions between functional classes.Significant connections between functional classes are mediated by protein-protein interactions. For each dataset and each class combination a P-value was calculated, reflecting the significance of the interaction density between classes in an interaction dataset of certain size and class coverage. Functional groups that exhibit cross-talk are highlighted (dotted lines are a guide to the eye).
Mentions: We grouped E. coli and yeast proteins according to broad functional classes that were defined by clusters of orthologous groups (COGs)2425 and counted the occurrence of inter-class PPIs within the different interaction datasets8. We determined a log-odds ratio of the observed and expected frequencies of interactions between proteins of the corresponding functional classes, allowing us to calculate a P-value with a Z-test (see Materials and Methods). Fig. 3 shows that interactions mostly appeared between the same classes in binary-Y2H, co-complex and literature curated binary data. Interestingly, we found significant cross-talk between different functions that was dependent on the species and method used. For instance, both binary-Y2H and co-complex data show enriched interactions among yeast cell cycle (letter “D”) and cytoskeleton proteins (“Z”). However, co-complex and literature-curated binary interactions in yeast also point to interactions between chromatin proteins and transcription/replication proteins/RNA processing (Fig. 3). By contrast, the difference between binary-Y2H and co-complex data is much more pronounced in E. coli. Here, binary-Y2H interaction data sets detect the strongest cross-talk signal between transcription and signal transduction while co-complex data indicates a strong connection between translation/ribosomes and a number of other processes. However, given the unusually strong connection of ribosomal proteins to several other processes we suspect that this observation is the consequence of an artifact of ribosome-associated proteins (see discussion).

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.


Related in: MedlinePlus