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Analysis of Protein Interaction Network and Extinction from the View of Evolution

Author: XuMeng
Tutor: NiuLiWen; ZuoMaiKun
School: University of Science and Technology of China
Course: Biochemistry and Molecular Biology
Keywords: coevolution PPI extinction genetic algorithm optimization
CLC: Q51
Type: PhD thesis
Year: 2010
Downloads: 6
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Abstract

Molecular evolution is one of the most active areas of research. Here, we explored a fundamental question on the role of coevolution in the shaping of yeast protein interaction network (PIN). We found that the extent of coevolu- tion between two proteins decreases rapidly as their distance on PIN increases. This suggests that coevolutionary constraint is a short-distance force and genetic perturbation on a protein damps rapidly. We also found that protein-protein interactions (PPIs) with strong coevolution tend to aggregate to form densely connected clusters while PPIs with weak coevolution are more frequently present at inter-cluster region. The finding indicates the close relationship between co- evolution and modular organization of yeast PIN. Using protein complexes de- posited at MIPS as a reference, we demonstrated that intra-complex PPIs have stronger coevolution than inter-complex PPIs and complexes/modules are the coevolutionary cores on yeast PIN. These observations suggest a coevolutionary landscape model for yeast PIN evolution and may provide insights into the evolu- tion and modularity of cellular networks. As an extension of molecular evolution, we also investigated a kind of widespread extinction form which select against the most fitted individual and its genetic family in a population. This kind of extinction is actually contrary to the classic’survival the fittest’mechanism. In silico simulation showed that periodical extinction events could accelerate evo- lution. We demonstrated that extinction could protect the weaker individuals and help the population escaping from fitness local maxima. Extinction events also increased the genetic diversity within the population. We suggested that’survival the fittest’might be a short-eyed selection mechanism which could lead to a overflow of genomes in local maxima. Protection for weaker individuals is essential for fast evolution. Our research may provide insights into evolution study and suggest a new way to improve optimization algorithms.

Analysis of Protein Interaction Network and Extinction from the View of Evolution

Abstract

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