Biological network modelling based on differentially expressed proteins in a bacilysin-deficient strain of bacillus subtilis

Date

2019

Author

Kutnu, Meltem

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Bacillus subtilis is a non-pathogenic, Gram-positive organism which is known for producing a broad range of secondary metabolites with pharmacological and antimicrobial activities. The dipeptide bacilysin is one of the many antibiotics synthesized by certain strains of B. subtilis, and it is composed of L-alanine and the non-proteinogenic amino acid L-anticapsin. Earlier silencing studies by our group have suggested that bacilysin acts as a pleiotropic molecule on its host. Therefore, the absence or lack of bacilysin would affect the host response. In this study, data from previous proteomic studies by our group on bacilysin-deleted derivative strain Bacillus subtilis OGU1 have been collected. We constructed time-dependent secretome and cytosolic proteome networks by using the Prize-collecting Steiner forest (PCSF) algorithm. Functional enrichment analyses on the resulting networks have confirmed our earlier findings, as well as revealing further hidden molecules including CcpA, BglH, HxlA and YwmD, along with pathways such as amino acid metabolism, ABC transporters, sugar metabolism, and one carbon pool by folate. Biological network modelling can facilitate the identification of unknown protein interactions, as well as interaction partners in organisms such as Bacillus subtilis under a particular condition, in addition to guiding further experiments.

Subject Keywords

Bacillus subtilis., Bacillus subtilis, Bacilysin, Proteomics, Network modeling, Pathway enrichment analysis.

URI

http://etd.lib.metu.edu.tr/upload/12624295/index.pdf
https://hdl.handle.net/11511/44343

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Graduate School of Natural and Applied Sciences, Thesis