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Modularity in the evolution of yeast protein interaction network.

Soichi Ogishima1, Hiroshi Tanaka2, Jun Nakaya1

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

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|April 28, 2015
PubMed
Summary
This summary is machine-generated.

This study proposes a new hypothesis for modularity in yeast protein interaction networks. New and existing proteins evolve together in modules, suggesting systems-level evolution.

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Area of Science:

  • Systems biology
  • Evolutionary biology
  • Bioinformatics

Background:

  • Protein interaction networks display complex structures like scale-free, small-world, and modularity.
  • Existing models like preferential attachment and duplication-divergence explain scale-free and small-world properties.
  • The evolutionary origins of modularity in these networks remain less understood.

Purpose of the Study:

  • To propose a hypothesis explaining the evolution of modularity in the yeast protein interaction network.
  • To investigate the evolutionary processes underlying the formation of protein complexes and modules.

Main Methods:

  • Constructed phylogenetic profiles to assign yeast proteins into six evolutionary ages.
  • Analyzed the evolutionary ages of hub proteins, protein complexes, functional modules, and topological modules.
  • Compared evolutionary rates of proteins within and outside these modules.

Main Results:

  • Nearly half of all hub proteins were found to be evolutionarily recent.
  • Proteins within modules (complexes, functional, topological) predominantly emerged in one or two evolutionary ages.
  • Proteins in complexes and topological modules exhibited significantly lower evolutionary rates compared to non-module proteins.

Conclusions:

  • The findings support a hypothesis of modularity arising through systems evolution in the yeast protein interaction network.
  • Suggests that modular structures evolve as coordinated units rather than through independent protein evolution.
  • Highlights the interplay between evolutionary age, protein function, and network topology.