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

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.


Topological features of protein-protein interaction sets in E. coli and S. cerevisiae.In (A) we schematically illustrate interactions between co-regulated and co-regulating genes. In particular, co-regulated genes are considered a set of target genes that are controlled by a transcription factor. In turn, co-regulating genes refer to transcription factors that control the expression of the same genes. In (B) we calculated the number of interactions between co-regulated genes. In turn, we also calculated the enrichment of interactions between co-regulating genes in both E. coli and S. cerevisiae. As for their expected levels, we randomized the set of target genes of each transcription factor 10,000 times. While enrichments were significant in all datasets (P < 10−4) transcription factors tend to interact more frequently with each other than their target genes.
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f5: Topological features of protein-protein interaction sets in E. coli and S. cerevisiae.In (A) we schematically illustrate interactions between co-regulated and co-regulating genes. In particular, co-regulated genes are considered a set of target genes that are controlled by a transcription factor. In turn, co-regulating genes refer to transcription factors that control the expression of the same genes. In (B) we calculated the number of interactions between co-regulated genes. In turn, we also calculated the enrichment of interactions between co-regulating genes in both E. coli and S. cerevisiae. As for their expected levels, we randomized the set of target genes of each transcription factor 10,000 times. While enrichments were significant in all datasets (P < 10−4) transcription factors tend to interact more frequently with each other than their target genes.

Mentions: Utilizing 4,442 regulatory interactions between 187 transcription factors and 1,638 genes in E. coli from RegulonDB21, we measured the number of interactions that appeared between co-regulated target genes (Fig. 5A). In addition, we determined the number of interactions between transcription factors co-regulating the same target genes (Fig. 5A). As a model we randomly assigned the same number of targeted genes to each corresponding transcription factor 10,000 times. Fig. 5B indicates that binary-Y2H as well as co-complex interactions between targets of transcription factors were significantly enriched (P < 10−4). Utilizing 48,082 regulatory interactions between 183 transcription factors and 6,403 genes from the YEASTRACT database22 we obtained similar results in yeast (P < 10−4), confirming that enrichment signals were stronger for interactions between transcription factors than among their target genes3.


Protein-protein Interaction Networks of E. coli and S. cerevisiae are similar
Topological features of protein-protein interaction sets in E. coli and S. cerevisiae.In (A) we schematically illustrate interactions between co-regulated and co-regulating genes. In particular, co-regulated genes are considered a set of target genes that are controlled by a transcription factor. In turn, co-regulating genes refer to transcription factors that control the expression of the same genes. In (B) we calculated the number of interactions between co-regulated genes. In turn, we also calculated the enrichment of interactions between co-regulating genes in both E. coli and S. cerevisiae. As for their expected levels, we randomized the set of target genes of each transcription factor 10,000 times. While enrichments were significant in all datasets (P < 10−4) transcription factors tend to interact more frequently with each other than their target genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: Topological features of protein-protein interaction sets in E. coli and S. cerevisiae.In (A) we schematically illustrate interactions between co-regulated and co-regulating genes. In particular, co-regulated genes are considered a set of target genes that are controlled by a transcription factor. In turn, co-regulating genes refer to transcription factors that control the expression of the same genes. In (B) we calculated the number of interactions between co-regulated genes. In turn, we also calculated the enrichment of interactions between co-regulating genes in both E. coli and S. cerevisiae. As for their expected levels, we randomized the set of target genes of each transcription factor 10,000 times. While enrichments were significant in all datasets (P < 10−4) transcription factors tend to interact more frequently with each other than their target genes.
Mentions: Utilizing 4,442 regulatory interactions between 187 transcription factors and 1,638 genes in E. coli from RegulonDB21, we measured the number of interactions that appeared between co-regulated target genes (Fig. 5A). In addition, we determined the number of interactions between transcription factors co-regulating the same target genes (Fig. 5A). As a model we randomly assigned the same number of targeted genes to each corresponding transcription factor 10,000 times. Fig. 5B indicates that binary-Y2H as well as co-complex interactions between targets of transcription factors were significantly enriched (P < 10−4). Utilizing 48,082 regulatory interactions between 183 transcription factors and 6,403 genes from the YEASTRACT database22 we obtained similar results in yeast (P < 10−4), confirming that enrichment signals were stronger for interactions between transcription factors than among their target genes3.

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.