Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs

BMC Evolutionary Biology

Research Article

Zhongyang Liu¹  Yunping Zhu¹  Hao Guo¹  Dong Li¹  Hanchang Sun²  Qijun Liu³  Fuchu He⁴  Lin Hou⁵ 

[1] State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, 100850, Beijing, China;State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, 100850, Beijing, China;Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, 109 Deya Road, 410073, Changsha, China;State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, 100850, Beijing, China;Department of Chemistry and Biology, College of Science, National University of Defense Technology, 109 Deya Road, 410073, Changsha, China;State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, 100850, Beijing, China;Institutes of Biomedical Sciences, Fudan University, 130 Dong-An Road, 200032, Shanghai, China;State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, 100850, Beijing, China;School of Mathematical Sciences, Peking University, 5 Yiheyuan Road, 100871, Beijing, China;

关键词: Orthologous Group;    Protein Interaction Network;    Network Motif;    Phylogenetic Profile;    Random Expectation;   

DOI  :  10.1186/1471-2148-11-133

 received in 2010-07-20, accepted in 2011-05-20,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundHigh-throughput screens have revealed large-scale protein interaction networks defining most cellular functions. How the proteins were added to the protein interaction network during its growth is a basic and important issue. Network motifs represent the simplest building blocks of cellular machines and are of biological significance.ResultsHere we study the evolution of protein interaction networks from the perspective of network motifs. We find that in current protein interaction networks, proteins of the same age class tend to form motifs and such co-origins of motif constituents are affected by their topologies and biological functions. Further, we find that the proteins within motifs whose constituents are of the same age class tend to be densely interconnected, co-evolve and share the same biological functions, and these motifs tend to be within protein complexes.ConclusionsOur findings provide novel evidence for the hypothesis of the additions of clustered interacting nodes and point out network motifs, especially the motifs with the dense topology and specific function may play important roles during this process. Our results suggest functional constraints may be the underlying driving force for such additions of clustered interacting nodes.

【 授权许可】

CC BY   
© Liu et al; licensee BioMed Central Ltd. 2011