title: Prediction and characterization of protein-protein interaction network in Bacillus licheniformis WX-02.
abstract: In this study, we constructed a protein-protein interaction (PPI) network of B. licheniformis strain WX-02 with interolog method and domain-based method, which contained 15,864 edges and 2,448 nodes. Although computationally predicted networks have relatively low coverage and high false-positive rate, our prediction was confirmed from three perspectives: local structural features, functional similarities and transcriptional correlations. Further analysis of the COG heat map showed that protein interactions in B. licheniformis WX-02 mainly occurred in the same functional categories. By incorporating the transcriptome data, we found that the topological properties of the PPI network were robust under normal and high salt conditions. In addition, 267 different protein complexes were identified and 117 poorly characterized proteins were annotated with certain functions based on the PPI network. Furthermore, the sub-network showed that a hub protein CcpA jointed directly or indirectly many proteins related to γ-PGA synthesis and regulation, such as PgsB, GltA, GltB, ProB, ProJ, YcgM and two signal transduction systems ComP-ComA and DegS-DegU. Thus, CcpA might play an important role in the regulation of γ-PGA synthesis. This study therefore will facilitate the understanding of the complex cellular behaviors and mechanisms of γ-PGA synthesis in B. licheniformis WX-02.
authors.affiliation: College of Informatics, Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Yi-Chao
authors.initials: YC
authors.lastname: Han
authors.affiliation: College of Informatics, Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Jia-Ming
authors.initials: JM
authors.lastname: Song
authors.affiliation: College of Informatics, Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Long
authors.initials: L
authors.lastname: Wang
authors.affiliation: College of Informatics, Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Cheng-Cheng
authors.initials: CC
authors.lastname: Shu
authors.affiliation: College of Informatics, Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Jing
authors.initials: J
authors.lastname: Guo
authors.affiliation: College of Informatics, Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Chen
mesh_terms: D000069976:Bacillus licheniformis / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D011099:Polyglutamic Acid / Q000031:analogs & derivatives / Q000235:genetics; D060066:Protein Interaction Maps / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics; D059467:Transcriptome / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; C511775:poly(gamma-glutamic acid); D011099:Polyglutamic Acid