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Modularity in the evolution of yeast protein interaction network.

Ogishima S, Tanaka H, Nakaya J - Bioinformation (2015)

Bottom Line: We found that all the almost half of hub proteins are evolutionarily new.Examining the evolutionary processes of protein complexes, functional modules and topological modules, we also found that member proteins of these modules tend to appear in one or two evolutionary ages.Our results suggest a hypothesis of modularity in the evolution of yeast protein interaction network as systems evolution.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioclinical Informatics, Tohoku Medical and Megabank Organization, Tohoku University, Seiryo-cho 4-1, Aoba-ku, Sendai-shi Miyagi 980-8575 Japan.

ABSTRACT
Protein interaction networks are known to exhibit remarkable structures: scale-free and small-world and modular structures. To explain the evolutionary processes of protein interaction networks possessing scale-free and small-world structures, preferential attachment and duplication-divergence models have been proposed as mathematical models. Protein interaction networks are also known to exhibit another remarkable structural characteristic, modular structure. How the protein interaction networks became to exhibit modularity in their evolution? Here, we propose a hypothesis of modularity in the evolution of yeast protein interaction network based on molecular evolutionary evidence. We assigned yeast proteins into six evolutionary ages by constructing a phylogenetic profile. We found that all the almost half of hub proteins are evolutionarily new. Examining the evolutionary processes of protein complexes, functional modules and topological modules, we also found that member proteins of these modules tend to appear in one or two evolutionary ages. Moreover, proteins in protein complexes and topological modules show significantly low evolutionary rates than those not in these modules. Our results suggest a hypothesis of modularity in the evolution of yeast protein interaction network as systems evolution.

No MeSH data available.


Related in: MedlinePlus

Modularity in the evolutionary process of protein complexes, functional modules and topological modules. Horizontalaxes indicates the proportion of the FSEP proteins to all member proteins (FSEP proportion), vertical axes indicates the proportionof the complexes having the designated FESP proportion to total complexes.
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Figure 2: Modularity in the evolutionary process of protein complexes, functional modules and topological modules. Horizontalaxes indicates the proportion of the FSEP proteins to all member proteins (FSEP proportion), vertical axes indicates the proportionof the complexes having the designated FESP proportion to total complexes.

Mentions: What are the correspondences with “modules”? Weconsidered that protein complexes, functional modules andtopological modules correspond with “modules”.We examined1,142 protein complexes, 598 functional modules and 43topological modules, and inferred the evolutionary processesof them by assigning each evolutionary age to member protein.We identified the firstly and secondly evolutionarilypopulated(FSEP) proteins in each module defined by proteinsof the top-two populated evolutionary ages. That is, weidentified the firstly and secondly largest groups of memberproteins in each module which appear in the sameevolutionary ages. We then examined their compositions toform protein complexes, functional modules and topologicalmodules (Figure 2). Our results showed that the FESPproportion is remarkably concentrated at 1. This tendency doesnot result from the background bias in the numbers of proteinsof each evolutionary age;67.2% of complexes, 56.0% offunctional modules and 45.5% of topological modules aresignificantly biased in their evolutionary compositions (χ2 testof goodness-of-fit, p-value<0.05).These results suggest thatprotein complexes, functional modules and topological modules tends to be formed by proteins that appeared in onlyone or two evolutionary ages, therefore they did not appear inall six ages continuously and incrementally, but instead in onlyone or two evolutionary ages simultaneously.


Modularity in the evolution of yeast protein interaction network.

Ogishima S, Tanaka H, Nakaya J - Bioinformation (2015)

Modularity in the evolutionary process of protein complexes, functional modules and topological modules. Horizontalaxes indicates the proportion of the FSEP proteins to all member proteins (FSEP proportion), vertical axes indicates the proportionof the complexes having the designated FESP proportion to total complexes.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4403033&req=5

Figure 2: Modularity in the evolutionary process of protein complexes, functional modules and topological modules. Horizontalaxes indicates the proportion of the FSEP proteins to all member proteins (FSEP proportion), vertical axes indicates the proportionof the complexes having the designated FESP proportion to total complexes.
Mentions: What are the correspondences with “modules”? Weconsidered that protein complexes, functional modules andtopological modules correspond with “modules”.We examined1,142 protein complexes, 598 functional modules and 43topological modules, and inferred the evolutionary processesof them by assigning each evolutionary age to member protein.We identified the firstly and secondly evolutionarilypopulated(FSEP) proteins in each module defined by proteinsof the top-two populated evolutionary ages. That is, weidentified the firstly and secondly largest groups of memberproteins in each module which appear in the sameevolutionary ages. We then examined their compositions toform protein complexes, functional modules and topologicalmodules (Figure 2). Our results showed that the FESPproportion is remarkably concentrated at 1. This tendency doesnot result from the background bias in the numbers of proteinsof each evolutionary age;67.2% of complexes, 56.0% offunctional modules and 45.5% of topological modules aresignificantly biased in their evolutionary compositions (χ2 testof goodness-of-fit, p-value<0.05).These results suggest thatprotein complexes, functional modules and topological modules tends to be formed by proteins that appeared in onlyone or two evolutionary ages, therefore they did not appear inall six ages continuously and incrementally, but instead in onlyone or two evolutionary ages simultaneously.

Bottom Line: We found that all the almost half of hub proteins are evolutionarily new.Examining the evolutionary processes of protein complexes, functional modules and topological modules, we also found that member proteins of these modules tend to appear in one or two evolutionary ages.Our results suggest a hypothesis of modularity in the evolution of yeast protein interaction network as systems evolution.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioclinical Informatics, Tohoku Medical and Megabank Organization, Tohoku University, Seiryo-cho 4-1, Aoba-ku, Sendai-shi Miyagi 980-8575 Japan.

ABSTRACT
Protein interaction networks are known to exhibit remarkable structures: scale-free and small-world and modular structures. To explain the evolutionary processes of protein interaction networks possessing scale-free and small-world structures, preferential attachment and duplication-divergence models have been proposed as mathematical models. Protein interaction networks are also known to exhibit another remarkable structural characteristic, modular structure. How the protein interaction networks became to exhibit modularity in their evolution? Here, we propose a hypothesis of modularity in the evolution of yeast protein interaction network based on molecular evolutionary evidence. We assigned yeast proteins into six evolutionary ages by constructing a phylogenetic profile. We found that all the almost half of hub proteins are evolutionarily new. Examining the evolutionary processes of protein complexes, functional modules and topological modules, we also found that member proteins of these modules tend to appear in one or two evolutionary ages. Moreover, proteins in protein complexes and topological modules show significantly low evolutionary rates than those not in these modules. Our results suggest a hypothesis of modularity in the evolution of yeast protein interaction network as systems evolution.

No MeSH data available.


Related in: MedlinePlus