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BMC Genomics. 2008; 9: 519.
Published online 2008 November 2. doi: 10.1186/1471-2164-9-519.
PMCID: PMC2601049
The prediction of protein-protein interaction networks in rice blast fungus
Fei He,1 Yan Zhang,2 Hao Chen,1 Ziding Zhang,corresponding author1 and You-Liang Peng2
1State Key Laboratory for ArgoBiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
2Department of Plant Pathology, China Agricultural University, Beijing 100193, PR China
corresponding authorCorresponding author.
Fei He: plane332000/at/yahoo.com.cn; Yan Zhang: yzhang/at/cau.edu.cn; Hao Chen: chenhao392/at/sohu.com; Ziding Zhang: zidingzhang/at/cau.edu.cn; You-Liang Peng: pengyl/at/cau.edu.cn
Received March 2, 2008; Accepted November 2, 2008.
Abstract
Background
Protein-protein interaction (PPI) maps are useful tools for investigating the cellular functions of genes. Thus far, large-scale PPI mapping projects have not been implemented for the rice blast fungus Magnaporthe grisea, which is responsible for the most severe rice disease. Inspired by recent advances in PPI prediction, we constructed a PPI map of this important fungus.
Results
Using a well-recognized interolog approach, we have predicted 11,674 interactions among 3,017 M. grisea proteins. Although the scale of the constructed map covers approximately only one-fourth of the M. grisea's proteome, it is the first PPI map for this crucial organism and will therefore provide new insights into the functional genomics of the rice blast fungus. Focusing on the network topology of proteins encoded by known pathogenicity genes, we have found that pathogenicity proteins tend to interact with higher numbers of proteins. The pathogenicity proteins and their interacting partners in the entire network were then used to construct a subnet called a pathogenicity network. These data may provide further clues for the study of these pathogenicity proteins. Finally, it has been established that secreted proteins in M. grisea interact with fewer proteins. These secreted proteins and their interacting partners were also compiled into a network of secreted proteins, which may be helpful in constructing an interactome between the rice blast fungus and rice.
Conclusion
We predicted the PPIs of M. grisea and compiled them into a database server called MPID. It is hoped that MPID will provide new hints as to the functional genomics of this fungus. MPID is available at http://bioinformatics.cau.edu.cn/zzd_lab/MPID.html.