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SynechoNET: integrated protein interaction database of Synechocystis

6 th InCoB 2007 HKUST, Hong Kong. SynechoNET: integrated protein interaction database of Synechocystis. Sungsoo Kang & Jongsoon Choi Korean BioInformation Center, KRIBB Korea Basic Science Institute.

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SynechoNET: integrated protein interaction database of Synechocystis

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  1. 6th InCoB 2007 HKUST, Hong Kong SynechoNET: integrated protein interaction database of Synechocystis Sungsoo Kang & Jongsoon Choi Korean BioInformation Center, KRIBB Korea Basic Science Institute

  2. The national bioinformatics center of Korea • Integration of diverse biological information • Genome information • Biodiversity information • Bioresource information • International training programs on bioinformatics • Collaborative development of bioinformatics tools and resources • BioWiki (online knowledge base of biology) • BioPipe (BioWorkflow engine) Korean BioInformation Center (KOBIC)

  3. BioWiki • Wiki • a web technology that enables anyone to create and update website contents. • suited for developing online knowledge bases (e.g., Wikipedia ). • BioWiki • To adopt the wiki paradigm in biology • Collaborative development of biological knowledge bases. • BioWiki Contest ( http://biowiki.net )

  4. BioPipe • BioWorkflow Engine • No installation required • ‘Drag and drop’ supported • BioPipe Contest • Open free Web 2.0 • Period: Aug 15th ~ Sep 20th • Website: http://www.biopipe.net • Easy way to do bioinformatics

  5. 6th InCoB 2007 HKUST, Hong Kong SynechoNET: integrated protein interaction database of Synechocystis Sungsoo Kang & Jongsoon Choi Korean BioInformation Center, KRIBB Korea Basic Science Institute

  6. Cyanobacteria (Synechocystis) • Photosynthetic bacteria with multi-layered membranes • Photo-autotrophic or photo-heterotrophic growth • Ancestor of plant chloroplast

  7. Photosynthesis of Synechocystis • Thylakoid membrane contains many phycobilisomes on its surface • Phycobilisomes contain accessory pigments absorbing light for photosynthesis

  8. Synechocystis sp. PCC 6803 • Model organism of higher plants • Plant-like oxygenic photosynthesis • High transformation efficiency • Light signal transduction mutants • Undergoing systems biology pilot study • ‘Genome-to-Life’ project of DOE, USA • The first complete genome sequence among photosynthetic bacteria (DNA Research 1996) Genome size: 3,573,470 bp, GC content : 47.7% 3167 proteins (92 two-component regulatory proteins)

  9. SynechoNET • Provides predicted protein interaction network of Synechocystis sp. PCC 6803 • Integrates four complementary and redundant public protein-protein interaction (PPI) databases • Generates prediction reliability based on redundancy • Provides predicted membrane protein information • trans-membrane topology and domain information

  10. Overview of SynechoNET System 1 2 3 4

  11. Web Pages of SynechoNET

  12. 1. Integration of Protein Protein Interaction Data structural interaction interaction from multi-contexts

  13. Display of predicted protein interactions and their evidences

  14. 2. Prediction of Membrane Proteins Membrane protein Amino acid sequence Phobius (HMM model) Signal peptide Profile of predicted TM topology and signal peptide PFAM (protein domain DB) Predicted TM topology Localizome (graphic module) Transmembrane (TM) topology Domain structure

  15. Display of predicted transmembrane topology and its evidence

  16. 3. External Links from SynechoNET

  17. 4-1. Interactive Network Analysis in SynechoNET

  18. 4-2. Keyword Search in SynechoNET

  19. 4-3. Functional Category Search in SynechoNET

  20. Application of SynechoNET • Analysis on highly interacting hub proteins in a specific functional category • Finding upstream or downstream interacting proteins in a cellular pathway • Functional prediction of unknown genes • Analysis on regulatory membrane proteins

  21. Interaction Network of Regulatory Proteins(further analysis in Cytoscape program) • No. of found genes: 279 • No. of interactions: 2754

  22. Highly-Interacting Regulatory Proteins with a Transmembrane Domain

  23. P53 T Sll0043 Sll0038 Sll0043 Sll0039 Lam T -His Experimental Verification ofPredicted Interactions for Further Study Real interaction verified by yeast two-hybrid analysis

  24. Conclusion • SynechoNET: Synechocystis-specific integrated protein-protein interaction (PPI) database with trans-membrane topology and domain information • Integrates PPI information from PSIMAP, iPFAM, InterDom, and STRING • Transmembrane topology and domain information from Phobius and Localizome • Available at http://synechocystis.org or directly at http://bioportal.kobic.re.kr/SynechoNET/

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